Starting phenix.real_space_refine on Sun Aug 24 09:10:04 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8g3o_29706/08_2025/8g3o_29706.cif Found real_map, /net/cci-nas-00/data/ceres_data/8g3o_29706/08_2025/8g3o_29706.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8g3o_29706/08_2025/8g3o_29706.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8g3o_29706/08_2025/8g3o_29706.map" model { file = "/net/cci-nas-00/data/ceres_data/8g3o_29706/08_2025/8g3o_29706.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8g3o_29706/08_2025/8g3o_29706.cif" } resolution = 3.1 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= 0.000 sd= 0.029 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: 5 Type Number sf(0) Gaussians Ca 5 9.91 5 S 109 5.16 5 C 11416 2.51 5 N 3132 2.21 5 O 3825 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 139 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: 18487 Number of models: 1 Model: "" Number of chains: 38 Chain: "E" Number of atoms: 986 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 986 Classifications: {'peptide': 130} Link IDs: {'PTRANS': 4, 'TRANS': 125} Chain: "F" Number of atoms: 848 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 848 Classifications: {'peptide': 110} Link IDs: {'PCIS': 2, 'PTRANS': 3, 'TRANS': 104} Chain: "A" Number of atoms: 986 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 986 Classifications: {'peptide': 130} Link IDs: {'PTRANS': 4, 'TRANS': 125} Chain: "D" Number of atoms: 848 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 848 Classifications: {'peptide': 110} Link IDs: {'PCIS': 2, 'PTRANS': 3, 'TRANS': 104} Chain: "C" Number of atoms: 986 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 986 Classifications: {'peptide': 130} Link IDs: {'PTRANS': 4, 'TRANS': 125} Chain: "I" Number of atoms: 848 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 848 Classifications: {'peptide': 110} Link IDs: {'PCIS': 2, 'PTRANS': 3, 'TRANS': 104} Chain: "G" Number of atoms: 3001 Number of conformers: 1 Conformer: "" Number of residues, atoms: 388, 3001 Classifications: {'peptide': 388} Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 10, 'TRANS': 374} Chain: "H" Number of atoms: 3001 Number of conformers: 1 Conformer: "" Number of residues, atoms: 388, 3001 Classifications: {'peptide': 388} Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 10, 'TRANS': 374} Chain: "B" Number of atoms: 3001 Number of conformers: 1 Conformer: "" Number of residues, atoms: 388, 3001 Classifications: {'peptide': 388} Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 10, 'TRANS': 374} Chain: "J" Number of atoms: 3001 Number of conformers: 1 Conformer: "" Number of residues, atoms: 388, 3001 Classifications: {'peptide': 388} Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 10, 'TRANS': 374} 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: "c" Number of atoms: 94 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 94 Unusual residues: {'BMA': 1, 'MAN': 5, 'NAG': 2} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "k" Number of atoms: 94 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 94 Unusual residues: {'BMA': 1, 'MAN': 5, 'NAG': 2} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "s" Number of atoms: 94 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 94 Unusual residues: {'BMA': 1, 'MAN': 5, 'NAG': 2} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "3" Number of atoms: 94 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 94 Unusual residues: {'BMA': 1, 'MAN': 5, 'NAG': 2} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "e" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "i" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "j" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "l" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "o" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "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: "t" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "w" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "1" 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: "2" 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: "4" 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: "5" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 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: "7" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "m" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "u" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 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: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "H" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Chain: "J" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.29, per 1000 atoms: 0.23 Number of scatterers: 18487 At special positions: 0 Unit cell: (112.88, 140.27, 170.15, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Ca 5 19.99 S 109 16.00 O 3825 8.00 N 3132 7.00 C 11416 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=42, symmetry=0 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " distance=2.02 Simple disulfide: pdb=" SG CYS F 23 " - pdb=" SG CYS F 88 " distance=2.05 Simple disulfide: pdb=" SG CYS A 22 " - pdb=" SG CYS A 96 " distance=2.03 Simple disulfide: pdb=" SG CYS D 23 " - pdb=" SG CYS D 88 " distance=2.06 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 96 " distance=2.02 Simple disulfide: pdb=" SG CYS I 23 " - pdb=" SG CYS I 88 " distance=2.06 Simple disulfide: pdb=" SG CYS G 92 " - pdb=" SG CYS G 417 " distance=2.07 Simple disulfide: pdb=" SG CYS G 124 " - pdb=" SG CYS G 129 " distance=2.07 Simple disulfide: pdb=" SG CYS G 175 " - pdb=" SG CYS G 193 " distance=2.06 Simple disulfide: pdb=" SG CYS G 183 " - pdb=" SG CYS G 230 " distance=2.06 Simple disulfide: pdb=" SG CYS G 232 " - pdb=" SG CYS G 237 " distance=2.08 Simple disulfide: pdb=" SG CYS G 278 " - pdb=" SG CYS G 291 " distance=2.06 Simple disulfide: pdb=" SG CYS G 280 " - pdb=" SG CYS G 289 " distance=2.07 Simple disulfide: pdb=" SG CYS G 318 " - pdb=" SG CYS G 337 " distance=2.10 Simple disulfide: pdb=" SG CYS G 421 " - pdb=" SG CYS G 447 " distance=2.13 Simple disulfide: pdb=" SG CYS H 92 " - pdb=" SG CYS H 417 " distance=2.06 Simple disulfide: pdb=" SG CYS H 124 " - pdb=" SG CYS H 129 " distance=2.07 Simple disulfide: pdb=" SG CYS H 175 " - pdb=" SG CYS H 193 " distance=2.05 Simple disulfide: pdb=" SG CYS H 183 " - pdb=" SG CYS H 230 " distance=2.02 Simple disulfide: pdb=" SG CYS H 232 " - pdb=" SG CYS H 237 " distance=2.09 Simple disulfide: pdb=" SG CYS H 278 " - pdb=" SG CYS H 291 " distance=2.07 Simple disulfide: pdb=" SG CYS H 280 " - pdb=" SG CYS H 289 " distance=2.08 Simple disulfide: pdb=" SG CYS H 318 " - pdb=" SG CYS H 337 " distance=2.08 Simple disulfide: pdb=" SG CYS H 421 " - pdb=" SG CYS H 447 " distance=2.12 Simple disulfide: pdb=" SG CYS B 92 " - pdb=" SG CYS B 417 " distance=2.05 Simple disulfide: pdb=" SG CYS B 124 " - pdb=" SG CYS B 129 " distance=2.07 Simple disulfide: pdb=" SG CYS B 175 " - pdb=" SG CYS B 193 " distance=2.06 Simple disulfide: pdb=" SG CYS B 183 " - pdb=" SG CYS B 230 " distance=2.06 Simple disulfide: pdb=" SG CYS B 232 " - pdb=" SG CYS B 237 " distance=2.07 Simple disulfide: pdb=" SG CYS B 278 " - pdb=" SG CYS B 291 " distance=2.06 Simple disulfide: pdb=" SG CYS B 280 " - pdb=" SG CYS B 289 " distance=2.07 Simple disulfide: pdb=" SG CYS B 318 " - pdb=" SG CYS B 337 " distance=2.08 Simple disulfide: pdb=" SG CYS B 421 " - pdb=" SG CYS B 447 " distance=2.13 Simple disulfide: pdb=" SG CYS J 92 " - pdb=" SG CYS J 417 " distance=2.05 Simple disulfide: pdb=" SG CYS J 124 " - pdb=" SG CYS J 129 " distance=2.09 Simple disulfide: pdb=" SG CYS J 175 " - pdb=" SG CYS J 193 " distance=2.06 Simple disulfide: pdb=" SG CYS J 183 " - pdb=" SG CYS J 230 " distance=2.09 Simple disulfide: pdb=" SG CYS J 232 " - pdb=" SG CYS J 237 " distance=2.08 Simple disulfide: pdb=" SG CYS J 278 " - pdb=" SG CYS J 291 " distance=2.05 Simple disulfide: pdb=" SG CYS J 280 " - pdb=" SG CYS J 289 " distance=2.10 Simple disulfide: pdb=" SG CYS J 318 " - pdb=" SG CYS J 337 " distance=2.09 Simple disulfide: pdb=" SG CYS J 421 " - pdb=" SG CYS J 447 " distance=2.12 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-2 " MAN 3 4 " - " MAN 3 5 " " MAN c 4 " - " MAN c 5 " " MAN k 4 " - " MAN k 5 " " MAN s 4 " - " MAN s 5 " ALPHA1-3 " BMA 3 3 " - " MAN 3 4 " " MAN 3 6 " - " MAN 3 7 " " BMA c 3 " - " MAN c 4 " " MAN c 6 " - " MAN c 7 " " BMA k 3 " - " MAN k 4 " " MAN k 6 " - " MAN k 7 " " BMA s 3 " - " MAN s 4 " " MAN s 6 " - " MAN s 7 " ALPHA1-6 " BMA 3 3 " - " MAN 3 6 " " MAN 3 6 " - " MAN 3 8 " " BMA c 3 " - " MAN c 6 " " MAN c 6 " - " MAN c 8 " " BMA k 3 " - " MAN k 6 " " MAN k 6 " - " MAN k 8 " " BMA s 3 " - " MAN s 6 " " MAN s 6 " - " MAN s 8 " BETA1-4 " NAG 1 1 " - " NAG 1 2 " " NAG 2 1 " - " NAG 2 2 " " NAG 3 1 " - " NAG 3 2 " " NAG 3 2 " - " BMA 3 3 " " NAG 4 1 " - " NAG 4 2 " " NAG 5 1 " - " NAG 5 2 " " NAG 7 1 " - " NAG 7 2 " " NAG a 1 " - " NAG a 2 " " NAG b 1 " - " NAG b 2 " " NAG c 1 " - " NAG c 2 " " NAG c 2 " - " BMA c 3 " " NAG d 1 " - " NAG d 2 " " NAG e 1 " - " NAG e 2 " " NAG g 1 " - " NAG g 2 " " NAG i 1 " - " NAG i 2 " " NAG j 1 " - " NAG j 2 " " NAG k 1 " - " NAG k 2 " " NAG k 2 " - " BMA k 3 " " NAG l 1 " - " NAG l 2 " " NAG m 1 " - " NAG m 2 " " NAG o 1 " - " NAG o 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 u 1 " - " NAG u 2 " " NAG w 1 " - " NAG w 2 " BETA1-6 " NAG 5 1 " - " FUC 5 3 " ~> Even though FUC is an alpha isomer, a beta linkage is required... " NAG e 1 " - " FUC e 3 " " NAG m 1 " - " FUC m 3 " " NAG u 1 " - " FUC u 3 " NAG-ASN " NAG 1 1 " - " ASN J 86 " " NAG 2 1 " - " ASN J 146 " " NAG 3 1 " - " ASN J 200 " " NAG 4 1 " - " ASN J 234 " " NAG 5 1 " - " ASN J 245 " " NAG 7 1 " - " ASN J 367 " " NAG a 1 " - " ASN G 86 " " NAG b 1 " - " ASN G 146 " " NAG c 1 " - " ASN G 200 " " NAG d 1 " - " ASN G 234 " " NAG e 1 " - " ASN G 245 " " NAG g 1 " - " ASN G 367 " " NAG i 1 " - " ASN H 86 " " NAG j 1 " - " ASN H 146 " " NAG k 1 " - " ASN H 200 " " NAG l 1 " - " ASN H 234 " " NAG m 1 " - " ASN H 245 " " NAG o 1 " - " ASN H 367 " " NAG q 1 " - " ASN B 86 " " NAG r 1 " - " ASN B 146 " " NAG s 1 " - " ASN B 200 " " NAG t 1 " - " ASN B 234 " " NAG u 1 " - " ASN B 245 " " NAG w 1 " - " ASN B 367 " Time building additional restraints: 2.10 Conformation dependent library (CDL) restraints added in 796.8 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 4504 Ramachandran restraints generated. 2252 Oldfield, 0 Emsley, 2252 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4108 Finding SS restraints... Secondary structure from input PDB file: 20 helices and 42 sheets defined 4.7% alpha, 41.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.79 Creating SS restraints... Processing helix chain 'E' and resid 62 through 65 Processing helix chain 'E' and resid 87 through 91 Processing helix chain 'F' and resid 79 through 83 removed outlier: 3.792A pdb=" N SER F 83 " --> pdb=" O SER F 80 " (cutoff:3.500A) Processing helix chain 'A' and resid 62 through 65 Processing helix chain 'A' and resid 87 through 91 Processing helix chain 'D' and resid 79 through 83 removed outlier: 3.780A pdb=" N SER D 83 " --> pdb=" O SER D 80 " (cutoff:3.500A) Processing helix chain 'C' and resid 62 through 65 Processing helix chain 'C' and resid 87 through 91 Processing helix chain 'I' and resid 79 through 83 removed outlier: 3.785A pdb=" N SER I 83 " --> pdb=" O SER I 80 " (cutoff:3.500A) Processing helix chain 'G' and resid 104 through 110 Processing helix chain 'G' and resid 142 through 146 removed outlier: 3.736A pdb=" N ASN G 146 " --> pdb=" O VAL G 143 " (cutoff:3.500A) Processing helix chain 'G' and resid 247 through 252 Processing helix chain 'H' and resid 104 through 110 Processing helix chain 'H' and resid 142 through 146 removed outlier: 3.740A pdb=" N ASN H 146 " --> pdb=" O VAL H 143 " (cutoff:3.500A) Processing helix chain 'H' and resid 247 through 252 Processing helix chain 'B' and resid 104 through 110 Processing helix chain 'B' and resid 142 through 146 removed outlier: 3.739A pdb=" N ASN B 146 " --> pdb=" O VAL B 143 " (cutoff:3.500A) Processing helix chain 'B' and resid 247 through 251 Processing helix chain 'J' and resid 104 through 110 Processing helix chain 'J' and resid 142 through 146 removed outlier: 3.731A pdb=" N ASN J 146 " --> pdb=" O VAL J 143 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'E' and resid 4 through 6 Processing sheet with id=AA2, first strand: chain 'E' and resid 10 through 12 removed outlier: 6.462A pdb=" N GLU E 10 " --> pdb=" O THR E 125 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N ILE E 34 " --> pdb=" O GLY E 50 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N GLY E 50 " --> pdb=" O ILE E 34 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N TRP E 36 " --> pdb=" O MET E 48 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'E' and resid 10 through 12 removed outlier: 6.462A pdb=" N GLU E 10 " --> pdb=" O THR E 125 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N CYS E 96 " --> pdb=" O TRP E 118 " (cutoff:3.500A) removed outlier: 4.784A pdb=" N TRP E 118 " --> pdb=" O CYS E 96 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N ARG E 98 " --> pdb=" O ALA E 116 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'E' and resid 104 through 105 Processing sheet with id=AA5, first strand: chain 'F' and resid 4 through 7 removed outlier: 3.629A pdb=" N GLU F 70 " --> pdb=" O SER F 67 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'F' and resid 10 through 13 removed outlier: 6.582A pdb=" N LEU F 33 " --> pdb=" O TYR F 49 " (cutoff:3.500A) removed outlier: 4.626A pdb=" N TYR F 49 " --> pdb=" O LEU F 33 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N TRP F 35 " --> pdb=" O LEU F 47 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 4 through 6 Processing sheet with id=AA8, first strand: chain 'A' and resid 10 through 12 removed outlier: 6.479A pdb=" N GLU A 10 " --> pdb=" O THR A 125 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N ILE A 34 " --> pdb=" O GLY A 50 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N GLY A 50 " --> pdb=" O ILE A 34 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N TRP A 36 " --> pdb=" O MET A 48 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 10 through 12 removed outlier: 6.479A pdb=" N GLU A 10 " --> pdb=" O THR A 125 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N CYS A 96 " --> pdb=" O TRP A 118 " (cutoff:3.500A) removed outlier: 4.751A pdb=" N TRP A 118 " --> pdb=" O CYS A 96 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N ARG A 98 " --> pdb=" O ALA A 116 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 104 through 105 Processing sheet with id=AB2, first strand: chain 'D' and resid 4 through 7 removed outlier: 3.632A pdb=" N GLU D 70 " --> pdb=" O SER D 67 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 10 through 13 removed outlier: 6.595A pdb=" N LEU D 33 " --> pdb=" O TYR D 49 " (cutoff:3.500A) removed outlier: 4.638A pdb=" N TYR D 49 " --> pdb=" O LEU D 33 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N TRP D 35 " --> pdb=" O LEU D 47 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 4 through 6 Processing sheet with id=AB5, first strand: chain 'C' and resid 10 through 12 removed outlier: 6.482A pdb=" N GLU C 10 " --> pdb=" O THR C 125 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N ILE C 34 " --> pdb=" O GLY C 50 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N GLY C 50 " --> pdb=" O ILE C 34 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N TRP C 36 " --> pdb=" O MET C 48 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 10 through 12 removed outlier: 6.482A pdb=" N GLU C 10 " --> pdb=" O THR C 125 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N CYS C 96 " --> pdb=" O TRP C 118 " (cutoff:3.500A) removed outlier: 4.765A pdb=" N TRP C 118 " --> pdb=" O CYS C 96 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N ARG C 98 " --> pdb=" O ALA C 116 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 104 through 105 Processing sheet with id=AB8, first strand: chain 'I' and resid 4 through 7 removed outlier: 3.631A pdb=" N GLU I 70 " --> pdb=" O SER I 67 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'I' and resid 10 through 13 removed outlier: 6.573A pdb=" N LEU I 33 " --> pdb=" O TYR I 49 " (cutoff:3.500A) removed outlier: 4.631A pdb=" N TYR I 49 " --> pdb=" O LEU I 33 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N TRP I 35 " --> pdb=" O LEU I 47 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'G' and resid 96 through 102 removed outlier: 5.470A pdb=" N PHE G 97 " --> pdb=" O THR G 449 " (cutoff:3.500A) removed outlier: 6.106A pdb=" N THR G 449 " --> pdb=" O PHE G 97 " (cutoff:3.500A) removed outlier: 5.624A pdb=" N CYS G 447 " --> pdb=" O PRO G 99 " (cutoff:3.500A) removed outlier: 5.833A pdb=" N ARG G 420 " --> pdb=" O GLY G 448 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'G' and resid 115 through 124 removed outlier: 4.802A pdb=" N TRP G 115 " --> pdb=" O THR G 138 " (cutoff:3.500A) removed outlier: 7.398A pdb=" N THR G 138 " --> pdb=" O TRP G 115 " (cutoff:3.500A) removed outlier: 7.610A pdb=" N THR G 117 " --> pdb=" O GLN G 136 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N GLN G 136 " --> pdb=" O THR G 117 " (cutoff:3.500A) removed outlier: 5.468A pdb=" N GLU G 119 " --> pdb=" O LEU G 134 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N LEU G 134 " --> pdb=" O GLU G 119 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N THR G 157 " --> pdb=" O GLY G 135 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N LEU G 158 " --> pdb=" O VAL G 174 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N LYS G 172 " --> pdb=" O MET G 160 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'G' and resid 179 through 184 removed outlier: 4.129A pdb=" N ASP G 197 " --> pdb=" O ASN G 200 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N TYR G 207 " --> pdb=" O LEU G 211 " (cutoff:3.500A) removed outlier: 5.188A pdb=" N LEU G 211 " --> pdb=" O TYR G 207 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'G' and resid 231 through 233 removed outlier: 6.447A pdb=" N GLU G 258 " --> pdb=" O ILE G 262 " (cutoff:3.500A) removed outlier: 5.438A pdb=" N ILE G 262 " --> pdb=" O GLU G 258 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'G' and resid 276 through 283 removed outlier: 5.414A pdb=" N GLU G 277 " --> pdb=" O ARG G 292 " (cutoff:3.500A) removed outlier: 4.994A pdb=" N ARG G 292 " --> pdb=" O GLU G 277 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'G' and resid 352 through 356 removed outlier: 4.485A pdb=" N TRP G 352 " --> pdb=" O GLY G 363 " (cutoff:3.500A) removed outlier: 7.011A pdb=" N ASP G 402 " --> pdb=" O GLY G 373 " (cutoff:3.500A) removed outlier: 9.712A pdb=" N GLU G 375 " --> pdb=" O ARG G 400 " (cutoff:3.500A) removed outlier: 10.452A pdb=" N ARG G 400 " --> pdb=" O GLU G 375 " (cutoff:3.500A) removed outlier: 11.501A pdb=" N PHE G 377 " --> pdb=" O VAL G 398 " (cutoff:3.500A) removed outlier: 13.554A pdb=" N VAL G 398 " --> pdb=" O PHE G 377 " (cutoff:3.500A) removed outlier: 15.764A pdb=" N VAL G 379 " --> pdb=" O VAL G 396 " (cutoff:3.500A) removed outlier: 16.338A pdb=" N VAL G 396 " --> pdb=" O VAL G 379 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'H' and resid 96 through 102 removed outlier: 3.782A pdb=" N GLY H 96 " --> pdb=" O THR H 449 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N VAL H 445 " --> pdb=" O PHE H 100 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N LYS H 102 " --> pdb=" O ILE H 443 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N ILE H 443 " --> pdb=" O LYS H 102 " (cutoff:3.500A) removed outlier: 5.840A pdb=" N ARG H 420 " --> pdb=" O GLY H 448 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'H' and resid 115 through 124 removed outlier: 4.778A pdb=" N TRP H 115 " --> pdb=" O THR H 138 " (cutoff:3.500A) removed outlier: 7.404A pdb=" N THR H 138 " --> pdb=" O TRP H 115 " (cutoff:3.500A) removed outlier: 7.646A pdb=" N THR H 117 " --> pdb=" O GLN H 136 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N GLN H 136 " --> pdb=" O THR H 117 " (cutoff:3.500A) removed outlier: 5.455A pdb=" N GLU H 119 " --> pdb=" O LEU H 134 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N LEU H 134 " --> pdb=" O GLU H 119 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N THR H 157 " --> pdb=" O GLY H 135 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N LEU H 158 " --> pdb=" O VAL H 174 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N LYS H 172 " --> pdb=" O MET H 160 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'H' and resid 179 through 184 removed outlier: 4.121A pdb=" N ASP H 197 " --> pdb=" O ASN H 200 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N TYR H 207 " --> pdb=" O LEU H 211 " (cutoff:3.500A) removed outlier: 5.172A pdb=" N LEU H 211 " --> pdb=" O TYR H 207 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'H' and resid 231 through 233 removed outlier: 6.427A pdb=" N GLU H 258 " --> pdb=" O ILE H 262 " (cutoff:3.500A) removed outlier: 5.450A pdb=" N ILE H 262 " --> pdb=" O GLU H 258 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'H' and resid 276 through 283 removed outlier: 5.404A pdb=" N GLU H 277 " --> pdb=" O ARG H 292 " (cutoff:3.500A) removed outlier: 4.975A pdb=" N ARG H 292 " --> pdb=" O GLU H 277 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'H' and resid 352 through 356 removed outlier: 4.461A pdb=" N TRP H 352 " --> pdb=" O GLY H 363 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N ASP H 402 " --> pdb=" O GLY H 373 " (cutoff:3.500A) removed outlier: 9.717A pdb=" N GLU H 375 " --> pdb=" O ARG H 400 " (cutoff:3.500A) removed outlier: 10.503A pdb=" N ARG H 400 " --> pdb=" O GLU H 375 " (cutoff:3.500A) removed outlier: 11.513A pdb=" N PHE H 377 " --> pdb=" O VAL H 398 " (cutoff:3.500A) removed outlier: 13.543A pdb=" N VAL H 398 " --> pdb=" O PHE H 377 " (cutoff:3.500A) removed outlier: 15.750A pdb=" N VAL H 379 " --> pdb=" O VAL H 396 " (cutoff:3.500A) removed outlier: 16.346A pdb=" N VAL H 396 " --> pdb=" O VAL H 379 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 96 through 102 removed outlier: 5.479A pdb=" N PHE B 97 " --> pdb=" O THR B 449 " (cutoff:3.500A) removed outlier: 6.124A pdb=" N THR B 449 " --> pdb=" O PHE B 97 " (cutoff:3.500A) removed outlier: 5.692A pdb=" N CYS B 447 " --> pdb=" O PRO B 99 " (cutoff:3.500A) removed outlier: 5.840A pdb=" N ARG B 420 " --> pdb=" O GLY B 448 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 115 through 124 removed outlier: 4.772A pdb=" N TRP B 115 " --> pdb=" O THR B 138 " (cutoff:3.500A) removed outlier: 7.371A pdb=" N THR B 138 " --> pdb=" O TRP B 115 " (cutoff:3.500A) removed outlier: 7.616A pdb=" N THR B 117 " --> pdb=" O GLN B 136 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N GLN B 136 " --> pdb=" O THR B 117 " (cutoff:3.500A) removed outlier: 5.470A pdb=" N GLU B 119 " --> pdb=" O LEU B 134 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N LEU B 134 " --> pdb=" O GLU B 119 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N THR B 157 " --> pdb=" O GLY B 135 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N LEU B 158 " --> pdb=" O VAL B 174 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N LYS B 172 " --> pdb=" O MET B 160 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 179 through 184 removed outlier: 4.123A pdb=" N ASP B 197 " --> pdb=" O ASN B 200 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N TYR B 207 " --> pdb=" O LEU B 211 " (cutoff:3.500A) removed outlier: 5.174A pdb=" N LEU B 211 " --> pdb=" O TYR B 207 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 231 through 233 removed outlier: 6.429A pdb=" N GLU B 258 " --> pdb=" O ILE B 262 " (cutoff:3.500A) removed outlier: 5.439A pdb=" N ILE B 262 " --> pdb=" O GLU B 258 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 276 through 283 removed outlier: 5.424A pdb=" N GLU B 277 " --> pdb=" O ARG B 292 " (cutoff:3.500A) removed outlier: 4.988A pdb=" N ARG B 292 " --> pdb=" O GLU B 277 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'B' and resid 352 through 356 removed outlier: 4.494A pdb=" N TRP B 352 " --> pdb=" O GLY B 363 " (cutoff:3.500A) removed outlier: 7.005A pdb=" N ASP B 402 " --> pdb=" O GLY B 373 " (cutoff:3.500A) removed outlier: 9.706A pdb=" N GLU B 375 " --> pdb=" O ARG B 400 " (cutoff:3.500A) removed outlier: 10.486A pdb=" N ARG B 400 " --> pdb=" O GLU B 375 " (cutoff:3.500A) removed outlier: 11.509A pdb=" N PHE B 377 " --> pdb=" O VAL B 398 " (cutoff:3.500A) removed outlier: 13.562A pdb=" N VAL B 398 " --> pdb=" O PHE B 377 " (cutoff:3.500A) removed outlier: 15.815A pdb=" N VAL B 379 " --> pdb=" O VAL B 396 " (cutoff:3.500A) removed outlier: 16.373A pdb=" N VAL B 396 " --> pdb=" O VAL B 379 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'J' and resid 96 through 102 removed outlier: 3.796A pdb=" N GLY J 96 " --> pdb=" O THR J 449 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N VAL J 445 " --> pdb=" O PHE J 100 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N LYS J 102 " --> pdb=" O ILE J 443 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N ILE J 443 " --> pdb=" O LYS J 102 " (cutoff:3.500A) removed outlier: 5.837A pdb=" N ARG J 420 " --> pdb=" O GLY J 448 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'J' and resid 115 through 124 removed outlier: 4.798A pdb=" N TRP J 115 " --> pdb=" O THR J 138 " (cutoff:3.500A) removed outlier: 7.420A pdb=" N THR J 138 " --> pdb=" O TRP J 115 " (cutoff:3.500A) removed outlier: 7.593A pdb=" N THR J 117 " --> pdb=" O GLN J 136 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N GLN J 136 " --> pdb=" O THR J 117 " (cutoff:3.500A) removed outlier: 5.449A pdb=" N GLU J 119 " --> pdb=" O LEU J 134 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N LEU J 134 " --> pdb=" O GLU J 119 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N THR J 157 " --> pdb=" O GLY J 135 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N LEU J 158 " --> pdb=" O VAL J 174 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N LYS J 172 " --> pdb=" O MET J 160 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'J' and resid 179 through 184 removed outlier: 4.117A pdb=" N ASP J 197 " --> pdb=" O ASN J 200 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N TYR J 207 " --> pdb=" O LEU J 211 " (cutoff:3.500A) removed outlier: 5.180A pdb=" N LEU J 211 " --> pdb=" O TYR J 207 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'J' and resid 231 through 233 removed outlier: 6.435A pdb=" N GLU J 258 " --> pdb=" O ILE J 262 " (cutoff:3.500A) removed outlier: 5.434A pdb=" N ILE J 262 " --> pdb=" O GLU J 258 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'J' and resid 276 through 283 removed outlier: 5.405A pdb=" N GLU J 277 " --> pdb=" O ARG J 292 " (cutoff:3.500A) removed outlier: 4.939A pdb=" N ARG J 292 " --> pdb=" O GLU J 277 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'J' and resid 352 through 356 removed outlier: 4.458A pdb=" N TRP J 352 " --> pdb=" O GLY J 363 " (cutoff:3.500A) removed outlier: 7.025A pdb=" N ASP J 402 " --> pdb=" O GLY J 373 " (cutoff:3.500A) removed outlier: 9.676A pdb=" N GLU J 375 " --> pdb=" O ARG J 400 " (cutoff:3.500A) removed outlier: 10.429A pdb=" N ARG J 400 " --> pdb=" O GLU J 375 " (cutoff:3.500A) removed outlier: 11.508A pdb=" N PHE J 377 " --> pdb=" O VAL J 398 " (cutoff:3.500A) removed outlier: 13.570A pdb=" N VAL J 398 " --> pdb=" O PHE J 377 " (cutoff:3.500A) removed outlier: 15.789A pdb=" N VAL J 379 " --> pdb=" O VAL J 396 " (cutoff:3.500A) removed outlier: 16.357A pdb=" N VAL J 396 " --> pdb=" O VAL J 379 " (cutoff:3.500A) 584 hydrogen bonds defined for protein. 1518 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: 3.87 Time building geometry restraints manager: 2.62 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.32: 3171 1.32 - 1.45: 5346 1.45 - 1.58: 10224 1.58 - 1.71: 0 1.71 - 1.85: 134 Bond restraints: 18875 Sorted by residual: bond pdb=" C SER J 404 " pdb=" O SER J 404 " ideal model delta sigma weight residual 1.235 1.298 -0.062 1.26e-02 6.30e+03 2.45e+01 bond pdb=" C LYS G 350 " pdb=" O LYS G 350 " ideal model delta sigma weight residual 1.235 1.288 -0.053 1.20e-02 6.94e+03 1.97e+01 bond pdb=" N GLY J 286 " pdb=" CA GLY J 286 " ideal model delta sigma weight residual 1.442 1.475 -0.033 7.70e-03 1.69e+04 1.87e+01 bond pdb=" N GLY G 286 " pdb=" CA GLY G 286 " ideal model delta sigma weight residual 1.442 1.474 -0.032 7.70e-03 1.69e+04 1.77e+01 bond pdb=" C PRO H 90 " pdb=" O PRO H 90 " ideal model delta sigma weight residual 1.233 1.184 0.049 1.18e-02 7.18e+03 1.73e+01 ... (remaining 18870 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.21: 20936 2.21 - 4.42: 4275 4.42 - 6.63: 365 6.63 - 8.84: 33 8.84 - 11.04: 8 Bond angle restraints: 25617 Sorted by residual: angle pdb=" N ILE J 397 " pdb=" CA ILE J 397 " pdb=" C ILE J 397 " ideal model delta sigma weight residual 111.81 106.63 5.18 8.60e-01 1.35e+00 3.63e+01 angle pdb=" N ILE B 397 " pdb=" CA ILE B 397 " pdb=" C ILE B 397 " ideal model delta sigma weight residual 111.81 106.70 5.11 8.60e-01 1.35e+00 3.53e+01 angle pdb=" N LYS J 128 " pdb=" CA LYS J 128 " pdb=" CB LYS J 128 " ideal model delta sigma weight residual 111.52 100.48 11.04 1.86e+00 2.89e-01 3.53e+01 angle pdb=" N ILE G 397 " pdb=" CA ILE G 397 " pdb=" C ILE G 397 " ideal model delta sigma weight residual 111.81 106.77 5.04 8.60e-01 1.35e+00 3.43e+01 angle pdb=" CA ASP H 125 " pdb=" CB ASP H 125 " pdb=" CG ASP H 125 " ideal model delta sigma weight residual 112.60 118.41 -5.81 1.00e+00 1.00e+00 3.38e+01 ... (remaining 25612 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 19.75: 11476 19.75 - 39.50: 466 39.50 - 59.25: 107 59.25 - 79.00: 55 79.00 - 98.75: 27 Dihedral angle restraints: 12131 sinusoidal: 5680 harmonic: 6451 Sorted by residual: dihedral pdb=" CA GLY J 244 " pdb=" C GLY J 244 " pdb=" N ASN J 245 " pdb=" CA ASN J 245 " ideal model delta harmonic sigma weight residual -180.00 -150.08 -29.92 0 5.00e+00 4.00e-02 3.58e+01 dihedral pdb=" CA ASP J 127 " pdb=" C ASP J 127 " pdb=" N LYS J 128 " pdb=" CA LYS J 128 " ideal model delta harmonic sigma weight residual -180.00 -155.41 -24.59 0 5.00e+00 4.00e-02 2.42e+01 dihedral pdb=" CA GLY J 297 " pdb=" C GLY J 297 " pdb=" N SER J 298 " pdb=" CA SER J 298 " ideal model delta harmonic sigma weight residual 180.00 155.95 24.05 0 5.00e+00 4.00e-02 2.31e+01 ... (remaining 12128 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.120: 2423 0.120 - 0.240: 576 0.240 - 0.361: 11 0.361 - 0.481: 5 0.481 - 0.601: 1 Chirality restraints: 3016 Sorted by residual: chirality pdb=" C1 BMA k 3 " pdb=" O4 NAG k 2 " pdb=" C2 BMA k 3 " pdb=" O5 BMA k 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.23 -0.17 2.00e-02 2.50e+03 7.21e+01 chirality pdb=" C1 MAN k 4 " pdb=" O3 BMA k 3 " pdb=" C2 MAN k 4 " pdb=" O5 MAN k 4 " both_signs ideal model delta sigma weight residual False 2.40 2.23 0.17 2.00e-02 2.50e+03 6.96e+01 chirality pdb=" C1 MAN 3 4 " pdb=" O3 BMA 3 3 " pdb=" C2 MAN 3 4 " pdb=" O5 MAN 3 4 " both_signs ideal model delta sigma weight residual False 2.40 2.25 0.15 2.00e-02 2.50e+03 5.46e+01 ... (remaining 3013 not shown) Planarity restraints: 3222 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG c 2 " 0.076 2.00e-02 2.50e+03 6.44e-02 5.18e+01 pdb=" C7 NAG c 2 " -0.036 2.00e-02 2.50e+03 pdb=" C8 NAG c 2 " 0.063 2.00e-02 2.50e+03 pdb=" N2 NAG c 2 " -0.098 2.00e-02 2.50e+03 pdb=" O7 NAG c 2 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG r 1 " -0.074 2.00e-02 2.50e+03 6.15e-02 4.73e+01 pdb=" C7 NAG r 1 " 0.032 2.00e-02 2.50e+03 pdb=" C8 NAG r 1 " -0.059 2.00e-02 2.50e+03 pdb=" N2 NAG r 1 " 0.094 2.00e-02 2.50e+03 pdb=" O7 NAG r 1 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR J 281 " -0.084 2.00e-02 2.50e+03 4.45e-02 3.97e+01 pdb=" CG TYR J 281 " 0.048 2.00e-02 2.50e+03 pdb=" CD1 TYR J 281 " 0.028 2.00e-02 2.50e+03 pdb=" CD2 TYR J 281 " 0.026 2.00e-02 2.50e+03 pdb=" CE1 TYR J 281 " 0.017 2.00e-02 2.50e+03 pdb=" CE2 TYR J 281 " 0.023 2.00e-02 2.50e+03 pdb=" CZ TYR J 281 " 0.007 2.00e-02 2.50e+03 pdb=" OH TYR J 281 " -0.064 2.00e-02 2.50e+03 ... (remaining 3219 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 1410 2.75 - 3.29: 18460 3.29 - 3.83: 30748 3.83 - 4.36: 42465 4.36 - 4.90: 67681 Nonbonded interactions: 160764 Sorted by model distance: nonbonded pdb=" OD2 ASP J 324 " pdb="CA CA J2000 " model vdw 2.218 2.510 nonbonded pdb=" OD2 ASP B 324 " pdb="CA CA B2000 " model vdw 2.239 2.510 nonbonded pdb=" O HIS G 347 " pdb="CA CA G 501 " model vdw 2.252 2.510 nonbonded pdb=" OD2 ASP H 324 " pdb="CA CA H2000 " model vdw 2.275 2.510 nonbonded pdb=" OD2 ASP G 324 " pdb="CA CA G 501 " model vdw 2.291 2.510 ... (remaining 160759 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 '1' selection = chain '2' selection = chain '4' selection = chain '7' selection = chain 'a' selection = chain 'b' selection = chain 'd' selection = chain 'g' selection = chain 'i' selection = chain 'j' selection = chain 'l' selection = chain 'o' selection = chain 'q' selection = chain 'r' selection = chain 't' selection = chain 'w' } ncs_group { reference = chain '3' selection = chain 'c' selection = chain 'k' selection = chain 's' } ncs_group { reference = chain '5' selection = chain 'e' selection = chain 'm' selection = chain 'u' } ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'E' } ncs_group { reference = chain 'B' selection = (chain 'G' and resid 82 through 501) selection = chain 'H' selection = chain 'J' } ncs_group { reference = chain 'D' selection = chain 'F' 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 individual isotropic 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: 5.550 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.240 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 18.840 Find NCS groups from input model: 0.460 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:1.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.260 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8935 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 : 0.015 0.102 18993 Z= 1.037 Angle : 1.752 14.536 25929 Z= 1.116 Chirality : 0.094 0.601 3016 Planarity : 0.010 0.064 3198 Dihedral : 13.443 98.749 7897 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 0.31 Ramachandran Plot: Outliers : 0.58 % Allowed : 3.77 % Favored : 95.65 % Rotamer: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Cbeta Deviations : 0.34 % Peptide Plane: Cis-proline : 18.67 % Cis-general : 0.18 % 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: -0.63 (0.17), residues: 2252 helix: -1.12 (0.70), residues: 24 sheet: 0.04 (0.16), residues: 925 loop : -0.70 (0.16), residues: 1303 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.030 0.003 ARG H 288 TYR 0.084 0.013 TYR J 281 PHE 0.057 0.013 PHE G 205 TRP 0.060 0.013 TRP B 458 HIS 0.046 0.007 HIS H 168 Details of bonding type rmsd covalent geometry : bond 0.01489 (18875) covalent geometry : angle 1.70803 (25617) SS BOND : bond 0.04676 ( 42) SS BOND : angle 2.40405 ( 84) hydrogen bonds : bond 0.16151 ( 572) hydrogen bonds : angle 8.58427 ( 1518) link_ALPHA1-2 : bond 0.00289 ( 4) link_ALPHA1-2 : angle 4.89940 ( 12) link_ALPHA1-3 : bond 0.01904 ( 8) link_ALPHA1-3 : angle 2.87221 ( 24) link_ALPHA1-6 : bond 0.01550 ( 8) link_ALPHA1-6 : angle 3.20270 ( 24) link_BETA1-4 : bond 0.01548 ( 28) link_BETA1-4 : angle 4.16160 ( 84) link_BETA1-6 : bond 0.01223 ( 4) link_BETA1-6 : angle 3.27205 ( 12) link_NAG-ASN : bond 0.01782 ( 24) link_NAG-ASN : angle 5.35011 ( 72) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4504 Ramachandran restraints generated. 2252 Oldfield, 0 Emsley, 2252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4504 Ramachandran restraints generated. 2252 Oldfield, 0 Emsley, 2252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 1939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 297 time to evaluate : 0.751 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: E 90 ASP cc_start: 0.7815 (m-30) cc_final: 0.6939 (m-30) REVERT: F 11 LEU cc_start: 0.8017 (tp) cc_final: 0.7664 (tt) REVERT: F 75 ILE cc_start: 0.9128 (mt) cc_final: 0.8911 (mp) REVERT: F 79 GLN cc_start: 0.7499 (mm-40) cc_final: 0.7050 (mp10) REVERT: A 43 GLN cc_start: 0.8830 (tt0) cc_final: 0.8480 (mt0) REVERT: A 65 GLN cc_start: 0.8812 (tt0) cc_final: 0.8611 (tp-100) REVERT: D 42 GLN cc_start: 0.8890 (mt0) cc_final: 0.8662 (mt0) REVERT: D 75 ILE cc_start: 0.9472 (mt) cc_final: 0.9241 (tt) REVERT: C 23 LYS cc_start: 0.9259 (ttmt) cc_final: 0.8999 (tttp) REVERT: C 36 TRP cc_start: 0.9275 (m100) cc_final: 0.8952 (m100) REVERT: C 64 PHE cc_start: 0.8594 (m-80) cc_final: 0.8256 (m-10) REVERT: C 81 MET cc_start: 0.8256 (tmm) cc_final: 0.8035 (tmm) REVERT: C 90 ASP cc_start: 0.7477 (m-30) cc_final: 0.6935 (m-30) REVERT: C 93 VAL cc_start: 0.9147 (t) cc_final: 0.8892 (p) REVERT: C 102 ASP cc_start: 0.9066 (p0) cc_final: 0.8703 (p0) REVERT: I 4 MET cc_start: 0.8606 (mmm) cc_final: 0.7799 (mmm) REVERT: I 6 GLN cc_start: 0.8277 (tt0) cc_final: 0.7883 (tt0) REVERT: I 42 GLN cc_start: 0.7786 (mt0) cc_final: 0.7228 (mp10) REVERT: I 82 ASP cc_start: 0.7994 (m-30) cc_final: 0.7645 (m-30) REVERT: I 109 ARG cc_start: 0.6332 (ptm160) cc_final: 0.5263 (pmt-80) REVERT: H 141 ASN cc_start: 0.9366 (t0) cc_final: 0.8904 (p0) REVERT: B 400 ARG cc_start: 0.8908 (ptm-80) cc_final: 0.8671 (ptp-110) outliers start: 0 outliers final: 0 residues processed: 297 average time/residue: 0.1815 time to fit residues: 75.5649 Evaluate side-chains 182 residues out of total 1939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 182 time to evaluate : 0.644 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 216 optimal weight: 0.9990 chunk 98 optimal weight: 1.9990 chunk 194 optimal weight: 1.9990 chunk 107 optimal weight: 0.9980 chunk 10 optimal weight: 0.5980 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 0.7980 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 0.7980 chunk 200 optimal weight: 0.5980 chunk 212 optimal weight: 2.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 39 GLN E 65 GLN A 120 GLN D 6 GLN C 6 GLN G 274 HIS G 468 HIS ** H 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 274 HIS J 468 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.083038 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.060029 restraints weight = 43484.172| |-----------------------------------------------------------------------------| r_work (start): 0.2964 rms_B_bonded: 2.86 r_work: 0.2845 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2711 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.2711 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8733 moved from start: 0.1952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 18993 Z= 0.144 Angle : 0.716 9.829 25929 Z= 0.373 Chirality : 0.048 0.326 3016 Planarity : 0.004 0.029 3198 Dihedral : 8.649 74.536 3998 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 2.92 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.29 % Favored : 96.54 % Rotamer: Outliers : 0.88 % Allowed : 6.19 % Favored : 92.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.67 % Cis-general : 0.18 % 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 (0.17), residues: 2252 helix: -0.70 (0.85), residues: 24 sheet: -0.03 (0.16), residues: 948 loop : -0.14 (0.17), residues: 1280 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 106 TYR 0.014 0.002 TYR F 49 PHE 0.016 0.002 PHE B 410 TRP 0.022 0.002 TRP G 178 HIS 0.007 0.001 HIS J 468 Details of bonding type rmsd covalent geometry : bond 0.00298 (18875) covalent geometry : angle 0.68278 (25617) SS BOND : bond 0.00604 ( 42) SS BOND : angle 1.38923 ( 84) hydrogen bonds : bond 0.05046 ( 572) hydrogen bonds : angle 7.31508 ( 1518) link_ALPHA1-2 : bond 0.00749 ( 4) link_ALPHA1-2 : angle 1.84979 ( 12) link_ALPHA1-3 : bond 0.01083 ( 8) link_ALPHA1-3 : angle 1.82181 ( 24) link_ALPHA1-6 : bond 0.00713 ( 8) link_ALPHA1-6 : angle 1.28105 ( 24) link_BETA1-4 : bond 0.00496 ( 28) link_BETA1-4 : angle 2.05894 ( 84) link_BETA1-6 : bond 0.00512 ( 4) link_BETA1-6 : angle 1.46074 ( 12) link_NAG-ASN : bond 0.00270 ( 24) link_NAG-ASN : angle 2.98534 ( 72) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4504 Ramachandran restraints generated. 2252 Oldfield, 0 Emsley, 2252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4504 Ramachandran restraints generated. 2252 Oldfield, 0 Emsley, 2252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 1939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 209 time to evaluate : 0.763 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 48 MET cc_start: 0.9078 (mtm) cc_final: 0.8868 (mtm) REVERT: E 65 GLN cc_start: 0.8336 (tp-100) cc_final: 0.8004 (tm-30) REVERT: E 67 ARG cc_start: 0.7531 (mtm-85) cc_final: 0.6196 (mtm110) REVERT: E 90 ASP cc_start: 0.7173 (m-30) cc_final: 0.6940 (m-30) REVERT: F 11 LEU cc_start: 0.8033 (tp) cc_final: 0.7774 (tt) REVERT: F 13 LEU cc_start: 0.8125 (mt) cc_final: 0.7344 (mt) REVERT: F 18 ARG cc_start: 0.8776 (tmm-80) cc_final: 0.8468 (ttp80) REVERT: F 79 GLN cc_start: 0.7591 (mm-40) cc_final: 0.7081 (mp10) REVERT: F 85 ILE cc_start: 0.8624 (mm) cc_final: 0.8383 (mm) REVERT: F 104 LYS cc_start: 0.8047 (tppt) cc_final: 0.7700 (tppt) REVERT: A 46 GLU cc_start: 0.8543 (tp30) cc_final: 0.8299 (tm-30) REVERT: A 77 THR cc_start: 0.7513 (OUTLIER) cc_final: 0.7248 (p) REVERT: A 81 MET cc_start: 0.8141 (tmm) cc_final: 0.7470 (ttp) REVERT: D 70 GLU cc_start: 0.8689 (tt0) cc_final: 0.8475 (tt0) REVERT: D 75 ILE cc_start: 0.9449 (mt) cc_final: 0.9165 (tt) REVERT: C 12 LYS cc_start: 0.8314 (mmtm) cc_final: 0.8106 (mmtm) REVERT: C 23 LYS cc_start: 0.8886 (ttmt) cc_final: 0.8470 (tttm) REVERT: C 31 ASN cc_start: 0.8725 (t0) cc_final: 0.8465 (t0) REVERT: C 36 TRP cc_start: 0.9146 (m100) cc_final: 0.8783 (m100) REVERT: C 102 ASP cc_start: 0.9110 (p0) cc_final: 0.8715 (p0) REVERT: I 4 MET cc_start: 0.8380 (mmm) cc_final: 0.7822 (mmm) REVERT: I 11 LEU cc_start: 0.8775 (tp) cc_final: 0.8469 (tt) REVERT: I 42 GLN cc_start: 0.7467 (mt0) cc_final: 0.7122 (mt0) REVERT: I 79 GLN cc_start: 0.8790 (mm-40) cc_final: 0.8589 (mm-40) REVERT: I 101 GLN cc_start: 0.8668 (mm110) cc_final: 0.8427 (pm20) REVERT: I 109 ARG cc_start: 0.6413 (ptm160) cc_final: 0.5016 (pmt-80) REVERT: H 103 ASP cc_start: 0.8275 (p0) cc_final: 0.8016 (m-30) outliers start: 17 outliers final: 8 residues processed: 219 average time/residue: 0.1729 time to fit residues: 53.7765 Evaluate side-chains 185 residues out of total 1939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 176 time to evaluate : 0.678 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 75 SER Chi-restraints excluded: chain A residue 77 THR Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 35 SER Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain I residue 107 ILE Chi-restraints excluded: chain H residue 230 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 173 optimal weight: 1.9990 chunk 39 optimal weight: 7.9990 chunk 119 optimal weight: 3.9990 chunk 120 optimal weight: 3.9990 chunk 190 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 197 optimal weight: 0.9980 chunk 142 optimal weight: 0.9990 chunk 207 optimal weight: 6.9990 chunk 70 optimal weight: 3.9990 chunk 211 optimal weight: 9.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 32 GLN A 65 GLN D 42 GLN I 6 GLN G 347 HIS G 468 HIS H 347 HIS ** H 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 347 HIS B 358 ASN J 468 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.080080 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2920 r_free = 0.2920 target = 0.057119 restraints weight = 44205.690| |-----------------------------------------------------------------------------| r_work (start): 0.2889 rms_B_bonded: 2.82 r_work: 0.2775 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2649 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.2649 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8811 moved from start: 0.2556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.058 18993 Z= 0.257 Angle : 0.721 9.102 25929 Z= 0.367 Chirality : 0.049 0.307 3016 Planarity : 0.004 0.032 3198 Dihedral : 7.975 67.942 3998 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.37 % Favored : 96.45 % Rotamer: Outliers : 1.39 % Allowed : 8.35 % Favored : 90.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.67 % Cis-general : 0.18 % 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 (0.17), residues: 2252 helix: -0.29 (0.88), residues: 24 sheet: -0.15 (0.16), residues: 930 loop : -0.10 (0.17), residues: 1298 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG I 54 TYR 0.021 0.002 TYR H 121 PHE 0.020 0.002 PHE C 64 TRP 0.020 0.002 TRP G 178 HIS 0.006 0.002 HIS G 347 Details of bonding type rmsd covalent geometry : bond 0.00587 (18875) covalent geometry : angle 0.69041 (25617) SS BOND : bond 0.00451 ( 42) SS BOND : angle 1.20280 ( 84) hydrogen bonds : bond 0.04937 ( 572) hydrogen bonds : angle 6.90742 ( 1518) link_ALPHA1-2 : bond 0.00312 ( 4) link_ALPHA1-2 : angle 2.42820 ( 12) link_ALPHA1-3 : bond 0.00571 ( 8) link_ALPHA1-3 : angle 2.19641 ( 24) link_ALPHA1-6 : bond 0.00384 ( 8) link_ALPHA1-6 : angle 1.52116 ( 24) link_BETA1-4 : bond 0.00419 ( 28) link_BETA1-4 : angle 1.98634 ( 84) link_BETA1-6 : bond 0.00565 ( 4) link_BETA1-6 : angle 2.27697 ( 12) link_NAG-ASN : bond 0.00435 ( 24) link_NAG-ASN : angle 2.69397 ( 72) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4504 Ramachandran restraints generated. 2252 Oldfield, 0 Emsley, 2252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4504 Ramachandran restraints generated. 2252 Oldfield, 0 Emsley, 2252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 1939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 185 time to evaluate : 0.487 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 12 LYS cc_start: 0.7806 (mmtt) cc_final: 0.7429 (mmtt) REVERT: F 77 SER cc_start: 0.8545 (t) cc_final: 0.8176 (p) REVERT: F 79 GLN cc_start: 0.7736 (mm-40) cc_final: 0.7302 (mp10) REVERT: F 104 LYS cc_start: 0.8427 (tppt) cc_final: 0.8209 (tppt) REVERT: A 12 LYS cc_start: 0.8154 (mmtt) cc_final: 0.7875 (mmmt) REVERT: A 23 LYS cc_start: 0.9028 (tttm) cc_final: 0.8662 (tttp) REVERT: A 46 GLU cc_start: 0.8757 (tp30) cc_final: 0.8387 (tm-30) REVERT: A 77 THR cc_start: 0.7604 (OUTLIER) cc_final: 0.7264 (p) REVERT: D 18 ARG cc_start: 0.8491 (ttp80) cc_final: 0.8284 (ttp80) REVERT: D 24 ARG cc_start: 0.8460 (ttm-80) cc_final: 0.8256 (ttm-80) REVERT: D 75 ILE cc_start: 0.9444 (mt) cc_final: 0.9206 (tt) REVERT: C 12 LYS cc_start: 0.8563 (mmtm) cc_final: 0.8188 (mmtm) REVERT: C 23 LYS cc_start: 0.8859 (ttmt) cc_final: 0.8441 (tttm) REVERT: C 31 ASN cc_start: 0.8785 (t0) cc_final: 0.8488 (t0) REVERT: C 65 GLN cc_start: 0.8712 (tp40) cc_final: 0.8046 (tm-30) REVERT: C 102 ASP cc_start: 0.9276 (p0) cc_final: 0.8845 (p0) REVERT: I 4 MET cc_start: 0.8392 (mmm) cc_final: 0.7881 (mmm) REVERT: I 13 LEU cc_start: 0.8316 (mp) cc_final: 0.7863 (mt) REVERT: I 42 GLN cc_start: 0.7731 (mt0) cc_final: 0.7408 (mt0) REVERT: I 101 GLN cc_start: 0.8625 (mm110) cc_final: 0.8384 (pm20) REVERT: I 104 LYS cc_start: 0.8748 (mtpp) cc_final: 0.8502 (mmtt) REVERT: I 109 ARG cc_start: 0.6410 (ptm160) cc_final: 0.4962 (pmt-80) outliers start: 27 outliers final: 17 residues processed: 207 average time/residue: 0.1761 time to fit residues: 51.7501 Evaluate side-chains 190 residues out of total 1939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 172 time to evaluate : 0.702 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain F residue 48 ILE Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 67 ARG Chi-restraints excluded: chain A residue 75 SER Chi-restraints excluded: chain A residue 77 THR Chi-restraints excluded: chain D residue 56 THR Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 35 SER Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain G residue 230 CYS Chi-restraints excluded: chain H residue 230 CYS Chi-restraints excluded: chain B residue 307 ILE Chi-restraints excluded: chain B residue 319 SER Chi-restraints excluded: chain J residue 230 CYS Chi-restraints excluded: chain J residue 245 ASN Chi-restraints excluded: chain J residue 376 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 146 optimal weight: 3.9990 chunk 79 optimal weight: 2.9990 chunk 157 optimal weight: 0.7980 chunk 168 optimal weight: 0.6980 chunk 21 optimal weight: 6.9990 chunk 135 optimal weight: 5.9990 chunk 24 optimal weight: 10.0000 chunk 69 optimal weight: 0.9990 chunk 66 optimal weight: 6.9990 chunk 108 optimal weight: 0.7980 chunk 183 optimal weight: 3.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 65 GLN D 79 GLN G 468 HIS ** H 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 468 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.080736 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2959 r_free = 0.2959 target = 0.058651 restraints weight = 43627.528| |-----------------------------------------------------------------------------| r_work (start): 0.2926 rms_B_bonded: 2.73 r_work: 0.2814 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2689 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.2689 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8781 moved from start: 0.2776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 18993 Z= 0.160 Angle : 0.641 9.122 25929 Z= 0.325 Chirality : 0.046 0.260 3016 Planarity : 0.003 0.037 3198 Dihedral : 7.269 58.437 3998 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 4.03 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.15 % Favored : 96.67 % Rotamer: Outliers : 1.24 % Allowed : 9.59 % Favored : 89.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.67 % Cis-general : 0.18 % 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: -0.31 (0.17), residues: 2252 helix: -1.28 (0.76), residues: 28 sheet: -0.16 (0.15), residues: 974 loop : -0.08 (0.17), residues: 1250 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG I 18 TYR 0.016 0.001 TYR F 49 PHE 0.015 0.002 PHE H 410 TRP 0.019 0.001 TRP J 178 HIS 0.009 0.001 HIS J 468 Details of bonding type rmsd covalent geometry : bond 0.00356 (18875) covalent geometry : angle 0.61235 (25617) SS BOND : bond 0.00288 ( 42) SS BOND : angle 1.27353 ( 84) hydrogen bonds : bond 0.04133 ( 572) hydrogen bonds : angle 6.66448 ( 1518) link_ALPHA1-2 : bond 0.00532 ( 4) link_ALPHA1-2 : angle 2.34999 ( 12) link_ALPHA1-3 : bond 0.00839 ( 8) link_ALPHA1-3 : angle 1.78514 ( 24) link_ALPHA1-6 : bond 0.00556 ( 8) link_ALPHA1-6 : angle 1.38675 ( 24) link_BETA1-4 : bond 0.00423 ( 28) link_BETA1-4 : angle 1.70733 ( 84) link_BETA1-6 : bond 0.00346 ( 4) link_BETA1-6 : angle 1.41626 ( 12) link_NAG-ASN : bond 0.00340 ( 24) link_NAG-ASN : angle 2.50070 ( 72) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4504 Ramachandran restraints generated. 2252 Oldfield, 0 Emsley, 2252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4504 Ramachandran restraints generated. 2252 Oldfield, 0 Emsley, 2252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 180 time to evaluate : 0.689 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: E 23 LYS cc_start: 0.8651 (mttt) cc_final: 0.8448 (mmtt) REVERT: E 65 GLN cc_start: 0.8319 (tp-100) cc_final: 0.7986 (tm-30) REVERT: F 74 THR cc_start: 0.7617 (OUTLIER) cc_final: 0.7307 (t) REVERT: F 79 GLN cc_start: 0.7612 (mm-40) cc_final: 0.6971 (mp10) REVERT: A 12 LYS cc_start: 0.8128 (mmtt) cc_final: 0.7866 (mmmt) REVERT: A 46 GLU cc_start: 0.8766 (tp30) cc_final: 0.8245 (tm-30) REVERT: A 77 THR cc_start: 0.7670 (OUTLIER) cc_final: 0.7376 (p) REVERT: A 107 ASP cc_start: 0.8536 (OUTLIER) cc_final: 0.8045 (m-30) REVERT: D 45 ARG cc_start: 0.8604 (ttm-80) cc_final: 0.8035 (ttp80) REVERT: C 12 LYS cc_start: 0.8556 (mmtm) cc_final: 0.8189 (mmtm) REVERT: C 23 LYS cc_start: 0.8876 (ttmt) cc_final: 0.8442 (tttm) REVERT: C 65 GLN cc_start: 0.8659 (tp40) cc_final: 0.8000 (tm-30) REVERT: C 94 TYR cc_start: 0.8186 (m-10) cc_final: 0.7882 (m-10) REVERT: C 102 ASP cc_start: 0.9247 (p0) cc_final: 0.8829 (p0) REVERT: C 107 ASP cc_start: 0.8852 (t0) cc_final: 0.8617 (t0) REVERT: I 4 MET cc_start: 0.8382 (mmm) cc_final: 0.7989 (mmm) REVERT: I 42 GLN cc_start: 0.7676 (mt0) cc_final: 0.7367 (mt0) REVERT: I 101 GLN cc_start: 0.8639 (mm110) cc_final: 0.8344 (pm20) REVERT: I 109 ARG cc_start: 0.6330 (ptm160) cc_final: 0.4982 (pmt-80) REVERT: H 101 SER cc_start: 0.9464 (t) cc_final: 0.9131 (m) REVERT: B 358 ASN cc_start: 0.8773 (OUTLIER) cc_final: 0.8239 (t0) outliers start: 24 outliers final: 15 residues processed: 201 average time/residue: 0.1727 time to fit residues: 49.0756 Evaluate side-chains 186 residues out of total 1939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 167 time to evaluate : 0.630 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain F residue 74 THR Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 75 SER Chi-restraints excluded: chain A residue 77 THR Chi-restraints excluded: chain A residue 107 ASP Chi-restraints excluded: chain D residue 33 LEU Chi-restraints excluded: chain D residue 56 THR Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 35 SER Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain G residue 230 CYS Chi-restraints excluded: chain H residue 230 CYS Chi-restraints excluded: chain B residue 319 SER Chi-restraints excluded: chain B residue 358 ASN Chi-restraints excluded: chain J residue 230 CYS Chi-restraints excluded: chain J residue 245 ASN Chi-restraints excluded: chain J residue 376 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 193 optimal weight: 3.9990 chunk 203 optimal weight: 2.9990 chunk 171 optimal weight: 4.9990 chunk 64 optimal weight: 10.0000 chunk 125 optimal weight: 1.9990 chunk 45 optimal weight: 6.9990 chunk 92 optimal weight: 0.0470 chunk 117 optimal weight: 2.9990 chunk 120 optimal weight: 2.9990 chunk 115 optimal weight: 0.6980 chunk 17 optimal weight: 0.0030 overall best weight: 1.1492 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 39 GLN F 6 GLN D 79 GLN G 468 HIS ** H 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 468 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.080749 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2961 r_free = 0.2961 target = 0.058618 restraints weight = 43339.009| |-----------------------------------------------------------------------------| r_work (start): 0.2931 rms_B_bonded: 2.74 r_work: 0.2817 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2691 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.2691 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8780 moved from start: 0.2968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 18993 Z= 0.153 Angle : 0.629 9.230 25929 Z= 0.315 Chirality : 0.046 0.250 3016 Planarity : 0.003 0.048 3198 Dihedral : 6.905 53.941 3998 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.46 % Favored : 96.36 % Rotamer: Outliers : 1.29 % Allowed : 10.16 % Favored : 88.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.67 % Cis-general : 0.18 % 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 (0.17), residues: 2252 helix: -1.07 (0.78), residues: 28 sheet: -0.16 (0.16), residues: 956 loop : -0.06 (0.17), residues: 1268 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG F 24 TYR 0.016 0.001 TYR F 49 PHE 0.015 0.002 PHE H 410 TRP 0.018 0.001 TRP J 178 HIS 0.009 0.001 HIS J 468 Details of bonding type rmsd covalent geometry : bond 0.00342 (18875) covalent geometry : angle 0.60430 (25617) SS BOND : bond 0.00334 ( 42) SS BOND : angle 1.05359 ( 84) hydrogen bonds : bond 0.03998 ( 572) hydrogen bonds : angle 6.54611 ( 1518) link_ALPHA1-2 : bond 0.00502 ( 4) link_ALPHA1-2 : angle 2.28888 ( 12) link_ALPHA1-3 : bond 0.00815 ( 8) link_ALPHA1-3 : angle 1.79614 ( 24) link_ALPHA1-6 : bond 0.00563 ( 8) link_ALPHA1-6 : angle 1.41821 ( 24) link_BETA1-4 : bond 0.00389 ( 28) link_BETA1-4 : angle 1.63739 ( 84) link_BETA1-6 : bond 0.00284 ( 4) link_BETA1-6 : angle 1.41430 ( 12) link_NAG-ASN : bond 0.00259 ( 24) link_NAG-ASN : angle 2.31831 ( 72) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4504 Ramachandran restraints generated. 2252 Oldfield, 0 Emsley, 2252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4504 Ramachandran restraints generated. 2252 Oldfield, 0 Emsley, 2252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 177 time to evaluate : 0.479 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 10 GLU cc_start: 0.8770 (mm-30) cc_final: 0.8347 (mp0) REVERT: E 65 GLN cc_start: 0.8378 (tp-100) cc_final: 0.8028 (tm-30) REVERT: F 79 GLN cc_start: 0.7649 (mm-40) cc_final: 0.7004 (mp10) REVERT: F 104 LYS cc_start: 0.8036 (tppt) cc_final: 0.7820 (tppt) REVERT: A 12 LYS cc_start: 0.8161 (mmtt) cc_final: 0.7937 (mmmt) REVERT: A 23 LYS cc_start: 0.8954 (tttm) cc_final: 0.8614 (tttp) REVERT: A 46 GLU cc_start: 0.8831 (tp30) cc_final: 0.8350 (tm-30) REVERT: A 77 THR cc_start: 0.7731 (OUTLIER) cc_final: 0.7380 (p) REVERT: A 107 ASP cc_start: 0.8420 (OUTLIER) cc_final: 0.7970 (m-30) REVERT: D 24 ARG cc_start: 0.8657 (ttm110) cc_final: 0.8113 (ttm-80) REVERT: D 45 ARG cc_start: 0.8619 (ttm-80) cc_final: 0.8037 (ttp80) REVERT: C 12 LYS cc_start: 0.8545 (mmtm) cc_final: 0.8201 (mmtm) REVERT: C 23 LYS cc_start: 0.8884 (ttmt) cc_final: 0.8450 (tttp) REVERT: C 65 GLN cc_start: 0.8658 (tp40) cc_final: 0.7953 (tm-30) REVERT: C 94 TYR cc_start: 0.8131 (m-10) cc_final: 0.7789 (m-10) REVERT: C 102 ASP cc_start: 0.9247 (p0) cc_final: 0.8840 (p0) REVERT: C 107 ASP cc_start: 0.8808 (t0) cc_final: 0.8603 (t0) REVERT: I 4 MET cc_start: 0.8361 (mmm) cc_final: 0.7942 (mmm) REVERT: I 42 GLN cc_start: 0.7687 (mt0) cc_final: 0.7380 (mt0) REVERT: I 47 LEU cc_start: 0.9065 (tp) cc_final: 0.8382 (tt) REVERT: I 54 ARG cc_start: 0.8543 (ttp-110) cc_final: 0.8171 (ttp-110) REVERT: I 101 GLN cc_start: 0.8623 (mm110) cc_final: 0.8320 (pm20) REVERT: I 109 ARG cc_start: 0.6219 (ptm160) cc_final: 0.4869 (pmt-80) REVERT: H 101 SER cc_start: 0.9440 (t) cc_final: 0.9122 (m) REVERT: B 358 ASN cc_start: 0.8767 (OUTLIER) cc_final: 0.8251 (t0) outliers start: 25 outliers final: 16 residues processed: 199 average time/residue: 0.1575 time to fit residues: 44.7376 Evaluate side-chains 188 residues out of total 1939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 169 time to evaluate : 0.456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain F residue 48 ILE Chi-restraints excluded: chain F residue 107 ILE Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 75 SER Chi-restraints excluded: chain A residue 77 THR Chi-restraints excluded: chain A residue 107 ASP Chi-restraints excluded: chain D residue 33 LEU Chi-restraints excluded: chain D residue 56 THR Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 35 SER Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain G residue 230 CYS Chi-restraints excluded: chain H residue 230 CYS Chi-restraints excluded: chain B residue 358 ASN Chi-restraints excluded: chain J residue 230 CYS Chi-restraints excluded: chain J residue 245 ASN Chi-restraints excluded: chain J residue 376 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 18 optimal weight: 10.0000 chunk 179 optimal weight: 4.9990 chunk 190 optimal weight: 2.9990 chunk 4 optimal weight: 7.9990 chunk 162 optimal weight: 3.9990 chunk 174 optimal weight: 5.9990 chunk 31 optimal weight: 5.9990 chunk 44 optimal weight: 5.9990 chunk 21 optimal weight: 5.9990 chunk 132 optimal weight: 1.9990 chunk 124 optimal weight: 4.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 65 GLN ** A 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 468 HIS ** H 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 468 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.077669 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2880 r_free = 0.2880 target = 0.055409 restraints weight = 44266.470| |-----------------------------------------------------------------------------| r_work (start): 0.2849 rms_B_bonded: 2.79 r_work: 0.2732 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2607 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.2607 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8867 moved from start: 0.3168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.080 18993 Z= 0.386 Angle : 0.776 9.719 25929 Z= 0.388 Chirality : 0.051 0.292 3016 Planarity : 0.004 0.041 3198 Dihedral : 7.821 61.184 3998 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.09 % Favored : 95.74 % Rotamer: Outliers : 1.50 % Allowed : 11.09 % Favored : 87.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.67 % Cis-general : 0.18 % 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: -0.63 (0.17), residues: 2252 helix: 0.23 (0.88), residues: 24 sheet: -0.39 (0.15), residues: 971 loop : -0.34 (0.17), residues: 1257 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 63 TYR 0.019 0.002 TYR H 121 PHE 0.020 0.003 PHE J 410 TRP 0.017 0.002 TRP G 178 HIS 0.008 0.002 HIS J 468 Details of bonding type rmsd covalent geometry : bond 0.00889 (18875) covalent geometry : angle 0.74395 (25617) SS BOND : bond 0.00722 ( 42) SS BOND : angle 1.38202 ( 84) hydrogen bonds : bond 0.05165 ( 572) hydrogen bonds : angle 6.88346 ( 1518) link_ALPHA1-2 : bond 0.00147 ( 4) link_ALPHA1-2 : angle 2.51062 ( 12) link_ALPHA1-3 : bond 0.00191 ( 8) link_ALPHA1-3 : angle 2.76292 ( 24) link_ALPHA1-6 : bond 0.00325 ( 8) link_ALPHA1-6 : angle 1.72793 ( 24) link_BETA1-4 : bond 0.00334 ( 28) link_BETA1-4 : angle 2.06251 ( 84) link_BETA1-6 : bond 0.00229 ( 4) link_BETA1-6 : angle 1.72242 ( 12) link_NAG-ASN : bond 0.00683 ( 24) link_NAG-ASN : angle 2.74302 ( 72) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4504 Ramachandran restraints generated. 2252 Oldfield, 0 Emsley, 2252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4504 Ramachandran restraints generated. 2252 Oldfield, 0 Emsley, 2252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 173 time to evaluate : 0.705 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: E 65 GLN cc_start: 0.8495 (tp-100) cc_final: 0.7920 (tm-30) REVERT: F 61 ARG cc_start: 0.8129 (ptm-80) cc_final: 0.6710 (ptm160) REVERT: F 74 THR cc_start: 0.7873 (OUTLIER) cc_final: 0.7403 (p) REVERT: F 79 GLN cc_start: 0.7951 (mm-40) cc_final: 0.7502 (mp10) REVERT: F 104 LYS cc_start: 0.8317 (tppt) cc_final: 0.8015 (tppt) REVERT: A 12 LYS cc_start: 0.8230 (mmtt) cc_final: 0.7908 (mmmt) REVERT: A 46 GLU cc_start: 0.8922 (tp30) cc_final: 0.8574 (tm-30) REVERT: A 77 THR cc_start: 0.7795 (OUTLIER) cc_final: 0.7506 (p) REVERT: C 12 LYS cc_start: 0.8625 (mmtm) cc_final: 0.8416 (mmtm) REVERT: C 23 LYS cc_start: 0.8907 (ttmt) cc_final: 0.8442 (tttp) REVERT: C 94 TYR cc_start: 0.8195 (m-10) cc_final: 0.7824 (m-10) REVERT: C 102 ASP cc_start: 0.9338 (p0) cc_final: 0.8967 (p0) REVERT: I 4 MET cc_start: 0.8442 (mmm) cc_final: 0.7960 (mmm) REVERT: I 42 GLN cc_start: 0.7929 (mt0) cc_final: 0.7629 (mt0) REVERT: I 47 LEU cc_start: 0.9028 (tp) cc_final: 0.8807 (tt) REVERT: I 54 ARG cc_start: 0.8607 (ttp-110) cc_final: 0.8313 (ttp-110) REVERT: I 101 GLN cc_start: 0.8588 (mm110) cc_final: 0.8343 (pm20) REVERT: I 109 ARG cc_start: 0.6232 (ptm160) cc_final: 0.4807 (pmt-80) outliers start: 29 outliers final: 21 residues processed: 196 average time/residue: 0.1811 time to fit residues: 49.8740 Evaluate side-chains 186 residues out of total 1939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 163 time to evaluate : 0.622 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 19 THR Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain F residue 48 ILE Chi-restraints excluded: chain F residue 74 THR Chi-restraints excluded: chain F residue 105 VAL Chi-restraints excluded: chain F residue 107 ILE Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 75 SER Chi-restraints excluded: chain A residue 77 THR Chi-restraints excluded: chain D residue 33 LEU Chi-restraints excluded: chain D residue 56 THR Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 123 LEU Chi-restraints excluded: chain G residue 230 CYS Chi-restraints excluded: chain H residue 140 LEU Chi-restraints excluded: chain H residue 230 CYS Chi-restraints excluded: chain B residue 157 THR Chi-restraints excluded: chain B residue 307 ILE Chi-restraints excluded: chain B residue 319 SER Chi-restraints excluded: chain J residue 230 CYS Chi-restraints excluded: chain J residue 245 ASN Chi-restraints excluded: chain J residue 376 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 162 optimal weight: 2.9990 chunk 170 optimal weight: 0.9980 chunk 88 optimal weight: 0.0980 chunk 63 optimal weight: 10.0000 chunk 125 optimal weight: 0.6980 chunk 100 optimal weight: 0.8980 chunk 209 optimal weight: 2.9990 chunk 34 optimal weight: 0.2980 chunk 182 optimal weight: 0.9980 chunk 160 optimal weight: 0.9980 chunk 39 optimal weight: 0.3980 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 120 GLN D 79 GLN G 468 HIS ** H 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 468 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.080538 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2963 r_free = 0.2963 target = 0.058667 restraints weight = 43377.511| |-----------------------------------------------------------------------------| r_work (start): 0.2931 rms_B_bonded: 2.74 r_work: 0.2816 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2689 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.2689 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8783 moved from start: 0.3294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 18993 Z= 0.123 Angle : 0.639 15.763 25929 Z= 0.317 Chirality : 0.045 0.242 3016 Planarity : 0.003 0.041 3198 Dihedral : 6.827 57.229 3998 Min Nonbonded Distance : 2.292 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.46 % Favored : 96.36 % Rotamer: Outliers : 1.08 % Allowed : 11.71 % Favored : 87.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.67 % Cis-general : 0.18 % 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: -0.41 (0.17), residues: 2252 helix: -1.07 (0.78), residues: 28 sheet: -0.21 (0.16), residues: 946 loop : -0.18 (0.17), residues: 1278 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E 63 TYR 0.016 0.001 TYR F 49 PHE 0.013 0.001 PHE J 410 TRP 0.020 0.001 TRP J 178 HIS 0.005 0.001 HIS J 468 Details of bonding type rmsd covalent geometry : bond 0.00262 (18875) covalent geometry : angle 0.61805 (25617) SS BOND : bond 0.00229 ( 42) SS BOND : angle 0.83123 ( 84) hydrogen bonds : bond 0.03800 ( 572) hydrogen bonds : angle 6.47030 ( 1518) link_ALPHA1-2 : bond 0.00546 ( 4) link_ALPHA1-2 : angle 2.51102 ( 12) link_ALPHA1-3 : bond 0.00997 ( 8) link_ALPHA1-3 : angle 1.62875 ( 24) link_ALPHA1-6 : bond 0.00675 ( 8) link_ALPHA1-6 : angle 1.37768 ( 24) link_BETA1-4 : bond 0.00449 ( 28) link_BETA1-4 : angle 1.45483 ( 84) link_BETA1-6 : bond 0.00289 ( 4) link_BETA1-6 : angle 1.38345 ( 12) link_NAG-ASN : bond 0.00202 ( 24) link_NAG-ASN : angle 2.22393 ( 72) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4504 Ramachandran restraints generated. 2252 Oldfield, 0 Emsley, 2252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4504 Ramachandran restraints generated. 2252 Oldfield, 0 Emsley, 2252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 180 time to evaluate : 0.603 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: E 10 GLU cc_start: 0.8911 (mm-30) cc_final: 0.8293 (mp0) REVERT: E 12 LYS cc_start: 0.8007 (mmtt) cc_final: 0.7481 (mmtt) REVERT: E 65 GLN cc_start: 0.8502 (tp-100) cc_final: 0.7941 (tm-30) REVERT: F 61 ARG cc_start: 0.7932 (ptm-80) cc_final: 0.5831 (ptm-80) REVERT: F 79 GLN cc_start: 0.7566 (mm-40) cc_final: 0.7156 (mp10) REVERT: F 104 LYS cc_start: 0.8286 (tppt) cc_final: 0.8015 (tppt) REVERT: A 12 LYS cc_start: 0.8329 (mmtt) cc_final: 0.7991 (mmmt) REVERT: A 46 GLU cc_start: 0.8856 (tp30) cc_final: 0.8378 (tm-30) REVERT: A 67 ARG cc_start: 0.8281 (mtp85) cc_final: 0.8033 (mtp85) REVERT: D 45 ARG cc_start: 0.8549 (ttm-80) cc_final: 0.8037 (ttp80) REVERT: C 12 LYS cc_start: 0.8614 (mmtm) cc_final: 0.8330 (mmtm) REVERT: C 23 LYS cc_start: 0.8883 (ttmt) cc_final: 0.8429 (tttp) REVERT: C 65 GLN cc_start: 0.8653 (tp40) cc_final: 0.7979 (tm-30) REVERT: C 94 TYR cc_start: 0.8072 (m-10) cc_final: 0.7750 (m-10) REVERT: C 102 ASP cc_start: 0.9280 (p0) cc_final: 0.8824 (p0) REVERT: I 4 MET cc_start: 0.8322 (mmm) cc_final: 0.7947 (mmm) REVERT: I 42 GLN cc_start: 0.7731 (mt0) cc_final: 0.7434 (mt0) REVERT: I 47 LEU cc_start: 0.9094 (tp) cc_final: 0.8505 (tt) REVERT: I 54 ARG cc_start: 0.8592 (ttp-110) cc_final: 0.8265 (ttp80) REVERT: I 101 GLN cc_start: 0.8586 (mm110) cc_final: 0.8383 (pm20) REVERT: I 104 LYS cc_start: 0.8718 (mtpp) cc_final: 0.8467 (mmtt) REVERT: I 109 ARG cc_start: 0.6364 (ptm160) cc_final: 0.5097 (pmt-80) outliers start: 21 outliers final: 15 residues processed: 196 average time/residue: 0.1981 time to fit residues: 54.3855 Evaluate side-chains 184 residues out of total 1939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 169 time to evaluate : 0.823 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 19 THR Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 75 SER Chi-restraints excluded: chain A residue 120 GLN Chi-restraints excluded: chain D residue 33 LEU Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 123 LEU Chi-restraints excluded: chain G residue 230 CYS Chi-restraints excluded: chain H residue 230 CYS Chi-restraints excluded: chain B residue 307 ILE Chi-restraints excluded: chain J residue 230 CYS Chi-restraints excluded: chain J residue 245 ASN Chi-restraints excluded: chain J residue 376 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 97 optimal weight: 0.5980 chunk 36 optimal weight: 9.9990 chunk 129 optimal weight: 0.9990 chunk 185 optimal weight: 3.9990 chunk 217 optimal weight: 4.9990 chunk 2 optimal weight: 8.9990 chunk 175 optimal weight: 2.9990 chunk 194 optimal weight: 2.9990 chunk 214 optimal weight: 1.9990 chunk 26 optimal weight: 5.9990 chunk 219 optimal weight: 1.9990 overall best weight: 1.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 6 GLN D 79 GLN G 468 HIS ** H 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 468 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.079713 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2940 r_free = 0.2940 target = 0.057808 restraints weight = 43767.106| |-----------------------------------------------------------------------------| r_work (start): 0.2912 rms_B_bonded: 2.72 r_work: 0.2798 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2672 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.2672 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8812 moved from start: 0.3351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 18993 Z= 0.202 Angle : 0.659 13.798 25929 Z= 0.325 Chirality : 0.046 0.248 3016 Planarity : 0.004 0.080 3198 Dihedral : 6.866 54.528 3998 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.00 % Favored : 95.83 % Rotamer: Outliers : 1.55 % Allowed : 11.50 % Favored : 86.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.67 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -0.39 (0.17), residues: 2252 helix: -0.81 (0.80), residues: 28 sheet: -0.18 (0.16), residues: 945 loop : -0.19 (0.17), residues: 1279 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG E 63 TYR 0.017 0.002 TYR F 49 PHE 0.015 0.002 PHE J 410 TRP 0.017 0.001 TRP J 178 HIS 0.004 0.001 HIS G 468 Details of bonding type rmsd covalent geometry : bond 0.00461 (18875) covalent geometry : angle 0.63652 (25617) SS BOND : bond 0.00311 ( 42) SS BOND : angle 0.90898 ( 84) hydrogen bonds : bond 0.04121 ( 572) hydrogen bonds : angle 6.45842 ( 1518) link_ALPHA1-2 : bond 0.00370 ( 4) link_ALPHA1-2 : angle 2.33528 ( 12) link_ALPHA1-3 : bond 0.00656 ( 8) link_ALPHA1-3 : angle 1.98963 ( 24) link_ALPHA1-6 : bond 0.00492 ( 8) link_ALPHA1-6 : angle 1.47294 ( 24) link_BETA1-4 : bond 0.00321 ( 28) link_BETA1-4 : angle 1.60585 ( 84) link_BETA1-6 : bond 0.00192 ( 4) link_BETA1-6 : angle 1.42574 ( 12) link_NAG-ASN : bond 0.00321 ( 24) link_NAG-ASN : angle 2.27117 ( 72) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4504 Ramachandran restraints generated. 2252 Oldfield, 0 Emsley, 2252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4504 Ramachandran restraints generated. 2252 Oldfield, 0 Emsley, 2252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 1939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 179 time to evaluate : 0.657 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: E 10 GLU cc_start: 0.8896 (mm-30) cc_final: 0.8335 (mp0) REVERT: E 12 LYS cc_start: 0.8039 (mmtt) cc_final: 0.7572 (mmtt) REVERT: E 29 PHE cc_start: 0.5823 (OUTLIER) cc_final: 0.5359 (m-80) REVERT: E 65 GLN cc_start: 0.8511 (tp-100) cc_final: 0.7908 (tm-30) REVERT: F 61 ARG cc_start: 0.8009 (ptm-80) cc_final: 0.5939 (ptm-80) REVERT: F 79 GLN cc_start: 0.7627 (mm-40) cc_final: 0.7225 (mp10) REVERT: F 104 LYS cc_start: 0.8308 (tppt) cc_final: 0.8047 (tppt) REVERT: A 12 LYS cc_start: 0.8301 (mmtt) cc_final: 0.8038 (mmmt) REVERT: A 46 GLU cc_start: 0.8880 (tp30) cc_final: 0.8366 (tm-30) REVERT: A 67 ARG cc_start: 0.8361 (mtp85) cc_final: 0.8138 (mtp85) REVERT: A 111 GLU cc_start: 0.8336 (tt0) cc_final: 0.8088 (pm20) REVERT: D 45 ARG cc_start: 0.8527 (ttm-80) cc_final: 0.8017 (ttp80) REVERT: C 12 LYS cc_start: 0.8615 (mmtm) cc_final: 0.8343 (mmtm) REVERT: C 23 LYS cc_start: 0.8911 (ttmt) cc_final: 0.8465 (tttp) REVERT: C 65 GLN cc_start: 0.8695 (tp40) cc_final: 0.7998 (tm-30) REVERT: C 94 TYR cc_start: 0.8116 (m-10) cc_final: 0.7755 (m-10) REVERT: C 102 ASP cc_start: 0.9256 (p0) cc_final: 0.8849 (p0) REVERT: I 4 MET cc_start: 0.8367 (mmm) cc_final: 0.7945 (mmm) REVERT: I 42 GLN cc_start: 0.7775 (mt0) cc_final: 0.7485 (mt0) REVERT: I 47 LEU cc_start: 0.9059 (tp) cc_final: 0.8850 (tt) REVERT: I 54 ARG cc_start: 0.8599 (ttp-110) cc_final: 0.8322 (ttp80) REVERT: I 101 GLN cc_start: 0.8558 (mm110) cc_final: 0.8335 (pm20) REVERT: I 104 LYS cc_start: 0.8718 (mtpp) cc_final: 0.8442 (mmtt) REVERT: I 109 ARG cc_start: 0.6268 (ptm160) cc_final: 0.4940 (pmt-80) outliers start: 30 outliers final: 22 residues processed: 202 average time/residue: 0.1961 time to fit residues: 55.5474 Evaluate side-chains 201 residues out of total 1939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 178 time to evaluate : 0.700 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 19 THR Chi-restraints excluded: chain E residue 29 PHE Chi-restraints excluded: chain E residue 38 ARG Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain F residue 13 LEU Chi-restraints excluded: chain F residue 24 ARG Chi-restraints excluded: chain F residue 107 ILE Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 75 SER Chi-restraints excluded: chain D residue 33 LEU Chi-restraints excluded: chain D residue 56 THR Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 123 LEU Chi-restraints excluded: chain I residue 21 LEU Chi-restraints excluded: chain G residue 230 CYS Chi-restraints excluded: chain H residue 140 LEU Chi-restraints excluded: chain H residue 230 CYS Chi-restraints excluded: chain B residue 307 ILE Chi-restraints excluded: chain B residue 319 SER Chi-restraints excluded: chain B residue 328 LYS Chi-restraints excluded: chain J residue 230 CYS Chi-restraints excluded: chain J residue 376 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 1 optimal weight: 30.0000 chunk 75 optimal weight: 4.9990 chunk 163 optimal weight: 0.8980 chunk 156 optimal weight: 3.9990 chunk 37 optimal weight: 8.9990 chunk 60 optimal weight: 9.9990 chunk 44 optimal weight: 9.9990 chunk 208 optimal weight: 5.9990 chunk 96 optimal weight: 1.9990 chunk 47 optimal weight: 9.9990 chunk 127 optimal weight: 2.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 79 GLN I 37 GLN G 468 HIS ** H 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 468 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.078406 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2902 r_free = 0.2902 target = 0.056367 restraints weight = 44057.926| |-----------------------------------------------------------------------------| r_work (start): 0.2867 rms_B_bonded: 2.78 r_work: 0.2749 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2622 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.2622 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8854 moved from start: 0.3427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.064 18993 Z= 0.319 Angle : 0.737 12.222 25929 Z= 0.364 Chirality : 0.049 0.267 3016 Planarity : 0.004 0.060 3198 Dihedral : 7.353 53.116 3998 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.26 % Favored : 95.56 % Rotamer: Outliers : 1.50 % Allowed : 11.96 % Favored : 86.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.67 % Cis-general : 0.18 % 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: -0.52 (0.17), residues: 2252 helix: 0.23 (0.86), residues: 24 sheet: -0.31 (0.16), residues: 949 loop : -0.28 (0.17), residues: 1279 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG E 63 TYR 0.020 0.002 TYR I 87 PHE 0.018 0.002 PHE C 29 TRP 0.015 0.002 TRP J 178 HIS 0.004 0.001 HIS G 336 Details of bonding type rmsd covalent geometry : bond 0.00734 (18875) covalent geometry : angle 0.70802 (25617) SS BOND : bond 0.00438 ( 42) SS BOND : angle 1.11972 ( 84) hydrogen bonds : bond 0.04725 ( 572) hydrogen bonds : angle 6.62473 ( 1518) link_ALPHA1-2 : bond 0.00167 ( 4) link_ALPHA1-2 : angle 2.45628 ( 12) link_ALPHA1-3 : bond 0.00320 ( 8) link_ALPHA1-3 : angle 2.47037 ( 24) link_ALPHA1-6 : bond 0.00369 ( 8) link_ALPHA1-6 : angle 1.62151 ( 24) link_BETA1-4 : bond 0.00375 ( 28) link_BETA1-4 : angle 1.80565 ( 84) link_BETA1-6 : bond 0.00226 ( 4) link_BETA1-6 : angle 1.69043 ( 12) link_NAG-ASN : bond 0.00560 ( 24) link_NAG-ASN : angle 2.78094 ( 72) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4504 Ramachandran restraints generated. 2252 Oldfield, 0 Emsley, 2252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4504 Ramachandran restraints generated. 2252 Oldfield, 0 Emsley, 2252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 177 time to evaluate : 0.735 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 10 GLU cc_start: 0.8924 (mm-30) cc_final: 0.8390 (mp0) REVERT: E 12 LYS cc_start: 0.8102 (mmtt) cc_final: 0.7651 (mmtt) REVERT: E 29 PHE cc_start: 0.5914 (OUTLIER) cc_final: 0.5441 (m-80) REVERT: E 63 ARG cc_start: 0.8188 (mtm110) cc_final: 0.7929 (mtm110) REVERT: E 65 GLN cc_start: 0.8565 (tp-100) cc_final: 0.7847 (tm-30) REVERT: F 61 ARG cc_start: 0.8051 (ptm-80) cc_final: 0.6038 (ptm160) REVERT: F 79 GLN cc_start: 0.7597 (mm-40) cc_final: 0.7213 (mp10) REVERT: F 104 LYS cc_start: 0.8325 (tppt) cc_final: 0.8061 (tppt) REVERT: A 12 LYS cc_start: 0.8398 (mmtt) cc_final: 0.8138 (mmmt) REVERT: A 46 GLU cc_start: 0.8913 (tp30) cc_final: 0.8587 (tm-30) REVERT: A 111 GLU cc_start: 0.8386 (tt0) cc_final: 0.8113 (pm20) REVERT: D 45 ARG cc_start: 0.8560 (ttm-80) cc_final: 0.8008 (ttp80) REVERT: C 12 LYS cc_start: 0.8634 (mmtm) cc_final: 0.8362 (mmtm) REVERT: C 23 LYS cc_start: 0.8866 (ttmt) cc_final: 0.8397 (tttp) REVERT: C 65 GLN cc_start: 0.8795 (tp40) cc_final: 0.8006 (tm-30) REVERT: C 102 ASP cc_start: 0.9325 (p0) cc_final: 0.8925 (p0) REVERT: I 4 MET cc_start: 0.8385 (mmm) cc_final: 0.7981 (mmm) REVERT: I 42 GLN cc_start: 0.7923 (mt0) cc_final: 0.7625 (mt0) REVERT: I 47 LEU cc_start: 0.9093 (tp) cc_final: 0.8890 (tt) REVERT: I 54 ARG cc_start: 0.8627 (ttp-110) cc_final: 0.8311 (ttp-110) REVERT: I 101 GLN cc_start: 0.8570 (mm110) cc_final: 0.8342 (pm20) REVERT: I 109 ARG cc_start: 0.6279 (ptm160) cc_final: 0.4869 (pmt-80) outliers start: 29 outliers final: 24 residues processed: 200 average time/residue: 0.2078 time to fit residues: 57.8329 Evaluate side-chains 197 residues out of total 1939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 172 time to evaluate : 0.693 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 19 THR Chi-restraints excluded: chain E residue 29 PHE Chi-restraints excluded: chain E residue 38 ARG Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain F residue 13 LEU Chi-restraints excluded: chain F residue 24 ARG Chi-restraints excluded: chain F residue 107 ILE Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 75 SER Chi-restraints excluded: chain D residue 33 LEU Chi-restraints excluded: chain D residue 56 THR Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 123 LEU Chi-restraints excluded: chain I residue 21 LEU Chi-restraints excluded: chain I residue 37 GLN Chi-restraints excluded: chain G residue 148 THR Chi-restraints excluded: chain G residue 230 CYS Chi-restraints excluded: chain H residue 140 LEU Chi-restraints excluded: chain H residue 230 CYS Chi-restraints excluded: chain B residue 157 THR Chi-restraints excluded: chain B residue 307 ILE Chi-restraints excluded: chain B residue 319 SER Chi-restraints excluded: chain J residue 230 CYS Chi-restraints excluded: chain J residue 376 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 126 optimal weight: 0.9990 chunk 2 optimal weight: 0.7980 chunk 117 optimal weight: 0.9990 chunk 185 optimal weight: 0.9980 chunk 168 optimal weight: 0.7980 chunk 43 optimal weight: 0.0980 chunk 143 optimal weight: 0.7980 chunk 125 optimal weight: 0.7980 chunk 83 optimal weight: 1.9990 chunk 127 optimal weight: 0.8980 chunk 140 optimal weight: 0.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 43 GLN A 65 GLN A 120 GLN G 468 HIS ** H 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 468 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.081491 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2958 r_free = 0.2958 target = 0.058787 restraints weight = 43625.161| |-----------------------------------------------------------------------------| r_work (start): 0.2930 rms_B_bonded: 2.82 r_work: 0.2816 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2689 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.2689 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8782 moved from start: 0.3537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 18993 Z= 0.124 Angle : 0.659 13.437 25929 Z= 0.323 Chirality : 0.045 0.246 3016 Planarity : 0.003 0.047 3198 Dihedral : 6.637 43.520 3998 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.73 % Favored : 96.09 % Rotamer: Outliers : 1.19 % Allowed : 12.48 % Favored : 86.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.67 % Cis-general : 0.18 % 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: -0.34 (0.17), residues: 2252 helix: -0.93 (0.77), residues: 28 sheet: -0.19 (0.16), residues: 933 loop : -0.12 (0.18), residues: 1291 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG E 63 TYR 0.024 0.001 TYR I 87 PHE 0.012 0.001 PHE H 410 TRP 0.021 0.001 TRP J 178 HIS 0.003 0.001 HIS J 468 Details of bonding type rmsd covalent geometry : bond 0.00268 (18875) covalent geometry : angle 0.63200 (25617) SS BOND : bond 0.00200 ( 42) SS BOND : angle 0.70049 ( 84) hydrogen bonds : bond 0.03736 ( 572) hydrogen bonds : angle 6.36514 ( 1518) link_ALPHA1-2 : bond 0.00515 ( 4) link_ALPHA1-2 : angle 2.50456 ( 12) link_ALPHA1-3 : bond 0.00993 ( 8) link_ALPHA1-3 : angle 1.59868 ( 24) link_ALPHA1-6 : bond 0.00622 ( 8) link_ALPHA1-6 : angle 1.39017 ( 24) link_BETA1-4 : bond 0.00497 ( 28) link_BETA1-4 : angle 1.40369 ( 84) link_BETA1-6 : bond 0.00332 ( 4) link_BETA1-6 : angle 1.41813 ( 12) link_NAG-ASN : bond 0.00211 ( 24) link_NAG-ASN : angle 2.88711 ( 72) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4504 Ramachandran restraints generated. 2252 Oldfield, 0 Emsley, 2252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4504 Ramachandran restraints generated. 2252 Oldfield, 0 Emsley, 2252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 1939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 185 time to evaluate : 0.765 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: E 10 GLU cc_start: 0.8890 (mm-30) cc_final: 0.8483 (mp0) REVERT: E 12 LYS cc_start: 0.8166 (mmtt) cc_final: 0.7581 (mmtt) REVERT: E 29 PHE cc_start: 0.5887 (OUTLIER) cc_final: 0.5461 (m-80) REVERT: E 65 GLN cc_start: 0.8491 (tp-100) cc_final: 0.7830 (tm-30) REVERT: F 61 ARG cc_start: 0.8007 (ptm-80) cc_final: 0.6008 (ptm-80) REVERT: F 79 GLN cc_start: 0.7516 (mm-40) cc_final: 0.7251 (mp10) REVERT: A 46 GLU cc_start: 0.8894 (tp30) cc_final: 0.8357 (tm-30) REVERT: D 18 ARG cc_start: 0.8341 (ttp80) cc_final: 0.8070 (ttp80) REVERT: D 45 ARG cc_start: 0.8509 (ttm-80) cc_final: 0.8009 (ttp80) REVERT: C 12 LYS cc_start: 0.8634 (mmtm) cc_final: 0.8361 (mmtm) REVERT: C 23 LYS cc_start: 0.8867 (ttmt) cc_final: 0.8410 (tttp) REVERT: C 46 GLU cc_start: 0.8726 (tp30) cc_final: 0.8276 (tt0) REVERT: C 65 GLN cc_start: 0.8649 (tp40) cc_final: 0.8009 (tm-30) REVERT: C 93 VAL cc_start: 0.8969 (t) cc_final: 0.8678 (p) REVERT: C 94 TYR cc_start: 0.8052 (m-10) cc_final: 0.7720 (m-10) REVERT: C 102 ASP cc_start: 0.9278 (p0) cc_final: 0.8845 (p0) REVERT: I 4 MET cc_start: 0.8312 (mmm) cc_final: 0.7948 (mmm) REVERT: I 42 GLN cc_start: 0.7783 (mt0) cc_final: 0.7514 (mt0) REVERT: I 54 ARG cc_start: 0.8642 (ttp-110) cc_final: 0.8362 (ttp-110) REVERT: I 87 TYR cc_start: 0.8963 (m-80) cc_final: 0.8543 (m-80) REVERT: I 109 ARG cc_start: 0.6352 (ptm160) cc_final: 0.5022 (pmt-80) outliers start: 23 outliers final: 16 residues processed: 202 average time/residue: 0.1954 time to fit residues: 55.4739 Evaluate side-chains 194 residues out of total 1939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 177 time to evaluate : 0.627 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 29 PHE Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain F residue 13 LEU Chi-restraints excluded: chain F residue 24 ARG Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 75 SER Chi-restraints excluded: chain D residue 33 LEU Chi-restraints excluded: chain D residue 56 THR Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 123 LEU Chi-restraints excluded: chain G residue 230 CYS Chi-restraints excluded: chain H residue 140 LEU Chi-restraints excluded: chain H residue 230 CYS Chi-restraints excluded: chain J residue 140 LEU Chi-restraints excluded: chain J residue 230 CYS Chi-restraints excluded: chain J residue 376 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 24 optimal weight: 6.9990 chunk 14 optimal weight: 20.0000 chunk 127 optimal weight: 3.9990 chunk 99 optimal weight: 1.9990 chunk 149 optimal weight: 4.9990 chunk 42 optimal weight: 7.9990 chunk 108 optimal weight: 0.9990 chunk 221 optimal weight: 3.9990 chunk 139 optimal weight: 3.9990 chunk 59 optimal weight: 5.9990 chunk 175 optimal weight: 0.6980 overall best weight: 2.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 37 GLN G 468 HIS ** H 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 468 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.078414 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2921 r_free = 0.2921 target = 0.056933 restraints weight = 43970.511| |-----------------------------------------------------------------------------| r_work (start): 0.2892 rms_B_bonded: 2.73 r_work: 0.2766 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2635 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.2635 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8839 moved from start: 0.3555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 18993 Z= 0.258 Angle : 0.708 11.474 25929 Z= 0.349 Chirality : 0.047 0.252 3016 Planarity : 0.004 0.077 3198 Dihedral : 6.930 47.604 3998 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.53 % Favored : 95.29 % Rotamer: Outliers : 1.34 % Allowed : 12.17 % Favored : 86.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.67 % Cis-general : 0.18 % 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: -0.42 (0.17), residues: 2252 helix: -0.53 (0.85), residues: 28 sheet: -0.23 (0.16), residues: 933 loop : -0.20 (0.18), residues: 1291 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG E 63 TYR 0.018 0.002 TYR F 49 PHE 0.017 0.002 PHE J 410 TRP 0.016 0.001 TRP J 178 HIS 0.004 0.001 HIS G 468 Details of bonding type rmsd covalent geometry : bond 0.00592 (18875) covalent geometry : angle 0.67948 (25617) SS BOND : bond 0.00379 ( 42) SS BOND : angle 0.98735 ( 84) hydrogen bonds : bond 0.04388 ( 572) hydrogen bonds : angle 6.48188 ( 1518) link_ALPHA1-2 : bond 0.00241 ( 4) link_ALPHA1-2 : angle 2.32890 ( 12) link_ALPHA1-3 : bond 0.00459 ( 8) link_ALPHA1-3 : angle 2.26433 ( 24) link_ALPHA1-6 : bond 0.00421 ( 8) link_ALPHA1-6 : angle 1.55675 ( 24) link_BETA1-4 : bond 0.00339 ( 28) link_BETA1-4 : angle 1.67401 ( 84) link_BETA1-6 : bond 0.00091 ( 4) link_BETA1-6 : angle 1.59072 ( 12) link_NAG-ASN : bond 0.00464 ( 24) link_NAG-ASN : angle 2.86450 ( 72) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4731.17 seconds wall clock time: 82 minutes 12.16 seconds (4932.16 seconds total)