Starting phenix.real_space_refine on Sun Aug 24 13:38:57 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8g85_29836/08_2025/8g85_29836.cif Found real_map, /net/cci-nas-00/data/ceres_data/8g85_29836/08_2025/8g85_29836.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.99 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8g85_29836/08_2025/8g85_29836.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8g85_29836/08_2025/8g85_29836.map" model { file = "/net/cci-nas-00/data/ceres_data/8g85_29836/08_2025/8g85_29836.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8g85_29836/08_2025/8g85_29836.cif" } resolution = 3.99 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.010 sd= 0.061 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 129 5.16 5 C 12577 2.51 5 N 3347 2.21 5 O 4037 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 95 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 20090 Number of models: 1 Model: "" Number of chains: 39 Chain: "G" Number of atoms: 3468 Number of conformers: 1 Conformer: "" Number of residues, atoms: 441, 3468 Classifications: {'peptide': 441} Link IDs: {'PTRANS': 22, 'TRANS': 418} Chain breaks: 3 Chain: "B" Number of atoms: 1059 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1059 Classifications: {'peptide': 135} Link IDs: {'PTRANS': 1, 'TRANS': 133} Chain breaks: 1 Chain: "D" Number of atoms: 3468 Number of conformers: 1 Conformer: "" Number of residues, atoms: 441, 3468 Classifications: {'peptide': 441} Link IDs: {'PTRANS': 22, 'TRANS': 418} Chain breaks: 3 Chain: "E" Number of atoms: 1059 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1059 Classifications: {'peptide': 135} Link IDs: {'PTRANS': 1, 'TRANS': 133} Chain breaks: 1 Chain: "J" Number of atoms: 3468 Number of conformers: 1 Conformer: "" Number of residues, atoms: 441, 3468 Classifications: {'peptide': 441} Link IDs: {'CIS': 1, 'PTRANS': 22, 'TRANS': 417} Chain breaks: 3 Chain: "K" Number of atoms: 1059 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1059 Classifications: {'peptide': 135} Link IDs: {'PTRANS': 1, 'TRANS': 133} Chain breaks: 1 Chain: "H" Number of atoms: 917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 917 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 5, 'TRANS': 109} Chain: "L" Number of atoms: 831 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 831 Classifications: {'peptide': 106} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 100} Chain: "A" Number of atoms: 917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 917 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 5, 'TRANS': 109} Chain: "C" Number of atoms: 831 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 831 Classifications: {'peptide': 106} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 100} Chain: "F" Number of atoms: 917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 917 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 5, 'TRANS': 109} Chain: "I" Number of atoms: 831 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 831 Classifications: {'peptide': 106} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 100} Chain: "M" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 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 dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "T" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 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 dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "a" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "b" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "c" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "d" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "e" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "f" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "g" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "h" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "i" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "G" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "K" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 5.18, per 1000 atoms: 0.26 Number of scatterers: 20090 At special positions: 0 Unit cell: (132.016, 145.969, 140.602, 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 129 16.00 O 4037 8.00 N 3347 7.00 C 12577 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=42, symmetry=0 Simple disulfide: pdb=" SG CYS G 54 " - pdb=" SG CYS G 74 " distance=2.03 Simple disulfide: pdb=" SG CYS G 119 " - pdb=" SG CYS G 205 " distance=2.03 Simple disulfide: pdb=" SG CYS G 126 " - pdb=" SG CYS G 196 " distance=2.03 Simple disulfide: pdb=" SG CYS G 131 " - pdb=" SG CYS G 157 " distance=2.03 Simple disulfide: pdb=" SG CYS G 201 " - pdb=" SG CYS G 433 " distance=2.04 Simple disulfide: pdb=" SG CYS G 218 " - pdb=" SG CYS G 247 " distance=2.05 Simple disulfide: pdb=" SG CYS G 228 " - pdb=" SG CYS G 239 " distance=2.03 Simple disulfide: pdb=" SG CYS G 296 " - pdb=" SG CYS G 331 " distance=2.03 Simple disulfide: pdb=" SG CYS G 378 " - pdb=" SG CYS G 445 " distance=2.03 Simple disulfide: pdb=" SG CYS G 385 " - pdb=" SG CYS G 418 " distance=2.03 Simple disulfide: pdb=" SG CYS G 501 " - pdb=" SG CYS B 605 " distance=2.03 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.03 Simple disulfide: pdb=" SG CYS D 54 " - pdb=" SG CYS D 74 " distance=2.03 Simple disulfide: pdb=" SG CYS D 119 " - pdb=" SG CYS D 205 " distance=2.03 Simple disulfide: pdb=" SG CYS D 126 " - pdb=" SG CYS D 196 " distance=2.03 Simple disulfide: pdb=" SG CYS D 131 " - pdb=" SG CYS D 157 " distance=2.03 Simple disulfide: pdb=" SG CYS D 201 " - pdb=" SG CYS D 433 " distance=2.04 Simple disulfide: pdb=" SG CYS D 218 " - pdb=" SG CYS D 247 " distance=2.05 Simple disulfide: pdb=" SG CYS D 228 " - pdb=" SG CYS D 239 " distance=2.03 Simple disulfide: pdb=" SG CYS D 296 " - pdb=" SG CYS D 331 " distance=2.03 Simple disulfide: pdb=" SG CYS D 378 " - pdb=" SG CYS D 445 " distance=2.03 Simple disulfide: pdb=" SG CYS D 385 " - pdb=" SG CYS D 418 " distance=2.03 Simple disulfide: pdb=" SG CYS D 501 " - pdb=" SG CYS E 605 " distance=2.03 Simple disulfide: pdb=" SG CYS E 598 " - pdb=" SG CYS E 604 " distance=2.03 Simple disulfide: pdb=" SG CYS J 54 " - pdb=" SG CYS J 74 " distance=2.04 Simple disulfide: pdb=" SG CYS J 119 " - pdb=" SG CYS J 205 " distance=2.03 Simple disulfide: pdb=" SG CYS J 126 " - pdb=" SG CYS J 196 " distance=2.03 Simple disulfide: pdb=" SG CYS J 131 " - pdb=" SG CYS J 157 " distance=2.03 Simple disulfide: pdb=" SG CYS J 201 " - pdb=" SG CYS J 433 " distance=2.03 Simple disulfide: pdb=" SG CYS J 218 " - pdb=" SG CYS J 247 " distance=2.03 Simple disulfide: pdb=" SG CYS J 228 " - pdb=" SG CYS J 239 " distance=2.03 Simple disulfide: pdb=" SG CYS J 296 " - pdb=" SG CYS J 331 " distance=2.03 Simple disulfide: pdb=" SG CYS J 378 " - pdb=" SG CYS J 445 " distance=2.03 Simple disulfide: pdb=" SG CYS J 385 " - pdb=" SG CYS J 418 " distance=2.03 Simple disulfide: pdb=" SG CYS J 501 " - pdb=" SG CYS K 605 " distance=2.03 Simple disulfide: pdb=" SG CYS K 598 " - pdb=" SG CYS K 604 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.04 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.04 Simple disulfide: pdb=" SG CYS A 22 " - pdb=" SG CYS A 92 " distance=2.03 Simple disulfide: pdb=" SG CYS C 23 " - pdb=" SG CYS C 88 " distance=2.03 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 92 " distance=2.04 Simple disulfide: pdb=" SG CYS I 23 " - pdb=" SG CYS I 88 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-3 " MAN M 4 " - " MAN M 5 " " BMA S 3 " - " MAN S 4 " " BMA T 3 " - " MAN T 4 " " BMA d 3 " - " MAN d 4 " ALPHA1-6 " BMA M 3 " - " MAN M 4 " " BMA T 3 " - " MAN T 5 " " BMA V 3 " - " MAN V 4 " " BMA d 3 " - " MAN d 5 " BETA1-4 " NAG M 1 " - " NAG M 2 " " NAG M 2 " - " BMA M 3 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG S 2 " - " BMA S 3 " " NAG T 1 " - " NAG T 2 " " NAG T 2 " - " BMA T 3 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG V 2 " - " BMA V 3 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " " NAG b 1 " - " NAG b 2 " " NAG b 2 " - " BMA b 3 " " NAG c 1 " - " NAG c 2 " " NAG c 2 " - " BMA c 3 " " NAG d 1 " - " NAG d 2 " " NAG d 2 " - " BMA d 3 " " NAG e 1 " - " NAG e 2 " " NAG f 1 " - " NAG f 2 " " NAG g 1 " - " NAG g 2 " " NAG h 1 " - " NAG h 2 " " NAG h 2 " - " BMA h 3 " " NAG i 1 " - " NAG i 2 " " NAG i 2 " - " BMA i 3 " NAG-ASN " NAG B 701 " - " ASN B 611 " " NAG B 702 " - " ASN B 637 " " NAG D 601 " - " ASN D 133 " " NAG D 602 " - " ASN D 156 " " NAG D 603 " - " ASN D 160 " " NAG D 604 " - " ASN D 197 " " NAG D 605 " - " ASN D 276 " " NAG D 606 " - " ASN D 301 " " NAG D 607 " - " ASN D 355 " " NAG D 608 " - " ASN D 339 " " NAG D 609 " - " ASN D 392 " " NAG D 610 " - " ASN D 234 " " NAG E 701 " - " ASN E 611 " " NAG E 702 " - " ASN E 637 " " NAG G 601 " - " ASN G 133 " " NAG G 602 " - " ASN G 156 " " NAG G 603 " - " ASN G 160 " " NAG G 604 " - " ASN G 197 " " NAG G 605 " - " ASN G 276 " " NAG G 606 " - " ASN G 301 " " NAG G 607 " - " ASN G 355 " " NAG G 608 " - " ASN G 339 " " NAG G 609 " - " ASN G 392 " " NAG G 610 " - " ASN G 234 " " NAG J 601 " - " ASN J 133 " " NAG J 602 " - " ASN J 156 " " NAG J 603 " - " ASN J 160 " " NAG J 604 " - " ASN J 197 " " NAG J 605 " - " ASN J 276 " " NAG J 606 " - " ASN J 301 " " NAG J 607 " - " ASN J 355 " " NAG J 608 " - " ASN J 339 " " NAG J 609 " - " ASN J 392 " " NAG J 610 " - " ASN J 234 " " NAG K 701 " - " ASN K 637 " " NAG M 1 " - " ASN G 262 " " NAG O 1 " - " ASN G 295 " " NAG P 1 " - " ASN G 332 " " NAG Q 1 " - " ASN G 363 " " NAG R 1 " - " ASN G 386 " " NAG S 1 " - " ASN G 448 " " NAG T 1 " - " ASN G 88 " " NAG U 1 " - " ASN D 88 " " NAG V 1 " - " ASN D 262 " " NAG X 1 " - " ASN D 295 " " NAG Y 1 " - " ASN D 332 " " NAG Z 1 " - " ASN D 363 " " NAG a 1 " - " ASN D 386 " " NAG b 1 " - " ASN D 448 " " NAG c 1 " - " ASN J 88 " " NAG d 1 " - " ASN J 262 " " NAG e 1 " - " ASN J 295 " " NAG f 1 " - " ASN J 332 " " NAG g 1 " - " ASN J 363 " " NAG h 1 " - " ASN J 386 " " NAG i 1 " - " ASN J 448 " Time building additional restraints: 1.98 Conformation dependent library (CDL) restraints added in 749.0 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 4440 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 42 sheets defined 19.0% alpha, 31.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.77 Creating SS restraints... Processing helix chain 'G' and resid 99 through 115 removed outlier: 3.504A pdb=" N ILE G 109 " --> pdb=" O HIS G 105 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N SER G 110 " --> pdb=" O THR G 106 " (cutoff:3.500A) Processing helix chain 'G' and resid 122 through 126 removed outlier: 3.681A pdb=" N LEU G 125 " --> pdb=" O LEU G 122 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N CYS G 126 " --> pdb=" O THR G 123 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 122 through 126' Processing helix chain 'G' and resid 334 through 350 removed outlier: 3.794A pdb=" N GLN G 348 " --> pdb=" O LYS G 344 " (cutoff:3.500A) Processing helix chain 'G' and resid 368 through 373 removed outlier: 3.820A pdb=" N THR G 373 " --> pdb=" O LEU G 369 " (cutoff:3.500A) Processing helix chain 'G' and resid 387 through 391 removed outlier: 4.104A pdb=" N LEU G 390 " --> pdb=" O THR G 387 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N PHE G 391 " --> pdb=" O SER G 388 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 387 through 391' Processing helix chain 'G' and resid 474 through 479 removed outlier: 3.761A pdb=" N ASP G 477 " --> pdb=" O ASP G 474 " (cutoff:3.500A) Processing helix chain 'B' and resid 513 through 517 removed outlier: 3.788A pdb=" N ALA B 517 " --> pdb=" O GLY B 514 " (cutoff:3.500A) Processing helix chain 'B' and resid 523 through 527 removed outlier: 3.818A pdb=" N ALA B 526 " --> pdb=" O LEU B 523 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N GLY B 527 " --> pdb=" O GLY B 524 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 523 through 527' Processing helix chain 'B' and resid 529 through 534 Processing helix chain 'B' and resid 536 through 543 removed outlier: 3.699A pdb=" N GLN B 540 " --> pdb=" O THR B 536 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ALA B 541 " --> pdb=" O LEU B 537 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N ASN B 543 " --> pdb=" O VAL B 539 " (cutoff:3.500A) Processing helix chain 'B' and resid 572 through 596 removed outlier: 3.945A pdb=" N LEU B 576 " --> pdb=" O GLY B 572 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ARG B 579 " --> pdb=" O GLN B 575 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LEU B 581 " --> pdb=" O GLN B 577 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ALA B 582 " --> pdb=" O ALA B 578 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N TRP B 596 " --> pdb=" O LEU B 592 " (cutoff:3.500A) Processing helix chain 'B' and resid 627 through 633 removed outlier: 4.168A pdb=" N LYS B 633 " --> pdb=" O LEU B 629 " (cutoff:3.500A) Processing helix chain 'B' and resid 635 through 637 No H-bonds generated for 'chain 'B' and resid 635 through 637' Processing helix chain 'B' and resid 638 through 662 removed outlier: 4.060A pdb=" N LEU B 646 " --> pdb=" O ILE B 642 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N GLU B 647 " --> pdb=" O TYR B 643 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N GLU B 648 " --> pdb=" O GLY B 644 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N SER B 649 " --> pdb=" O LEU B 645 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N GLN B 652 " --> pdb=" O GLU B 648 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N GLN B 653 " --> pdb=" O SER B 649 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N GLU B 654 " --> pdb=" O GLN B 650 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ALA B 662 " --> pdb=" O GLN B 658 " (cutoff:3.500A) Processing helix chain 'D' and resid 98 through 115 removed outlier: 4.274A pdb=" N GLU D 102 " --> pdb=" O ASN D 98 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ILE D 109 " --> pdb=" O HIS D 105 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLN D 114 " --> pdb=" O SER D 110 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N SER D 115 " --> pdb=" O LEU D 111 " (cutoff:3.500A) Processing helix chain 'D' and resid 122 through 127 removed outlier: 3.558A pdb=" N LEU D 125 " --> pdb=" O LEU D 122 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N CYS D 126 " --> pdb=" O THR D 123 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N VAL D 127 " --> pdb=" O PRO D 124 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 122 through 127' Processing helix chain 'D' and resid 139 through 151 removed outlier: 3.570A pdb=" N MET D 150 " --> pdb=" O THR D 139 " (cutoff:3.500A) Processing helix chain 'D' and resid 195 through 198 Processing helix chain 'D' and resid 334 through 350 removed outlier: 3.543A pdb=" N LYS D 347 " --> pdb=" O GLY D 343 " (cutoff:3.500A) Processing helix chain 'D' and resid 368 through 373 removed outlier: 3.887A pdb=" N THR D 373 " --> pdb=" O LEU D 369 " (cutoff:3.500A) Processing helix chain 'D' and resid 476 through 481 removed outlier: 4.045A pdb=" N SER D 481 " --> pdb=" O ASP D 477 " (cutoff:3.500A) Processing helix chain 'E' and resid 513 through 517 Processing helix chain 'E' and resid 531 through 535 removed outlier: 4.105A pdb=" N MET E 535 " --> pdb=" O ALA E 532 " (cutoff:3.500A) Processing helix chain 'E' and resid 536 through 542 removed outlier: 4.070A pdb=" N GLN E 540 " --> pdb=" O THR E 536 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ALA E 541 " --> pdb=" O LEU E 537 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ARG E 542 " --> pdb=" O THR E 538 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 536 through 542' Processing helix chain 'E' and resid 572 through 596 removed outlier: 3.913A pdb=" N TYR E 586 " --> pdb=" O ALA E 582 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LEU E 593 " --> pdb=" O ASP E 589 " (cutoff:3.500A) Processing helix chain 'E' and resid 618 through 622 removed outlier: 3.517A pdb=" N ILE E 622 " --> pdb=" O LEU E 619 " (cutoff:3.500A) Processing helix chain 'E' and resid 630 through 636 removed outlier: 4.087A pdb=" N GLU E 634 " --> pdb=" O GLN E 630 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ILE E 635 " --> pdb=" O TRP E 631 " (cutoff:3.500A) Processing helix chain 'E' and resid 638 through 662 removed outlier: 3.679A pdb=" N LEU E 645 " --> pdb=" O ILE E 641 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LEU E 646 " --> pdb=" O ILE E 642 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N GLU E 647 " --> pdb=" O TYR E 643 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ASN E 651 " --> pdb=" O GLU E 647 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N LYS E 655 " --> pdb=" O ASN E 651 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ASN E 656 " --> pdb=" O GLN E 652 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LEU E 660 " --> pdb=" O ASN E 656 " (cutoff:3.500A) Processing helix chain 'J' and resid 98 through 115 removed outlier: 4.102A pdb=" N GLU J 102 " --> pdb=" O ASN J 98 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ILE J 109 " --> pdb=" O HIS J 105 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N SER J 115 " --> pdb=" O LEU J 111 " (cutoff:3.500A) Processing helix chain 'J' and resid 122 through 127 removed outlier: 3.759A pdb=" N CYS J 126 " --> pdb=" O THR J 123 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N VAL J 127 " --> pdb=" O PRO J 124 " (cutoff:3.500A) Processing helix chain 'J' and resid 334 through 353 removed outlier: 3.977A pdb=" N LYS J 347 " --> pdb=" O GLY J 343 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N GLN J 348 " --> pdb=" O LYS J 344 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N LYS J 351 " --> pdb=" O LYS J 347 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N HIS J 352 " --> pdb=" O GLN J 348 " (cutoff:3.500A) Processing helix chain 'J' and resid 368 through 373 removed outlier: 3.787A pdb=" N THR J 373 " --> pdb=" O LEU J 369 " (cutoff:3.500A) Processing helix chain 'J' and resid 377 through 381 removed outlier: 4.135A pdb=" N GLY J 380 " --> pdb=" O ASN J 377 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N GLU J 381 " --> pdb=" O CYS J 378 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 377 through 381' Processing helix chain 'J' and resid 474 through 482 removed outlier: 3.561A pdb=" N TRP J 479 " --> pdb=" O ARG J 476 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ARG J 480 " --> pdb=" O ASP J 477 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N SER J 481 " --> pdb=" O ASN J 478 " (cutoff:3.500A) Processing helix chain 'K' and resid 513 through 517 removed outlier: 3.699A pdb=" N ALA K 517 " --> pdb=" O GLY K 514 " (cutoff:3.500A) Processing helix chain 'K' and resid 529 through 534 Processing helix chain 'K' and resid 575 through 596 removed outlier: 3.502A pdb=" N LEU K 592 " --> pdb=" O ARG K 588 " (cutoff:3.500A) Processing helix chain 'K' and resid 627 through 635 removed outlier: 3.533A pdb=" N TRP K 631 " --> pdb=" O THR K 627 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N LYS K 633 " --> pdb=" O LEU K 629 " (cutoff:3.500A) Processing helix chain 'K' and resid 638 through 662 removed outlier: 3.689A pdb=" N ILE K 642 " --> pdb=" O TYR K 638 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLY K 644 " --> pdb=" O GLN K 640 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N LEU K 646 " --> pdb=" O ILE K 642 " (cutoff:3.500A) removed outlier: 4.721A pdb=" N GLU K 647 " --> pdb=" O TYR K 643 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N GLU K 648 " --> pdb=" O GLY K 644 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N GLN K 652 " --> pdb=" O GLU K 648 " (cutoff:3.500A) Processing helix chain 'H' and resid 61 through 64 Processing helix chain 'H' and resid 83 through 87 Processing helix chain 'L' and resid 79 through 83 Processing helix chain 'A' and resid 61 through 64 Processing helix chain 'A' and resid 83 through 87 Processing helix chain 'C' and resid 79 through 83 removed outlier: 3.524A pdb=" N ASP C 82 " --> pdb=" O GLN C 79 " (cutoff:3.500A) Processing helix chain 'F' and resid 61 through 64 Processing helix chain 'F' and resid 83 through 87 Processing helix chain 'I' and resid 79 through 83 Processing sheet with id=AA1, first strand: chain 'G' and resid 494 through 499 removed outlier: 3.551A pdb=" N CYS B 604 " --> pdb=" O VAL G 38 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'G' and resid 45 through 46 removed outlier: 3.899A pdb=" N ILE G 225 " --> pdb=" O VAL G 245 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'G' and resid 91 through 93 removed outlier: 3.835A pdb=" N GLU G 91 " --> pdb=" O CYS G 239 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLY G 237 " --> pdb=" O PHE G 93 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'G' and resid 130 through 133 Processing sheet with id=AA5, first strand: chain 'G' and resid 181 through 182 Processing sheet with id=AA6, first strand: chain 'G' and resid 271 through 273 removed outlier: 3.621A pdb=" N MET G 271 " --> pdb=" O GLN G 287 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N THR G 297 " --> pdb=" O HIS G 330 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N HIS G 330 " --> pdb=" O THR G 297 " (cutoff:3.500A) removed outlier: 4.743A pdb=" N ALA G 329 " --> pdb=" O CYS G 418 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N PHE G 383 " --> pdb=" O PHE G 376 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N PHE G 376 " --> pdb=" O PHE G 383 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'G' and resid 271 through 273 removed outlier: 3.621A pdb=" N MET G 271 " --> pdb=" O GLN G 287 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N THR G 450 " --> pdb=" O PHE G 288 " (cutoff:3.500A) removed outlier: 10.782A pdb=" N THR G 290 " --> pdb=" O ASN G 448 " (cutoff:3.500A) removed outlier: 9.811A pdb=" N ASN G 448 " --> pdb=" O THR G 290 " (cutoff:3.500A) removed outlier: 10.652A pdb=" N VAL G 292 " --> pdb=" O VAL G 446 " (cutoff:3.500A) removed outlier: 9.754A pdb=" N VAL G 446 " --> pdb=" O VAL G 292 " (cutoff:3.500A) removed outlier: 11.186A pdb=" N ILE G 294 " --> pdb=" O ARG G 444 " (cutoff:3.500A) removed outlier: 9.955A pdb=" N ARG G 444 " --> pdb=" O ILE G 294 " (cutoff:3.500A) removed outlier: 10.634A pdb=" N CYS G 296 " --> pdb=" O VAL G 442 " (cutoff:3.500A) removed outlier: 10.163A pdb=" N VAL G 442 " --> pdb=" O CYS G 296 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N ARG G 360 " --> pdb=" O PHE G 468 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'G' and resid 304 through 312 removed outlier: 6.910A pdb=" N GLN G 315 " --> pdb=" O ILE G 309 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 494 through 495 Processing sheet with id=AB1, first strand: chain 'D' and resid 494 through 495 Processing sheet with id=AB2, first strand: chain 'D' and resid 45 through 46 removed outlier: 3.918A pdb=" N ILE D 225 " --> pdb=" O VAL D 245 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 75 through 76 removed outlier: 4.339A pdb=" N VAL D 75 " --> pdb=" O CYS D 54 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N SER D 56 " --> pdb=" O VAL D 75 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 91 through 93 removed outlier: 3.547A pdb=" N GLU D 91 " --> pdb=" O CYS D 239 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 132 through 133 removed outlier: 3.690A pdb=" N VAL D 172 " --> pdb=" O PHE D 159 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 181 through 182 Processing sheet with id=AB7, first strand: chain 'D' and resid 259 through 261 removed outlier: 6.337A pdb=" N LEU D 260 " --> pdb=" O THR D 450 " (cutoff:3.500A) removed outlier: 10.007A pdb=" N ARG D 444 " --> pdb=" O ILE D 294 " (cutoff:3.500A) removed outlier: 11.235A pdb=" N ILE D 294 " --> pdb=" O ARG D 444 " (cutoff:3.500A) removed outlier: 9.647A pdb=" N VAL D 446 " --> pdb=" O VAL D 292 " (cutoff:3.500A) removed outlier: 10.609A pdb=" N VAL D 292 " --> pdb=" O VAL D 446 " (cutoff:3.500A) removed outlier: 8.611A pdb=" N ASN D 448 " --> pdb=" O THR D 290 " (cutoff:3.500A) removed outlier: 10.033A pdb=" N THR D 290 " --> pdb=" O ASN D 448 " (cutoff:3.500A) removed outlier: 7.116A pdb=" N THR D 450 " --> pdb=" O PHE D 288 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N HIS D 330 " --> pdb=" O THR D 297 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N VAL D 333 " --> pdb=" O ILE D 414 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N PHE D 383 " --> pdb=" O PHE D 376 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N PHE D 376 " --> pdb=" O PHE D 383 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 271 through 273 removed outlier: 3.503A pdb=" N LEU D 285 " --> pdb=" O ARG D 273 " (cutoff:3.500A) removed outlier: 7.116A pdb=" N THR D 450 " --> pdb=" O PHE D 288 " (cutoff:3.500A) removed outlier: 10.033A pdb=" N THR D 290 " --> pdb=" O ASN D 448 " (cutoff:3.500A) removed outlier: 8.611A pdb=" N ASN D 448 " --> pdb=" O THR D 290 " (cutoff:3.500A) removed outlier: 10.609A pdb=" N VAL D 292 " --> pdb=" O VAL D 446 " (cutoff:3.500A) removed outlier: 9.647A pdb=" N VAL D 446 " --> pdb=" O VAL D 292 " (cutoff:3.500A) removed outlier: 11.235A pdb=" N ILE D 294 " --> pdb=" O ARG D 444 " (cutoff:3.500A) removed outlier: 10.007A pdb=" N ARG D 444 " --> pdb=" O ILE D 294 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N ARG D 360 " --> pdb=" O PHE D 468 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N SER D 393 " --> pdb=" O PHE D 361 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 304 through 312 removed outlier: 6.843A pdb=" N GLN D 315 " --> pdb=" O ILE D 309 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'J' and resid 494 through 499 removed outlier: 4.979A pdb=" N VAL J 36 " --> pdb=" O THR K 606 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'J' and resid 45 through 46 removed outlier: 3.787A pdb=" N ILE J 225 " --> pdb=" O VAL J 245 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'J' and resid 91 through 93 Processing sheet with id=AC4, first strand: chain 'J' and resid 130 through 133 Processing sheet with id=AC5, first strand: chain 'J' and resid 181 through 182 Processing sheet with id=AC6, first strand: chain 'J' and resid 259 through 261 removed outlier: 6.172A pdb=" N LEU J 260 " --> pdb=" O THR J 450 " (cutoff:3.500A) removed outlier: 10.514A pdb=" N VAL J 442 " --> pdb=" O CYS J 296 " (cutoff:3.500A) removed outlier: 11.451A pdb=" N CYS J 296 " --> pdb=" O VAL J 442 " (cutoff:3.500A) removed outlier: 9.996A pdb=" N ARG J 444 " --> pdb=" O ILE J 294 " (cutoff:3.500A) removed outlier: 11.160A pdb=" N ILE J 294 " --> pdb=" O ARG J 444 " (cutoff:3.500A) removed outlier: 9.729A pdb=" N VAL J 446 " --> pdb=" O VAL J 292 " (cutoff:3.500A) removed outlier: 10.896A pdb=" N VAL J 292 " --> pdb=" O VAL J 446 " (cutoff:3.500A) removed outlier: 9.531A pdb=" N ASN J 448 " --> pdb=" O THR J 290 " (cutoff:3.500A) removed outlier: 10.584A pdb=" N THR J 290 " --> pdb=" O ASN J 448 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N THR J 450 " --> pdb=" O PHE J 288 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N HIS J 330 " --> pdb=" O THR J 297 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N VAL J 333 " --> pdb=" O ILE J 414 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N PHE J 376 " --> pdb=" O PHE J 383 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'J' and resid 271 through 273 removed outlier: 3.934A pdb=" N MET J 271 " --> pdb=" O GLN J 287 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N GLN J 287 " --> pdb=" O MET J 271 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LEU J 285 " --> pdb=" O ARG J 273 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N THR J 450 " --> pdb=" O PHE J 288 " (cutoff:3.500A) removed outlier: 10.584A pdb=" N THR J 290 " --> pdb=" O ASN J 448 " (cutoff:3.500A) removed outlier: 9.531A pdb=" N ASN J 448 " --> pdb=" O THR J 290 " (cutoff:3.500A) removed outlier: 10.896A pdb=" N VAL J 292 " --> pdb=" O VAL J 446 " (cutoff:3.500A) removed outlier: 9.729A pdb=" N VAL J 446 " --> pdb=" O VAL J 292 " (cutoff:3.500A) removed outlier: 11.160A pdb=" N ILE J 294 " --> pdb=" O ARG J 444 " (cutoff:3.500A) removed outlier: 9.996A pdb=" N ARG J 444 " --> pdb=" O ILE J 294 " (cutoff:3.500A) removed outlier: 11.451A pdb=" N CYS J 296 " --> pdb=" O VAL J 442 " (cutoff:3.500A) removed outlier: 10.514A pdb=" N VAL J 442 " --> pdb=" O CYS J 296 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N ARG J 360 " --> pdb=" O PHE J 468 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N SER J 393 " --> pdb=" O PHE J 361 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'J' and resid 305 through 312 removed outlier: 6.840A pdb=" N GLN J 315 " --> pdb=" O ILE J 309 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'J' and resid 423 through 425 Processing sheet with id=AD1, first strand: chain 'H' and resid 3 through 7 removed outlier: 3.563A pdb=" N GLN H 3 " --> pdb=" O THR H 25 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N SER H 68 " --> pdb=" O LYS H 81 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'H' and resid 11 through 12 removed outlier: 3.674A pdb=" N THR H 107 " --> pdb=" O TYR H 90 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N LEU H 109 " --> pdb=" O ALA H 88 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N ALA H 88 " --> pdb=" O LEU H 109 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N GLU H 95 " --> pdb=" O TYR H 34 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N TYR H 34 " --> pdb=" O GLU H 95 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N TRP H 35 " --> pdb=" O TYR H 50 " (cutoff:3.500A) removed outlier: 4.635A pdb=" N TYR H 50 " --> pdb=" O TRP H 35 " (cutoff:3.500A) removed outlier: 7.066A pdb=" N TRP H 36 " --> pdb=" O MET H 48 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N GLY H 58 " --> pdb=" O TYR H 50 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'H' and resid 11 through 12 removed outlier: 3.674A pdb=" N THR H 107 " --> pdb=" O TYR H 90 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N LEU H 109 " --> pdb=" O ALA H 88 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N ALA H 88 " --> pdb=" O LEU H 109 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'L' and resid 5 through 6 removed outlier: 3.504A pdb=" N THR L 5 " --> pdb=" O LYS L 24 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LYS L 24 " --> pdb=" O THR L 5 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N PHE L 71 " --> pdb=" O CYS L 23 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'L' and resid 10 through 12 removed outlier: 6.336A pdb=" N MET L 11 " --> pdb=" O GLU L 105 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N VAL L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) removed outlier: 4.893A pdb=" N TYR L 49 " --> pdb=" O VAL L 33 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N TYR L 49 " --> pdb=" O THR L 53 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N THR L 53 " --> pdb=" O TYR L 49 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'A' and resid 3 through 7 removed outlier: 3.553A pdb=" N PHE A 78 " --> pdb=" O CYS A 22 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'A' and resid 11 through 12 removed outlier: 3.702A pdb=" N LEU A 109 " --> pdb=" O ALA A 88 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ALA A 88 " --> pdb=" O LEU A 109 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N TRP A 35 " --> pdb=" O TYR A 50 " (cutoff:3.500A) removed outlier: 4.964A pdb=" N TYR A 50 " --> pdb=" O TRP A 35 " (cutoff:3.500A) removed outlier: 7.355A pdb=" N TRP A 36 " --> pdb=" O MET A 48 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N MET A 48 " --> pdb=" O TRP A 36 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ARG A 38 " --> pdb=" O GLU A 46 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N LYS A 44 " --> pdb=" O PHE A 40 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N GLY A 58 " --> pdb=" O TYR A 50 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'A' and resid 11 through 12 removed outlier: 3.702A pdb=" N LEU A 109 " --> pdb=" O ALA A 88 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ALA A 88 " --> pdb=" O LEU A 109 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 4 through 6 Processing sheet with id=AE1, first strand: chain 'C' and resid 10 through 12 removed outlier: 6.553A pdb=" N MET C 11 " --> pdb=" O GLU C 105 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N VAL C 33 " --> pdb=" O TYR C 49 " (cutoff:3.500A) removed outlier: 4.745A pdb=" N TYR C 49 " --> pdb=" O VAL C 33 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N TRP C 35 " --> pdb=" O LEU C 47 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N TYR C 49 " --> pdb=" O THR C 53 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N THR C 53 " --> pdb=" O TYR C 49 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'F' and resid 3 through 7 Processing sheet with id=AE3, first strand: chain 'F' and resid 11 through 12 removed outlier: 3.652A pdb=" N VAL F 12 " --> pdb=" O ILE F 110 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N THR F 107 " --> pdb=" O TYR F 90 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N LEU F 109 " --> pdb=" O ALA F 88 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N ALA F 88 " --> pdb=" O LEU F 109 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N TRP F 35 " --> pdb=" O TYR F 50 " (cutoff:3.500A) removed outlier: 4.683A pdb=" N TYR F 50 " --> pdb=" O TRP F 35 " (cutoff:3.500A) removed outlier: 7.304A pdb=" N TRP F 36 " --> pdb=" O MET F 48 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N MET F 48 " --> pdb=" O TRP F 36 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ARG F 38 " --> pdb=" O GLU F 46 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N LYS F 44 " --> pdb=" O PHE F 40 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N GLY F 58 " --> pdb=" O TYR F 50 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'F' and resid 11 through 12 removed outlier: 3.652A pdb=" N VAL F 12 " --> pdb=" O ILE F 110 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N THR F 107 " --> pdb=" O TYR F 90 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N LEU F 109 " --> pdb=" O ALA F 88 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N ALA F 88 " --> pdb=" O LEU F 109 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'I' and resid 4 through 6 Processing sheet with id=AE6, first strand: chain 'I' and resid 10 through 12 removed outlier: 6.616A pdb=" N MET I 11 " --> pdb=" O GLU I 105 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N VAL I 33 " --> pdb=" O TYR I 49 " (cutoff:3.500A) removed outlier: 4.759A pdb=" N TYR I 49 " --> pdb=" O VAL I 33 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N TRP I 35 " --> pdb=" O LEU I 47 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N TYR I 49 " --> pdb=" O THR I 53 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N THR I 53 " --> pdb=" O TYR I 49 " (cutoff:3.500A) 585 hydrogen bonds defined for protein. 1485 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: 3.60 Time building geometry restraints manager: 2.55 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 6274 1.34 - 1.47: 5131 1.47 - 1.59: 8916 1.59 - 1.71: 0 1.71 - 1.83: 174 Bond restraints: 20495 Sorted by residual: bond pdb=" C1 NAG D 610 " pdb=" O5 NAG D 610 " ideal model delta sigma weight residual 1.406 1.494 -0.088 2.00e-02 2.50e+03 1.95e+01 bond pdb=" C1 NAG G 610 " pdb=" O5 NAG G 610 " ideal model delta sigma weight residual 1.406 1.489 -0.083 2.00e-02 2.50e+03 1.72e+01 bond pdb=" C1 NAG c 1 " pdb=" O5 NAG c 1 " ideal model delta sigma weight residual 1.406 1.487 -0.081 2.00e-02 2.50e+03 1.63e+01 bond pdb=" C1 MAN M 5 " pdb=" C2 MAN M 5 " ideal model delta sigma weight residual 1.526 1.581 -0.055 2.00e-02 2.50e+03 7.46e+00 bond pdb=" C1 MAN M 5 " pdb=" O5 MAN M 5 " ideal model delta sigma weight residual 1.399 1.454 -0.055 2.00e-02 2.50e+03 7.46e+00 ... (remaining 20490 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.22: 27586 4.22 - 8.43: 225 8.43 - 12.65: 14 12.65 - 16.86: 3 16.86 - 21.08: 2 Bond angle restraints: 27830 Sorted by residual: angle pdb=" CG ARG H 94 " pdb=" CD ARG H 94 " pdb=" NE ARG H 94 " ideal model delta sigma weight residual 112.00 90.92 21.08 2.20e+00 2.07e-01 9.18e+01 angle pdb=" C ALA H 32 " pdb=" N TYR H 33 " pdb=" CA TYR H 33 " ideal model delta sigma weight residual 121.74 136.28 -14.54 1.58e+00 4.01e-01 8.47e+01 angle pdb=" CB ARG H 94 " pdb=" CG ARG H 94 " pdb=" CD ARG H 94 " ideal model delta sigma weight residual 111.30 128.66 -17.36 2.30e+00 1.89e-01 5.70e+01 angle pdb=" CA ARG H 94 " pdb=" CB ARG H 94 " pdb=" CG ARG H 94 " ideal model delta sigma weight residual 114.10 128.29 -14.19 2.00e+00 2.50e-01 5.03e+01 angle pdb=" C LYS H 64 " pdb=" CA LYS H 64 " pdb=" CB LYS H 64 " ideal model delta sigma weight residual 116.54 109.04 7.50 1.15e+00 7.56e-01 4.25e+01 ... (remaining 27825 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.04: 12508 24.04 - 48.07: 712 48.07 - 72.11: 146 72.11 - 96.15: 65 96.15 - 120.18: 50 Dihedral angle restraints: 13481 sinusoidal: 6593 harmonic: 6888 Sorted by residual: dihedral pdb=" CB CYS G 218 " pdb=" SG CYS G 218 " pdb=" SG CYS G 247 " pdb=" CB CYS G 247 " ideal model delta sinusoidal sigma weight residual -86.00 -5.65 -80.35 1 1.00e+01 1.00e-02 7.99e+01 dihedral pdb=" CB CYS G 201 " pdb=" SG CYS G 201 " pdb=" SG CYS G 433 " pdb=" CB CYS G 433 " ideal model delta sinusoidal sigma weight residual -86.00 -16.38 -69.62 1 1.00e+01 1.00e-02 6.26e+01 dihedral pdb=" CB CYS J 54 " pdb=" SG CYS J 54 " pdb=" SG CYS J 74 " pdb=" CB CYS J 74 " ideal model delta sinusoidal sigma weight residual -86.00 -16.88 -69.12 1 1.00e+01 1.00e-02 6.18e+01 ... (remaining 13478 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.095: 3035 0.095 - 0.190: 333 0.190 - 0.285: 20 0.285 - 0.380: 5 0.380 - 0.474: 2 Chirality restraints: 3395 Sorted by residual: chirality pdb=" C1 NAG B 701 " pdb=" ND2 ASN B 611 " pdb=" C2 NAG B 701 " pdb=" O5 NAG B 701 " both_signs ideal model delta sigma weight residual False -2.40 -1.93 -0.47 2.00e-01 2.50e+01 5.63e+00 chirality pdb=" C1 NAG E 701 " pdb=" ND2 ASN E 611 " pdb=" C2 NAG E 701 " pdb=" O5 NAG E 701 " both_signs ideal model delta sigma weight residual False -2.40 -2.00 -0.40 2.00e-01 2.50e+01 4.05e+00 chirality pdb=" C1 NAG D 605 " pdb=" ND2 ASN D 276 " pdb=" C2 NAG D 605 " pdb=" O5 NAG D 605 " both_signs ideal model delta sigma weight residual False -2.40 -2.07 -0.33 2.00e-01 2.50e+01 2.68e+00 ... (remaining 3392 not shown) Planarity restraints: 3472 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG F 94 " 0.096 9.50e-02 1.11e+02 5.47e-02 1.54e+01 pdb=" NE ARG F 94 " -0.027 2.00e-02 2.50e+03 pdb=" CZ ARG F 94 " 0.064 2.00e-02 2.50e+03 pdb=" NH1 ARG F 94 " -0.023 2.00e-02 2.50e+03 pdb=" NH2 ARG F 94 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA D 497 " -0.062 5.00e-02 4.00e+02 9.49e-02 1.44e+01 pdb=" N PRO D 498 " 0.164 5.00e-02 4.00e+02 pdb=" CA PRO D 498 " -0.051 5.00e-02 4.00e+02 pdb=" CD PRO D 498 " -0.051 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL G 42 " 0.042 5.00e-02 4.00e+02 6.48e-02 6.72e+00 pdb=" N PRO G 43 " -0.112 5.00e-02 4.00e+02 pdb=" CA PRO G 43 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO G 43 " 0.036 5.00e-02 4.00e+02 ... (remaining 3469 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 4061 2.79 - 3.32: 16698 3.32 - 3.84: 31260 3.84 - 4.37: 34508 4.37 - 4.90: 60633 Nonbonded interactions: 147160 Sorted by model distance: nonbonded pdb=" OG SER C 12 " pdb=" OE1 GLU C 105 " model vdw 2.259 3.040 nonbonded pdb=" O ILE J 277 " pdb=" NH2 ARG J 456 " model vdw 2.309 3.120 nonbonded pdb=" NZ LYS L 24 " pdb=" OD2 ASP L 70 " model vdw 2.315 3.120 nonbonded pdb=" OG SER G 264 " pdb=" OE2 GLU G 482 " model vdw 2.319 3.040 nonbonded pdb=" OD1 ASN G 283 " pdb=" OG1 THR G 455 " model vdw 2.327 3.040 ... (remaining 147155 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'F' selection = chain 'H' } ncs_group { reference = (chain 'B' and resid 512 through 701) selection = (chain 'E' and resid 512 through 701) selection = chain 'K' } ncs_group { reference = chain 'C' selection = chain 'I' selection = chain 'L' } ncs_group { reference = chain 'D' selection = chain 'G' selection = chain 'J' } ncs_group { reference = chain 'M' selection = chain 'T' selection = chain 'd' } ncs_group { reference = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'U' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' selection = chain 'e' selection = chain 'f' selection = chain 'g' } ncs_group { reference = chain 'S' selection = chain 'V' } ncs_group { reference = chain 'b' selection = chain 'c' selection = chain 'h' selection = chain 'i' } 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: 2.130 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: 0.020 Extract box with map and model: 0.240 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 19.150 Find NCS groups from input model: 0.310 Set up NCS constraints: 0.060 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:1.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.190 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7327 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 : 0.005 0.088 20631 Z= 0.268 Angle : 1.025 21.075 28196 Z= 0.509 Chirality : 0.058 0.474 3395 Planarity : 0.005 0.095 3416 Dihedral : 17.496 120.185 8915 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 3.76 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.61 % Favored : 95.31 % Rotamer: Outliers : 0.09 % Allowed : 1.09 % Favored : 98.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.62 (0.16), residues: 2343 helix: -3.31 (0.18), residues: 337 sheet: 0.51 (0.21), residues: 552 loop : -1.18 (0.15), residues: 1454 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.065 0.002 ARG F 94 TYR 0.029 0.002 TYR F 50 PHE 0.020 0.001 PHE I 98 TRP 0.028 0.002 TRP G 427 HIS 0.006 0.001 HIS I 89 Details of bonding type rmsd covalent geometry : bond 0.00533 (20495) covalent geometry : angle 0.96941 (27830) SS BOND : bond 0.00537 ( 42) SS BOND : angle 1.55605 ( 84) hydrogen bonds : bond 0.28576 ( 564) hydrogen bonds : angle 9.96664 ( 1485) link_ALPHA1-3 : bond 0.00996 ( 4) link_ALPHA1-3 : angle 1.78245 ( 12) link_ALPHA1-6 : bond 0.00903 ( 4) link_ALPHA1-6 : angle 1.85980 ( 12) link_BETA1-4 : bond 0.01073 ( 30) link_BETA1-4 : angle 3.32834 ( 90) link_NAG-ASN : bond 0.00663 ( 56) link_NAG-ASN : angle 3.59677 ( 168) *********************** 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 274 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 272 time to evaluate : 0.776 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: B 581 LEU cc_start: 0.7663 (tp) cc_final: 0.7320 (tp) REVERT: K 536 THR cc_start: 0.7416 (p) cc_final: 0.7183 (p) REVERT: K 624 ASP cc_start: 0.7083 (p0) cc_final: 0.6474 (p0) REVERT: H 77 GLN cc_start: 0.8602 (mt0) cc_final: 0.7868 (mt0) REVERT: L 20 SER cc_start: 0.7916 (p) cc_final: 0.7284 (t) REVERT: A 77 GLN cc_start: 0.8585 (mt0) cc_final: 0.8155 (mt0) REVERT: C 1 ASP cc_start: 0.7041 (m-30) cc_final: 0.6327 (t0) REVERT: C 3 VAL cc_start: 0.9264 (t) cc_final: 0.9009 (m) REVERT: F 35 TRP cc_start: 0.8002 (m100) cc_final: 0.7496 (m100) REVERT: F 48 MET cc_start: 0.7397 (ptp) cc_final: 0.7142 (mpp) REVERT: F 109 LEU cc_start: 0.6502 (mt) cc_final: 0.6221 (mm) REVERT: I 3 VAL cc_start: 0.8156 (t) cc_final: 0.7756 (p) REVERT: I 4 MET cc_start: 0.6818 (mmm) cc_final: 0.4642 (mtp) outliers start: 2 outliers final: 1 residues processed: 274 average time/residue: 0.1753 time to fit residues: 69.3995 Evaluate side-chains 125 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 124 time to evaluate : 0.981 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 19 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 216 optimal weight: 20.0000 chunk 98 optimal weight: 6.9990 chunk 194 optimal weight: 9.9990 chunk 227 optimal weight: 20.0000 chunk 107 optimal weight: 6.9990 chunk 10 optimal weight: 9.9990 chunk 66 optimal weight: 9.9990 chunk 130 optimal weight: 0.4980 chunk 124 optimal weight: 9.9990 chunk 103 optimal weight: 10.0000 chunk 200 optimal weight: 9.9990 overall best weight: 6.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 203 GLN ** G 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 543 ASN ** D 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 216 HIS D 398 ASN E 653 GLN ** J 377 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 398 ASN J 478 ASN K 550 GLN K 651 ASN ** K 656 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 98 ASN L 37 GLN ** L 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 3 GLN ** A 35AASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 37 GLN ** C 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 6 GLN ** I 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.049416 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2829 r_free = 0.2829 target = 0.033434 restraints weight = 165186.040| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.2867 r_free = 0.2867 target = 0.034372 restraints weight = 92601.982| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.2892 r_free = 0.2892 target = 0.034978 restraints weight = 65803.597| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 50)----------------| | r_work = 0.2907 r_free = 0.2907 target = 0.035355 restraints weight = 53509.674| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.2916 r_free = 0.2916 target = 0.035594 restraints weight = 47283.094| |-----------------------------------------------------------------------------| r_work (final): 0.2879 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8339 moved from start: 0.3230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.098 20631 Z= 0.395 Angle : 1.005 15.978 28196 Z= 0.485 Chirality : 0.052 0.395 3395 Planarity : 0.006 0.084 3416 Dihedral : 14.142 106.688 4497 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 13.26 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.16 % Favored : 94.71 % Rotamer: Outliers : 1.70 % Allowed : 9.09 % Favored : 89.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.84 (0.17), residues: 2343 helix: -1.11 (0.26), residues: 358 sheet: -0.01 (0.20), residues: 672 loop : -0.62 (0.18), residues: 1313 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG L 61 TYR 0.025 0.002 TYR H 33 PHE 0.041 0.003 PHE D 382 TRP 0.024 0.003 TRP J 338 HIS 0.018 0.002 HIS C 8 Details of bonding type rmsd covalent geometry : bond 0.00856 (20495) covalent geometry : angle 0.95518 (27830) SS BOND : bond 0.00657 ( 42) SS BOND : angle 2.08513 ( 84) hydrogen bonds : bond 0.04647 ( 564) hydrogen bonds : angle 6.35839 ( 1485) link_ALPHA1-3 : bond 0.01295 ( 4) link_ALPHA1-3 : angle 3.22363 ( 12) link_ALPHA1-6 : bond 0.00862 ( 4) link_ALPHA1-6 : angle 2.59579 ( 12) link_BETA1-4 : bond 0.00736 ( 30) link_BETA1-4 : angle 2.57050 ( 90) link_NAG-ASN : bond 0.00808 ( 56) link_NAG-ASN : angle 3.36349 ( 168) *********************** 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 158 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 122 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: B 573 ILE cc_start: 0.9084 (pt) cc_final: 0.8832 (mp) REVERT: D 150 MET cc_start: 0.8836 (OUTLIER) cc_final: 0.8071 (mpp) REVERT: E 530 MET cc_start: 0.8875 (mtp) cc_final: 0.8605 (mtp) REVERT: J 390 LEU cc_start: 0.9591 (mt) cc_final: 0.9304 (tp) REVERT: K 581 LEU cc_start: 0.9686 (tt) cc_final: 0.9438 (pp) REVERT: K 589 ASP cc_start: 0.9429 (m-30) cc_final: 0.9217 (m-30) REVERT: L 11 MET cc_start: 0.2751 (ttp) cc_final: 0.2491 (ttp) REVERT: L 70 ASP cc_start: 0.9098 (t0) cc_final: 0.8799 (p0) REVERT: A 65 ASN cc_start: 0.9454 (t0) cc_final: 0.9210 (p0) REVERT: I 4 MET cc_start: 0.6236 (mmm) cc_final: 0.4829 (mtt) outliers start: 36 outliers final: 24 residues processed: 150 average time/residue: 0.1553 time to fit residues: 35.8094 Evaluate side-chains 125 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 100 time to evaluate : 0.815 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 37 THR Chi-restraints excluded: chain G residue 53 PHE Chi-restraints excluded: chain G residue 75 VAL Chi-restraints excluded: chain G residue 247 CYS Chi-restraints excluded: chain G residue 390 LEU Chi-restraints excluded: chain G residue 494 LEU Chi-restraints excluded: chain B residue 589 ASP Chi-restraints excluded: chain D residue 110 SER Chi-restraints excluded: chain D residue 150 MET Chi-restraints excluded: chain D residue 307 ILE Chi-restraints excluded: chain E residue 581 LEU Chi-restraints excluded: chain E residue 629 LEU Chi-restraints excluded: chain J residue 120 VAL Chi-restraints excluded: chain K residue 518 VAL Chi-restraints excluded: chain K residue 569 THR Chi-restraints excluded: chain K residue 632 ASP Chi-restraints excluded: chain H residue 15 SER Chi-restraints excluded: chain H residue 94 ARG Chi-restraints excluded: chain L residue 1 ASP Chi-restraints excluded: chain L residue 63 THR Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain C residue 11 MET Chi-restraints excluded: chain F residue 40 PHE Chi-restraints excluded: chain F residue 67 ILE Chi-restraints excluded: chain I residue 5 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 231 optimal weight: 30.0000 chunk 182 optimal weight: 30.0000 chunk 205 optimal weight: 9.9990 chunk 42 optimal weight: 4.9990 chunk 127 optimal weight: 2.9990 chunk 189 optimal weight: 20.0000 chunk 166 optimal weight: 0.0970 chunk 31 optimal weight: 5.9990 chunk 149 optimal weight: 0.7980 chunk 85 optimal weight: 5.9990 chunk 136 optimal weight: 2.9990 overall best weight: 2.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 105 HIS J 377 ASN ** H 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 65 ASN H 77 GLN A 35AASN ** C 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 97 ASN ** 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 = 0.3405 r_free = 0.3405 target = 0.050139 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2867 r_free = 0.2867 target = 0.034288 restraints weight = 163440.124| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.2909 r_free = 0.2909 target = 0.035354 restraints weight = 88063.005| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.2935 r_free = 0.2935 target = 0.036010 restraints weight = 60985.906| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.036404 restraints weight = 48723.059| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2961 r_free = 0.2961 target = 0.036671 restraints weight = 42563.109| |-----------------------------------------------------------------------------| r_work (final): 0.2924 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8280 moved from start: 0.3409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 20631 Z= 0.161 Angle : 0.722 14.794 28196 Z= 0.343 Chirality : 0.047 0.392 3395 Planarity : 0.004 0.065 3416 Dihedral : 12.227 104.662 4496 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 9.65 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.44 % Favored : 95.52 % Rotamer: Outliers : 2.04 % Allowed : 10.46 % Favored : 87.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.45 (0.18), residues: 2343 helix: -0.22 (0.28), residues: 358 sheet: 0.12 (0.20), residues: 666 loop : -0.47 (0.18), residues: 1319 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 9 TYR 0.023 0.001 TYR F 53 PHE 0.021 0.002 PHE H 78 TRP 0.012 0.001 TRP G 479 HIS 0.012 0.001 HIS C 8 Details of bonding type rmsd covalent geometry : bond 0.00349 (20495) covalent geometry : angle 0.66768 (27830) SS BOND : bond 0.00340 ( 42) SS BOND : angle 1.47284 ( 84) hydrogen bonds : bond 0.03862 ( 564) hydrogen bonds : angle 5.71631 ( 1485) link_ALPHA1-3 : bond 0.01778 ( 4) link_ALPHA1-3 : angle 2.97446 ( 12) link_ALPHA1-6 : bond 0.01437 ( 4) link_ALPHA1-6 : angle 2.60169 ( 12) link_BETA1-4 : bond 0.00572 ( 30) link_BETA1-4 : angle 2.35147 ( 90) link_NAG-ASN : bond 0.00477 ( 56) link_NAG-ASN : angle 2.90664 ( 168) *********************** 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 159 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 116 time to evaluate : 0.819 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: G 119 CYS cc_start: 0.8593 (OUTLIER) cc_final: 0.8386 (p) REVERT: G 475 MET cc_start: 0.8496 (tpp) cc_final: 0.8270 (tpp) REVERT: B 530 MET cc_start: 0.8919 (mmp) cc_final: 0.6707 (mmm) REVERT: B 573 ILE cc_start: 0.9119 (pt) cc_final: 0.8872 (mp) REVERT: B 626 MET cc_start: 0.7874 (tmm) cc_final: 0.7447 (tmm) REVERT: D 150 MET cc_start: 0.8774 (OUTLIER) cc_final: 0.8036 (mpp) REVERT: E 530 MET cc_start: 0.8802 (mtp) cc_final: 0.8536 (mtp) REVERT: J 104 MET cc_start: 0.9098 (ppp) cc_final: 0.8703 (ppp) REVERT: J 390 LEU cc_start: 0.9583 (mt) cc_final: 0.9208 (tp) REVERT: K 581 LEU cc_start: 0.9690 (tt) cc_final: 0.9398 (mm) REVERT: K 589 ASP cc_start: 0.9406 (m-30) cc_final: 0.9041 (m-30) REVERT: K 624 ASP cc_start: 0.9134 (p0) cc_final: 0.8804 (p0) REVERT: K 626 MET cc_start: 0.7627 (ppp) cc_final: 0.7010 (ppp) REVERT: H 65 ASN cc_start: 0.8850 (m-40) cc_final: 0.8493 (m110) REVERT: L 4 MET cc_start: 0.4327 (ptp) cc_final: 0.3773 (pmm) REVERT: L 11 MET cc_start: 0.2863 (ttp) cc_final: 0.2648 (ttp) REVERT: L 70 ASP cc_start: 0.9071 (t0) cc_final: 0.8754 (p0) REVERT: I 4 MET cc_start: 0.6425 (mmm) cc_final: 0.5022 (mtp) REVERT: I 11 MET cc_start: 0.4806 (ptt) cc_final: 0.4055 (pmm) outliers start: 43 outliers final: 24 residues processed: 155 average time/residue: 0.1330 time to fit residues: 31.8562 Evaluate side-chains 124 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 98 time to evaluate : 0.502 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 53 PHE Chi-restraints excluded: chain G residue 119 CYS Chi-restraints excluded: chain G residue 205 CYS Chi-restraints excluded: chain G residue 218 CYS Chi-restraints excluded: chain G residue 247 CYS Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain D residue 104 MET Chi-restraints excluded: chain D residue 110 SER Chi-restraints excluded: chain D residue 150 MET Chi-restraints excluded: chain D residue 307 ILE Chi-restraints excluded: chain E residue 569 THR Chi-restraints excluded: chain E residue 581 LEU Chi-restraints excluded: chain J residue 120 VAL Chi-restraints excluded: chain K residue 518 VAL Chi-restraints excluded: chain K residue 569 THR Chi-restraints excluded: chain H residue 15 SER Chi-restraints excluded: chain H residue 94 ARG Chi-restraints excluded: chain L residue 1 ASP Chi-restraints excluded: chain L residue 9 ARG Chi-restraints excluded: chain L residue 63 THR Chi-restraints excluded: chain A residue 64 LYS Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain C residue 11 MET Chi-restraints excluded: chain F residue 40 PHE Chi-restraints excluded: chain I residue 5 THR Chi-restraints excluded: chain I residue 75 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 46 optimal weight: 6.9990 chunk 129 optimal weight: 0.5980 chunk 177 optimal weight: 6.9990 chunk 41 optimal weight: 6.9990 chunk 70 optimal weight: 3.9990 chunk 111 optimal weight: 1.9990 chunk 113 optimal weight: 8.9990 chunk 12 optimal weight: 7.9990 chunk 155 optimal weight: 7.9990 chunk 73 optimal weight: 4.9990 chunk 4 optimal weight: 4.9990 overall best weight: 3.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 656 ASN ** H 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 97 ASN L 37 GLN C 6 GLN ** C 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 39 GLN ** F 97 ASN ** 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 = 0.3394 r_free = 0.3394 target = 0.049647 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.2845 r_free = 0.2845 target = 0.033796 restraints weight = 163779.056| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.2885 r_free = 0.2885 target = 0.034827 restraints weight = 89140.457| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.2911 r_free = 0.2911 target = 0.035473 restraints weight = 62024.204| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.2926 r_free = 0.2926 target = 0.035871 restraints weight = 49749.089| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 50)----------------| | r_work = 0.2934 r_free = 0.2934 target = 0.036100 restraints weight = 43510.450| |-----------------------------------------------------------------------------| r_work (final): 0.2892 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8318 moved from start: 0.3882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 20631 Z= 0.208 Angle : 0.748 14.633 28196 Z= 0.352 Chirality : 0.047 0.384 3395 Planarity : 0.004 0.067 3416 Dihedral : 10.901 99.812 4496 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 10.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.46 % Favored : 94.54 % Rotamer: Outliers : 2.46 % Allowed : 11.70 % Favored : 85.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.31 (0.18), residues: 2343 helix: 0.35 (0.29), residues: 357 sheet: 0.07 (0.20), residues: 672 loop : -0.44 (0.18), residues: 1314 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG K 542 TYR 0.017 0.001 TYR F 53 PHE 0.016 0.002 PHE G 53 TRP 0.019 0.002 TRP D 479 HIS 0.009 0.001 HIS C 8 Details of bonding type rmsd covalent geometry : bond 0.00457 (20495) covalent geometry : angle 0.69439 (27830) SS BOND : bond 0.00392 ( 42) SS BOND : angle 1.58436 ( 84) hydrogen bonds : bond 0.03483 ( 564) hydrogen bonds : angle 5.42110 ( 1485) link_ALPHA1-3 : bond 0.01868 ( 4) link_ALPHA1-3 : angle 3.15070 ( 12) link_ALPHA1-6 : bond 0.01577 ( 4) link_ALPHA1-6 : angle 2.61994 ( 12) link_BETA1-4 : bond 0.00546 ( 30) link_BETA1-4 : angle 2.31356 ( 90) link_NAG-ASN : bond 0.00524 ( 56) link_NAG-ASN : angle 2.96046 ( 168) *********************** 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 156 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 104 time to evaluate : 0.677 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: G 475 MET cc_start: 0.8459 (tpp) cc_final: 0.8166 (tpp) REVERT: B 530 MET cc_start: 0.8963 (mmp) cc_final: 0.6702 (mmm) REVERT: B 626 MET cc_start: 0.8009 (tmm) cc_final: 0.7673 (tmm) REVERT: D 150 MET cc_start: 0.8765 (OUTLIER) cc_final: 0.8032 (mpp) REVERT: E 530 MET cc_start: 0.8780 (mtp) cc_final: 0.8517 (mtp) REVERT: J 390 LEU cc_start: 0.9580 (mt) cc_final: 0.9270 (tp) REVERT: J 475 MET cc_start: 0.9278 (mmm) cc_final: 0.9004 (mmm) REVERT: K 530 MET cc_start: 0.7732 (mmp) cc_final: 0.7243 (mmt) REVERT: K 581 LEU cc_start: 0.9695 (tt) cc_final: 0.9407 (mm) REVERT: K 589 ASP cc_start: 0.9435 (m-30) cc_final: 0.9218 (m-30) REVERT: K 624 ASP cc_start: 0.9148 (p0) cc_final: 0.8849 (p0) REVERT: L 4 MET cc_start: 0.4667 (ptp) cc_final: 0.4134 (pmm) REVERT: L 70 ASP cc_start: 0.9145 (t0) cc_final: 0.8830 (p0) REVERT: F 29 ILE cc_start: 0.7500 (pt) cc_final: 0.6936 (mp) REVERT: F 35 TRP cc_start: 0.9060 (m100) cc_final: 0.8480 (m100) REVERT: I 4 MET cc_start: 0.6205 (mmm) cc_final: 0.5164 (mtt) outliers start: 52 outliers final: 31 residues processed: 146 average time/residue: 0.1438 time to fit residues: 33.3481 Evaluate side-chains 128 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 96 time to evaluate : 0.809 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 37 THR Chi-restraints excluded: chain G residue 53 PHE Chi-restraints excluded: chain G residue 218 CYS Chi-restraints excluded: chain G residue 247 CYS Chi-restraints excluded: chain B residue 573 ILE Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain D residue 110 SER Chi-restraints excluded: chain D residue 120 VAL Chi-restraints excluded: chain D residue 150 MET Chi-restraints excluded: chain D residue 162 THR Chi-restraints excluded: chain D residue 164 GLU Chi-restraints excluded: chain D residue 244 THR Chi-restraints excluded: chain D residue 245 VAL Chi-restraints excluded: chain D residue 307 ILE Chi-restraints excluded: chain D residue 423 ILE Chi-restraints excluded: chain E residue 569 THR Chi-restraints excluded: chain E residue 581 LEU Chi-restraints excluded: chain E residue 629 LEU Chi-restraints excluded: chain J residue 120 VAL Chi-restraints excluded: chain J residue 434 MET Chi-restraints excluded: chain K residue 518 VAL Chi-restraints excluded: chain K residue 569 THR Chi-restraints excluded: chain H residue 15 SER Chi-restraints excluded: chain H residue 33 TYR Chi-restraints excluded: chain H residue 94 ARG Chi-restraints excluded: chain L residue 63 THR Chi-restraints excluded: chain A residue 64 LYS Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain C residue 11 MET Chi-restraints excluded: chain F residue 40 PHE Chi-restraints excluded: chain F residue 67 ILE Chi-restraints excluded: chain I residue 75 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 224 optimal weight: 5.9990 chunk 177 optimal weight: 6.9990 chunk 6 optimal weight: 7.9990 chunk 143 optimal weight: 3.9990 chunk 172 optimal weight: 0.9990 chunk 41 optimal weight: 0.8980 chunk 159 optimal weight: 9.9990 chunk 187 optimal weight: 30.0000 chunk 75 optimal weight: 9.9990 chunk 137 optimal weight: 2.9990 chunk 209 optimal weight: 20.0000 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 170 GLN ** H 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 6 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.049531 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.2847 r_free = 0.2847 target = 0.033760 restraints weight = 163610.954| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.2889 r_free = 0.2889 target = 0.034791 restraints weight = 88826.830| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.2915 r_free = 0.2915 target = 0.035434 restraints weight = 62059.951| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2930 r_free = 0.2930 target = 0.035772 restraints weight = 50043.001| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 64)----------------| | r_work = 0.2938 r_free = 0.2938 target = 0.036038 restraints weight = 44241.755| |-----------------------------------------------------------------------------| r_work (final): 0.2889 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8325 moved from start: 0.4146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 20631 Z= 0.182 Angle : 0.720 14.317 28196 Z= 0.340 Chirality : 0.046 0.392 3395 Planarity : 0.004 0.059 3416 Dihedral : 9.844 92.266 4496 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 10.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 2.41 % Allowed : 12.74 % Favored : 84.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.24 (0.18), residues: 2343 helix: 0.54 (0.30), residues: 359 sheet: 0.08 (0.20), residues: 678 loop : -0.43 (0.18), residues: 1306 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 66 TYR 0.018 0.001 TYR F 53 PHE 0.014 0.001 PHE H 78 TRP 0.022 0.001 TRP D 45 HIS 0.007 0.001 HIS C 8 Details of bonding type rmsd covalent geometry : bond 0.00397 (20495) covalent geometry : angle 0.66485 (27830) SS BOND : bond 0.00370 ( 42) SS BOND : angle 1.54656 ( 84) hydrogen bonds : bond 0.03318 ( 564) hydrogen bonds : angle 5.20584 ( 1485) link_ALPHA1-3 : bond 0.02060 ( 4) link_ALPHA1-3 : angle 3.31126 ( 12) link_ALPHA1-6 : bond 0.01797 ( 4) link_ALPHA1-6 : angle 2.67346 ( 12) link_BETA1-4 : bond 0.00545 ( 30) link_BETA1-4 : angle 2.22835 ( 90) link_NAG-ASN : bond 0.00496 ( 56) link_NAG-ASN : angle 2.93032 ( 168) *********************** 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 151 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 100 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: B 530 MET cc_start: 0.8952 (mmp) cc_final: 0.6681 (mmm) REVERT: B 626 MET cc_start: 0.7999 (tmm) cc_final: 0.7600 (tmm) REVERT: D 104 MET cc_start: 0.9548 (OUTLIER) cc_final: 0.8934 (ppp) REVERT: J 390 LEU cc_start: 0.9585 (mt) cc_final: 0.9280 (tp) REVERT: K 530 MET cc_start: 0.7792 (mmp) cc_final: 0.7573 (mmm) REVERT: K 581 LEU cc_start: 0.9696 (tt) cc_final: 0.9353 (mm) REVERT: K 589 ASP cc_start: 0.9390 (m-30) cc_final: 0.9151 (m-30) REVERT: K 624 ASP cc_start: 0.9188 (p0) cc_final: 0.8873 (p0) REVERT: K 626 MET cc_start: 0.7034 (ppp) cc_final: 0.6764 (ppp) REVERT: L 4 MET cc_start: 0.4875 (ptp) cc_final: 0.4325 (pmm) REVERT: L 70 ASP cc_start: 0.9168 (t0) cc_final: 0.8823 (p0) REVERT: F 35 TRP cc_start: 0.9042 (m100) cc_final: 0.8688 (m100) REVERT: I 4 MET cc_start: 0.6127 (mmm) cc_final: 0.5074 (mtt) outliers start: 51 outliers final: 39 residues processed: 139 average time/residue: 0.1288 time to fit residues: 29.1786 Evaluate side-chains 131 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 91 time to evaluate : 0.588 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 37 THR Chi-restraints excluded: chain G residue 53 PHE Chi-restraints excluded: chain G residue 119 CYS Chi-restraints excluded: chain G residue 218 CYS Chi-restraints excluded: chain G residue 244 THR Chi-restraints excluded: chain G residue 247 CYS Chi-restraints excluded: chain G residue 272 ILE Chi-restraints excluded: chain B residue 573 ILE Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain D residue 45 TRP Chi-restraints excluded: chain D residue 104 MET Chi-restraints excluded: chain D residue 110 SER Chi-restraints excluded: chain D residue 162 THR Chi-restraints excluded: chain D residue 164 GLU Chi-restraints excluded: chain D residue 245 VAL Chi-restraints excluded: chain D residue 307 ILE Chi-restraints excluded: chain D residue 433 CYS Chi-restraints excluded: chain D residue 488 VAL Chi-restraints excluded: chain E residue 569 THR Chi-restraints excluded: chain E residue 581 LEU Chi-restraints excluded: chain J residue 36 VAL Chi-restraints excluded: chain J residue 53 PHE Chi-restraints excluded: chain J residue 120 VAL Chi-restraints excluded: chain J residue 434 MET Chi-restraints excluded: chain J residue 488 VAL Chi-restraints excluded: chain K residue 518 VAL Chi-restraints excluded: chain K residue 569 THR Chi-restraints excluded: chain K residue 573 ILE Chi-restraints excluded: chain H residue 15 SER Chi-restraints excluded: chain H residue 67 ILE Chi-restraints excluded: chain H residue 94 ARG Chi-restraints excluded: chain L residue 1 ASP Chi-restraints excluded: chain L residue 63 THR Chi-restraints excluded: chain A residue 64 LYS Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain C residue 11 MET Chi-restraints excluded: chain C residue 13 THR Chi-restraints excluded: chain F residue 40 PHE Chi-restraints excluded: chain F residue 67 ILE Chi-restraints excluded: chain I residue 75 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 37 optimal weight: 7.9990 chunk 105 optimal weight: 0.1980 chunk 171 optimal weight: 30.0000 chunk 96 optimal weight: 4.9990 chunk 20 optimal weight: 2.9990 chunk 165 optimal weight: 3.9990 chunk 216 optimal weight: 30.0000 chunk 65 optimal weight: 10.0000 chunk 67 optimal weight: 9.9990 chunk 48 optimal weight: 10.0000 chunk 89 optimal weight: 6.9990 overall best weight: 3.8388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 72 HIS J 377 ASN ** H 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 77 GLN ** C 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 6 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.048811 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2814 r_free = 0.2814 target = 0.033225 restraints weight = 170914.266| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2856 r_free = 0.2856 target = 0.034218 restraints weight = 94177.151| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.2881 r_free = 0.2881 target = 0.034854 restraints weight = 66595.983| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.2896 r_free = 0.2896 target = 0.035233 restraints weight = 53887.981| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.2904 r_free = 0.2904 target = 0.035398 restraints weight = 47442.632| |-----------------------------------------------------------------------------| r_work (final): 0.2852 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8376 moved from start: 0.4586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 20631 Z= 0.228 Angle : 0.760 14.396 28196 Z= 0.358 Chirality : 0.046 0.379 3395 Planarity : 0.004 0.064 3416 Dihedral : 9.128 91.252 4496 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 12.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.19 % Favored : 93.81 % Rotamer: Outliers : 3.03 % Allowed : 13.30 % Favored : 83.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.29 (0.18), residues: 2343 helix: 0.61 (0.29), residues: 359 sheet: -0.04 (0.20), residues: 681 loop : -0.43 (0.18), residues: 1303 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 94 TYR 0.015 0.001 TYR F 53 PHE 0.016 0.002 PHE G 53 TRP 0.018 0.002 TRP G 45 HIS 0.005 0.001 HIS C 8 Details of bonding type rmsd covalent geometry : bond 0.00499 (20495) covalent geometry : angle 0.70377 (27830) SS BOND : bond 0.00454 ( 42) SS BOND : angle 1.73904 ( 84) hydrogen bonds : bond 0.03377 ( 564) hydrogen bonds : angle 5.15836 ( 1485) link_ALPHA1-3 : bond 0.02246 ( 4) link_ALPHA1-3 : angle 3.47513 ( 12) link_ALPHA1-6 : bond 0.01867 ( 4) link_ALPHA1-6 : angle 2.78005 ( 12) link_BETA1-4 : bond 0.00570 ( 30) link_BETA1-4 : angle 2.23639 ( 90) link_NAG-ASN : bond 0.00579 ( 56) link_NAG-ASN : angle 3.04693 ( 168) *********************** 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 153 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 89 time to evaluate : 0.734 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: G 161 MET cc_start: 0.8920 (tpt) cc_final: 0.8616 (tpp) REVERT: B 530 MET cc_start: 0.8954 (mmp) cc_final: 0.6685 (mmm) REVERT: B 626 MET cc_start: 0.8004 (tmm) cc_final: 0.7569 (tmm) REVERT: D 104 MET cc_start: 0.9535 (OUTLIER) cc_final: 0.8978 (ppp) REVERT: J 100 MET cc_start: 0.9099 (mtp) cc_final: 0.8852 (mtm) REVERT: J 104 MET cc_start: 0.9176 (ppp) cc_final: 0.8973 (tmm) REVERT: J 271 MET cc_start: 0.8917 (mpp) cc_final: 0.8715 (mpp) REVERT: K 530 MET cc_start: 0.7814 (mmp) cc_final: 0.7302 (mmt) REVERT: K 581 LEU cc_start: 0.9697 (tt) cc_final: 0.9356 (mm) REVERT: K 589 ASP cc_start: 0.9407 (m-30) cc_final: 0.9169 (m-30) REVERT: K 626 MET cc_start: 0.7339 (ppp) cc_final: 0.6919 (ppp) REVERT: L 4 MET cc_start: 0.5260 (ptp) cc_final: 0.4810 (pmm) REVERT: L 70 ASP cc_start: 0.9257 (t0) cc_final: 0.8930 (p0) REVERT: F 35 TRP cc_start: 0.9063 (m100) cc_final: 0.8761 (m100) REVERT: I 4 MET cc_start: 0.5561 (mmm) cc_final: 0.4658 (mtt) outliers start: 64 outliers final: 48 residues processed: 144 average time/residue: 0.1331 time to fit residues: 30.7170 Evaluate side-chains 133 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 84 time to evaluate : 0.834 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 36 VAL Chi-restraints excluded: chain G residue 37 THR Chi-restraints excluded: chain G residue 53 PHE Chi-restraints excluded: chain G residue 119 CYS Chi-restraints excluded: chain G residue 141 ASP Chi-restraints excluded: chain G residue 218 CYS Chi-restraints excluded: chain G residue 244 THR Chi-restraints excluded: chain G residue 247 CYS Chi-restraints excluded: chain G residue 272 ILE Chi-restraints excluded: chain B residue 573 ILE Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain D residue 45 TRP Chi-restraints excluded: chain D residue 47 ASP Chi-restraints excluded: chain D residue 89 VAL Chi-restraints excluded: chain D residue 104 MET Chi-restraints excluded: chain D residue 110 SER Chi-restraints excluded: chain D residue 120 VAL Chi-restraints excluded: chain D residue 162 THR Chi-restraints excluded: chain D residue 164 GLU Chi-restraints excluded: chain D residue 244 THR Chi-restraints excluded: chain D residue 245 VAL Chi-restraints excluded: chain D residue 307 ILE Chi-restraints excluded: chain D residue 423 ILE Chi-restraints excluded: chain D residue 488 VAL Chi-restraints excluded: chain E residue 569 THR Chi-restraints excluded: chain E residue 581 LEU Chi-restraints excluded: chain E residue 610 TRP Chi-restraints excluded: chain E residue 629 LEU Chi-restraints excluded: chain J residue 36 VAL Chi-restraints excluded: chain J residue 120 VAL Chi-restraints excluded: chain J residue 434 MET Chi-restraints excluded: chain J residue 488 VAL Chi-restraints excluded: chain K residue 518 VAL Chi-restraints excluded: chain K residue 569 THR Chi-restraints excluded: chain K residue 573 ILE Chi-restraints excluded: chain K residue 610 TRP Chi-restraints excluded: chain H residue 15 SER Chi-restraints excluded: chain H residue 33 TYR Chi-restraints excluded: chain H residue 67 ILE Chi-restraints excluded: chain H residue 94 ARG Chi-restraints excluded: chain L residue 1 ASP Chi-restraints excluded: chain L residue 63 THR Chi-restraints excluded: chain A residue 64 LYS Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain C residue 11 MET Chi-restraints excluded: chain C residue 13 THR Chi-restraints excluded: chain F residue 40 PHE Chi-restraints excluded: chain F residue 67 ILE Chi-restraints excluded: chain I residue 75 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 33 optimal weight: 6.9990 chunk 65 optimal weight: 7.9990 chunk 182 optimal weight: 50.0000 chunk 150 optimal weight: 6.9990 chunk 233 optimal weight: 0.0970 chunk 183 optimal weight: 5.9990 chunk 143 optimal weight: 0.9980 chunk 230 optimal weight: 4.9990 chunk 75 optimal weight: 2.9990 chunk 48 optimal weight: 8.9990 chunk 87 optimal weight: 4.9990 overall best weight: 2.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.048923 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2836 r_free = 0.2836 target = 0.033536 restraints weight = 163386.034| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.2876 r_free = 0.2876 target = 0.034512 restraints weight = 90379.794| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.2900 r_free = 0.2900 target = 0.035100 restraints weight = 62999.295| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.2915 r_free = 0.2915 target = 0.035437 restraints weight = 51010.759| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.2925 r_free = 0.2925 target = 0.035671 restraints weight = 45205.668| |-----------------------------------------------------------------------------| r_work (final): 0.2883 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8348 moved from start: 0.4691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 20631 Z= 0.178 Angle : 0.718 14.171 28196 Z= 0.337 Chirality : 0.046 0.396 3395 Planarity : 0.004 0.058 3416 Dihedral : 8.669 91.118 4496 Min Nonbonded Distance : 2.314 Molprobity Statistics. All-atom Clashscore : 11.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.46 % Favored : 94.54 % Rotamer: Outliers : 2.89 % Allowed : 13.83 % Favored : 83.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.23 (0.18), residues: 2343 helix: 0.76 (0.30), residues: 359 sheet: -0.04 (0.20), residues: 678 loop : -0.40 (0.18), residues: 1306 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 94 TYR 0.011 0.001 TYR F 53 PHE 0.014 0.001 PHE H 78 TRP 0.021 0.002 TRP G 45 HIS 0.004 0.001 HIS D 105 Details of bonding type rmsd covalent geometry : bond 0.00388 (20495) covalent geometry : angle 0.66121 (27830) SS BOND : bond 0.00429 ( 42) SS BOND : angle 1.59918 ( 84) hydrogen bonds : bond 0.03178 ( 564) hydrogen bonds : angle 5.04149 ( 1485) link_ALPHA1-3 : bond 0.02482 ( 4) link_ALPHA1-3 : angle 3.53615 ( 12) link_ALPHA1-6 : bond 0.01841 ( 4) link_ALPHA1-6 : angle 2.88914 ( 12) link_BETA1-4 : bond 0.00554 ( 30) link_BETA1-4 : angle 2.18867 ( 90) link_NAG-ASN : bond 0.00500 ( 56) link_NAG-ASN : angle 2.96625 ( 168) *********************** 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 149 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 88 time to evaluate : 0.837 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: B 530 MET cc_start: 0.8960 (mmp) cc_final: 0.6737 (mmm) REVERT: B 626 MET cc_start: 0.8001 (tmm) cc_final: 0.7556 (tmm) REVERT: D 104 MET cc_start: 0.9537 (OUTLIER) cc_final: 0.9001 (ppp) REVERT: E 530 MET cc_start: 0.8790 (mtp) cc_final: 0.8479 (mtm) REVERT: J 271 MET cc_start: 0.8900 (mpp) cc_final: 0.8678 (mpp) REVERT: K 530 MET cc_start: 0.7747 (mmp) cc_final: 0.7237 (mmt) REVERT: K 581 LEU cc_start: 0.9689 (tt) cc_final: 0.9361 (mm) REVERT: K 589 ASP cc_start: 0.9393 (m-30) cc_final: 0.9143 (m-30) REVERT: K 624 ASP cc_start: 0.9216 (p0) cc_final: 0.8925 (p0) REVERT: K 626 MET cc_start: 0.7261 (ppp) cc_final: 0.6643 (ppp) REVERT: L 4 MET cc_start: 0.5294 (ptp) cc_final: 0.4818 (pmm) REVERT: L 70 ASP cc_start: 0.9241 (t0) cc_final: 0.8910 (p0) REVERT: C 13 THR cc_start: 0.6648 (OUTLIER) cc_final: 0.6405 (p) REVERT: I 4 MET cc_start: 0.5727 (mmm) cc_final: 0.4844 (mtt) outliers start: 61 outliers final: 47 residues processed: 138 average time/residue: 0.1372 time to fit residues: 30.6071 Evaluate side-chains 135 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 86 time to evaluate : 0.735 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 36 VAL Chi-restraints excluded: chain G residue 37 THR Chi-restraints excluded: chain G residue 53 PHE Chi-restraints excluded: chain G residue 141 ASP Chi-restraints excluded: chain G residue 218 CYS Chi-restraints excluded: chain G residue 244 THR Chi-restraints excluded: chain G residue 247 CYS Chi-restraints excluded: chain G residue 272 ILE Chi-restraints excluded: chain B residue 573 ILE Chi-restraints excluded: chain B residue 593 LEU Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain D residue 45 TRP Chi-restraints excluded: chain D residue 89 VAL Chi-restraints excluded: chain D residue 104 MET Chi-restraints excluded: chain D residue 110 SER Chi-restraints excluded: chain D residue 120 VAL Chi-restraints excluded: chain D residue 162 THR Chi-restraints excluded: chain D residue 164 GLU Chi-restraints excluded: chain D residue 245 VAL Chi-restraints excluded: chain D residue 257 THR Chi-restraints excluded: chain D residue 307 ILE Chi-restraints excluded: chain D residue 423 ILE Chi-restraints excluded: chain D residue 433 CYS Chi-restraints excluded: chain D residue 488 VAL Chi-restraints excluded: chain E residue 569 THR Chi-restraints excluded: chain E residue 581 LEU Chi-restraints excluded: chain E residue 610 TRP Chi-restraints excluded: chain E residue 629 LEU Chi-restraints excluded: chain J residue 36 VAL Chi-restraints excluded: chain J residue 120 VAL Chi-restraints excluded: chain J residue 373 THR Chi-restraints excluded: chain J residue 434 MET Chi-restraints excluded: chain J residue 488 VAL Chi-restraints excluded: chain K residue 518 VAL Chi-restraints excluded: chain K residue 569 THR Chi-restraints excluded: chain K residue 573 ILE Chi-restraints excluded: chain K residue 610 TRP Chi-restraints excluded: chain H residue 33 TYR Chi-restraints excluded: chain H residue 67 ILE Chi-restraints excluded: chain H residue 94 ARG Chi-restraints excluded: chain L residue 1 ASP Chi-restraints excluded: chain L residue 63 THR Chi-restraints excluded: chain A residue 64 LYS Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain C residue 13 THR Chi-restraints excluded: chain F residue 40 PHE Chi-restraints excluded: chain F residue 67 ILE Chi-restraints excluded: chain I residue 3 VAL Chi-restraints excluded: chain I residue 75 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 152 optimal weight: 2.9990 chunk 129 optimal weight: 3.9990 chunk 226 optimal weight: 20.0000 chunk 92 optimal weight: 5.9990 chunk 42 optimal weight: 0.7980 chunk 9 optimal weight: 7.9990 chunk 186 optimal weight: 7.9990 chunk 228 optimal weight: 6.9990 chunk 83 optimal weight: 8.9990 chunk 114 optimal weight: 6.9990 chunk 119 optimal weight: 1.9990 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 99 ASN ** G 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 38 GLN ** F 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.048624 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2817 r_free = 0.2817 target = 0.033010 restraints weight = 165575.340| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2858 r_free = 0.2858 target = 0.034019 restraints weight = 89904.910| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2883 r_free = 0.2883 target = 0.034654 restraints weight = 63071.034| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2897 r_free = 0.2897 target = 0.034979 restraints weight = 50885.508| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 57)----------------| | r_work = 0.2905 r_free = 0.2905 target = 0.035225 restraints weight = 45113.239| |-----------------------------------------------------------------------------| r_work (final): 0.2861 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8365 moved from start: 0.4918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 20631 Z= 0.194 Angle : 0.733 14.099 28196 Z= 0.343 Chirality : 0.046 0.389 3395 Planarity : 0.004 0.062 3416 Dihedral : 8.326 91.280 4496 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 11.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.10 % Favored : 93.90 % Rotamer: Outliers : 2.84 % Allowed : 14.20 % Favored : 82.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.04 % Twisted Proline : 1.01 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.25 (0.18), residues: 2343 helix: 0.80 (0.30), residues: 359 sheet: -0.14 (0.19), residues: 696 loop : -0.38 (0.19), residues: 1288 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 94 TYR 0.012 0.001 TYR J 217 PHE 0.015 0.002 PHE G 53 TRP 0.019 0.002 TRP G 45 HIS 0.005 0.001 HIS D 105 Details of bonding type rmsd covalent geometry : bond 0.00425 (20495) covalent geometry : angle 0.67666 (27830) SS BOND : bond 0.00479 ( 42) SS BOND : angle 1.56661 ( 84) hydrogen bonds : bond 0.03223 ( 564) hydrogen bonds : angle 5.01071 ( 1485) link_ALPHA1-3 : bond 0.02658 ( 4) link_ALPHA1-3 : angle 3.52627 ( 12) link_ALPHA1-6 : bond 0.01853 ( 4) link_ALPHA1-6 : angle 2.93989 ( 12) link_BETA1-4 : bond 0.00568 ( 30) link_BETA1-4 : angle 2.20365 ( 90) link_NAG-ASN : bond 0.00517 ( 56) link_NAG-ASN : angle 2.99386 ( 168) *********************** 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 148 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 88 time to evaluate : 0.924 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 104 MET cc_start: 0.9738 (ttm) cc_final: 0.9194 (ttm) REVERT: B 530 MET cc_start: 0.8908 (mmp) cc_final: 0.6713 (mmm) REVERT: B 626 MET cc_start: 0.8070 (tmm) cc_final: 0.7656 (tmm) REVERT: D 104 MET cc_start: 0.9540 (OUTLIER) cc_final: 0.9010 (ppp) REVERT: E 530 MET cc_start: 0.8708 (mtp) cc_final: 0.8163 (mtm) REVERT: J 104 MET cc_start: 0.9188 (ppp) cc_final: 0.8954 (ppp) REVERT: J 271 MET cc_start: 0.8903 (mpp) cc_final: 0.8668 (mpp) REVERT: K 530 MET cc_start: 0.7552 (mmp) cc_final: 0.7024 (mmt) REVERT: K 581 LEU cc_start: 0.9690 (tt) cc_final: 0.9415 (mm) REVERT: K 589 ASP cc_start: 0.9394 (m-30) cc_final: 0.9138 (m-30) REVERT: K 626 MET cc_start: 0.7233 (ppp) cc_final: 0.6817 (ppp) REVERT: L 4 MET cc_start: 0.5721 (ptp) cc_final: 0.5352 (pmm) REVERT: L 70 ASP cc_start: 0.9279 (t0) cc_final: 0.8965 (p0) REVERT: F 71 ARG cc_start: 0.5531 (ptt-90) cc_final: 0.5316 (ptt-90) outliers start: 60 outliers final: 48 residues processed: 139 average time/residue: 0.1429 time to fit residues: 31.7796 Evaluate side-chains 132 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 83 time to evaluate : 0.832 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 36 VAL Chi-restraints excluded: chain G residue 37 THR Chi-restraints excluded: chain G residue 53 PHE Chi-restraints excluded: chain G residue 141 ASP Chi-restraints excluded: chain G residue 205 CYS Chi-restraints excluded: chain G residue 218 CYS Chi-restraints excluded: chain G residue 244 THR Chi-restraints excluded: chain G residue 247 CYS Chi-restraints excluded: chain G residue 272 ILE Chi-restraints excluded: chain B residue 573 ILE Chi-restraints excluded: chain B residue 593 LEU Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain D residue 37 THR Chi-restraints excluded: chain D residue 45 TRP Chi-restraints excluded: chain D residue 89 VAL Chi-restraints excluded: chain D residue 104 MET Chi-restraints excluded: chain D residue 110 SER Chi-restraints excluded: chain D residue 120 VAL Chi-restraints excluded: chain D residue 162 THR Chi-restraints excluded: chain D residue 164 GLU Chi-restraints excluded: chain D residue 244 THR Chi-restraints excluded: chain D residue 245 VAL Chi-restraints excluded: chain D residue 307 ILE Chi-restraints excluded: chain D residue 423 ILE Chi-restraints excluded: chain D residue 433 CYS Chi-restraints excluded: chain D residue 488 VAL Chi-restraints excluded: chain E residue 569 THR Chi-restraints excluded: chain E residue 581 LEU Chi-restraints excluded: chain E residue 610 TRP Chi-restraints excluded: chain E residue 629 LEU Chi-restraints excluded: chain J residue 36 VAL Chi-restraints excluded: chain J residue 53 PHE Chi-restraints excluded: chain J residue 120 VAL Chi-restraints excluded: chain J residue 373 THR Chi-restraints excluded: chain J residue 434 MET Chi-restraints excluded: chain J residue 488 VAL Chi-restraints excluded: chain K residue 518 VAL Chi-restraints excluded: chain K residue 569 THR Chi-restraints excluded: chain K residue 573 ILE Chi-restraints excluded: chain K residue 610 TRP Chi-restraints excluded: chain H residue 33 TYR Chi-restraints excluded: chain H residue 67 ILE Chi-restraints excluded: chain L residue 1 ASP Chi-restraints excluded: chain L residue 63 THR Chi-restraints excluded: chain A residue 64 LYS Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain F residue 40 PHE Chi-restraints excluded: chain F residue 67 ILE Chi-restraints excluded: chain I residue 3 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 106 optimal weight: 0.9990 chunk 220 optimal weight: 4.9990 chunk 55 optimal weight: 4.9990 chunk 0 optimal weight: 7.9990 chunk 96 optimal weight: 8.9990 chunk 200 optimal weight: 9.9990 chunk 141 optimal weight: 5.9990 chunk 153 optimal weight: 9.9990 chunk 122 optimal weight: 1.9990 chunk 196 optimal weight: 7.9990 chunk 176 optimal weight: 3.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 77 GLN ** F 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.048514 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.2825 r_free = 0.2825 target = 0.033270 restraints weight = 159668.081| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.2862 r_free = 0.2862 target = 0.034184 restraints weight = 87028.386| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.2887 r_free = 0.2887 target = 0.034775 restraints weight = 60604.797| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.2901 r_free = 0.2901 target = 0.035094 restraints weight = 48739.770| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.2910 r_free = 0.2910 target = 0.035356 restraints weight = 43122.338| |-----------------------------------------------------------------------------| r_work (final): 0.2869 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8352 moved from start: 0.5079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 20631 Z= 0.204 Angle : 0.752 14.095 28196 Z= 0.354 Chirality : 0.046 0.390 3395 Planarity : 0.004 0.128 3416 Dihedral : 8.277 91.735 4496 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 12.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.15 % Favored : 93.85 % Rotamer: Outliers : 2.84 % Allowed : 14.54 % Favored : 82.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.28 (0.18), residues: 2343 helix: 0.83 (0.30), residues: 359 sheet: -0.17 (0.19), residues: 690 loop : -0.41 (0.19), residues: 1294 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 94 TYR 0.011 0.001 TYR J 217 PHE 0.014 0.002 PHE G 53 TRP 0.020 0.002 TRP G 45 HIS 0.008 0.001 HIS C 8 Details of bonding type rmsd covalent geometry : bond 0.00448 (20495) covalent geometry : angle 0.69608 (27830) SS BOND : bond 0.00437 ( 42) SS BOND : angle 1.66292 ( 84) hydrogen bonds : bond 0.03277 ( 564) hydrogen bonds : angle 5.04157 ( 1485) link_ALPHA1-3 : bond 0.02602 ( 4) link_ALPHA1-3 : angle 3.49078 ( 12) link_ALPHA1-6 : bond 0.01811 ( 4) link_ALPHA1-6 : angle 2.92805 ( 12) link_BETA1-4 : bond 0.00558 ( 30) link_BETA1-4 : angle 2.20263 ( 90) link_NAG-ASN : bond 0.00522 ( 56) link_NAG-ASN : angle 3.01388 ( 168) *********************** 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 143 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 83 time to evaluate : 0.981 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 530 MET cc_start: 0.8922 (mmp) cc_final: 0.6643 (mmm) REVERT: B 626 MET cc_start: 0.8051 (tmm) cc_final: 0.7510 (tmm) REVERT: D 104 MET cc_start: 0.9532 (OUTLIER) cc_final: 0.8973 (ppp) REVERT: E 530 MET cc_start: 0.8692 (mtp) cc_final: 0.8121 (mtm) REVERT: J 104 MET cc_start: 0.9104 (ppp) cc_final: 0.8866 (ppp) REVERT: J 271 MET cc_start: 0.8882 (mpp) cc_final: 0.8638 (mpp) REVERT: K 530 MET cc_start: 0.7527 (mmp) cc_final: 0.7001 (mmt) REVERT: K 589 ASP cc_start: 0.9393 (m-30) cc_final: 0.9141 (m-30) REVERT: K 626 MET cc_start: 0.7245 (ppp) cc_final: 0.6803 (ppp) REVERT: H 64 LYS cc_start: 0.9513 (pptt) cc_final: 0.9289 (pptt) REVERT: H 65 ASN cc_start: 0.8829 (m-40) cc_final: 0.8559 (t0) REVERT: L 4 MET cc_start: 0.5801 (ptp) cc_final: 0.5461 (pmm) REVERT: L 70 ASP cc_start: 0.9277 (t0) cc_final: 0.8972 (p0) REVERT: F 71 ARG cc_start: 0.5892 (ptt-90) cc_final: 0.5648 (ptt-90) outliers start: 60 outliers final: 49 residues processed: 133 average time/residue: 0.1361 time to fit residues: 29.9321 Evaluate side-chains 131 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 81 time to evaluate : 0.787 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 36 VAL Chi-restraints excluded: chain G residue 37 THR Chi-restraints excluded: chain G residue 53 PHE Chi-restraints excluded: chain G residue 141 ASP Chi-restraints excluded: chain G residue 205 CYS Chi-restraints excluded: chain G residue 218 CYS Chi-restraints excluded: chain G residue 244 THR Chi-restraints excluded: chain G residue 247 CYS Chi-restraints excluded: chain G residue 272 ILE Chi-restraints excluded: chain B residue 573 ILE Chi-restraints excluded: chain B residue 593 LEU Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain D residue 37 THR Chi-restraints excluded: chain D residue 45 TRP Chi-restraints excluded: chain D residue 89 VAL Chi-restraints excluded: chain D residue 104 MET Chi-restraints excluded: chain D residue 110 SER Chi-restraints excluded: chain D residue 120 VAL Chi-restraints excluded: chain D residue 162 THR Chi-restraints excluded: chain D residue 164 GLU Chi-restraints excluded: chain D residue 244 THR Chi-restraints excluded: chain D residue 245 VAL Chi-restraints excluded: chain D residue 257 THR Chi-restraints excluded: chain D residue 307 ILE Chi-restraints excluded: chain D residue 423 ILE Chi-restraints excluded: chain D residue 433 CYS Chi-restraints excluded: chain D residue 488 VAL Chi-restraints excluded: chain E residue 569 THR Chi-restraints excluded: chain E residue 610 TRP Chi-restraints excluded: chain E residue 629 LEU Chi-restraints excluded: chain J residue 36 VAL Chi-restraints excluded: chain J residue 53 PHE Chi-restraints excluded: chain J residue 120 VAL Chi-restraints excluded: chain J residue 373 THR Chi-restraints excluded: chain J residue 434 MET Chi-restraints excluded: chain J residue 488 VAL Chi-restraints excluded: chain K residue 518 VAL Chi-restraints excluded: chain K residue 569 THR Chi-restraints excluded: chain K residue 573 ILE Chi-restraints excluded: chain K residue 610 TRP Chi-restraints excluded: chain H residue 33 TYR Chi-restraints excluded: chain H residue 67 ILE Chi-restraints excluded: chain H residue 94 ARG Chi-restraints excluded: chain L residue 1 ASP Chi-restraints excluded: chain L residue 63 THR Chi-restraints excluded: chain A residue 64 LYS Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain F residue 40 PHE Chi-restraints excluded: chain F residue 67 ILE Chi-restraints excluded: chain I residue 3 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 208 optimal weight: 5.9990 chunk 213 optimal weight: 20.0000 chunk 82 optimal weight: 7.9990 chunk 149 optimal weight: 4.9990 chunk 18 optimal weight: 6.9990 chunk 27 optimal weight: 0.0970 chunk 20 optimal weight: 2.9990 chunk 160 optimal weight: 9.9990 chunk 13 optimal weight: 6.9990 chunk 128 optimal weight: 0.7980 chunk 70 optimal weight: 5.9990 overall best weight: 2.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 216 HIS ** G 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.048586 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2820 r_free = 0.2820 target = 0.033028 restraints weight = 166222.145| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.2860 r_free = 0.2860 target = 0.034036 restraints weight = 91505.568| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 67)----------------| | r_work = 0.2885 r_free = 0.2885 target = 0.034650 restraints weight = 64373.066| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2898 r_free = 0.2898 target = 0.034952 restraints weight = 52142.198| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.2908 r_free = 0.2908 target = 0.035215 restraints weight = 46372.168| |-----------------------------------------------------------------------------| r_work (final): 0.2862 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8369 moved from start: 0.5193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 20631 Z= 0.186 Angle : 0.735 13.938 28196 Z= 0.346 Chirality : 0.046 0.393 3395 Planarity : 0.004 0.105 3416 Dihedral : 8.166 92.188 4496 Min Nonbonded Distance : 2.303 Molprobity Statistics. All-atom Clashscore : 12.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.19 % Favored : 93.81 % Rotamer: Outliers : 2.51 % Allowed : 14.91 % Favored : 82.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.25 (0.18), residues: 2343 helix: 1.10 (0.30), residues: 341 sheet: -0.19 (0.19), residues: 690 loop : -0.41 (0.18), residues: 1312 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG H 94 TYR 0.010 0.001 TYR J 217 PHE 0.015 0.001 PHE G 53 TRP 0.020 0.002 TRP G 45 HIS 0.009 0.001 HIS C 8 Details of bonding type rmsd covalent geometry : bond 0.00408 (20495) covalent geometry : angle 0.67903 (27830) SS BOND : bond 0.00404 ( 42) SS BOND : angle 1.67921 ( 84) hydrogen bonds : bond 0.03144 ( 564) hydrogen bonds : angle 5.03515 ( 1485) link_ALPHA1-3 : bond 0.02559 ( 4) link_ALPHA1-3 : angle 3.48878 ( 12) link_ALPHA1-6 : bond 0.01782 ( 4) link_ALPHA1-6 : angle 2.93610 ( 12) link_BETA1-4 : bond 0.00556 ( 30) link_BETA1-4 : angle 2.18628 ( 90) link_NAG-ASN : bond 0.00496 ( 56) link_NAG-ASN : angle 2.99016 ( 168) ********************** 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 136 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 83 time to evaluate : 0.811 Fit side-chains revert: symmetry clash REVERT: G 104 MET cc_start: 0.9705 (ttm) cc_final: 0.9489 (ttm) REVERT: B 530 MET cc_start: 0.8921 (mmp) cc_final: 0.6652 (mmm) REVERT: B 626 MET cc_start: 0.8069 (OUTLIER) cc_final: 0.7520 (tmm) REVERT: D 104 MET cc_start: 0.9526 (OUTLIER) cc_final: 0.8957 (ppp) REVERT: E 530 MET cc_start: 0.8630 (mtp) cc_final: 0.8022 (mtm) REVERT: J 104 MET cc_start: 0.9144 (ppp) cc_final: 0.8884 (ppp) REVERT: J 271 MET cc_start: 0.8843 (mpp) cc_final: 0.8558 (mpp) REVERT: K 530 MET cc_start: 0.7478 (mmp) cc_final: 0.6927 (mmt) REVERT: K 589 ASP cc_start: 0.9397 (m-30) cc_final: 0.9145 (m-30) REVERT: K 626 MET cc_start: 0.7249 (ppp) cc_final: 0.6727 (ppp) REVERT: L 4 MET cc_start: 0.5738 (ptp) cc_final: 0.5425 (pmm) REVERT: L 70 ASP cc_start: 0.9312 (t0) cc_final: 0.9044 (p0) outliers start: 53 outliers final: 48 residues processed: 127 average time/residue: 0.1316 time to fit residues: 27.8875 Evaluate side-chains 130 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 80 time to evaluate : 0.871 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 36 VAL Chi-restraints excluded: chain G residue 53 PHE Chi-restraints excluded: chain G residue 141 ASP Chi-restraints excluded: chain G residue 205 CYS Chi-restraints excluded: chain G residue 218 CYS Chi-restraints excluded: chain G residue 244 THR Chi-restraints excluded: chain G residue 247 CYS Chi-restraints excluded: chain G residue 272 ILE Chi-restraints excluded: chain B residue 573 ILE Chi-restraints excluded: chain B residue 593 LEU Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 626 MET Chi-restraints excluded: chain D residue 37 THR Chi-restraints excluded: chain D residue 45 TRP Chi-restraints excluded: chain D residue 89 VAL Chi-restraints excluded: chain D residue 104 MET Chi-restraints excluded: chain D residue 110 SER Chi-restraints excluded: chain D residue 120 VAL Chi-restraints excluded: chain D residue 162 THR Chi-restraints excluded: chain D residue 244 THR Chi-restraints excluded: chain D residue 245 VAL Chi-restraints excluded: chain D residue 257 THR Chi-restraints excluded: chain D residue 307 ILE Chi-restraints excluded: chain D residue 423 ILE Chi-restraints excluded: chain D residue 433 CYS Chi-restraints excluded: chain D residue 488 VAL Chi-restraints excluded: chain E residue 569 THR Chi-restraints excluded: chain E residue 581 LEU Chi-restraints excluded: chain E residue 610 TRP Chi-restraints excluded: chain E residue 629 LEU Chi-restraints excluded: chain J residue 36 VAL Chi-restraints excluded: chain J residue 53 PHE Chi-restraints excluded: chain J residue 120 VAL Chi-restraints excluded: chain J residue 373 THR Chi-restraints excluded: chain J residue 434 MET Chi-restraints excluded: chain J residue 488 VAL Chi-restraints excluded: chain K residue 518 VAL Chi-restraints excluded: chain K residue 569 THR Chi-restraints excluded: chain K residue 573 ILE Chi-restraints excluded: chain K residue 610 TRP Chi-restraints excluded: chain H residue 33 TYR Chi-restraints excluded: chain H residue 67 ILE Chi-restraints excluded: chain H residue 94 ARG Chi-restraints excluded: chain L residue 1 ASP Chi-restraints excluded: chain L residue 63 THR Chi-restraints excluded: chain A residue 64 LYS Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain F residue 40 PHE Chi-restraints excluded: chain F residue 67 ILE Chi-restraints excluded: chain I residue 3 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 182 optimal weight: 40.0000 chunk 118 optimal weight: 0.0370 chunk 191 optimal weight: 10.0000 chunk 1 optimal weight: 9.9990 chunk 107 optimal weight: 0.9990 chunk 127 optimal weight: 0.0170 chunk 201 optimal weight: 20.0000 chunk 155 optimal weight: 4.9990 chunk 49 optimal weight: 0.8980 chunk 50 optimal weight: 1.9990 chunk 136 optimal weight: 0.9990 overall best weight: 0.5900 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 656 ASN H 105 GLN L 37 GLN ** A 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 6 GLN ** I 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.049471 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2865 r_free = 0.2865 target = 0.034072 restraints weight = 161917.837| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.2905 r_free = 0.2905 target = 0.035080 restraints weight = 85912.630| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.2931 r_free = 0.2931 target = 0.035721 restraints weight = 59101.746| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.2947 r_free = 0.2947 target = 0.036120 restraints weight = 47095.883| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2956 r_free = 0.2956 target = 0.036322 restraints weight = 41074.653| |-----------------------------------------------------------------------------| r_work (final): 0.2919 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8294 moved from start: 0.5073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 20631 Z= 0.116 Angle : 0.701 15.879 28196 Z= 0.327 Chirality : 0.046 0.416 3395 Planarity : 0.004 0.090 3416 Dihedral : 7.675 91.521 4496 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 10.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer: Outliers : 1.70 % Allowed : 15.77 % Favored : 82.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.08 (0.18), residues: 2343 helix: 1.28 (0.31), residues: 332 sheet: 0.16 (0.20), residues: 657 loop : -0.46 (0.18), residues: 1354 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG K 579 TYR 0.011 0.001 TYR A 90 PHE 0.015 0.001 PHE F 78 TRP 0.017 0.002 TRP D 45 HIS 0.007 0.001 HIS C 8 Details of bonding type rmsd covalent geometry : bond 0.00252 (20495) covalent geometry : angle 0.64817 (27830) SS BOND : bond 0.00247 ( 42) SS BOND : angle 1.37672 ( 84) hydrogen bonds : bond 0.02921 ( 564) hydrogen bonds : angle 4.83177 ( 1485) link_ALPHA1-3 : bond 0.02517 ( 4) link_ALPHA1-3 : angle 3.65278 ( 12) link_ALPHA1-6 : bond 0.01786 ( 4) link_ALPHA1-6 : angle 2.98600 ( 12) link_BETA1-4 : bond 0.00622 ( 30) link_BETA1-4 : angle 2.13111 ( 90) link_NAG-ASN : bond 0.00478 ( 56) link_NAG-ASN : angle 2.79719 ( 168) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3652.23 seconds wall clock time: 64 minutes 15.24 seconds (3855.24 seconds total)