Starting phenix.real_space_refine on Sun Sep 13 04:02:10 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6orn_20175/09_2026/6orn_20175.cif Found real_map, /net/cci-nas-00/data/ceres_data/6orn_20175/09_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_20175/09_2026/6orn_20175.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6orn_20175/09_2026/6orn_20175.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6orn_20175/09_2026/6orn_20175.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6orn_20175/09_2026/6orn_20175.map" restraint_files = "/net/cci-nas-00/data/ceres_data/6orn_20175/09_2026/6orn_20175.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6orn_20175/09_2026/6orn_20175.cif" } 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 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 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 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 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 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 chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen chiralities: 7 Chain: "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 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 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 chiralities: 2 Chain: "Y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "a" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "b" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen chiralities: 6 Chain: "c" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "d" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "e" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen chiralities: 6 Chain: "f" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "g" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "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 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 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 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 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 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 chiralities: 5 Time building chain proxies: 4.34, per 1000 atoms: 0.21 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: 2.07 Conformation dependent library (CDL) restraints added in 817.2 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: 0.70 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: 3.68 Time building geometry restraints manager: 2.66 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 - 15.16: 10848 15.16 - 30.32: 559 30.32 - 45.47: 173 45.47 - 60.63: 27 60.63 - 75.79: 24 Dihedral angle restraints: 11631 sinusoidal: 4674 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 11628 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: 0.570 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: 0.270 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 19.020 Find NCS groups from input model: 0.580 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.890 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8498 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 : 10.575 75.788 7038 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/Z covalent geometry : bond 0.00753 / 0.36 (20752) covalent geometry : angle 1.13637 / 0.58 (28176) SS BOND : bond 0.00737 / 0.45 ( 39) SS BOND : angle 2.29379 / 1.59 ( 78) hydrogen bonds : bond 0.27066 / 18.14 ( 467) hydrogen bonds : angle 8.68981 / 6.26 ( 1251) link_ALPHA1-2 : bond 0.00758 / 0.42 ( 5) link_ALPHA1-2 : angle 3.51331 / 2.09 ( 15) link_ALPHA1-3 : bond 0.00935 / 0.75 ( 8) link_ALPHA1-3 : angle 2.70721 / 1.67 ( 24) link_ALPHA1-6 : bond 0.01014 / 0.48 ( 7) link_ALPHA1-6 : angle 2.44177 / 1.40 ( 21) link_BETA1-4 : bond 0.01034 / 0.65 ( 30) link_BETA1-4 : angle 5.51101 / 3.70 ( 90) link_NAG-ASN : bond 0.00980 / 0.57 ( 51) link_NAG-ASN : angle 5.19139 / 3.55 ( 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 : 0.805 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: 0.1722 time to fit residues: 121.4613 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 : 0.749 ------------------------------------------------------------------------------- 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... C 590 GLN G 103 GLN G 133 ASN G 137 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 52 GLN P 89 HIS Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.073252 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2740 r_free = 0.2740 target = 0.054784 restraints weight = 69434.257| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2791 r_free = 0.2791 target = 0.056981 restraints weight = 33033.846| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.2825 r_free = 0.2825 target = 0.058463 restraints weight = 20797.085| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.2847 r_free = 0.2847 target = 0.059446 restraints weight = 15432.110| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.2862 r_free = 0.2862 target = 0.060108 restraints weight = 12664.259| |-----------------------------------------------------------------------------| r_work (final): 0.2854 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8429 moved from start: 0.1722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 20892 Z= 0.140 Angle : 0.793 15.225 28557 Z= 0.367 Chirality : 0.048 0.449 3436 Planarity : 0.004 0.041 3447 Dihedral : 5.652 40.257 2604 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.82 % Favored : 95.05 % Rotamer: Outliers : 0.05 % Allowed : 2.32 % Favored : 97.63 % 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: -3.57 (0.15), residues: 2364 helix: -2.87 (0.20), residues: 369 sheet: -1.41 (0.21), residues: 533 loop : -2.74 (0.14), residues: 1462 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG I 31 TYR 0.016 0.001 TYR Q 586 PHE 0.014 0.001 PHE K 320 TRP 0.022 0.001 TRP G 69 HIS 0.002 0.001 HIS G 105 Details of bonding type rmsd/Z covalent geometry : bond 0.00297 / 0.14 (20752) covalent geometry : angle 0.72917 / 0.35 (28176) SS BOND : bond 0.00226 / 0.14 ( 39) SS BOND : angle 1.52518 / 1.04 ( 78) hydrogen bonds : bond 0.04984 / 3.38 ( 467) hydrogen bonds : angle 5.83374 / 4.13 ( 1251) link_ALPHA1-2 : bond 0.00803 / 0.48 ( 5) link_ALPHA1-2 : angle 2.80469 / 1.73 ( 15) link_ALPHA1-3 : bond 0.00785 / 0.61 ( 8) link_ALPHA1-3 : angle 1.73714 / 1.01 ( 24) link_ALPHA1-6 : bond 0.00678 / 0.31 ( 7) link_ALPHA1-6 : angle 1.86190 / 1.15 ( 21) link_BETA1-4 : bond 0.00662 / 0.47 ( 30) link_BETA1-4 : angle 2.95064 / 2.00 ( 90) link_NAG-ASN : bond 0.00475 / 0.31 ( 51) link_NAG-ASN : angle 3.39343 / 2.32 ( 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 431 residues out of total 2109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 430 time to evaluate : 0.780 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 543 ASN cc_start: 0.8737 (t0) cc_final: 0.8373 (t0) REVERT: C 577 GLN cc_start: 0.8839 (mt0) cc_final: 0.8492 (mt0) REVERT: C 580 VAL cc_start: 0.9370 (p) cc_final: 0.8990 (p) REVERT: C 584 GLU cc_start: 0.9317 (pm20) cc_final: 0.8978 (pm20) REVERT: C 647 GLU cc_start: 0.8700 (tm-30) cc_final: 0.8388 (tm-30) REVERT: G 49 GLU cc_start: 0.8782 (pp20) cc_final: 0.8436 (tm-30) REVERT: G 95 MET cc_start: 0.9209 (ptt) cc_final: 0.8722 (ptt) REVERT: G 150 MET cc_start: 0.8855 (mtt) cc_final: 0.8530 (mtt) REVERT: G 164 GLU cc_start: 0.8162 (tt0) cc_final: 0.7928 (tt0) REVERT: G 322 ILE cc_start: 0.9243 (mm) cc_final: 0.9017 (mm) REVERT: J 543 ASN cc_start: 0.9061 (m-40) cc_final: 0.8654 (t0) REVERT: J 577 GLN cc_start: 0.8906 (mt0) cc_final: 0.8391 (mt0) REVERT: J 624 ASP cc_start: 0.8864 (m-30) cc_final: 0.8482 (p0) REVERT: J 632 ASP cc_start: 0.8956 (t70) cc_final: 0.8566 (t70) REVERT: K 475 MET cc_start: 0.8704 (mmm) cc_final: 0.8491 (mmm) REVERT: Q 543 ASN cc_start: 0.8726 (t0) cc_final: 0.8416 (t0) REVERT: Q 573 ILE cc_start: 0.9084 (mm) cc_final: 0.8742 (tp) REVERT: Q 577 GLN cc_start: 0.8861 (mt0) cc_final: 0.8444 (mt0) REVERT: Q 584 GLU cc_start: 0.9309 (pm20) cc_final: 0.8919 (pm20) REVERT: Q 591 GLN cc_start: 0.9708 (tm-30) cc_final: 0.9324 (tm-30) REVERT: Q 601 LYS cc_start: 0.8990 (mppt) cc_final: 0.8730 (mmtt) REVERT: Q 624 ASP cc_start: 0.8999 (m-30) cc_final: 0.8671 (m-30) REVERT: Q 632 ASP cc_start: 0.8922 (t70) cc_final: 0.8607 (t70) REVERT: Q 643 TYR cc_start: 0.9471 (m-10) cc_final: 0.9191 (m-80) REVERT: R 95 MET cc_start: 0.9105 (ptm) cc_final: 0.8625 (ptt) REVERT: R 377 ASN cc_start: 0.9365 (p0) cc_final: 0.8615 (t0) REVERT: R 434 MET cc_start: 0.9007 (ttm) cc_final: 0.8672 (ttm) REVERT: R 492 GLU cc_start: 0.8754 (tm-30) cc_final: 0.7908 (tm-30) REVERT: R 494 LEU cc_start: 0.9244 (tp) cc_final: 0.8658 (tt) REVERT: A 29 MET cc_start: 0.6749 (ptm) cc_final: 0.5870 (ptp) REVERT: A 34 TRP cc_start: 0.8657 (m100) cc_final: 0.7931 (m100) REVERT: A 48 ILE cc_start: 0.9104 (mt) cc_final: 0.8598 (mp) REVERT: A 64 ASN cc_start: 0.8942 (m-40) cc_final: 0.8699 (m110) REVERT: A 81 LYS cc_start: 0.9550 (mttt) cc_final: 0.9191 (tptt) REVERT: A 82 LEU cc_start: 0.8804 (mp) cc_final: 0.8216 (mp) REVERT: A 91 TYR cc_start: 0.9077 (m-80) cc_final: 0.8695 (m-80) REVERT: F 1 GLN cc_start: 0.7287 (tp40) cc_final: 0.6266 (tm-30) REVERT: F 3 GLN cc_start: 0.9280 (mm110) cc_final: 0.8567 (mm110) REVERT: F 48 ILE cc_start: 0.9133 (mt) cc_final: 0.8655 (mp) REVERT: F 80 LEU cc_start: 0.8502 (mt) cc_final: 0.7471 (mt) REVERT: F 81 LYS cc_start: 0.9563 (mttt) cc_final: 0.8979 (mmmm) REVERT: F 82 ASN cc_start: 0.8901 (m-40) cc_final: 0.8646 (p0) REVERT: F 90 TYR cc_start: 0.9269 (m-10) cc_final: 0.9035 (m-10) REVERT: F 91 TYR cc_start: 0.8944 (m-80) cc_final: 0.8731 (m-80) REVERT: F 105 LYS cc_start: 0.8517 (ptmt) cc_final: 0.8266 (mtmm) REVERT: O 3 GLN cc_start: 0.9289 (mm110) cc_final: 0.8695 (mp10) REVERT: O 13 LYS cc_start: 0.9204 (pttm) cc_final: 0.8961 (tppt) REVERT: O 46 GLU cc_start: 0.8830 (tt0) cc_final: 0.8391 (tm-30) REVERT: O 77 GLN cc_start: 0.8958 (mm110) cc_final: 0.8636 (mm110) REVERT: O 80 LEU cc_start: 0.8698 (mt) cc_final: 0.8436 (mt) REVERT: O 81 LYS cc_start: 0.9547 (mttt) cc_final: 0.9046 (mmmm) REVERT: O 82 ASN cc_start: 0.8811 (m-40) cc_final: 0.8522 (p0) REVERT: O 99 GLN cc_start: 0.8628 (pp30) cc_final: 0.8348 (pp30) REVERT: O 100 GLU cc_start: 0.8714 (tt0) cc_final: 0.7952 (tt0) REVERT: B 37 GLN cc_start: 0.8202 (tp40) cc_final: 0.7585 (tp-100) REVERT: B 42 GLN cc_start: 0.8388 (mp10) cc_final: 0.8063 (mp10) REVERT: B 47 LEU cc_start: 0.9665 (mt) cc_final: 0.9463 (mp) REVERT: B 70 ARG cc_start: 0.7992 (mmm160) cc_final: 0.6616 (tpt170) REVERT: B 85 ASP cc_start: 0.8378 (m-30) cc_final: 0.7675 (p0) REVERT: B 90 MET cc_start: 0.9070 (tpp) cc_final: 0.8814 (tpp) REVERT: I 31 ARG cc_start: 0.9057 (mtm110) cc_final: 0.8627 (ptp-170) REVERT: I 37 GLN cc_start: 0.8800 (tt0) cc_final: 0.8574 (tm-30) REVERT: I 42 GLN cc_start: 0.8519 (mp10) cc_final: 0.8157 (mp10) REVERT: I 47 LEU cc_start: 0.9699 (mt) cc_final: 0.9231 (mp) REVERT: I 70 ARG cc_start: 0.7996 (mmm160) cc_final: 0.7325 (mmt180) REVERT: I 83 GLU cc_start: 0.7982 (tp30) cc_final: 0.7564 (tp30) REVERT: I 85 ASP cc_start: 0.8413 (m-30) cc_final: 0.7805 (p0) REVERT: I 92 ASP cc_start: 0.8706 (p0) cc_final: 0.8495 (p0) REVERT: I 104 LEU cc_start: 0.8452 (tp) cc_final: 0.7743 (tp) REVERT: P 18 THR cc_start: 0.9057 (p) cc_final: 0.8822 (t) REVERT: P 31 ARG cc_start: 0.8786 (mtm110) cc_final: 0.8548 (ptp-170) REVERT: P 33 VAL cc_start: 0.9304 (m) cc_final: 0.8923 (m) REVERT: P 37 GLN cc_start: 0.8866 (tt0) cc_final: 0.8523 (tp40) REVERT: P 42 GLN cc_start: 0.8411 (mp10) cc_final: 0.8085 (mp10) REVERT: P 47 LEU cc_start: 0.9671 (mt) cc_final: 0.9328 (mp) REVERT: P 70 ARG cc_start: 0.7945 (mmm160) cc_final: 0.7512 (mmt180) REVERT: P 83 GLU cc_start: 0.7819 (tp30) cc_final: 0.7592 (tp30) REVERT: P 85 ASP cc_start: 0.8211 (m-30) cc_final: 0.7456 (p0) outliers start: 1 outliers final: 0 residues processed: 430 average time/residue: 0.1539 time to fit residues: 101.1385 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 : 0.765 ------------------------------------------------------------------------------- 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: 10.0000 chunk 107 optimal weight: 0.7980 chunk 80 optimal weight: 4.9990 chunk 48 optimal weight: 6.9990 chunk 16 optimal weight: 0.0070 chunk 113 optimal weight: 9.9990 chunk 127 optimal weight: 1.9990 chunk 220 optimal weight: 10.0000 chunk 184 optimal weight: 9.9990 chunk 105 optimal weight: 8.9990 chunk 122 optimal weight: 9.9990 overall best weight: 2.9604 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Q 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** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.071628 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2701 r_free = 0.2701 target = 0.053033 restraints weight = 70244.380| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2752 r_free = 0.2752 target = 0.055189 restraints weight = 33598.076| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2786 r_free = 0.2786 target = 0.056660 restraints weight = 21285.048| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.2808 r_free = 0.2808 target = 0.057630 restraints weight = 15823.656| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2821 r_free = 0.2821 target = 0.058238 restraints weight = 13017.017| |-----------------------------------------------------------------------------| r_work (final): 0.2808 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8456 moved from start: 0.2203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 20892 Z= 0.177 Angle : 0.767 15.170 28557 Z= 0.354 Chirality : 0.048 0.425 3436 Planarity : 0.004 0.048 3447 Dihedral : 5.387 41.139 2604 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.96 % Favored : 93.95 % 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 : 0.13 % 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: -3.09 (0.15), residues: 2364 helix: -1.89 (0.24), residues: 342 sheet: -1.28 (0.20), residues: 591 loop : -2.55 (0.14), residues: 1431 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 103 TYR 0.016 0.001 TYR C 643 PHE 0.013 0.001 PHE K 320 TRP 0.019 0.002 TRP G 69 HIS 0.005 0.001 HIS K 330 Details of bonding type rmsd/Z covalent geometry : bond 0.00392 / 0.18 (20752) covalent geometry : angle 0.70725 / 0.34 (28176) SS BOND : bond 0.00385 / 0.24 ( 39) SS BOND : angle 1.66229 / 1.17 ( 78) hydrogen bonds : bond 0.04437 / 3.03 ( 467) hydrogen bonds : angle 5.35576 / 3.79 ( 1251) link_ALPHA1-2 : bond 0.00718 / 0.45 ( 5) link_ALPHA1-2 : angle 2.72487 / 1.69 ( 15) link_ALPHA1-3 : bond 0.00755 / 0.59 ( 8) link_ALPHA1-3 : angle 1.81053 / 1.10 ( 24) link_ALPHA1-6 : bond 0.00553 / 0.25 ( 7) link_ALPHA1-6 : angle 1.64688 / 1.04 ( 21) link_BETA1-4 : bond 0.00688 / 0.47 ( 30) link_BETA1-4 : angle 2.82712 / 1.91 ( 90) link_NAG-ASN : bond 0.00490 / 0.32 ( 51) link_NAG-ASN : angle 3.15926 / 2.16 ( 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 388 residues out of total 2109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 388 time to evaluate : 0.700 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: C 530 MET cc_start: 0.9042 (ttm) cc_final: 0.8659 (ttm) REVERT: C 543 ASN cc_start: 0.8935 (t0) cc_final: 0.8500 (t0) REVERT: C 574 LYS cc_start: 0.9230 (mttm) cc_final: 0.8770 (mtmt) REVERT: C 577 GLN cc_start: 0.8913 (mt0) cc_final: 0.8474 (mt0) REVERT: C 584 GLU cc_start: 0.9209 (pm20) cc_final: 0.8916 (pm20) REVERT: C 647 GLU cc_start: 0.8605 (tm-30) cc_final: 0.8333 (tm-30) REVERT: C 657 GLU cc_start: 0.9512 (mm-30) cc_final: 0.9309 (mm-30) REVERT: G 95 MET cc_start: 0.9302 (ptt) cc_final: 0.8780 (ptt) REVERT: J 530 MET cc_start: 0.9224 (ttm) cc_final: 0.8863 (ttm) REVERT: J 543 ASN cc_start: 0.9121 (m-40) cc_final: 0.8768 (t0) REVERT: J 577 GLN cc_start: 0.8982 (mt0) cc_final: 0.8434 (mt0) REVERT: J 624 ASP cc_start: 0.8938 (m-30) cc_final: 0.8548 (p0) REVERT: J 632 ASP cc_start: 0.9049 (t70) cc_final: 0.8733 (t70) REVERT: J 654 GLU cc_start: 0.9476 (mm-30) cc_final: 0.9258 (mm-30) REVERT: K 217 TYR cc_start: 0.8849 (m-80) cc_final: 0.8279 (m-80) REVERT: K 475 MET cc_start: 0.8850 (mmm) cc_final: 0.8589 (mmm) REVERT: Q 543 ASN cc_start: 0.8881 (t0) cc_final: 0.8470 (t0) REVERT: Q 573 ILE cc_start: 0.9182 (mm) cc_final: 0.8658 (tp) REVERT: Q 577 GLN cc_start: 0.8961 (mt0) cc_final: 0.8554 (mt0) REVERT: Q 584 GLU cc_start: 0.9186 (pm20) cc_final: 0.8882 (pm20) REVERT: Q 624 ASP cc_start: 0.9028 (m-30) cc_final: 0.8757 (p0) REVERT: Q 626 MET cc_start: 0.8194 (ptm) cc_final: 0.7778 (ptm) REVERT: Q 632 ASP cc_start: 0.9089 (t70) cc_final: 0.8771 (t70) REVERT: R 95 MET cc_start: 0.9055 (ptm) cc_final: 0.8376 (ptp) REVERT: R 377 ASN cc_start: 0.9344 (p0) cc_final: 0.8549 (t0) REVERT: R 434 MET cc_start: 0.9125 (ttm) cc_final: 0.8807 (ttm) REVERT: R 492 GLU cc_start: 0.8676 (tm-30) cc_final: 0.8317 (tm-30) REVERT: R 494 LEU cc_start: 0.9254 (tp) cc_final: 0.8907 (tt) REVERT: A 64 ASN cc_start: 0.8992 (m-40) cc_final: 0.8763 (m110) REVERT: A 81 LYS cc_start: 0.9581 (mttt) cc_final: 0.9206 (tptt) REVERT: A 82 LEU cc_start: 0.8857 (mp) cc_final: 0.8284 (mp) REVERT: A 100 GLU cc_start: 0.8758 (tt0) cc_final: 0.8288 (tt0) REVERT: A 100 MET cc_start: 0.9034 (mpp) cc_final: 0.8774 (mpp) REVERT: A 124 LYS cc_start: 0.8882 (ptpp) cc_final: 0.8469 (ptpp) REVERT: F 1 GLN cc_start: 0.7291 (tp40) cc_final: 0.6239 (tm-30) REVERT: F 3 GLN cc_start: 0.9283 (mm110) cc_final: 0.8824 (mm110) REVERT: F 48 ILE cc_start: 0.9075 (mt) cc_final: 0.8724 (mp) REVERT: F 80 LEU cc_start: 0.8622 (mt) cc_final: 0.7668 (mt) REVERT: F 81 LYS cc_start: 0.9577 (mttt) cc_final: 0.9042 (mmmm) REVERT: F 82 ASN cc_start: 0.8896 (m-40) cc_final: 0.8674 (p0) REVERT: F 105 LYS cc_start: 0.8560 (ptmt) cc_final: 0.8262 (mtmm) REVERT: O 3 GLN cc_start: 0.9246 (mm110) cc_final: 0.8834 (mm110) REVERT: O 13 LYS cc_start: 0.9225 (pttm) cc_final: 0.8991 (tppt) REVERT: O 46 GLU cc_start: 0.8731 (tt0) cc_final: 0.8245 (tm-30) REVERT: O 80 LEU cc_start: 0.8808 (mt) cc_final: 0.8484 (mt) REVERT: O 81 LYS cc_start: 0.9534 (mttt) cc_final: 0.9044 (mmmm) REVERT: O 82 ASN cc_start: 0.8822 (m-40) cc_final: 0.8511 (p0) REVERT: O 86 ASP cc_start: 0.9011 (t0) cc_final: 0.8544 (p0) REVERT: O 99 GLN cc_start: 0.8711 (pp30) cc_final: 0.8377 (pp30) REVERT: O 100 GLU cc_start: 0.8651 (tt0) cc_final: 0.7851 (tt0) REVERT: O 101 ASP cc_start: 0.9292 (p0) cc_final: 0.8876 (p0) REVERT: O 105 LYS cc_start: 0.8743 (ptpp) cc_final: 0.8267 (pttm) REVERT: B 37 GLN cc_start: 0.8278 (tp40) cc_final: 0.7646 (tp-100) REVERT: B 42 GLN cc_start: 0.8381 (mp10) cc_final: 0.8019 (mp10) REVERT: B 47 LEU cc_start: 0.9658 (mt) cc_final: 0.9452 (mp) REVERT: B 70 ARG cc_start: 0.7971 (mmm160) cc_final: 0.7199 (mmt180) REVERT: B 85 ASP cc_start: 0.8389 (m-30) cc_final: 0.7714 (p0) REVERT: B 90 MET cc_start: 0.8969 (tpp) cc_final: 0.8670 (tpp) REVERT: I 26 GLN cc_start: 0.9292 (tp-100) cc_final: 0.8881 (tp-100) REVERT: I 37 GLN cc_start: 0.8814 (tt0) cc_final: 0.8232 (tm-30) REVERT: I 42 GLN cc_start: 0.8539 (mp10) cc_final: 0.8102 (mp10) REVERT: I 47 LEU cc_start: 0.9699 (mt) cc_final: 0.9368 (mp) REVERT: I 70 ARG cc_start: 0.7886 (mmm160) cc_final: 0.7198 (tpt170) REVERT: I 83 GLU cc_start: 0.8037 (tp30) cc_final: 0.7756 (mm-30) REVERT: I 85 ASP cc_start: 0.8415 (m-30) cc_final: 0.7832 (p0) REVERT: P 18 THR cc_start: 0.8999 (p) cc_final: 0.8781 (t) REVERT: P 33 VAL cc_start: 0.9304 (m) cc_final: 0.8936 (m) REVERT: P 37 GLN cc_start: 0.8948 (tt0) cc_final: 0.8454 (tm-30) REVERT: P 42 GLN cc_start: 0.8468 (mp10) cc_final: 0.8195 (mp10) REVERT: P 47 LEU cc_start: 0.9615 (mt) cc_final: 0.9289 (mp) REVERT: P 70 ARG cc_start: 0.7826 (mmm160) cc_final: 0.7449 (mmt180) REVERT: P 83 GLU cc_start: 0.7870 (tp30) cc_final: 0.7640 (tp30) REVERT: P 85 ASP cc_start: 0.8292 (m-30) cc_final: 0.7528 (p0) outliers start: 0 outliers final: 0 residues processed: 388 average time/residue: 0.1484 time to fit residues: 88.5885 Evaluate side-chains 289 residues out of total 2109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 289 time to evaluate : 0.725 ------------------------------------------------------------------------------- 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: 9.9990 chunk 222 optimal weight: 20.0000 chunk 177 optimal weight: 5.9990 chunk 65 optimal weight: 0.9980 chunk 47 optimal weight: 20.0000 chunk 17 optimal weight: 3.9990 chunk 71 optimal weight: 3.9990 chunk 70 optimal weight: 5.9990 chunk 6 optimal weight: 0.0670 chunk 136 optimal weight: 5.9990 chunk 73 optimal weight: 10.0000 overall best weight: 3.0124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 650 GLN R 137 ASN ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.071006 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2687 r_free = 0.2687 target = 0.052478 restraints weight = 70690.114| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.2737 r_free = 0.2737 target = 0.054613 restraints weight = 33910.003| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2769 r_free = 0.2769 target = 0.056014 restraints weight = 21596.991| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.2791 r_free = 0.2791 target = 0.056964 restraints weight = 16175.928| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.2806 r_free = 0.2806 target = 0.057595 restraints weight = 13390.333| |-----------------------------------------------------------------------------| r_work (final): 0.2797 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8466 moved from start: 0.2506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 20892 Z= 0.176 Angle : 0.764 15.035 28557 Z= 0.351 Chirality : 0.048 0.405 3436 Planarity : 0.004 0.038 3447 Dihedral : 5.280 40.454 2604 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.09 % Favored : 93.82 % Rotamer: Outliers : 0.14 % Allowed : 1.90 % Favored : 97.96 % 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: -2.78 (0.16), residues: 2364 helix: -1.40 (0.26), residues: 342 sheet: -1.08 (0.20), residues: 603 loop : -2.41 (0.15), residues: 1419 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG I 31 TYR 0.017 0.001 TYR J 586 PHE 0.013 0.001 PHE K 320 TRP 0.018 0.001 TRP K 69 HIS 0.005 0.001 HIS K 330 Details of bonding type rmsd/Z covalent geometry : bond 0.00391 / 0.17 (20752) covalent geometry : angle 0.70564 / 0.34 (28176) SS BOND : bond 0.00307 / 0.19 ( 39) SS BOND : angle 1.59257 / 1.08 ( 78) hydrogen bonds : bond 0.04001 / 2.74 ( 467) hydrogen bonds : angle 5.07523 / 3.59 ( 1251) link_ALPHA1-2 : bond 0.00612 / 0.37 ( 5) link_ALPHA1-2 : angle 2.62888 / 1.63 ( 15) link_ALPHA1-3 : bond 0.00627 / 0.49 ( 8) link_ALPHA1-3 : angle 1.80138 / 1.09 ( 24) link_ALPHA1-6 : bond 0.00569 / 0.26 ( 7) link_ALPHA1-6 : angle 1.63310 / 1.02 ( 21) link_BETA1-4 : bond 0.00687 / 0.48 ( 30) link_BETA1-4 : angle 2.71317 / 1.83 ( 90) link_NAG-ASN : bond 0.00546 / 0.33 ( 51) link_NAG-ASN : angle 3.16319 / 2.15 ( 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 390 residues out of total 2109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 387 time to evaluate : 0.820 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: 0.9082 (ttm) cc_final: 0.8447 (ttm) REVERT: C 540 GLN cc_start: 0.9030 (mp10) cc_final: 0.8823 (mp10) REVERT: C 543 ASN cc_start: 0.8995 (t0) cc_final: 0.8571 (t0) REVERT: C 574 LYS cc_start: 0.9292 (mttm) cc_final: 0.9005 (mtmt) REVERT: C 575 GLN cc_start: 0.9066 (mp10) cc_final: 0.8663 (mp10) REVERT: C 584 GLU cc_start: 0.9055 (pm20) cc_final: 0.8754 (pm20) REVERT: C 590 GLN cc_start: 0.9537 (tp40) cc_final: 0.9069 (tp40) REVERT: C 591 GLN cc_start: 0.9666 (tm-30) cc_final: 0.9269 (tm-30) REVERT: C 624 ASP cc_start: 0.9158 (m-30) cc_final: 0.8955 (m-30) REVERT: C 654 GLU cc_start: 0.9404 (mm-30) cc_final: 0.9124 (mm-30) REVERT: C 657 GLU cc_start: 0.9478 (mm-30) cc_final: 0.9271 (mm-30) REVERT: G 69 TRP cc_start: 0.7735 (p-90) cc_final: 0.7022 (p-90) REVERT: G 95 MET cc_start: 0.9305 (ptt) cc_final: 0.8539 (ptt) REVERT: G 106 GLU cc_start: 0.8671 (tm-30) cc_final: 0.8433 (tm-30) REVERT: J 543 ASN cc_start: 0.9096 (m-40) cc_final: 0.8708 (t0) REVERT: J 577 GLN cc_start: 0.8991 (mt0) cc_final: 0.8510 (mt0) REVERT: J 624 ASP cc_start: 0.8945 (m-30) cc_final: 0.8619 (p0) REVERT: J 632 ASP cc_start: 0.9087 (t70) cc_final: 0.8779 (t70) REVERT: K 478 ASN cc_start: 0.9148 (m110) cc_final: 0.8911 (m110) REVERT: Q 530 MET cc_start: 0.9225 (ttp) cc_final: 0.8954 (mmm) REVERT: Q 540 GLN cc_start: 0.8801 (mp10) cc_final: 0.8600 (mp10) REVERT: Q 543 ASN cc_start: 0.8921 (t0) cc_final: 0.8480 (t0) REVERT: Q 573 ILE cc_start: 0.8843 (mm) cc_final: 0.8643 (tp) REVERT: Q 577 GLN cc_start: 0.9008 (mt0) cc_final: 0.8598 (mt0) REVERT: Q 584 GLU cc_start: 0.9104 (pm20) cc_final: 0.8785 (pm20) REVERT: Q 591 GLN cc_start: 0.9736 (tm-30) cc_final: 0.9347 (tm-30) REVERT: Q 624 ASP cc_start: 0.8960 (m-30) cc_final: 0.8627 (m-30) REVERT: Q 626 MET cc_start: 0.8226 (ptm) cc_final: 0.7784 (ptm) REVERT: Q 632 ASP cc_start: 0.9102 (t70) cc_final: 0.8840 (t70) REVERT: Q 643 TYR cc_start: 0.9450 (m-10) cc_final: 0.9159 (m-10) REVERT: Q 654 GLU cc_start: 0.9117 (OUTLIER) cc_final: 0.8845 (mt-10) REVERT: R 95 MET cc_start: 0.9034 (ptm) cc_final: 0.8385 (ptp) REVERT: R 137 ASN cc_start: 0.9183 (OUTLIER) cc_final: 0.8946 (p0) REVERT: R 377 ASN cc_start: 0.9325 (p0) cc_final: 0.8578 (t0) REVERT: R 434 MET cc_start: 0.9092 (ttm) cc_final: 0.8795 (ttm) REVERT: R 492 GLU cc_start: 0.8709 (tm-30) cc_final: 0.8305 (tm-30) REVERT: R 494 LEU cc_start: 0.9255 (tp) cc_final: 0.8927 (tt) REVERT: A 64 ASN cc_start: 0.9013 (m-40) cc_final: 0.8784 (m110) REVERT: A 81 LYS cc_start: 0.9559 (mttt) cc_final: 0.9227 (tptt) REVERT: A 82 LEU cc_start: 0.8842 (mp) cc_final: 0.8315 (mp) REVERT: A 100 GLU cc_start: 0.8742 (tt0) cc_final: 0.8220 (tt0) REVERT: A 100 MET cc_start: 0.9080 (mpp) cc_final: 0.8879 (mpp) REVERT: F 1 GLN cc_start: 0.7447 (tp40) cc_final: 0.6407 (tm-30) REVERT: F 3 GLN cc_start: 0.9288 (mm110) cc_final: 0.8796 (mm110) REVERT: F 48 ILE cc_start: 0.9102 (mt) cc_final: 0.8869 (mp) REVERT: F 77 GLN cc_start: 0.8718 (mm110) cc_final: 0.8338 (tp40) REVERT: F 80 LEU cc_start: 0.8696 (mt) cc_final: 0.7654 (mt) REVERT: F 81 LYS cc_start: 0.9590 (mttt) cc_final: 0.9045 (mmmm) REVERT: F 82 ASN cc_start: 0.8977 (m-40) cc_final: 0.8700 (p0) REVERT: F 105 LYS cc_start: 0.8576 (ptmt) cc_final: 0.8275 (mtmm) REVERT: O 3 GLN cc_start: 0.9263 (mm110) cc_final: 0.8835 (mm110) REVERT: O 13 LYS cc_start: 0.9244 (pttm) cc_final: 0.8991 (tppt) REVERT: O 46 GLU cc_start: 0.8788 (tt0) cc_final: 0.8219 (tm-30) REVERT: O 80 LEU cc_start: 0.8853 (mt) cc_final: 0.8475 (mt) REVERT: O 81 LYS cc_start: 0.9547 (mttt) cc_final: 0.9056 (mmmm) REVERT: O 82 ASN cc_start: 0.8747 (m-40) cc_final: 0.8527 (p0) REVERT: O 86 ASP cc_start: 0.8935 (t0) cc_final: 0.8547 (p0) REVERT: O 99 GLN cc_start: 0.8724 (pp30) cc_final: 0.8369 (pp30) REVERT: O 100 GLU cc_start: 0.8815 (tt0) cc_final: 0.8088 (tt0) REVERT: O 100 MET cc_start: 0.8930 (mpp) cc_final: 0.8728 (mpp) REVERT: O 101 ASP cc_start: 0.9312 (p0) cc_final: 0.8874 (p0) REVERT: B 26 GLN cc_start: 0.8958 (tp-100) cc_final: 0.8495 (tp-100) REVERT: B 37 GLN cc_start: 0.8271 (tp40) cc_final: 0.7682 (tp40) REVERT: B 42 GLN cc_start: 0.8393 (mp10) cc_final: 0.8006 (mp10) REVERT: B 47 LEU cc_start: 0.9678 (mt) cc_final: 0.9385 (mp) REVERT: B 85 ASP cc_start: 0.8390 (m-30) cc_final: 0.7784 (p0) REVERT: B 90 MET cc_start: 0.8988 (tpp) cc_final: 0.8672 (tpp) REVERT: I 26 GLN cc_start: 0.9281 (tp-100) cc_final: 0.8914 (tp-100) REVERT: I 31 ARG cc_start: 0.9359 (mtm110) cc_final: 0.8575 (ptp90) REVERT: I 42 GLN cc_start: 0.8522 (mp10) cc_final: 0.8061 (mp10) REVERT: I 47 LEU cc_start: 0.9707 (mt) cc_final: 0.9393 (mp) REVERT: I 70 ARG cc_start: 0.7857 (mmm160) cc_final: 0.7301 (tpt170) REVERT: I 83 GLU cc_start: 0.8075 (tp30) cc_final: 0.7806 (mm-30) REVERT: I 85 ASP cc_start: 0.8436 (m-30) cc_final: 0.7679 (p0) REVERT: P 18 THR cc_start: 0.8993 (p) cc_final: 0.8779 (t) REVERT: P 37 GLN cc_start: 0.8944 (tt0) cc_final: 0.8436 (tm-30) REVERT: P 42 GLN cc_start: 0.8473 (mp10) cc_final: 0.8198 (mp10) REVERT: P 47 LEU cc_start: 0.9644 (mt) cc_final: 0.9296 (mp) REVERT: P 48 ILE cc_start: 0.9551 (mm) cc_final: 0.9238 (mm) REVERT: P 53 ASP cc_start: 0.8675 (t70) cc_final: 0.8464 (t70) REVERT: P 70 ARG cc_start: 0.7912 (mmm160) cc_final: 0.7466 (mmt180) REVERT: P 83 GLU cc_start: 0.7933 (tp30) cc_final: 0.7713 (mm-30) REVERT: P 85 ASP cc_start: 0.8345 (m-30) cc_final: 0.7554 (p0) outliers start: 3 outliers final: 0 residues processed: 389 average time/residue: 0.1497 time to fit residues: 89.3600 Evaluate side-chains 294 residues out of total 2109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 292 time to evaluate : 0.711 ------------------------------------------------------------------------------- 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: 1.9990 chunk 56 optimal weight: 10.0000 chunk 209 optimal weight: 10.0000 chunk 173 optimal weight: 9.9990 chunk 86 optimal weight: 8.9990 chunk 131 optimal weight: 0.2980 chunk 22 optimal weight: 6.9990 chunk 127 optimal weight: 1.9990 chunk 78 optimal weight: 9.9990 chunk 190 optimal weight: 2.9990 chunk 29 optimal weight: 8.9990 overall best weight: 2.8588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 300 ASN J 575 GLN ** A 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 26 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.071066 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2688 r_free = 0.2688 target = 0.052523 restraints weight = 70573.189| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2738 r_free = 0.2738 target = 0.054642 restraints weight = 33832.976| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.2771 r_free = 0.2771 target = 0.056074 restraints weight = 21504.998| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.2793 r_free = 0.2793 target = 0.057012 restraints weight = 16061.507| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.2807 r_free = 0.2807 target = 0.057611 restraints weight = 13300.414| |-----------------------------------------------------------------------------| r_work (final): 0.2796 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8488 moved from start: 0.2700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 20892 Z= 0.167 Angle : 0.749 14.745 28557 Z= 0.345 Chirality : 0.048 0.396 3436 Planarity : 0.004 0.054 3447 Dihedral : 5.145 33.715 2604 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.22 % Favored : 93.74 % Rotamer: Outliers : 0.05 % Allowed : 2.23 % Favored : 97.72 % 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: -2.60 (0.16), residues: 2364 helix: -1.17 (0.27), residues: 342 sheet: -0.92 (0.21), residues: 561 loop : -2.30 (0.15), residues: 1461 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG I 31 TYR 0.018 0.001 TYR Q 586 PHE 0.013 0.001 PHE K 320 TRP 0.018 0.001 TRP R 112 HIS 0.005 0.001 HIS I 38 Details of bonding type rmsd/Z covalent geometry : bond 0.00370 / 0.17 (20752) covalent geometry : angle 0.69389 / 0.33 (28176) SS BOND : bond 0.00335 / 0.21 ( 39) SS BOND : angle 1.60874 / 1.09 ( 78) hydrogen bonds : bond 0.03810 / 2.63 ( 467) hydrogen bonds : angle 4.92033 / 3.47 ( 1251) link_ALPHA1-2 : bond 0.00607 / 0.36 ( 5) link_ALPHA1-2 : angle 2.57115 / 1.59 ( 15) link_ALPHA1-3 : bond 0.00623 / 0.48 ( 8) link_ALPHA1-3 : angle 1.79024 / 1.09 ( 24) link_ALPHA1-6 : bond 0.00550 / 0.26 ( 7) link_ALPHA1-6 : angle 1.57340 / 0.99 ( 21) link_BETA1-4 : bond 0.00660 / 0.46 ( 30) link_BETA1-4 : angle 2.63097 / 1.77 ( 90) link_NAG-ASN : bond 0.00433 / 0.28 ( 51) link_NAG-ASN : angle 3.04921 / 2.08 ( 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 389 residues out of total 2109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 388 time to evaluate : 0.830 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: C 530 MET cc_start: 0.9087 (ttm) cc_final: 0.8455 (ttm) REVERT: C 540 GLN cc_start: 0.9024 (mp10) cc_final: 0.8810 (mp10) REVERT: C 543 ASN cc_start: 0.8983 (t0) cc_final: 0.8540 (t0) REVERT: C 574 LYS cc_start: 0.9288 (mttm) cc_final: 0.9035 (mttt) REVERT: C 575 GLN cc_start: 0.9072 (mp10) cc_final: 0.8677 (mp10) REVERT: C 584 GLU cc_start: 0.8974 (pm20) cc_final: 0.8687 (pm20) REVERT: C 590 GLN cc_start: 0.9529 (tp40) cc_final: 0.9074 (tp40) REVERT: C 591 GLN cc_start: 0.9677 (tm-30) cc_final: 0.9293 (tm-30) REVERT: C 654 GLU cc_start: 0.9371 (mm-30) cc_final: 0.9009 (mm-30) REVERT: C 657 GLU cc_start: 0.9493 (mm-30) cc_final: 0.9274 (mm-30) REVERT: G 69 TRP cc_start: 0.7747 (p-90) cc_final: 0.7495 (p-90) REVERT: G 95 MET cc_start: 0.9298 (ptt) cc_final: 0.8560 (ptt) REVERT: G 106 GLU cc_start: 0.8723 (tm-30) cc_final: 0.8468 (tm-30) REVERT: G 150 MET cc_start: 0.9058 (mtm) cc_final: 0.8734 (mtt) REVERT: J 543 ASN cc_start: 0.9095 (m-40) cc_final: 0.8655 (t0) REVERT: J 573 ILE cc_start: 0.9158 (mm) cc_final: 0.8295 (tp) REVERT: J 574 LYS cc_start: 0.9144 (mppt) cc_final: 0.8757 (pttt) REVERT: J 575 GLN cc_start: 0.9027 (mp10) cc_final: 0.8746 (mp10) REVERT: J 577 GLN cc_start: 0.8938 (mt0) cc_final: 0.8607 (mt0) REVERT: J 591 GLN cc_start: 0.9781 (tm-30) cc_final: 0.9320 (tm-30) REVERT: J 624 ASP cc_start: 0.8809 (m-30) cc_final: 0.8576 (p0) REVERT: J 632 ASP cc_start: 0.9093 (t70) cc_final: 0.8835 (t70) REVERT: J 650 GLN cc_start: 0.8831 (tp40) cc_final: 0.8535 (tp40) REVERT: J 654 GLU cc_start: 0.9372 (mm-30) cc_final: 0.9005 (mp0) REVERT: K 194 ILE cc_start: 0.9319 (tp) cc_final: 0.8933 (tp) REVERT: K 217 TYR cc_start: 0.8827 (m-80) cc_final: 0.8313 (m-80) REVERT: K 478 ASN cc_start: 0.9113 (m110) cc_final: 0.8910 (m110) REVERT: Q 530 MET cc_start: 0.9230 (ttp) cc_final: 0.8936 (mmm) REVERT: Q 542 ARG cc_start: 0.9346 (ttt180) cc_final: 0.8902 (ttp80) REVERT: Q 543 ASN cc_start: 0.8924 (t0) cc_final: 0.8495 (t0) REVERT: Q 584 GLU cc_start: 0.9017 (pm20) cc_final: 0.8700 (pm20) REVERT: Q 624 ASP cc_start: 0.8848 (m-30) cc_final: 0.8545 (m-30) REVERT: Q 632 ASP cc_start: 0.9216 (t70) cc_final: 0.8939 (t70) REVERT: Q 654 GLU cc_start: 0.9354 (mm-30) cc_final: 0.9124 (mm-30) REVERT: R 95 MET cc_start: 0.8977 (ptm) cc_final: 0.8557 (ptp) REVERT: R 377 ASN cc_start: 0.9329 (p0) cc_final: 0.8619 (t0) REVERT: R 434 MET cc_start: 0.9093 (ttm) cc_final: 0.8862 (ttm) REVERT: R 492 GLU cc_start: 0.8724 (tm-30) cc_final: 0.8270 (tm-30) REVERT: R 494 LEU cc_start: 0.9266 (tp) cc_final: 0.8905 (tp) REVERT: A 16 GLU cc_start: 0.7781 (pm20) cc_final: 0.7488 (pm20) REVERT: A 46 GLU cc_start: 0.8384 (tm-30) cc_final: 0.8174 (tm-30) REVERT: A 64 ASN cc_start: 0.9017 (m-40) cc_final: 0.8765 (m110) REVERT: A 81 LYS cc_start: 0.9575 (mttt) cc_final: 0.9240 (tptt) REVERT: A 82 LEU cc_start: 0.8843 (mp) cc_final: 0.8367 (mp) REVERT: A 100 MET cc_start: 0.9114 (mpp) cc_final: 0.8897 (mpp) REVERT: F 1 GLN cc_start: 0.7415 (tp40) cc_final: 0.6432 (tm-30) REVERT: F 3 GLN cc_start: 0.9292 (mm110) cc_final: 0.8776 (mm110) REVERT: F 77 GLN cc_start: 0.8620 (mm110) cc_final: 0.8255 (tp40) REVERT: F 80 LEU cc_start: 0.8786 (mt) cc_final: 0.7746 (mt) REVERT: F 81 LYS cc_start: 0.9604 (mttt) cc_final: 0.9005 (mmmm) REVERT: F 105 LYS cc_start: 0.8563 (ptmt) cc_final: 0.8269 (mtmm) REVERT: O 3 GLN cc_start: 0.9247 (mm110) cc_final: 0.8551 (mp-120) REVERT: O 13 LYS cc_start: 0.9251 (pttm) cc_final: 0.8989 (tppt) REVERT: O 46 GLU cc_start: 0.8822 (tt0) cc_final: 0.8492 (tm-30) REVERT: O 80 LEU cc_start: 0.8829 (mt) cc_final: 0.8486 (mt) REVERT: O 81 LYS cc_start: 0.9551 (mttt) cc_final: 0.9057 (mmmm) REVERT: O 82 ASN cc_start: 0.8844 (m-40) cc_final: 0.8561 (p0) REVERT: O 86 ASP cc_start: 0.8894 (t0) cc_final: 0.8387 (p0) REVERT: O 99 GLN cc_start: 0.8790 (pp30) cc_final: 0.8399 (pp30) REVERT: O 100 GLU cc_start: 0.8753 (tt0) cc_final: 0.8048 (tt0) REVERT: O 101 ASP cc_start: 0.9343 (p0) cc_final: 0.8866 (p0) REVERT: B 26 GLN cc_start: 0.9077 (tp40) cc_final: 0.8673 (tp-100) REVERT: B 37 GLN cc_start: 0.8381 (tp40) cc_final: 0.7857 (tp-100) REVERT: B 42 GLN cc_start: 0.8398 (mp10) cc_final: 0.8082 (mp10) REVERT: B 47 LEU cc_start: 0.9690 (mt) cc_final: 0.9468 (mp) REVERT: B 85 ASP cc_start: 0.8410 (m-30) cc_final: 0.7794 (p0) REVERT: B 90 MET cc_start: 0.9026 (tpp) cc_final: 0.8709 (tpp) REVERT: I 26 GLN cc_start: 0.9296 (tp-100) cc_final: 0.9037 (tp-100) REVERT: I 31 ARG cc_start: 0.9327 (mtm110) cc_final: 0.8606 (ptp90) REVERT: I 42 GLN cc_start: 0.8454 (mp10) cc_final: 0.8046 (mp10) REVERT: I 47 LEU cc_start: 0.9654 (mt) cc_final: 0.9342 (mp) REVERT: I 70 ARG cc_start: 0.7834 (mmm160) cc_final: 0.7276 (tpt170) REVERT: I 83 GLU cc_start: 0.8012 (tp30) cc_final: 0.7725 (mm-30) REVERT: I 85 ASP cc_start: 0.8529 (m-30) cc_final: 0.7823 (p0) REVERT: P 37 GLN cc_start: 0.8937 (tt0) cc_final: 0.8467 (tm-30) REVERT: P 42 GLN cc_start: 0.8463 (mp10) cc_final: 0.8091 (mp10) REVERT: P 47 LEU cc_start: 0.9664 (mt) cc_final: 0.9334 (mp) REVERT: P 48 ILE cc_start: 0.9528 (mm) cc_final: 0.9229 (mm) REVERT: P 53 ASP cc_start: 0.8676 (t70) cc_final: 0.8471 (t0) REVERT: P 70 ARG cc_start: 0.8000 (mmm160) cc_final: 0.7611 (mmt180) REVERT: P 83 GLU cc_start: 0.8008 (tp30) cc_final: 0.7707 (tp30) REVERT: P 85 ASP cc_start: 0.8372 (m-30) cc_final: 0.7431 (p0) outliers start: 1 outliers final: 0 residues processed: 389 average time/residue: 0.1470 time to fit residues: 87.5400 Evaluate side-chains 299 residues out of total 2109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 299 time to evaluate : 0.720 ------------------------------------------------------------------------------- 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: 10.0000 chunk 178 optimal weight: 4.9990 chunk 2 optimal weight: 5.9990 chunk 222 optimal weight: 0.2980 chunk 137 optimal weight: 0.8980 chunk 62 optimal weight: 0.0170 chunk 156 optimal weight: 1.9990 chunk 145 optimal weight: 5.9990 chunk 54 optimal weight: 1.9990 chunk 179 optimal weight: 0.9980 chunk 74 optimal weight: 4.9990 overall best weight: 0.8420 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 650 GLN G 258 GLN G 422 GLN K 258 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.072764 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2728 r_free = 0.2728 target = 0.054103 restraints weight = 68932.870| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2779 r_free = 0.2779 target = 0.056279 restraints weight = 33002.985| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.2812 r_free = 0.2812 target = 0.057727 restraints weight = 20949.918| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2832 r_free = 0.2832 target = 0.058649 restraints weight = 15627.481| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.2848 r_free = 0.2848 target = 0.059324 restraints weight = 12972.498| |-----------------------------------------------------------------------------| r_work (final): 0.2835 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8431 moved from start: 0.2901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 20892 Z= 0.106 Angle : 0.711 13.869 28557 Z= 0.326 Chirality : 0.048 0.347 3436 Planarity : 0.003 0.035 3447 Dihedral : 4.955 37.907 2604 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.25 % Favored : 94.71 % Rotamer: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % 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: -2.30 (0.16), residues: 2364 helix: -1.00 (0.27), residues: 342 sheet: -0.51 (0.22), residues: 529 loop : -2.16 (0.15), residues: 1493 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 38 TYR 0.027 0.001 TYR J 643 PHE 0.009 0.001 PHE K 320 TRP 0.013 0.001 TRP K 69 HIS 0.006 0.001 HIS I 89 Details of bonding type rmsd/Z covalent geometry : bond 0.00228 / 0.10 (20752) covalent geometry : angle 0.66160 / 0.31 (28176) SS BOND : bond 0.00234 / 0.15 ( 39) SS BOND : angle 1.36576 / 0.93 ( 78) hydrogen bonds : bond 0.03337 / 2.29 ( 467) hydrogen bonds : angle 4.70699 / 3.34 ( 1251) link_ALPHA1-2 : bond 0.00645 / 0.37 ( 5) link_ALPHA1-2 : angle 2.29064 / 1.40 ( 15) link_ALPHA1-3 : bond 0.00623 / 0.47 ( 8) link_ALPHA1-3 : angle 1.76906 / 1.07 ( 24) link_ALPHA1-6 : bond 0.00546 / 0.26 ( 7) link_ALPHA1-6 : angle 1.45689 / 0.88 ( 21) link_BETA1-4 : bond 0.00670 / 0.47 ( 30) link_BETA1-4 : angle 2.48756 / 1.67 ( 90) link_NAG-ASN : bond 0.00453 / 0.28 ( 51) link_NAG-ASN : angle 2.79768 / 1.90 ( 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 413 residues out of total 2109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 413 time to evaluate : 0.788 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: 0.9075 (ttm) cc_final: 0.8450 (ttm) REVERT: C 543 ASN cc_start: 0.8890 (t0) cc_final: 0.8408 (t0) REVERT: C 574 LYS cc_start: 0.9267 (mttm) cc_final: 0.8978 (mttt) REVERT: C 584 GLU cc_start: 0.8846 (pm20) cc_final: 0.8583 (pm20) REVERT: C 621 GLU cc_start: 0.8691 (pt0) cc_final: 0.8191 (pt0) REVERT: C 654 GLU cc_start: 0.9175 (mm-30) cc_final: 0.8858 (mt-10) REVERT: G 69 TRP cc_start: 0.7797 (p-90) cc_final: 0.7377 (p-90) REVERT: G 95 MET cc_start: 0.9264 (ptt) cc_final: 0.8590 (ptt) REVERT: G 106 GLU cc_start: 0.8555 (tm-30) cc_final: 0.8261 (tm-30) REVERT: G 150 MET cc_start: 0.9070 (mtm) cc_final: 0.8676 (mtm) REVERT: G 440 GLN cc_start: 0.8858 (tt0) cc_final: 0.8550 (pm20) REVERT: J 543 ASN cc_start: 0.9116 (m-40) cc_final: 0.8607 (t0) REVERT: J 573 ILE cc_start: 0.9126 (mm) cc_final: 0.8437 (tp) REVERT: J 577 GLN cc_start: 0.8911 (mt0) cc_final: 0.8444 (mt0) REVERT: J 591 GLN cc_start: 0.9792 (tm-30) cc_final: 0.9340 (tm-30) REVERT: J 632 ASP cc_start: 0.9157 (t70) cc_final: 0.8829 (t70) REVERT: J 654 GLU cc_start: 0.9344 (mm-30) cc_final: 0.9091 (mp0) REVERT: K 217 TYR cc_start: 0.8657 (m-80) cc_final: 0.8238 (m-80) REVERT: K 478 ASN cc_start: 0.9105 (m110) cc_final: 0.8760 (m110) REVERT: Q 530 MET cc_start: 0.9214 (ttp) cc_final: 0.8910 (mmm) REVERT: Q 542 ARG cc_start: 0.9334 (ttt180) cc_final: 0.8931 (ttp80) REVERT: Q 543 ASN cc_start: 0.8846 (t0) cc_final: 0.8424 (t0) REVERT: Q 577 GLN cc_start: 0.8974 (mt0) cc_final: 0.8642 (mt0) REVERT: Q 584 GLU cc_start: 0.9031 (pm20) cc_final: 0.8665 (pm20) REVERT: Q 590 GLN cc_start: 0.9528 (tp-100) cc_final: 0.9250 (tp40) REVERT: Q 591 GLN cc_start: 0.9732 (tm-30) cc_final: 0.9323 (tm-30) REVERT: Q 624 ASP cc_start: 0.8825 (m-30) cc_final: 0.8535 (m-30) REVERT: Q 632 ASP cc_start: 0.9032 (t70) cc_final: 0.8788 (t70) REVERT: Q 654 GLU cc_start: 0.9357 (mm-30) cc_final: 0.9016 (mm-30) REVERT: R 95 MET cc_start: 0.8891 (ptm) cc_final: 0.8447 (ptp) REVERT: R 106 GLU cc_start: 0.8713 (tp30) cc_final: 0.8401 (tp30) REVERT: R 377 ASN cc_start: 0.9284 (p0) cc_final: 0.8545 (t0) REVERT: R 492 GLU cc_start: 0.8678 (tm-30) cc_final: 0.8170 (tm-30) REVERT: R 494 LEU cc_start: 0.9278 (tp) cc_final: 0.8880 (tt) REVERT: A 16 GLU cc_start: 0.7767 (pm20) cc_final: 0.7421 (pm20) REVERT: A 64 ASN cc_start: 0.8992 (m-40) cc_final: 0.8738 (m110) REVERT: A 81 LYS cc_start: 0.9565 (mttt) cc_final: 0.9101 (tptt) REVERT: A 82 LEU cc_start: 0.8687 (mp) cc_final: 0.8170 (mp) REVERT: A 100 MET cc_start: 0.9119 (mpp) cc_final: 0.8887 (mpp) REVERT: F 3 GLN cc_start: 0.9281 (mm110) cc_final: 0.8803 (mp10) REVERT: F 13 LYS cc_start: 0.9128 (tptp) cc_final: 0.8864 (tppt) REVERT: F 77 GLN cc_start: 0.8755 (mm110) cc_final: 0.8305 (tp40) REVERT: F 80 LEU cc_start: 0.8820 (mt) cc_final: 0.7899 (mt) REVERT: F 81 LYS cc_start: 0.9610 (mttt) cc_final: 0.9203 (mmtm) REVERT: F 82 ASN cc_start: 0.9050 (m110) cc_final: 0.8720 (p0) REVERT: F 99 GLN cc_start: 0.8801 (pp30) cc_final: 0.8600 (pp30) REVERT: F 105 LYS cc_start: 0.8516 (ptmt) cc_final: 0.8262 (mtmm) REVERT: O 3 GLN cc_start: 0.9257 (mm110) cc_final: 0.8604 (mp10) REVERT: O 46 GLU cc_start: 0.8821 (tt0) cc_final: 0.8511 (tm-30) REVERT: O 80 LEU cc_start: 0.8916 (mt) cc_final: 0.8606 (mt) REVERT: O 81 LYS cc_start: 0.9542 (mttt) cc_final: 0.9040 (mmmm) REVERT: O 82 ASN cc_start: 0.8878 (m-40) cc_final: 0.8615 (p0) REVERT: O 86 ASP cc_start: 0.8922 (t0) cc_final: 0.8606 (t0) REVERT: O 99 GLN cc_start: 0.8779 (pp30) cc_final: 0.8487 (pp30) REVERT: O 100 GLU cc_start: 0.8789 (tt0) cc_final: 0.8050 (tt0) REVERT: O 101 ASP cc_start: 0.9400 (p0) cc_final: 0.8909 (p0) REVERT: B 26 GLN cc_start: 0.9078 (tp40) cc_final: 0.8824 (tp-100) REVERT: B 37 GLN cc_start: 0.8385 (tp40) cc_final: 0.8081 (tp40) REVERT: B 42 GLN cc_start: 0.8359 (mp10) cc_final: 0.7955 (mp10) REVERT: B 47 LEU cc_start: 0.9729 (mt) cc_final: 0.9469 (mp) REVERT: B 70 ARG cc_start: 0.8482 (mmm160) cc_final: 0.7762 (tpt170) REVERT: B 83 GLU cc_start: 0.7711 (mm-30) cc_final: 0.7511 (mm-30) REVERT: B 85 ASP cc_start: 0.8421 (m-30) cc_final: 0.7787 (p0) REVERT: B 90 MET cc_start: 0.9029 (tpp) cc_final: 0.8745 (tmm) REVERT: I 26 GLN cc_start: 0.9288 (tp-100) cc_final: 0.8926 (tp-100) REVERT: I 31 ARG cc_start: 0.9252 (mtm110) cc_final: 0.8564 (ptp90) REVERT: I 42 GLN cc_start: 0.8424 (mp10) cc_final: 0.7994 (mp10) REVERT: I 47 LEU cc_start: 0.9630 (mt) cc_final: 0.9316 (mp) REVERT: I 70 ARG cc_start: 0.7895 (mmm160) cc_final: 0.7324 (tpt170) REVERT: I 83 GLU cc_start: 0.7955 (tp30) cc_final: 0.7576 (tp30) REVERT: I 85 ASP cc_start: 0.8525 (m-30) cc_final: 0.7935 (p0) REVERT: I 104 LEU cc_start: 0.8280 (tp) cc_final: 0.7857 (tp) REVERT: P 37 GLN cc_start: 0.8892 (tt0) cc_final: 0.8447 (tm-30) REVERT: P 42 GLN cc_start: 0.8407 (mp10) cc_final: 0.8027 (mp10) REVERT: P 47 LEU cc_start: 0.9636 (mt) cc_final: 0.9291 (mp) REVERT: P 70 ARG cc_start: 0.8019 (mmm160) cc_final: 0.7694 (tpt170) REVERT: P 83 GLU cc_start: 0.7926 (tp30) cc_final: 0.7606 (tp30) REVERT: P 85 ASP cc_start: 0.8372 (m-30) cc_final: 0.7491 (p0) outliers start: 0 outliers final: 0 residues processed: 413 average time/residue: 0.1499 time to fit residues: 95.5347 Evaluate side-chains 320 residues out of total 2109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 320 time to evaluate : 0.794 ------------------------------------------------------------------------------- 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: 9.9990 chunk 132 optimal weight: 0.0060 chunk 225 optimal weight: 9.9990 chunk 48 optimal weight: 0.9980 chunk 98 optimal weight: 7.9990 chunk 124 optimal weight: 7.9990 chunk 122 optimal weight: 3.9990 chunk 121 optimal weight: 1.9990 chunk 6 optimal weight: 10.0000 chunk 27 optimal weight: 9.9990 chunk 171 optimal weight: 20.0000 overall best weight: 3.0002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... J 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 = 0.3108 r_free = 0.3108 target = 0.071049 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2686 r_free = 0.2686 target = 0.052552 restraints weight = 70657.239| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.2736 r_free = 0.2736 target = 0.054666 restraints weight = 34063.959| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2769 r_free = 0.2769 target = 0.056063 restraints weight = 21749.953| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.2791 r_free = 0.2791 target = 0.057015 restraints weight = 16313.514| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.2806 r_free = 0.2806 target = 0.057635 restraints weight = 13502.147| |-----------------------------------------------------------------------------| r_work (final): 0.2795 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8480 moved from start: 0.3069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 20892 Z= 0.172 Angle : 0.755 14.368 28557 Z= 0.346 Chirality : 0.048 0.390 3436 Planarity : 0.004 0.041 3447 Dihedral : 5.068 36.770 2604 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.68 % Favored : 93.27 % Rotamer: Outliers : 0.00 % Allowed : 0.95 % Favored : 99.05 % 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: -2.23 (0.16), residues: 2364 helix: -0.75 (0.28), residues: 339 sheet: -0.65 (0.20), residues: 627 loop : -2.16 (0.15), residues: 1398 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 38 TYR 0.022 0.001 TYR J 586 PHE 0.011 0.001 PHE G 391 TRP 0.018 0.001 TRP R 112 HIS 0.005 0.001 HIS K 330 Details of bonding type rmsd/Z covalent geometry : bond 0.00384 / 0.17 (20752) covalent geometry : angle 0.70392 / 0.33 (28176) SS BOND : bond 0.00265 / 0.16 ( 39) SS BOND : angle 1.79668 / 1.24 ( 78) hydrogen bonds : bond 0.03630 / 2.49 ( 467) hydrogen bonds : angle 4.75989 / 3.38 ( 1251) link_ALPHA1-2 : bond 0.00583 / 0.34 ( 5) link_ALPHA1-2 : angle 2.54365 / 1.60 ( 15) link_ALPHA1-3 : bond 0.00507 / 0.38 ( 8) link_ALPHA1-3 : angle 1.76804 / 1.07 ( 24) link_ALPHA1-6 : bond 0.00502 / 0.24 ( 7) link_ALPHA1-6 : angle 1.59240 / 1.00 ( 21) link_BETA1-4 : bond 0.00635 / 0.44 ( 30) link_BETA1-4 : angle 2.54384 / 1.72 ( 90) link_NAG-ASN : bond 0.00459 / 0.30 ( 51) link_NAG-ASN : angle 2.86328 / 1.93 ( 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 388 residues out of total 2109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 388 time to evaluate : 0.800 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: C 530 MET cc_start: 0.8983 (ttm) cc_final: 0.8325 (ttm) REVERT: C 543 ASN cc_start: 0.9021 (t0) cc_final: 0.8578 (t0) REVERT: C 574 LYS cc_start: 0.9309 (mttm) cc_final: 0.9045 (mttt) REVERT: C 584 GLU cc_start: 0.9106 (pm20) cc_final: 0.8672 (pm20) REVERT: G 69 TRP cc_start: 0.7846 (p-90) cc_final: 0.7206 (p-90) REVERT: G 95 MET cc_start: 0.9298 (ptt) cc_final: 0.8530 (ptt) REVERT: G 106 GLU cc_start: 0.8647 (tm-30) cc_final: 0.8363 (tm-30) REVERT: G 150 MET cc_start: 0.8843 (mtm) cc_final: 0.8496 (mtm) REVERT: G 161 MET cc_start: 0.8445 (tpp) cc_final: 0.7961 (tpt) REVERT: G 440 GLN cc_start: 0.8876 (tt0) cc_final: 0.8584 (pm20) REVERT: G 475 MET cc_start: 0.8767 (mmm) cc_final: 0.8526 (mmm) REVERT: J 543 ASN cc_start: 0.9132 (m-40) cc_final: 0.8658 (t0) REVERT: J 573 ILE cc_start: 0.8976 (mm) cc_final: 0.8631 (tp) REVERT: J 577 GLN cc_start: 0.8879 (mt0) cc_final: 0.8437 (mt0) REVERT: J 591 GLN cc_start: 0.9782 (tm-30) cc_final: 0.9307 (tm-30) REVERT: J 632 ASP cc_start: 0.9067 (t70) cc_final: 0.8806 (t70) REVERT: K 217 TYR cc_start: 0.8806 (m-80) cc_final: 0.8445 (m-80) REVERT: K 328 MET cc_start: 0.8603 (tpp) cc_final: 0.8388 (tpp) REVERT: K 478 ASN cc_start: 0.9071 (m110) cc_final: 0.8670 (m110) REVERT: Q 530 MET cc_start: 0.9137 (ttp) cc_final: 0.8800 (mmm) REVERT: Q 543 ASN cc_start: 0.9021 (t0) cc_final: 0.8634 (t0) REVERT: Q 584 GLU cc_start: 0.9170 (pm20) cc_final: 0.8706 (pm20) REVERT: Q 624 ASP cc_start: 0.8813 (m-30) cc_final: 0.8546 (m-30) REVERT: Q 632 ASP cc_start: 0.9128 (t70) cc_final: 0.8854 (t70) REVERT: Q 654 GLU cc_start: 0.9330 (mm-30) cc_final: 0.9057 (mm-30) REVERT: R 106 GLU cc_start: 0.8800 (tp30) cc_final: 0.8519 (tp30) REVERT: R 377 ASN cc_start: 0.9280 (p0) cc_final: 0.8525 (t0) REVERT: R 434 MET cc_start: 0.8966 (ttm) cc_final: 0.8558 (ttm) REVERT: R 475 MET cc_start: 0.8798 (mmm) cc_final: 0.8237 (mmm) REVERT: A 64 ASN cc_start: 0.9010 (m-40) cc_final: 0.8759 (m110) REVERT: A 81 LYS cc_start: 0.9605 (mttt) cc_final: 0.9269 (tptt) REVERT: A 82 LEU cc_start: 0.8685 (mp) cc_final: 0.8232 (mp) REVERT: A 100 GLU cc_start: 0.8659 (tt0) cc_final: 0.8036 (tt0) REVERT: A 100 MET cc_start: 0.9140 (mpp) cc_final: 0.8917 (mpp) REVERT: F 37 ILE cc_start: 0.9552 (mm) cc_final: 0.9350 (mm) REVERT: F 46 GLU cc_start: 0.8125 (tm-30) cc_final: 0.7894 (tm-30) REVERT: F 80 LEU cc_start: 0.8753 (mt) cc_final: 0.7808 (mt) REVERT: F 81 LYS cc_start: 0.9619 (mttt) cc_final: 0.9150 (mmtm) REVERT: F 99 GLN cc_start: 0.8783 (pp30) cc_final: 0.8497 (pp30) REVERT: F 100 GLU cc_start: 0.8411 (tt0) cc_final: 0.8058 (tt0) REVERT: F 105 LYS cc_start: 0.8530 (ptmt) cc_final: 0.8254 (mtmm) REVERT: O 3 GLN cc_start: 0.9282 (mm110) cc_final: 0.8843 (mm110) REVERT: O 16 GLU cc_start: 0.8412 (pt0) cc_final: 0.7669 (pt0) REVERT: O 46 GLU cc_start: 0.8881 (tt0) cc_final: 0.8588 (tm-30) REVERT: O 77 GLN cc_start: 0.8830 (mm110) cc_final: 0.8426 (mm110) REVERT: O 80 LEU cc_start: 0.8991 (mt) cc_final: 0.8155 (mt) REVERT: O 81 LYS cc_start: 0.9530 (mttt) cc_final: 0.8949 (mmmm) REVERT: O 82 LEU cc_start: 0.8339 (mp) cc_final: 0.8094 (mp) REVERT: O 86 ASP cc_start: 0.8890 (t0) cc_final: 0.8621 (t0) REVERT: O 99 GLN cc_start: 0.8866 (pp30) cc_final: 0.8544 (pp30) REVERT: O 100 GLU cc_start: 0.8703 (tt0) cc_final: 0.7953 (tt0) REVERT: O 101 ASP cc_start: 0.9423 (p0) cc_final: 0.8968 (p0) REVERT: B 26 GLN cc_start: 0.9080 (tp40) cc_final: 0.8762 (tp-100) REVERT: B 37 GLN cc_start: 0.8429 (tp40) cc_final: 0.8147 (tp-100) REVERT: B 42 GLN cc_start: 0.8405 (mp10) cc_final: 0.7979 (mp10) REVERT: B 47 LEU cc_start: 0.9703 (mt) cc_final: 0.9470 (mp) REVERT: B 70 ARG cc_start: 0.8390 (mmm160) cc_final: 0.7560 (tpt170) REVERT: B 85 ASP cc_start: 0.8498 (m-30) cc_final: 0.7906 (p0) REVERT: I 26 GLN cc_start: 0.9318 (tp-100) cc_final: 0.9087 (tp-100) REVERT: I 42 GLN cc_start: 0.8337 (mp10) cc_final: 0.7898 (mp10) REVERT: I 47 LEU cc_start: 0.9633 (mt) cc_final: 0.9408 (mp) REVERT: I 70 ARG cc_start: 0.7795 (mmm160) cc_final: 0.7170 (tpt170) REVERT: I 83 GLU cc_start: 0.8004 (tp30) cc_final: 0.7652 (tp30) REVERT: I 85 ASP cc_start: 0.8421 (m-30) cc_final: 0.7821 (p0) REVERT: I 104 LEU cc_start: 0.8549 (tp) cc_final: 0.8187 (tp) REVERT: P 37 GLN cc_start: 0.8919 (tt0) cc_final: 0.8456 (tm-30) REVERT: P 42 GLN cc_start: 0.8390 (mp10) cc_final: 0.8022 (mp10) REVERT: P 47 LEU cc_start: 0.9607 (mt) cc_final: 0.9380 (mp) REVERT: P 70 ARG cc_start: 0.7976 (mmm160) cc_final: 0.7601 (mmt180) REVERT: P 83 GLU cc_start: 0.8030 (tp30) cc_final: 0.7770 (tp30) REVERT: P 85 ASP cc_start: 0.8412 (m-30) cc_final: 0.7511 (p0) outliers start: 0 outliers final: 0 residues processed: 388 average time/residue: 0.1576 time to fit residues: 92.6500 Evaluate side-chains 297 residues out of total 2109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 297 time to evaluate : 0.755 ------------------------------------------------------------------------------- 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: 8.9990 chunk 127 optimal weight: 3.9990 chunk 75 optimal weight: 0.8980 chunk 93 optimal weight: 6.9990 chunk 206 optimal weight: 3.9990 chunk 233 optimal weight: 9.9990 chunk 163 optimal weight: 5.9990 chunk 60 optimal weight: 0.8980 chunk 222 optimal weight: 0.0060 chunk 0 optimal weight: 10.0000 chunk 126 optimal weight: 9.9990 overall best weight: 1.9600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... J 575 GLN A 77 GLN O 82AASN ** B 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 = 0.3125 r_free = 0.3125 target = 0.071818 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2708 r_free = 0.2708 target = 0.053235 restraints weight = 70062.011| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2759 r_free = 0.2759 target = 0.055400 restraints weight = 33602.869| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.2792 r_free = 0.2792 target = 0.056839 restraints weight = 21347.142| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.2813 r_free = 0.2813 target = 0.057791 restraints weight = 15908.901| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2826 r_free = 0.2826 target = 0.058381 restraints weight = 13134.325| |-----------------------------------------------------------------------------| r_work (final): 0.2813 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8447 moved from start: 0.3192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 20892 Z= 0.129 Angle : 0.723 14.061 28557 Z= 0.331 Chirality : 0.047 0.362 3436 Planarity : 0.004 0.042 3447 Dihedral : 4.935 36.538 2604 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.37 % Favored : 94.59 % Rotamer: Outliers : 0.00 % Allowed : 0.43 % Favored : 99.57 % 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: -2.10 (0.16), residues: 2364 helix: -0.67 (0.28), residues: 342 sheet: -0.40 (0.22), residues: 534 loop : -2.06 (0.15), residues: 1488 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG I 31 TYR 0.024 0.001 TYR J 586 PHE 0.011 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/Z covalent geometry : bond 0.00287 / 0.13 (20752) covalent geometry : angle 0.67517 / 0.32 (28176) SS BOND : bond 0.00320 / 0.20 ( 39) SS BOND : angle 1.54339 / 1.07 ( 78) hydrogen bonds : bond 0.03398 / 2.31 ( 467) hydrogen bonds : angle 4.66676 / 3.31 ( 1251) link_ALPHA1-2 : bond 0.00608 / 0.35 ( 5) link_ALPHA1-2 : angle 2.30993 / 1.42 ( 15) link_ALPHA1-3 : bond 0.00585 / 0.45 ( 8) link_ALPHA1-3 : angle 1.78072 / 1.08 ( 24) link_ALPHA1-6 : bond 0.00517 / 0.26 ( 7) link_ALPHA1-6 : angle 1.44070 / 0.89 ( 21) link_BETA1-4 : bond 0.00657 / 0.46 ( 30) link_BETA1-4 : angle 2.43770 / 1.65 ( 90) link_NAG-ASN : bond 0.00424 / 0.26 ( 51) link_NAG-ASN : angle 2.76137 / 1.86 ( 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 386 residues out of total 2109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 386 time to evaluate : 0.809 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: 0.9059 (ttm) cc_final: 0.8370 (ttm) REVERT: C 543 ASN cc_start: 0.8949 (t0) cc_final: 0.8475 (t0) REVERT: C 574 LYS cc_start: 0.9300 (mttm) cc_final: 0.9033 (mttt) REVERT: C 584 GLU cc_start: 0.8997 (pm20) cc_final: 0.8717 (pm20) REVERT: C 624 ASP cc_start: 0.9107 (m-30) cc_final: 0.8889 (m-30) REVERT: C 626 MET cc_start: 0.8375 (ttm) cc_final: 0.8010 (ttm) REVERT: G 69 TRP cc_start: 0.7901 (p-90) cc_final: 0.7125 (p-90) REVERT: G 95 MET cc_start: 0.9304 (ptt) cc_final: 0.8613 (ptt) REVERT: G 106 GLU cc_start: 0.8659 (tm-30) cc_final: 0.8367 (tm-30) REVERT: G 161 MET cc_start: 0.8420 (tpp) cc_final: 0.8009 (tpt) REVERT: G 440 GLN cc_start: 0.8869 (tt0) cc_final: 0.8570 (pm20) REVERT: G 475 MET cc_start: 0.8790 (mmm) cc_final: 0.8503 (mmm) REVERT: J 543 ASN cc_start: 0.9129 (m-40) cc_final: 0.8609 (t0) REVERT: J 573 ILE cc_start: 0.8998 (mm) cc_final: 0.8406 (tp) REVERT: J 577 GLN cc_start: 0.8864 (mt0) cc_final: 0.8433 (mt0) REVERT: J 591 GLN cc_start: 0.9775 (tm-30) cc_final: 0.9308 (tm-30) REVERT: J 632 ASP cc_start: 0.9072 (t70) cc_final: 0.8809 (t70) REVERT: J 650 GLN cc_start: 0.8939 (tp40) cc_final: 0.8537 (mm-40) REVERT: J 654 GLU cc_start: 0.9446 (mm-30) cc_final: 0.9052 (mt-10) REVERT: K 217 TYR cc_start: 0.8686 (m-80) cc_final: 0.8265 (m-80) REVERT: K 328 MET cc_start: 0.8493 (tpp) cc_final: 0.8147 (tpp) REVERT: K 475 MET cc_start: 0.9025 (mmm) cc_final: 0.8720 (mmm) REVERT: K 478 ASN cc_start: 0.9114 (m110) cc_final: 0.8624 (m110) REVERT: Q 543 ASN cc_start: 0.8992 (t0) cc_final: 0.8589 (t0) REVERT: Q 584 GLU cc_start: 0.9078 (pm20) cc_final: 0.8782 (pm20) REVERT: Q 624 ASP cc_start: 0.8856 (m-30) cc_final: 0.8588 (m-30) REVERT: Q 632 ASP cc_start: 0.9101 (t70) cc_final: 0.8858 (t70) REVERT: R 69 TRP cc_start: 0.7215 (p-90) cc_final: 0.5968 (p-90) REVERT: R 106 GLU cc_start: 0.8773 (tp30) cc_final: 0.8524 (tp30) REVERT: R 377 ASN cc_start: 0.9212 (p0) cc_final: 0.8491 (t0) REVERT: R 434 MET cc_start: 0.8934 (ttm) cc_final: 0.8426 (ttm) REVERT: R 475 MET cc_start: 0.8813 (mmm) cc_final: 0.8177 (mmm) REVERT: A 64 ASN cc_start: 0.8997 (m-40) cc_final: 0.8744 (m110) REVERT: A 81 LYS cc_start: 0.9580 (mttt) cc_final: 0.9125 (tptt) REVERT: A 82 LEU cc_start: 0.8701 (mp) cc_final: 0.8240 (mp) REVERT: A 100 MET cc_start: 0.9220 (mpp) cc_final: 0.8956 (mpp) REVERT: F 3 GLN cc_start: 0.9234 (mm110) cc_final: 0.9018 (mm110) REVERT: F 80 LEU cc_start: 0.8788 (mt) cc_final: 0.7902 (mt) REVERT: F 81 LYS cc_start: 0.9609 (mttt) cc_final: 0.9168 (mmtm) REVERT: F 99 GLN cc_start: 0.8788 (pp30) cc_final: 0.8468 (pp30) REVERT: F 100 GLU cc_start: 0.8424 (tt0) cc_final: 0.8021 (tt0) REVERT: O 3 GLN cc_start: 0.9263 (mm110) cc_final: 0.8608 (mp10) REVERT: O 18 LEU cc_start: 0.8378 (tt) cc_final: 0.7968 (mp) REVERT: O 46 GLU cc_start: 0.8868 (tt0) cc_final: 0.8492 (tm-30) REVERT: O 77 GLN cc_start: 0.8897 (mm110) cc_final: 0.8468 (mm110) REVERT: O 80 LEU cc_start: 0.8993 (mt) cc_final: 0.8072 (mt) REVERT: O 81 LYS cc_start: 0.9521 (mttt) cc_final: 0.8916 (mmmm) REVERT: O 82 LEU cc_start: 0.8284 (mp) cc_final: 0.7968 (mp) REVERT: O 86 ASP cc_start: 0.8903 (t0) cc_final: 0.8585 (t0) REVERT: O 99 GLN cc_start: 0.8824 (pp30) cc_final: 0.8488 (pp30) REVERT: O 100 GLU cc_start: 0.8830 (tt0) cc_final: 0.8029 (tt0) REVERT: O 101 ASP cc_start: 0.9425 (p0) cc_final: 0.8943 (p0) REVERT: B 26 GLN cc_start: 0.9051 (tp40) cc_final: 0.8846 (tp-100) REVERT: B 37 GLN cc_start: 0.8534 (tp40) cc_final: 0.8206 (tp40) REVERT: B 42 GLN cc_start: 0.8449 (mp10) cc_final: 0.7999 (mp10) REVERT: B 47 LEU cc_start: 0.9712 (mt) cc_final: 0.9441 (mp) REVERT: B 70 ARG cc_start: 0.8367 (mmm160) cc_final: 0.7567 (tpt170) REVERT: B 85 ASP cc_start: 0.8492 (m-30) cc_final: 0.7881 (p0) REVERT: B 90 MET cc_start: 0.9058 (tpp) cc_final: 0.8751 (tmm) REVERT: I 26 GLN cc_start: 0.9327 (tp-100) cc_final: 0.9002 (tp-100) REVERT: I 31 ARG cc_start: 0.9303 (mtm110) cc_final: 0.8397 (ptp90) REVERT: I 42 GLN cc_start: 0.8338 (mp10) cc_final: 0.7870 (mp10) REVERT: I 47 LEU cc_start: 0.9599 (mt) cc_final: 0.9326 (mp) REVERT: I 70 ARG cc_start: 0.7793 (mmm160) cc_final: 0.7286 (tpt170) REVERT: I 83 GLU cc_start: 0.8005 (tp30) cc_final: 0.7626 (tp30) REVERT: I 85 ASP cc_start: 0.8425 (m-30) cc_final: 0.7803 (p0) REVERT: I 104 LEU cc_start: 0.8550 (tp) cc_final: 0.7972 (tp) REVERT: P 37 GLN cc_start: 0.8911 (tt0) cc_final: 0.8436 (tm-30) REVERT: P 42 GLN cc_start: 0.8374 (mp10) cc_final: 0.8002 (mp10) REVERT: P 47 LEU cc_start: 0.9571 (mt) cc_final: 0.9350 (mp) REVERT: P 70 ARG cc_start: 0.7970 (mmm160) cc_final: 0.7643 (tpt170) REVERT: P 83 GLU cc_start: 0.8050 (tp30) cc_final: 0.7782 (tp30) REVERT: P 85 ASP cc_start: 0.8419 (m-30) cc_final: 0.7508 (p0) outliers start: 0 outliers final: 0 residues processed: 386 average time/residue: 0.1438 time to fit residues: 85.8912 Evaluate side-chains 309 residues out of total 2109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 309 time to evaluate : 0.760 ------------------------------------------------------------------------------- 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: 9.9990 chunk 55 optimal weight: 0.7980 chunk 173 optimal weight: 7.9990 chunk 201 optimal weight: 7.9990 chunk 148 optimal weight: 10.0000 chunk 128 optimal weight: 9.9990 chunk 122 optimal weight: 0.9990 chunk 1 optimal weight: 8.9990 chunk 97 optimal weight: 6.9990 chunk 71 optimal weight: 0.9990 chunk 139 optimal weight: 0.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... O 82AASN ** 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 = 0.3122 r_free = 0.3122 target = 0.071624 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2702 r_free = 0.2702 target = 0.053007 restraints weight = 70113.204| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2753 r_free = 0.2753 target = 0.055167 restraints weight = 33774.986| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.2786 r_free = 0.2786 target = 0.056602 restraints weight = 21475.534| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2808 r_free = 0.2808 target = 0.057541 restraints weight = 16055.334| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.2822 r_free = 0.2822 target = 0.058173 restraints weight = 13282.884| |-----------------------------------------------------------------------------| r_work (final): 0.2810 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8449 moved from start: 0.3303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 20892 Z= 0.137 Angle : 0.728 13.973 28557 Z= 0.334 Chirality : 0.047 0.371 3436 Planarity : 0.004 0.051 3447 Dihedral : 4.911 36.685 2604 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.22 % Favored : 93.74 % 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 : 0.09 % 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: -2.01 (0.17), residues: 2364 helix: -0.48 (0.29), residues: 339 sheet: -0.46 (0.21), residues: 590 loop : -2.03 (0.15), residues: 1435 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG I 31 TYR 0.020 0.001 TYR Q 586 PHE 0.011 0.001 PHE K 320 TRP 0.017 0.001 TRP R 112 HIS 0.004 0.001 HIS G 216 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.14 (20752) covalent geometry : angle 0.68131 / 0.32 (28176) SS BOND : bond 0.00309 / 0.19 ( 39) SS BOND : angle 1.50483 / 1.05 ( 78) hydrogen bonds : bond 0.03406 / 2.33 ( 467) hydrogen bonds : angle 4.64625 / 3.29 ( 1251) link_ALPHA1-2 : bond 0.00579 / 0.33 ( 5) link_ALPHA1-2 : angle 2.32792 / 1.45 ( 15) link_ALPHA1-3 : bond 0.00550 / 0.41 ( 8) link_ALPHA1-3 : angle 1.76171 / 1.06 ( 24) link_ALPHA1-6 : bond 0.00521 / 0.26 ( 7) link_ALPHA1-6 : angle 1.46975 / 0.92 ( 21) link_BETA1-4 : bond 0.00634 / 0.44 ( 30) link_BETA1-4 : angle 2.43273 / 1.65 ( 90) link_NAG-ASN : bond 0.00422 / 0.26 ( 51) link_NAG-ASN : angle 2.74057 / 1.84 ( 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 378 residues out of total 2109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 378 time to evaluate : 0.807 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: 0.9086 (ttm) cc_final: 0.8443 (ttm) REVERT: C 543 ASN cc_start: 0.8970 (t0) cc_final: 0.8561 (t0) REVERT: C 574 LYS cc_start: 0.9298 (mttm) cc_final: 0.9033 (mttt) REVERT: C 584 GLU cc_start: 0.8998 (pm20) cc_final: 0.8699 (pm20) REVERT: C 595 ILE cc_start: 0.9359 (tp) cc_final: 0.9134 (tp) REVERT: C 624 ASP cc_start: 0.9144 (m-30) cc_final: 0.8938 (m-30) REVERT: C 626 MET cc_start: 0.8488 (ttm) cc_final: 0.8247 (ttm) REVERT: C 651 ASN cc_start: 0.8779 (m110) cc_final: 0.8513 (m110) REVERT: C 654 GLU cc_start: 0.8531 (pt0) cc_final: 0.8165 (tm-30) REVERT: G 69 TRP cc_start: 0.7905 (p-90) cc_final: 0.7279 (p-90) REVERT: G 95 MET cc_start: 0.9289 (ptt) cc_final: 0.8577 (ptt) REVERT: G 106 GLU cc_start: 0.8682 (tm-30) cc_final: 0.8389 (tm-30) REVERT: G 161 MET cc_start: 0.8513 (tpp) cc_final: 0.8091 (tpt) REVERT: G 217 TYR cc_start: 0.8947 (m-80) cc_final: 0.8611 (m-80) REVERT: G 440 GLN cc_start: 0.8874 (tt0) cc_final: 0.8570 (pm20) REVERT: G 475 MET cc_start: 0.8901 (mmm) cc_final: 0.8657 (tpp) REVERT: J 543 ASN cc_start: 0.9140 (m-40) cc_final: 0.8609 (t0) REVERT: J 573 ILE cc_start: 0.9008 (mm) cc_final: 0.8774 (tp) REVERT: J 575 GLN cc_start: 0.9165 (mp10) cc_final: 0.8880 (mp10) REVERT: J 632 ASP cc_start: 0.9119 (t70) cc_final: 0.8878 (t70) REVERT: J 647 GLU cc_start: 0.8935 (pp20) cc_final: 0.8732 (pp20) REVERT: J 650 GLN cc_start: 0.8949 (tp40) cc_final: 0.8248 (mm-40) REVERT: J 654 GLU cc_start: 0.9505 (mm-30) cc_final: 0.9099 (mt-10) REVERT: K 195 ASN cc_start: 0.8957 (t0) cc_final: 0.8714 (t0) REVERT: K 217 TYR cc_start: 0.8652 (m-80) cc_final: 0.8074 (m-80) REVERT: K 328 MET cc_start: 0.8498 (tpp) cc_final: 0.8147 (tpp) REVERT: K 475 MET cc_start: 0.9089 (mmm) cc_final: 0.8764 (mmm) REVERT: K 478 ASN cc_start: 0.9112 (m110) cc_final: 0.8605 (m110) REVERT: Q 543 ASN cc_start: 0.9012 (t0) cc_final: 0.8615 (t0) REVERT: Q 584 GLU cc_start: 0.9075 (pm20) cc_final: 0.8764 (pm20) REVERT: Q 624 ASP cc_start: 0.8832 (m-30) cc_final: 0.8543 (m-30) REVERT: Q 632 ASP cc_start: 0.9122 (t70) cc_final: 0.8890 (t70) REVERT: Q 654 GLU cc_start: 0.9312 (mm-30) cc_final: 0.9068 (mm-30) REVERT: R 69 TRP cc_start: 0.7176 (p-90) cc_final: 0.6014 (p-90) REVERT: R 106 GLU cc_start: 0.8819 (tp30) cc_final: 0.8552 (tp30) REVERT: R 377 ASN cc_start: 0.9181 (p0) cc_final: 0.8458 (t0) REVERT: R 434 MET cc_start: 0.8951 (ttm) cc_final: 0.8468 (ttm) REVERT: R 475 MET cc_start: 0.8915 (mmm) cc_final: 0.8580 (mmm) REVERT: A 16 GLU cc_start: 0.7761 (pm20) cc_final: 0.7448 (pm20) REVERT: A 64 ASN cc_start: 0.8995 (m-40) cc_final: 0.8743 (m110) REVERT: A 81 LYS cc_start: 0.9602 (mttt) cc_final: 0.9151 (tptt) REVERT: A 82 LEU cc_start: 0.8696 (mp) cc_final: 0.8275 (mp) REVERT: A 100 GLU cc_start: 0.8645 (tt0) cc_final: 0.8040 (tt0) REVERT: A 100 MET cc_start: 0.9230 (mpp) cc_final: 0.8961 (mpp) REVERT: F 3 GLN cc_start: 0.9240 (mm110) cc_final: 0.9027 (mm110) REVERT: F 81 LYS cc_start: 0.9647 (mttt) cc_final: 0.9110 (tptt) REVERT: F 82 LEU cc_start: 0.8564 (mp) cc_final: 0.8232 (mp) REVERT: F 99 GLN cc_start: 0.8786 (pp30) cc_final: 0.8429 (pp30) REVERT: F 100 GLU cc_start: 0.8414 (tt0) cc_final: 0.8010 (tt0) REVERT: O 3 GLN cc_start: 0.9271 (mm110) cc_final: 0.8603 (mp-120) REVERT: O 46 GLU cc_start: 0.8886 (tt0) cc_final: 0.8502 (tm-30) REVERT: O 77 GLN cc_start: 0.8883 (mm110) cc_final: 0.8482 (mm110) REVERT: O 80 LEU cc_start: 0.9031 (mt) cc_final: 0.8129 (mt) REVERT: O 81 LYS cc_start: 0.9538 (mttt) cc_final: 0.8970 (mmmm) REVERT: O 86 ASP cc_start: 0.8886 (t0) cc_final: 0.8555 (t0) REVERT: O 99 GLN cc_start: 0.8868 (pp30) cc_final: 0.8510 (pp30) REVERT: O 100 GLU cc_start: 0.8858 (tt0) cc_final: 0.8057 (tt0) REVERT: O 101 ASP cc_start: 0.9500 (p0) cc_final: 0.8978 (p0) REVERT: B 26 GLN cc_start: 0.9054 (tp40) cc_final: 0.8791 (tp-100) REVERT: B 37 GLN cc_start: 0.8546 (tp40) cc_final: 0.8212 (tp40) REVERT: B 42 GLN cc_start: 0.8450 (mp10) cc_final: 0.7966 (mp10) REVERT: B 47 LEU cc_start: 0.9686 (mt) cc_final: 0.9437 (mp) REVERT: B 70 ARG cc_start: 0.8337 (mmm160) cc_final: 0.7390 (tpt170) REVERT: B 85 ASP cc_start: 0.8412 (m-30) cc_final: 0.7747 (p0) REVERT: B 90 MET cc_start: 0.9062 (tpp) cc_final: 0.8770 (tmm) REVERT: I 26 GLN cc_start: 0.9337 (tp-100) cc_final: 0.9009 (tp-100) REVERT: I 31 ARG cc_start: 0.9310 (mtm110) cc_final: 0.8377 (ptp90) REVERT: I 42 GLN cc_start: 0.8326 (mp10) cc_final: 0.7869 (mp10) REVERT: I 47 LEU cc_start: 0.9602 (mt) cc_final: 0.9277 (mp) REVERT: I 48 ILE cc_start: 0.9506 (mm) cc_final: 0.9232 (mm) REVERT: I 70 ARG cc_start: 0.7769 (mmm160) cc_final: 0.7315 (tpt170) REVERT: I 83 GLU cc_start: 0.8049 (tp30) cc_final: 0.7667 (tp30) REVERT: I 85 ASP cc_start: 0.8436 (m-30) cc_final: 0.7839 (p0) REVERT: I 104 LEU cc_start: 0.8571 (tp) cc_final: 0.7993 (tp) REVERT: P 37 GLN cc_start: 0.8928 (tt0) cc_final: 0.8305 (tm-30) REVERT: P 42 GLN cc_start: 0.8385 (mp10) cc_final: 0.8007 (mp10) REVERT: P 47 LEU cc_start: 0.9546 (mt) cc_final: 0.9340 (mp) REVERT: P 70 ARG cc_start: 0.7964 (mmm160) cc_final: 0.7641 (tpt170) REVERT: P 83 GLU cc_start: 0.8101 (tp30) cc_final: 0.7841 (tp30) REVERT: P 85 ASP cc_start: 0.8486 (m-30) cc_final: 0.7657 (p0) outliers start: 0 outliers final: 0 residues processed: 378 average time/residue: 0.1474 time to fit residues: 85.6455 Evaluate side-chains 317 residues out of total 2109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 317 time to evaluate : 0.662 ------------------------------------------------------------------------------- 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: 30.0000 chunk 236 optimal weight: 5.9990 chunk 129 optimal weight: 6.9990 chunk 99 optimal weight: 6.9990 chunk 40 optimal weight: 5.9990 chunk 27 optimal weight: 0.7980 chunk 3 optimal weight: 2.9990 chunk 74 optimal weight: 0.4980 chunk 38 optimal weight: 4.9990 chunk 91 optimal weight: 0.9990 chunk 61 optimal weight: 0.9980 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... O 82AASN ** 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 = 0.3137 r_free = 0.3137 target = 0.072444 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2722 r_free = 0.2722 target = 0.053833 restraints weight = 70266.036| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2772 r_free = 0.2772 target = 0.056004 restraints weight = 33676.010| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2807 r_free = 0.2807 target = 0.057492 restraints weight = 21337.421| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2828 r_free = 0.2828 target = 0.058436 restraints weight = 15855.971| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.2843 r_free = 0.2843 target = 0.059083 restraints weight = 13104.882| |-----------------------------------------------------------------------------| r_work (final): 0.2829 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8428 moved from start: 0.3423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 20892 Z= 0.113 Angle : 0.723 13.676 28557 Z= 0.329 Chirality : 0.047 0.346 3436 Planarity : 0.004 0.047 3447 Dihedral : 4.785 31.255 2604 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.20 % Favored : 94.75 % 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 : 0.09 % 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: -1.91 (0.17), residues: 2364 helix: -0.51 (0.29), residues: 342 sheet: -0.29 (0.22), residues: 549 loop : -1.94 (0.15), residues: 1473 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG I 31 TYR 0.023 0.001 TYR C 643 PHE 0.011 0.001 PHE R 391 TRP 0.020 0.001 TRP R 96 HIS 0.004 0.001 HIS R 216 Details of bonding type rmsd/Z covalent geometry : bond 0.00249 / 0.11 (20752) covalent geometry : angle 0.67642 / 0.32 (28176) SS BOND : bond 0.00289 / 0.18 ( 39) SS BOND : angle 1.43101 / 0.97 ( 78) hydrogen bonds : bond 0.03176 / 2.17 ( 467) hydrogen bonds : angle 4.57953 / 3.24 ( 1251) link_ALPHA1-2 : bond 0.00600 / 0.33 ( 5) link_ALPHA1-2 : angle 2.21375 / 1.36 ( 15) link_ALPHA1-3 : bond 0.00564 / 0.41 ( 8) link_ALPHA1-3 : angle 1.73861 / 1.03 ( 24) link_ALPHA1-6 : bond 0.00507 / 0.25 ( 7) link_ALPHA1-6 : angle 1.41051 / 0.87 ( 21) link_BETA1-4 : bond 0.00652 / 0.46 ( 30) link_BETA1-4 : angle 2.37351 / 1.62 ( 90) link_NAG-ASN : bond 0.00418 / 0.25 ( 51) link_NAG-ASN : angle 2.77642 / 1.90 ( 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 386 residues out of total 2109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 386 time to evaluate : 0.822 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 543 ASN cc_start: 0.8916 (t0) cc_final: 0.8488 (t0) REVERT: C 574 LYS cc_start: 0.9283 (mttm) cc_final: 0.9029 (mttt) REVERT: C 584 GLU cc_start: 0.9050 (pm20) cc_final: 0.8735 (pm20) REVERT: C 651 ASN cc_start: 0.8857 (m110) cc_final: 0.8559 (m-40) REVERT: G 69 TRP cc_start: 0.7716 (p-90) cc_final: 0.7236 (p-90) REVERT: G 95 MET cc_start: 0.9266 (ptt) cc_final: 0.8575 (ptt) REVERT: G 106 GLU cc_start: 0.8644 (tm-30) cc_final: 0.8343 (tm-30) REVERT: G 440 GLN cc_start: 0.8869 (tt0) cc_final: 0.8570 (pm20) REVERT: G 475 MET cc_start: 0.8883 (mmm) cc_final: 0.8637 (tpp) REVERT: J 530 MET cc_start: 0.9714 (mmm) cc_final: 0.9428 (tpp) REVERT: J 543 ASN cc_start: 0.9130 (m-40) cc_final: 0.8582 (t0) REVERT: J 575 GLN cc_start: 0.9170 (mp10) cc_final: 0.8844 (mp10) REVERT: J 632 ASP cc_start: 0.9111 (t70) cc_final: 0.8875 (t70) REVERT: J 647 GLU cc_start: 0.8906 (pp20) cc_final: 0.8695 (pp20) REVERT: J 654 GLU cc_start: 0.9463 (mm-30) cc_final: 0.9078 (mt-10) REVERT: K 217 TYR cc_start: 0.8359 (m-80) cc_final: 0.8119 (m-80) REVERT: K 256 SER cc_start: 0.9374 (p) cc_final: 0.9167 (p) REVERT: K 328 MET cc_start: 0.8493 (tpp) cc_final: 0.8140 (tpp) REVERT: K 475 MET cc_start: 0.9092 (mmm) cc_final: 0.8807 (mmm) REVERT: K 478 ASN cc_start: 0.9098 (m110) cc_final: 0.8589 (m110) REVERT: Q 543 ASN cc_start: 0.8984 (t0) cc_final: 0.8559 (t0) REVERT: Q 584 GLU cc_start: 0.9117 (pm20) cc_final: 0.8786 (pm20) REVERT: Q 624 ASP cc_start: 0.8878 (m-30) cc_final: 0.8604 (m-30) REVERT: Q 632 ASP cc_start: 0.9085 (t70) cc_final: 0.8862 (t70) REVERT: Q 654 GLU cc_start: 0.9293 (mm-30) cc_final: 0.9042 (mm-30) REVERT: R 69 TRP cc_start: 0.7126 (p-90) cc_final: 0.5987 (p-90) REVERT: R 106 GLU cc_start: 0.8757 (tp30) cc_final: 0.8516 (tp30) REVERT: R 150 MET cc_start: 0.8835 (mpp) cc_final: 0.8625 (mtt) REVERT: R 174 SER cc_start: 0.9438 (t) cc_final: 0.9109 (t) REVERT: R 195 ASN cc_start: 0.8990 (m-40) cc_final: 0.8737 (m-40) REVERT: R 377 ASN cc_start: 0.9135 (p0) cc_final: 0.8457 (t0) REVERT: R 434 MET cc_start: 0.8962 (ttm) cc_final: 0.8485 (ttm) REVERT: R 475 MET cc_start: 0.8848 (mmm) cc_final: 0.8532 (mmm) REVERT: A 16 GLU cc_start: 0.7756 (pm20) cc_final: 0.7486 (pm20) REVERT: A 64 ASN cc_start: 0.8973 (m-40) cc_final: 0.8720 (m110) REVERT: A 81 LYS cc_start: 0.9595 (mttt) cc_final: 0.9151 (tptt) REVERT: A 82 LEU cc_start: 0.8699 (mp) cc_final: 0.8277 (mp) REVERT: A 100 MET cc_start: 0.9205 (mpp) cc_final: 0.8917 (mpp) REVERT: F 3 GLN cc_start: 0.9246 (mm110) cc_final: 0.9028 (mm110) REVERT: F 81 LYS cc_start: 0.9639 (mttt) cc_final: 0.9075 (tptt) REVERT: F 82 LEU cc_start: 0.8564 (mp) cc_final: 0.8240 (mp) REVERT: F 99 GLN cc_start: 0.8790 (pp30) cc_final: 0.8394 (pp30) REVERT: F 100 ILE cc_start: 0.9479 (pt) cc_final: 0.9258 (pt) REVERT: F 100 GLU cc_start: 0.8372 (tt0) cc_final: 0.7983 (tt0) REVERT: O 3 GLN cc_start: 0.9265 (mm110) cc_final: 0.8605 (mp10) REVERT: O 18 LEU cc_start: 0.7963 (tt) cc_final: 0.6995 (mp) REVERT: O 37 ILE cc_start: 0.9486 (mm) cc_final: 0.9254 (mm) REVERT: O 46 GLU cc_start: 0.8874 (tt0) cc_final: 0.8502 (tm-30) REVERT: O 77 GLN cc_start: 0.8902 (mm110) cc_final: 0.8493 (mm110) REVERT: O 80 LEU cc_start: 0.9032 (mt) cc_final: 0.8194 (mt) REVERT: O 81 LYS cc_start: 0.9525 (mttt) cc_final: 0.8978 (mmmm) REVERT: O 82 ASN cc_start: 0.8871 (m-40) cc_final: 0.8598 (p0) REVERT: O 86 ASP cc_start: 0.8892 (t0) cc_final: 0.8588 (t0) REVERT: O 99 GLN cc_start: 0.8869 (pp30) cc_final: 0.8493 (pp30) REVERT: O 100 GLU cc_start: 0.8818 (tt0) cc_final: 0.8035 (tt0) REVERT: O 101 ASP cc_start: 0.9490 (p0) cc_final: 0.8936 (p0) REVERT: B 37 GLN cc_start: 0.8556 (tp40) cc_final: 0.8161 (tp40) REVERT: B 42 GLN cc_start: 0.8451 (mp10) cc_final: 0.7968 (mp10) REVERT: B 47 LEU cc_start: 0.9706 (mt) cc_final: 0.9395 (mp) REVERT: B 70 ARG cc_start: 0.8312 (mmm160) cc_final: 0.7568 (mmt180) REVERT: B 85 ASP cc_start: 0.8423 (m-30) cc_final: 0.7734 (p0) REVERT: B 90 MET cc_start: 0.9057 (tpp) cc_final: 0.8752 (tpp) REVERT: I 26 GLN cc_start: 0.9349 (tp-100) cc_final: 0.9045 (tp-100) REVERT: I 31 ARG cc_start: 0.9278 (mtm110) cc_final: 0.8365 (ptp90) REVERT: I 42 GLN cc_start: 0.8344 (mp10) cc_final: 0.7862 (mp10) REVERT: I 47 LEU cc_start: 0.9614 (mt) cc_final: 0.9291 (mp) REVERT: I 70 ARG cc_start: 0.7789 (mmm160) cc_final: 0.7351 (tpt170) REVERT: I 83 GLU cc_start: 0.8035 (tp30) cc_final: 0.7794 (mm-30) REVERT: I 85 ASP cc_start: 0.8442 (m-30) cc_final: 0.7808 (p0) REVERT: P 37 GLN cc_start: 0.8922 (tt0) cc_final: 0.8308 (tm-30) REVERT: P 42 GLN cc_start: 0.8378 (mp10) cc_final: 0.8027 (mp10) REVERT: P 70 ARG cc_start: 0.7973 (mmm160) cc_final: 0.7633 (tpt170) REVERT: P 83 GLU cc_start: 0.8087 (tp30) cc_final: 0.7827 (tp30) REVERT: P 85 ASP cc_start: 0.8460 (m-30) cc_final: 0.7526 (p0) outliers start: 0 outliers final: 0 residues processed: 386 average time/residue: 0.1488 time to fit residues: 88.3550 Evaluate side-chains 316 residues out of total 2109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 316 time to evaluate : 0.586 ------------------------------------------------------------------------------- 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: 9.9990 chunk 64 optimal weight: 5.9990 chunk 235 optimal weight: 10.0000 chunk 79 optimal weight: 10.0000 chunk 185 optimal weight: 30.0000 chunk 180 optimal weight: 8.9990 chunk 91 optimal weight: 6.9990 chunk 63 optimal weight: 3.9990 chunk 98 optimal weight: 7.9990 chunk 158 optimal weight: 0.7980 chunk 30 optimal weight: 5.9990 overall best weight: 4.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 422 GLN ** K 99 ASN ** 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 = 0.3081 r_free = 0.3081 target = 0.069617 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2656 r_free = 0.2656 target = 0.051096 restraints weight = 72394.253| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2705 r_free = 0.2705 target = 0.053169 restraints weight = 35282.052| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2738 r_free = 0.2738 target = 0.054561 restraints weight = 22674.285| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.2759 r_free = 0.2759 target = 0.055460 restraints weight = 17050.138| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.2774 r_free = 0.2774 target = 0.056077 restraints weight = 14218.236| |-----------------------------------------------------------------------------| r_work (final): 0.2760 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8520 moved from start: 0.3440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 20892 Z= 0.249 Angle : 0.815 14.856 28557 Z= 0.376 Chirality : 0.049 0.440 3436 Planarity : 0.004 0.051 3447 Dihedral : 5.155 33.561 2604 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.04 % Allowed : 8.16 % Favored : 91.79 % Rotamer: Outliers : 0.00 % Allowed : 0.09 % Favored : 99.91 % 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: -2.04 (0.17), residues: 2364 helix: -0.47 (0.28), residues: 342 sheet: -0.55 (0.20), residues: 635 loop : -2.07 (0.16), residues: 1387 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG I 31 TYR 0.027 0.002 TYR J 586 PHE 0.015 0.002 PHE K 320 TRP 0.028 0.002 TRP R 112 HIS 0.006 0.001 HIS K 330 Details of bonding type rmsd/Z covalent geometry : bond 0.00557 / 0.25 (20752) covalent geometry : angle 0.76548 / 0.36 (28176) SS BOND : bond 0.00323 / 0.20 ( 39) SS BOND : angle 1.85076 / 1.29 ( 78) hydrogen bonds : bond 0.03877 / 2.64 ( 467) hydrogen bonds : angle 4.84266 / 3.44 ( 1251) link_ALPHA1-2 : bond 0.00558 / 0.31 ( 5) link_ALPHA1-2 : angle 2.65930 / 1.70 ( 15) link_ALPHA1-3 : bond 0.00518 / 0.39 ( 8) link_ALPHA1-3 : angle 1.85103 / 1.12 ( 24) link_ALPHA1-6 : bond 0.00612 / 0.27 ( 7) link_ALPHA1-6 : angle 1.67695 / 1.08 ( 21) link_BETA1-4 : bond 0.00601 / 0.42 ( 30) link_BETA1-4 : angle 2.54832 / 1.74 ( 90) link_NAG-ASN : bond 0.00560 / 0.39 ( 51) link_NAG-ASN : angle 2.96907 / 2.01 ( 153) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3515.83 seconds wall clock time: 61 minutes 39.93 seconds (3699.93 seconds total)