Starting phenix.real_space_refine on Sun Sep 13 02:45:57 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6orp_20177/09_2026/6orp_20177.cif Found real_map, /net/cci-nas-00/data/ceres_data/6orp_20177/09_2026/6orp_20177.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/6orp_20177/09_2026/6orp_20177.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6orp_20177/09_2026/6orp_20177.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6orp_20177/09_2026/6orp_20177.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6orp_20177/09_2026/6orp_20177.map" model { file = "/net/cci-nas-00/data/ceres_data/6orp_20177/09_2026/6orp_20177.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6orp_20177/09_2026/6orp_20177.cif" } resolution = 4.4 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= -0.002 sd= 0.204 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 114 5.16 5 C 12487 2.51 5 N 3317 2.21 5 O 4054 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 18 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: 19972 Number of models: 1 Model: "" Number of chains: 47 Chain: "A" 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: "B" 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: "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: "D" Number of atoms: 938 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 938 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 6, 'TRANS': 117} Chain: "E" Number of atoms: 808 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 808 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 6, 'TRANS': 102} Chain: "F" 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: "H" Number of atoms: 938 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 938 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 6, 'TRANS': 117} Chain: "I" 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: 938 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 938 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 6, 'TRANS': 117} Chain: "K" Number of atoms: 808 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 808 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 6, 'TRANS': 102} Chain: "L" Number of atoms: 808 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 808 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 6, 'TRANS': 102} Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 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: "P" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 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: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "Y" Number of atoms: 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: "Z" 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: "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: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Chain: "c" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "d" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "e" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "f" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "g" Number of atoms: 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: 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: "i" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "j" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Chain: "k" 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: "l" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "m" Number of atoms: 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: "n" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "o" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "A" 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: "B" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 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: "F" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "G" 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 Chain: "I" 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: 4.53, per 1000 atoms: 0.23 Number of scatterers: 19972 At special positions: 0 Unit cell: (139.292, 133.548, 150.78, 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 114 16.00 O 4054 8.00 N 3317 7.00 C 12487 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=30, symmetry=0 Simple disulfide: pdb=" SG CYS A 598 " - pdb=" SG CYS A 604 " distance=2.03 Simple disulfide: pdb=" SG CYS A 605 " - pdb=" SG CYS B 501 " distance=2.05 Simple disulfide: pdb=" SG CYS B 119 " - pdb=" SG CYS B 205 " distance=2.05 Simple disulfide: pdb=" SG CYS B 126 " - pdb=" SG CYS B 196 " distance=2.02 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 157 " distance=2.07 Simple disulfide: pdb=" SG CYS B 218 " - pdb=" SG CYS B 247 " distance=2.03 Simple disulfide: pdb=" SG CYS B 228 " - pdb=" SG CYS B 239 " distance=2.03 Simple disulfide: pdb=" SG CYS B 296 " - pdb=" SG CYS B 331 " distance=2.02 Simple disulfide: pdb=" SG CYS B 378 " - pdb=" SG CYS B 445 " distance=2.04 Simple disulfide: pdb=" SG CYS B 385 " - pdb=" SG CYS B 418 " distance=2.05 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=2.06 Simple disulfide: pdb=" SG CYS F 598 " - pdb=" SG CYS F 604 " distance=2.03 Simple disulfide: pdb=" SG CYS F 605 " - pdb=" SG CYS I 501 " distance=2.05 Simple disulfide: pdb=" SG CYS G 119 " - pdb=" SG CYS G 205 " distance=2.04 Simple disulfide: pdb=" SG CYS G 126 " - pdb=" SG CYS G 196 " distance=2.02 Simple disulfide: pdb=" SG CYS G 131 " - pdb=" SG CYS G 157 " distance=2.04 Simple disulfide: pdb=" SG CYS G 218 " - pdb=" SG CYS G 247 " distance=2.03 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=2.09 Simple disulfide: pdb=" SG CYS G 378 " - pdb=" SG CYS G 445 " distance=2.04 Simple disulfide: pdb=" SG CYS G 385 " - pdb=" SG CYS G 418 " distance=2.03 Simple disulfide: pdb=" SG CYS I 119 " - pdb=" SG CYS I 205 " distance=2.04 Simple disulfide: pdb=" SG CYS I 126 " - pdb=" SG CYS I 196 " distance=2.03 Simple disulfide: pdb=" SG CYS I 131 " - pdb=" SG CYS I 157 " distance=2.05 Simple disulfide: pdb=" SG CYS I 218 " - pdb=" SG CYS I 247 " distance=2.03 Simple disulfide: pdb=" SG CYS I 228 " - pdb=" SG CYS I 239 " distance=2.03 Simple disulfide: pdb=" SG CYS I 296 " - pdb=" SG CYS I 331 " distance=2.09 Simple disulfide: pdb=" SG CYS I 378 " - pdb=" SG CYS I 445 " distance=2.04 Simple disulfide: pdb=" SG CYS I 385 " - pdb=" SG CYS I 418 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-3 " BMA P 3 " - " MAN P 4 " " BMA b 3 " - " MAN b 4 " " BMA j 3 " - " MAN j 4 " ALPHA1-6 " BMA P 3 " - " MAN P 5 " " BMA j 3 " - " MAN j 5 " BETA1-4 " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG O 2 " - " BMA O 3 " " NAG P 1 " - " NAG P 2 " " NAG P 2 " - " BMA P 3 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG R 2 " - " BMA R 3 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG V 2 " - " BMA V 3 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Y 2 " - " BMA Y 3 " " NAG Z 1 " - " NAG Z 2 " " NAG Z 2 " - " BMA Z 3 " " 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 f 1 " - " NAG f 2 " " NAG g 1 " - " NAG g 2 " " NAG g 2 " - " BMA g 3 " " NAG h 1 " - " NAG h 2 " " NAG h 2 " - " BMA h 3 " " NAG i 1 " - " NAG i 2 " " NAG i 2 " - " BMA i 3 " " NAG j 1 " - " NAG j 2 " " NAG j 2 " - " BMA j 3 " " NAG k 1 " - " NAG k 2 " " NAG k 2 " - " BMA k 3 " " NAG l 1 " - " NAG l 2 " " NAG m 1 " - " NAG m 2 " " NAG m 2 " - " BMA m 3 " " NAG n 1 " - " NAG n 2 " " NAG o 1 " - " NAG o 2 " NAG-ASN " NAG A 701 " - " ASN A 611 " " NAG A 702 " - " ASN A 618 " " NAG A 703 " - " ASN A 637 " " NAG B 601 " - " ASN B 88 " " NAG B 614 " - " ASN B 295 " " NAG B 620 " - " ASN B 339 " " NAG B 621 " - " ASN B 355 " " NAG C 703 " - " ASN C 618 " " NAG C 704 " - " ASN C 637 " " NAG F 701 " - " ASN F 611 " " NAG F 702 " - " ASN F 618 " " NAG F 703 " - " ASN F 637 " " NAG G 615 " - " ASN G 295 " " NAG G 620 " - " ASN G 339 " " NAG G 621 " - " ASN G 355 " " NAG G 622 " - " ASN G 392 " " NAG G 627 " - " ASN G 448 " " NAG I 601 " - " ASN I 88 " " NAG I 619 " - " ASN I 295 " " NAG I 625 " - " ASN I 339 " " NAG I 626 " - " ASN I 355 " " NAG I 631 " - " ASN I 448 " " NAG M 1 " - " ASN B 160 " " NAG N 1 " - " ASN B 197 " " NAG O 1 " - " ASN B 234 " " NAG P 1 " - " ASN B 262 " " NAG Q 1 " - " ASN B 301 " " NAG R 1 " - " ASN B 332 " " NAG S 1 " - " ASN B 386 " " NAG T 1 " - " ASN B 448 " " NAG U 1 " - " ASN B 392 " " NAG V 1 " - " ASN B 276 " " NAG W 1 " - " ASN C 611 " " NAG X 1 " - " ASN G 88 " " NAG Y 1 " - " ASN G 160 " " NAG Z 1 " - " ASN G 197 " " NAG a 1 " - " ASN G 234 " " NAG b 1 " - " ASN G 262 " " NAG c 1 " - " ASN G 301 " " NAG d 1 " - " ASN G 332 " " NAG e 1 " - " ASN G 279 " " NAG f 1 " - " ASN G 386 " " NAG g 1 " - " ASN I 160 " " NAG h 1 " - " ASN I 197 " " NAG i 1 " - " ASN I 234 " " NAG j 1 " - " ASN I 262 " " NAG k 1 " - " ASN I 279 " " NAG l 1 " - " ASN I 301 " " NAG m 1 " - " ASN I 332 " " NAG n 1 " - " ASN I 386 " " NAG o 1 " - " ASN I 392 " Time building additional restraints: 2.45 Conformation dependent library (CDL) restraints added in 889.2 milliseconds 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4422 Finding SS restraints... Secondary structure from input PDB file: 42 helices and 43 sheets defined 16.8% alpha, 20.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.63 Creating SS restraints... Processing helix chain 'A' and resid 529 through 534 Processing helix chain 'A' and resid 537 through 543 removed outlier: 3.666A pdb=" N ALA A 541 " --> pdb=" O LEU A 537 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N ASN A 543 " --> pdb=" O VAL A 539 " (cutoff:3.500A) Processing helix chain 'A' and resid 572 through 595 removed outlier: 3.579A pdb=" N VAL A 580 " --> pdb=" O LEU A 576 " (cutoff:3.500A) removed outlier: 4.641A pdb=" N ASP A 589 " --> pdb=" O HIS A 585 " (cutoff:3.500A) Processing helix chain 'A' and resid 618 through 625 removed outlier: 3.611A pdb=" N ILE A 622 " --> pdb=" O ASN A 618 " (cutoff:3.500A) Processing helix chain 'A' and resid 627 through 632 removed outlier: 3.502A pdb=" N ASP A 632 " --> pdb=" O TRP A 628 " (cutoff:3.500A) Processing helix chain 'A' and resid 638 through 648 removed outlier: 3.696A pdb=" N GLU A 647 " --> pdb=" O TYR A 643 " (cutoff:3.500A) Processing helix chain 'A' and resid 652 through 661 Processing helix chain 'B' and resid 99 through 116 removed outlier: 3.782A pdb=" N ILE B 109 " --> pdb=" O HIS B 105 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N LEU B 116 " --> pdb=" O TRP B 112 " (cutoff:3.500A) Processing helix chain 'B' and resid 335 through 350 Processing helix chain 'B' and resid 351 through 353 No H-bonds generated for 'chain 'B' and resid 351 through 353' Processing helix chain 'B' and resid 368 through 373 removed outlier: 3.602A pdb=" N THR B 373 " --> pdb=" O LEU B 369 " (cutoff:3.500A) Processing helix chain 'B' and resid 475 through 481 removed outlier: 4.208A pdb=" N TRP B 479 " --> pdb=" O MET B 475 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ARG B 480 " --> pdb=" O ARG B 476 " (cutoff:3.500A) Processing helix chain 'C' and resid 529 through 534 Processing helix chain 'C' and resid 537 through 546 removed outlier: 3.695A pdb=" N ALA C 541 " --> pdb=" O LEU C 537 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N ASN C 543 " --> pdb=" O VAL C 539 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N LEU C 545 " --> pdb=" O ALA C 541 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N SER C 546 " --> pdb=" O ARG C 542 " (cutoff:3.500A) Processing helix chain 'C' and resid 572 through 595 removed outlier: 3.641A pdb=" N VAL C 580 " --> pdb=" O LEU C 576 " (cutoff:3.500A) removed outlier: 4.833A pdb=" N ASP C 589 " --> pdb=" O HIS C 585 " (cutoff:3.500A) Processing helix chain 'C' and resid 618 through 625 Processing helix chain 'C' and resid 627 through 632 removed outlier: 3.618A pdb=" N ASP C 632 " --> pdb=" O TRP C 628 " (cutoff:3.500A) Processing helix chain 'C' and resid 638 through 649 removed outlier: 4.967A pdb=" N GLU C 647 " --> pdb=" O TYR C 643 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N GLU C 648 " --> pdb=" O GLY C 644 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N SER C 649 " --> pdb=" O LEU C 645 " (cutoff:3.500A) Processing helix chain 'C' and resid 652 through 661 Processing helix chain 'D' and resid 28 through 32 removed outlier: 3.760A pdb=" N SER D 31 " --> pdb=" O SER D 28 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N SER D 32 " --> pdb=" O ILE D 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 28 through 32' Processing helix chain 'E' and resid 26 through 29 Processing helix chain 'F' and resid 529 through 534 Processing helix chain 'F' and resid 537 through 543 removed outlier: 3.764A pdb=" N ALA F 541 " --> pdb=" O LEU F 537 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N ASN F 543 " --> pdb=" O VAL F 539 " (cutoff:3.500A) Processing helix chain 'F' and resid 571 through 595 removed outlier: 4.415A pdb=" N GLN F 575 " --> pdb=" O TRP F 571 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N VAL F 580 " --> pdb=" O LEU F 576 " (cutoff:3.500A) removed outlier: 4.715A pdb=" N ASP F 589 " --> pdb=" O HIS F 585 " (cutoff:3.500A) Processing helix chain 'F' and resid 618 through 625 removed outlier: 3.595A pdb=" N ILE F 622 " --> pdb=" O ASN F 618 " (cutoff:3.500A) Processing helix chain 'F' and resid 627 through 632 Processing helix chain 'F' and resid 638 through 648 removed outlier: 4.451A pdb=" N GLU F 647 " --> pdb=" O TYR F 643 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N GLU F 648 " --> pdb=" O GLY F 644 " (cutoff:3.500A) Processing helix chain 'F' and resid 652 through 661 Processing helix chain 'G' and resid 99 through 116 removed outlier: 3.641A pdb=" N GLN G 103 " --> pdb=" O ASN G 99 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ILE G 109 " --> pdb=" O HIS G 105 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N LEU G 116 " --> pdb=" O TRP G 112 " (cutoff:3.500A) Processing helix chain 'G' and resid 335 through 350 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: 3.634A pdb=" N THR G 373 " --> pdb=" O LEU G 369 " (cutoff:3.500A) Processing helix chain 'G' and resid 476 through 481 removed outlier: 3.722A pdb=" N ARG G 480 " --> pdb=" O ARG G 476 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N SER G 481 " --> pdb=" O ASP G 477 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 476 through 481' Processing helix chain 'H' and resid 28 through 32 removed outlier: 3.761A pdb=" N SER H 31 " --> pdb=" O SER H 28 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N SER H 32 " --> pdb=" O ILE H 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 28 through 32' Processing helix chain 'I' and resid 99 through 116 removed outlier: 3.618A pdb=" N ILE I 109 " --> pdb=" O HIS I 105 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LEU I 116 " --> pdb=" O TRP I 112 " (cutoff:3.500A) Processing helix chain 'I' and resid 335 through 350 Processing helix chain 'I' and resid 351 through 353 No H-bonds generated for 'chain 'I' and resid 351 through 353' Processing helix chain 'I' and resid 368 through 373 removed outlier: 3.557A pdb=" N THR I 373 " --> pdb=" O LEU I 369 " (cutoff:3.500A) Processing helix chain 'I' and resid 476 through 481 removed outlier: 3.830A pdb=" N ARG I 480 " --> pdb=" O ARG I 476 " (cutoff:3.500A) Processing helix chain 'J' and resid 28 through 32 removed outlier: 3.760A pdb=" N SER J 31 " --> pdb=" O SER J 28 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N SER J 32 " --> pdb=" O ILE J 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 28 through 32' Processing helix chain 'K' and resid 26 through 29 Processing helix chain 'L' and resid 26 through 29 Processing sheet with id=AA1, first strand: chain 'B' and resid 35 through 46 removed outlier: 9.153A pdb=" N ILE B 491 " --> pdb=" O PRO B 43 " (cutoff:3.500A) removed outlier: 8.360A pdb=" N TRP B 45 " --> pdb=" O VAL B 489 " (cutoff:3.500A) removed outlier: 8.909A pdb=" N VAL B 489 " --> pdb=" O TRP B 45 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 75 through 76 removed outlier: 4.360A pdb=" N VAL B 75 " --> pdb=" O CYS B 54 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 172 through 176 removed outlier: 3.734A pdb=" N VAL B 172 " --> pdb=" O PHE B 159 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N PHE B 159 " --> pdb=" O VAL B 172 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N CYS B 131 " --> pdb=" O LYS B 189 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N LYS B 189 " --> pdb=" O CYS B 131 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N GLU B 190 " --> pdb=" O ILE B 184 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 202 through 203 removed outlier: 6.249A pdb=" N THR B 202 " --> pdb=" O TYR B 435 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 259 through 261 removed outlier: 4.130A pdb=" N LEU B 260 " --> pdb=" O THR B 450 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N ILE B 443 " --> pdb=" O ARG B 298 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N VAL B 292 " --> pdb=" O ILE B 449 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 271 through 273 removed outlier: 3.511A pdb=" N ILE B 271 " --> pdb=" O GLN B 287 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N LEU B 452 " --> pdb=" O VAL B 286 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N ARG B 360 " --> pdb=" O PHE B 468 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 304 through 307 removed outlier: 3.903A pdb=" N LYS B 305 " --> pdb=" O TYR B 319 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 329 through 334 removed outlier: 3.785A pdb=" N ALA B 329 " --> pdb=" O CYS B 418 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 6 through 8 removed outlier: 3.621A pdb=" N GLY D 8 " --> pdb=" O THR D 21 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N THR D 21 " --> pdb=" O GLY D 8 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 17 through 18 removed outlier: 3.884A pdb=" N THR D 69 " --> pdb=" O LYS D 82 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 47 through 49 removed outlier: 4.514A pdb=" N TRP D 37 " --> pdb=" O ILE D 49 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 19 through 24 removed outlier: 4.042A pdb=" N VAL E 19 " --> pdb=" O ILE E 75 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 90 through 92 removed outlier: 3.644A pdb=" N ALA E 95B" --> pdb=" O ASP E 92 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'G' and resid 35 through 46 removed outlier: 3.540A pdb=" N GLY G 495 " --> pdb=" O TYR G 39 " (cutoff:3.500A) removed outlier: 9.051A pdb=" N ILE G 491 " --> pdb=" O PRO G 43 " (cutoff:3.500A) removed outlier: 7.912A pdb=" N TRP G 45 " --> pdb=" O VAL G 489 " (cutoff:3.500A) removed outlier: 9.014A pdb=" N VAL G 489 " --> pdb=" O TRP G 45 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ILE G 225 " --> pdb=" O VAL G 245 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'G' and resid 75 through 76 removed outlier: 4.458A pdb=" N VAL G 75 " --> pdb=" O CYS G 54 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'G' and resid 92 through 94 removed outlier: 4.142A pdb=" N GLY G 237 " --> pdb=" O PHE G 93 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'G' and resid 169 through 176 removed outlier: 3.923A pdb=" N VAL G 172 " --> pdb=" O PHE G 159 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N PHE G 159 " --> pdb=" O VAL G 172 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N CYS G 131 " --> pdb=" O LYS G 189 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N LYS G 189 " --> pdb=" O CYS G 131 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'G' and resid 202 through 203 removed outlier: 6.269A pdb=" N THR G 202 " --> pdb=" O TYR G 435 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'G' and resid 256 through 257 Processing sheet with id=AC2, first strand: chain 'G' and resid 259 through 260 removed outlier: 3.728A pdb=" N LEU G 452 " --> pdb=" O VAL G 286 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ILE G 271 " --> pdb=" O GLN G 287 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'G' and resid 259 through 260 removed outlier: 6.589A pdb=" N ARG G 360 " --> pdb=" O PHE G 468 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'G' and resid 383 through 385 removed outlier: 3.756A pdb=" N ALA G 329 " --> pdb=" O CYS G 418 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'G' and resid 383 through 385 removed outlier: 3.756A pdb=" N ALA G 329 " --> pdb=" O CYS G 418 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N HIS G 330 " --> pdb=" O THR G 297 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N THR G 297 " --> pdb=" O HIS G 330 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ASN G 295 " --> pdb=" O ASN G 332 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ILE G 443 " --> pdb=" O ARG G 298 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'G' and resid 304 through 307 removed outlier: 3.576A pdb=" N LYS G 305 " --> pdb=" O TYR G 319 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'H' and resid 6 through 8 removed outlier: 3.620A pdb=" N GLY H 8 " --> pdb=" O THR H 21 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N THR H 21 " --> pdb=" O GLY H 8 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'H' and resid 17 through 18 removed outlier: 3.884A pdb=" N THR H 69 " --> pdb=" O LYS H 82 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'H' and resid 47 through 49 removed outlier: 4.514A pdb=" N TRP H 37 " --> pdb=" O ILE H 49 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'I' and resid 35 through 46 removed outlier: 9.239A pdb=" N ILE I 491 " --> pdb=" O PRO I 43 " (cutoff:3.500A) removed outlier: 8.491A pdb=" N TRP I 45 " --> pdb=" O VAL I 489 " (cutoff:3.500A) removed outlier: 9.079A pdb=" N VAL I 489 " --> pdb=" O TRP I 45 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ILE I 225 " --> pdb=" O VAL I 245 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'I' and resid 53 through 55 removed outlier: 5.853A pdb=" N ILE I 215 " --> pdb=" O GLY I 250 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N GLY I 250 " --> pdb=" O ILE I 215 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N TYR I 217 " --> pdb=" O THR I 248 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'I' and resid 92 through 94 removed outlier: 4.139A pdb=" N GLY I 237 " --> pdb=" O PHE I 93 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'I' and resid 169 through 176 removed outlier: 3.840A pdb=" N PHE I 159 " --> pdb=" O VAL I 172 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N CYS I 131 " --> pdb=" O LYS I 189 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N LYS I 189 " --> pdb=" O CYS I 131 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'I' and resid 202 through 203 removed outlier: 5.852A pdb=" N THR I 202 " --> pdb=" O TYR I 435 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'I' and resid 271 through 273 removed outlier: 3.823A pdb=" N ILE I 271 " --> pdb=" O GLN I 287 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N ARG I 360 " --> pdb=" O PHE I 468 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'I' and resid 383 through 385 removed outlier: 3.673A pdb=" N ALA I 329 " --> pdb=" O CYS I 418 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'I' and resid 383 through 385 removed outlier: 3.673A pdb=" N ALA I 329 " --> pdb=" O CYS I 418 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N HIS I 330 " --> pdb=" O THR I 297 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N THR I 297 " --> pdb=" O HIS I 330 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ASN I 295 " --> pdb=" O ASN I 332 " (cutoff:3.500A) removed outlier: 5.099A pdb=" N SER I 334 " --> pdb=" O GLN I 293 " (cutoff:3.500A) removed outlier: 7.326A pdb=" N GLN I 293 " --> pdb=" O SER I 334 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N VAL I 292 " --> pdb=" O ILE I 449 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N ILE I 443 " --> pdb=" O ARG I 298 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'I' and resid 301 through 308 removed outlier: 7.656A pdb=" N ASN I 301 " --> pdb=" O ILE I 322 " (cutoff:3.500A) removed outlier: 5.241A pdb=" N ILE I 322 " --> pdb=" O ASN I 301 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N THR I 303 " --> pdb=" O GLY I 321 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N LYS I 305 " --> pdb=" O TYR I 319 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'J' and resid 6 through 8 removed outlier: 3.620A pdb=" N GLY J 8 " --> pdb=" O THR J 21 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N THR J 21 " --> pdb=" O GLY J 8 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'J' and resid 17 through 18 removed outlier: 3.884A pdb=" N THR J 69 " --> pdb=" O LYS J 82 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'J' and resid 47 through 49 removed outlier: 4.513A pdb=" N TRP J 37 " --> pdb=" O ILE J 49 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'K' and resid 19 through 24 removed outlier: 4.042A pdb=" N VAL K 19 " --> pdb=" O ILE K 75 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'K' and resid 90 through 92 removed outlier: 3.646A pdb=" N ALA K 95B" --> pdb=" O ASP K 92 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'L' and resid 19 through 24 removed outlier: 4.042A pdb=" N VAL L 19 " --> pdb=" O ILE L 75 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'L' and resid 90 through 92 removed outlier: 3.645A pdb=" N ALA L 95B" --> pdb=" O ASP L 92 " (cutoff:3.500A) 459 hydrogen bonds defined for protein. 1239 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: 3.61 Time building geometry restraints manager: 3.11 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.31: 3206 1.31 - 1.45: 6838 1.45 - 1.59: 10176 1.59 - 1.73: 1 1.73 - 1.87: 150 Bond restraints: 20371 Sorted by residual: bond pdb=" C4 NAG e 1 " pdb=" O4 NAG e 1 " ideal model delta sigma weight residual 1.409 1.524 -0.115 2.00e-02 2.50e+03 3.33e+01 bond pdb=" C7 NAG B 614 " pdb=" N2 NAG B 614 " ideal model delta sigma weight residual 1.346 1.243 0.103 2.00e-02 2.50e+03 2.64e+01 bond pdb=" C1 NAG B 614 " pdb=" C2 NAG B 614 " ideal model delta sigma weight residual 1.532 1.434 0.098 2.00e-02 2.50e+03 2.40e+01 bond pdb=" C2 NAG B 614 " pdb=" N2 NAG B 614 " ideal model delta sigma weight residual 1.439 1.342 0.097 2.00e-02 2.50e+03 2.37e+01 bond pdb=" C3 NAG B 614 " pdb=" C4 NAG B 614 " ideal model delta sigma weight residual 1.524 1.432 0.092 2.00e-02 2.50e+03 2.12e+01 ... (remaining 20366 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.28: 27250 5.28 - 10.56: 362 10.56 - 15.84: 48 15.84 - 21.12: 10 21.12 - 26.40: 4 Bond angle restraints: 27674 Sorted by residual: angle pdb=" CA ASN G 448 " pdb=" C ASN G 448 " pdb=" O ASN G 448 " ideal model delta sigma weight residual 119.32 104.70 14.62 1.19e+00 7.06e-01 1.51e+02 angle pdb=" C ASN G 448 " pdb=" N ILE G 449 " pdb=" CA ILE G 449 " ideal model delta sigma weight residual 121.97 140.56 -18.59 1.80e+00 3.09e-01 1.07e+02 angle pdb=" O SER G 447 " pdb=" C SER G 447 " pdb=" N ASN G 448 " ideal model delta sigma weight residual 123.10 133.55 -10.45 1.15e+00 7.56e-01 8.26e+01 angle pdb=" C3 NAG C 704 " pdb=" C2 NAG C 704 " pdb=" N2 NAG C 704 " ideal model delta sigma weight residual 110.74 84.34 26.40 3.00e+00 1.11e-01 7.75e+01 angle pdb=" C1 NAG j 1 " pdb=" C2 NAG j 1 " pdb=" N2 NAG j 1 " ideal model delta sigma weight residual 110.79 88.76 22.03 3.00e+00 1.11e-01 5.39e+01 ... (remaining 27669 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.78: 10376 17.78 - 35.56: 781 35.56 - 53.33: 191 53.33 - 71.11: 18 71.11 - 88.89: 19 Dihedral angle restraints: 11385 sinusoidal: 4515 harmonic: 6870 Sorted by residual: dihedral pdb=" CB CYS F 605 " pdb=" SG CYS F 605 " pdb=" SG CYS I 501 " pdb=" CB CYS I 501 " ideal model delta sinusoidal sigma weight residual -86.00 2.89 -88.89 1 1.00e+01 1.00e-02 9.41e+01 dihedral pdb=" CA GLN K 34 " pdb=" C GLN K 34 " pdb=" N TRP K 35 " pdb=" CA TRP K 35 " ideal model delta harmonic sigma weight residual 180.00 134.99 45.01 0 5.00e+00 4.00e-02 8.10e+01 dihedral pdb=" CA GLN L 34 " pdb=" C GLN L 34 " pdb=" N TRP L 35 " pdb=" CA TRP L 35 " ideal model delta harmonic sigma weight residual 180.00 135.03 44.97 0 5.00e+00 4.00e-02 8.09e+01 ... (remaining 11382 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.241: 3307 0.241 - 0.483: 73 0.483 - 0.724: 5 0.724 - 0.965: 2 0.965 - 1.207: 4 Chirality restraints: 3391 Sorted by residual: chirality pdb=" C1 NAG e 2 " pdb=" O4 NAG e 1 " pdb=" C2 NAG e 2 " pdb=" O5 NAG e 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.81 0.41 2.00e-02 2.50e+03 4.13e+02 chirality pdb=" C1 BMA V 3 " pdb=" O4 NAG V 2 " pdb=" C2 BMA V 3 " pdb=" O5 BMA V 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.72 0.32 2.00e-02 2.50e+03 2.63e+02 chirality pdb=" C1 NAG j 2 " pdb=" O4 NAG j 1 " pdb=" C2 NAG j 2 " pdb=" O5 NAG j 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.08 -0.32 2.00e-02 2.50e+03 2.54e+02 ... (remaining 3388 not shown) Planarity restraints: 3440 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG f 1 " -0.366 2.00e-02 2.50e+03 3.06e-01 1.17e+03 pdb=" C7 NAG f 1 " 0.096 2.00e-02 2.50e+03 pdb=" C8 NAG f 1 " -0.192 2.00e-02 2.50e+03 pdb=" N2 NAG f 1 " 0.533 2.00e-02 2.50e+03 pdb=" O7 NAG f 1 " -0.071 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG U 2 " 0.344 2.00e-02 2.50e+03 2.97e-01 1.10e+03 pdb=" C7 NAG U 2 " -0.078 2.00e-02 2.50e+03 pdb=" C8 NAG U 2 " 0.100 2.00e-02 2.50e+03 pdb=" N2 NAG U 2 " -0.529 2.00e-02 2.50e+03 pdb=" O7 NAG U 2 " 0.164 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG j 1 " -0.336 2.00e-02 2.50e+03 2.90e-01 1.05e+03 pdb=" C7 NAG j 1 " 0.120 2.00e-02 2.50e+03 pdb=" C8 NAG j 1 " -0.180 2.00e-02 2.50e+03 pdb=" N2 NAG j 1 " 0.499 2.00e-02 2.50e+03 pdb=" O7 NAG j 1 " -0.104 2.00e-02 2.50e+03 ... (remaining 3437 not shown) Histogram of nonbonded interaction distances: 1.54 - 2.21: 15 2.21 - 2.88: 7971 2.88 - 3.56: 27575 3.56 - 4.23: 44211 4.23 - 4.90: 67651 Nonbonded interactions: 147423 Sorted by model distance: nonbonded pdb=" CE2 PHE B 391 " pdb=" CG PRO B 470 " model vdw 1.539 3.740 nonbonded pdb=" CE3 TRP G 96 " pdb=" OE2 GLU G 275 " model vdw 1.863 3.340 nonbonded pdb=" CE2 PHE B 391 " pdb=" CB PRO B 470 " model vdw 1.868 3.740 nonbonded pdb=" O4 NAG C 704 " pdb=" O6 NAG C 704 " model vdw 1.983 3.040 nonbonded pdb=" O4 NAG A 703 " pdb=" O6 NAG A 703 " model vdw 1.998 3.040 ... (remaining 147418 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' and resid 518 through 702) selection = chain 'C' selection = (chain 'F' and resid 518 through 702) } ncs_group { reference = chain 'B' selection = (chain 'G' and resid 31 through 622) selection = (chain 'I' and resid 31 through 626) } ncs_group { reference = chain 'D' selection = chain 'H' selection = chain 'J' } ncs_group { reference = chain 'E' selection = chain 'K' selection = chain 'L' } ncs_group { reference = chain 'M' selection = chain 'N' selection = chain 'Q' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'W' selection = chain 'X' selection = chain 'a' selection = chain 'c' selection = chain 'd' selection = chain 'e' selection = chain 'f' selection = chain 'l' selection = chain 'n' selection = chain 'o' } ncs_group { reference = chain 'O' selection = chain 'R' selection = chain 'V' selection = chain 'Y' selection = chain 'Z' selection = chain 'g' selection = chain 'h' selection = chain 'i' selection = chain 'k' selection = chain 'm' } ncs_group { reference = chain 'P' selection = chain 'j' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.230 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: 0.310 Check model and map are aligned: 0.070 Set scattering table: 0.050 Process input model: 19.700 Find NCS groups from input model: 0.650 Set up NCS constraints: 0.090 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:1.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.220 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6140 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 : 0.010 0.115 20499 Z= 0.485 Angle : 1.752 26.404 28028 Z= 0.845 Chirality : 0.099 1.207 3391 Planarity : 0.015 0.306 3389 Dihedral : 13.275 79.327 6873 Min Nonbonded Distance : 1.539 Molprobity Statistics. All-atom Clashscore : 13.49 Ramachandran Plot: Outliers : 0.43 % Allowed : 15.83 % Favored : 83.74 % Rotamer: Outliers : 1.05 % Allowed : 8.24 % Favored : 90.71 % Cbeta Deviations : 0.32 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.98 % Twisted General : 1.59 % 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: -4.88 (0.14), residues: 2343 helix: -3.44 (0.19), residues: 333 sheet: -2.48 (0.19), residues: 564 loop : -3.71 (0.14), residues: 1446 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 429 TYR 0.073 0.004 TYR B 173 PHE 0.033 0.004 PHE B 320 TRP 0.036 0.005 TRP H 100B HIS 0.021 0.003 HIS F 585 Details of bonding type rmsd/Z covalent geometry : bond 0.00964 / 0.48 (20371) covalent geometry : angle 1.62168 / 0.82 (27674) SS BOND : bond 0.01905 / 1.16 ( 30) SS BOND : angle 3.09748 / 1.96 ( 60) hydrogen bonds : bond 0.22160 / 14.57 ( 451) hydrogen bonds : angle 10.22535 / 7.30 ( 1239) link_ALPHA1-3 : bond 0.01473 / 0.60 ( 3) link_ALPHA1-3 : angle 4.22306 / 2.34 ( 9) link_ALPHA1-6 : bond 0.00717 / 0.38 ( 2) link_ALPHA1-6 : angle 2.29520 / 1.22 ( 6) link_BETA1-4 : bond 0.01917 / 1.37 ( 42) link_BETA1-4 : angle 6.75584 / 5.16 ( 126) link_NAG-ASN : bond 0.02066 / 1.43 ( 51) link_NAG-ASN : angle 6.64536 / 4.51 ( 153) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 918 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 896 time to evaluate : 0.792 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 523 LEU cc_start: 0.8845 (mt) cc_final: 0.8627 (mt) REVERT: A 534 SER cc_start: 0.8967 (p) cc_final: 0.8602 (p) REVERT: A 543 ASN cc_start: 0.8175 (t0) cc_final: 0.7759 (t0) REVERT: A 624 ASP cc_start: 0.8398 (m-30) cc_final: 0.8198 (m-30) REVERT: B 97 LYS cc_start: 0.8313 (mmtp) cc_final: 0.8066 (mmmm) REVERT: B 116 LEU cc_start: 0.7173 (pp) cc_final: 0.6712 (pp) REVERT: B 131 CYS cc_start: 0.5986 (t) cc_final: 0.5698 (t) REVERT: B 150 MET cc_start: 0.7943 (mpp) cc_final: 0.7681 (mpp) REVERT: B 181 VAL cc_start: 0.7815 (t) cc_final: 0.7579 (t) REVERT: B 265 LEU cc_start: 0.8160 (mt) cc_final: 0.7825 (mm) REVERT: B 269 GLU cc_start: 0.8504 (tp30) cc_final: 0.8261 (tp30) REVERT: B 289 ASN cc_start: 0.8274 (p0) cc_final: 0.8045 (p0) REVERT: B 307 ILE cc_start: 0.7410 (mm) cc_final: 0.7120 (tp) REVERT: B 474 ASP cc_start: 0.7988 (t70) cc_final: 0.6688 (t0) REVERT: B 485 LYS cc_start: 0.6351 (ptpt) cc_final: 0.6107 (ptpp) REVERT: C 534 SER cc_start: 0.8972 (p) cc_final: 0.8582 (p) REVERT: C 543 ASN cc_start: 0.7901 (t0) cc_final: 0.7693 (t0) REVERT: C 583 VAL cc_start: 0.6947 (m) cc_final: 0.6677 (m) REVERT: C 624 ASP cc_start: 0.8131 (m-30) cc_final: 0.7794 (m-30) REVERT: C 658 GLN cc_start: 0.8632 (tp-100) cc_final: 0.8272 (tp-100) REVERT: E 58 LEU cc_start: 0.7936 (tp) cc_final: 0.7497 (tp) REVERT: E 60 ASP cc_start: 0.6980 (t0) cc_final: 0.6147 (t0) REVERT: E 92 ASP cc_start: 0.7970 (t0) cc_final: 0.7703 (m-30) REVERT: F 522 PHE cc_start: 0.7390 (t80) cc_final: 0.6343 (t80) REVERT: F 534 SER cc_start: 0.8840 (p) cc_final: 0.8476 (p) REVERT: F 543 ASN cc_start: 0.7950 (t0) cc_final: 0.7700 (t0) REVERT: F 590 GLN cc_start: 0.8423 (tp-100) cc_final: 0.8180 (tm-30) REVERT: F 624 ASP cc_start: 0.8025 (m-30) cc_final: 0.7739 (m-30) REVERT: G 82 GLN cc_start: 0.8764 (mm-40) cc_final: 0.7937 (mp10) REVERT: G 94 ASN cc_start: 0.7961 (t0) cc_final: 0.7542 (t0) REVERT: G 98 ASN cc_start: 0.8262 (t0) cc_final: 0.8033 (t0) REVERT: G 171 LYS cc_start: 0.7794 (mtpt) cc_final: 0.7576 (mtmt) REVERT: G 203 GLN cc_start: 0.7278 (pp30) cc_final: 0.6736 (pp30) REVERT: G 230 ASP cc_start: 0.8519 (t0) cc_final: 0.7990 (p0) REVERT: G 239 CYS cc_start: 0.5349 (t) cc_final: 0.5060 (t) REVERT: G 269 GLU cc_start: 0.8300 (tp30) cc_final: 0.7882 (tp30) REVERT: G 289 ASN cc_start: 0.8341 (p0) cc_final: 0.7920 (p0) REVERT: G 320 PHE cc_start: 0.8099 (t80) cc_final: 0.7384 (t80) REVERT: G 321 ASP cc_start: 0.7970 (m-30) cc_final: 0.7731 (m-30) REVERT: G 328 MET cc_start: 0.7465 (ptm) cc_final: 0.7044 (pmm) REVERT: G 369 LEU cc_start: 0.8293 (pp) cc_final: 0.8021 (mm) REVERT: G 426 MET cc_start: 0.7626 (ptt) cc_final: 0.7313 (ptm) REVERT: G 474 ASP cc_start: 0.7070 (t70) cc_final: 0.6542 (t70) REVERT: G 478 ASN cc_start: 0.6955 (m110) cc_final: 0.6556 (m110) REVERT: G 488 VAL cc_start: 0.5941 (p) cc_final: 0.5301 (p) REVERT: H 57 ASN cc_start: 0.6348 (t0) cc_final: 0.6066 (t0) REVERT: I 50 THR cc_start: 0.9334 (p) cc_final: 0.8962 (p) REVERT: I 53 PHE cc_start: 0.6691 (p90) cc_final: 0.6394 (p90) REVERT: I 87 GLU cc_start: 0.7019 (tm-30) cc_final: 0.6672 (tm-30) REVERT: I 97 LYS cc_start: 0.8596 (mmtp) cc_final: 0.8260 (mmmm) REVERT: I 171 LYS cc_start: 0.8170 (pmmt) cc_final: 0.7560 (ptmt) REVERT: I 172 VAL cc_start: 0.8136 (p) cc_final: 0.7845 (p) REVERT: I 261 LEU cc_start: 0.7152 (tp) cc_final: 0.6906 (tp) REVERT: I 269 GLU cc_start: 0.8282 (tp30) cc_final: 0.8069 (tp30) REVERT: I 278 THR cc_start: 0.9055 (m) cc_final: 0.8830 (t) REVERT: I 289 ASN cc_start: 0.8238 (p0) cc_final: 0.7674 (p0) REVERT: I 308 ARG cc_start: 0.7783 (mpp80) cc_final: 0.7351 (mtm-85) REVERT: I 383 PHE cc_start: 0.6136 (m-10) cc_final: 0.5810 (m-10) REVERT: I 443 ILE cc_start: 0.8020 (mm) cc_final: 0.7788 (mp) REVERT: J 9 PRO cc_start: 0.8372 (Cg_endo) cc_final: 0.8110 (Cg_exo) REVERT: J 78 GLN cc_start: 0.7794 (mp10) cc_final: 0.7460 (mp10) REVERT: J 91 TYR cc_start: 0.7187 (m-80) cc_final: 0.6972 (m-10) REVERT: K 22 SER cc_start: 0.9111 (m) cc_final: 0.8885 (t) REVERT: K 58 LEU cc_start: 0.7898 (tp) cc_final: 0.7639 (tp) REVERT: K 60 ASP cc_start: 0.6306 (t0) cc_final: 0.5118 (t0) REVERT: K 92 ASP cc_start: 0.8340 (t0) cc_final: 0.8104 (m-30) REVERT: L 34 GLN cc_start: 0.7034 (pp30) cc_final: 0.6797 (pp30) REVERT: L 58 LEU cc_start: 0.7707 (tp) cc_final: 0.7460 (tp) REVERT: L 60 ASP cc_start: 0.7037 (t0) cc_final: 0.6207 (t0) REVERT: L 92 ASP cc_start: 0.8116 (t0) cc_final: 0.7791 (m-30) outliers start: 22 outliers final: 9 residues processed: 909 average time/residue: 0.1444 time to fit residues: 201.6975 Evaluate side-chains 569 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 560 time to evaluate : 0.733 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 216 optimal weight: 6.9990 chunk 98 optimal weight: 5.9990 chunk 194 optimal weight: 0.7980 chunk 227 optimal weight: 5.9990 chunk 107 optimal weight: 0.9980 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 0.8980 chunk 130 optimal weight: 9.9990 chunk 124 optimal weight: 0.7980 chunk 103 optimal weight: 1.9990 chunk 200 optimal weight: 0.0060 overall best weight: 0.6996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 577 GLN A 651 ASN ** B 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 137 ASN ** B 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 203 GLN B 258 GLN C 651 ASN C 656 ASN F 651 ASN ** G 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 137 ASN G 156 GLN G 170 GLN G 425 ASN I 137 ASN I 156 GLN I 170 GLN I 302 ASN I 425 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.135453 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.110205 restraints weight = 40372.379| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.113687 restraints weight = 23905.000| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.116110 restraints weight = 16428.981| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.117785 restraints weight = 12492.704| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.119023 restraints weight = 10218.202| |-----------------------------------------------------------------------------| r_work (final): 0.3368 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7872 moved from start: 0.3174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 20499 Z= 0.175 Angle : 1.081 16.237 28028 Z= 0.493 Chirality : 0.060 0.606 3391 Planarity : 0.006 0.059 3389 Dihedral : 8.027 39.468 2544 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 11.38 Ramachandran Plot: Outliers : 0.09 % Allowed : 11.01 % Favored : 88.90 % Rotamer: Outliers : 0.29 % Allowed : 5.65 % Favored : 94.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.98 % Twisted General : 0.62 % 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: -4.30 (0.15), residues: 2343 helix: -2.49 (0.23), residues: 336 sheet: -1.70 (0.23), residues: 438 loop : -3.54 (0.13), residues: 1569 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 500 TYR 0.034 0.002 TYR I 173 PHE 0.040 0.002 PHE K 31 TRP 0.029 0.002 TRP F 610 HIS 0.006 0.001 HIS G 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00363 / 0.17 (20371) covalent geometry : angle 0.99526 / 0.47 (27674) SS BOND : bond 0.00473 / 0.37 ( 30) SS BOND : angle 1.66345 / 0.98 ( 60) hydrogen bonds : bond 0.05348 / 3.59 ( 451) hydrogen bonds : angle 7.51204 / 5.34 ( 1239) link_ALPHA1-3 : bond 0.01234 / 0.60 ( 3) link_ALPHA1-3 : angle 2.68811 / 1.47 ( 9) link_ALPHA1-6 : bond 0.00749 / 0.38 ( 2) link_ALPHA1-6 : angle 1.78240 / 0.86 ( 6) link_BETA1-4 : bond 0.01120 / 0.93 ( 42) link_BETA1-4 : angle 3.87526 / 2.97 ( 126) link_NAG-ASN : bond 0.00906 / 0.63 ( 51) link_NAG-ASN : angle 4.55904 / 3.16 ( 153) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 767 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 761 time to evaluate : 0.828 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 522 PHE cc_start: 0.8779 (t80) cc_final: 0.8496 (t80) REVERT: A 523 LEU cc_start: 0.9407 (mt) cc_final: 0.9070 (mt) REVERT: A 543 ASN cc_start: 0.9040 (t0) cc_final: 0.8339 (t0) REVERT: A 588 ARG cc_start: 0.8584 (ttt90) cc_final: 0.7773 (tmm-80) REVERT: A 661 LEU cc_start: 0.8639 (tp) cc_final: 0.8339 (tt) REVERT: B 96 TRP cc_start: 0.9375 (m100) cc_final: 0.9017 (m100) REVERT: B 97 LYS cc_start: 0.9043 (mmtp) cc_final: 0.8510 (mmmm) REVERT: B 106 GLU cc_start: 0.8748 (pt0) cc_final: 0.8350 (tm-30) REVERT: B 182 VAL cc_start: 0.9001 (t) cc_final: 0.8739 (p) REVERT: B 265 LEU cc_start: 0.9148 (mt) cc_final: 0.8858 (mm) REVERT: B 270 VAL cc_start: 0.9559 (m) cc_final: 0.9320 (t) REVERT: B 279 ASN cc_start: 0.8270 (t0) cc_final: 0.7863 (t0) REVERT: B 321 ASP cc_start: 0.8900 (m-30) cc_final: 0.8624 (m-30) REVERT: B 474 ASP cc_start: 0.8574 (t70) cc_final: 0.7977 (t0) REVERT: B 485 LYS cc_start: 0.8675 (ptpt) cc_final: 0.8247 (ptpt) REVERT: B 492 GLU cc_start: 0.8769 (tp30) cc_final: 0.8293 (tm-30) REVERT: C 588 ARG cc_start: 0.8702 (ttt90) cc_final: 0.7989 (ttt180) REVERT: C 607 ASN cc_start: 0.8198 (t0) cc_final: 0.7851 (t0) REVERT: C 658 GLN cc_start: 0.8758 (tp-100) cc_final: 0.8065 (tp-100) REVERT: D 48 TRP cc_start: 0.8832 (t60) cc_final: 0.8258 (t60) REVERT: D 57 ASN cc_start: 0.7600 (t0) cc_final: 0.7381 (t0) REVERT: D 58 THR cc_start: 0.8872 (p) cc_final: 0.8569 (m) REVERT: D 59 TYR cc_start: 0.7700 (m-80) cc_final: 0.7256 (m-10) REVERT: D 61 ASN cc_start: 0.7933 (t0) cc_final: 0.7693 (t0) REVERT: D 79 PHE cc_start: 0.8705 (p90) cc_final: 0.8460 (p90) REVERT: D 100 ASN cc_start: 0.8362 (p0) cc_final: 0.8126 (p0) REVERT: E 49 TYR cc_start: 0.7370 (t80) cc_final: 0.6998 (t80) REVERT: E 60 ASP cc_start: 0.7748 (t0) cc_final: 0.6861 (t0) REVERT: E 85 ASP cc_start: 0.7916 (m-30) cc_final: 0.7695 (m-30) REVERT: E 92 ASP cc_start: 0.8953 (t0) cc_final: 0.8657 (m-30) REVERT: E 104 LEU cc_start: 0.8487 (pt) cc_final: 0.8221 (pp) REVERT: F 522 PHE cc_start: 0.8540 (t80) cc_final: 0.7964 (t80) REVERT: F 523 LEU cc_start: 0.9388 (mt) cc_final: 0.9163 (mt) REVERT: F 543 ASN cc_start: 0.8817 (t0) cc_final: 0.8159 (t0) REVERT: G 82 GLN cc_start: 0.8953 (mm-40) cc_final: 0.8101 (mp10) REVERT: G 94 ASN cc_start: 0.8588 (t0) cc_final: 0.7983 (t0) REVERT: G 122 LEU cc_start: 0.8050 (tt) cc_final: 0.7729 (tt) REVERT: G 156 GLN cc_start: 0.8043 (OUTLIER) cc_final: 0.7506 (pm20) REVERT: G 193 LEU cc_start: 0.7777 (pt) cc_final: 0.7456 (pp) REVERT: G 203 GLN cc_start: 0.8759 (pp30) cc_final: 0.8384 (pp30) REVERT: G 226 LEU cc_start: 0.8421 (pp) cc_final: 0.8084 (pp) REVERT: G 270 VAL cc_start: 0.9548 (t) cc_final: 0.9250 (t) REVERT: G 325 ASP cc_start: 0.8999 (p0) cc_final: 0.8785 (p0) REVERT: G 328 MET cc_start: 0.7478 (ptm) cc_final: 0.7171 (pmm) REVERT: G 368 ASP cc_start: 0.8391 (p0) cc_final: 0.8072 (t70) REVERT: G 369 LEU cc_start: 0.8672 (pp) cc_final: 0.8364 (mm) REVERT: G 425 ASN cc_start: 0.8181 (OUTLIER) cc_final: 0.7599 (p0) REVERT: G 449 ILE cc_start: 0.6897 (mm) cc_final: 0.6646 (mm) REVERT: G 494 LEU cc_start: 0.8887 (tt) cc_final: 0.8683 (tt) REVERT: H 79 PHE cc_start: 0.8930 (p90) cc_final: 0.8669 (p90) REVERT: H 91 TYR cc_start: 0.8430 (m-10) cc_final: 0.7780 (m-10) REVERT: I 50 THR cc_start: 0.9587 (p) cc_final: 0.9313 (p) REVERT: I 53 PHE cc_start: 0.8609 (p90) cc_final: 0.8358 (p90) REVERT: I 87 GLU cc_start: 0.8072 (tm-30) cc_final: 0.7760 (tm-30) REVERT: I 97 LYS cc_start: 0.9177 (mmtp) cc_final: 0.8668 (mmmm) REVERT: I 110 SER cc_start: 0.9545 (m) cc_final: 0.9296 (t) REVERT: I 114 GLN cc_start: 0.9245 (tm-30) cc_final: 0.8929 (tm-30) REVERT: I 269 GLU cc_start: 0.9262 (tp30) cc_final: 0.8731 (tp30) REVERT: I 368 ASP cc_start: 0.8587 (t70) cc_final: 0.8263 (t70) REVERT: I 370 GLU cc_start: 0.8244 (mp0) cc_final: 0.7948 (mp0) REVERT: I 421 LYS cc_start: 0.9207 (ttmt) cc_final: 0.8960 (mtmt) REVERT: I 425 ASN cc_start: 0.8084 (OUTLIER) cc_final: 0.7806 (p0) REVERT: I 426 MET cc_start: 0.7407 (ptt) cc_final: 0.6985 (ptm) REVERT: I 427 TRP cc_start: 0.8726 (m100) cc_final: 0.8046 (m100) REVERT: I 434 MET cc_start: 0.8748 (ttm) cc_final: 0.8486 (ttm) REVERT: I 499 THR cc_start: 0.8851 (t) cc_final: 0.8631 (t) REVERT: J 13 LYS cc_start: 0.7236 (mtmt) cc_final: 0.6903 (mtmt) REVERT: J 57 ASN cc_start: 0.7451 (t0) cc_final: 0.7204 (t0) REVERT: K 60 ASP cc_start: 0.8127 (t0) cc_final: 0.7157 (t0) REVERT: K 92 ASP cc_start: 0.9025 (t0) cc_final: 0.8658 (m-30) REVERT: L 49 TYR cc_start: 0.6894 (t80) cc_final: 0.6537 (t80) REVERT: L 85 ASP cc_start: 0.7704 (m-30) cc_final: 0.7433 (m-30) REVERT: L 92 ASP cc_start: 0.8885 (t0) cc_final: 0.8534 (m-30) outliers start: 6 outliers final: 1 residues processed: 763 average time/residue: 0.1261 time to fit residues: 151.7274 Evaluate side-chains 556 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 552 time to evaluate : 0.672 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 96 optimal weight: 3.9990 chunk 230 optimal weight: 8.9990 chunk 148 optimal weight: 0.9980 chunk 135 optimal weight: 2.9990 chunk 211 optimal weight: 4.9990 chunk 132 optimal weight: 3.9990 chunk 27 optimal weight: 3.9990 chunk 15 optimal weight: 0.2980 chunk 154 optimal weight: 9.9990 chunk 117 optimal weight: 0.9980 chunk 176 optimal weight: 5.9990 overall best weight: 1.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 577 GLN A 652 GLN A 658 GLN B 156 GLN G 156 GLN ** I 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 103 GLN I 137 ASN I 156 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.129128 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.104354 restraints weight = 40468.530| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.107666 restraints weight = 23728.326| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.109993 restraints weight = 16221.683| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.111573 restraints weight = 12284.788| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.112668 restraints weight = 10055.760| |-----------------------------------------------------------------------------| r_work (final): 0.3293 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8015 moved from start: 0.3870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.091 20499 Z= 0.198 Angle : 1.020 14.694 28028 Z= 0.467 Chirality : 0.057 0.528 3391 Planarity : 0.005 0.058 3389 Dihedral : 7.447 41.056 2544 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 11.99 Ramachandran Plot: Outliers : 0.09 % Allowed : 13.40 % Favored : 86.51 % Rotamer: Outliers : 0.34 % Allowed : 5.12 % Favored : 94.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.57 % 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: -4.02 (0.15), residues: 2343 helix: -2.07 (0.24), residues: 345 sheet: -1.50 (0.21), residues: 504 loop : -3.46 (0.14), residues: 1494 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG K 54 TYR 0.035 0.002 TYR I 173 PHE 0.020 0.002 PHE I 320 TRP 0.054 0.002 TRP A 596 HIS 0.005 0.001 HIS G 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00431 / 0.20 (20371) covalent geometry : angle 0.94057 / 0.45 (27674) SS BOND : bond 0.00314 / 0.21 ( 30) SS BOND : angle 1.64819 / 0.99 ( 60) hydrogen bonds : bond 0.04861 / 3.23 ( 451) hydrogen bonds : angle 6.97049 / 4.96 ( 1239) link_ALPHA1-3 : bond 0.00927 / 0.45 ( 3) link_ALPHA1-3 : angle 2.64383 / 1.45 ( 9) link_ALPHA1-6 : bond 0.00736 / 0.38 ( 2) link_ALPHA1-6 : angle 1.21848 / 0.63 ( 6) link_BETA1-4 : bond 0.00988 / 0.76 ( 42) link_BETA1-4 : angle 3.60529 / 2.80 ( 126) link_NAG-ASN : bond 0.01066 / 0.73 ( 51) link_NAG-ASN : angle 4.28949 / 2.94 ( 153) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 667 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 660 time to evaluate : 0.655 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 522 PHE cc_start: 0.9028 (t80) cc_final: 0.8638 (t80) REVERT: A 523 LEU cc_start: 0.9426 (mt) cc_final: 0.9049 (mt) REVERT: A 543 ASN cc_start: 0.9202 (t0) cc_final: 0.8472 (t0) REVERT: A 588 ARG cc_start: 0.9004 (ttt90) cc_final: 0.8606 (tpt-90) REVERT: A 607 ASN cc_start: 0.8177 (t0) cc_final: 0.7924 (t0) REVERT: A 620 SER cc_start: 0.8616 (p) cc_final: 0.8134 (p) REVERT: B 96 TRP cc_start: 0.9417 (m100) cc_final: 0.8980 (m100) REVERT: B 97 LYS cc_start: 0.9099 (mmtp) cc_final: 0.8618 (mmmm) REVERT: B 106 GLU cc_start: 0.8870 (pt0) cc_final: 0.8469 (tm-30) REVERT: B 217 TYR cc_start: 0.7292 (m-10) cc_final: 0.6886 (m-10) REVERT: B 265 LEU cc_start: 0.9134 (mt) cc_final: 0.8825 (mm) REVERT: B 279 ASN cc_start: 0.8460 (t0) cc_final: 0.8047 (t0) REVERT: B 474 ASP cc_start: 0.8417 (t70) cc_final: 0.7791 (t70) REVERT: B 475 MET cc_start: 0.7981 (mmm) cc_final: 0.7573 (mmm) REVERT: B 485 LYS cc_start: 0.8830 (ptpt) cc_final: 0.8423 (ptpt) REVERT: B 492 GLU cc_start: 0.8737 (tp30) cc_final: 0.8309 (tm-30) REVERT: C 530 MET cc_start: 0.8302 (ttm) cc_final: 0.7738 (ptm) REVERT: C 588 ARG cc_start: 0.8930 (ttt90) cc_final: 0.8502 (tpt-90) REVERT: C 607 ASN cc_start: 0.8266 (t0) cc_final: 0.7844 (t0) REVERT: C 654 GLU cc_start: 0.8380 (pt0) cc_final: 0.8095 (pt0) REVERT: C 658 GLN cc_start: 0.8759 (tp-100) cc_final: 0.8196 (tp40) REVERT: D 13 LYS cc_start: 0.7805 (mtpt) cc_final: 0.7596 (mtpt) REVERT: D 47 GLU cc_start: 0.7738 (tp30) cc_final: 0.7533 (tp30) REVERT: D 48 TRP cc_start: 0.8864 (t60) cc_final: 0.8196 (t60) REVERT: D 58 THR cc_start: 0.9019 (p) cc_final: 0.8710 (m) REVERT: D 61 ASN cc_start: 0.8394 (t0) cc_final: 0.7903 (t0) REVERT: D 100 ASN cc_start: 0.8428 (p0) cc_final: 0.8174 (p0) REVERT: E 92 ASP cc_start: 0.9077 (t0) cc_final: 0.8794 (m-30) REVERT: E 104 LEU cc_start: 0.8446 (pt) cc_final: 0.8117 (pp) REVERT: F 522 PHE cc_start: 0.8882 (t80) cc_final: 0.8626 (t80) REVERT: F 543 ASN cc_start: 0.8948 (t0) cc_final: 0.8254 (t0) REVERT: F 638 TYR cc_start: 0.8320 (m-10) cc_final: 0.8101 (m-10) REVERT: G 82 GLN cc_start: 0.8932 (mm-40) cc_final: 0.8124 (mp10) REVERT: G 92 GLU cc_start: 0.7651 (pp20) cc_final: 0.7104 (pp20) REVERT: G 94 ASN cc_start: 0.8781 (t0) cc_final: 0.8187 (t0) REVERT: G 156 GLN cc_start: 0.7559 (OUTLIER) cc_final: 0.7155 (pm20) REVERT: G 164 GLU cc_start: 0.9131 (pp20) cc_final: 0.8895 (pp20) REVERT: G 211 GLU cc_start: 0.8325 (tm-30) cc_final: 0.8072 (tm-30) REVERT: G 226 LEU cc_start: 0.8724 (pp) cc_final: 0.8341 (pp) REVERT: H 57 ASN cc_start: 0.7889 (t0) cc_final: 0.7677 (t0) REVERT: H 91 TYR cc_start: 0.8599 (m-10) cc_final: 0.8028 (m-10) REVERT: I 50 THR cc_start: 0.9465 (p) cc_final: 0.9185 (p) REVERT: I 97 LYS cc_start: 0.9030 (mmtp) cc_final: 0.8655 (mmmm) REVERT: I 106 GLU cc_start: 0.8568 (tt0) cc_final: 0.8132 (tm-30) REVERT: I 114 GLN cc_start: 0.9234 (tm-30) cc_final: 0.9007 (tm-30) REVERT: I 180 ASP cc_start: 0.8146 (m-30) cc_final: 0.7940 (m-30) REVERT: I 320 PHE cc_start: 0.8066 (t80) cc_final: 0.7705 (t80) REVERT: I 340 GLU cc_start: 0.9143 (tt0) cc_final: 0.8602 (tp30) REVERT: I 368 ASP cc_start: 0.8482 (t70) cc_final: 0.8046 (t0) REVERT: I 423 ILE cc_start: 0.9132 (pt) cc_final: 0.8837 (pt) REVERT: I 434 MET cc_start: 0.8842 (ttm) cc_final: 0.8295 (ttm) REVERT: I 480 ARG cc_start: 0.8784 (mtt180) cc_final: 0.8560 (mtm180) REVERT: I 499 THR cc_start: 0.8860 (t) cc_final: 0.8624 (t) REVERT: J 13 LYS cc_start: 0.7526 (mtmt) cc_final: 0.7066 (mtmt) REVERT: J 57 ASN cc_start: 0.7582 (t0) cc_final: 0.7350 (t0) REVERT: J 61 ASN cc_start: 0.8079 (t0) cc_final: 0.7790 (t0) REVERT: K 92 ASP cc_start: 0.9061 (t0) cc_final: 0.8743 (m-30) REVERT: L 39 LEU cc_start: 0.5878 (tp) cc_final: 0.5629 (tp) REVERT: L 49 TYR cc_start: 0.6908 (t80) cc_final: 0.6590 (t80) REVERT: L 92 ASP cc_start: 0.9058 (t0) cc_final: 0.8719 (m-30) outliers start: 7 outliers final: 3 residues processed: 662 average time/residue: 0.1364 time to fit residues: 142.6671 Evaluate side-chains 526 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 522 time to evaluate : 0.769 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 97 optimal weight: 1.9990 chunk 51 optimal weight: 4.9990 chunk 111 optimal weight: 3.9990 chunk 80 optimal weight: 0.0670 chunk 59 optimal weight: 6.9990 chunk 183 optimal weight: 0.9990 chunk 148 optimal weight: 0.8980 chunk 81 optimal weight: 1.9990 chunk 168 optimal weight: 7.9990 chunk 218 optimal weight: 2.9990 chunk 199 optimal weight: 3.9990 overall best weight: 1.1924 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 195 ASN D 77 ASN G 99 ASN G 156 GLN H 78 GLN ** I 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.129700 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.104968 restraints weight = 40447.314| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.108276 restraints weight = 23888.352| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.110595 restraints weight = 16410.359| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.112190 restraints weight = 12462.226| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.113267 restraints weight = 10199.229| |-----------------------------------------------------------------------------| r_work (final): 0.3303 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7993 moved from start: 0.4313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 20499 Z= 0.155 Angle : 0.963 13.779 28028 Z= 0.437 Chirality : 0.055 0.471 3391 Planarity : 0.005 0.063 3389 Dihedral : 7.079 39.601 2544 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 10.87 Ramachandran Plot: Outliers : 0.09 % Allowed : 12.42 % Favored : 87.49 % Rotamer: Outliers : 0.14 % Allowed : 3.30 % Favored : 96.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.98 % Twisted General : 0.53 % 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: -3.88 (0.16), residues: 2343 helix: -1.85 (0.24), residues: 351 sheet: -1.47 (0.23), residues: 474 loop : -3.35 (0.14), residues: 1518 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG I 429 TYR 0.026 0.002 TYR G 173 PHE 0.016 0.001 PHE B 53 TRP 0.024 0.002 TRP A 596 HIS 0.006 0.001 HIS I 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00341 / 0.15 (20371) covalent geometry : angle 0.88957 / 0.42 (27674) SS BOND : bond 0.00516 / 0.37 ( 30) SS BOND : angle 1.83581 / 1.09 ( 60) hydrogen bonds : bond 0.04050 / 2.74 ( 451) hydrogen bonds : angle 6.46980 / 4.60 ( 1239) link_ALPHA1-3 : bond 0.00708 / 0.35 ( 3) link_ALPHA1-3 : angle 2.65731 / 1.45 ( 9) link_ALPHA1-6 : bond 0.00641 / 0.33 ( 2) link_ALPHA1-6 : angle 1.28983 / 0.64 ( 6) link_BETA1-4 : bond 0.00938 / 0.72 ( 42) link_BETA1-4 : angle 3.45115 / 2.65 ( 126) link_NAG-ASN : bond 0.00688 / 0.54 ( 51) link_NAG-ASN : angle 3.91224 / 2.70 ( 153) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 659 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 656 time to evaluate : 0.783 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 522 PHE cc_start: 0.8948 (t80) cc_final: 0.8570 (t80) REVERT: A 523 LEU cc_start: 0.9406 (mt) cc_final: 0.9014 (mt) REVERT: A 535 MET cc_start: 0.8929 (mmt) cc_final: 0.8669 (mmp) REVERT: A 543 ASN cc_start: 0.9240 (t0) cc_final: 0.8454 (t0) REVERT: A 588 ARG cc_start: 0.8994 (ttt90) cc_final: 0.8631 (tpt-90) REVERT: A 595 ILE cc_start: 0.9395 (tp) cc_final: 0.9153 (tp) REVERT: A 620 SER cc_start: 0.8487 (p) cc_final: 0.7911 (p) REVERT: A 630 GLN cc_start: 0.8938 (mp10) cc_final: 0.8699 (mp10) REVERT: B 47 ASP cc_start: 0.8361 (t0) cc_final: 0.8082 (t0) REVERT: B 92 GLU cc_start: 0.5586 (pp20) cc_final: 0.5051 (pp20) REVERT: B 106 GLU cc_start: 0.8596 (pt0) cc_final: 0.8256 (tm-30) REVERT: B 149 ASN cc_start: 0.9294 (p0) cc_final: 0.7754 (p0) REVERT: B 195 ASN cc_start: 0.8014 (OUTLIER) cc_final: 0.7742 (t160) REVERT: B 217 TYR cc_start: 0.7299 (m-10) cc_final: 0.7057 (m-10) REVERT: B 265 LEU cc_start: 0.9102 (mt) cc_final: 0.8833 (mm) REVERT: B 270 VAL cc_start: 0.9558 (m) cc_final: 0.9279 (t) REVERT: B 279 ASN cc_start: 0.8705 (t0) cc_final: 0.8261 (t0) REVERT: B 474 ASP cc_start: 0.8498 (t70) cc_final: 0.7774 (t70) REVERT: B 485 LYS cc_start: 0.8832 (ptpt) cc_final: 0.8448 (ptpt) REVERT: B 492 GLU cc_start: 0.8685 (tp30) cc_final: 0.8336 (tt0) REVERT: C 530 MET cc_start: 0.8239 (ttm) cc_final: 0.7701 (ptm) REVERT: C 588 ARG cc_start: 0.9104 (ttt90) cc_final: 0.8901 (tpt-90) REVERT: C 607 ASN cc_start: 0.8167 (t0) cc_final: 0.7748 (t0) REVERT: C 658 GLN cc_start: 0.8840 (tp-100) cc_final: 0.8185 (tp40) REVERT: D 22 CYS cc_start: 0.7546 (t) cc_final: 0.7267 (t) REVERT: D 48 TRP cc_start: 0.8738 (t60) cc_final: 0.8218 (t60) REVERT: D 58 THR cc_start: 0.8878 (p) cc_final: 0.8533 (m) REVERT: D 61 ASN cc_start: 0.8405 (t0) cc_final: 0.7929 (t0) REVERT: D 100 ASN cc_start: 0.8308 (p0) cc_final: 0.7918 (p0) REVERT: E 31 PHE cc_start: 0.6471 (t80) cc_final: 0.5798 (t80) REVERT: E 92 ASP cc_start: 0.9090 (t0) cc_final: 0.8737 (m-30) REVERT: E 104 LEU cc_start: 0.8342 (pt) cc_final: 0.8059 (pp) REVERT: F 522 PHE cc_start: 0.8972 (t80) cc_final: 0.8497 (t80) REVERT: F 523 LEU cc_start: 0.9341 (mt) cc_final: 0.8954 (mt) REVERT: F 543 ASN cc_start: 0.8990 (t0) cc_final: 0.8338 (t0) REVERT: F 588 ARG cc_start: 0.8213 (ttt180) cc_final: 0.7898 (tpt-90) REVERT: F 607 ASN cc_start: 0.7781 (t0) cc_final: 0.7546 (t0) REVERT: F 630 GLN cc_start: 0.8728 (mp10) cc_final: 0.8256 (mp10) REVERT: F 638 TYR cc_start: 0.8469 (m-10) cc_final: 0.8041 (m-10) REVERT: G 82 GLN cc_start: 0.8879 (mm-40) cc_final: 0.8118 (mp10) REVERT: G 92 GLU cc_start: 0.7503 (pp20) cc_final: 0.6975 (pp20) REVERT: G 94 ASN cc_start: 0.8776 (t0) cc_final: 0.8221 (t0) REVERT: G 156 GLN cc_start: 0.7792 (OUTLIER) cc_final: 0.7393 (pm20) REVERT: G 164 GLU cc_start: 0.9128 (pp20) cc_final: 0.8876 (pp20) REVERT: G 211 GLU cc_start: 0.8278 (tm-30) cc_final: 0.8032 (tm-30) REVERT: G 226 LEU cc_start: 0.8685 (pp) cc_final: 0.8285 (pp) REVERT: G 477 ASP cc_start: 0.9492 (m-30) cc_final: 0.9259 (m-30) REVERT: G 499 THR cc_start: 0.8462 (t) cc_final: 0.8241 (t) REVERT: H 57 ASN cc_start: 0.7899 (t0) cc_final: 0.7574 (t0) REVERT: H 61 ASN cc_start: 0.8596 (t0) cc_final: 0.8389 (t0) REVERT: H 78 GLN cc_start: 0.7305 (mp10) cc_final: 0.6745 (mp10) REVERT: H 91 TYR cc_start: 0.8695 (m-10) cc_final: 0.8385 (m-10) REVERT: I 50 THR cc_start: 0.9472 (p) cc_final: 0.9195 (p) REVERT: I 97 LYS cc_start: 0.8982 (mmtp) cc_final: 0.8576 (mmmm) REVERT: I 106 GLU cc_start: 0.8716 (tt0) cc_final: 0.8265 (tm-30) REVERT: I 114 GLN cc_start: 0.9298 (tm-30) cc_final: 0.8900 (tm-30) REVERT: I 150 MET cc_start: 0.8773 (mpp) cc_final: 0.7398 (mpp) REVERT: I 156 GLN cc_start: 0.8678 (pp30) cc_final: 0.7603 (pm20) REVERT: I 307 ILE cc_start: 0.8866 (mm) cc_final: 0.8591 (tp) REVERT: I 328 MET cc_start: 0.7575 (ptm) cc_final: 0.7028 (ptp) REVERT: I 340 GLU cc_start: 0.9158 (tt0) cc_final: 0.8592 (tp30) REVERT: I 368 ASP cc_start: 0.8370 (t70) cc_final: 0.8086 (t0) REVERT: I 370 GLU cc_start: 0.8239 (pm20) cc_final: 0.7653 (pm20) REVERT: I 434 MET cc_start: 0.8823 (ttm) cc_final: 0.8477 (ttm) REVERT: I 499 THR cc_start: 0.8803 (t) cc_final: 0.8586 (t) REVERT: J 13 LYS cc_start: 0.7473 (mtmt) cc_final: 0.7068 (mtmt) REVERT: J 40 GLN cc_start: 0.8562 (tm-30) cc_final: 0.8091 (tm-30) REVERT: J 57 ASN cc_start: 0.7531 (t0) cc_final: 0.7268 (t0) REVERT: J 61 ASN cc_start: 0.8240 (t0) cc_final: 0.7692 (t0) REVERT: J 70 ILE cc_start: 0.9201 (mp) cc_final: 0.8933 (tp) REVERT: K 60 ASP cc_start: 0.8021 (t0) cc_final: 0.7377 (t0) REVERT: K 92 ASP cc_start: 0.9061 (t0) cc_final: 0.8713 (m-30) REVERT: L 22 SER cc_start: 0.9043 (m) cc_final: 0.8697 (m) REVERT: L 39 LEU cc_start: 0.5928 (tp) cc_final: 0.5659 (tp) REVERT: L 92 ASP cc_start: 0.9089 (t0) cc_final: 0.8612 (m-30) outliers start: 3 outliers final: 0 residues processed: 659 average time/residue: 0.1390 time to fit residues: 144.0680 Evaluate side-chains 508 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 506 time to evaluate : 0.853 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 57 optimal weight: 0.5980 chunk 100 optimal weight: 0.9990 chunk 178 optimal weight: 2.9990 chunk 71 optimal weight: 6.9990 chunk 14 optimal weight: 6.9990 chunk 28 optimal weight: 4.9990 chunk 191 optimal weight: 1.9990 chunk 155 optimal weight: 0.8980 chunk 10 optimal weight: 1.9990 chunk 146 optimal weight: 20.0000 chunk 42 optimal weight: 2.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 616 ASN A 652 GLN B 99 ASN ** B 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 99 ASN G 156 GLN G 276 ASN ** G 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 103 GLN I 137 ASN I 156 GLN I 478 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.128498 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.103681 restraints weight = 40438.856| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.106952 restraints weight = 23997.275| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.109256 restraints weight = 16569.231| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.110828 restraints weight = 12623.313| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.111978 restraints weight = 10368.321| |-----------------------------------------------------------------------------| r_work (final): 0.3288 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8014 moved from start: 0.4648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 20499 Z= 0.155 Angle : 0.927 13.259 28028 Z= 0.422 Chirality : 0.054 0.450 3391 Planarity : 0.005 0.069 3389 Dihedral : 6.858 40.766 2544 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 10.93 Ramachandran Plot: Outliers : 0.09 % Allowed : 12.80 % Favored : 87.11 % Rotamer: Outliers : 0.19 % Allowed : 3.54 % Favored : 96.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.35 % 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: -3.78 (0.16), residues: 2343 helix: -1.64 (0.25), residues: 354 sheet: -1.50 (0.23), residues: 486 loop : -3.30 (0.14), residues: 1503 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 617 TYR 0.065 0.002 TYR B 173 PHE 0.020 0.001 PHE I 320 TRP 0.021 0.002 TRP E 35 HIS 0.005 0.001 HIS G 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00345 / 0.15 (20371) covalent geometry : angle 0.85914 / 0.41 (27674) SS BOND : bond 0.00509 / 0.34 ( 30) SS BOND : angle 1.85102 / 1.15 ( 60) hydrogen bonds : bond 0.03892 / 2.64 ( 451) hydrogen bonds : angle 6.27092 / 4.50 ( 1239) link_ALPHA1-3 : bond 0.00731 / 0.36 ( 3) link_ALPHA1-3 : angle 2.58914 / 1.41 ( 9) link_ALPHA1-6 : bond 0.00682 / 0.35 ( 2) link_ALPHA1-6 : angle 1.29658 / 0.65 ( 6) link_BETA1-4 : bond 0.00874 / 0.67 ( 42) link_BETA1-4 : angle 3.23021 / 2.50 ( 126) link_NAG-ASN : bond 0.00641 / 0.50 ( 51) link_NAG-ASN : angle 3.68669 / 2.55 ( 153) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 652 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 648 time to evaluate : 0.761 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 522 PHE cc_start: 0.8986 (t80) cc_final: 0.8783 (t80) REVERT: A 523 LEU cc_start: 0.9360 (mt) cc_final: 0.9024 (mt) REVERT: A 535 MET cc_start: 0.8983 (mmt) cc_final: 0.8766 (mmp) REVERT: A 543 ASN cc_start: 0.9301 (t0) cc_final: 0.8596 (t0) REVERT: A 588 ARG cc_start: 0.8997 (ttt90) cc_final: 0.8525 (tpt-90) REVERT: A 607 ASN cc_start: 0.8149 (t0) cc_final: 0.7906 (t0) REVERT: A 620 SER cc_start: 0.8748 (p) cc_final: 0.8162 (p) REVERT: A 630 GLN cc_start: 0.8922 (mp10) cc_final: 0.8337 (mp10) REVERT: B 104 MET cc_start: 0.8580 (ttp) cc_final: 0.7948 (ttp) REVERT: B 106 GLU cc_start: 0.8590 (pt0) cc_final: 0.8344 (tm-30) REVERT: B 217 TYR cc_start: 0.7643 (m-10) cc_final: 0.7261 (m-10) REVERT: B 265 LEU cc_start: 0.9074 (mt) cc_final: 0.8815 (mm) REVERT: B 270 VAL cc_start: 0.9522 (m) cc_final: 0.9289 (t) REVERT: B 279 ASN cc_start: 0.8796 (t0) cc_final: 0.8359 (t0) REVERT: B 474 ASP cc_start: 0.8490 (t70) cc_final: 0.7815 (t70) REVERT: B 475 MET cc_start: 0.7843 (mmm) cc_final: 0.6917 (mmm) REVERT: B 479 TRP cc_start: 0.8928 (m-90) cc_final: 0.8433 (m-90) REVERT: B 485 LYS cc_start: 0.8771 (ptpt) cc_final: 0.8381 (ptpt) REVERT: B 492 GLU cc_start: 0.8714 (tp30) cc_final: 0.8239 (tt0) REVERT: C 530 MET cc_start: 0.8323 (ttm) cc_final: 0.7733 (ptm) REVERT: C 588 ARG cc_start: 0.9285 (ttt90) cc_final: 0.9024 (tpt-90) REVERT: C 607 ASN cc_start: 0.8194 (t0) cc_final: 0.7815 (t0) REVERT: C 630 GLN cc_start: 0.9111 (mp10) cc_final: 0.8904 (mp10) REVERT: C 658 GLN cc_start: 0.8711 (tp-100) cc_final: 0.7999 (tp40) REVERT: D 48 TRP cc_start: 0.8715 (t60) cc_final: 0.8379 (t60) REVERT: D 61 ASN cc_start: 0.8300 (t0) cc_final: 0.8001 (t0) REVERT: D 100 ASN cc_start: 0.8789 (p0) cc_final: 0.8491 (p0) REVERT: E 31 PHE cc_start: 0.6486 (t80) cc_final: 0.5752 (t80) REVERT: E 92 ASP cc_start: 0.9163 (t0) cc_final: 0.8794 (m-30) REVERT: E 104 LEU cc_start: 0.8328 (pt) cc_final: 0.8105 (pp) REVERT: F 522 PHE cc_start: 0.9046 (t80) cc_final: 0.8632 (t80) REVERT: F 523 LEU cc_start: 0.9340 (mt) cc_final: 0.9021 (mt) REVERT: F 543 ASN cc_start: 0.9061 (t0) cc_final: 0.8458 (t0) REVERT: F 607 ASN cc_start: 0.7753 (t0) cc_final: 0.7460 (t0) REVERT: F 630 GLN cc_start: 0.8747 (mp10) cc_final: 0.8396 (mp10) REVERT: F 638 TYR cc_start: 0.8417 (m-10) cc_final: 0.8183 (m-10) REVERT: F 664 ASP cc_start: 0.6825 (p0) cc_final: 0.6607 (p0) REVERT: G 82 GLN cc_start: 0.8847 (mm-40) cc_final: 0.8128 (mp10) REVERT: G 92 GLU cc_start: 0.7600 (pp20) cc_final: 0.7204 (pp20) REVERT: G 94 ASN cc_start: 0.8809 (t0) cc_final: 0.8269 (t0) REVERT: G 156 GLN cc_start: 0.7726 (OUTLIER) cc_final: 0.7146 (pm20) REVERT: G 164 GLU cc_start: 0.9115 (pp20) cc_final: 0.8873 (pp20) REVERT: G 211 GLU cc_start: 0.8188 (tm-30) cc_final: 0.7921 (tm-30) REVERT: G 276 ASN cc_start: 0.8754 (OUTLIER) cc_final: 0.8263 (t0) REVERT: G 363 GLN cc_start: 0.8989 (pp30) cc_final: 0.8723 (pp30) REVERT: G 368 ASP cc_start: 0.8400 (t70) cc_final: 0.8145 (t70) REVERT: G 475 MET cc_start: 0.8351 (tpp) cc_final: 0.7478 (tpp) REVERT: G 477 ASP cc_start: 0.9514 (m-30) cc_final: 0.9290 (m-30) REVERT: G 499 THR cc_start: 0.8445 (t) cc_final: 0.8186 (t) REVERT: H 47 GLU cc_start: 0.7921 (tp30) cc_final: 0.7576 (tp30) REVERT: H 57 ASN cc_start: 0.8001 (t0) cc_final: 0.7767 (t0) REVERT: H 91 TYR cc_start: 0.8772 (m-10) cc_final: 0.8420 (m-10) REVERT: I 50 THR cc_start: 0.9445 (p) cc_final: 0.9179 (p) REVERT: I 97 LYS cc_start: 0.8969 (mmtp) cc_final: 0.8547 (mmmm) REVERT: I 114 GLN cc_start: 0.9398 (tm-30) cc_final: 0.8991 (tm-30) REVERT: I 150 MET cc_start: 0.8786 (mpp) cc_final: 0.8178 (mpp) REVERT: I 156 GLN cc_start: 0.8681 (OUTLIER) cc_final: 0.7677 (pm20) REVERT: I 195 ASN cc_start: 0.7730 (t0) cc_final: 0.7428 (t0) REVERT: I 307 ILE cc_start: 0.8892 (mm) cc_final: 0.8585 (tp) REVERT: I 320 PHE cc_start: 0.8020 (t80) cc_final: 0.7593 (t80) REVERT: I 340 GLU cc_start: 0.9167 (tt0) cc_final: 0.8513 (tp30) REVERT: I 368 ASP cc_start: 0.8351 (t70) cc_final: 0.7866 (t0) REVERT: I 370 GLU cc_start: 0.8311 (pm20) cc_final: 0.7860 (pm20) REVERT: I 426 MET cc_start: 0.8823 (ppp) cc_final: 0.8450 (ppp) REVERT: I 434 MET cc_start: 0.8871 (ttm) cc_final: 0.8299 (ttm) REVERT: I 482 GLU cc_start: 0.7182 (tm-30) cc_final: 0.6922 (tm-30) REVERT: J 13 LYS cc_start: 0.7390 (mtmt) cc_final: 0.7175 (mtmt) REVERT: J 40 GLN cc_start: 0.8645 (tm-30) cc_final: 0.8196 (tm-30) REVERT: J 57 ASN cc_start: 0.7626 (t0) cc_final: 0.7370 (t0) REVERT: J 61 ASN cc_start: 0.8229 (t0) cc_final: 0.7707 (t0) REVERT: K 60 ASP cc_start: 0.8121 (t0) cc_final: 0.7485 (t0) REVERT: K 92 ASP cc_start: 0.9059 (t0) cc_final: 0.8591 (m-30) REVERT: L 22 SER cc_start: 0.9064 (m) cc_final: 0.8788 (m) REVERT: L 39 LEU cc_start: 0.5980 (tp) cc_final: 0.5729 (tp) outliers start: 4 outliers final: 0 residues processed: 649 average time/residue: 0.1330 time to fit residues: 136.4759 Evaluate side-chains 518 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 515 time to evaluate : 0.749 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 187 optimal weight: 4.9990 chunk 41 optimal weight: 4.9990 chunk 35 optimal weight: 6.9990 chunk 19 optimal weight: 0.0470 chunk 17 optimal weight: 0.0020 chunk 91 optimal weight: 4.9990 chunk 164 optimal weight: 0.8980 chunk 220 optimal weight: 0.6980 chunk 195 optimal weight: 4.9990 chunk 192 optimal weight: 8.9990 chunk 171 optimal weight: 0.2980 overall best weight: 0.3886 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 616 ASN A 652 GLN B 156 GLN D 77 ASN E 6 GLN G 99 ASN G 258 GLN ** G 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 276 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.132686 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.107950 restraints weight = 39491.001| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.111280 restraints weight = 23451.202| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.113611 restraints weight = 16104.664| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.115230 restraints weight = 12206.212| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.116413 restraints weight = 9952.873| |-----------------------------------------------------------------------------| r_work (final): 0.3345 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7969 moved from start: 0.4962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 20499 Z= 0.133 Angle : 0.900 12.604 28028 Z= 0.409 Chirality : 0.053 0.452 3391 Planarity : 0.005 0.073 3389 Dihedral : 6.537 39.378 2544 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.09 % Allowed : 12.08 % Favored : 87.84 % Rotamer: Outliers : 0.05 % Allowed : 2.78 % Favored : 97.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.98 % Twisted General : 0.26 % 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: -3.63 (0.16), residues: 2343 helix: -1.45 (0.26), residues: 342 sheet: -1.43 (0.23), residues: 486 loop : -3.19 (0.15), residues: 1515 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 151 TYR 0.019 0.001 TYR G 173 PHE 0.017 0.001 PHE B 53 TRP 0.029 0.002 TRP B 427 HIS 0.005 0.001 HIS B 249 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.13 (20371) covalent geometry : angle 0.83927 / 0.39 (27674) SS BOND : bond 0.00449 / 0.31 ( 30) SS BOND : angle 1.83564 / 1.09 ( 60) hydrogen bonds : bond 0.03394 / 2.30 ( 451) hydrogen bonds : angle 5.95905 / 4.28 ( 1239) link_ALPHA1-3 : bond 0.00655 / 0.32 ( 3) link_ALPHA1-3 : angle 2.59013 / 1.42 ( 9) link_ALPHA1-6 : bond 0.00677 / 0.34 ( 2) link_ALPHA1-6 : angle 1.32337 / 0.64 ( 6) link_BETA1-4 : bond 0.00880 / 0.67 ( 42) link_BETA1-4 : angle 3.03453 / 2.32 ( 126) link_NAG-ASN : bond 0.00622 / 0.48 ( 51) link_NAG-ASN : angle 3.39284 / 2.34 ( 153) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 676 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 675 time to evaluate : 0.754 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 522 PHE cc_start: 0.8927 (t80) cc_final: 0.8654 (t80) REVERT: A 523 LEU cc_start: 0.9253 (mt) cc_final: 0.8900 (mt) REVERT: A 530 MET cc_start: 0.9294 (mmm) cc_final: 0.9065 (tpp) REVERT: A 535 MET cc_start: 0.8832 (mmt) cc_final: 0.8600 (mmp) REVERT: A 543 ASN cc_start: 0.9109 (t0) cc_final: 0.8284 (t0) REVERT: A 620 SER cc_start: 0.8754 (p) cc_final: 0.8118 (p) REVERT: A 630 GLN cc_start: 0.8824 (mp10) cc_final: 0.8543 (mp10) REVERT: B 96 TRP cc_start: 0.9373 (m100) cc_final: 0.8692 (m100) REVERT: B 104 MET cc_start: 0.8508 (ttp) cc_final: 0.8037 (ttp) REVERT: B 166 ARG cc_start: 0.7634 (ptm160) cc_final: 0.7203 (ttm-80) REVERT: B 167 ASP cc_start: 0.9512 (p0) cc_final: 0.9216 (p0) REVERT: B 173 TYR cc_start: 0.6965 (m-80) cc_final: 0.6718 (m-80) REVERT: B 265 LEU cc_start: 0.8993 (mt) cc_final: 0.8764 (mm) REVERT: B 270 VAL cc_start: 0.9480 (m) cc_final: 0.9275 (t) REVERT: B 279 ASN cc_start: 0.8806 (t0) cc_final: 0.8482 (t0) REVERT: B 368 ASP cc_start: 0.7813 (t70) cc_final: 0.7576 (t70) REVERT: B 426 MET cc_start: 0.8981 (ppp) cc_final: 0.8614 (tmm) REVERT: B 474 ASP cc_start: 0.8437 (t70) cc_final: 0.7871 (t0) REVERT: B 479 TRP cc_start: 0.8632 (m-90) cc_final: 0.8349 (m-90) REVERT: B 485 LYS cc_start: 0.8639 (ptpt) cc_final: 0.8309 (ptpt) REVERT: B 492 GLU cc_start: 0.8674 (tp30) cc_final: 0.8129 (tp30) REVERT: C 528 SER cc_start: 0.9274 (m) cc_final: 0.8935 (p) REVERT: C 607 ASN cc_start: 0.8208 (t0) cc_final: 0.7827 (t0) REVERT: C 658 GLN cc_start: 0.8600 (tp-100) cc_final: 0.7860 (tp40) REVERT: D 40 GLN cc_start: 0.8644 (tm-30) cc_final: 0.8154 (tm-30) REVERT: D 52 ILE cc_start: 0.7202 (tp) cc_final: 0.6666 (tp) REVERT: D 58 THR cc_start: 0.8767 (m) cc_final: 0.8549 (m) REVERT: D 61 ASN cc_start: 0.8389 (t0) cc_final: 0.8110 (t0) REVERT: D 67 ARG cc_start: 0.8299 (mmm160) cc_final: 0.7949 (mmm160) REVERT: D 70 ILE cc_start: 0.9327 (mp) cc_final: 0.8517 (mm) REVERT: E 31 PHE cc_start: 0.6627 (t80) cc_final: 0.5965 (t80) REVERT: E 85 ASP cc_start: 0.7822 (m-30) cc_final: 0.7598 (m-30) REVERT: E 104 LEU cc_start: 0.8193 (pt) cc_final: 0.7912 (pp) REVERT: F 522 PHE cc_start: 0.9026 (t80) cc_final: 0.8477 (t80) REVERT: F 523 LEU cc_start: 0.9252 (mt) cc_final: 0.8973 (mt) REVERT: F 528 SER cc_start: 0.8975 (m) cc_final: 0.8714 (p) REVERT: F 543 ASN cc_start: 0.9063 (t0) cc_final: 0.8459 (t0) REVERT: F 607 ASN cc_start: 0.7815 (t0) cc_final: 0.7548 (t0) REVERT: F 624 ASP cc_start: 0.8089 (m-30) cc_final: 0.7878 (m-30) REVERT: F 630 GLN cc_start: 0.8740 (mp10) cc_final: 0.8428 (mp10) REVERT: F 638 TYR cc_start: 0.8283 (m-10) cc_final: 0.7918 (m-10) REVERT: F 658 GLN cc_start: 0.8896 (mt0) cc_final: 0.8669 (mt0) REVERT: F 664 ASP cc_start: 0.6961 (p0) cc_final: 0.6679 (p0) REVERT: G 82 GLN cc_start: 0.8822 (mm-40) cc_final: 0.8183 (mp10) REVERT: G 92 GLU cc_start: 0.7678 (pp20) cc_final: 0.7333 (pp20) REVERT: G 94 ASN cc_start: 0.8658 (t0) cc_final: 0.8070 (t0) REVERT: G 164 GLU cc_start: 0.9063 (pp20) cc_final: 0.8855 (pp20) REVERT: G 195 ASN cc_start: 0.7929 (t0) cc_final: 0.7705 (t0) REVERT: G 211 GLU cc_start: 0.8194 (tm-30) cc_final: 0.7906 (tm-30) REVERT: G 243 SER cc_start: 0.8292 (m) cc_final: 0.7670 (t) REVERT: G 244 THR cc_start: 0.9488 (t) cc_final: 0.9282 (t) REVERT: G 350 ARG cc_start: 0.8336 (tpt-90) cc_final: 0.8096 (tpt-90) REVERT: G 363 GLN cc_start: 0.9043 (pp30) cc_final: 0.8743 (pp30) REVERT: G 368 ASP cc_start: 0.8029 (t70) cc_final: 0.7829 (t70) REVERT: G 475 MET cc_start: 0.8020 (tpp) cc_final: 0.7430 (tpp) REVERT: G 499 THR cc_start: 0.8389 (t) cc_final: 0.8102 (t) REVERT: H 40 GLN cc_start: 0.8587 (tm-30) cc_final: 0.8269 (tm-30) REVERT: H 47 GLU cc_start: 0.8238 (tp30) cc_final: 0.7963 (tp30) REVERT: H 48 TRP cc_start: 0.9189 (t60) cc_final: 0.8464 (t60) REVERT: H 67 ARG cc_start: 0.7973 (mmm160) cc_final: 0.7209 (mmm160) REVERT: H 78 GLN cc_start: 0.7681 (mp-120) cc_final: 0.7082 (mp10) REVERT: I 50 THR cc_start: 0.9422 (p) cc_final: 0.9174 (p) REVERT: I 106 GLU cc_start: 0.8996 (tt0) cc_final: 0.8777 (tt0) REVERT: I 114 GLN cc_start: 0.9395 (tm-30) cc_final: 0.9180 (tm-30) REVERT: I 149 ASN cc_start: 0.9309 (t0) cc_final: 0.9101 (m-40) REVERT: I 150 MET cc_start: 0.8740 (mpp) cc_final: 0.8198 (mpp) REVERT: I 195 ASN cc_start: 0.7810 (t0) cc_final: 0.7470 (t0) REVERT: I 205 CYS cc_start: 0.6855 (t) cc_final: 0.6340 (t) REVERT: I 340 GLU cc_start: 0.9132 (tt0) cc_final: 0.8654 (tp30) REVERT: I 368 ASP cc_start: 0.8288 (t70) cc_final: 0.7731 (t70) REVERT: I 370 GLU cc_start: 0.8375 (pm20) cc_final: 0.7420 (pm20) REVERT: I 434 MET cc_start: 0.8786 (ttm) cc_final: 0.8229 (ttm) REVERT: I 482 GLU cc_start: 0.7091 (tm-30) cc_final: 0.6844 (tm-30) REVERT: J 40 GLN cc_start: 0.8723 (tm-30) cc_final: 0.8345 (tm-30) REVERT: J 61 ASN cc_start: 0.8389 (t0) cc_final: 0.7868 (t0) REVERT: K 31 PHE cc_start: 0.7262 (t80) cc_final: 0.6285 (t80) REVERT: K 60 ASP cc_start: 0.8320 (t0) cc_final: 0.7792 (t0) REVERT: L 22 SER cc_start: 0.8983 (m) cc_final: 0.8462 (t) REVERT: L 31 PHE cc_start: 0.7101 (t80) cc_final: 0.6213 (t80) REVERT: L 34 GLN cc_start: 0.6929 (pp30) cc_final: 0.6466 (pp30) outliers start: 1 outliers final: 1 residues processed: 675 average time/residue: 0.1363 time to fit residues: 147.3428 Evaluate side-chains 530 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 529 time to evaluate : 0.815 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 22 optimal weight: 6.9990 chunk 29 optimal weight: 0.2980 chunk 183 optimal weight: 8.9990 chunk 198 optimal weight: 0.6980 chunk 145 optimal weight: 0.9980 chunk 65 optimal weight: 3.9990 chunk 165 optimal weight: 0.7980 chunk 184 optimal weight: 4.9990 chunk 74 optimal weight: 0.7980 chunk 52 optimal weight: 2.9990 chunk 2 optimal weight: 3.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 616 ASN B 103 GLN ** B 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 77 ASN D 78 GLN G 133 ASN ** G 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 33 ASN H 78 GLN ** I 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.131809 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.106974 restraints weight = 39599.494| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.110265 restraints weight = 23527.743| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.112568 restraints weight = 16182.681| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.114183 restraints weight = 12286.712| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.115231 restraints weight = 10010.901| |-----------------------------------------------------------------------------| r_work (final): 0.3334 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7983 moved from start: 0.5189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 20499 Z= 0.135 Angle : 0.902 13.519 28028 Z= 0.410 Chirality : 0.053 0.446 3391 Planarity : 0.004 0.054 3389 Dihedral : 6.374 38.564 2544 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 10.01 Ramachandran Plot: Outliers : 0.04 % Allowed : 12.08 % Favored : 87.88 % Rotamer: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.26 % 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: -3.53 (0.16), residues: 2343 helix: -1.28 (0.26), residues: 342 sheet: -1.20 (0.23), residues: 510 loop : -3.23 (0.15), residues: 1491 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 95 TYR 0.018 0.001 TYR E 36 PHE 0.022 0.001 PHE G 53 TRP 0.064 0.002 TRP A 596 HIS 0.004 0.001 HIS B 249 Details of bonding type rmsd/Z covalent geometry : bond 0.00297 / 0.13 (20371) covalent geometry : angle 0.83833 / 0.39 (27674) SS BOND : bond 0.00438 / 0.31 ( 30) SS BOND : angle 2.07977 / 1.35 ( 60) hydrogen bonds : bond 0.03407 / 2.31 ( 451) hydrogen bonds : angle 5.92626 / 4.23 ( 1239) link_ALPHA1-3 : bond 0.00554 / 0.27 ( 3) link_ALPHA1-3 : angle 2.57267 / 1.41 ( 9) link_ALPHA1-6 : bond 0.00676 / 0.34 ( 2) link_ALPHA1-6 : angle 1.30347 / 0.64 ( 6) link_BETA1-4 : bond 0.00812 / 0.60 ( 42) link_BETA1-4 : angle 2.93448 / 2.26 ( 126) link_NAG-ASN : bond 0.00596 / 0.46 ( 51) link_NAG-ASN : angle 3.57742 / 2.48 ( 153) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 652 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 652 time to evaluate : 0.774 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 522 PHE cc_start: 0.8930 (t80) cc_final: 0.8689 (t80) REVERT: A 523 LEU cc_start: 0.9275 (mt) cc_final: 0.8911 (mt) REVERT: A 535 MET cc_start: 0.8792 (mmt) cc_final: 0.8557 (mmp) REVERT: A 543 ASN cc_start: 0.9124 (t0) cc_final: 0.8306 (t0) REVERT: A 588 ARG cc_start: 0.8948 (tpt-90) cc_final: 0.8181 (ttt180) REVERT: A 620 SER cc_start: 0.8744 (p) cc_final: 0.8067 (p) REVERT: A 622 ILE cc_start: 0.8801 (mm) cc_final: 0.8542 (mt) REVERT: B 96 TRP cc_start: 0.9359 (m100) cc_final: 0.8631 (m100) REVERT: B 106 GLU cc_start: 0.8392 (tm-30) cc_final: 0.8021 (tm-30) REVERT: B 166 ARG cc_start: 0.7539 (ptm160) cc_final: 0.7212 (ptp-170) REVERT: B 265 LEU cc_start: 0.8985 (mt) cc_final: 0.8742 (mm) REVERT: B 270 VAL cc_start: 0.9553 (m) cc_final: 0.9338 (t) REVERT: B 279 ASN cc_start: 0.8807 (t0) cc_final: 0.8505 (t0) REVERT: B 368 ASP cc_start: 0.7954 (t70) cc_final: 0.7694 (t70) REVERT: B 474 ASP cc_start: 0.8489 (t70) cc_final: 0.7790 (t70) REVERT: B 479 TRP cc_start: 0.8827 (m-90) cc_final: 0.8512 (m-90) REVERT: B 485 LYS cc_start: 0.8700 (ptpt) cc_final: 0.8391 (ptpt) REVERT: B 492 GLU cc_start: 0.8643 (tp30) cc_final: 0.8169 (tp30) REVERT: C 528 SER cc_start: 0.9281 (m) cc_final: 0.8895 (p) REVERT: C 535 MET cc_start: 0.8717 (mmt) cc_final: 0.8494 (mmm) REVERT: C 607 ASN cc_start: 0.8257 (t0) cc_final: 0.7867 (t0) REVERT: C 658 GLN cc_start: 0.8615 (tp-100) cc_final: 0.7839 (tp40) REVERT: D 61 ASN cc_start: 0.8446 (t0) cc_final: 0.8170 (t0) REVERT: D 70 ILE cc_start: 0.9311 (mp) cc_final: 0.8716 (mm) REVERT: E 31 PHE cc_start: 0.6592 (t80) cc_final: 0.5890 (t80) REVERT: E 85 ASP cc_start: 0.7795 (m-30) cc_final: 0.7557 (m-30) REVERT: E 92 ASP cc_start: 0.9165 (t0) cc_final: 0.8227 (t70) REVERT: E 104 LEU cc_start: 0.8188 (pt) cc_final: 0.7868 (pp) REVERT: F 522 PHE cc_start: 0.9016 (t80) cc_final: 0.8628 (t80) REVERT: F 523 LEU cc_start: 0.9259 (mt) cc_final: 0.9005 (mt) REVERT: F 528 SER cc_start: 0.8943 (m) cc_final: 0.8677 (p) REVERT: F 530 MET cc_start: 0.8432 (ptm) cc_final: 0.7957 (mtm) REVERT: F 543 ASN cc_start: 0.9079 (t0) cc_final: 0.8576 (t0) REVERT: F 607 ASN cc_start: 0.7775 (t0) cc_final: 0.7330 (t0) REVERT: F 624 ASP cc_start: 0.8109 (m-30) cc_final: 0.7856 (m-30) REVERT: F 630 GLN cc_start: 0.8719 (mp10) cc_final: 0.8481 (mp10) REVERT: F 638 TYR cc_start: 0.8276 (m-10) cc_final: 0.8034 (m-10) REVERT: F 664 ASP cc_start: 0.6620 (p0) cc_final: 0.6226 (p0) REVERT: G 82 GLN cc_start: 0.8839 (mm-40) cc_final: 0.8206 (mp10) REVERT: G 92 GLU cc_start: 0.7652 (pp20) cc_final: 0.7346 (pp20) REVERT: G 94 ASN cc_start: 0.8692 (t0) cc_final: 0.8151 (t0) REVERT: G 104 MET cc_start: 0.9114 (ttt) cc_final: 0.8299 (ttt) REVERT: G 164 GLU cc_start: 0.9065 (pp20) cc_final: 0.8827 (pp20) REVERT: G 170 GLN cc_start: 0.6928 (tt0) cc_final: 0.6725 (mt0) REVERT: G 171 LYS cc_start: 0.8895 (mtpt) cc_final: 0.8677 (mtmt) REVERT: G 195 ASN cc_start: 0.8014 (t0) cc_final: 0.7782 (t0) REVERT: G 211 GLU cc_start: 0.8268 (tm-30) cc_final: 0.7969 (tm-30) REVERT: G 217 TYR cc_start: 0.8201 (m-10) cc_final: 0.7912 (m-10) REVERT: G 243 SER cc_start: 0.8296 (m) cc_final: 0.7696 (t) REVERT: G 244 THR cc_start: 0.9479 (t) cc_final: 0.9253 (t) REVERT: G 350 ARG cc_start: 0.8359 (tpt-90) cc_final: 0.8107 (tpt-90) REVERT: G 368 ASP cc_start: 0.8017 (t70) cc_final: 0.7773 (t70) REVERT: G 475 MET cc_start: 0.8007 (tpp) cc_final: 0.7445 (tpp) REVERT: G 499 THR cc_start: 0.8409 (t) cc_final: 0.8133 (t) REVERT: H 47 GLU cc_start: 0.8298 (tp30) cc_final: 0.7968 (tp30) REVERT: H 48 TRP cc_start: 0.9182 (t60) cc_final: 0.8572 (t60) REVERT: H 67 ARG cc_start: 0.7817 (mmm160) cc_final: 0.7461 (mmm160) REVERT: I 50 THR cc_start: 0.9445 (p) cc_final: 0.9156 (p) REVERT: I 97 LYS cc_start: 0.8946 (mmtp) cc_final: 0.8612 (mmmm) REVERT: I 106 GLU cc_start: 0.9050 (tt0) cc_final: 0.8804 (tt0) REVERT: I 114 GLN cc_start: 0.9386 (tm-30) cc_final: 0.9174 (tm-30) REVERT: I 150 MET cc_start: 0.8733 (mpp) cc_final: 0.8183 (mpp) REVERT: I 195 ASN cc_start: 0.7961 (t0) cc_final: 0.7433 (t0) REVERT: I 319 TYR cc_start: 0.8560 (p90) cc_final: 0.8357 (p90) REVERT: I 320 PHE cc_start: 0.7869 (t80) cc_final: 0.7629 (t80) REVERT: I 340 GLU cc_start: 0.9183 (tt0) cc_final: 0.8528 (tp30) REVERT: I 363 GLN cc_start: 0.8579 (pp30) cc_final: 0.8263 (pp30) REVERT: I 368 ASP cc_start: 0.8276 (t70) cc_final: 0.7647 (t0) REVERT: I 370 GLU cc_start: 0.8450 (pm20) cc_final: 0.8119 (pm20) REVERT: I 434 MET cc_start: 0.8755 (ttm) cc_final: 0.8180 (ttm) REVERT: I 477 ASP cc_start: 0.9195 (m-30) cc_final: 0.8893 (m-30) REVERT: J 38 ILE cc_start: 0.9278 (mm) cc_final: 0.8981 (tp) REVERT: J 40 GLN cc_start: 0.8713 (tm-30) cc_final: 0.8308 (tm-30) REVERT: J 48 TRP cc_start: 0.9254 (t60) cc_final: 0.9023 (t60) REVERT: J 52 ILE cc_start: 0.7341 (tp) cc_final: 0.7050 (tp) REVERT: J 61 ASN cc_start: 0.8296 (t0) cc_final: 0.7711 (t0) REVERT: J 70 ILE cc_start: 0.9200 (mp) cc_final: 0.8756 (tp) REVERT: K 60 ASP cc_start: 0.8340 (t0) cc_final: 0.7869 (t0) REVERT: L 22 SER cc_start: 0.8932 (m) cc_final: 0.8442 (t) REVERT: L 34 GLN cc_start: 0.7142 (pp30) cc_final: 0.6853 (pp30) outliers start: 0 outliers final: 0 residues processed: 652 average time/residue: 0.1289 time to fit residues: 134.2633 Evaluate side-chains 530 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 530 time to evaluate : 0.765 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 215 optimal weight: 4.9990 chunk 65 optimal weight: 3.9990 chunk 58 optimal weight: 5.9990 chunk 202 optimal weight: 8.9990 chunk 103 optimal weight: 1.9990 chunk 14 optimal weight: 8.9990 chunk 179 optimal weight: 0.5980 chunk 157 optimal weight: 7.9990 chunk 192 optimal weight: 2.9990 chunk 198 optimal weight: 2.9990 chunk 110 optimal weight: 3.9990 overall best weight: 2.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 616 ASN ** A 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 170 GLN D 78 GLN G 99 ASN G 156 GLN ** G 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 38 GLN ** K 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.122554 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.097699 restraints weight = 40994.187| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.100757 restraints weight = 24630.834| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.102839 restraints weight = 17187.266| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.104384 restraints weight = 13247.347| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.105484 restraints weight = 10921.736| |-----------------------------------------------------------------------------| r_work (final): 0.3196 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8099 moved from start: 0.5533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 20499 Z= 0.215 Angle : 0.990 12.570 28028 Z= 0.457 Chirality : 0.055 0.499 3391 Planarity : 0.005 0.064 3389 Dihedral : 6.792 43.775 2544 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 13.16 Ramachandran Plot: Outliers : 0.04 % Allowed : 14.38 % Favored : 85.57 % Rotamer: Outliers : 0.05 % Allowed : 1.58 % Favored : 98.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.98 % Twisted General : 0.40 % 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: -3.52 (0.16), residues: 2343 helix: -1.10 (0.28), residues: 321 sheet: -1.19 (0.23), residues: 516 loop : -3.26 (0.14), residues: 1506 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG H 95 TYR 0.022 0.002 TYR K 36 PHE 0.021 0.002 PHE G 53 TRP 0.052 0.003 TRP A 596 HIS 0.004 0.001 HIS B 216 Details of bonding type rmsd/Z covalent geometry : bond 0.00487 / 0.21 (20371) covalent geometry : angle 0.92410 / 0.44 (27674) SS BOND : bond 0.00360 / 0.24 ( 30) SS BOND : angle 2.71082 / 1.81 ( 60) hydrogen bonds : bond 0.04285 / 2.96 ( 451) hydrogen bonds : angle 6.19587 / 4.45 ( 1239) link_ALPHA1-3 : bond 0.00369 / 0.18 ( 3) link_ALPHA1-3 : angle 2.63207 / 1.44 ( 9) link_ALPHA1-6 : bond 0.00662 / 0.34 ( 2) link_ALPHA1-6 : angle 1.29655 / 0.66 ( 6) link_BETA1-4 : bond 0.00823 / 0.56 ( 42) link_BETA1-4 : angle 3.08567 / 2.38 ( 126) link_NAG-ASN : bond 0.00565 / 0.43 ( 51) link_NAG-ASN : angle 3.73532 / 2.55 ( 153) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 636 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 635 time to evaluate : 0.693 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 535 MET cc_start: 0.8975 (mmt) cc_final: 0.8719 (mmp) REVERT: A 543 ASN cc_start: 0.9422 (t0) cc_final: 0.8666 (t0) REVERT: B 92 GLU cc_start: 0.5569 (pp20) cc_final: 0.5028 (pp20) REVERT: B 95 MET cc_start: 0.9284 (tmm) cc_final: 0.9025 (tmm) REVERT: B 106 GLU cc_start: 0.8616 (tm-30) cc_final: 0.8333 (tm-30) REVERT: B 265 LEU cc_start: 0.9095 (mt) cc_final: 0.8835 (mm) REVERT: B 426 MET cc_start: 0.8844 (ppp) cc_final: 0.8574 (ppp) REVERT: B 475 MET cc_start: 0.8220 (mmm) cc_final: 0.7605 (mmm) REVERT: B 485 LYS cc_start: 0.8876 (ptpt) cc_final: 0.8438 (ptpt) REVERT: B 492 GLU cc_start: 0.8758 (tp30) cc_final: 0.8358 (tp30) REVERT: C 543 ASN cc_start: 0.9042 (t0) cc_final: 0.8551 (t0) REVERT: C 607 ASN cc_start: 0.8291 (t0) cc_final: 0.8009 (t0) REVERT: C 630 GLN cc_start: 0.9047 (mp10) cc_final: 0.8718 (mp10) REVERT: C 654 GLU cc_start: 0.8297 (pt0) cc_final: 0.7825 (pt0) REVERT: C 658 GLN cc_start: 0.8712 (tp-100) cc_final: 0.7896 (tp40) REVERT: D 61 ASN cc_start: 0.8813 (t0) cc_final: 0.8595 (t0) REVERT: D 67 ARG cc_start: 0.8358 (mmm160) cc_final: 0.8108 (mmm160) REVERT: D 100 TRP cc_start: 0.7391 (m-10) cc_final: 0.6989 (m-10) REVERT: E 31 PHE cc_start: 0.6829 (t80) cc_final: 0.6074 (t80) REVERT: E 35 TRP cc_start: 0.7964 (m100) cc_final: 0.7720 (m100) REVERT: E 85 ASP cc_start: 0.8129 (m-30) cc_final: 0.7868 (m-30) REVERT: E 92 ASP cc_start: 0.9303 (t0) cc_final: 0.8919 (t0) REVERT: F 522 PHE cc_start: 0.9219 (t80) cc_final: 0.8770 (t80) REVERT: F 523 LEU cc_start: 0.9453 (mt) cc_final: 0.9128 (mt) REVERT: F 528 SER cc_start: 0.9257 (m) cc_final: 0.8885 (p) REVERT: F 530 MET cc_start: 0.8743 (ptm) cc_final: 0.8071 (mtm) REVERT: F 543 ASN cc_start: 0.9129 (t0) cc_final: 0.8544 (t0) REVERT: F 588 ARG cc_start: 0.8609 (ttt180) cc_final: 0.8214 (tpt-90) REVERT: F 607 ASN cc_start: 0.7829 (t0) cc_final: 0.7579 (t0) REVERT: F 622 ILE cc_start: 0.8943 (mt) cc_final: 0.8701 (mt) REVERT: F 630 GLN cc_start: 0.8767 (mp10) cc_final: 0.7923 (mp10) REVERT: F 638 TYR cc_start: 0.8562 (m-10) cc_final: 0.8290 (m-10) REVERT: F 664 ASP cc_start: 0.6863 (p0) cc_final: 0.6544 (p0) REVERT: G 82 GLN cc_start: 0.8905 (mm-40) cc_final: 0.8078 (mp10) REVERT: G 92 GLU cc_start: 0.7718 (pp20) cc_final: 0.7351 (pp20) REVERT: G 94 ASN cc_start: 0.8914 (t0) cc_final: 0.8396 (t0) REVERT: G 104 MET cc_start: 0.9149 (ttt) cc_final: 0.8623 (ttt) REVERT: G 110 SER cc_start: 0.9557 (m) cc_final: 0.9223 (t) REVERT: G 138 LEU cc_start: 0.8837 (tt) cc_final: 0.8565 (tt) REVERT: G 156 GLN cc_start: 0.7801 (OUTLIER) cc_final: 0.7291 (pm20) REVERT: G 164 GLU cc_start: 0.9152 (pp20) cc_final: 0.8809 (pp20) REVERT: G 213 ILE cc_start: 0.9248 (mm) cc_final: 0.9011 (mt) REVERT: G 357 THR cc_start: 0.8923 (m) cc_final: 0.8672 (p) REVERT: G 368 ASP cc_start: 0.8166 (t70) cc_final: 0.7902 (t70) REVERT: G 474 ASP cc_start: 0.8713 (t70) cc_final: 0.8450 (t70) REVERT: G 477 ASP cc_start: 0.9617 (m-30) cc_final: 0.9410 (m-30) REVERT: G 479 TRP cc_start: 0.9083 (m-90) cc_final: 0.8595 (m-90) REVERT: H 47 GLU cc_start: 0.8273 (tp30) cc_final: 0.8008 (tp30) REVERT: H 48 TRP cc_start: 0.9213 (t60) cc_final: 0.8414 (t60) REVERT: H 67 ARG cc_start: 0.7820 (mmm160) cc_final: 0.7471 (mmm160) REVERT: I 50 THR cc_start: 0.9439 (p) cc_final: 0.9204 (p) REVERT: I 106 GLU cc_start: 0.9271 (tt0) cc_final: 0.8410 (tm-30) REVERT: I 107 ASP cc_start: 0.8692 (p0) cc_final: 0.8337 (p0) REVERT: I 114 GLN cc_start: 0.9525 (tm-30) cc_final: 0.9185 (tm-30) REVERT: I 195 ASN cc_start: 0.8085 (t0) cc_final: 0.7691 (t0) REVERT: I 320 PHE cc_start: 0.8134 (t80) cc_final: 0.7866 (t80) REVERT: I 340 GLU cc_start: 0.9265 (tt0) cc_final: 0.8572 (tp30) REVERT: I 363 GLN cc_start: 0.8645 (pp30) cc_final: 0.8394 (pp30) REVERT: I 426 MET cc_start: 0.8852 (ppp) cc_final: 0.8478 (ppp) REVERT: I 434 MET cc_start: 0.8882 (ttm) cc_final: 0.8356 (ttm) REVERT: I 474 ASP cc_start: 0.8822 (t70) cc_final: 0.8312 (t70) REVERT: I 477 ASP cc_start: 0.9211 (m-30) cc_final: 0.8928 (m-30) REVERT: I 499 THR cc_start: 0.8815 (t) cc_final: 0.8608 (t) REVERT: J 40 GLN cc_start: 0.8565 (tm-30) cc_final: 0.8098 (tm-30) REVERT: J 48 TRP cc_start: 0.9306 (t60) cc_final: 0.8756 (t60) REVERT: J 57 ASN cc_start: 0.7765 (t0) cc_final: 0.7483 (t0) REVERT: J 61 ASN cc_start: 0.8710 (t0) cc_final: 0.8167 (t0) REVERT: K 35 TRP cc_start: 0.8130 (m100) cc_final: 0.7838 (m100) REVERT: K 60 ASP cc_start: 0.8203 (t0) cc_final: 0.7590 (t0) REVERT: K 85 ASP cc_start: 0.7947 (m-30) cc_final: 0.7649 (m-30) REVERT: K 92 ASP cc_start: 0.8936 (t0) cc_final: 0.8729 (t70) REVERT: L 22 SER cc_start: 0.9123 (m) cc_final: 0.8786 (t) REVERT: L 27 ASN cc_start: 0.8563 (t0) cc_final: 0.8329 (t0) REVERT: L 31 PHE cc_start: 0.7061 (t80) cc_final: 0.6097 (t80) REVERT: L 37 GLN cc_start: 0.8145 (mp10) cc_final: 0.7451 (mp10) REVERT: L 39 LEU cc_start: 0.6115 (tp) cc_final: 0.5867 (tp) REVERT: L 60 ASP cc_start: 0.7928 (t0) cc_final: 0.7369 (t0) REVERT: L 92 ASP cc_start: 0.8819 (t70) cc_final: 0.8005 (t70) outliers start: 1 outliers final: 0 residues processed: 635 average time/residue: 0.1324 time to fit residues: 134.0432 Evaluate side-chains 501 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 500 time to evaluate : 0.775 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 65 optimal weight: 4.9990 chunk 12 optimal weight: 0.1980 chunk 211 optimal weight: 2.9990 chunk 229 optimal weight: 9.9990 chunk 32 optimal weight: 3.9990 chunk 169 optimal weight: 2.9990 chunk 114 optimal weight: 0.8980 chunk 176 optimal weight: 6.9990 chunk 188 optimal weight: 0.9980 chunk 137 optimal weight: 3.9990 chunk 9 optimal weight: 4.9990 overall best weight: 1.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 203 GLN D 78 GLN G 99 ASN G 103 GLN G 188 ASN ** G 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 78 GLN ** I 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 38 GLN ** K 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.124041 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.099204 restraints weight = 40609.062| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.102234 restraints weight = 24683.875| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.104368 restraints weight = 17348.839| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.105858 restraints weight = 13408.642| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.106955 restraints weight = 11097.716| |-----------------------------------------------------------------------------| r_work (final): 0.3218 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8115 moved from start: 0.5720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 20499 Z= 0.164 Angle : 0.955 14.213 28028 Z= 0.437 Chirality : 0.054 0.599 3391 Planarity : 0.005 0.048 3389 Dihedral : 6.579 40.456 2544 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 11.84 Ramachandran Plot: Outliers : 0.04 % Allowed : 12.51 % Favored : 87.45 % Rotamer: Outliers : 0.05 % Allowed : 0.91 % Favored : 99.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.98 % Twisted General : 0.26 % 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: -3.50 (0.16), residues: 2343 helix: -0.99 (0.29), residues: 321 sheet: -1.21 (0.24), residues: 486 loop : -3.23 (0.14), residues: 1536 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 166 TYR 0.026 0.002 TYR A 586 PHE 0.020 0.001 PHE I 320 TRP 0.050 0.002 TRP A 596 HIS 0.004 0.001 HIS G 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00374 / 0.16 (20371) covalent geometry : angle 0.88963 / 0.42 (27674) SS BOND : bond 0.00445 / 0.29 ( 30) SS BOND : angle 2.49210 / 1.63 ( 60) hydrogen bonds : bond 0.03801 / 2.59 ( 451) hydrogen bonds : angle 6.01801 / 4.32 ( 1239) link_ALPHA1-3 : bond 0.00512 / 0.25 ( 3) link_ALPHA1-3 : angle 2.62909 / 1.43 ( 9) link_ALPHA1-6 : bond 0.00666 / 0.34 ( 2) link_ALPHA1-6 : angle 1.31362 / 0.65 ( 6) link_BETA1-4 : bond 0.00819 / 0.58 ( 42) link_BETA1-4 : angle 2.97270 / 2.28 ( 126) link_NAG-ASN : bond 0.00544 / 0.40 ( 51) link_NAG-ASN : angle 3.72318 / 2.56 ( 153) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 635 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 634 time to evaluate : 0.770 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 535 MET cc_start: 0.8875 (mmt) cc_final: 0.8665 (mmp) REVERT: A 543 ASN cc_start: 0.9240 (t0) cc_final: 0.8422 (t0) REVERT: B 92 GLU cc_start: 0.8373 (pp20) cc_final: 0.8065 (pp20) REVERT: B 95 MET cc_start: 0.9239 (tmm) cc_final: 0.8794 (tmm) REVERT: B 96 TRP cc_start: 0.9408 (m100) cc_final: 0.8480 (m100) REVERT: B 106 GLU cc_start: 0.8514 (tm-30) cc_final: 0.8251 (tm-30) REVERT: B 150 MET cc_start: 0.8285 (mpp) cc_final: 0.7712 (mpp) REVERT: B 166 ARG cc_start: 0.7669 (ttp80) cc_final: 0.7133 (ptm-80) REVERT: B 205 CYS cc_start: 0.6160 (t) cc_final: 0.5666 (t) REVERT: B 265 LEU cc_start: 0.9044 (mt) cc_final: 0.8730 (mm) REVERT: B 416 LEU cc_start: 0.8971 (tp) cc_final: 0.8763 (tp) REVERT: B 426 MET cc_start: 0.9018 (ppp) cc_final: 0.8721 (ppp) REVERT: B 475 MET cc_start: 0.7641 (mmm) cc_final: 0.7036 (mmm) REVERT: B 479 TRP cc_start: 0.8641 (m-90) cc_final: 0.8432 (m-90) REVERT: B 485 LYS cc_start: 0.8848 (ptpt) cc_final: 0.8390 (ptpt) REVERT: B 492 GLU cc_start: 0.8670 (tp30) cc_final: 0.8271 (tp30) REVERT: C 607 ASN cc_start: 0.8346 (t0) cc_final: 0.8068 (t0) REVERT: D 40 GLN cc_start: 0.8475 (tm-30) cc_final: 0.8123 (tm-30) REVERT: D 67 ARG cc_start: 0.8331 (mmm160) cc_final: 0.8029 (mmm160) REVERT: E 35 TRP cc_start: 0.8045 (m100) cc_final: 0.7505 (m100) REVERT: E 60 ASP cc_start: 0.7737 (t0) cc_final: 0.7068 (t0) REVERT: E 85 ASP cc_start: 0.7966 (m-30) cc_final: 0.7736 (m-30) REVERT: E 92 ASP cc_start: 0.9313 (t0) cc_final: 0.8960 (t0) REVERT: F 522 PHE cc_start: 0.9221 (t80) cc_final: 0.8754 (t80) REVERT: F 523 LEU cc_start: 0.9379 (mt) cc_final: 0.9130 (mt) REVERT: F 528 SER cc_start: 0.9221 (m) cc_final: 0.8959 (p) REVERT: F 543 ASN cc_start: 0.9159 (t0) cc_final: 0.8724 (t0) REVERT: F 588 ARG cc_start: 0.8513 (ttt180) cc_final: 0.8132 (tpt-90) REVERT: F 616 ASN cc_start: 0.8454 (p0) cc_final: 0.8170 (p0) REVERT: F 622 ILE cc_start: 0.8943 (mt) cc_final: 0.8694 (mt) REVERT: F 627 THR cc_start: 0.8236 (p) cc_final: 0.8007 (p) REVERT: F 638 TYR cc_start: 0.8531 (m-10) cc_final: 0.8216 (m-10) REVERT: F 664 ASP cc_start: 0.6473 (p0) cc_final: 0.6165 (p0) REVERT: G 82 GLN cc_start: 0.8817 (mm-40) cc_final: 0.8055 (mp10) REVERT: G 92 GLU cc_start: 0.7672 (pp20) cc_final: 0.7326 (pp20) REVERT: G 94 ASN cc_start: 0.8865 (t0) cc_final: 0.8280 (t0) REVERT: G 138 LEU cc_start: 0.8925 (tt) cc_final: 0.8624 (tt) REVERT: G 357 THR cc_start: 0.8885 (m) cc_final: 0.8671 (p) REVERT: G 368 ASP cc_start: 0.8162 (t70) cc_final: 0.7942 (t70) REVERT: G 474 ASP cc_start: 0.8664 (t70) cc_final: 0.8301 (t70) REVERT: H 47 GLU cc_start: 0.8331 (tp30) cc_final: 0.8113 (tp30) REVERT: H 48 TRP cc_start: 0.9242 (t60) cc_final: 0.8466 (t60) REVERT: H 67 ARG cc_start: 0.7779 (mmm160) cc_final: 0.7414 (mmm160) REVERT: I 50 THR cc_start: 0.9402 (p) cc_final: 0.9139 (p) REVERT: I 92 GLU cc_start: 0.8513 (pp20) cc_final: 0.8304 (pp20) REVERT: I 106 GLU cc_start: 0.9194 (tt0) cc_final: 0.8100 (tm-30) REVERT: I 107 ASP cc_start: 0.8478 (p0) cc_final: 0.8249 (p0) REVERT: I 114 GLN cc_start: 0.9408 (tm-30) cc_final: 0.9087 (tm-30) REVERT: I 174 SER cc_start: 0.9022 (m) cc_final: 0.8320 (p) REVERT: I 181 VAL cc_start: 0.9799 (m) cc_final: 0.9556 (p) REVERT: I 195 ASN cc_start: 0.8211 (t0) cc_final: 0.7815 (t0) REVERT: I 205 CYS cc_start: 0.7352 (t) cc_final: 0.7004 (t) REVERT: I 340 GLU cc_start: 0.9212 (tt0) cc_final: 0.8433 (tp30) REVERT: I 363 GLN cc_start: 0.8589 (pp30) cc_final: 0.8222 (pp30) REVERT: I 434 MET cc_start: 0.8854 (ttm) cc_final: 0.8328 (ttm) REVERT: I 499 THR cc_start: 0.8691 (t) cc_final: 0.8471 (t) REVERT: J 40 GLN cc_start: 0.8572 (tm-30) cc_final: 0.8246 (tm-30) REVERT: J 44 LYS cc_start: 0.7306 (mptt) cc_final: 0.6915 (mptt) REVERT: J 48 TRP cc_start: 0.9295 (t60) cc_final: 0.8701 (t60) REVERT: J 61 ASN cc_start: 0.8741 (t0) cc_final: 0.8253 (t0) REVERT: K 31 PHE cc_start: 0.7285 (t80) cc_final: 0.6365 (t80) REVERT: K 60 ASP cc_start: 0.8206 (t0) cc_final: 0.7705 (t0) REVERT: K 85 ASP cc_start: 0.7777 (m-30) cc_final: 0.7554 (m-30) REVERT: L 22 SER cc_start: 0.9140 (m) cc_final: 0.8891 (t) REVERT: L 36 TYR cc_start: 0.8356 (p90) cc_final: 0.7985 (p90) REVERT: L 37 GLN cc_start: 0.8193 (mp10) cc_final: 0.6649 (mp10) REVERT: L 39 LEU cc_start: 0.6129 (tp) cc_final: 0.5921 (tp) REVERT: L 92 ASP cc_start: 0.8877 (t70) cc_final: 0.8081 (t70) outliers start: 1 outliers final: 0 residues processed: 634 average time/residue: 0.1277 time to fit residues: 128.9909 Evaluate side-chains 505 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 505 time to evaluate : 0.744 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 53 optimal weight: 0.2980 chunk 147 optimal weight: 5.9990 chunk 45 optimal weight: 1.9990 chunk 6 optimal weight: 0.9990 chunk 75 optimal weight: 9.9990 chunk 183 optimal weight: 1.9990 chunk 174 optimal weight: 0.9990 chunk 138 optimal weight: 4.9990 chunk 7 optimal weight: 6.9990 chunk 22 optimal weight: 3.9990 chunk 27 optimal weight: 2.9990 overall best weight: 1.2588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 203 GLN D 78 GLN E 51 ASN G 33 ASN G 99 ASN G 188 ASN ** G 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 78 GLN ** I 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 38 GLN ** K 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.124913 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.099958 restraints weight = 40818.348| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.103077 restraints weight = 24630.376| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.105256 restraints weight = 17176.638| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.106783 restraints weight = 13216.635| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.107867 restraints weight = 10890.449| |-----------------------------------------------------------------------------| r_work (final): 0.3231 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8077 moved from start: 0.5879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 20499 Z= 0.152 Angle : 0.940 13.881 28028 Z= 0.431 Chirality : 0.054 0.555 3391 Planarity : 0.005 0.049 3389 Dihedral : 6.524 39.689 2544 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 11.20 Ramachandran Plot: Outliers : 0.04 % Allowed : 13.53 % Favored : 86.43 % Rotamer: Outliers : 0.10 % Allowed : 0.48 % Favored : 99.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.26 % 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: -3.46 (0.16), residues: 2343 helix: -0.91 (0.29), residues: 321 sheet: -1.28 (0.23), residues: 516 loop : -3.21 (0.14), residues: 1506 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 166 TYR 0.062 0.002 TYR I 173 PHE 0.015 0.001 PHE B 53 TRP 0.040 0.002 TRP A 596 HIS 0.004 0.001 HIS G 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00346 / 0.15 (20371) covalent geometry : angle 0.87971 / 0.42 (27674) SS BOND : bond 0.00505 / 0.30 ( 30) SS BOND : angle 2.35324 / 1.56 ( 60) hydrogen bonds : bond 0.03664 / 2.50 ( 451) hydrogen bonds : angle 5.93916 / 4.27 ( 1239) link_ALPHA1-3 : bond 0.00538 / 0.26 ( 3) link_ALPHA1-3 : angle 2.57291 / 1.40 ( 9) link_ALPHA1-6 : bond 0.00662 / 0.34 ( 2) link_ALPHA1-6 : angle 1.32444 / 0.66 ( 6) link_BETA1-4 : bond 0.00786 / 0.56 ( 42) link_BETA1-4 : angle 2.86699 / 2.20 ( 126) link_NAG-ASN : bond 0.00478 / 0.38 ( 51) link_NAG-ASN : angle 3.53018 / 2.43 ( 153) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 635 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 633 time to evaluate : 0.736 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: A 535 MET cc_start: 0.8788 (mmt) cc_final: 0.8554 (mmp) REVERT: A 543 ASN cc_start: 0.9200 (t0) cc_final: 0.8397 (t0) REVERT: A 588 ARG cc_start: 0.9051 (ttt90) cc_final: 0.8145 (ttt180) REVERT: B 92 GLU cc_start: 0.8421 (pp20) cc_final: 0.8104 (pp20) REVERT: B 95 MET cc_start: 0.9234 (tmm) cc_final: 0.8787 (tmm) REVERT: B 96 TRP cc_start: 0.9403 (m100) cc_final: 0.8488 (m100) REVERT: B 104 MET cc_start: 0.8766 (ttp) cc_final: 0.8297 (ttp) REVERT: B 106 GLU cc_start: 0.8437 (tm-30) cc_final: 0.8191 (tm-30) REVERT: B 205 CYS cc_start: 0.6639 (t) cc_final: 0.6352 (t) REVERT: B 265 LEU cc_start: 0.9041 (mt) cc_final: 0.8692 (mm) REVERT: B 368 ASP cc_start: 0.8001 (t70) cc_final: 0.7668 (t70) REVERT: B 416 LEU cc_start: 0.8907 (tp) cc_final: 0.8703 (tp) REVERT: B 474 ASP cc_start: 0.8729 (t70) cc_final: 0.8227 (t0) REVERT: B 475 MET cc_start: 0.7736 (mmm) cc_final: 0.7348 (mmm) REVERT: B 479 TRP cc_start: 0.8663 (m-90) cc_final: 0.8407 (m-90) REVERT: B 485 LYS cc_start: 0.8815 (ptpt) cc_final: 0.8363 (ptpt) REVERT: B 492 GLU cc_start: 0.8678 (tp30) cc_final: 0.8334 (tp30) REVERT: C 528 SER cc_start: 0.9224 (m) cc_final: 0.8660 (p) REVERT: D 40 GLN cc_start: 0.8464 (tm-30) cc_final: 0.8107 (tm-30) REVERT: D 67 ARG cc_start: 0.8262 (mmm160) cc_final: 0.7952 (mmm160) REVERT: E 31 PHE cc_start: 0.6936 (t80) cc_final: 0.6307 (t80) REVERT: E 60 ASP cc_start: 0.7907 (t0) cc_final: 0.7318 (t0) REVERT: E 85 ASP cc_start: 0.7989 (m-30) cc_final: 0.7763 (m-30) REVERT: E 92 ASP cc_start: 0.9340 (t0) cc_final: 0.8969 (t0) REVERT: F 522 PHE cc_start: 0.9192 (t80) cc_final: 0.8872 (t80) REVERT: F 528 SER cc_start: 0.9239 (m) cc_final: 0.8923 (p) REVERT: F 543 ASN cc_start: 0.9170 (t0) cc_final: 0.8685 (t0) REVERT: F 588 ARG cc_start: 0.8514 (ttt180) cc_final: 0.8124 (tpt-90) REVERT: F 616 ASN cc_start: 0.8541 (p0) cc_final: 0.8172 (p0) REVERT: F 622 ILE cc_start: 0.8945 (mt) cc_final: 0.8702 (mt) REVERT: F 627 THR cc_start: 0.8328 (p) cc_final: 0.8049 (p) REVERT: F 638 TYR cc_start: 0.8677 (m-10) cc_final: 0.8267 (m-10) REVERT: F 654 GLU cc_start: 0.8976 (tm-30) cc_final: 0.8619 (tm-30) REVERT: F 658 GLN cc_start: 0.8619 (pt0) cc_final: 0.8342 (pt0) REVERT: F 664 ASP cc_start: 0.5927 (p0) cc_final: 0.5650 (p0) REVERT: G 82 GLN cc_start: 0.8815 (mm-40) cc_final: 0.7991 (mp10) REVERT: G 92 GLU cc_start: 0.7677 (pp20) cc_final: 0.7324 (pp20) REVERT: G 94 ASN cc_start: 0.8612 (t0) cc_final: 0.8148 (t0) REVERT: G 106 GLU cc_start: 0.9209 (tt0) cc_final: 0.8964 (tt0) REVERT: G 138 LEU cc_start: 0.8856 (tt) cc_final: 0.8521 (tt) REVERT: G 243 SER cc_start: 0.8457 (m) cc_final: 0.7877 (t) REVERT: G 328 MET cc_start: 0.7479 (pmm) cc_final: 0.7102 (pmm) REVERT: G 357 THR cc_start: 0.8892 (m) cc_final: 0.8664 (p) REVERT: G 368 ASP cc_start: 0.8130 (t70) cc_final: 0.7868 (t70) REVERT: G 475 MET cc_start: 0.8218 (tpp) cc_final: 0.7140 (tpp) REVERT: G 479 TRP cc_start: 0.9040 (m-90) cc_final: 0.8418 (m-90) REVERT: H 47 GLU cc_start: 0.8282 (tp30) cc_final: 0.8045 (tp30) REVERT: H 48 TRP cc_start: 0.9217 (t60) cc_final: 0.8595 (t60) REVERT: H 67 ARG cc_start: 0.7805 (mmm160) cc_final: 0.7431 (mmm160) REVERT: I 50 THR cc_start: 0.9416 (p) cc_final: 0.9123 (p) REVERT: I 82 GLN cc_start: 0.8910 (mm-40) cc_final: 0.8179 (mp10) REVERT: I 102 GLU cc_start: 0.9031 (mm-30) cc_final: 0.8550 (tp30) REVERT: I 106 GLU cc_start: 0.9206 (tt0) cc_final: 0.8871 (tt0) REVERT: I 114 GLN cc_start: 0.9437 (tm-30) cc_final: 0.9099 (tm-30) REVERT: I 150 MET cc_start: 0.8772 (mpp) cc_final: 0.7361 (mpp) REVERT: I 181 VAL cc_start: 0.9785 (m) cc_final: 0.9534 (p) REVERT: I 195 ASN cc_start: 0.8168 (t0) cc_final: 0.7723 (t0) REVERT: I 321 ASP cc_start: 0.9086 (m-30) cc_final: 0.8646 (m-30) REVERT: I 328 MET cc_start: 0.7470 (ptm) cc_final: 0.6998 (ptp) REVERT: I 340 GLU cc_start: 0.9165 (tt0) cc_final: 0.8460 (tp30) REVERT: I 434 MET cc_start: 0.8838 (ttm) cc_final: 0.8291 (ttm) REVERT: J 40 GLN cc_start: 0.8332 (tm-30) cc_final: 0.8060 (tm-30) REVERT: J 48 TRP cc_start: 0.9318 (t60) cc_final: 0.8769 (t60) REVERT: J 61 ASN cc_start: 0.8754 (t0) cc_final: 0.8288 (t0) REVERT: J 67 ARG cc_start: 0.8345 (mmm160) cc_final: 0.7888 (mmm160) REVERT: K 31 PHE cc_start: 0.7333 (t80) cc_final: 0.6454 (t80) REVERT: K 38 GLN cc_start: 0.6702 (mm-40) cc_final: 0.6382 (mm-40) REVERT: K 60 ASP cc_start: 0.8359 (t0) cc_final: 0.7702 (t0) REVERT: K 92 ASP cc_start: 0.8867 (t0) cc_final: 0.8328 (t70) REVERT: L 22 SER cc_start: 0.9118 (m) cc_final: 0.8866 (t) REVERT: L 27 ASN cc_start: 0.8473 (t0) cc_final: 0.8237 (t0) REVERT: L 39 LEU cc_start: 0.6127 (tp) cc_final: 0.5908 (tp) REVERT: L 60 ASP cc_start: 0.8129 (t0) cc_final: 0.7577 (t0) REVERT: L 92 ASP cc_start: 0.8874 (t70) cc_final: 0.8091 (t70) outliers start: 2 outliers final: 1 residues processed: 633 average time/residue: 0.1275 time to fit residues: 128.9050 Evaluate side-chains 515 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 514 time to evaluate : 0.830 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 25 optimal weight: 6.9990 chunk 229 optimal weight: 0.2980 chunk 4 optimal weight: 0.9980 chunk 170 optimal weight: 0.9980 chunk 119 optimal weight: 0.7980 chunk 139 optimal weight: 6.9990 chunk 59 optimal weight: 7.9990 chunk 222 optimal weight: 10.0000 chunk 10 optimal weight: 0.8980 chunk 152 optimal weight: 0.1980 chunk 154 optimal weight: 8.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 577 GLN A 652 GLN B 156 GLN B 203 GLN G 33 ASN ** G 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 40 GLN ** I 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 93 ASN L 38 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.127338 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.102435 restraints weight = 40272.183| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.105615 restraints weight = 24066.502| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.107816 restraints weight = 16667.547| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.109378 restraints weight = 12756.883| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.110444 restraints weight = 10472.192| |-----------------------------------------------------------------------------| r_work (final): 0.3265 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8052 moved from start: 0.6032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 20499 Z= 0.141 Angle : 0.934 13.615 28028 Z= 0.426 Chirality : 0.054 0.541 3391 Planarity : 0.004 0.047 3389 Dihedral : 6.314 39.269 2544 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 10.72 Ramachandran Plot: Outliers : 0.04 % Allowed : 11.99 % Favored : 87.96 % Rotamer: Outliers : 0.10 % Allowed : 0.57 % Favored : 99.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.26 % 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: -3.40 (0.16), residues: 2343 helix: -0.80 (0.28), residues: 330 sheet: -1.16 (0.24), residues: 516 loop : -3.22 (0.14), residues: 1497 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 166 TYR 0.032 0.002 TYR B 173 PHE 0.021 0.001 PHE C 522 TRP 0.038 0.002 TRP A 596 HIS 0.004 0.001 HIS G 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00317 / 0.14 (20371) covalent geometry : angle 0.87902 / 0.41 (27674) SS BOND : bond 0.00525 / 0.32 ( 30) SS BOND : angle 2.18249 / 1.41 ( 60) hydrogen bonds : bond 0.03441 / 2.34 ( 451) hydrogen bonds : angle 5.79950 / 4.17 ( 1239) link_ALPHA1-3 : bond 0.00557 / 0.27 ( 3) link_ALPHA1-3 : angle 2.55735 / 1.40 ( 9) link_ALPHA1-6 : bond 0.00650 / 0.33 ( 2) link_ALPHA1-6 : angle 1.33220 / 0.65 ( 6) link_BETA1-4 : bond 0.00813 / 0.58 ( 42) link_BETA1-4 : angle 2.76142 / 2.11 ( 126) link_NAG-ASN : bond 0.00524 / 0.41 ( 51) link_NAG-ASN : angle 3.39101 / 2.32 ( 153) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3592.74 seconds wall clock time: 63 minutes 6.37 seconds (3786.37 seconds total)