Starting phenix.real_space_refine on Thu Mar 5 08:16:45 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6orn_20175/03_2026/6orn_20175.cif Found real_map, /net/cci-nas-00/data/ceres_data/6orn_20175/03_2026/6orn_20175.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.05 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6orn_20175/03_2026/6orn_20175.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6orn_20175/03_2026/6orn_20175.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6orn_20175/03_2026/6orn_20175.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6orn_20175/03_2026/6orn_20175.map" } resolution = 4.05 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.012 sd= 0.158 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 123 5.16 5 C 12729 2.51 5 N 3402 2.21 5 O 4084 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 28 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 20338 Number of models: 1 Model: "" Number of chains: 39 Chain: "C" Number of atoms: 987 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 987 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 1, 'TRANS': 122} Chain breaks: 1 Chain: "G" Number of atoms: 3485 Number of conformers: 1 Conformer: "" Number of residues, atoms: 442, 3485 Classifications: {'peptide': 442} Link IDs: {'PTRANS': 22, 'TRANS': 419} Chain breaks: 4 Chain: "J" Number of atoms: 987 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 987 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 1, 'TRANS': 122} Chain breaks: 1 Chain: "K" Number of atoms: 3485 Number of conformers: 1 Conformer: "" Number of residues, atoms: 442, 3485 Classifications: {'peptide': 442} Link IDs: {'PTRANS': 22, 'TRANS': 419} Chain breaks: 4 Chain: "Q" Number of atoms: 987 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 987 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 1, 'TRANS': 122} Chain breaks: 1 Chain: "R" Number of atoms: 3485 Number of conformers: 1 Conformer: "" Number of residues, atoms: 442, 3485 Classifications: {'peptide': 442} Link IDs: {'PTRANS': 22, 'TRANS': 419} Chain breaks: 4 Chain: "A" Number of atoms: 1041 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 1041 Classifications: {'peptide': 133} Link IDs: {'PTRANS': 5, 'TRANS': 127} Chain: "F" Number of atoms: 1041 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 1041 Classifications: {'peptide': 133} Link IDs: {'PTRANS': 5, 'TRANS': 127} Chain: "O" Number of atoms: 1041 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 1041 Classifications: {'peptide': 133} Link IDs: {'PTRANS': 5, 'TRANS': 127} Chain: "B" Number of atoms: 824 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 824 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 6, 'TRANS': 100} Chain: "I" Number of atoms: 824 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 824 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 6, 'TRANS': 100} Chain: "P" Number of atoms: 824 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 824 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 6, 'TRANS': 100} Chain: "D" 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: "E" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 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: "L" 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: "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: "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: 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: "U" 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: "V" 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: "W" 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: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen 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: 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: "b" 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: "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: 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: "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: "C" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "G" 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: "J" 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: "K" 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: "Q" 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: "R" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} 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 Time building chain proxies: 4.92, per 1000 atoms: 0.24 Number of scatterers: 20338 At special positions: 0 Unit cell: (150.78, 157.96, 159.396, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 123 16.00 O 4084 8.00 N 3402 7.00 C 12729 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=39, symmetry=0 Simple disulfide: pdb=" SG CYS C 598 " - pdb=" SG CYS C 604 " distance=2.03 Simple disulfide: pdb=" SG CYS C 605 " - pdb=" SG CYS G 501 " distance=2.03 Simple disulfide: pdb=" SG CYS G 54 " - pdb=" SG CYS G 74 " distance=2.03 Simple disulfide: pdb=" SG CYS G 119 " - pdb=" SG CYS G 205 " distance=2.03 Simple disulfide: pdb=" SG CYS G 126 " - pdb=" SG CYS G 196 " distance=2.03 Simple disulfide: pdb=" SG CYS G 131 " - pdb=" SG CYS G 157 " distance=2.03 Simple disulfide: pdb=" SG CYS G 218 " - pdb=" SG CYS G 247 " distance=2.05 Simple disulfide: pdb=" SG CYS G 228 " - pdb=" SG CYS G 239 " distance=2.03 Simple disulfide: pdb=" SG CYS G 296 " - pdb=" SG CYS G 331 " distance=2.03 Simple disulfide: pdb=" SG CYS G 378 " - pdb=" SG CYS G 445 " distance=2.02 Simple disulfide: pdb=" SG CYS G 385 " - pdb=" SG CYS G 418 " distance=2.03 Simple disulfide: pdb=" SG CYS J 598 " - pdb=" SG CYS J 604 " distance=2.03 Simple disulfide: pdb=" SG CYS J 605 " - pdb=" SG CYS K 501 " distance=2.03 Simple disulfide: pdb=" SG CYS K 54 " - pdb=" SG CYS K 74 " distance=2.03 Simple disulfide: pdb=" SG CYS K 119 " - pdb=" SG CYS K 205 " distance=2.03 Simple disulfide: pdb=" SG CYS K 126 " - pdb=" SG CYS K 196 " distance=2.03 Simple disulfide: pdb=" SG CYS K 131 " - pdb=" SG CYS K 157 " distance=2.03 Simple disulfide: pdb=" SG CYS K 218 " - pdb=" SG CYS K 247 " distance=2.06 Simple disulfide: pdb=" SG CYS K 228 " - pdb=" SG CYS K 239 " distance=2.03 Simple disulfide: pdb=" SG CYS K 296 " - pdb=" SG CYS K 331 " distance=2.03 Simple disulfide: pdb=" SG CYS K 378 " - pdb=" SG CYS K 445 " distance=2.02 Simple disulfide: pdb=" SG CYS K 385 " - pdb=" SG CYS K 418 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 598 " - pdb=" SG CYS Q 604 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 605 " - pdb=" SG CYS R 501 " distance=2.03 Simple disulfide: pdb=" SG CYS R 54 " - pdb=" SG CYS R 74 " distance=2.03 Simple disulfide: pdb=" SG CYS R 119 " - pdb=" SG CYS R 205 " distance=2.03 Simple disulfide: pdb=" SG CYS R 126 " - pdb=" SG CYS R 196 " distance=2.03 Simple disulfide: pdb=" SG CYS R 131 " - pdb=" SG CYS R 157 " distance=2.03 Simple disulfide: pdb=" SG CYS R 218 " - pdb=" SG CYS R 247 " distance=2.06 Simple disulfide: pdb=" SG CYS R 228 " - pdb=" SG CYS R 239 " distance=2.03 Simple disulfide: pdb=" SG CYS R 296 " - pdb=" SG CYS R 331 " distance=2.03 Simple disulfide: pdb=" SG CYS R 378 " - pdb=" SG CYS R 445 " distance=2.02 Simple disulfide: pdb=" SG CYS R 385 " - pdb=" SG CYS R 418 " distance=2.03 Simple disulfide: pdb=" SG CYS A 22 " - pdb=" SG CYS A 92 " distance=2.03 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 92 " distance=2.03 Simple disulfide: pdb=" SG CYS O 22 " - pdb=" SG CYS O 92 " distance=2.03 Simple disulfide: pdb=" SG CYS B 23 " - pdb=" SG CYS B 88 " distance=2.03 Simple disulfide: pdb=" SG CYS I 23 " - pdb=" SG CYS I 88 " distance=2.03 Simple disulfide: pdb=" SG CYS P 23 " - pdb=" SG CYS P 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 ALPHA1-2 " MAN D 4 " - " MAN D 5 " " MAN H 4 " - " MAN H 5 " " MAN U 4 " - " MAN U 5 " " MAN W 4 " - " MAN W 5 " " MAN b 4 " - " MAN b 5 " ALPHA1-3 " BMA D 3 " - " MAN D 4 " " BMA H 3 " - " MAN H 4 " " MAN H 6 " - " MAN H 7 " " BMA U 3 " - " MAN U 4 " " MAN U 6 " - " MAN U 7 " " BMA W 3 " - " MAN W 4 " " BMA b 3 " - " MAN b 4 " " BMA e 3 " - " MAN e 6 " ALPHA1-6 " BMA D 3 " - " MAN D 6 " " BMA H 3 " - " MAN H 6 " " BMA U 3 " - " MAN U 6 " " BMA W 3 " - " MAN W 6 " " BMA b 3 " - " MAN b 6 " " BMA e 3 " - " MAN e 4 " " MAN e 4 " - " MAN e 5 " BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG D 2 " - " BMA D 3 " " NAG E 1 " - " NAG E 2 " " NAG E 2 " - " BMA E 3 " " NAG H 1 " - " NAG H 2 " " NAG H 2 " - " BMA H 3 " " NAG L 1 " - " NAG L 2 " " NAG L 2 " - " BMA L 3 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG U 2 " - " BMA U 3 " " NAG V 1 " - " NAG V 2 " " NAG V 2 " - " BMA V 3 " " NAG W 1 " - " NAG W 2 " " NAG W 2 " - " BMA W 3 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " " NAG b 1 " - " NAG b 2 " " NAG b 2 " - " BMA b 3 " " NAG c 1 " - " NAG c 2 " " NAG d 1 " - " NAG d 2 " " NAG e 1 " - " NAG e 2 " " NAG e 2 " - " BMA e 3 " " NAG f 1 " - " NAG f 2 " " NAG g 1 " - " NAG g 2 " NAG-ASN " NAG C 701 " - " ASN C 637 " " NAG C 702 " - " ASN C 618 " " NAG C 703 " - " ASN C 611 " " NAG D 1 " - " ASN G 262 " " NAG E 1 " - " ASN G 276 " " NAG G 601 " - " ASN G 88 " " NAG G 602 " - " ASN G 160 " " NAG G 603 " - " ASN G 197 " " NAG G 604 " - " ASN G 234 " " NAG G 614 " - " ASN G 295 " " NAG G 615 " - " ASN G 301 " " NAG G 623 " - " ASN G 339 " " NAG G 624 " - " ASN G 355 " " NAG G 628 " - " ASN G 392 " " NAG H 1 " - " ASN G 332 " " NAG J 701 " - " ASN J 611 " " NAG J 702 " - " ASN J 618 " " NAG J 703 " - " ASN J 637 " " NAG K 601 " - " ASN K 448 " " NAG K 608 " - " ASN K 234 " " NAG K 619 " - " ASN K 295 " " NAG K 620 " - " ASN K 301 " " NAG K 627 " - " ASN K 339 " " NAG K 628 " - " ASN K 355 " " NAG K 631 " - " ASN K 392 " " NAG L 1 " - " ASN G 386 " " NAG M 1 " - " ASN G 448 " " NAG N 1 " - " ASN K 88 " " NAG Q 701 " - " ASN Q 611 " " NAG Q 702 " - " ASN Q 618 " " NAG Q 703 " - " ASN Q 637 " " NAG R 607 " - " ASN R 234 " " NAG R 616 " - " ASN R 295 " " NAG R 625 " - " ASN R 339 " " NAG R 626 " - " ASN R 355 " " NAG R 629 " - " ASN R 392 " " NAG S 1 " - " ASN K 160 " " NAG T 1 " - " ASN K 197 " " NAG U 1 " - " ASN K 262 " " NAG V 1 " - " ASN K 276 " " NAG W 1 " - " ASN K 332 " " NAG X 1 " - " ASN K 386 " " NAG Y 1 " - " ASN R 88 " " NAG Z 1 " - " ASN R 160 " " NAG a 1 " - " ASN R 197 " " NAG b 1 " - " ASN R 262 " " NAG c 1 " - " ASN R 276 " " NAG d 1 " - " ASN R 301 " " NAG e 1 " - " ASN R 332 " " NAG f 1 " - " ASN R 386 " " NAG g 1 " - " ASN R 448 " Time building additional restraints: 1.67 Conformation dependent library (CDL) restraints added in 741.0 milliseconds 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4476 Finding SS restraints... Secondary structure from input PDB file: 39 helices and 41 sheets defined 16.5% alpha, 25.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.57 Creating SS restraints... Processing helix chain 'C' and resid 529 through 534 Processing helix chain 'C' and resid 537 through 543 removed outlier: 3.677A pdb=" N ALA C 541 " --> pdb=" O LEU C 537 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N ASN C 543 " --> pdb=" O VAL C 539 " (cutoff:3.500A) Processing helix chain 'C' and resid 573 through 596 removed outlier: 3.604A pdb=" N ALA C 578 " --> pdb=" O LYS C 574 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N ARG C 579 " --> pdb=" O GLN C 575 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N LEU C 581 " --> pdb=" O GLN C 577 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N VAL C 583 " --> pdb=" O ARG C 579 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N GLU C 584 " --> pdb=" O VAL C 580 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N HIS C 585 " --> pdb=" O LEU C 581 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N ASP C 589 " --> pdb=" O HIS C 585 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N TRP C 596 " --> pdb=" O LEU C 592 " (cutoff:3.500A) Processing helix chain 'C' and resid 627 through 636 removed outlier: 4.253A pdb=" N LYS C 633 " --> pdb=" O LEU C 629 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N GLU C 634 " --> pdb=" O GLN C 630 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N ILE C 635 " --> pdb=" O TRP C 631 " (cutoff:3.500A) Processing helix chain 'C' and resid 638 through 662 removed outlier: 3.631A pdb=" N GLU C 647 " --> pdb=" O TYR C 643 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N SER C 649 " --> pdb=" O LEU C 645 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N GLN C 650 " --> pdb=" O LEU C 646 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N ASN C 651 " --> pdb=" O GLU C 647 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N GLN C 652 " --> pdb=" O GLU C 648 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ASN C 656 " --> pdb=" O GLN C 652 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N GLU C 657 " --> pdb=" O GLN C 653 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N GLN C 658 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ASP C 659 " --> pdb=" O LYS C 655 " (cutoff:3.500A) Processing helix chain 'G' and resid 99 through 115 removed outlier: 3.631A pdb=" N GLU G 106 " --> pdb=" O GLU G 102 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N ILE G 109 " --> pdb=" O HIS G 105 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N LEU G 111 " --> pdb=" O ASP G 107 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N SER G 115 " --> pdb=" O LEU G 111 " (cutoff:3.500A) Processing helix chain 'G' and resid 177 through 179 No H-bonds generated for 'chain 'G' and resid 177 through 179' Processing helix chain 'G' and resid 335 through 350 removed outlier: 3.506A pdb=" N LYS G 347 " --> pdb=" O GLY G 343 " (cutoff:3.500A) Processing helix chain 'G' and resid 351 through 353 No H-bonds generated for 'chain 'G' and resid 351 through 353' Processing helix chain 'G' and resid 368 through 373 removed outlier: 3.583A pdb=" N THR G 373 " --> pdb=" O LEU G 369 " (cutoff:3.500A) Processing helix chain 'G' and resid 387 through 391 removed outlier: 3.694A pdb=" N LEU G 390 " --> pdb=" O THR G 387 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N PHE G 391 " --> pdb=" O SER G 388 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 387 through 391' Processing helix chain 'G' and resid 425 through 429 removed outlier: 4.044A pdb=" N GLN G 428 " --> pdb=" O ASN G 425 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N ARG G 429 " --> pdb=" O MET G 426 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 425 through 429' Processing helix chain 'G' and resid 476 through 481 Processing helix chain 'J' and resid 529 through 534 Processing helix chain 'J' and resid 537 through 543 removed outlier: 3.676A pdb=" N ALA J 541 " --> pdb=" O LEU J 537 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N ASN J 543 " --> pdb=" O VAL J 539 " (cutoff:3.500A) Processing helix chain 'J' and resid 573 through 596 removed outlier: 3.604A pdb=" N ALA J 578 " --> pdb=" O LYS J 574 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N ARG J 579 " --> pdb=" O GLN J 575 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N LEU J 581 " --> pdb=" O GLN J 577 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N VAL J 583 " --> pdb=" O ARG J 579 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N GLU J 584 " --> pdb=" O VAL J 580 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N HIS J 585 " --> pdb=" O LEU J 581 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N ASP J 589 " --> pdb=" O HIS J 585 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N TRP J 596 " --> pdb=" O LEU J 592 " (cutoff:3.500A) Processing helix chain 'J' and resid 627 through 636 removed outlier: 4.253A pdb=" N LYS J 633 " --> pdb=" O LEU J 629 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N GLU J 634 " --> pdb=" O GLN J 630 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N ILE J 635 " --> pdb=" O TRP J 631 " (cutoff:3.500A) Processing helix chain 'J' and resid 638 through 662 removed outlier: 3.632A pdb=" N GLU J 647 " --> pdb=" O TYR J 643 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N SER J 649 " --> pdb=" O LEU J 645 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N GLN J 650 " --> pdb=" O LEU J 646 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N ASN J 651 " --> pdb=" O GLU J 647 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N GLN J 652 " --> pdb=" O GLU J 648 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ASN J 656 " --> pdb=" O GLN J 652 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N GLU J 657 " --> pdb=" O GLN J 653 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N GLN J 658 " --> pdb=" O GLU J 654 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ASP J 659 " --> pdb=" O LYS J 655 " (cutoff:3.500A) Processing helix chain 'K' and resid 99 through 115 removed outlier: 3.559A pdb=" N GLU K 106 " --> pdb=" O GLU K 102 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N ILE K 109 " --> pdb=" O HIS K 105 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LEU K 111 " --> pdb=" O ASP K 107 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N SER K 115 " --> pdb=" O LEU K 111 " (cutoff:3.500A) Processing helix chain 'K' and resid 177 through 179 No H-bonds generated for 'chain 'K' and resid 177 through 179' Processing helix chain 'K' and resid 335 through 350 removed outlier: 3.610A pdb=" N LYS K 347 " --> pdb=" O GLY K 343 " (cutoff:3.500A) Processing helix chain 'K' and resid 351 through 353 No H-bonds generated for 'chain 'K' and resid 351 through 353' Processing helix chain 'K' and resid 368 through 373 removed outlier: 3.668A pdb=" N THR K 373 " --> pdb=" O LEU K 369 " (cutoff:3.500A) Processing helix chain 'K' and resid 387 through 391 removed outlier: 3.759A pdb=" N LEU K 390 " --> pdb=" O THR K 387 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N PHE K 391 " --> pdb=" O SER K 388 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 387 through 391' Processing helix chain 'K' and resid 425 through 429 removed outlier: 4.056A pdb=" N GLN K 428 " --> pdb=" O ASN K 425 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N ARG K 429 " --> pdb=" O MET K 426 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 425 through 429' Processing helix chain 'K' and resid 476 through 481 Processing helix chain 'Q' and resid 529 through 534 Processing helix chain 'Q' and resid 537 through 543 removed outlier: 3.676A pdb=" N ALA Q 541 " --> pdb=" O LEU Q 537 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N ASN Q 543 " --> pdb=" O VAL Q 539 " (cutoff:3.500A) Processing helix chain 'Q' and resid 573 through 596 removed outlier: 3.604A pdb=" N ALA Q 578 " --> pdb=" O LYS Q 574 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N ARG Q 579 " --> pdb=" O GLN Q 575 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N LEU Q 581 " --> pdb=" O GLN Q 577 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N VAL Q 583 " --> pdb=" O ARG Q 579 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N GLU Q 584 " --> pdb=" O VAL Q 580 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N HIS Q 585 " --> pdb=" O LEU Q 581 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N ASP Q 589 " --> pdb=" O HIS Q 585 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N TRP Q 596 " --> pdb=" O LEU Q 592 " (cutoff:3.500A) Processing helix chain 'Q' and resid 627 through 636 removed outlier: 4.253A pdb=" N LYS Q 633 " --> pdb=" O LEU Q 629 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N GLU Q 634 " --> pdb=" O GLN Q 630 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ILE Q 635 " --> pdb=" O TRP Q 631 " (cutoff:3.500A) Processing helix chain 'Q' and resid 638 through 662 removed outlier: 3.633A pdb=" N GLU Q 647 " --> pdb=" O TYR Q 643 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N SER Q 649 " --> pdb=" O LEU Q 645 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N GLN Q 650 " --> pdb=" O LEU Q 646 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N ASN Q 651 " --> pdb=" O GLU Q 647 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N GLN Q 652 " --> pdb=" O GLU Q 648 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ASN Q 656 " --> pdb=" O GLN Q 652 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N GLU Q 657 " --> pdb=" O GLN Q 653 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N GLN Q 658 " --> pdb=" O GLU Q 654 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ASP Q 659 " --> pdb=" O LYS Q 655 " (cutoff:3.500A) Processing helix chain 'R' and resid 99 through 115 removed outlier: 3.561A pdb=" N GLN R 103 " --> pdb=" O ASN R 99 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N GLU R 106 " --> pdb=" O GLU R 102 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N ILE R 109 " --> pdb=" O HIS R 105 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LEU R 111 " --> pdb=" O ASP R 107 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N GLN R 114 " --> pdb=" O SER R 110 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N SER R 115 " --> pdb=" O LEU R 111 " (cutoff:3.500A) Processing helix chain 'R' and resid 177 through 179 No H-bonds generated for 'chain 'R' and resid 177 through 179' Processing helix chain 'R' and resid 335 through 350 removed outlier: 3.501A pdb=" N LYS R 347 " --> pdb=" O GLY R 343 " (cutoff:3.500A) Processing helix chain 'R' and resid 351 through 353 No H-bonds generated for 'chain 'R' and resid 351 through 353' Processing helix chain 'R' and resid 368 through 373 removed outlier: 3.525A pdb=" N THR R 373 " --> pdb=" O LEU R 369 " (cutoff:3.500A) Processing helix chain 'R' and resid 387 through 391 removed outlier: 3.633A pdb=" N LEU R 390 " --> pdb=" O THR R 387 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N PHE R 391 " --> pdb=" O SER R 388 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 387 through 391' Processing helix chain 'R' and resid 425 through 429 removed outlier: 4.164A pdb=" N GLN R 428 " --> pdb=" O ASN R 425 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N ARG R 429 " --> pdb=" O MET R 426 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 425 through 429' Processing helix chain 'R' and resid 476 through 481 Processing sheet with id=AA1, first strand: chain 'G' and resid 35 through 40 Processing sheet with id=AA2, first strand: chain 'G' and resid 45 through 46 removed outlier: 3.801A pdb=" N ILE G 225 " --> pdb=" O VAL G 245 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'G' and resid 91 through 94 removed outlier: 3.838A pdb=" N GLU G 91 " --> pdb=" O CYS G 239 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N GLY G 237 " --> pdb=" O PHE G 93 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'G' and resid 169 through 176 removed outlier: 3.604A pdb=" N VAL G 172 " --> pdb=" O PHE G 159 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N PHE G 159 " --> pdb=" O VAL G 172 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N CYS G 131 " --> pdb=" O LYS G 189 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N LYS G 189 " --> pdb=" O CYS G 131 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'G' and resid 199 through 203 removed outlier: 6.384A pdb=" N ALA G 200 " --> pdb=" O ALA G 433 " (cutoff:3.500A) removed outlier: 7.952A pdb=" N TYR G 435 " --> pdb=" O ALA G 200 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N THR G 202 " --> pdb=" O TYR G 435 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'G' and resid 271 through 273 Processing sheet with id=AA7, first strand: chain 'G' and resid 384 through 385 removed outlier: 4.699A pdb=" N SER G 334 " --> pdb=" O GLN G 293 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N GLN G 293 " --> pdb=" O SER G 334 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N VAL G 292 " --> pdb=" O ILE G 449 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ILE G 294 " --> pdb=" O SER G 447 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ILE G 443 " --> pdb=" O ARG G 298 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'G' and resid 304 through 307 removed outlier: 3.753A pdb=" N LYS G 305 " --> pdb=" O TYR G 319 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N TYR G 319 " --> pdb=" O LYS G 305 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'G' and resid 377 through 378 removed outlier: 3.590A pdb=" N GLU G 381 " --> pdb=" O CYS G 378 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'K' and resid 35 through 40 Processing sheet with id=AB2, first strand: chain 'K' and resid 45 through 46 removed outlier: 3.693A pdb=" N ILE K 225 " --> pdb=" O VAL K 245 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'K' and resid 91 through 94 removed outlier: 3.758A pdb=" N GLU K 91 " --> pdb=" O CYS K 239 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N GLY K 237 " --> pdb=" O PHE K 93 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'K' and resid 169 through 176 removed outlier: 3.533A pdb=" N VAL K 172 " --> pdb=" O PHE K 159 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N PHE K 159 " --> pdb=" O VAL K 172 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N CYS K 131 " --> pdb=" O LYS K 189 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N LYS K 189 " --> pdb=" O CYS K 131 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'K' and resid 200 through 203 removed outlier: 4.045A pdb=" N ALA K 433 " --> pdb=" O ALA K 200 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'K' and resid 259 through 261 removed outlier: 4.883A pdb=" N LEU K 260 " --> pdb=" O THR K 450 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N ILE K 358 " --> pdb=" O GLU K 466 " (cutoff:3.500A) removed outlier: 7.849A pdb=" N PHE K 468 " --> pdb=" O ILE K 358 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N ARG K 360 " --> pdb=" O PHE K 468 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'K' and resid 271 through 273 removed outlier: 3.503A pdb=" N VAL K 286 " --> pdb=" O LEU K 452 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N LEU K 452 " --> pdb=" O VAL K 286 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N ILE K 443 " --> pdb=" O ARG K 298 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N SER K 447 " --> pdb=" O ILE K 294 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N ILE K 294 " --> pdb=" O SER K 447 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N VAL K 292 " --> pdb=" O ILE K 449 " (cutoff:3.500A) removed outlier: 7.092A pdb=" N GLN K 293 " --> pdb=" O SER K 334 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N SER K 334 " --> pdb=" O GLN K 293 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N HIS K 330 " --> pdb=" O THR K 297 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N GLU K 381 " --> pdb=" O CYS K 378 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N CYS K 378 " --> pdb=" O GLU K 381 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N PHE K 376 " --> pdb=" O PHE K 383 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'K' and resid 302 through 307 removed outlier: 6.637A pdb=" N THR K 303 " --> pdb=" O GLY K 321 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N LYS K 305 " --> pdb=" O TYR K 319 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N TYR K 319 " --> pdb=" O LYS K 305 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'R' and resid 35 through 40 Processing sheet with id=AC1, first strand: chain 'R' and resid 45 through 46 removed outlier: 3.754A pdb=" N ILE R 225 " --> pdb=" O VAL R 245 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'R' and resid 91 through 94 removed outlier: 3.825A pdb=" N GLU R 91 " --> pdb=" O CYS R 239 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N GLY R 237 " --> pdb=" O PHE R 93 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'R' and resid 169 through 176 removed outlier: 3.608A pdb=" N VAL R 172 " --> pdb=" O PHE R 159 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N PHE R 159 " --> pdb=" O VAL R 172 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N LYS R 189 " --> pdb=" O CYS R 131 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'R' and resid 200 through 203 removed outlier: 6.798A pdb=" N ALA R 200 " --> pdb=" O ALA R 433 " (cutoff:3.500A) removed outlier: 7.791A pdb=" N TYR R 435 " --> pdb=" O ALA R 200 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N THR R 202 " --> pdb=" O TYR R 435 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC4 Processing sheet with id=AC5, first strand: chain 'R' and resid 271 through 273 Processing sheet with id=AC6, first strand: chain 'R' and resid 374 through 378 removed outlier: 3.732A pdb=" N PHE R 376 " --> pdb=" O PHE R 383 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N HIS R 330 " --> pdb=" O THR R 297 " (cutoff:3.500A) removed outlier: 4.720A pdb=" N SER R 334 " --> pdb=" O GLN R 293 " (cutoff:3.500A) removed outlier: 7.636A pdb=" N GLN R 293 " --> pdb=" O SER R 334 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N VAL R 292 " --> pdb=" O ILE R 449 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ILE R 294 " --> pdb=" O SER R 447 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ILE R 443 " --> pdb=" O ARG R 298 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'R' and resid 302 through 307 removed outlier: 6.495A pdb=" N THR R 303 " --> pdb=" O GLY R 321 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N LYS R 305 " --> pdb=" O TYR R 319 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N TYR R 319 " --> pdb=" O LYS R 305 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'R' and resid 360 through 361 removed outlier: 6.645A pdb=" N ARG R 360 " --> pdb=" O PHE R 468 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC8 Processing sheet with id=AC9, first strand: chain 'A' and resid 3 through 7 removed outlier: 3.520A pdb=" N LEU A 78 " --> pdb=" O CYS A 22 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'A' and resid 11 through 12 removed outlier: 3.500A pdb=" N VAL A 12 " --> pdb=" O THR A 129 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N THR A 126 " --> pdb=" O TYR A 90 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N VAL A 128 " --> pdb=" O ALA A 88 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N VAL A 89 " --> pdb=" O GLN A 39 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ALA A 93 " --> pdb=" O THR A 35 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N TRP A 34 " --> pdb=" O TYR A 50 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N TYR A 50 " --> pdb=" O TRP A 34 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N TRP A 36 " --> pdb=" O ILE A 48 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N TYR A 50 " --> pdb=" O THR A 58 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N THR A 58 " --> pdb=" O TYR A 50 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'A' and resid 11 through 12 removed outlier: 3.500A pdb=" N VAL A 12 " --> pdb=" O THR A 129 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N THR A 126 " --> pdb=" O TYR A 90 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N VAL A 128 " --> pdb=" O ALA A 88 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N PHE A 100K" --> pdb=" O ARG A 100 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'F' and resid 3 through 7 removed outlier: 3.520A pdb=" N LEU F 78 " --> pdb=" O CYS F 22 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'F' and resid 11 through 12 removed outlier: 3.501A pdb=" N VAL F 12 " --> pdb=" O THR F 110 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N THR F 107 " --> pdb=" O TYR F 90 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N VAL F 109 " --> pdb=" O ALA F 88 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N VAL F 89 " --> pdb=" O GLN F 39 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ALA F 93 " --> pdb=" O THR F 35 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N TRP F 34 " --> pdb=" O TYR F 50 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N TYR F 50 " --> pdb=" O TRP F 34 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N TRP F 36 " --> pdb=" O ILE F 48 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N TYR F 50 " --> pdb=" O THR F 58 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N THR F 58 " --> pdb=" O TYR F 50 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'F' and resid 11 through 12 removed outlier: 3.501A pdb=" N VAL F 12 " --> pdb=" O THR F 110 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N THR F 107 " --> pdb=" O TYR F 90 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N VAL F 109 " --> pdb=" O ALA F 88 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N PHE F 100K" --> pdb=" O ARG F 100 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'O' and resid 3 through 7 removed outlier: 3.520A pdb=" N LEU O 78 " --> pdb=" O CYS O 22 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'O' and resid 11 through 12 removed outlier: 3.500A pdb=" N VAL O 12 " --> pdb=" O THR O 110 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N THR O 107 " --> pdb=" O TYR O 90 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N VAL O 109 " --> pdb=" O ALA O 88 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N VAL O 89 " --> pdb=" O GLN O 39 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ALA O 93 " --> pdb=" O THR O 35 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N TRP O 34 " --> pdb=" O TYR O 50 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N TYR O 50 " --> pdb=" O TRP O 34 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N TRP O 36 " --> pdb=" O ILE O 48 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N TYR O 50 " --> pdb=" O THR O 58 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N THR O 58 " --> pdb=" O TYR O 50 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'O' and resid 11 through 12 removed outlier: 3.500A pdb=" N VAL O 12 " --> pdb=" O THR O 110 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N THR O 107 " --> pdb=" O TYR O 90 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N VAL O 109 " --> pdb=" O ALA O 88 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N PHE O 100K" --> pdb=" O ARG O 100 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'B' and resid 9 through 11 removed outlier: 6.499A pdb=" N ARG B 9 " --> pdb=" O ARG B 103 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N THR B 102 " --> pdb=" O TYR B 86 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ASP B 85 " --> pdb=" O HIS B 38 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N TYR B 87 " --> pdb=" O TYR B 36 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N TYR B 36 " --> pdb=" O TYR B 87 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N TRP B 35 " --> pdb=" O LEU B 47 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'B' and resid 19 through 22 Processing sheet with id=AE2, first strand: chain 'I' and resid 9 through 11 removed outlier: 6.500A pdb=" N ARG I 9 " --> pdb=" O ARG I 103 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N THR I 102 " --> pdb=" O TYR I 86 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ASP I 85 " --> pdb=" O HIS I 38 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N TYR I 87 " --> pdb=" O TYR I 36 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N TYR I 36 " --> pdb=" O TYR I 87 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N TRP I 35 " --> pdb=" O LEU I 47 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'I' and resid 19 through 22 Processing sheet with id=AE4, first strand: chain 'P' and resid 9 through 11 removed outlier: 6.500A pdb=" N ARG P 9 " --> pdb=" O ARG P 103 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N THR P 102 " --> pdb=" O TYR P 86 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ASP P 85 " --> pdb=" O HIS P 38 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N TYR P 87 " --> pdb=" O TYR P 36 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N TYR P 36 " --> pdb=" O TYR P 87 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N TRP P 35 " --> pdb=" O LEU P 47 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'P' and resid 19 through 22 473 hydrogen bonds defined for protein. 1251 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.62 Time building geometry restraints manager: 2.29 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 5907 1.33 - 1.46: 5361 1.46 - 1.58: 9311 1.58 - 1.71: 5 1.71 - 1.84: 168 Bond restraints: 20752 Sorted by residual: bond pdb=" C1 MAN W 6 " pdb=" O5 MAN W 6 " ideal model delta sigma weight residual 1.399 1.485 -0.086 2.00e-02 2.50e+03 1.85e+01 bond pdb=" C5 MAN W 6 " pdb=" O5 MAN W 6 " ideal model delta sigma weight residual 1.418 1.496 -0.078 2.00e-02 2.50e+03 1.54e+01 bond pdb=" C1 MAN e 6 " pdb=" C2 MAN e 6 " ideal model delta sigma weight residual 1.526 1.602 -0.076 2.00e-02 2.50e+03 1.45e+01 bond pdb=" C1 NAG S 1 " pdb=" O5 NAG S 1 " ideal model delta sigma weight residual 1.406 1.331 0.075 2.00e-02 2.50e+03 1.40e+01 bond pdb=" C5 MAN H 5 " pdb=" O5 MAN H 5 " ideal model delta sigma weight residual 1.418 1.483 -0.065 2.00e-02 2.50e+03 1.04e+01 ... (remaining 20747 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.13: 27872 4.13 - 8.26: 263 8.26 - 12.39: 36 12.39 - 16.51: 3 16.51 - 20.64: 2 Bond angle restraints: 28176 Sorted by residual: angle pdb=" C ASN C 618 " pdb=" CA ASN C 618 " pdb=" CB ASN C 618 " ideal model delta sigma weight residual 109.46 88.82 20.64 1.84e+00 2.95e-01 1.26e+02 angle pdb=" N ASN G 302 " pdb=" CA ASN G 302 " pdb=" C ASN G 302 " ideal model delta sigma weight residual 110.91 117.78 -6.87 1.17e+00 7.31e-01 3.44e+01 angle pdb=" CA GLU C 584 " pdb=" CB GLU C 584 " pdb=" CG GLU C 584 " ideal model delta sigma weight residual 114.10 125.34 -11.24 2.00e+00 2.50e-01 3.16e+01 angle pdb=" CA GLU Q 584 " pdb=" CB GLU Q 584 " pdb=" CG GLU Q 584 " ideal model delta sigma weight residual 114.10 125.31 -11.21 2.00e+00 2.50e-01 3.14e+01 angle pdb=" CA GLU J 584 " pdb=" CB GLU J 584 " pdb=" CG GLU J 584 " ideal model delta sigma weight residual 114.10 125.31 -11.21 2.00e+00 2.50e-01 3.14e+01 ... (remaining 28171 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.92: 12919 21.92 - 43.84: 515 43.84 - 65.75: 149 65.75 - 87.67: 67 87.67 - 109.59: 44 Dihedral angle restraints: 13694 sinusoidal: 6737 harmonic: 6957 Sorted by residual: dihedral pdb=" C ASN C 618 " pdb=" N ASN C 618 " pdb=" CA ASN C 618 " pdb=" CB ASN C 618 " ideal model delta harmonic sigma weight residual -122.60 -96.33 -26.27 0 2.50e+00 1.60e-01 1.10e+02 dihedral pdb=" CA ASN R 386 " pdb=" C ASN R 386 " pdb=" N THR R 387 " pdb=" CA THR R 387 " ideal model delta harmonic sigma weight residual -180.00 -127.74 -52.26 0 5.00e+00 4.00e-02 1.09e+02 dihedral pdb=" CA LEU R 261 " pdb=" C LEU R 261 " pdb=" N ASN R 262 " pdb=" CA ASN R 262 " ideal model delta harmonic sigma weight residual -180.00 -134.34 -45.66 0 5.00e+00 4.00e-02 8.34e+01 ... (remaining 13691 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.158: 3336 0.158 - 0.315: 85 0.315 - 0.473: 14 0.473 - 0.630: 0 0.630 - 0.788: 1 Chirality restraints: 3436 Sorted by residual: chirality pdb=" C1 NAG D 1 " pdb=" ND2 ASN G 262 " pdb=" C2 NAG D 1 " pdb=" O5 NAG D 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.61 -0.79 2.00e-01 2.50e+01 1.55e+01 chirality pdb=" CA ASN C 618 " pdb=" N ASN C 618 " pdb=" C ASN C 618 " pdb=" CB ASN C 618 " both_signs ideal model delta sigma weight residual False 2.51 2.95 -0.44 2.00e-01 2.50e+01 4.93e+00 chirality pdb=" C1 NAG J 702 " pdb=" ND2 ASN J 618 " pdb=" C2 NAG J 702 " pdb=" O5 NAG J 702 " both_signs ideal model delta sigma weight residual False -2.40 -2.00 -0.40 2.00e-01 2.50e+01 4.03e+00 ... (remaining 3433 not shown) Planarity restraints: 3498 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG C 702 " -0.391 2.00e-02 2.50e+03 3.31e-01 1.37e+03 pdb=" C7 NAG C 702 " 0.100 2.00e-02 2.50e+03 pdb=" C8 NAG C 702 " -0.100 2.00e-02 2.50e+03 pdb=" N2 NAG C 702 " 0.581 2.00e-02 2.50e+03 pdb=" O7 NAG C 702 " -0.191 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG C 703 " 0.044 2.00e-02 2.50e+03 3.62e-02 1.64e+01 pdb=" C7 NAG C 703 " -0.011 2.00e-02 2.50e+03 pdb=" C8 NAG C 703 " 0.033 2.00e-02 2.50e+03 pdb=" N2 NAG C 703 " -0.058 2.00e-02 2.50e+03 pdb=" O7 NAG C 703 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN R 386 " -0.017 2.00e-02 2.50e+03 3.35e-02 1.12e+01 pdb=" C ASN R 386 " 0.058 2.00e-02 2.50e+03 pdb=" O ASN R 386 " -0.021 2.00e-02 2.50e+03 pdb=" N THR R 387 " -0.020 2.00e-02 2.50e+03 ... (remaining 3495 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 4669 2.79 - 3.31: 17379 3.31 - 3.84: 31083 3.84 - 4.37: 32362 4.37 - 4.90: 57173 Nonbonded interactions: 142666 Sorted by model distance: nonbonded pdb=" OG1 THR R 278 " pdb=" O7 NAG c 1 " model vdw 2.257 3.040 nonbonded pdb=" O TRP Q 571 " pdb=" NE2 GLN Q 575 " model vdw 2.298 3.120 nonbonded pdb=" O TRP J 571 " pdb=" NE2 GLN J 575 " model vdw 2.299 3.120 nonbonded pdb=" O TRP C 571 " pdb=" NE2 GLN C 575 " model vdw 2.299 3.120 nonbonded pdb=" O4 MAN e 6 " pdb=" O6 MAN e 6 " model vdw 2.335 3.040 ... (remaining 142661 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 'F' selection = chain 'O' } ncs_group { reference = chain 'B' selection = chain 'I' selection = chain 'P' } ncs_group { reference = chain 'C' selection = chain 'J' selection = chain 'Q' } ncs_group { reference = (chain 'D' and (resid 1 or resid 4 through 6)) selection = (chain 'H' and (resid 2 or resid 5 through 7)) selection = (chain 'U' and (resid 2 or resid 5 through 7)) selection = (chain 'W' and (resid 1 or resid 4 through 6)) selection = (chain 'b' and (resid 1 or resid 4 through 6)) selection = (chain 'e' and (resid 1 or resid 4 through 6)) } ncs_group { reference = chain 'E' selection = chain 'L' selection = chain 'V' } ncs_group { reference = (chain 'G' and resid 31 through 614) selection = (chain 'K' and resid 31 through 627) selection = chain 'R' } ncs_group { reference = chain 'M' selection = chain 'N' selection = chain 'S' selection = chain 'T' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' selection = chain 'c' selection = chain 'd' selection = chain 'f' selection = chain 'g' } 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: 0.710 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.200 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 18.030 Find NCS groups from input model: 0.440 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8447 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 : 0.008 0.086 20892 Z= 0.363 Angle : 1.243 21.919 28557 Z= 0.601 Chirality : 0.068 0.788 3436 Planarity : 0.009 0.331 3447 Dihedral : 15.034 109.588 9101 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.17 % Allowed : 7.45 % Favored : 92.39 % Rotamer: Outliers : 0.62 % Allowed : 3.03 % Favored : 96.35 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.01 % Twisted General : 0.22 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.42 (0.14), residues: 2364 helix: -4.07 (0.15), residues: 351 sheet: -2.00 (0.20), residues: 558 loop : -3.17 (0.13), residues: 1455 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.047 0.001 ARG O 54 TYR 0.014 0.002 TYR K 319 PHE 0.022 0.003 PHE R 53 TRP 0.035 0.003 TRP R 96 HIS 0.004 0.001 HIS I 38 Details of bonding type rmsd covalent geometry : bond 0.00753 (20752) covalent geometry : angle 1.13637 (28176) SS BOND : bond 0.00737 ( 39) SS BOND : angle 2.29379 ( 78) hydrogen bonds : bond 0.27066 ( 467) hydrogen bonds : angle 8.68981 ( 1251) link_ALPHA1-2 : bond 0.00758 ( 5) link_ALPHA1-2 : angle 3.51331 ( 15) link_ALPHA1-3 : bond 0.00935 ( 8) link_ALPHA1-3 : angle 2.70721 ( 24) link_ALPHA1-6 : bond 0.01014 ( 7) link_ALPHA1-6 : angle 2.44177 ( 21) link_BETA1-4 : bond 0.01034 ( 30) link_BETA1-4 : angle 5.51101 ( 90) link_NAG-ASN : bond 0.00980 ( 51) link_NAG-ASN : angle 5.19139 ( 153) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 489 residues out of total 2109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 476 time to evaluate : 0.682 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: C 573 ILE cc_start: 0.9088 (mm) cc_final: 0.8508 (tp) REVERT: C 575 GLN cc_start: 0.8690 (mp-120) cc_final: 0.8077 (mp-120) REVERT: C 576 LEU cc_start: 0.9637 (OUTLIER) cc_final: 0.9394 (mt) REVERT: C 590 GLN cc_start: 0.9436 (tp-100) cc_final: 0.9021 (tp-100) REVERT: C 632 ASP cc_start: 0.8763 (t70) cc_final: 0.7896 (t70) REVERT: C 654 GLU cc_start: 0.9580 (mm-30) cc_final: 0.9241 (mm-30) REVERT: G 95 MET cc_start: 0.9155 (ptt) cc_final: 0.8806 (ptt) REVERT: G 161 MET cc_start: 0.8726 (tpp) cc_final: 0.8288 (tpt) REVERT: G 322 ILE cc_start: 0.9199 (mm) cc_final: 0.8981 (mm) REVERT: J 543 ASN cc_start: 0.9006 (m-40) cc_final: 0.8721 (t0) REVERT: J 576 LEU cc_start: 0.9615 (OUTLIER) cc_final: 0.9399 (mt) REVERT: J 577 GLN cc_start: 0.9158 (mt0) cc_final: 0.8527 (mt0) REVERT: J 588 ARG cc_start: 0.8766 (ttm-80) cc_final: 0.8520 (ttm170) REVERT: J 616 ASN cc_start: 0.9222 (p0) cc_final: 0.8923 (m-40) REVERT: J 632 ASP cc_start: 0.8923 (t70) cc_final: 0.8577 (t70) REVERT: J 654 GLU cc_start: 0.9421 (mm-30) cc_final: 0.9186 (mm-30) REVERT: K 475 MET cc_start: 0.8699 (mmm) cc_final: 0.8427 (tpp) REVERT: K 482 GLU cc_start: 0.8916 (tp30) cc_final: 0.8364 (tp30) REVERT: K 492 GLU cc_start: 0.8563 (tm-30) cc_final: 0.7889 (tm-30) REVERT: Q 530 MET cc_start: 0.9067 (mtp) cc_final: 0.8815 (ttm) REVERT: Q 573 ILE cc_start: 0.8993 (mm) cc_final: 0.8481 (tp) REVERT: Q 575 GLN cc_start: 0.9041 (mp-120) cc_final: 0.8659 (mp10) REVERT: Q 576 LEU cc_start: 0.9591 (OUTLIER) cc_final: 0.9370 (mt) REVERT: Q 577 GLN cc_start: 0.9121 (mt0) cc_final: 0.8877 (mt0) REVERT: Q 601 LYS cc_start: 0.9158 (mppt) cc_final: 0.8938 (mmtt) REVERT: Q 632 ASP cc_start: 0.8835 (t70) cc_final: 0.8403 (t70) REVERT: R 95 MET cc_start: 0.9165 (ptm) cc_final: 0.8951 (ptt) REVERT: R 99 ASN cc_start: 0.9493 (m-40) cc_final: 0.9246 (m-40) REVERT: R 377 ASN cc_start: 0.9314 (p0) cc_final: 0.8584 (t0) REVERT: R 434 MET cc_start: 0.8836 (ttm) cc_final: 0.8381 (ttm) REVERT: R 492 GLU cc_start: 0.8735 (tm-30) cc_final: 0.8079 (tm-30) REVERT: A 13 LYS cc_start: 0.8996 (pmtt) cc_final: 0.8655 (mmmt) REVERT: A 29 MET cc_start: 0.6694 (ptm) cc_final: 0.5534 (ptp) REVERT: A 34 TRP cc_start: 0.8817 (m100) cc_final: 0.8444 (m100) REVERT: A 37 ILE cc_start: 0.9483 (mm) cc_final: 0.9279 (mm) REVERT: A 46 GLU cc_start: 0.8887 (tt0) cc_final: 0.8573 (tm-30) REVERT: A 64 ASN cc_start: 0.8945 (m-40) cc_final: 0.8718 (m110) REVERT: A 78 LEU cc_start: 0.9118 (mt) cc_final: 0.8709 (mt) REVERT: A 81 LYS cc_start: 0.9437 (mttt) cc_final: 0.9063 (mtpp) REVERT: A 91 TYR cc_start: 0.9160 (m-80) cc_final: 0.8639 (m-80) REVERT: A 100 GLU cc_start: 0.8658 (tt0) cc_final: 0.8294 (tt0) REVERT: F 1 GLN cc_start: 0.7273 (tp40) cc_final: 0.6471 (tm-30) REVERT: F 3 GLN cc_start: 0.9348 (mm110) cc_final: 0.9009 (mm110) REVERT: F 13 LYS cc_start: 0.9360 (pmtt) cc_final: 0.9111 (tppt) REVERT: F 29 MET cc_start: 0.6131 (ptm) cc_final: 0.5533 (ptm) REVERT: F 46 GLU cc_start: 0.8640 (tt0) cc_final: 0.8422 (tm-30) REVERT: F 77 GLN cc_start: 0.8757 (mm-40) cc_final: 0.8428 (tp40) REVERT: F 78 LEU cc_start: 0.9126 (mt) cc_final: 0.8725 (mt) REVERT: F 80 LEU cc_start: 0.8559 (mt) cc_final: 0.7335 (mt) REVERT: F 81 LYS cc_start: 0.9531 (mttt) cc_final: 0.8982 (mmmm) REVERT: F 105 LYS cc_start: 0.8776 (ptmt) cc_final: 0.8295 (mtmm) REVERT: O 3 GLN cc_start: 0.9350 (mm110) cc_final: 0.8757 (mp10) REVERT: O 13 LYS cc_start: 0.9110 (pmtt) cc_final: 0.8751 (tppt) REVERT: O 29 MET cc_start: 0.5098 (ptm) cc_final: 0.4724 (ptp) REVERT: O 46 GLU cc_start: 0.8703 (tt0) cc_final: 0.8488 (tm-30) REVERT: O 77 GLN cc_start: 0.9002 (mm-40) cc_final: 0.8702 (tp40) REVERT: O 78 LEU cc_start: 0.9193 (mt) cc_final: 0.8549 (mt) REVERT: O 81 LYS cc_start: 0.9449 (mttt) cc_final: 0.9008 (mmmm) REVERT: O 82 ASN cc_start: 0.9019 (m-40) cc_final: 0.8667 (p0) REVERT: O 100 GLU cc_start: 0.8568 (tt0) cc_final: 0.8024 (tt0) REVERT: B 26 GLN cc_start: 0.8623 (mm-40) cc_final: 0.8245 (tp-100) REVERT: B 42 GLN cc_start: 0.8329 (mp10) cc_final: 0.8046 (mp10) REVERT: B 47 LEU cc_start: 0.9690 (mt) cc_final: 0.9472 (mp) REVERT: B 70 ARG cc_start: 0.7924 (mmm160) cc_final: 0.6501 (tpt90) REVERT: B 83 GLU cc_start: 0.7642 (tp30) cc_final: 0.7315 (tp30) REVERT: B 85 ASP cc_start: 0.8270 (m-30) cc_final: 0.7730 (p0) REVERT: B 104 LEU cc_start: 0.8741 (tp) cc_final: 0.8086 (tp) REVERT: I 37 GLN cc_start: 0.8835 (tt0) cc_final: 0.8514 (tm-30) REVERT: I 42 GLN cc_start: 0.8453 (mp10) cc_final: 0.8091 (mp10) REVERT: I 47 LEU cc_start: 0.9626 (mt) cc_final: 0.9120 (mp) REVERT: I 70 ARG cc_start: 0.7944 (mmm160) cc_final: 0.7007 (mmt180) REVERT: I 83 GLU cc_start: 0.7915 (tp30) cc_final: 0.7518 (tp30) REVERT: I 85 ASP cc_start: 0.8388 (m-30) cc_final: 0.8040 (p0) REVERT: I 92 ASP cc_start: 0.8807 (p0) cc_final: 0.8559 (p0) REVERT: I 104 LEU cc_start: 0.8637 (tp) cc_final: 0.8072 (tp) REVERT: P 18 THR cc_start: 0.9108 (p) cc_final: 0.8883 (t) REVERT: P 33 VAL cc_start: 0.9416 (m) cc_final: 0.8921 (m) REVERT: P 37 GLN cc_start: 0.9017 (tt0) cc_final: 0.8428 (tp40) REVERT: P 42 GLN cc_start: 0.8172 (mp10) cc_final: 0.7878 (mp10) REVERT: P 47 LEU cc_start: 0.9637 (mt) cc_final: 0.9342 (mp) REVERT: P 53 ASP cc_start: 0.9030 (m-30) cc_final: 0.8738 (t0) REVERT: P 70 ARG cc_start: 0.7818 (mmm160) cc_final: 0.6338 (tpt90) REVERT: P 83 GLU cc_start: 0.7863 (tp30) cc_final: 0.7535 (tp30) REVERT: P 85 ASP cc_start: 0.8192 (m-30) cc_final: 0.7741 (p0) REVERT: P 104 LEU cc_start: 0.8701 (tp) cc_final: 0.8500 (tp) outliers start: 13 outliers final: 6 residues processed: 482 average time/residue: 0.1620 time to fit residues: 113.3282 Evaluate side-chains 318 residues out of total 2109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 309 time to evaluate : 0.645 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 216 optimal weight: 0.3980 chunk 98 optimal weight: 5.9990 chunk 194 optimal weight: 0.4980 chunk 227 optimal weight: 9.9990 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 0.9990 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 9.9990 chunk 235 optimal weight: 5.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 590 GLN G 103 GLN G 133 ASN G 188 ASN G 352 HIS K 103 GLN K 133 ASN K 302 ASN R 103 GLN R 133 ASN R 188 ASN R 300 ASN R 478 ASN ** F 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 77 GLN O 77 GLN ** B 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 89 HIS I 89 HIS P 89 HIS Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.073348 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2743 r_free = 0.2743 target = 0.054913 restraints weight = 69090.092| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2794 r_free = 0.2794 target = 0.057110 restraints weight = 32794.924| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2828 r_free = 0.2828 target = 0.058598 restraints weight = 20600.449| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.2850 r_free = 0.2850 target = 0.059589 restraints weight = 15233.931| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.2864 r_free = 0.2864 target = 0.060215 restraints weight = 12500.213| |-----------------------------------------------------------------------------| r_work (final): 0.2852 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8362 moved from start: 0.1778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 20892 Z= 0.140 Angle : 0.805 15.535 28557 Z= 0.369 Chirality : 0.049 0.485 3436 Planarity : 0.004 0.041 3447 Dihedral : 13.206 113.358 4667 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.70 % Favored : 95.18 % Rotamer: Outliers : 0.09 % Allowed : 2.37 % Favored : 97.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.58 (0.15), residues: 2364 helix: -2.90 (0.20), residues: 369 sheet: -1.52 (0.20), residues: 569 loop : -2.70 (0.14), residues: 1426 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG I 31 TYR 0.016 0.001 TYR Q 586 PHE 0.013 0.001 PHE K 320 TRP 0.021 0.001 TRP G 69 HIS 0.002 0.001 HIS G 105 Details of bonding type rmsd covalent geometry : bond 0.00302 (20752) covalent geometry : angle 0.73717 (28176) SS BOND : bond 0.00179 ( 39) SS BOND : angle 1.50974 ( 78) hydrogen bonds : bond 0.04650 ( 467) hydrogen bonds : angle 5.75891 ( 1251) link_ALPHA1-2 : bond 0.00866 ( 5) link_ALPHA1-2 : angle 3.18082 ( 15) link_ALPHA1-3 : bond 0.01197 ( 8) link_ALPHA1-3 : angle 1.52187 ( 24) link_ALPHA1-6 : bond 0.01074 ( 7) link_ALPHA1-6 : angle 2.43203 ( 21) link_BETA1-4 : bond 0.00745 ( 30) link_BETA1-4 : angle 3.25502 ( 90) link_NAG-ASN : bond 0.00488 ( 51) link_NAG-ASN : angle 3.38014 ( 153) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 433 residues out of total 2109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 431 time to evaluate : 0.747 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: C 543 ASN cc_start: 0.8806 (t0) cc_final: 0.8422 (t0) REVERT: C 577 GLN cc_start: 0.8829 (mt0) cc_final: 0.8486 (mt0) REVERT: C 580 VAL cc_start: 0.9356 (p) cc_final: 0.8965 (p) REVERT: C 584 GLU cc_start: 0.9311 (pm20) cc_final: 0.8961 (pm20) REVERT: C 647 GLU cc_start: 0.8703 (tm-30) cc_final: 0.8390 (tm-30) REVERT: G 49 GLU cc_start: 0.8783 (pp20) cc_final: 0.8432 (tm-30) REVERT: G 95 MET cc_start: 0.9221 (ptt) cc_final: 0.8724 (ptt) REVERT: J 543 ASN cc_start: 0.9069 (m-40) cc_final: 0.8654 (t0) REVERT: J 577 GLN cc_start: 0.8927 (mt0) cc_final: 0.8498 (mt0) REVERT: J 616 ASN cc_start: 0.9082 (p0) cc_final: 0.8876 (m-40) REVERT: J 624 ASP cc_start: 0.8876 (m-30) cc_final: 0.8483 (p0) REVERT: J 632 ASP cc_start: 0.9015 (t70) cc_final: 0.8644 (t70) REVERT: Q 543 ASN cc_start: 0.8741 (t0) cc_final: 0.8426 (t0) REVERT: Q 571 TRP cc_start: 0.7498 (m100) cc_final: 0.7150 (m100) REVERT: Q 573 ILE cc_start: 0.9087 (mm) cc_final: 0.8570 (tp) REVERT: Q 577 GLN cc_start: 0.8849 (mt0) cc_final: 0.8433 (mt0) REVERT: Q 584 GLU cc_start: 0.9302 (pm20) cc_final: 0.8898 (pm20) REVERT: Q 591 GLN cc_start: 0.9723 (tm-30) cc_final: 0.9351 (tm-30) REVERT: Q 601 LYS cc_start: 0.8977 (mppt) cc_final: 0.8714 (mmtt) REVERT: Q 624 ASP cc_start: 0.9005 (m-30) cc_final: 0.8675 (m-30) REVERT: Q 632 ASP cc_start: 0.8893 (t70) cc_final: 0.8578 (t70) REVERT: Q 643 TYR cc_start: 0.9471 (m-10) cc_final: 0.9199 (m-80) REVERT: Q 647 GLU cc_start: 0.8615 (tm-30) cc_final: 0.8396 (tm-30) REVERT: R 95 MET cc_start: 0.9106 (ptm) cc_final: 0.8613 (ptt) REVERT: R 377 ASN cc_start: 0.9366 (p0) cc_final: 0.8602 (t0) REVERT: R 434 MET cc_start: 0.8962 (ttm) cc_final: 0.8650 (ttm) REVERT: R 492 GLU cc_start: 0.8690 (tm-30) cc_final: 0.7799 (tm-30) REVERT: R 494 LEU cc_start: 0.9230 (tp) cc_final: 0.8640 (tt) REVERT: A 29 MET cc_start: 0.6740 (ptm) cc_final: 0.5860 (ptp) REVERT: A 34 TRP cc_start: 0.8641 (m100) cc_final: 0.7938 (m100) REVERT: A 48 ILE cc_start: 0.9099 (mt) cc_final: 0.8587 (mp) REVERT: A 64 ASN cc_start: 0.8944 (m-40) cc_final: 0.8703 (m110) REVERT: A 81 LYS cc_start: 0.9550 (mttt) cc_final: 0.9192 (tptt) REVERT: A 82 LEU cc_start: 0.8795 (mp) cc_final: 0.8210 (mp) REVERT: A 91 TYR cc_start: 0.9069 (m-80) cc_final: 0.8690 (m-80) REVERT: F 1 GLN cc_start: 0.7279 (tp40) cc_final: 0.6240 (tm-30) REVERT: F 3 GLN cc_start: 0.9273 (mm110) cc_final: 0.8556 (mm110) REVERT: F 48 ILE cc_start: 0.9130 (mt) cc_final: 0.8649 (mp) REVERT: F 80 LEU cc_start: 0.8503 (mt) cc_final: 0.7476 (mt) REVERT: F 81 LYS cc_start: 0.9563 (mttt) cc_final: 0.8980 (mmmm) REVERT: F 82 ASN cc_start: 0.8893 (m-40) cc_final: 0.8655 (p0) REVERT: F 90 TYR cc_start: 0.9266 (m-10) cc_final: 0.8964 (m-10) REVERT: F 91 TYR cc_start: 0.8951 (m-80) cc_final: 0.8745 (m-80) REVERT: F 105 LYS cc_start: 0.8521 (ptmt) cc_final: 0.8268 (mtmm) REVERT: O 3 GLN cc_start: 0.9284 (mm110) cc_final: 0.8687 (mp10) REVERT: O 13 LYS cc_start: 0.9204 (pttm) cc_final: 0.8960 (tppt) REVERT: O 46 GLU cc_start: 0.8805 (tt0) cc_final: 0.8362 (tm-30) REVERT: O 77 GLN cc_start: 0.8963 (mm110) cc_final: 0.8635 (mm110) REVERT: O 80 LEU cc_start: 0.8695 (mt) cc_final: 0.8432 (mt) REVERT: O 81 LYS cc_start: 0.9548 (mttt) cc_final: 0.9048 (mmmm) REVERT: O 82 ASN cc_start: 0.8806 (m-40) cc_final: 0.8526 (p0) REVERT: O 99 GLN cc_start: 0.8634 (pp30) cc_final: 0.8352 (pp30) REVERT: O 100 GLU cc_start: 0.8721 (tt0) cc_final: 0.7942 (tt0) REVERT: B 37 GLN cc_start: 0.8163 (tp40) cc_final: 0.7542 (tp-100) REVERT: B 42 GLN cc_start: 0.8386 (mp10) cc_final: 0.8060 (mp10) REVERT: B 47 LEU cc_start: 0.9661 (mt) cc_final: 0.9458 (mp) REVERT: B 70 ARG cc_start: 0.7991 (mmm160) cc_final: 0.6642 (tpt170) REVERT: B 85 ASP cc_start: 0.8365 (m-30) cc_final: 0.7671 (p0) REVERT: B 90 MET cc_start: 0.9072 (tpp) cc_final: 0.8812 (tpp) REVERT: I 31 ARG cc_start: 0.9040 (mtm110) cc_final: 0.8560 (ptp-170) REVERT: I 37 GLN cc_start: 0.8799 (tt0) cc_final: 0.8572 (tm-30) REVERT: I 42 GLN cc_start: 0.8517 (mp10) cc_final: 0.8153 (mp10) REVERT: I 47 LEU cc_start: 0.9698 (mt) cc_final: 0.9224 (mp) REVERT: I 70 ARG cc_start: 0.7982 (mmm160) cc_final: 0.7303 (mmt180) REVERT: I 83 GLU cc_start: 0.7981 (tp30) cc_final: 0.7566 (tp30) REVERT: I 85 ASP cc_start: 0.8397 (m-30) cc_final: 0.7791 (p0) REVERT: I 92 ASP cc_start: 0.8707 (p0) cc_final: 0.8502 (p0) REVERT: I 104 LEU cc_start: 0.8443 (tp) cc_final: 0.7747 (tp) REVERT: P 18 THR cc_start: 0.9048 (p) cc_final: 0.8810 (t) REVERT: P 31 ARG cc_start: 0.8768 (mtm110) cc_final: 0.8533 (ptp90) REVERT: P 33 VAL cc_start: 0.9301 (m) cc_final: 0.8939 (m) REVERT: P 37 GLN cc_start: 0.8864 (tt0) cc_final: 0.8510 (tp40) REVERT: P 42 GLN cc_start: 0.8411 (mp10) cc_final: 0.8081 (mp10) REVERT: P 47 LEU cc_start: 0.9666 (mt) cc_final: 0.9322 (mp) REVERT: P 70 ARG cc_start: 0.7930 (mmm160) cc_final: 0.7415 (mmt180) REVERT: P 83 GLU cc_start: 0.7761 (tp30) cc_final: 0.7541 (tp30) REVERT: P 85 ASP cc_start: 0.8217 (m-30) cc_final: 0.7449 (p0) outliers start: 2 outliers final: 0 residues processed: 431 average time/residue: 0.1415 time to fit residues: 92.9910 Evaluate side-chains 315 residues out of total 2109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 315 time to evaluate : 0.637 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 219 optimal weight: 3.9990 chunk 107 optimal weight: 1.9990 chunk 80 optimal weight: 2.9990 chunk 48 optimal weight: 4.9990 chunk 16 optimal weight: 5.9990 chunk 113 optimal weight: 10.0000 chunk 127 optimal weight: 7.9990 chunk 220 optimal weight: 5.9990 chunk 184 optimal weight: 5.9990 chunk 105 optimal weight: 6.9990 chunk 122 optimal weight: 6.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 575 GLN Q 616 ASN ** A 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 5 GLN ** B 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 52 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.070538 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2678 r_free = 0.2678 target = 0.052011 restraints weight = 70689.316| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2728 r_free = 0.2728 target = 0.054136 restraints weight = 33958.792| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2760 r_free = 0.2760 target = 0.055537 restraints weight = 21639.310| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.2783 r_free = 0.2783 target = 0.056490 restraints weight = 16182.593| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2796 r_free = 0.2796 target = 0.057093 restraints weight = 13368.423| |-----------------------------------------------------------------------------| r_work (final): 0.2783 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8429 moved from start: 0.2288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 20892 Z= 0.223 Angle : 0.818 15.739 28557 Z= 0.376 Chirality : 0.050 0.498 3436 Planarity : 0.004 0.044 3447 Dihedral : 11.990 105.685 4667 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.77 % Favored : 93.15 % Rotamer: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.12 (0.15), residues: 2364 helix: -1.78 (0.25), residues: 342 sheet: -1.38 (0.20), residues: 597 loop : -2.56 (0.14), residues: 1425 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG K 444 TYR 0.016 0.001 TYR C 643 PHE 0.015 0.001 PHE K 320 TRP 0.021 0.002 TRP R 112 HIS 0.007 0.001 HIS K 330 Details of bonding type rmsd covalent geometry : bond 0.00495 (20752) covalent geometry : angle 0.75274 (28176) SS BOND : bond 0.00433 ( 39) SS BOND : angle 1.71801 ( 78) hydrogen bonds : bond 0.04733 ( 467) hydrogen bonds : angle 5.41022 ( 1251) link_ALPHA1-2 : bond 0.01023 ( 5) link_ALPHA1-2 : angle 3.36339 ( 15) link_ALPHA1-3 : bond 0.00792 ( 8) link_ALPHA1-3 : angle 1.47222 ( 24) link_ALPHA1-6 : bond 0.00726 ( 7) link_ALPHA1-6 : angle 1.97137 ( 21) link_BETA1-4 : bond 0.00748 ( 30) link_BETA1-4 : angle 3.26180 ( 90) link_NAG-ASN : bond 0.00545 ( 51) link_NAG-ASN : angle 3.27400 ( 153) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 374 residues out of total 2109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 374 time to evaluate : 0.695 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: C 530 MET cc_start: 0.9057 (ttm) cc_final: 0.8671 (ttm) REVERT: C 543 ASN cc_start: 0.8982 (t0) cc_final: 0.8574 (t0) REVERT: C 574 LYS cc_start: 0.9234 (mttm) cc_final: 0.8849 (mttt) REVERT: C 577 GLN cc_start: 0.8945 (mt0) cc_final: 0.8499 (mt0) REVERT: C 584 GLU cc_start: 0.9194 (pm20) cc_final: 0.8908 (pm20) REVERT: C 647 GLU cc_start: 0.8725 (tm-30) cc_final: 0.8476 (tm-30) REVERT: C 657 GLU cc_start: 0.9534 (mm-30) cc_final: 0.9326 (mm-30) REVERT: G 95 MET cc_start: 0.9327 (ptt) cc_final: 0.8780 (ptt) REVERT: G 106 GLU cc_start: 0.8778 (tm-30) cc_final: 0.8530 (tm-30) REVERT: G 150 MET cc_start: 0.8963 (mtt) cc_final: 0.8611 (mtt) REVERT: J 530 MET cc_start: 0.9226 (ttm) cc_final: 0.8865 (ttm) REVERT: J 543 ASN cc_start: 0.9106 (m-40) cc_final: 0.8760 (t0) REVERT: J 577 GLN cc_start: 0.8999 (mt0) cc_final: 0.8388 (mt0) REVERT: J 624 ASP cc_start: 0.8936 (m-30) cc_final: 0.8638 (p0) REVERT: J 632 ASP cc_start: 0.9097 (t70) cc_final: 0.8788 (t70) REVERT: J 654 GLU cc_start: 0.9482 (mm-30) cc_final: 0.9260 (mm-30) REVERT: K 217 TYR cc_start: 0.8933 (m-80) cc_final: 0.8378 (m-80) REVERT: K 475 MET cc_start: 0.8876 (mmm) cc_final: 0.8592 (mmm) REVERT: Q 535 MET cc_start: 0.9175 (tpt) cc_final: 0.8674 (tmm) REVERT: Q 543 ASN cc_start: 0.8937 (t0) cc_final: 0.8525 (t0) REVERT: Q 573 ILE cc_start: 0.8998 (mm) cc_final: 0.8474 (tp) REVERT: Q 577 GLN cc_start: 0.8995 (mt0) cc_final: 0.8696 (mt0) REVERT: Q 584 GLU cc_start: 0.9213 (pm20) cc_final: 0.8922 (pm20) REVERT: Q 624 ASP cc_start: 0.9011 (m-30) cc_final: 0.8749 (m-30) REVERT: Q 626 MET cc_start: 0.8210 (ptm) cc_final: 0.7818 (ptm) REVERT: Q 632 ASP cc_start: 0.9153 (t70) cc_final: 0.8844 (t70) REVERT: Q 643 TYR cc_start: 0.9492 (m-10) cc_final: 0.9180 (m-80) REVERT: Q 647 GLU cc_start: 0.8593 (tm-30) cc_final: 0.8275 (tm-30) REVERT: R 95 MET cc_start: 0.9124 (ptm) cc_final: 0.8622 (ptp) REVERT: R 377 ASN cc_start: 0.9378 (p0) cc_final: 0.8570 (t0) REVERT: R 434 MET cc_start: 0.9152 (ttm) cc_final: 0.8823 (ttm) REVERT: A 64 ASN cc_start: 0.9004 (m-40) cc_final: 0.8774 (m110) REVERT: A 81 LYS cc_start: 0.9591 (mttt) cc_final: 0.9217 (tptt) REVERT: A 82 LEU cc_start: 0.8885 (mp) cc_final: 0.8319 (mp) REVERT: A 100 GLU cc_start: 0.8780 (tt0) cc_final: 0.8353 (tt0) REVERT: A 100 MET cc_start: 0.9067 (mpp) cc_final: 0.8791 (mpp) REVERT: A 124 LYS cc_start: 0.8887 (ptpp) cc_final: 0.8474 (ptpp) REVERT: F 1 GLN cc_start: 0.7333 (tp40) cc_final: 0.6258 (tm-30) REVERT: F 3 GLN cc_start: 0.9287 (mm110) cc_final: 0.8842 (mm110) REVERT: F 48 ILE cc_start: 0.9073 (mt) cc_final: 0.8676 (mp) REVERT: F 80 LEU cc_start: 0.8670 (mt) cc_final: 0.7734 (mt) REVERT: F 81 LYS cc_start: 0.9589 (mttt) cc_final: 0.9056 (mmmm) REVERT: F 82 ASN cc_start: 0.8947 (m-40) cc_final: 0.8671 (p0) REVERT: F 105 LYS cc_start: 0.8584 (ptmt) cc_final: 0.8279 (mtmm) REVERT: O 3 GLN cc_start: 0.9249 (mm110) cc_final: 0.8833 (mm110) REVERT: O 13 LYS cc_start: 0.9246 (pttm) cc_final: 0.8988 (tppt) REVERT: O 46 GLU cc_start: 0.8735 (tt0) cc_final: 0.8464 (tm-30) REVERT: O 80 LEU cc_start: 0.8852 (mt) cc_final: 0.8518 (mt) REVERT: O 81 LYS cc_start: 0.9544 (mttt) cc_final: 0.9057 (mmmm) REVERT: O 82 ASN cc_start: 0.8777 (m-40) cc_final: 0.8549 (p0) REVERT: O 86 ASP cc_start: 0.8982 (t0) cc_final: 0.8537 (p0) REVERT: O 99 GLN cc_start: 0.8740 (pp30) cc_final: 0.8397 (pp30) REVERT: O 100 GLU cc_start: 0.8704 (tt0) cc_final: 0.7962 (tt0) REVERT: O 105 LYS cc_start: 0.8745 (ptpp) cc_final: 0.8302 (pttm) REVERT: B 37 GLN cc_start: 0.8301 (tp40) cc_final: 0.7712 (tp40) REVERT: B 42 GLN cc_start: 0.8409 (mp10) cc_final: 0.8053 (mp10) REVERT: B 70 ARG cc_start: 0.8029 (mmm160) cc_final: 0.7286 (mmt180) REVERT: B 85 ASP cc_start: 0.8389 (m-30) cc_final: 0.7750 (p0) REVERT: B 90 MET cc_start: 0.8963 (tpp) cc_final: 0.8651 (tpp) REVERT: I 26 GLN cc_start: 0.9301 (tp-100) cc_final: 0.8798 (tp-100) REVERT: I 37 GLN cc_start: 0.8830 (tt0) cc_final: 0.8247 (tm-30) REVERT: I 42 GLN cc_start: 0.8445 (mp10) cc_final: 0.7971 (mp10) REVERT: I 47 LEU cc_start: 0.9693 (mt) cc_final: 0.9370 (mp) REVERT: I 70 ARG cc_start: 0.7866 (mmm160) cc_final: 0.7237 (tpt170) REVERT: I 83 GLU cc_start: 0.8090 (tp30) cc_final: 0.7816 (mm-30) REVERT: I 85 ASP cc_start: 0.8427 (m-30) cc_final: 0.7822 (p0) REVERT: P 18 THR cc_start: 0.8999 (p) cc_final: 0.8783 (t) REVERT: P 31 ARG cc_start: 0.8930 (mtm110) cc_final: 0.8704 (ptp90) REVERT: P 33 VAL cc_start: 0.9336 (m) cc_final: 0.8999 (m) REVERT: P 37 GLN cc_start: 0.8957 (tt0) cc_final: 0.8455 (tm-30) REVERT: P 42 GLN cc_start: 0.8490 (mp10) cc_final: 0.8227 (mp10) REVERT: P 47 LEU cc_start: 0.9662 (mt) cc_final: 0.9374 (mp) REVERT: P 70 ARG cc_start: 0.7803 (mmm160) cc_final: 0.7478 (mmt180) REVERT: P 83 GLU cc_start: 0.7972 (tp30) cc_final: 0.7651 (tp30) REVERT: P 85 ASP cc_start: 0.8311 (m-30) cc_final: 0.7557 (p0) REVERT: P 104 LEU cc_start: 0.8425 (tp) cc_final: 0.8158 (tp) outliers start: 0 outliers final: 0 residues processed: 374 average time/residue: 0.1363 time to fit residues: 78.4289 Evaluate side-chains 286 residues out of total 2109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 286 time to evaluate : 0.746 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 209 optimal weight: 10.0000 chunk 222 optimal weight: 30.0000 chunk 177 optimal weight: 9.9990 chunk 65 optimal weight: 3.9990 chunk 47 optimal weight: 6.9990 chunk 17 optimal weight: 6.9990 chunk 71 optimal weight: 5.9990 chunk 70 optimal weight: 5.9990 chunk 6 optimal weight: 0.0470 chunk 136 optimal weight: 2.9990 chunk 73 optimal weight: 6.9990 overall best weight: 3.8086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 650 GLN ** A 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.070194 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2667 r_free = 0.2667 target = 0.051597 restraints weight = 70785.675| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2716 r_free = 0.2716 target = 0.053700 restraints weight = 34096.223| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2749 r_free = 0.2749 target = 0.055107 restraints weight = 21757.425| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.2771 r_free = 0.2771 target = 0.056042 restraints weight = 16308.199| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.2785 r_free = 0.2785 target = 0.056660 restraints weight = 13508.089| |-----------------------------------------------------------------------------| r_work (final): 0.2773 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8441 moved from start: 0.2595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 20892 Z= 0.210 Angle : 0.797 15.686 28557 Z= 0.366 Chirality : 0.050 0.460 3436 Planarity : 0.004 0.042 3447 Dihedral : 11.290 108.348 4667 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.39 % Favored : 93.53 % Rotamer: Outliers : 0.05 % Allowed : 2.70 % Favored : 97.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.82 (0.16), residues: 2364 helix: -1.31 (0.26), residues: 342 sheet: -1.07 (0.20), residues: 573 loop : -2.47 (0.15), residues: 1449 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG I 31 TYR 0.017 0.001 TYR Q 586 PHE 0.015 0.001 PHE K 320 TRP 0.020 0.002 TRP K 69 HIS 0.006 0.001 HIS K 330 Details of bonding type rmsd covalent geometry : bond 0.00466 (20752) covalent geometry : angle 0.73266 (28176) SS BOND : bond 0.00431 ( 39) SS BOND : angle 1.72146 ( 78) hydrogen bonds : bond 0.04206 ( 467) hydrogen bonds : angle 5.10627 ( 1251) link_ALPHA1-2 : bond 0.00870 ( 5) link_ALPHA1-2 : angle 3.17607 ( 15) link_ALPHA1-3 : bond 0.00877 ( 8) link_ALPHA1-3 : angle 1.42413 ( 24) link_ALPHA1-6 : bond 0.00786 ( 7) link_ALPHA1-6 : angle 1.92459 ( 21) link_BETA1-4 : bond 0.00688 ( 30) link_BETA1-4 : angle 3.13504 ( 90) link_NAG-ASN : bond 0.00516 ( 51) link_NAG-ASN : angle 3.25853 ( 153) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 381 residues out of total 2109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 380 time to evaluate : 0.636 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: C 530 MET cc_start: 0.9067 (ttm) cc_final: 0.8459 (ttm) REVERT: C 540 GLN cc_start: 0.9030 (mp10) cc_final: 0.8786 (mp10) REVERT: C 543 ASN cc_start: 0.9024 (t0) cc_final: 0.8588 (t0) REVERT: C 574 LYS cc_start: 0.9272 (mttm) cc_final: 0.8996 (mtmt) REVERT: C 575 GLN cc_start: 0.9073 (mp10) cc_final: 0.8689 (mp10) REVERT: C 584 GLU cc_start: 0.9029 (pm20) cc_final: 0.8750 (pm20) REVERT: C 590 GLN cc_start: 0.9539 (tp40) cc_final: 0.9078 (tp40) REVERT: C 591 GLN cc_start: 0.9696 (tm-30) cc_final: 0.9319 (tm-30) REVERT: C 624 ASP cc_start: 0.9118 (m-30) cc_final: 0.8846 (m-30) REVERT: C 654 GLU cc_start: 0.9407 (mm-30) cc_final: 0.9135 (mm-30) REVERT: C 657 GLU cc_start: 0.9509 (mm-30) cc_final: 0.9286 (mm-30) REVERT: G 69 TRP cc_start: 0.7972 (p-90) cc_final: 0.7419 (p-90) REVERT: G 95 MET cc_start: 0.9328 (ptt) cc_final: 0.8558 (ptt) REVERT: G 106 GLU cc_start: 0.8711 (tm-30) cc_final: 0.8475 (tm-30) REVERT: G 150 MET cc_start: 0.8925 (mtt) cc_final: 0.8537 (mtt) REVERT: J 543 ASN cc_start: 0.9120 (m-40) cc_final: 0.8671 (t0) REVERT: J 577 GLN cc_start: 0.8988 (mt0) cc_final: 0.8562 (mt0) REVERT: J 591 GLN cc_start: 0.9789 (tm-30) cc_final: 0.9344 (tm-30) REVERT: J 624 ASP cc_start: 0.8833 (m-30) cc_final: 0.8590 (p0) REVERT: J 632 ASP cc_start: 0.9134 (t70) cc_final: 0.8846 (t70) REVERT: K 475 MET cc_start: 0.8927 (mmm) cc_final: 0.8594 (mmm) REVERT: Q 540 GLN cc_start: 0.8816 (mp10) cc_final: 0.8596 (mp10) REVERT: Q 543 ASN cc_start: 0.8943 (t0) cc_final: 0.8568 (t0) REVERT: Q 574 LYS cc_start: 0.9167 (mtpt) cc_final: 0.8956 (mmtm) REVERT: Q 575 GLN cc_start: 0.9145 (mp10) cc_final: 0.8896 (mp10) REVERT: Q 577 GLN cc_start: 0.9041 (mt0) cc_final: 0.8680 (mt0) REVERT: Q 584 GLU cc_start: 0.9064 (pm20) cc_final: 0.8857 (pm20) REVERT: Q 591 GLN cc_start: 0.9741 (tm-30) cc_final: 0.9316 (tm-30) REVERT: Q 624 ASP cc_start: 0.8958 (m-30) cc_final: 0.8650 (m-30) REVERT: Q 632 ASP cc_start: 0.9159 (t70) cc_final: 0.8876 (t70) REVERT: Q 643 TYR cc_start: 0.9489 (m-10) cc_final: 0.9208 (m-80) REVERT: Q 654 GLU cc_start: 0.9137 (mm-30) cc_final: 0.8733 (mm-30) REVERT: R 95 MET cc_start: 0.9056 (ptm) cc_final: 0.8643 (ptp) REVERT: R 377 ASN cc_start: 0.9376 (p0) cc_final: 0.8627 (t0) REVERT: R 434 MET cc_start: 0.9107 (ttm) cc_final: 0.8856 (ttm) REVERT: A 46 GLU cc_start: 0.8298 (tm-30) cc_final: 0.8091 (tm-30) REVERT: A 64 ASN cc_start: 0.9019 (m-40) cc_final: 0.8782 (m110) REVERT: A 81 LYS cc_start: 0.9574 (mttt) cc_final: 0.9242 (tptt) REVERT: A 82 LEU cc_start: 0.8911 (mp) cc_final: 0.8364 (mp) REVERT: A 100 MET cc_start: 0.9129 (mpp) cc_final: 0.8872 (mpp) REVERT: F 1 GLN cc_start: 0.7425 (tp40) cc_final: 0.6429 (tm-30) REVERT: F 3 GLN cc_start: 0.9293 (mm110) cc_final: 0.8805 (mm110) REVERT: F 77 GLN cc_start: 0.8598 (mm110) cc_final: 0.8293 (tp40) REVERT: F 80 LEU cc_start: 0.8747 (mt) cc_final: 0.7704 (mt) REVERT: F 81 LYS cc_start: 0.9599 (mttt) cc_final: 0.9008 (mmmm) REVERT: F 105 LYS cc_start: 0.8580 (ptmt) cc_final: 0.8315 (mtmm) REVERT: O 3 GLN cc_start: 0.9259 (mm110) cc_final: 0.8832 (mm110) REVERT: O 13 LYS cc_start: 0.9259 (pttm) cc_final: 0.8985 (tppt) REVERT: O 46 GLU cc_start: 0.8823 (tt0) cc_final: 0.8451 (tm-30) REVERT: O 80 LEU cc_start: 0.8826 (mt) cc_final: 0.8421 (mt) REVERT: O 81 LYS cc_start: 0.9559 (mttt) cc_final: 0.9069 (mmmm) REVERT: O 82 ASN cc_start: 0.8753 (m-40) cc_final: 0.8534 (p0) REVERT: O 86 ASP cc_start: 0.8866 (t0) cc_final: 0.8475 (p0) REVERT: O 99 GLN cc_start: 0.8779 (pp30) cc_final: 0.8408 (pp30) REVERT: O 100 GLU cc_start: 0.8696 (tt0) cc_final: 0.8032 (tt0) REVERT: O 105 LYS cc_start: 0.8781 (ptpp) cc_final: 0.8290 (ptpp) REVERT: B 37 GLN cc_start: 0.8393 (tp40) cc_final: 0.7594 (tp40) REVERT: B 42 GLN cc_start: 0.8421 (mp10) cc_final: 0.8028 (mp10) REVERT: B 70 ARG cc_start: 0.7999 (mmm160) cc_final: 0.7484 (mmt180) REVERT: B 85 ASP cc_start: 0.8407 (m-30) cc_final: 0.7811 (p0) REVERT: B 90 MET cc_start: 0.8988 (tpp) cc_final: 0.8657 (tpp) REVERT: I 26 GLN cc_start: 0.9302 (tp-100) cc_final: 0.8953 (tp-100) REVERT: I 31 ARG cc_start: 0.9367 (mtm110) cc_final: 0.8540 (ptp90) REVERT: I 42 GLN cc_start: 0.8559 (mp10) cc_final: 0.8104 (mp10) REVERT: I 47 LEU cc_start: 0.9696 (mt) cc_final: 0.9386 (mp) REVERT: I 70 ARG cc_start: 0.7825 (mmm160) cc_final: 0.7239 (tpt170) REVERT: I 83 GLU cc_start: 0.8121 (tp30) cc_final: 0.7860 (mm-30) REVERT: I 85 ASP cc_start: 0.8440 (m-30) cc_final: 0.7644 (p0) REVERT: P 18 THR cc_start: 0.8987 (p) cc_final: 0.8776 (t) REVERT: P 37 GLN cc_start: 0.8958 (tt0) cc_final: 0.8499 (tm-30) REVERT: P 42 GLN cc_start: 0.8454 (mp10) cc_final: 0.8158 (mp10) REVERT: P 47 LEU cc_start: 0.9651 (mt) cc_final: 0.9325 (mp) REVERT: P 48 ILE cc_start: 0.9592 (mm) cc_final: 0.9236 (mm) REVERT: P 70 ARG cc_start: 0.7712 (mmm160) cc_final: 0.7253 (mmt180) REVERT: P 83 GLU cc_start: 0.8026 (tp30) cc_final: 0.7736 (tp30) REVERT: P 85 ASP cc_start: 0.8361 (m-30) cc_final: 0.7485 (p0) outliers start: 1 outliers final: 0 residues processed: 381 average time/residue: 0.1350 time to fit residues: 78.8315 Evaluate side-chains 292 residues out of total 2109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 292 time to evaluate : 0.704 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 159 optimal weight: 0.0070 chunk 56 optimal weight: 10.0000 chunk 209 optimal weight: 0.9990 chunk 173 optimal weight: 4.9990 chunk 86 optimal weight: 0.5980 chunk 131 optimal weight: 4.9990 chunk 22 optimal weight: 0.9990 chunk 127 optimal weight: 2.9990 chunk 78 optimal weight: 5.9990 chunk 190 optimal weight: 9.9990 chunk 29 optimal weight: 8.9990 overall best weight: 1.1204 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 137 ASN G 258 GLN K 258 GLN ** A 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.072275 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2715 r_free = 0.2715 target = 0.053582 restraints weight = 69612.012| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.2765 r_free = 0.2765 target = 0.055739 restraints weight = 33270.675| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2798 r_free = 0.2798 target = 0.057194 restraints weight = 21170.335| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.2820 r_free = 0.2820 target = 0.058162 restraints weight = 15778.521| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2833 r_free = 0.2833 target = 0.058765 restraints weight = 13039.326| |-----------------------------------------------------------------------------| r_work (final): 0.2820 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8384 moved from start: 0.2816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 20892 Z= 0.115 Angle : 0.735 14.817 28557 Z= 0.335 Chirality : 0.049 0.402 3436 Planarity : 0.003 0.040 3447 Dihedral : 10.507 108.669 4667 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.61 % Favored : 95.35 % Rotamer: Outliers : 0.05 % Allowed : 2.18 % Favored : 97.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.50 (0.16), residues: 2364 helix: -1.04 (0.27), residues: 342 sheet: -0.86 (0.21), residues: 585 loop : -2.27 (0.15), residues: 1437 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG P 31 TYR 0.019 0.001 TYR J 586 PHE 0.009 0.001 PHE K 320 TRP 0.014 0.001 TRP K 69 HIS 0.008 0.001 HIS I 89 Details of bonding type rmsd covalent geometry : bond 0.00245 (20752) covalent geometry : angle 0.67582 (28176) SS BOND : bond 0.00285 ( 39) SS BOND : angle 1.52351 ( 78) hydrogen bonds : bond 0.03503 ( 467) hydrogen bonds : angle 4.80274 ( 1251) link_ALPHA1-2 : bond 0.00796 ( 5) link_ALPHA1-2 : angle 2.75795 ( 15) link_ALPHA1-3 : bond 0.00993 ( 8) link_ALPHA1-3 : angle 1.27469 ( 24) link_ALPHA1-6 : bond 0.00959 ( 7) link_ALPHA1-6 : angle 1.74829 ( 21) link_BETA1-4 : bond 0.00697 ( 30) link_BETA1-4 : angle 2.97241 ( 90) link_NAG-ASN : bond 0.00440 ( 51) link_NAG-ASN : angle 2.99859 ( 153) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 410 residues out of total 2109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 409 time to evaluate : 0.706 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: C 530 MET cc_start: 0.9202 (ttm) cc_final: 0.8604 (ttm) REVERT: C 540 GLN cc_start: 0.9023 (mp10) cc_final: 0.8804 (mp10) REVERT: C 543 ASN cc_start: 0.8911 (t0) cc_final: 0.8449 (t0) REVERT: C 574 LYS cc_start: 0.9285 (mttm) cc_final: 0.9058 (mttt) REVERT: C 575 GLN cc_start: 0.9135 (mp10) cc_final: 0.8758 (mp10) REVERT: C 584 GLU cc_start: 0.8925 (pm20) cc_final: 0.8642 (pm20) REVERT: C 590 GLN cc_start: 0.9536 (tp40) cc_final: 0.9108 (tp40) REVERT: C 591 GLN cc_start: 0.9683 (tm-30) cc_final: 0.9277 (tm-30) REVERT: C 621 GLU cc_start: 0.8871 (pt0) cc_final: 0.8210 (pt0) REVERT: C 654 GLU cc_start: 0.9377 (mm-30) cc_final: 0.9061 (mm-30) REVERT: G 69 TRP cc_start: 0.7874 (p-90) cc_final: 0.7277 (p-90) REVERT: G 95 MET cc_start: 0.9274 (ptt) cc_final: 0.8603 (ptt) REVERT: G 106 GLU cc_start: 0.8708 (tm-30) cc_final: 0.8440 (tm-30) REVERT: G 150 MET cc_start: 0.8886 (mtt) cc_final: 0.8259 (mtt) REVERT: G 217 TYR cc_start: 0.9025 (m-80) cc_final: 0.8733 (m-80) REVERT: G 381 GLU cc_start: 0.7898 (mp0) cc_final: 0.7259 (mp0) REVERT: J 543 ASN cc_start: 0.9106 (m-40) cc_final: 0.8621 (t0) REVERT: J 574 LYS cc_start: 0.9273 (mmtm) cc_final: 0.8857 (mttt) REVERT: J 624 ASP cc_start: 0.8875 (m-30) cc_final: 0.8492 (p0) REVERT: J 632 ASP cc_start: 0.9064 (t70) cc_final: 0.8754 (t70) REVERT: J 650 GLN cc_start: 0.8776 (tp40) cc_final: 0.8448 (mm-40) REVERT: J 654 GLU cc_start: 0.9443 (mm-30) cc_final: 0.9152 (mp0) REVERT: K 150 MET cc_start: 0.9027 (mtt) cc_final: 0.8657 (mtt) REVERT: K 194 ILE cc_start: 0.9251 (tp) cc_final: 0.8795 (tp) REVERT: K 217 TYR cc_start: 0.8716 (m-80) cc_final: 0.8262 (m-80) REVERT: K 328 MET cc_start: 0.8227 (tpp) cc_final: 0.8018 (tpp) REVERT: K 478 ASN cc_start: 0.9101 (m110) cc_final: 0.8713 (m110) REVERT: Q 542 ARG cc_start: 0.9307 (ttt180) cc_final: 0.8914 (ttp80) REVERT: Q 543 ASN cc_start: 0.8868 (t0) cc_final: 0.8433 (t0) REVERT: Q 573 ILE cc_start: 0.8934 (mm) cc_final: 0.8408 (tp) REVERT: Q 575 GLN cc_start: 0.9093 (mp10) cc_final: 0.8856 (mp10) REVERT: Q 584 GLU cc_start: 0.8977 (pm20) cc_final: 0.8624 (pm20) REVERT: Q 590 GLN cc_start: 0.9539 (tp-100) cc_final: 0.9290 (tp40) REVERT: Q 591 GLN cc_start: 0.9738 (tm-30) cc_final: 0.9323 (tm-30) REVERT: Q 624 ASP cc_start: 0.8833 (m-30) cc_final: 0.8532 (m-30) REVERT: Q 632 ASP cc_start: 0.9136 (t70) cc_final: 0.8867 (t70) REVERT: Q 643 TYR cc_start: 0.9428 (m-10) cc_final: 0.9138 (m-10) REVERT: Q 654 GLU cc_start: 0.9105 (mm-30) cc_final: 0.8673 (mm-30) REVERT: R 95 MET cc_start: 0.8949 (ptm) cc_final: 0.8468 (ptp) REVERT: R 377 ASN cc_start: 0.9320 (p0) cc_final: 0.8552 (t0) REVERT: R 492 GLU cc_start: 0.8703 (tm-30) cc_final: 0.8216 (tm-30) REVERT: R 494 LEU cc_start: 0.9252 (tp) cc_final: 0.8908 (tt) REVERT: A 64 ASN cc_start: 0.9000 (m-40) cc_final: 0.8765 (m110) REVERT: A 81 LYS cc_start: 0.9563 (mttt) cc_final: 0.9231 (tptt) REVERT: A 82 LEU cc_start: 0.8811 (mp) cc_final: 0.8278 (mp) REVERT: A 100 MET cc_start: 0.9125 (mpp) cc_final: 0.8882 (mpp) REVERT: F 3 GLN cc_start: 0.9271 (mm110) cc_final: 0.8979 (mp10) REVERT: F 13 LYS cc_start: 0.8992 (tptt) cc_final: 0.8597 (pptt) REVERT: F 77 GLN cc_start: 0.8512 (mm110) cc_final: 0.8224 (tp40) REVERT: F 80 LEU cc_start: 0.8760 (mt) cc_final: 0.7738 (mt) REVERT: F 81 LYS cc_start: 0.9608 (mttt) cc_final: 0.8994 (mmmm) REVERT: O 3 GLN cc_start: 0.9256 (mm110) cc_final: 0.8616 (mp10) REVERT: O 13 LYS cc_start: 0.9253 (pttm) cc_final: 0.8997 (tppt) REVERT: O 46 GLU cc_start: 0.8797 (tt0) cc_final: 0.8485 (tm-30) REVERT: O 80 LEU cc_start: 0.8939 (mt) cc_final: 0.8664 (mt) REVERT: O 81 LYS cc_start: 0.9543 (mttt) cc_final: 0.9050 (mmmm) REVERT: O 82 ASN cc_start: 0.8846 (m-40) cc_final: 0.8565 (p0) REVERT: O 86 ASP cc_start: 0.8916 (t0) cc_final: 0.8365 (p0) REVERT: O 99 GLN cc_start: 0.8782 (pp30) cc_final: 0.8384 (pp30) REVERT: O 100 MET cc_start: 0.9028 (mpp) cc_final: 0.8808 (mpp) REVERT: O 101 ASP cc_start: 0.9336 (p0) cc_final: 0.8858 (p0) REVERT: B 37 GLN cc_start: 0.8306 (tp40) cc_final: 0.7629 (tp-100) REVERT: B 42 GLN cc_start: 0.8380 (mp10) cc_final: 0.8053 (mp10) REVERT: B 47 LEU cc_start: 0.9675 (mp) cc_final: 0.9353 (mp) REVERT: B 70 ARG cc_start: 0.8101 (mmm160) cc_final: 0.7584 (mmt180) REVERT: B 85 ASP cc_start: 0.8393 (m-30) cc_final: 0.7774 (p0) REVERT: B 90 MET cc_start: 0.9014 (tpp) cc_final: 0.8715 (tpp) REVERT: I 26 GLN cc_start: 0.9280 (tp-100) cc_final: 0.8931 (tp-100) REVERT: I 31 ARG cc_start: 0.9273 (mtm110) cc_final: 0.8543 (ptp90) REVERT: I 37 GLN cc_start: 0.8023 (tp40) cc_final: 0.7639 (tp-100) REVERT: I 42 GLN cc_start: 0.8479 (mp10) cc_final: 0.8009 (mp10) REVERT: I 47 LEU cc_start: 0.9644 (mt) cc_final: 0.9319 (mp) REVERT: I 70 ARG cc_start: 0.7870 (mmm160) cc_final: 0.7329 (tpt170) REVERT: I 83 GLU cc_start: 0.7968 (tp30) cc_final: 0.7587 (tp30) REVERT: I 85 ASP cc_start: 0.8502 (m-30) cc_final: 0.7740 (p0) REVERT: I 104 LEU cc_start: 0.8461 (tp) cc_final: 0.8069 (tp) REVERT: P 31 ARG cc_start: 0.8895 (mtm110) cc_final: 0.8524 (ptp90) REVERT: P 37 GLN cc_start: 0.8910 (tt0) cc_final: 0.8493 (tm-30) REVERT: P 42 GLN cc_start: 0.8433 (mp10) cc_final: 0.8049 (mp10) REVERT: P 47 LEU cc_start: 0.9635 (mt) cc_final: 0.9332 (mp) REVERT: P 70 ARG cc_start: 0.7846 (mmm160) cc_final: 0.7570 (mmt180) REVERT: P 83 GLU cc_start: 0.7921 (tp30) cc_final: 0.7599 (tp30) REVERT: P 85 ASP cc_start: 0.8360 (m-30) cc_final: 0.7535 (p0) outliers start: 1 outliers final: 0 residues processed: 410 average time/residue: 0.1412 time to fit residues: 88.0687 Evaluate side-chains 314 residues out of total 2109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 314 time to evaluate : 0.778 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 225 optimal weight: 7.9990 chunk 178 optimal weight: 0.0020 chunk 2 optimal weight: 0.0980 chunk 222 optimal weight: 0.9980 chunk 137 optimal weight: 0.6980 chunk 62 optimal weight: 0.0000 chunk 156 optimal weight: 0.9990 chunk 145 optimal weight: 6.9990 chunk 54 optimal weight: 1.9990 chunk 179 optimal weight: 0.3980 chunk 74 optimal weight: 7.9990 overall best weight: 0.2392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 82AASN ** B 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.073861 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2751 r_free = 0.2751 target = 0.055129 restraints weight = 68663.699| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2802 r_free = 0.2802 target = 0.057326 restraints weight = 32848.627| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2834 r_free = 0.2834 target = 0.058782 restraints weight = 20893.393| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.2857 r_free = 0.2857 target = 0.059772 restraints weight = 15600.583| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.2871 r_free = 0.2871 target = 0.060417 restraints weight = 12866.600| |-----------------------------------------------------------------------------| r_work (final): 0.2855 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8339 moved from start: 0.3075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 20892 Z= 0.110 Angle : 0.716 13.991 28557 Z= 0.326 Chirality : 0.048 0.370 3436 Planarity : 0.003 0.051 3447 Dihedral : 9.879 110.384 4667 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.20 % Favored : 94.75 % Rotamer: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.23 (0.16), residues: 2364 helix: -0.84 (0.28), residues: 333 sheet: -0.52 (0.22), residues: 535 loop : -2.11 (0.15), residues: 1496 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 38 TYR 0.028 0.001 TYR J 643 PHE 0.008 0.001 PHE R 391 TRP 0.011 0.001 TRP K 69 HIS 0.005 0.001 HIS R 216 Details of bonding type rmsd covalent geometry : bond 0.00228 (20752) covalent geometry : angle 0.66347 (28176) SS BOND : bond 0.00469 ( 39) SS BOND : angle 1.35138 ( 78) hydrogen bonds : bond 0.03108 ( 467) hydrogen bonds : angle 4.61996 ( 1251) link_ALPHA1-2 : bond 0.01027 ( 5) link_ALPHA1-2 : angle 2.65191 ( 15) link_ALPHA1-3 : bond 0.01079 ( 8) link_ALPHA1-3 : angle 1.21721 ( 24) link_ALPHA1-6 : bond 0.00976 ( 7) link_ALPHA1-6 : angle 1.58678 ( 21) link_BETA1-4 : bond 0.00784 ( 30) link_BETA1-4 : angle 2.90039 ( 90) link_NAG-ASN : bond 0.00493 ( 51) link_NAG-ASN : angle 2.75728 ( 153) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 411 residues out of total 2109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 411 time to evaluate : 0.737 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: C 530 MET cc_start: 0.9110 (ttm) cc_final: 0.8466 (ttm) REVERT: C 540 GLN cc_start: 0.9046 (mp10) cc_final: 0.8841 (mp10) REVERT: C 543 ASN cc_start: 0.8862 (t0) cc_final: 0.8417 (t0) REVERT: C 574 LYS cc_start: 0.9258 (mttm) cc_final: 0.9047 (mttt) REVERT: C 575 GLN cc_start: 0.9130 (mp10) cc_final: 0.8765 (mp10) REVERT: C 584 GLU cc_start: 0.8828 (pm20) cc_final: 0.8553 (pm20) REVERT: C 590 GLN cc_start: 0.9532 (tp40) cc_final: 0.9132 (tp40) REVERT: C 591 GLN cc_start: 0.9681 (tm-30) cc_final: 0.9143 (tm-30) REVERT: C 621 GLU cc_start: 0.8678 (pt0) cc_final: 0.8181 (pt0) REVERT: C 654 GLU cc_start: 0.9395 (mm-30) cc_final: 0.8877 (mt-10) REVERT: G 69 TRP cc_start: 0.7614 (p-90) cc_final: 0.7283 (p90) REVERT: G 95 MET cc_start: 0.9233 (ptt) cc_final: 0.8487 (ptt) REVERT: G 106 GLU cc_start: 0.8576 (tm-30) cc_final: 0.8272 (tm-30) REVERT: G 161 MET cc_start: 0.8437 (tpp) cc_final: 0.8005 (tpt) REVERT: G 217 TYR cc_start: 0.8704 (m-80) cc_final: 0.8390 (m-80) REVERT: G 440 GLN cc_start: 0.8784 (tt0) cc_final: 0.8461 (pm20) REVERT: J 543 ASN cc_start: 0.9118 (m-40) cc_final: 0.8716 (t0) REVERT: J 574 LYS cc_start: 0.9288 (mmtm) cc_final: 0.8862 (mttt) REVERT: J 624 ASP cc_start: 0.8884 (m-30) cc_final: 0.8519 (p0) REVERT: J 632 ASP cc_start: 0.9013 (t70) cc_final: 0.8698 (t70) REVERT: J 654 GLU cc_start: 0.9358 (mm-30) cc_final: 0.9001 (mt-10) REVERT: K 150 MET cc_start: 0.9063 (mtt) cc_final: 0.8856 (mtt) REVERT: K 478 ASN cc_start: 0.9054 (m110) cc_final: 0.8708 (m110) REVERT: Q 530 MET cc_start: 0.9253 (ttm) cc_final: 0.8840 (mmm) REVERT: Q 542 ARG cc_start: 0.9349 (ttt180) cc_final: 0.8938 (ttp80) REVERT: Q 543 ASN cc_start: 0.8815 (t0) cc_final: 0.8369 (t0) REVERT: Q 575 GLN cc_start: 0.9105 (mp10) cc_final: 0.8889 (mp10) REVERT: Q 584 GLU cc_start: 0.8991 (pm20) cc_final: 0.8638 (pm20) REVERT: Q 590 GLN cc_start: 0.9542 (tp-100) cc_final: 0.9311 (tp40) REVERT: Q 591 GLN cc_start: 0.9735 (tm-30) cc_final: 0.9278 (tm-30) REVERT: Q 624 ASP cc_start: 0.8979 (m-30) cc_final: 0.8700 (m-30) REVERT: Q 654 GLU cc_start: 0.9032 (mm-30) cc_final: 0.8336 (mm-30) REVERT: R 95 MET cc_start: 0.8793 (ptm) cc_final: 0.8389 (ptp) REVERT: R 106 GLU cc_start: 0.8639 (tp30) cc_final: 0.8311 (tp30) REVERT: R 377 ASN cc_start: 0.9227 (p0) cc_final: 0.8549 (t0) REVERT: R 434 MET cc_start: 0.8945 (ttm) cc_final: 0.8554 (ttm) REVERT: R 492 GLU cc_start: 0.8697 (tm-30) cc_final: 0.8122 (tm-30) REVERT: R 494 LEU cc_start: 0.9223 (tp) cc_final: 0.8916 (tt) REVERT: A 64 ASN cc_start: 0.8966 (m-40) cc_final: 0.8714 (m110) REVERT: A 81 LYS cc_start: 0.9560 (mttt) cc_final: 0.9117 (tptt) REVERT: A 82 LEU cc_start: 0.8810 (mp) cc_final: 0.8260 (mp) REVERT: F 3 GLN cc_start: 0.9235 (mm110) cc_final: 0.9021 (mm110) REVERT: F 80 LEU cc_start: 0.8747 (mt) cc_final: 0.7804 (mt) REVERT: F 81 LYS cc_start: 0.9597 (mttt) cc_final: 0.9197 (mmtm) REVERT: F 82 ASN cc_start: 0.9044 (m-40) cc_final: 0.8792 (p0) REVERT: F 99 GLN cc_start: 0.8809 (pp30) cc_final: 0.8602 (pp30) REVERT: O 3 GLN cc_start: 0.9277 (mm110) cc_final: 0.8674 (mp10) REVERT: O 13 LYS cc_start: 0.9271 (pttm) cc_final: 0.9061 (tppt) REVERT: O 46 GLU cc_start: 0.8791 (tt0) cc_final: 0.8506 (tm-30) REVERT: O 80 LEU cc_start: 0.8926 (mt) cc_final: 0.8614 (mt) REVERT: O 81 LYS cc_start: 0.9507 (mttt) cc_final: 0.9029 (mmmm) REVERT: O 82 ASN cc_start: 0.8952 (m-40) cc_final: 0.8573 (p0) REVERT: O 86 ASP cc_start: 0.8937 (t0) cc_final: 0.8337 (p0) REVERT: O 99 GLN cc_start: 0.8818 (pp30) cc_final: 0.8535 (pp30) REVERT: O 101 ASP cc_start: 0.9404 (p0) cc_final: 0.8910 (p0) REVERT: B 37 GLN cc_start: 0.8358 (tp40) cc_final: 0.7782 (tp-100) REVERT: B 42 GLN cc_start: 0.8364 (mp10) cc_final: 0.7937 (mp10) REVERT: B 47 LEU cc_start: 0.9633 (mp) cc_final: 0.9303 (mp) REVERT: B 70 ARG cc_start: 0.8146 (mmm160) cc_final: 0.7644 (mmt180) REVERT: B 85 ASP cc_start: 0.8426 (m-30) cc_final: 0.7763 (p0) REVERT: B 90 MET cc_start: 0.9071 (tpp) cc_final: 0.8780 (tpp) REVERT: I 26 GLN cc_start: 0.9293 (tp-100) cc_final: 0.8973 (tp-100) REVERT: I 31 ARG cc_start: 0.9248 (mtm110) cc_final: 0.8546 (ptp90) REVERT: I 37 GLN cc_start: 0.8063 (tp40) cc_final: 0.7652 (tp-100) REVERT: I 42 GLN cc_start: 0.8388 (mp10) cc_final: 0.7973 (mp10) REVERT: I 47 LEU cc_start: 0.9620 (mt) cc_final: 0.9271 (mp) REVERT: I 70 ARG cc_start: 0.7882 (mmm160) cc_final: 0.7342 (tpt170) REVERT: I 83 GLU cc_start: 0.7936 (tp30) cc_final: 0.7545 (tp30) REVERT: I 85 ASP cc_start: 0.8497 (m-30) cc_final: 0.7733 (p0) REVERT: I 104 LEU cc_start: 0.8275 (tp) cc_final: 0.7842 (tp) REVERT: P 31 ARG cc_start: 0.8793 (mtm110) cc_final: 0.8538 (ptp90) REVERT: P 37 GLN cc_start: 0.8868 (tt0) cc_final: 0.8469 (tm-30) REVERT: P 42 GLN cc_start: 0.8355 (mp10) cc_final: 0.7980 (mp10) REVERT: P 47 LEU cc_start: 0.9619 (mt) cc_final: 0.9343 (mp) REVERT: P 70 ARG cc_start: 0.7853 (mmm160) cc_final: 0.7625 (mmt180) REVERT: P 83 GLU cc_start: 0.7909 (tp30) cc_final: 0.7689 (tp30) REVERT: P 85 ASP cc_start: 0.8375 (m-30) cc_final: 0.7487 (p0) outliers start: 0 outliers final: 0 residues processed: 411 average time/residue: 0.1366 time to fit residues: 85.7713 Evaluate side-chains 326 residues out of total 2109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 326 time to evaluate : 0.517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 148 optimal weight: 5.9990 chunk 132 optimal weight: 5.9990 chunk 225 optimal weight: 10.0000 chunk 48 optimal weight: 3.9990 chunk 98 optimal weight: 6.9990 chunk 124 optimal weight: 0.4980 chunk 122 optimal weight: 2.9990 chunk 121 optimal weight: 2.9990 chunk 6 optimal weight: 0.6980 chunk 27 optimal weight: 10.0000 chunk 171 optimal weight: 20.0000 overall best weight: 2.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Q 650 GLN ** A 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.072184 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2715 r_free = 0.2715 target = 0.053623 restraints weight = 70401.557| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2765 r_free = 0.2765 target = 0.055783 restraints weight = 33795.553| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.2798 r_free = 0.2798 target = 0.057225 restraints weight = 21540.923| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.2821 r_free = 0.2821 target = 0.058191 restraints weight = 16088.606| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2834 r_free = 0.2834 target = 0.058787 restraints weight = 13280.343| |-----------------------------------------------------------------------------| r_work (final): 0.2823 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8408 moved from start: 0.3175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 20892 Z= 0.143 Angle : 0.734 14.335 28557 Z= 0.334 Chirality : 0.048 0.413 3436 Planarity : 0.003 0.054 3447 Dihedral : 9.652 107.080 4667 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.67 % Favored : 94.29 % Rotamer: Outliers : 0.00 % Allowed : 1.04 % Favored : 98.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.13 (0.16), residues: 2364 helix: -0.60 (0.28), residues: 339 sheet: -0.38 (0.22), residues: 524 loop : -2.11 (0.15), residues: 1501 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG P 31 TYR 0.019 0.001 TYR Q 586 PHE 0.016 0.001 PHE A 100G TRP 0.015 0.001 TRP R 112 HIS 0.004 0.001 HIS K 216 Details of bonding type rmsd covalent geometry : bond 0.00319 (20752) covalent geometry : angle 0.68000 (28176) SS BOND : bond 0.00292 ( 39) SS BOND : angle 1.63253 ( 78) hydrogen bonds : bond 0.03288 ( 467) hydrogen bonds : angle 4.61427 ( 1251) link_ALPHA1-2 : bond 0.00998 ( 5) link_ALPHA1-2 : angle 2.82967 ( 15) link_ALPHA1-3 : bond 0.00775 ( 8) link_ALPHA1-3 : angle 1.28141 ( 24) link_ALPHA1-6 : bond 0.00942 ( 7) link_ALPHA1-6 : angle 1.73338 ( 21) link_BETA1-4 : bond 0.00719 ( 30) link_BETA1-4 : angle 2.88876 ( 90) link_NAG-ASN : bond 0.00426 ( 51) link_NAG-ASN : angle 2.78892 ( 153) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 400 residues out of total 2109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 400 time to evaluate : 0.702 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: C 530 MET cc_start: 0.9020 (ttm) cc_final: 0.8327 (ttm) REVERT: C 540 GLN cc_start: 0.9050 (mp10) cc_final: 0.8839 (mp10) REVERT: C 543 ASN cc_start: 0.8968 (t0) cc_final: 0.8502 (t0) REVERT: C 574 LYS cc_start: 0.9299 (mttm) cc_final: 0.9068 (mttt) REVERT: C 575 GLN cc_start: 0.9121 (mp10) cc_final: 0.8779 (mp10) REVERT: C 584 GLU cc_start: 0.9064 (pm20) cc_final: 0.8793 (pm20) REVERT: C 590 GLN cc_start: 0.9501 (tp40) cc_final: 0.9041 (tp40) REVERT: C 591 GLN cc_start: 0.9678 (tm-30) cc_final: 0.9282 (tm-30) REVERT: C 621 GLU cc_start: 0.8769 (pt0) cc_final: 0.8172 (pt0) REVERT: G 69 TRP cc_start: 0.7880 (p-90) cc_final: 0.7475 (p90) REVERT: G 95 MET cc_start: 0.9242 (ptt) cc_final: 0.8527 (ptt) REVERT: G 106 GLU cc_start: 0.8623 (tm-30) cc_final: 0.8324 (tm-30) REVERT: G 440 GLN cc_start: 0.8801 (tt0) cc_final: 0.8532 (pm20) REVERT: J 543 ASN cc_start: 0.9054 (m-40) cc_final: 0.8664 (t0) REVERT: J 574 LYS cc_start: 0.9287 (mmtm) cc_final: 0.8891 (mttt) REVERT: J 624 ASP cc_start: 0.8829 (m-30) cc_final: 0.8589 (p0) REVERT: J 632 ASP cc_start: 0.9014 (t70) cc_final: 0.8800 (t70) REVERT: J 654 GLU cc_start: 0.9373 (mm-30) cc_final: 0.9040 (mt-10) REVERT: K 150 MET cc_start: 0.9058 (mtt) cc_final: 0.8719 (mtt) REVERT: K 175 LEU cc_start: 0.8958 (mm) cc_final: 0.8631 (mm) REVERT: K 217 TYR cc_start: 0.8451 (m-80) cc_final: 0.8111 (m-80) REVERT: K 328 MET cc_start: 0.8303 (tpp) cc_final: 0.7984 (tpp) REVERT: K 478 ASN cc_start: 0.9025 (m110) cc_final: 0.8671 (m110) REVERT: Q 530 MET cc_start: 0.9231 (ttm) cc_final: 0.8736 (mmm) REVERT: Q 543 ASN cc_start: 0.8881 (t0) cc_final: 0.8437 (t0) REVERT: Q 584 GLU cc_start: 0.9063 (pm20) cc_final: 0.8770 (pm20) REVERT: Q 624 ASP cc_start: 0.8800 (m-30) cc_final: 0.8522 (m-30) REVERT: Q 643 TYR cc_start: 0.9443 (m-10) cc_final: 0.9166 (m-10) REVERT: R 106 GLU cc_start: 0.8752 (tp30) cc_final: 0.8465 (tp30) REVERT: R 377 ASN cc_start: 0.9228 (p0) cc_final: 0.8572 (t0) REVERT: R 434 MET cc_start: 0.8962 (ttm) cc_final: 0.8602 (ttm) REVERT: R 475 MET cc_start: 0.8724 (mmm) cc_final: 0.8019 (mmm) REVERT: A 16 GLU cc_start: 0.7711 (mt-10) cc_final: 0.7491 (mt-10) REVERT: A 46 GLU cc_start: 0.8481 (tm-30) cc_final: 0.8177 (tm-30) REVERT: A 64 ASN cc_start: 0.8974 (m-40) cc_final: 0.8721 (m110) REVERT: A 81 LYS cc_start: 0.9578 (mttt) cc_final: 0.9136 (tptt) REVERT: A 82 LEU cc_start: 0.8743 (mp) cc_final: 0.8180 (mp) REVERT: A 100 GLU cc_start: 0.8639 (tt0) cc_final: 0.8112 (tt0) REVERT: F 3 GLN cc_start: 0.9246 (mm110) cc_final: 0.9040 (mm110) REVERT: F 46 GLU cc_start: 0.8190 (tm-30) cc_final: 0.7886 (tm-30) REVERT: F 80 LEU cc_start: 0.8760 (mt) cc_final: 0.7869 (mt) REVERT: F 81 LYS cc_start: 0.9611 (mttt) cc_final: 0.9182 (mmtm) REVERT: F 82 ASN cc_start: 0.9038 (m-40) cc_final: 0.8783 (p0) REVERT: F 99 GLN cc_start: 0.8828 (pp30) cc_final: 0.8567 (pp30) REVERT: F 100 GLU cc_start: 0.8347 (tt0) cc_final: 0.8035 (tt0) REVERT: O 3 GLN cc_start: 0.9275 (mm110) cc_final: 0.8834 (mm110) REVERT: O 18 LEU cc_start: 0.8311 (tt) cc_final: 0.7991 (mp) REVERT: O 46 GLU cc_start: 0.8871 (tt0) cc_final: 0.8542 (tm-30) REVERT: O 80 LEU cc_start: 0.8982 (mt) cc_final: 0.8093 (mt) REVERT: O 81 LYS cc_start: 0.9524 (mttt) cc_final: 0.8915 (mmmm) REVERT: O 82 ASN cc_start: 0.8868 (m-40) cc_final: 0.8627 (p0) REVERT: O 86 ASP cc_start: 0.8900 (t0) cc_final: 0.8587 (t0) REVERT: O 99 GLN cc_start: 0.8824 (pp30) cc_final: 0.8490 (pp30) REVERT: O 100 GLU cc_start: 0.8736 (tt0) cc_final: 0.7963 (tt0) REVERT: O 101 ASP cc_start: 0.9454 (p0) cc_final: 0.8975 (p0) REVERT: B 37 GLN cc_start: 0.8368 (tp40) cc_final: 0.7699 (tp40) REVERT: B 42 GLN cc_start: 0.8400 (mp10) cc_final: 0.7984 (mp10) REVERT: B 47 LEU cc_start: 0.9684 (mp) cc_final: 0.9356 (mp) REVERT: B 70 ARG cc_start: 0.8156 (mmm160) cc_final: 0.7897 (tpt170) REVERT: B 85 ASP cc_start: 0.8483 (m-30) cc_final: 0.7870 (p0) REVERT: B 90 MET cc_start: 0.9087 (tpp) cc_final: 0.8810 (tpp) REVERT: I 26 GLN cc_start: 0.9311 (tp-100) cc_final: 0.9108 (tp-100) REVERT: I 37 GLN cc_start: 0.8154 (tp40) cc_final: 0.7728 (tp-100) REVERT: I 42 GLN cc_start: 0.8338 (mp10) cc_final: 0.7865 (mp10) REVERT: I 47 LEU cc_start: 0.9647 (mt) cc_final: 0.9333 (mp) REVERT: I 70 ARG cc_start: 0.7851 (mmm160) cc_final: 0.7207 (tpt170) REVERT: I 83 GLU cc_start: 0.8021 (tp30) cc_final: 0.7713 (mm-30) REVERT: I 85 ASP cc_start: 0.8409 (m-30) cc_final: 0.7596 (p0) REVERT: P 31 ARG cc_start: 0.8889 (mtm110) cc_final: 0.8620 (ptp90) REVERT: P 37 GLN cc_start: 0.8887 (tt0) cc_final: 0.8519 (tm-30) REVERT: P 42 GLN cc_start: 0.8347 (mp10) cc_final: 0.7981 (mp10) REVERT: P 47 LEU cc_start: 0.9668 (mt) cc_final: 0.9404 (mp) REVERT: P 83 GLU cc_start: 0.8006 (tp30) cc_final: 0.7732 (tp30) REVERT: P 85 ASP cc_start: 0.8400 (m-30) cc_final: 0.7469 (p0) outliers start: 0 outliers final: 0 residues processed: 400 average time/residue: 0.1392 time to fit residues: 84.9912 Evaluate side-chains 313 residues out of total 2109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 313 time to evaluate : 0.740 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 14 optimal weight: 9.9990 chunk 127 optimal weight: 2.9990 chunk 75 optimal weight: 7.9990 chunk 93 optimal weight: 0.7980 chunk 206 optimal weight: 7.9990 chunk 233 optimal weight: 6.9990 chunk 163 optimal weight: 7.9990 chunk 60 optimal weight: 1.9990 chunk 222 optimal weight: 0.0270 chunk 0 optimal weight: 10.0000 chunk 126 optimal weight: 5.9990 overall best weight: 2.3644 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.071861 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2706 r_free = 0.2706 target = 0.053238 restraints weight = 70842.200| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2756 r_free = 0.2756 target = 0.055388 restraints weight = 34078.771| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.2790 r_free = 0.2790 target = 0.056839 restraints weight = 21750.782| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.2812 r_free = 0.2812 target = 0.057784 restraints weight = 16268.189| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2826 r_free = 0.2826 target = 0.058417 restraints weight = 13479.791| |-----------------------------------------------------------------------------| r_work (final): 0.2813 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8407 moved from start: 0.3301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 20892 Z= 0.145 Angle : 0.738 14.515 28557 Z= 0.336 Chirality : 0.048 0.418 3436 Planarity : 0.004 0.049 3447 Dihedral : 9.527 107.831 4667 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.30 % Favored : 93.65 % Rotamer: Outliers : 0.00 % Allowed : 0.52 % Favored : 99.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.05 (0.16), residues: 2364 helix: -0.52 (0.28), residues: 342 sheet: -0.26 (0.22), residues: 542 loop : -2.11 (0.15), residues: 1480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG I 31 TYR 0.021 0.001 TYR C 643 PHE 0.011 0.001 PHE K 320 TRP 0.018 0.001 TRP R 112 HIS 0.004 0.001 HIS K 216 Details of bonding type rmsd covalent geometry : bond 0.00323 (20752) covalent geometry : angle 0.68541 (28176) SS BOND : bond 0.00350 ( 39) SS BOND : angle 1.56155 ( 78) hydrogen bonds : bond 0.03353 ( 467) hydrogen bonds : angle 4.60632 ( 1251) link_ALPHA1-2 : bond 0.00974 ( 5) link_ALPHA1-2 : angle 2.75435 ( 15) link_ALPHA1-3 : bond 0.00844 ( 8) link_ALPHA1-3 : angle 1.28855 ( 24) link_ALPHA1-6 : bond 0.00983 ( 7) link_ALPHA1-6 : angle 1.77454 ( 21) link_BETA1-4 : bond 0.00668 ( 30) link_BETA1-4 : angle 2.83018 ( 90) link_NAG-ASN : bond 0.00428 ( 51) link_NAG-ASN : angle 2.78153 ( 153) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 384 residues out of total 2109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 384 time to evaluate : 0.661 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: C 530 MET cc_start: 0.9048 (ttm) cc_final: 0.8408 (ttm) REVERT: C 540 GLN cc_start: 0.9090 (mp10) cc_final: 0.8867 (mp10) REVERT: C 543 ASN cc_start: 0.8978 (t0) cc_final: 0.8510 (t0) REVERT: C 574 LYS cc_start: 0.9296 (mttm) cc_final: 0.9066 (mttt) REVERT: C 575 GLN cc_start: 0.9109 (mp10) cc_final: 0.8756 (mp10) REVERT: C 584 GLU cc_start: 0.8969 (pm20) cc_final: 0.8697 (pm20) REVERT: C 590 GLN cc_start: 0.9515 (tp40) cc_final: 0.9132 (tp40) REVERT: C 591 GLN cc_start: 0.9685 (tm-30) cc_final: 0.9277 (tm-30) REVERT: C 626 MET cc_start: 0.8498 (ttm) cc_final: 0.8260 (ttm) REVERT: C 651 ASN cc_start: 0.8755 (m110) cc_final: 0.8499 (m110) REVERT: G 69 TRP cc_start: 0.7831 (p-90) cc_final: 0.7280 (p-90) REVERT: G 95 MET cc_start: 0.9270 (ptt) cc_final: 0.8557 (ptt) REVERT: G 106 GLU cc_start: 0.8677 (tm-30) cc_final: 0.8388 (tm-30) REVERT: G 150 MET cc_start: 0.8833 (mmm) cc_final: 0.8286 (mmt) REVERT: G 161 MET cc_start: 0.8521 (tpp) cc_final: 0.8097 (tpt) REVERT: G 440 GLN cc_start: 0.8821 (tt0) cc_final: 0.8597 (pm20) REVERT: J 543 ASN cc_start: 0.9072 (m-40) cc_final: 0.8616 (t0) REVERT: J 574 LYS cc_start: 0.9215 (mmtm) cc_final: 0.8855 (mttt) REVERT: J 624 ASP cc_start: 0.8834 (m-30) cc_final: 0.8581 (p0) REVERT: J 632 ASP cc_start: 0.9063 (t70) cc_final: 0.8800 (t70) REVERT: J 654 GLU cc_start: 0.9407 (mm-30) cc_final: 0.9061 (mt-10) REVERT: K 150 MET cc_start: 0.8992 (mtt) cc_final: 0.8719 (mtt) REVERT: K 217 TYR cc_start: 0.8550 (m-80) cc_final: 0.8056 (m-80) REVERT: K 328 MET cc_start: 0.8356 (tpp) cc_final: 0.7962 (tpp) REVERT: K 475 MET cc_start: 0.9069 (mmm) cc_final: 0.8799 (mmm) REVERT: K 478 ASN cc_start: 0.9059 (m110) cc_final: 0.8558 (m110) REVERT: Q 543 ASN cc_start: 0.8932 (t0) cc_final: 0.8471 (t0) REVERT: Q 584 GLU cc_start: 0.9051 (pm20) cc_final: 0.8759 (pm20) REVERT: Q 624 ASP cc_start: 0.8810 (m-30) cc_final: 0.8527 (m-30) REVERT: Q 643 TYR cc_start: 0.9419 (m-10) cc_final: 0.9114 (m-10) REVERT: R 106 GLU cc_start: 0.8773 (tp30) cc_final: 0.8504 (tp30) REVERT: R 377 ASN cc_start: 0.9194 (p0) cc_final: 0.8516 (t0) REVERT: R 434 MET cc_start: 0.8974 (ttm) cc_final: 0.8594 (ttm) REVERT: R 475 MET cc_start: 0.8843 (mmm) cc_final: 0.8208 (mmm) REVERT: A 16 GLU cc_start: 0.7624 (mt-10) cc_final: 0.7406 (mt-10) REVERT: A 64 ASN cc_start: 0.8975 (m-40) cc_final: 0.8722 (m110) REVERT: A 81 LYS cc_start: 0.9597 (mttt) cc_final: 0.9155 (tptt) REVERT: A 82 LEU cc_start: 0.8698 (mp) cc_final: 0.8199 (mp) REVERT: A 100 GLU cc_start: 0.8675 (tt0) cc_final: 0.8092 (tt0) REVERT: A 100 MET cc_start: 0.9213 (mpp) cc_final: 0.8996 (mpp) REVERT: F 3 GLN cc_start: 0.9250 (mm110) cc_final: 0.9039 (mm110) REVERT: F 77 GLN cc_start: 0.8966 (mp10) cc_final: 0.8721 (mp10) REVERT: F 80 LEU cc_start: 0.8760 (mt) cc_final: 0.7815 (mt) REVERT: F 81 LYS cc_start: 0.9598 (mttt) cc_final: 0.9175 (mmtm) REVERT: F 82 ASN cc_start: 0.9045 (m-40) cc_final: 0.8793 (p0) REVERT: F 99 GLN cc_start: 0.8828 (pp30) cc_final: 0.8535 (pp30) REVERT: F 100 GLU cc_start: 0.8406 (tt0) cc_final: 0.8020 (tt0) REVERT: O 3 GLN cc_start: 0.9274 (mm110) cc_final: 0.8832 (mm110) REVERT: O 18 LEU cc_start: 0.8196 (tt) cc_final: 0.7748 (mp) REVERT: O 46 GLU cc_start: 0.8884 (tt0) cc_final: 0.8514 (tm-30) REVERT: O 77 GLN cc_start: 0.8902 (mm110) cc_final: 0.8489 (mm110) REVERT: O 80 LEU cc_start: 0.9016 (mt) cc_final: 0.8086 (mt) REVERT: O 81 LYS cc_start: 0.9532 (mttt) cc_final: 0.8936 (mmmm) REVERT: O 82 ASN cc_start: 0.8784 (m-40) cc_final: 0.8577 (p0) REVERT: O 86 ASP cc_start: 0.8910 (t0) cc_final: 0.8585 (t0) REVERT: O 99 GLN cc_start: 0.8861 (pp30) cc_final: 0.8502 (pp30) REVERT: O 100 GLU cc_start: 0.8760 (tt0) cc_final: 0.8014 (tt0) REVERT: O 101 ASP cc_start: 0.9508 (p0) cc_final: 0.9015 (p0) REVERT: B 37 GLN cc_start: 0.8387 (tp40) cc_final: 0.7915 (tp-100) REVERT: B 42 GLN cc_start: 0.8343 (mp10) cc_final: 0.7898 (mp10) REVERT: B 47 LEU cc_start: 0.9612 (mp) cc_final: 0.9359 (mp) REVERT: B 85 ASP cc_start: 0.8384 (m-30) cc_final: 0.7672 (p0) REVERT: I 31 ARG cc_start: 0.9316 (mtm110) cc_final: 0.8330 (ptp90) REVERT: I 37 GLN cc_start: 0.8183 (tp40) cc_final: 0.7763 (tp-100) REVERT: I 42 GLN cc_start: 0.8361 (mp10) cc_final: 0.7869 (mp10) REVERT: I 47 LEU cc_start: 0.9639 (mt) cc_final: 0.9302 (mp) REVERT: I 70 ARG cc_start: 0.7796 (mmm160) cc_final: 0.7284 (tpt170) REVERT: I 83 GLU cc_start: 0.8015 (tp30) cc_final: 0.7720 (mm-30) REVERT: I 85 ASP cc_start: 0.8404 (m-30) cc_final: 0.7631 (p0) REVERT: P 31 ARG cc_start: 0.8849 (mtm110) cc_final: 0.8595 (ptp90) REVERT: P 37 GLN cc_start: 0.8886 (tt0) cc_final: 0.8507 (tm-30) REVERT: P 42 GLN cc_start: 0.8328 (mp10) cc_final: 0.7949 (mp10) REVERT: P 47 LEU cc_start: 0.9664 (mt) cc_final: 0.9399 (mp) REVERT: P 70 ARG cc_start: 0.7794 (mmm160) cc_final: 0.7567 (mmt180) REVERT: P 83 GLU cc_start: 0.8052 (tp30) cc_final: 0.7778 (tp30) REVERT: P 85 ASP cc_start: 0.8416 (m-30) cc_final: 0.7470 (p0) outliers start: 0 outliers final: 0 residues processed: 384 average time/residue: 0.1363 time to fit residues: 80.1979 Evaluate side-chains 314 residues out of total 2109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 314 time to evaluate : 0.596 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 42 optimal weight: 6.9990 chunk 55 optimal weight: 9.9990 chunk 173 optimal weight: 4.9990 chunk 201 optimal weight: 6.9990 chunk 148 optimal weight: 0.4980 chunk 128 optimal weight: 1.9990 chunk 122 optimal weight: 6.9990 chunk 1 optimal weight: 10.0000 chunk 97 optimal weight: 6.9990 chunk 71 optimal weight: 0.8980 chunk 139 optimal weight: 0.8980 overall best weight: 1.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 650 GLN A 77 GLN ** B 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.072274 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2715 r_free = 0.2715 target = 0.053616 restraints weight = 70377.241| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2765 r_free = 0.2765 target = 0.055765 restraints weight = 33865.350| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2799 r_free = 0.2799 target = 0.057236 restraints weight = 21605.448| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.2821 r_free = 0.2821 target = 0.058196 restraints weight = 16147.826| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2834 r_free = 0.2834 target = 0.058782 restraints weight = 13377.987| |-----------------------------------------------------------------------------| r_work (final): 0.2822 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8391 moved from start: 0.3380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 20892 Z= 0.128 Angle : 0.727 14.310 28557 Z= 0.330 Chirality : 0.047 0.413 3436 Planarity : 0.004 0.051 3447 Dihedral : 9.375 107.392 4667 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.01 % Favored : 93.95 % Rotamer: Outliers : 0.00 % Allowed : 0.19 % Favored : 99.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.98 (0.17), residues: 2364 helix: -0.46 (0.29), residues: 342 sheet: -0.30 (0.21), residues: 603 loop : -2.09 (0.15), residues: 1419 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG I 31 TYR 0.021 0.001 TYR Q 586 PHE 0.009 0.001 PHE K 320 TRP 0.015 0.001 TRP R 112 HIS 0.004 0.001 HIS R 216 Details of bonding type rmsd covalent geometry : bond 0.00284 (20752) covalent geometry : angle 0.67358 (28176) SS BOND : bond 0.00293 ( 39) SS BOND : angle 1.42688 ( 78) hydrogen bonds : bond 0.03233 ( 467) hydrogen bonds : angle 4.56150 ( 1251) link_ALPHA1-2 : bond 0.00962 ( 5) link_ALPHA1-2 : angle 2.67959 ( 15) link_ALPHA1-3 : bond 0.00856 ( 8) link_ALPHA1-3 : angle 1.28931 ( 24) link_ALPHA1-6 : bond 0.00993 ( 7) link_ALPHA1-6 : angle 1.78140 ( 21) link_BETA1-4 : bond 0.00654 ( 30) link_BETA1-4 : angle 2.79107 ( 90) link_NAG-ASN : bond 0.00431 ( 51) link_NAG-ASN : angle 2.85090 ( 153) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 388 residues out of total 2109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 388 time to evaluate : 0.619 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: C 530 MET cc_start: 0.9061 (ttm) cc_final: 0.8435 (ttm) REVERT: C 543 ASN cc_start: 0.8963 (t0) cc_final: 0.8502 (t0) REVERT: C 574 LYS cc_start: 0.9278 (mttm) cc_final: 0.9032 (mttt) REVERT: C 584 GLU cc_start: 0.9036 (pm20) cc_final: 0.8738 (pm20) REVERT: C 595 ILE cc_start: 0.9463 (tp) cc_final: 0.9191 (tp) REVERT: C 624 ASP cc_start: 0.9131 (m-30) cc_final: 0.8870 (p0) REVERT: C 626 MET cc_start: 0.8493 (ttm) cc_final: 0.8255 (ttm) REVERT: G 69 TRP cc_start: 0.7802 (p-90) cc_final: 0.7199 (p-90) REVERT: G 95 MET cc_start: 0.9262 (ptt) cc_final: 0.8554 (ptt) REVERT: G 106 GLU cc_start: 0.8683 (tm-30) cc_final: 0.8395 (tm-30) REVERT: G 150 MET cc_start: 0.8843 (mmm) cc_final: 0.8196 (mmt) REVERT: G 161 MET cc_start: 0.8519 (tpp) cc_final: 0.8105 (tpt) REVERT: G 440 GLN cc_start: 0.8816 (tt0) cc_final: 0.8579 (pm20) REVERT: J 543 ASN cc_start: 0.9044 (m-40) cc_final: 0.8581 (t0) REVERT: J 574 LYS cc_start: 0.9101 (mmtm) cc_final: 0.8782 (mttt) REVERT: J 624 ASP cc_start: 0.8840 (m-30) cc_final: 0.8567 (p0) REVERT: J 632 ASP cc_start: 0.9058 (t70) cc_final: 0.8807 (t70) REVERT: J 654 GLU cc_start: 0.9361 (mm-30) cc_final: 0.9007 (mt-10) REVERT: K 150 MET cc_start: 0.9000 (mtt) cc_final: 0.8751 (mtt) REVERT: K 217 TYR cc_start: 0.8507 (m-80) cc_final: 0.8034 (m-80) REVERT: K 256 SER cc_start: 0.9383 (p) cc_final: 0.9174 (p) REVERT: K 328 MET cc_start: 0.8385 (tpp) cc_final: 0.7964 (tpp) REVERT: K 475 MET cc_start: 0.9080 (mmm) cc_final: 0.8877 (mmm) REVERT: K 478 ASN cc_start: 0.9054 (m110) cc_final: 0.8679 (m110) REVERT: Q 530 MET cc_start: 0.9321 (ttm) cc_final: 0.8795 (mmm) REVERT: Q 543 ASN cc_start: 0.8936 (t0) cc_final: 0.8490 (t0) REVERT: Q 584 GLU cc_start: 0.9068 (pm20) cc_final: 0.8760 (pm20) REVERT: Q 595 ILE cc_start: 0.9628 (tp) cc_final: 0.9407 (tp) REVERT: Q 624 ASP cc_start: 0.8838 (m-30) cc_final: 0.8569 (m-30) REVERT: Q 643 TYR cc_start: 0.9412 (m-10) cc_final: 0.9098 (m-10) REVERT: Q 651 ASN cc_start: 0.8984 (m110) cc_final: 0.8631 (m110) REVERT: R 69 TRP cc_start: 0.7170 (p-90) cc_final: 0.5965 (p-90) REVERT: R 106 GLU cc_start: 0.8774 (tp30) cc_final: 0.8505 (tp30) REVERT: R 174 SER cc_start: 0.9453 (t) cc_final: 0.9128 (t) REVERT: R 217 TYR cc_start: 0.8945 (m-10) cc_final: 0.8653 (m-10) REVERT: R 377 ASN cc_start: 0.9149 (p0) cc_final: 0.8464 (t0) REVERT: R 434 MET cc_start: 0.8959 (ttm) cc_final: 0.8608 (ttm) REVERT: R 475 MET cc_start: 0.8817 (mmm) cc_final: 0.8519 (mmm) REVERT: A 16 GLU cc_start: 0.7553 (mt-10) cc_final: 0.7326 (mt-10) REVERT: A 64 ASN cc_start: 0.8967 (m-40) cc_final: 0.8716 (m110) REVERT: A 81 LYS cc_start: 0.9587 (mttt) cc_final: 0.9152 (tptt) REVERT: A 82 LEU cc_start: 0.8663 (mp) cc_final: 0.8195 (mp) REVERT: A 100 GLU cc_start: 0.8670 (tt0) cc_final: 0.8064 (tt0) REVERT: F 3 GLN cc_start: 0.9239 (mm110) cc_final: 0.9029 (mm110) REVERT: F 80 LEU cc_start: 0.8783 (mt) cc_final: 0.7868 (mt) REVERT: F 81 LYS cc_start: 0.9591 (mttt) cc_final: 0.9178 (mmtm) REVERT: F 82 ASN cc_start: 0.9035 (m-40) cc_final: 0.8762 (p0) REVERT: F 99 GLN cc_start: 0.8745 (pp30) cc_final: 0.8430 (pp30) REVERT: F 100 GLU cc_start: 0.8428 (tt0) cc_final: 0.8002 (tt0) REVERT: O 3 GLN cc_start: 0.9304 (mm110) cc_final: 0.8690 (mp10) REVERT: O 18 LEU cc_start: 0.8378 (tt) cc_final: 0.8024 (mp) REVERT: O 37 ILE cc_start: 0.9478 (mm) cc_final: 0.9251 (mm) REVERT: O 46 GLU cc_start: 0.8886 (tt0) cc_final: 0.8623 (tm-30) REVERT: O 77 GLN cc_start: 0.8933 (mm110) cc_final: 0.8496 (mm110) REVERT: O 80 LEU cc_start: 0.9024 (mt) cc_final: 0.8155 (mt) REVERT: O 81 LYS cc_start: 0.9532 (mttt) cc_final: 0.8928 (mmmm) REVERT: O 82 ASN cc_start: 0.8890 (m-40) cc_final: 0.8624 (p0) REVERT: O 86 ASP cc_start: 0.8906 (t0) cc_final: 0.8557 (t0) REVERT: O 99 GLN cc_start: 0.8882 (pp30) cc_final: 0.8526 (pp30) REVERT: O 100 GLU cc_start: 0.8811 (tt0) cc_final: 0.8019 (tt0) REVERT: O 101 ASP cc_start: 0.9509 (p0) cc_final: 0.8976 (p0) REVERT: B 37 GLN cc_start: 0.8377 (tp40) cc_final: 0.7931 (tp40) REVERT: B 42 GLN cc_start: 0.8284 (mp10) cc_final: 0.7822 (mp10) REVERT: B 47 LEU cc_start: 0.9634 (mp) cc_final: 0.9262 (mp) REVERT: B 70 ARG cc_start: 0.8022 (mmt180) cc_final: 0.7338 (tpt170) REVERT: B 85 ASP cc_start: 0.8398 (m-30) cc_final: 0.7710 (p0) REVERT: B 90 MET cc_start: 0.9078 (tpp) cc_final: 0.8801 (tpp) REVERT: I 26 GLN cc_start: 0.9319 (tp-100) cc_final: 0.8960 (tp-100) REVERT: I 31 ARG cc_start: 0.9321 (mtm110) cc_final: 0.8461 (ptp90) REVERT: I 37 GLN cc_start: 0.8219 (tp40) cc_final: 0.7826 (tp-100) REVERT: I 42 GLN cc_start: 0.8355 (mp10) cc_final: 0.7858 (mp10) REVERT: I 47 LEU cc_start: 0.9650 (mt) cc_final: 0.9336 (mp) REVERT: I 70 ARG cc_start: 0.7775 (mmm160) cc_final: 0.7367 (tpt170) REVERT: I 83 GLU cc_start: 0.8020 (tp30) cc_final: 0.7719 (mm-30) REVERT: I 85 ASP cc_start: 0.8407 (m-30) cc_final: 0.7631 (p0) REVERT: P 31 ARG cc_start: 0.8818 (mtm110) cc_final: 0.8576 (ptp90) REVERT: P 37 GLN cc_start: 0.8894 (tt0) cc_final: 0.8337 (tm-30) REVERT: P 42 GLN cc_start: 0.8340 (mp10) cc_final: 0.8003 (mp10) REVERT: P 47 LEU cc_start: 0.9661 (mt) cc_final: 0.9395 (mp) REVERT: P 70 ARG cc_start: 0.7758 (mmm160) cc_final: 0.7436 (tpt170) REVERT: P 83 GLU cc_start: 0.8073 (tp30) cc_final: 0.7798 (tp30) REVERT: P 85 ASP cc_start: 0.8425 (m-30) cc_final: 0.7524 (p0) outliers start: 0 outliers final: 0 residues processed: 388 average time/residue: 0.1366 time to fit residues: 81.1931 Evaluate side-chains 321 residues out of total 2109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 321 time to evaluate : 0.752 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 195 optimal weight: 10.0000 chunk 236 optimal weight: 1.9990 chunk 129 optimal weight: 0.0170 chunk 99 optimal weight: 6.9990 chunk 40 optimal weight: 2.9990 chunk 27 optimal weight: 10.0000 chunk 3 optimal weight: 4.9990 chunk 74 optimal weight: 3.9990 chunk 38 optimal weight: 4.9990 chunk 91 optimal weight: 0.5980 chunk 61 optimal weight: 3.9990 overall best weight: 1.9224 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 651 ASN ** K 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.072326 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2715 r_free = 0.2715 target = 0.053639 restraints weight = 70316.555| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2766 r_free = 0.2766 target = 0.055811 restraints weight = 33927.928| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.2800 r_free = 0.2800 target = 0.057286 restraints weight = 21593.987| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.2821 r_free = 0.2821 target = 0.058227 restraints weight = 16105.473| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.2836 r_free = 0.2836 target = 0.058876 restraints weight = 13346.607| |-----------------------------------------------------------------------------| r_work (final): 0.2823 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8396 moved from start: 0.3485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 20892 Z= 0.132 Angle : 0.740 14.357 28557 Z= 0.336 Chirality : 0.048 0.415 3436 Planarity : 0.004 0.046 3447 Dihedral : 9.314 106.943 4667 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.18 % Favored : 93.78 % Rotamer: Outliers : 0.00 % Allowed : 0.28 % Favored : 99.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.93 (0.17), residues: 2364 helix: -0.45 (0.28), residues: 345 sheet: -0.26 (0.21), residues: 608 loop : -2.06 (0.15), residues: 1411 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG I 31 TYR 0.021 0.001 TYR C 643 PHE 0.011 0.001 PHE A 100G TRP 0.016 0.001 TRP R 112 HIS 0.004 0.001 HIS R 216 Details of bonding type rmsd covalent geometry : bond 0.00293 (20752) covalent geometry : angle 0.68647 (28176) SS BOND : bond 0.00305 ( 39) SS BOND : angle 1.41721 ( 78) hydrogen bonds : bond 0.03188 ( 467) hydrogen bonds : angle 4.57453 ( 1251) link_ALPHA1-2 : bond 0.00990 ( 5) link_ALPHA1-2 : angle 2.68286 ( 15) link_ALPHA1-3 : bond 0.00818 ( 8) link_ALPHA1-3 : angle 1.31075 ( 24) link_ALPHA1-6 : bond 0.00992 ( 7) link_ALPHA1-6 : angle 1.80031 ( 21) link_BETA1-4 : bond 0.00672 ( 30) link_BETA1-4 : angle 2.76635 ( 90) link_NAG-ASN : bond 0.00430 ( 51) link_NAG-ASN : angle 2.91603 ( 153) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 387 residues out of total 2109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 387 time to evaluate : 0.683 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: C 530 MET cc_start: 0.9057 (ttm) cc_final: 0.8446 (ttm) REVERT: C 543 ASN cc_start: 0.8979 (t0) cc_final: 0.8518 (t0) REVERT: C 574 LYS cc_start: 0.9223 (mttm) cc_final: 0.8988 (mttt) REVERT: C 584 GLU cc_start: 0.9029 (pm20) cc_final: 0.8719 (pm20) REVERT: C 624 ASP cc_start: 0.9141 (m-30) cc_final: 0.8887 (p0) REVERT: C 626 MET cc_start: 0.8484 (ttm) cc_final: 0.8129 (ttm) REVERT: G 69 TRP cc_start: 0.7792 (p-90) cc_final: 0.7213 (p-90) REVERT: G 95 MET cc_start: 0.9265 (ptt) cc_final: 0.8565 (ptt) REVERT: G 106 GLU cc_start: 0.8688 (tm-30) cc_final: 0.8399 (tm-30) REVERT: G 161 MET cc_start: 0.8528 (tpp) cc_final: 0.8108 (tpt) REVERT: G 440 GLN cc_start: 0.8809 (tt0) cc_final: 0.8582 (pm20) REVERT: J 543 ASN cc_start: 0.9047 (m-40) cc_final: 0.8582 (t0) REVERT: J 574 LYS cc_start: 0.9083 (mmtm) cc_final: 0.8735 (mttt) REVERT: J 624 ASP cc_start: 0.8816 (m-30) cc_final: 0.8560 (p0) REVERT: J 632 ASP cc_start: 0.9058 (t70) cc_final: 0.8812 (t70) REVERT: J 654 GLU cc_start: 0.9411 (mm-30) cc_final: 0.9061 (mt-10) REVERT: K 217 TYR cc_start: 0.8499 (m-80) cc_final: 0.8076 (m-80) REVERT: K 256 SER cc_start: 0.9366 (p) cc_final: 0.9159 (p) REVERT: K 478 ASN cc_start: 0.9053 (m110) cc_final: 0.8656 (m110) REVERT: Q 543 ASN cc_start: 0.8943 (t0) cc_final: 0.8501 (t0) REVERT: Q 584 GLU cc_start: 0.9091 (pm20) cc_final: 0.8763 (pm20) REVERT: Q 624 ASP cc_start: 0.8878 (m-30) cc_final: 0.8616 (m-30) REVERT: Q 643 TYR cc_start: 0.9406 (m-10) cc_final: 0.9082 (m-10) REVERT: Q 655 LYS cc_start: 0.9419 (pttt) cc_final: 0.9211 (pttm) REVERT: R 69 TRP cc_start: 0.7085 (p-90) cc_final: 0.5919 (p-90) REVERT: R 106 GLU cc_start: 0.8774 (tp30) cc_final: 0.8511 (tp30) REVERT: R 174 SER cc_start: 0.9452 (t) cc_final: 0.9120 (t) REVERT: R 217 TYR cc_start: 0.8937 (m-10) cc_final: 0.8660 (m-10) REVERT: R 377 ASN cc_start: 0.9141 (p0) cc_final: 0.8473 (t0) REVERT: R 434 MET cc_start: 0.8953 (ttm) cc_final: 0.8621 (ttm) REVERT: R 475 MET cc_start: 0.8857 (mmm) cc_final: 0.8550 (mmm) REVERT: A 16 GLU cc_start: 0.7165 (mt-10) cc_final: 0.6923 (mt-10) REVERT: A 64 ASN cc_start: 0.8965 (m-40) cc_final: 0.8714 (m110) REVERT: A 81 LYS cc_start: 0.9591 (mttt) cc_final: 0.9156 (tptt) REVERT: A 82 LEU cc_start: 0.8676 (mp) cc_final: 0.8205 (mp) REVERT: A 100 GLU cc_start: 0.8696 (tt0) cc_final: 0.8067 (tt0) REVERT: A 100 MET cc_start: 0.9260 (mpp) cc_final: 0.9029 (mpp) REVERT: A 124 LYS cc_start: 0.8655 (ptpp) cc_final: 0.8332 (pttm) REVERT: F 3 GLN cc_start: 0.9254 (mm110) cc_final: 0.9042 (mm110) REVERT: F 46 GLU cc_start: 0.8286 (tm-30) cc_final: 0.8081 (tm-30) REVERT: F 80 LEU cc_start: 0.8790 (mt) cc_final: 0.8198 (mt) REVERT: F 81 LYS cc_start: 0.9617 (mttt) cc_final: 0.9148 (mmtm) REVERT: F 82 ASN cc_start: 0.9018 (m-40) cc_final: 0.8761 (p0) REVERT: F 99 GLN cc_start: 0.8799 (pp30) cc_final: 0.8489 (pp30) REVERT: F 100 GLU cc_start: 0.8419 (tt0) cc_final: 0.7994 (tt0) REVERT: O 3 GLN cc_start: 0.9280 (mm110) cc_final: 0.8612 (mp10) REVERT: O 18 LEU cc_start: 0.8387 (tt) cc_final: 0.8008 (mp) REVERT: O 46 GLU cc_start: 0.8900 (tt0) cc_final: 0.8634 (tm-30) REVERT: O 77 GLN cc_start: 0.8921 (mm110) cc_final: 0.8491 (mm110) REVERT: O 80 LEU cc_start: 0.9049 (mt) cc_final: 0.8392 (mt) REVERT: O 81 LYS cc_start: 0.9547 (mttt) cc_final: 0.9026 (mmtm) REVERT: O 82 ASN cc_start: 0.8874 (m-40) cc_final: 0.8593 (p0) REVERT: O 86 ASP cc_start: 0.8890 (t0) cc_final: 0.8579 (t0) REVERT: O 99 GLN cc_start: 0.8894 (pp30) cc_final: 0.8525 (pp30) REVERT: O 100 ILE cc_start: 0.9417 (pt) cc_final: 0.9214 (pt) REVERT: O 100 GLU cc_start: 0.8815 (tt0) cc_final: 0.8042 (tt0) REVERT: O 101 ASP cc_start: 0.9516 (p0) cc_final: 0.8975 (p0) REVERT: B 37 GLN cc_start: 0.8395 (tp40) cc_final: 0.7931 (tp40) REVERT: B 42 GLN cc_start: 0.8116 (mp10) cc_final: 0.7618 (mp10) REVERT: B 47 LEU cc_start: 0.9574 (mp) cc_final: 0.9304 (mp) REVERT: B 85 ASP cc_start: 0.8419 (m-30) cc_final: 0.7715 (p0) REVERT: B 90 MET cc_start: 0.9076 (tpp) cc_final: 0.8795 (tpp) REVERT: I 26 GLN cc_start: 0.9325 (tp-100) cc_final: 0.8969 (tp-100) REVERT: I 31 ARG cc_start: 0.9299 (mtm110) cc_final: 0.8425 (ptp90) REVERT: I 37 GLN cc_start: 0.8239 (tp40) cc_final: 0.7832 (tp-100) REVERT: I 42 GLN cc_start: 0.8384 (mp10) cc_final: 0.7875 (mp10) REVERT: I 47 LEU cc_start: 0.9641 (mt) cc_final: 0.9266 (mp) REVERT: I 70 ARG cc_start: 0.7756 (mmm160) cc_final: 0.7366 (tpt170) REVERT: I 83 GLU cc_start: 0.8047 (tp30) cc_final: 0.7748 (mm-30) REVERT: I 85 ASP cc_start: 0.8436 (m-30) cc_final: 0.7644 (p0) REVERT: P 31 ARG cc_start: 0.8831 (mtm110) cc_final: 0.8550 (ptp90) REVERT: P 37 GLN cc_start: 0.8894 (tt0) cc_final: 0.8346 (tm-30) REVERT: P 42 GLN cc_start: 0.8405 (mp10) cc_final: 0.8005 (mp10) REVERT: P 47 LEU cc_start: 0.9664 (mt) cc_final: 0.9356 (mp) REVERT: P 70 ARG cc_start: 0.7750 (mmm160) cc_final: 0.7439 (tpt170) REVERT: P 83 GLU cc_start: 0.8106 (tp30) cc_final: 0.7833 (tp30) REVERT: P 85 ASP cc_start: 0.8428 (m-30) cc_final: 0.7523 (p0) outliers start: 0 outliers final: 0 residues processed: 387 average time/residue: 0.1369 time to fit residues: 81.7962 Evaluate side-chains 319 residues out of total 2109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 319 time to evaluate : 0.740 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 113 optimal weight: 10.0000 chunk 64 optimal weight: 3.9990 chunk 235 optimal weight: 10.0000 chunk 79 optimal weight: 6.9990 chunk 185 optimal weight: 30.0000 chunk 180 optimal weight: 0.7980 chunk 91 optimal weight: 0.9980 chunk 63 optimal weight: 7.9990 chunk 98 optimal weight: 8.9990 chunk 158 optimal weight: 4.9990 chunk 30 optimal weight: 7.9990 overall best weight: 3.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 651 ASN ** K 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 651 ASN ** B 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.070596 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2673 r_free = 0.2673 target = 0.051921 restraints weight = 71776.848| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2722 r_free = 0.2722 target = 0.054010 restraints weight = 34979.517| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2756 r_free = 0.2756 target = 0.055431 restraints weight = 22479.609| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.2777 r_free = 0.2777 target = 0.056350 restraints weight = 16906.096| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.2792 r_free = 0.2792 target = 0.056960 restraints weight = 14083.790| |-----------------------------------------------------------------------------| r_work (final): 0.2781 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8447 moved from start: 0.3511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 20892 Z= 0.197 Angle : 0.787 15.095 28557 Z= 0.360 Chirality : 0.048 0.468 3436 Planarity : 0.004 0.047 3447 Dihedral : 9.398 101.719 4667 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.04 % Allowed : 7.40 % Favored : 92.55 % Rotamer: Outliers : 0.00 % Allowed : 0.14 % Favored : 99.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.96 (0.17), residues: 2364 helix: -0.37 (0.28), residues: 345 sheet: -0.39 (0.21), residues: 642 loop : -2.10 (0.16), residues: 1377 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG I 31 TYR 0.023 0.001 TYR Q 586 PHE 0.012 0.001 PHE G 391 TRP 0.026 0.002 TRP R 112 HIS 0.005 0.001 HIS K 330 Details of bonding type rmsd covalent geometry : bond 0.00441 (20752) covalent geometry : angle 0.73411 (28176) SS BOND : bond 0.00341 ( 39) SS BOND : angle 1.64767 ( 78) hydrogen bonds : bond 0.03600 ( 467) hydrogen bonds : angle 4.70848 ( 1251) link_ALPHA1-2 : bond 0.01020 ( 5) link_ALPHA1-2 : angle 2.95339 ( 15) link_ALPHA1-3 : bond 0.00756 ( 8) link_ALPHA1-3 : angle 1.37478 ( 24) link_ALPHA1-6 : bond 0.01042 ( 7) link_ALPHA1-6 : angle 1.96472 ( 21) link_BETA1-4 : bond 0.00645 ( 30) link_BETA1-4 : angle 2.82258 ( 90) link_NAG-ASN : bond 0.00466 ( 51) link_NAG-ASN : angle 2.94982 ( 153) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3202.03 seconds wall clock time: 56 minutes 7.12 seconds (3367.12 seconds total)