Starting phenix.real_space_refine on Tue Apr 29 16:22:24 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9b4l_44184/04_2025/9b4l_44184.cif Found real_map, /net/cci-nas-00/data/ceres_data/9b4l_44184/04_2025/9b4l_44184.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/9b4l_44184/04_2025/9b4l_44184.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9b4l_44184/04_2025/9b4l_44184.map" model { file = "/net/cci-nas-00/data/ceres_data/9b4l_44184/04_2025/9b4l_44184.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9b4l_44184/04_2025/9b4l_44184.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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= 1.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 12 5.16 5 C 5520 2.51 5 N 1524 2.21 5 O 1596 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/chem_data/mon_lib" Total number of atoms: 8652 Number of models: 1 Model: "" Number of chains: 42 Chain: "A" Number of atoms: 587 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 587 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 3, 'TRANS': 73} Chain: "B" Number of atoms: 587 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 587 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 3, 'TRANS': 73} Chain: "C" Number of atoms: 587 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 587 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 3, 'TRANS': 73} Chain: "D" Number of atoms: 587 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 587 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 3, 'TRANS': 73} Chain: "E" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 62 Classifications: {'peptide': 7} Modifications used: {'COO': 1, 'DIL_chir_02_both': 2, 'DTH_chir_02_both': 1, 'PEPT-D': 7} Link IDs: {'TRANS': 6} Chain: "F" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 62 Classifications: {'peptide': 7} Modifications used: {'COO': 1, 'DIL_chir_02_both': 2, 'DTH_chir_02_both': 1, 'PEPT-D': 7} Link IDs: {'TRANS': 6} Chain: "G" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 62 Classifications: {'peptide': 7} Modifications used: {'COO': 1, 'DIL_chir_02_both': 2, 'DTH_chir_02_both': 1, 'PEPT-D': 7} Link IDs: {'TRANS': 6} Chain: "H" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 62 Classifications: {'peptide': 7} Modifications used: {'COO': 1, 'DIL_chir_02_both': 2, 'DTH_chir_02_both': 1, 'PEPT-D': 7} Link IDs: {'TRANS': 6} Chain: "I" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 62 Classifications: {'peptide': 7} Modifications used: {'COO': 1, 'DIL_chir_02_both': 2, 'DTH_chir_02_both': 1, 'PEPT-D': 7} Link IDs: {'TRANS': 6} Chain: "J" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 62 Classifications: {'peptide': 7} Modifications used: {'COO': 1, 'DIL_chir_02_both': 2, 'DTH_chir_02_both': 1, 'PEPT-D': 7} Link IDs: {'TRANS': 6} Chain: "K" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 62 Classifications: {'peptide': 7} Modifications used: {'COO': 1, 'DIL_chir_02_both': 2, 'DTH_chir_02_both': 1, 'PEPT-D': 7} Link IDs: {'TRANS': 6} Chain: "L" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 62 Classifications: {'peptide': 7} Modifications used: {'COO': 1, 'DIL_chir_02_both': 2, 'DTH_chir_02_both': 1, 'PEPT-D': 7} Link IDs: {'TRANS': 6} Chain: "M" Number of atoms: 587 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 587 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 3, 'TRANS': 73} Chain: "N" Number of atoms: 587 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 587 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 3, 'TRANS': 73} Chain: "O" Number of atoms: 587 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 587 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 3, 'TRANS': 73} Chain: "P" Number of atoms: 587 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 587 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 3, 'TRANS': 73} Chain: "Q" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 62 Classifications: {'peptide': 7} Modifications used: {'COO': 1, 'DIL_chir_02_both': 2, 'DTH_chir_02_both': 1, 'PEPT-D': 7} Link IDs: {'TRANS': 6} Chain: "R" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 62 Classifications: {'peptide': 7} Modifications used: {'COO': 1, 'DIL_chir_02_both': 2, 'DTH_chir_02_both': 1, 'PEPT-D': 7} Link IDs: {'TRANS': 6} Chain: "S" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 62 Classifications: {'peptide': 7} Modifications used: {'COO': 1, 'DIL_chir_02_both': 2, 'DTH_chir_02_both': 1, 'PEPT-D': 7} Link IDs: {'TRANS': 6} Chain: "T" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 62 Classifications: {'peptide': 7} Modifications used: {'COO': 1, 'DIL_chir_02_both': 2, 'DTH_chir_02_both': 1, 'PEPT-D': 7} Link IDs: {'TRANS': 6} Chain: "U" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 62 Classifications: {'peptide': 7} Modifications used: {'COO': 1, 'DIL_chir_02_both': 2, 'DTH_chir_02_both': 1, 'PEPT-D': 7} Link IDs: {'TRANS': 6} Chain: "V" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 62 Classifications: {'peptide': 7} Modifications used: {'COO': 1, 'DIL_chir_02_both': 2, 'DTH_chir_02_both': 1, 'PEPT-D': 7} Link IDs: {'TRANS': 6} Chain: "W" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 62 Classifications: {'peptide': 7} Modifications used: {'COO': 1, 'DIL_chir_02_both': 2, 'DTH_chir_02_both': 1, 'PEPT-D': 7} Link IDs: {'TRANS': 6} Chain: "X" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 62 Classifications: {'peptide': 7} Modifications used: {'COO': 1, 'DIL_chir_02_both': 2, 'DTH_chir_02_both': 1, 'PEPT-D': 7} Link IDs: {'TRANS': 6} Chain: "Y" Number of atoms: 587 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 587 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 3, 'TRANS': 73} Chain: "Z" Number of atoms: 587 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 587 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 3, 'TRANS': 73} Chain: "0" Number of atoms: 587 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 587 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 3, 'TRANS': 73} Chain: "1" Number of atoms: 587 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 587 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 3, 'TRANS': 73} Chain: "2" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 62 Classifications: {'peptide': 7} Modifications used: {'COO': 1, 'DIL_chir_02_both': 2, 'DTH_chir_02_both': 1, 'PEPT-D': 7} Link IDs: {'TRANS': 6} Chain: "3" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 62 Classifications: {'peptide': 7} Modifications used: {'COO': 1, 'DIL_chir_02_both': 2, 'DTH_chir_02_both': 1, 'PEPT-D': 7} Link IDs: {'TRANS': 6} Chain: "4" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 62 Classifications: {'peptide': 7} Modifications used: {'COO': 1, 'DIL_chir_02_both': 2, 'DTH_chir_02_both': 1, 'PEPT-D': 7} Link IDs: {'TRANS': 6} Chain: "5" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 62 Classifications: {'peptide': 7} Modifications used: {'COO': 1, 'DIL_chir_02_both': 2, 'DTH_chir_02_both': 1, 'PEPT-D': 7} Link IDs: {'TRANS': 6} Chain: "6" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 62 Classifications: {'peptide': 7} Modifications used: {'COO': 1, 'DIL_chir_02_both': 2, 'DTH_chir_02_both': 1, 'PEPT-D': 7} Link IDs: {'TRANS': 6} Chain: "7" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 62 Classifications: {'peptide': 7} Modifications used: {'COO': 1, 'DIL_chir_02_both': 2, 'DTH_chir_02_both': 1, 'PEPT-D': 7} Link IDs: {'TRANS': 6} Chain: "8" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 62 Classifications: {'peptide': 7} Modifications used: {'COO': 1, 'DIL_chir_02_both': 2, 'DTH_chir_02_both': 1, 'PEPT-D': 7} Link IDs: {'TRANS': 6} Chain: "9" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 62 Classifications: {'peptide': 7} Modifications used: {'COO': 1, 'DIL_chir_02_both': 2, 'DTH_chir_02_both': 1, 'PEPT-D': 7} Link IDs: {'TRANS': 6} Chain: "A" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 20 Unusual residues: {'EDT': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 20 Unusual residues: {'EDT': 1} Classifications: {'undetermined': 1} Chain: "M" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 20 Unusual residues: {'EDT': 1} Classifications: {'undetermined': 1} Chain: "O" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 20 Unusual residues: {'EDT': 1} Classifications: {'undetermined': 1} Chain: "0" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 20 Unusual residues: {'EDT': 1} Classifications: {'undetermined': 1} Chain: "3" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 20 Unusual residues: {'EDT': 1} Classifications: {'undetermined': 1} Time building chain proxies: 8.30, per 1000 atoms: 0.96 Number of scatterers: 8652 At special positions: 0 Unit cell: (167.32, 109.04, 52.64, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 12 16.00 O 1596 8.00 N 1524 7.00 C 5520 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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=6, symmetry=0 Number of additional bonds: simple=6, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.47 Conformation dependent library (CDL) restraints added in 918.0 milliseconds 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Skipped Input residue name is d-peptide pdb=" CB DTH E 1 " pdb=" CB DLE E 2 " pdb=" CB DLY E 3 " pdb=" CB DIL E 4 " pdb=" CB DVA E 5 " pdb=" CB DTR E 6 " pdb=" CB DIL E 7 " pdb=" CB DTH F 1 " pdb=" CB DLE F 2 " pdb=" CB DLY F 3 " pdb=" CB DIL F 4 " pdb=" CB DVA F 5 " pdb=" CB DTR F 6 " pdb=" CB DIL F 7 " pdb=" CB DTH G 1 " pdb=" CB DLE G 2 " pdb=" CB DLY G 3 " pdb=" CB DIL G 4 " pdb=" CB DVA G 5 " pdb=" CB DTR G 6 " pdb=" CB DIL G 7 " pdb=" CB DTH H 1 " pdb=" CB DLE H 2 " pdb=" CB DLY H 3 " pdb=" CB DIL H 4 " pdb=" CB DVA H 5 " pdb=" CB DTR H 6 " pdb=" CB DIL H 7 " pdb=" CB DTH I 1 " pdb=" CB DLE I 2 " pdb=" CB DLY I 3 " pdb=" CB DIL I 4 " pdb=" CB DVA I 5 " pdb=" CB DTR I 6 " pdb=" CB DIL I 7 " pdb=" CB DTH J 1 " pdb=" CB DLE J 2 " pdb=" CB DLY J 3 " pdb=" CB DIL J 4 " pdb=" CB DVA J 5 " pdb=" CB DTR J 6 " pdb=" CB DIL J 7 " pdb=" CB DTH K 1 " pdb=" CB DLE K 2 " pdb=" CB DLY K 3 " pdb=" CB DIL K 4 " pdb=" CB DVA K 5 " pdb=" CB DTR K 6 " pdb=" CB DIL K 7 " pdb=" CB DTH L 1 " pdb=" CB DLE L 2 " pdb=" CB DLY L 3 " pdb=" CB DIL L 4 " pdb=" CB DVA L 5 " pdb=" CB DTR L 6 " pdb=" CB DIL L 7 " pdb=" CB DTH Q 1 " pdb=" CB DLE Q 2 " pdb=" CB DLY Q 3 " pdb=" CB DIL Q 4 " pdb=" CB DVA Q 5 " pdb=" CB DTR Q 6 " pdb=" CB DIL Q 7 " pdb=" CB DTH R 1 " pdb=" CB DLE R 2 " pdb=" CB DLY R 3 " pdb=" CB DIL R 4 " pdb=" CB DVA R 5 " pdb=" CB DTR R 6 " pdb=" CB DIL R 7 " pdb=" CB DTH S 1 " pdb=" CB DLE S 2 " pdb=" CB DLY S 3 " pdb=" CB DIL S 4 " pdb=" CB DVA S 5 " pdb=" CB DTR S 6 " pdb=" CB DIL S 7 " pdb=" CB DTH T 1 " pdb=" CB DLE T 2 " pdb=" CB DLY T 3 " pdb=" CB DIL T 4 " pdb=" CB DVA T 5 " pdb=" CB DTR T 6 " pdb=" CB DIL T 7 " pdb=" CB DTH U 1 " pdb=" CB DLE U 2 " pdb=" CB DLY U 3 " pdb=" CB DIL U 4 " pdb=" CB DVA U 5 " pdb=" CB DTR U 6 " pdb=" CB DIL U 7 " pdb=" CB DTH V 1 " pdb=" CB DLE V 2 " pdb=" CB DLY V 3 " pdb=" CB DIL V 4 " pdb=" CB DVA V 5 " pdb=" CB DTR V 6 " pdb=" CB DIL V 7 " pdb=" CB DTH W 1 " pdb=" CB DLE W 2 " pdb=" CB DLY W 3 " pdb=" CB DIL W 4 " pdb=" CB DVA W 5 " pdb=" CB DTR W 6 " pdb=" CB DIL W 7 " pdb=" CB DTH X 1 " pdb=" CB DLE X 2 " pdb=" CB DLY X 3 " pdb=" CB DIL X 4 " pdb=" CB DVA X 5 " pdb=" CB DTR X 6 " pdb=" CB DIL X 7 " pdb=" CB DTH 2 1 " pdb=" CB DLE 2 2 " pdb=" CB DLY 2 3 " pdb=" CB DIL 2 4 " pdb=" CB DVA 2 5 " pdb=" CB DTR 2 6 " pdb=" CB DIL 2 7 " pdb=" CB DTH 3 1 " pdb=" CB DLE 3 2 " pdb=" CB DLY 3 3 " pdb=" CB DIL 3 4 " pdb=" CB DVA 3 5 " pdb=" CB DTR 3 6 " pdb=" CB DIL 3 7 " pdb=" CB DTH 4 1 " pdb=" CB DLE 4 2 " pdb=" CB DLY 4 3 " pdb=" CB DIL 4 4 " pdb=" CB DVA 4 5 " pdb=" CB DTR 4 6 " pdb=" CB DIL 4 7 " pdb=" CB DTH 5 1 " pdb=" CB DLE 5 2 " pdb=" CB DLY 5 3 " pdb=" CB DIL 5 4 " pdb=" CB DVA 5 5 " pdb=" CB DTR 5 6 " pdb=" CB DIL 5 7 " pdb=" CB DTH 6 1 " pdb=" CB DLE 6 2 " pdb=" CB DLY 6 3 " pdb=" CB DIL 6 4 " pdb=" CB DVA 6 5 " pdb=" CB DTR 6 6 " pdb=" CB DIL 6 7 " pdb=" CB DTH 7 1 " pdb=" CB DLE 7 2 " pdb=" CB DLY 7 3 " pdb=" CB DIL 7 4 " pdb=" CB DVA 7 5 " pdb=" CB DTR 7 6 " pdb=" CB DIL 7 7 " pdb=" CB DTH 8 1 " pdb=" CB DLE 8 2 " pdb=" CB DLY 8 3 " pdb=" CB DIL 8 4 " pdb=" CB DVA 8 5 " pdb=" CB DTR 8 6 " pdb=" CB DIL 8 7 " pdb=" CB DTH 9 1 " pdb=" CB DLE 9 2 " pdb=" CB DLY 9 3 " pdb=" CB DIL 9 4 " pdb=" CB DVA 9 5 " pdb=" CB DTR 9 6 " pdb=" CB DIL 9 7 " Number of C-beta restraints generated: 1608 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 22 sheets defined 0.0% alpha, 57.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.63 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'N' and resid 306 through 310 removed outlier: 6.527A pdb=" N GLN A 307 " --> pdb=" O ILE Z 308 " (cutoff:3.500A) removed outlier: 7.824A pdb=" N TYR Z 310 " --> pdb=" O GLN A 307 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N VAL A 309 " --> pdb=" O TYR Z 310 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'N' and resid 313 through 314 removed outlier: 6.760A pdb=" N VAL A 313 " --> pdb=" O ASP Z 314 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'N' and resid 317 through 318 removed outlier: 6.343A pdb=" N LYS A 317 " --> pdb=" O VAL Z 318 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'N' and resid 321 through 330 removed outlier: 6.996A pdb=" N CYS N 322 " --> pdb=" O LYS M 321 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N GLY M 323 " --> pdb=" O CYS N 322 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N ILE N 328 " --> pdb=" O ASN M 327 " (cutoff:3.500A) removed outlier: 6.994A pdb=" N HIS M 329 " --> pdb=" O ILE N 328 " (cutoff:3.500A) removed outlier: 7.007A pdb=" N HIS N 330 " --> pdb=" O HIS M 329 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N CYS M 322 " --> pdb=" O LYS B 321 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N GLY B 323 " --> pdb=" O CYS M 322 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N ILE M 328 " --> pdb=" O ASN B 327 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N HIS B 329 " --> pdb=" O ILE M 328 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N HIS M 330 " --> pdb=" O HIS B 329 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N CYS B 322 " --> pdb=" O LYS A 321 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N GLY A 323 " --> pdb=" O CYS B 322 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N ILE B 328 " --> pdb=" O ASN A 327 " (cutoff:3.500A) removed outlier: 6.994A pdb=" N HIS A 329 " --> pdb=" O ILE B 328 " (cutoff:3.500A) removed outlier: 7.007A pdb=" N HIS B 330 " --> pdb=" O HIS A 329 " (cutoff:3.500A) removed outlier: 5.961A pdb=" N CYS A 322 " --> pdb=" O GLY Z 323 " (cutoff:3.500A) removed outlier: 7.499A pdb=" N LEU Z 325 " --> pdb=" O CYS A 322 " (cutoff:3.500A) removed outlier: 5.958A pdb=" N SER A 324 " --> pdb=" O LEU Z 325 " (cutoff:3.500A) removed outlier: 7.705A pdb=" N ASN Z 327 " --> pdb=" O SER A 324 " (cutoff:3.500A) removed outlier: 8.937A pdb=" N GLY A 326 " --> pdb=" O ASN Z 327 " (cutoff:3.500A) removed outlier: 8.428A pdb=" N HIS Z 329 " --> pdb=" O GLY A 326 " (cutoff:3.500A) removed outlier: 9.258A pdb=" N ILE A 328 " --> pdb=" O HIS Z 329 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N CYS Z 322 " --> pdb=" O LYS Y 321 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N GLY Y 323 " --> pdb=" O CYS Z 322 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N ILE Z 328 " --> pdb=" O ASN Y 327 " (cutoff:3.500A) removed outlier: 6.994A pdb=" N HIS Y 329 " --> pdb=" O ILE Z 328 " (cutoff:3.500A) removed outlier: 7.007A pdb=" N HIS Z 330 " --> pdb=" O HIS Y 329 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'N' and resid 336 through 340 removed outlier: 6.359A pdb=" N VAL B 337 " --> pdb=" O GLU M 338 " (cutoff:3.500A) removed outlier: 8.051A pdb=" N LYS M 340 " --> pdb=" O VAL B 337 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N VAL B 339 " --> pdb=" O LYS M 340 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'N' and resid 343 through 346 removed outlier: 6.536A pdb=" N LYS A 343 " --> pdb=" O LEU Z 344 " (cutoff:3.500A) removed outlier: 7.839A pdb=" N PHE Z 346 " --> pdb=" O LYS A 343 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N ASP A 345 " --> pdb=" O PHE Z 346 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'N' and resid 354 through 356 removed outlier: 8.309A pdb=" N ILE M 354 " --> pdb=" O GLY N 355 " (cutoff:3.500A) removed outlier: 8.329A pdb=" N ILE B 354 " --> pdb=" O GLY M 355 " (cutoff:3.500A) removed outlier: 8.309A pdb=" N ILE A 354 " --> pdb=" O GLY B 355 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N SER Z 356 " --> pdb=" O GLY A 355 " (cutoff:3.500A) removed outlier: 8.309A pdb=" N ILE Y 354 " --> pdb=" O GLY Z 355 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'N' and resid 359 through 362 removed outlier: 6.603A pdb=" N ASN M 359 " --> pdb=" O ILE N 360 " (cutoff:3.500A) removed outlier: 7.792A pdb=" N HIS N 362 " --> pdb=" O ASN M 359 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N THR M 361 " --> pdb=" O HIS N 362 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N ASN B 359 " --> pdb=" O ILE M 360 " (cutoff:3.500A) removed outlier: 7.763A pdb=" N HIS M 362 " --> pdb=" O ASN B 359 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N THR B 361 " --> pdb=" O HIS M 362 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N ASN A 359 " --> pdb=" O ILE B 360 " (cutoff:3.500A) removed outlier: 7.792A pdb=" N HIS B 362 " --> pdb=" O ASN A 359 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N THR A 361 " --> pdb=" O HIS B 362 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N ASN Y 359 " --> pdb=" O ILE Z 360 " (cutoff:3.500A) removed outlier: 7.792A pdb=" N HIS Z 362 " --> pdb=" O ASN Y 359 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N THR Y 361 " --> pdb=" O HIS Z 362 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'N' and resid 369 through 378 removed outlier: 6.550A pdb=" N LYS A 369 " --> pdb=" O LYS Z 370 " (cutoff:3.500A) removed outlier: 8.037A pdb=" N GLU Z 372 " --> pdb=" O LYS A 369 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N ILE A 371 " --> pdb=" O GLU Z 372 " (cutoff:3.500A) removed outlier: 7.823A pdb=" N HIS Z 374 " --> pdb=" O ILE A 371 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N THR A 373 " --> pdb=" O HIS Z 374 " (cutoff:3.500A) removed outlier: 7.737A pdb=" N LEU Z 376 " --> pdb=" O THR A 373 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N LYS A 375 " --> pdb=" O LEU Z 376 " (cutoff:3.500A) removed outlier: 7.751A pdb=" N PHE Z 378 " --> pdb=" O LYS A 375 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N THR A 377 " --> pdb=" O PHE Z 378 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'P' and resid 306 through 310 removed outlier: 6.480A pdb=" N GLN C 307 " --> pdb=" O ILE 1 308 " (cutoff:3.500A) removed outlier: 7.780A pdb=" N TYR 1 310 " --> pdb=" O GLN C 307 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N VAL C 309 " --> pdb=" O TYR 1 310 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'P' and resid 313 through 314 removed outlier: 6.716A pdb=" N VAL C 313 " --> pdb=" O ASP 1 314 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'P' and resid 317 through 318 removed outlier: 6.348A pdb=" N LYS C 317 " --> pdb=" O VAL 1 318 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'P' and resid 321 through 330 removed outlier: 6.931A pdb=" N CYS P 322 " --> pdb=" O LYS O 321 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N GLY O 323 " --> pdb=" O CYS P 322 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N ILE P 328 " --> pdb=" O ASN O 327 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N HIS O 329 " --> pdb=" O ILE P 328 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N HIS P 330 " --> pdb=" O HIS O 329 " (cutoff:3.500A) removed outlier: 6.973A pdb=" N CYS O 322 " --> pdb=" O LYS D 321 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N GLY D 323 " --> pdb=" O CYS O 322 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N ILE O 328 " --> pdb=" O ASN D 327 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N HIS D 329 " --> pdb=" O ILE O 328 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N HIS O 330 " --> pdb=" O HIS D 329 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N CYS D 322 " --> pdb=" O LYS C 321 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N GLY C 323 " --> pdb=" O CYS D 322 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N ILE D 328 " --> pdb=" O ASN C 327 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N HIS C 329 " --> pdb=" O ILE D 328 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N HIS D 330 " --> pdb=" O HIS C 329 " (cutoff:3.500A) removed outlier: 5.943A pdb=" N CYS C 322 " --> pdb=" O GLY 1 323 " (cutoff:3.500A) removed outlier: 7.527A pdb=" N LEU 1 325 " --> pdb=" O CYS C 322 " (cutoff:3.500A) removed outlier: 6.012A pdb=" N SER C 324 " --> pdb=" O LEU 1 325 " (cutoff:3.500A) removed outlier: 7.744A pdb=" N ASN 1 327 " --> pdb=" O SER C 324 " (cutoff:3.500A) removed outlier: 8.971A pdb=" N GLY C 326 " --> pdb=" O ASN 1 327 " (cutoff:3.500A) removed outlier: 8.480A pdb=" N HIS 1 329 " --> pdb=" O GLY C 326 " (cutoff:3.500A) removed outlier: 9.308A pdb=" N ILE C 328 " --> pdb=" O HIS 1 329 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N CYS 1 322 " --> pdb=" O LYS 0 321 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N GLY 0 323 " --> pdb=" O CYS 1 322 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N ILE 1 328 " --> pdb=" O ASN 0 327 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N HIS 0 329 " --> pdb=" O ILE 1 328 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N HIS 1 330 " --> pdb=" O HIS 0 329 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'P' and resid 336 through 340 removed outlier: 6.362A pdb=" N VAL O 337 " --> pdb=" O GLU P 338 " (cutoff:3.500A) removed outlier: 8.052A pdb=" N LYS P 340 " --> pdb=" O VAL O 337 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N VAL O 339 " --> pdb=" O LYS P 340 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N VAL D 337 " --> pdb=" O GLU O 338 " (cutoff:3.500A) removed outlier: 8.030A pdb=" N LYS O 340 " --> pdb=" O VAL D 337 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N VAL D 339 " --> pdb=" O LYS O 340 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N VAL C 337 " --> pdb=" O GLU D 338 " (cutoff:3.500A) removed outlier: 8.053A pdb=" N LYS D 340 " --> pdb=" O VAL C 337 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N VAL C 339 " --> pdb=" O LYS D 340 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N VAL 0 337 " --> pdb=" O GLU 1 338 " (cutoff:3.500A) removed outlier: 8.053A pdb=" N LYS 1 340 " --> pdb=" O VAL 0 337 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N VAL 0 339 " --> pdb=" O LYS 1 340 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'P' and resid 343 through 346 removed outlier: 6.474A pdb=" N LYS C 343 " --> pdb=" O LEU 1 344 " (cutoff:3.500A) removed outlier: 7.775A pdb=" N PHE 1 346 " --> pdb=" O LYS C 343 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N ASP C 345 " --> pdb=" O PHE 1 346 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'P' and resid 354 through 356 removed outlier: 8.335A pdb=" N ILE O 354 " --> pdb=" O GLY P 355 " (cutoff:3.500A) removed outlier: 8.321A pdb=" N ILE D 354 " --> pdb=" O GLY O 355 " (cutoff:3.500A) removed outlier: 8.335A pdb=" N ILE C 354 " --> pdb=" O GLY D 355 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N SER 1 356 " --> pdb=" O GLY C 355 " (cutoff:3.500A) removed outlier: 8.335A pdb=" N ILE 0 354 " --> pdb=" O GLY 1 355 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'P' and resid 359 through 362 removed outlier: 6.621A pdb=" N ASN O 359 " --> pdb=" O ILE P 360 " (cutoff:3.500A) removed outlier: 7.808A pdb=" N HIS P 362 " --> pdb=" O ASN O 359 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N THR O 361 " --> pdb=" O HIS P 362 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N ASN D 359 " --> pdb=" O ILE O 360 " (cutoff:3.500A) removed outlier: 7.822A pdb=" N HIS O 362 " --> pdb=" O ASN D 359 " (cutoff:3.500A) removed outlier: 6.286A pdb=" N THR D 361 " --> pdb=" O HIS O 362 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N ASN C 359 " --> pdb=" O ILE D 360 " (cutoff:3.500A) removed outlier: 7.808A pdb=" N HIS D 362 " --> pdb=" O ASN C 359 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N THR C 361 " --> pdb=" O HIS D 362 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N ASN 0 359 " --> pdb=" O ILE 1 360 " (cutoff:3.500A) removed outlier: 7.808A pdb=" N HIS 1 362 " --> pdb=" O ASN 0 359 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N THR 0 361 " --> pdb=" O HIS 1 362 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'P' and resid 369 through 378 removed outlier: 6.570A pdb=" N LYS C 369 " --> pdb=" O LYS 1 370 " (cutoff:3.500A) removed outlier: 8.058A pdb=" N GLU 1 372 " --> pdb=" O LYS C 369 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N ILE C 371 " --> pdb=" O GLU 1 372 " (cutoff:3.500A) removed outlier: 7.836A pdb=" N HIS 1 374 " --> pdb=" O ILE C 371 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N THR C 373 " --> pdb=" O HIS 1 374 " (cutoff:3.500A) removed outlier: 7.756A pdb=" N LEU 1 376 " --> pdb=" O THR C 373 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N LYS C 375 " --> pdb=" O LEU 1 376 " (cutoff:3.500A) removed outlier: 7.772A pdb=" N PHE 1 378 " --> pdb=" O LYS C 375 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N THR C 377 " --> pdb=" O PHE 1 378 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'Q' and resid 2 through 6 Processing sheet with id=AC2, first strand: chain 'S' and resid 2 through 6 Processing sheet with id=AC3, first strand: chain 'U' and resid 2 through 6 Processing sheet with id=AC4, first strand: chain 'W' and resid 2 through 6 300 hydrogen bonds defined for protein. 852 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: 2.54 Time building geometry restraints manager: 2.78 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1446 1.32 - 1.44: 2046 1.44 - 1.56: 5274 1.56 - 1.68: 0 1.68 - 1.80: 12 Bond restraints: 8778 Sorted by residual: bond pdb=" C LYS D 321 " pdb=" O LYS D 321 " ideal model delta sigma weight residual 1.235 1.199 0.036 1.14e-02 7.69e+03 9.98e+00 bond pdb=" C LYS 1 321 " pdb=" O LYS 1 321 " ideal model delta sigma weight residual 1.235 1.199 0.036 1.14e-02 7.69e+03 9.96e+00 bond pdb=" C LYS P 321 " pdb=" O LYS P 321 " ideal model delta sigma weight residual 1.235 1.199 0.036 1.14e-02 7.69e+03 9.92e+00 bond pdb=" C LYS O 321 " pdb=" O LYS O 321 " ideal model delta sigma weight residual 1.235 1.201 0.034 1.14e-02 7.69e+03 9.06e+00 bond pdb=" C LYS 0 321 " pdb=" O LYS 0 321 " ideal model delta sigma weight residual 1.235 1.201 0.034 1.14e-02 7.69e+03 9.02e+00 ... (remaining 8773 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.63: 10878 1.63 - 3.25: 745 3.25 - 4.88: 83 4.88 - 6.50: 42 6.50 - 8.13: 24 Bond angle restraints: 11772 Sorted by residual: angle pdb=" C LYS 0 321 " pdb=" CA LYS 0 321 " pdb=" CB LYS 0 321 " ideal model delta sigma weight residual 109.70 104.19 5.51 1.81e+00 3.05e-01 9.28e+00 angle pdb=" C LYS O 321 " pdb=" CA LYS O 321 " pdb=" CB LYS O 321 " ideal model delta sigma weight residual 109.70 104.19 5.51 1.81e+00 3.05e-01 9.27e+00 angle pdb=" C LYS C 321 " pdb=" CA LYS C 321 " pdb=" CB LYS C 321 " ideal model delta sigma weight residual 109.70 104.19 5.51 1.81e+00 3.05e-01 9.26e+00 angle pdb=" C SER C 320 " pdb=" N LYS C 321 " pdb=" CA LYS C 321 " ideal model delta sigma weight residual 122.74 118.54 4.20 1.54e+00 4.22e-01 7.43e+00 angle pdb=" C SER O 320 " pdb=" N LYS O 321 " pdb=" CA LYS O 321 " ideal model delta sigma weight residual 122.74 118.54 4.20 1.54e+00 4.22e-01 7.42e+00 ... (remaining 11767 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.49: 4188 13.49 - 26.98: 504 26.98 - 40.47: 108 40.47 - 53.96: 42 53.96 - 67.45: 84 Dihedral angle restraints: 4926 sinusoidal: 2250 harmonic: 2676 Sorted by residual: dihedral pdb=" C LYS 0 321 " pdb=" N LYS 0 321 " pdb=" CA LYS 0 321 " pdb=" CB LYS 0 321 " ideal model delta harmonic sigma weight residual -122.60 -113.10 -9.50 0 2.50e+00 1.60e-01 1.44e+01 dihedral pdb=" C LYS O 321 " pdb=" N LYS O 321 " pdb=" CA LYS O 321 " pdb=" CB LYS O 321 " ideal model delta harmonic sigma weight residual -122.60 -113.10 -9.50 0 2.50e+00 1.60e-01 1.44e+01 dihedral pdb=" C LYS C 321 " pdb=" N LYS C 321 " pdb=" CA LYS C 321 " pdb=" CB LYS C 321 " ideal model delta harmonic sigma weight residual -122.60 -113.10 -9.50 0 2.50e+00 1.60e-01 1.44e+01 ... (remaining 4923 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 795 0.036 - 0.071: 240 0.071 - 0.107: 166 0.107 - 0.142: 113 0.142 - 0.178: 42 Chirality restraints: 1356 Sorted by residual: chirality pdb=" CA LYS 0 321 " pdb=" N LYS 0 321 " pdb=" C LYS 0 321 " pdb=" CB LYS 0 321 " both_signs ideal model delta sigma weight residual False 2.51 2.69 -0.18 2.00e-01 2.50e+01 7.91e-01 chirality pdb=" CA LYS O 321 " pdb=" N LYS O 321 " pdb=" C LYS O 321 " pdb=" CB LYS O 321 " both_signs ideal model delta sigma weight residual False 2.51 2.69 -0.18 2.00e-01 2.50e+01 7.90e-01 chirality pdb=" CA LYS C 321 " pdb=" N LYS C 321 " pdb=" C LYS C 321 " pdb=" CB LYS C 321 " both_signs ideal model delta sigma weight residual False 2.51 2.69 -0.18 2.00e-01 2.50e+01 7.83e-01 ... (remaining 1353 not shown) Planarity restraints: 1440 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS N 343 " 0.010 2.00e-02 2.50e+03 2.08e-02 4.31e+00 pdb=" C LYS N 343 " -0.036 2.00e-02 2.50e+03 pdb=" O LYS N 343 " 0.014 2.00e-02 2.50e+03 pdb=" N LEU N 344 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS 1 343 " -0.010 2.00e-02 2.50e+03 2.08e-02 4.31e+00 pdb=" C LYS 1 343 " 0.036 2.00e-02 2.50e+03 pdb=" O LYS 1 343 " -0.014 2.00e-02 2.50e+03 pdb=" N LEU 1 344 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS D 343 " -0.010 2.00e-02 2.50e+03 2.07e-02 4.27e+00 pdb=" C LYS D 343 " 0.036 2.00e-02 2.50e+03 pdb=" O LYS D 343 " -0.013 2.00e-02 2.50e+03 pdb=" N LEU D 344 " -0.012 2.00e-02 2.50e+03 ... (remaining 1437 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 2064 2.81 - 3.34: 6564 3.34 - 3.86: 14647 3.86 - 4.38: 15223 4.38 - 4.90: 30376 Nonbonded interactions: 68874 Sorted by model distance: nonbonded pdb=" O DLE G 2 " pdb=" O DTR T 6 " model vdw 2.292 3.040 nonbonded pdb=" O DTR H 6 " pdb=" O DLE 4 2 " model vdw 2.293 3.040 nonbonded pdb=" NZ LYS M 343 " pdb=" OE2 GLU N 342 " model vdw 2.342 3.120 nonbonded pdb=" NZ LYS Y 343 " pdb=" OE2 GLU Z 342 " model vdw 2.343 3.120 nonbonded pdb=" NZ LYS A 343 " pdb=" OE2 GLU B 342 " model vdw 2.343 3.120 ... (remaining 68869 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 '0' and resid 304 through 380) selection = chain '1' selection = (chain 'A' and resid 304 through 380) selection = chain 'B' selection = (chain 'C' and resid 304 through 380) selection = chain 'D' selection = (chain 'M' and resid 304 through 380) selection = chain 'N' selection = (chain 'O' and resid 304 through 380) selection = chain 'P' selection = chain 'Y' selection = chain 'Z' } ncs_group { reference = chain '2' selection = chain '4' selection = chain '5' selection = chain '6' selection = chain '7' selection = chain '8' selection = chain '9' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' } 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: 5.600 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.380 Check model and map are aligned: 0.070 Set scattering table: 0.100 Process input model: 27.110 Find NCS groups from input model: 0.710 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:2.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.720 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7854 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 : 0.039 1.497 8784 Z= 3.851 Angle : 0.951 8.126 11772 Z= 0.447 Chirality : 0.061 0.178 1356 Planarity : 0.006 0.026 1440 Dihedral : 15.498 67.454 3318 Min Nonbonded Distance : 2.292 Molprobity Statistics. All-atom Clashscore : 15.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.67 % Favored : 89.33 % Rotamer: Outliers : 7.46 % Allowed : 5.97 % Favored : 86.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.54 (0.22), residues: 900 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.93 (0.17), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS 1 362 PHE 0.008 0.002 PHE Y 346 TYR 0.011 0.003 TYR 0 310 ARG 0.002 0.001 ARG M 379 Details of bonding type rmsd hydrogen bonds : bond 0.19442 ( 300) hydrogen bonds : angle 11.44775 ( 852) covalent geometry : bond 0.00798 ( 8778) covalent geometry : angle 0.95150 (11772) Misc. bond : bond 1.46647 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 507 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 447 time to evaluate : 0.987 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 331 LYS cc_start: 0.9241 (mttt) cc_final: 0.9016 (mtpt) REVERT: A 353 LYS cc_start: 0.9245 (tttt) cc_final: 0.8875 (tttt) REVERT: B 321 LYS cc_start: 0.9225 (mttt) cc_final: 0.8944 (mttp) REVERT: B 331 LYS cc_start: 0.9346 (mttt) cc_final: 0.8952 (mtmt) REVERT: B 353 LYS cc_start: 0.9194 (tttt) cc_final: 0.8958 (tttm) REVERT: B 356 SER cc_start: 0.9327 (p) cc_final: 0.9054 (p) REVERT: C 321 LYS cc_start: 0.9302 (mttt) cc_final: 0.9099 (mttp) REVERT: C 331 LYS cc_start: 0.9354 (mttt) cc_final: 0.9087 (mttm) REVERT: C 343 LYS cc_start: 0.8205 (mmtm) cc_final: 0.7972 (mtpp) REVERT: C 349 ARG cc_start: 0.7912 (mtm-85) cc_final: 0.7555 (mtm-85) REVERT: C 375 LYS cc_start: 0.8967 (tttt) cc_final: 0.8731 (tttt) REVERT: D 313 VAL cc_start: 0.9302 (t) cc_final: 0.9036 (p) REVERT: D 314 ASP cc_start: 0.8759 (t0) cc_final: 0.8496 (t0) REVERT: D 343 LYS cc_start: 0.8697 (mmtm) cc_final: 0.8368 (mmtp) REVERT: M 331 LYS cc_start: 0.9368 (mttt) cc_final: 0.9120 (mtmt) REVERT: M 336 GLN cc_start: 0.9274 (tt0) cc_final: 0.9009 (tt0) REVERT: M 343 LYS cc_start: 0.8279 (mmtm) cc_final: 0.7918 (mtpp) REVERT: M 353 LYS cc_start: 0.9305 (tttt) cc_final: 0.9026 (tttp) REVERT: N 331 LYS cc_start: 0.9404 (mttt) cc_final: 0.9135 (mtpt) REVERT: N 343 LYS cc_start: 0.8493 (mmtm) cc_final: 0.7914 (mtpp) REVERT: N 347 LYS cc_start: 0.8101 (ptpt) cc_final: 0.7887 (ptpt) REVERT: N 356 SER cc_start: 0.9265 (p) cc_final: 0.8944 (p) REVERT: O 321 LYS cc_start: 0.9264 (mttt) cc_final: 0.8937 (mttp) REVERT: P 327 ASN cc_start: 0.9099 (t0) cc_final: 0.8858 (t0) REVERT: Y 314 ASP cc_start: 0.8677 (t0) cc_final: 0.8431 (t0) REVERT: Z 321 LYS cc_start: 0.9154 (mttt) cc_final: 0.8835 (mttp) REVERT: Z 331 LYS cc_start: 0.9293 (mttt) cc_final: 0.8835 (mtpt) REVERT: Z 353 LYS cc_start: 0.9225 (tttt) cc_final: 0.8833 (tttm) REVERT: Z 356 SER cc_start: 0.9358 (p) cc_final: 0.9088 (p) REVERT: Z 375 LYS cc_start: 0.9041 (tttt) cc_final: 0.8651 (ttpp) REVERT: 0 310 TYR cc_start: 0.8705 (t80) cc_final: 0.8139 (t80) REVERT: 0 375 LYS cc_start: 0.8811 (tttt) cc_final: 0.8588 (tttm) REVERT: 1 343 LYS cc_start: 0.8572 (mmtm) cc_final: 0.8284 (mmtp) REVERT: 1 349 ARG cc_start: 0.7549 (mtm-85) cc_final: 0.7214 (mtm180) outliers start: 60 outliers final: 21 residues processed: 454 average time/residue: 0.2931 time to fit residues: 167.2713 Evaluate side-chains 441 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 420 time to evaluate : 0.889 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 342 GLU Chi-restraints excluded: chain B residue 311 LYS Chi-restraints excluded: chain B residue 342 GLU Chi-restraints excluded: chain B residue 358 ASP Chi-restraints excluded: chain C residue 339 VAL Chi-restraints excluded: chain C residue 342 GLU Chi-restraints excluded: chain D residue 342 GLU Chi-restraints excluded: chain M residue 339 VAL Chi-restraints excluded: chain M residue 342 GLU Chi-restraints excluded: chain M residue 358 ASP Chi-restraints excluded: chain N residue 339 VAL Chi-restraints excluded: chain O residue 339 VAL Chi-restraints excluded: chain O residue 342 GLU Chi-restraints excluded: chain P residue 339 VAL Chi-restraints excluded: chain P residue 342 GLU Chi-restraints excluded: chain Y residue 339 VAL Chi-restraints excluded: chain Z residue 311 LYS Chi-restraints excluded: chain Z residue 342 GLU Chi-restraints excluded: chain 0 residue 339 VAL Chi-restraints excluded: chain 0 residue 358 ASP Chi-restraints excluded: chain 1 residue 358 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 70 optimal weight: 10.0000 chunk 63 optimal weight: 5.9990 chunk 35 optimal weight: 7.9990 chunk 21 optimal weight: 0.6980 chunk 42 optimal weight: 2.9990 chunk 34 optimal weight: 0.6980 chunk 65 optimal weight: 3.9990 chunk 25 optimal weight: 0.7980 chunk 40 optimal weight: 0.5980 chunk 49 optimal weight: 7.9990 chunk 76 optimal weight: 6.9990 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 351 GLN 0 327 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4885 r_free = 0.4885 target = 0.200383 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4083 r_free = 0.4083 target = 0.132710 restraints weight = 9399.274| |-----------------------------------------------------------------------------| r_work (start): 0.4036 rms_B_bonded: 2.89 r_work: 0.3896 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.3775 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3775 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8276 moved from start: 0.2549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 8784 Z= 0.128 Angle : 0.655 8.065 11772 Z= 0.317 Chirality : 0.048 0.145 1356 Planarity : 0.003 0.022 1440 Dihedral : 12.644 66.186 1565 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.44 % Favored : 91.56 % Rotamer: Outliers : 2.99 % Allowed : 20.90 % Favored : 76.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.42 (0.23), residues: 900 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.83 (0.17), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS N 374 PHE 0.016 0.003 PHE 1 378 TYR 0.010 0.002 TYR M 310 ARG 0.005 0.000 ARG O 349 Details of bonding type rmsd hydrogen bonds : bond 0.03155 ( 300) hydrogen bonds : angle 6.28462 ( 852) covalent geometry : bond 0.00291 ( 8778) covalent geometry : angle 0.65509 (11772) Misc. bond : bond 0.00102 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 445 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 421 time to evaluate : 1.439 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 311 LYS cc_start: 0.8790 (ptpt) cc_final: 0.8570 (ptpt) REVERT: A 324 SER cc_start: 0.8902 (t) cc_final: 0.8636 (m) REVERT: A 331 LYS cc_start: 0.9298 (mttt) cc_final: 0.9027 (mtpt) REVERT: A 344 LEU cc_start: 0.9411 (mp) cc_final: 0.9208 (mp) REVERT: A 353 LYS cc_start: 0.9261 (tttt) cc_final: 0.8848 (tttt) REVERT: B 321 LYS cc_start: 0.9398 (mttt) cc_final: 0.9177 (mttm) REVERT: B 331 LYS cc_start: 0.9383 (mttt) cc_final: 0.9075 (mtmt) REVERT: B 343 LYS cc_start: 0.8804 (mtpp) cc_final: 0.8564 (mtpp) REVERT: C 314 ASP cc_start: 0.8801 (t0) cc_final: 0.8407 (t0) REVERT: C 321 LYS cc_start: 0.9285 (mttt) cc_final: 0.9063 (mttp) REVERT: C 331 LYS cc_start: 0.9390 (mttt) cc_final: 0.9189 (mttm) REVERT: C 343 LYS cc_start: 0.8886 (mmtm) cc_final: 0.8347 (mptt) REVERT: C 347 LYS cc_start: 0.8473 (ptpt) cc_final: 0.8257 (ptpt) REVERT: C 349 ARG cc_start: 0.8014 (mtm-85) cc_final: 0.7735 (mtm-85) REVERT: C 375 LYS cc_start: 0.8994 (tttt) cc_final: 0.8764 (tttt) REVERT: D 327 ASN cc_start: 0.9223 (t0) cc_final: 0.9009 (t0) REVERT: D 343 LYS cc_start: 0.8908 (mmtm) cc_final: 0.8680 (mptt) REVERT: M 325 LEU cc_start: 0.9344 (tp) cc_final: 0.9074 (tp) REVERT: M 331 LYS cc_start: 0.9365 (mttt) cc_final: 0.9133 (mtmt) REVERT: M 343 LYS cc_start: 0.8606 (mmtm) cc_final: 0.8265 (mmtm) REVERT: N 317 LYS cc_start: 0.8302 (ptpp) cc_final: 0.8015 (ptmt) REVERT: N 331 LYS cc_start: 0.9374 (mttt) cc_final: 0.9160 (mtpt) REVERT: N 343 LYS cc_start: 0.8366 (mmtm) cc_final: 0.8008 (mtpp) REVERT: N 349 ARG cc_start: 0.7906 (mtm-85) cc_final: 0.7656 (mtm-85) REVERT: O 321 LYS cc_start: 0.9405 (mttt) cc_final: 0.9099 (mttp) REVERT: O 342 GLU cc_start: 0.6973 (OUTLIER) cc_final: 0.6594 (pt0) REVERT: O 375 LYS cc_start: 0.8881 (tttt) cc_final: 0.8599 (tttt) REVERT: P 313 VAL cc_start: 0.9182 (t) cc_final: 0.8770 (p) REVERT: P 331 LYS cc_start: 0.9369 (mttt) cc_final: 0.7722 (tmtt) REVERT: Y 314 ASP cc_start: 0.8963 (t0) cc_final: 0.8760 (t0) REVERT: Z 321 LYS cc_start: 0.9359 (mttt) cc_final: 0.9110 (mttp) REVERT: Z 331 LYS cc_start: 0.9332 (mttt) cc_final: 0.8913 (mtpt) REVERT: Z 353 LYS cc_start: 0.9287 (tttt) cc_final: 0.8972 (tttm) REVERT: Z 356 SER cc_start: 0.9415 (p) cc_final: 0.9073 (p) REVERT: Z 375 LYS cc_start: 0.9080 (tttt) cc_final: 0.8690 (ttmm) REVERT: 0 310 TYR cc_start: 0.8808 (t80) cc_final: 0.8226 (t80) REVERT: 0 343 LYS cc_start: 0.8761 (mtpp) cc_final: 0.8521 (mttp) REVERT: 0 375 LYS cc_start: 0.8969 (tttt) cc_final: 0.8683 (tttm) REVERT: 1 314 ASP cc_start: 0.9028 (t0) cc_final: 0.8749 (t0) REVERT: 1 343 LYS cc_start: 0.8992 (mmtm) cc_final: 0.8773 (mptt) outliers start: 24 outliers final: 14 residues processed: 424 average time/residue: 0.3420 time to fit residues: 182.7184 Evaluate side-chains 423 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 408 time to evaluate : 1.159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain B residue 311 LYS Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain B residue 342 GLU Chi-restraints excluded: chain C residue 339 VAL Chi-restraints excluded: chain D residue 342 GLU Chi-restraints excluded: chain M residue 306 VAL Chi-restraints excluded: chain M residue 373 THR Chi-restraints excluded: chain O residue 339 VAL Chi-restraints excluded: chain O residue 342 GLU Chi-restraints excluded: chain Y residue 373 THR Chi-restraints excluded: chain Z residue 342 GLU Chi-restraints excluded: chain 0 residue 315 LEU Chi-restraints excluded: chain 0 residue 339 VAL Chi-restraints excluded: chain 1 residue 315 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 23 optimal weight: 8.9990 chunk 34 optimal weight: 5.9990 chunk 44 optimal weight: 2.9990 chunk 42 optimal weight: 10.0000 chunk 54 optimal weight: 2.9990 chunk 19 optimal weight: 5.9990 chunk 13 optimal weight: 0.9980 chunk 7 optimal weight: 10.0000 chunk 21 optimal weight: 0.4980 chunk 47 optimal weight: 2.9990 chunk 66 optimal weight: 5.9990 overall best weight: 2.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 374 HIS O 327 ASN P 327 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4842 r_free = 0.4842 target = 0.196299 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.126386 restraints weight = 9628.712| |-----------------------------------------------------------------------------| r_work (start): 0.3954 rms_B_bonded: 2.96 r_work: 0.3812 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.3693 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.3693 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8328 moved from start: 0.3013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 8784 Z= 0.167 Angle : 0.649 6.803 11772 Z= 0.318 Chirality : 0.048 0.185 1356 Planarity : 0.003 0.025 1440 Dihedral : 11.662 65.673 1537 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.67 % Favored : 91.33 % Rotamer: Outliers : 3.98 % Allowed : 22.26 % Favored : 73.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.27 (0.23), residues: 900 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.72 (0.18), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS N 374 PHE 0.012 0.002 PHE Y 346 TYR 0.014 0.002 TYR M 310 ARG 0.005 0.001 ARG O 349 Details of bonding type rmsd hydrogen bonds : bond 0.02849 ( 300) hydrogen bonds : angle 5.65926 ( 852) covalent geometry : bond 0.00397 ( 8778) covalent geometry : angle 0.64869 (11772) Misc. bond : bond 0.00022 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 439 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 407 time to evaluate : 0.972 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 324 SER cc_start: 0.9136 (t) cc_final: 0.8867 (m) REVERT: A 344 LEU cc_start: 0.9408 (mp) cc_final: 0.9183 (mp) REVERT: B 331 LYS cc_start: 0.9313 (mttt) cc_final: 0.8959 (mtmt) REVERT: B 343 LYS cc_start: 0.8904 (mtpp) cc_final: 0.8631 (mtpp) REVERT: B 353 LYS cc_start: 0.9235 (tttm) cc_final: 0.9015 (tttm) REVERT: B 375 LYS cc_start: 0.9091 (tttt) cc_final: 0.8688 (ttmm) REVERT: C 314 ASP cc_start: 0.8910 (t0) cc_final: 0.8442 (t0) REVERT: C 331 LYS cc_start: 0.9317 (mttt) cc_final: 0.9079 (mttm) REVERT: C 343 LYS cc_start: 0.8980 (mmtm) cc_final: 0.8475 (mptt) REVERT: C 375 LYS cc_start: 0.8920 (tttt) cc_final: 0.8488 (tttt) REVERT: D 343 LYS cc_start: 0.9024 (mmtm) cc_final: 0.8782 (mmtp) REVERT: M 336 GLN cc_start: 0.9286 (tt0) cc_final: 0.9056 (tt0) REVERT: M 343 LYS cc_start: 0.8694 (mmtm) cc_final: 0.8074 (mtpp) REVERT: N 317 LYS cc_start: 0.8310 (ptpp) cc_final: 0.7989 (ptmm) REVERT: N 331 LYS cc_start: 0.9314 (mttt) cc_final: 0.9057 (mtpt) REVERT: N 343 LYS cc_start: 0.8591 (mmtm) cc_final: 0.8116 (mmmm) REVERT: N 345 ASP cc_start: 0.8924 (m-30) cc_final: 0.8651 (m-30) REVERT: N 379 ARG cc_start: 0.3677 (mmp-170) cc_final: 0.3469 (mmp-170) REVERT: O 321 LYS cc_start: 0.9394 (mttt) cc_final: 0.9134 (mttp) REVERT: O 375 LYS cc_start: 0.8839 (tttt) cc_final: 0.8555 (tttt) REVERT: P 313 VAL cc_start: 0.9143 (t) cc_final: 0.8697 (p) REVERT: P 370 LYS cc_start: 0.8979 (tttm) cc_final: 0.8764 (tttp) REVERT: Z 321 LYS cc_start: 0.9333 (mttt) cc_final: 0.9081 (mttp) REVERT: Z 331 LYS cc_start: 0.9314 (mttt) cc_final: 0.8904 (mtpt) REVERT: Z 347 LYS cc_start: 0.8518 (ptpt) cc_final: 0.7779 (ptmm) REVERT: Z 353 LYS cc_start: 0.9369 (tttt) cc_final: 0.9058 (tttm) REVERT: Z 356 SER cc_start: 0.9560 (p) cc_final: 0.9225 (p) REVERT: Z 375 LYS cc_start: 0.9053 (tttt) cc_final: 0.8686 (ttmm) REVERT: 0 310 TYR cc_start: 0.8845 (t80) cc_final: 0.8560 (t80) REVERT: 0 331 LYS cc_start: 0.9416 (mttt) cc_final: 0.9156 (mtmt) REVERT: 0 343 LYS cc_start: 0.8914 (mtpp) cc_final: 0.8595 (mptt) REVERT: 1 313 VAL cc_start: 0.9083 (t) cc_final: 0.8551 (p) REVERT: 1 327 ASN cc_start: 0.9267 (t0) cc_final: 0.9060 (t0) REVERT: 1 331 LYS cc_start: 0.9379 (mtmm) cc_final: 0.9139 (mtmt) REVERT: 1 356 SER cc_start: 0.9491 (p) cc_final: 0.9207 (p) REVERT: 1 375 LYS cc_start: 0.8628 (tttt) cc_final: 0.8219 (tttm) outliers start: 32 outliers final: 20 residues processed: 412 average time/residue: 0.2826 time to fit residues: 146.4327 Evaluate side-chains 415 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 395 time to evaluate : 0.999 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain C residue 313 VAL Chi-restraints excluded: chain C residue 339 VAL Chi-restraints excluded: chain C residue 358 ASP Chi-restraints excluded: chain D residue 319 THR Chi-restraints excluded: chain D residue 342 GLU Chi-restraints excluded: chain M residue 306 VAL Chi-restraints excluded: chain N residue 306 VAL Chi-restraints excluded: chain N residue 339 VAL Chi-restraints excluded: chain N residue 352 SER Chi-restraints excluded: chain O residue 339 VAL Chi-restraints excluded: chain P residue 319 THR Chi-restraints excluded: chain P residue 358 ASP Chi-restraints excluded: chain Y residue 339 VAL Chi-restraints excluded: chain Z residue 320 SER Chi-restraints excluded: chain Z residue 373 THR Chi-restraints excluded: chain 1 residue 319 THR Chi-restraints excluded: chain 1 residue 358 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 4 optimal weight: 7.9990 chunk 68 optimal weight: 4.9990 chunk 56 optimal weight: 7.9990 chunk 35 optimal weight: 6.9990 chunk 48 optimal weight: 8.9990 chunk 75 optimal weight: 7.9990 chunk 54 optimal weight: 3.9990 chunk 19 optimal weight: 4.9990 chunk 31 optimal weight: 5.9990 chunk 57 optimal weight: 5.9990 chunk 60 optimal weight: 5.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 307 GLN 1 374 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4780 r_free = 0.4780 target = 0.189891 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.119867 restraints weight = 9684.850| |-----------------------------------------------------------------------------| r_work (start): 0.3868 rms_B_bonded: 3.06 r_work: 0.3726 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.3606 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3606 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8399 moved from start: 0.3550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.053 8784 Z= 0.362 Angle : 0.788 8.308 11772 Z= 0.392 Chirality : 0.051 0.197 1356 Planarity : 0.003 0.029 1440 Dihedral : 12.016 66.363 1523 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 9.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.89 % Favored : 91.11 % Rotamer: Outliers : 5.60 % Allowed : 23.01 % Favored : 71.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.47 (0.23), residues: 900 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.87 (0.17), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS 0 329 PHE 0.014 0.003 PHE A 346 TYR 0.017 0.003 TYR M 310 ARG 0.006 0.001 ARG O 349 Details of bonding type rmsd hydrogen bonds : bond 0.03456 ( 300) hydrogen bonds : angle 5.70659 ( 852) covalent geometry : bond 0.00866 ( 8778) covalent geometry : angle 0.78840 (11772) Misc. bond : bond 0.00071 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 427 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 382 time to evaluate : 0.988 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 343 LYS cc_start: 0.8843 (mmtm) cc_final: 0.8577 (mmtm) REVERT: A 344 LEU cc_start: 0.9428 (mp) cc_final: 0.9213 (mp) REVERT: A 353 LYS cc_start: 0.9392 (tttt) cc_final: 0.9035 (tttt) REVERT: B 331 LYS cc_start: 0.9320 (mttt) cc_final: 0.9078 (mtmt) REVERT: B 336 GLN cc_start: 0.9357 (tt0) cc_final: 0.8796 (tp40) REVERT: B 375 LYS cc_start: 0.9069 (tttt) cc_final: 0.8671 (ttmm) REVERT: C 331 LYS cc_start: 0.9358 (mttt) cc_final: 0.9138 (mttm) REVERT: C 342 GLU cc_start: 0.8809 (mt-10) cc_final: 0.8491 (mt-10) REVERT: C 343 LYS cc_start: 0.8953 (mmtm) cc_final: 0.8742 (mptt) REVERT: D 343 LYS cc_start: 0.9165 (mmtm) cc_final: 0.8902 (mmtt) REVERT: M 336 GLN cc_start: 0.9340 (tt0) cc_final: 0.9121 (tt0) REVERT: M 343 LYS cc_start: 0.8783 (mmtm) cc_final: 0.8209 (mtpp) REVERT: N 343 LYS cc_start: 0.8853 (mmtm) cc_final: 0.8286 (mtpp) REVERT: N 345 ASP cc_start: 0.8908 (m-30) cc_final: 0.8586 (m-30) REVERT: N 347 LYS cc_start: 0.8593 (ptpt) cc_final: 0.7952 (ptmm) REVERT: O 321 LYS cc_start: 0.9416 (mttt) cc_final: 0.9171 (mttp) REVERT: O 343 LYS cc_start: 0.9145 (mtpp) cc_final: 0.8911 (mtpp) REVERT: O 375 LYS cc_start: 0.8814 (tttt) cc_final: 0.8354 (tttm) REVERT: P 313 VAL cc_start: 0.9265 (t) cc_final: 0.8864 (p) REVERT: P 315 LEU cc_start: 0.9251 (OUTLIER) cc_final: 0.9016 (mp) REVERT: Y 315 LEU cc_start: 0.9337 (OUTLIER) cc_final: 0.9124 (mp) REVERT: Z 331 LYS cc_start: 0.9307 (mttt) cc_final: 0.8919 (mtpt) REVERT: Z 347 LYS cc_start: 0.8604 (ptpt) cc_final: 0.7938 (ptmm) REVERT: Z 353 LYS cc_start: 0.9330 (tttt) cc_final: 0.9008 (tttm) REVERT: Z 375 LYS cc_start: 0.9033 (tttt) cc_final: 0.8638 (ttmm) REVERT: 0 343 LYS cc_start: 0.8998 (mtpp) cc_final: 0.8706 (mtmm) REVERT: 0 378 PHE cc_start: 0.8898 (t80) cc_final: 0.8502 (t80) outliers start: 45 outliers final: 35 residues processed: 394 average time/residue: 0.2701 time to fit residues: 135.0193 Evaluate side-chains 410 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 373 time to evaluate : 0.968 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 352 SER Chi-restraints excluded: chain A residue 358 ASP Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain B residue 319 THR Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain B residue 352 SER Chi-restraints excluded: chain B residue 358 ASP Chi-restraints excluded: chain C residue 309 VAL Chi-restraints excluded: chain C residue 339 VAL Chi-restraints excluded: chain D residue 319 THR Chi-restraints excluded: chain M residue 306 VAL Chi-restraints excluded: chain M residue 315 LEU Chi-restraints excluded: chain M residue 358 ASP Chi-restraints excluded: chain N residue 306 VAL Chi-restraints excluded: chain N residue 339 VAL Chi-restraints excluded: chain N residue 352 SER Chi-restraints excluded: chain O residue 339 VAL Chi-restraints excluded: chain O residue 340 LYS Chi-restraints excluded: chain O residue 372 GLU Chi-restraints excluded: chain P residue 315 LEU Chi-restraints excluded: chain P residue 319 THR Chi-restraints excluded: chain Y residue 306 VAL Chi-restraints excluded: chain Y residue 315 LEU Chi-restraints excluded: chain Y residue 339 VAL Chi-restraints excluded: chain Z residue 306 VAL Chi-restraints excluded: chain Z residue 319 THR Chi-restraints excluded: chain Z residue 320 SER Chi-restraints excluded: chain Z residue 339 VAL Chi-restraints excluded: chain Z residue 351 GLN Chi-restraints excluded: chain Z residue 373 THR Chi-restraints excluded: chain 0 residue 315 LEU Chi-restraints excluded: chain 0 residue 339 VAL Chi-restraints excluded: chain 0 residue 358 ASP Chi-restraints excluded: chain 1 residue 319 THR Chi-restraints excluded: chain 1 residue 358 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 53 optimal weight: 3.9990 chunk 2 optimal weight: 2.9990 chunk 0 optimal weight: 7.9990 chunk 48 optimal weight: 7.9990 chunk 50 optimal weight: 10.0000 chunk 72 optimal weight: 1.9990 chunk 60 optimal weight: 2.9990 chunk 75 optimal weight: 0.5980 chunk 82 optimal weight: 0.6980 chunk 43 optimal weight: 2.9990 chunk 9 optimal weight: 0.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 307 GLN M 327 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4845 r_free = 0.4845 target = 0.196001 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.126532 restraints weight = 9562.175| |-----------------------------------------------------------------------------| r_work (start): 0.3970 rms_B_bonded: 3.05 r_work: 0.3834 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.3713 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3713 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8354 moved from start: 0.3727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8784 Z= 0.130 Angle : 0.638 7.353 11772 Z= 0.313 Chirality : 0.048 0.134 1356 Planarity : 0.002 0.022 1440 Dihedral : 11.437 65.039 1520 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.00 % Favored : 93.00 % Rotamer: Outliers : 4.73 % Allowed : 26.24 % Favored : 69.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.34 (0.23), residues: 900 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.78 (0.18), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS M 374 PHE 0.012 0.002 PHE N 378 TYR 0.011 0.002 TYR M 310 ARG 0.004 0.000 ARG O 349 Details of bonding type rmsd hydrogen bonds : bond 0.02269 ( 300) hydrogen bonds : angle 5.04820 ( 852) covalent geometry : bond 0.00302 ( 8778) covalent geometry : angle 0.63829 (11772) Misc. bond : bond 0.00019 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 431 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 393 time to evaluate : 0.995 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 331 LYS cc_start: 0.9350 (mtpt) cc_final: 0.9150 (mtpt) REVERT: A 344 LEU cc_start: 0.9411 (mp) cc_final: 0.9154 (mp) REVERT: A 353 LYS cc_start: 0.9360 (tttt) cc_final: 0.8948 (tttt) REVERT: B 331 LYS cc_start: 0.9277 (mttt) cc_final: 0.8939 (mtmt) REVERT: B 336 GLN cc_start: 0.9221 (tt0) cc_final: 0.8603 (tp40) REVERT: B 343 LYS cc_start: 0.8985 (mtpp) cc_final: 0.8714 (mtpp) REVERT: B 375 LYS cc_start: 0.9042 (tttt) cc_final: 0.8617 (ttmm) REVERT: C 314 ASP cc_start: 0.8914 (t0) cc_final: 0.8614 (t0) REVERT: D 343 LYS cc_start: 0.9117 (mmtm) cc_final: 0.8738 (mmtp) REVERT: M 336 GLN cc_start: 0.9265 (tt0) cc_final: 0.8957 (tt0) REVERT: M 343 LYS cc_start: 0.8764 (mmtm) cc_final: 0.8188 (mtpp) REVERT: N 343 LYS cc_start: 0.8761 (mmtm) cc_final: 0.8236 (mtpp) REVERT: N 345 ASP cc_start: 0.8893 (m-30) cc_final: 0.8693 (m-30) REVERT: O 321 LYS cc_start: 0.9397 (mttt) cc_final: 0.9143 (mttp) REVERT: O 343 LYS cc_start: 0.9129 (mtpp) cc_final: 0.8373 (mttm) REVERT: O 375 LYS cc_start: 0.8853 (tttt) cc_final: 0.8398 (tttm) REVERT: P 313 VAL cc_start: 0.9150 (t) cc_final: 0.8744 (p) REVERT: P 315 LEU cc_start: 0.9309 (OUTLIER) cc_final: 0.9083 (mp) REVERT: Y 315 LEU cc_start: 0.9328 (OUTLIER) cc_final: 0.9083 (mp) REVERT: Z 311 LYS cc_start: 0.9299 (ptpt) cc_final: 0.8775 (pttt) REVERT: Z 331 LYS cc_start: 0.9252 (mttt) cc_final: 0.8856 (mtpt) REVERT: Z 347 LYS cc_start: 0.8574 (ptpt) cc_final: 0.7939 (ptmm) REVERT: Z 353 LYS cc_start: 0.9369 (tttt) cc_final: 0.9069 (tttm) REVERT: Z 375 LYS cc_start: 0.9033 (tttt) cc_final: 0.8668 (ttmm) REVERT: 1 313 VAL cc_start: 0.9132 (t) cc_final: 0.8650 (p) REVERT: 1 331 LYS cc_start: 0.9394 (mtmm) cc_final: 0.9189 (mtmt) outliers start: 38 outliers final: 30 residues processed: 398 average time/residue: 0.2763 time to fit residues: 139.1238 Evaluate side-chains 414 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 382 time to evaluate : 0.906 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 351 GLN Chi-restraints excluded: chain A residue 352 SER Chi-restraints excluded: chain A residue 358 ASP Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain B residue 352 SER Chi-restraints excluded: chain B residue 358 ASP Chi-restraints excluded: chain C residue 339 VAL Chi-restraints excluded: chain C residue 358 ASP Chi-restraints excluded: chain D residue 319 THR Chi-restraints excluded: chain M residue 306 VAL Chi-restraints excluded: chain M residue 352 SER Chi-restraints excluded: chain M residue 358 ASP Chi-restraints excluded: chain N residue 339 VAL Chi-restraints excluded: chain N residue 352 SER Chi-restraints excluded: chain O residue 339 VAL Chi-restraints excluded: chain P residue 315 LEU Chi-restraints excluded: chain P residue 319 THR Chi-restraints excluded: chain Y residue 315 LEU Chi-restraints excluded: chain Y residue 339 VAL Chi-restraints excluded: chain Z residue 306 VAL Chi-restraints excluded: chain Z residue 319 THR Chi-restraints excluded: chain Z residue 351 GLN Chi-restraints excluded: chain Z residue 358 ASP Chi-restraints excluded: chain Z residue 373 THR Chi-restraints excluded: chain 0 residue 315 LEU Chi-restraints excluded: chain 0 residue 339 VAL Chi-restraints excluded: chain 0 residue 358 ASP Chi-restraints excluded: chain 0 residue 376 LEU Chi-restraints excluded: chain 1 residue 319 THR Chi-restraints excluded: chain 1 residue 358 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 9 optimal weight: 0.5980 chunk 14 optimal weight: 9.9990 chunk 80 optimal weight: 6.9990 chunk 1 optimal weight: 1.9990 chunk 77 optimal weight: 3.9990 chunk 74 optimal weight: 4.9990 chunk 28 optimal weight: 5.9990 chunk 4 optimal weight: 7.9990 chunk 71 optimal weight: 3.9990 chunk 79 optimal weight: 6.9990 chunk 45 optimal weight: 4.9990 overall best weight: 3.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 307 GLN M 327 ASN P 374 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4806 r_free = 0.4806 target = 0.192424 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3942 r_free = 0.3942 target = 0.122776 restraints weight = 9532.270| |-----------------------------------------------------------------------------| r_work (start): 0.3916 rms_B_bonded: 2.98 r_work: 0.3777 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3660 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3660 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8403 moved from start: 0.3903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 8784 Z= 0.230 Angle : 0.704 8.706 11772 Z= 0.344 Chirality : 0.049 0.157 1356 Planarity : 0.003 0.032 1440 Dihedral : 11.515 64.741 1520 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.78 % Favored : 91.22 % Rotamer: Outliers : 5.60 % Allowed : 25.87 % Favored : 68.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.43 (0.23), residues: 900 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.85 (0.17), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS M 374 PHE 0.012 0.003 PHE N 378 TYR 0.015 0.002 TYR M 310 ARG 0.006 0.001 ARG O 349 Details of bonding type rmsd hydrogen bonds : bond 0.02824 ( 300) hydrogen bonds : angle 5.17757 ( 852) covalent geometry : bond 0.00550 ( 8778) covalent geometry : angle 0.70431 (11772) Misc. bond : bond 0.00045 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 423 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 378 time to evaluate : 0.899 Fit side-chains revert: symmetry clash REVERT: A 344 LEU cc_start: 0.9434 (mp) cc_final: 0.9165 (mp) REVERT: A 353 LYS cc_start: 0.9406 (tttt) cc_final: 0.8993 (tttt) REVERT: B 331 LYS cc_start: 0.9303 (mttt) cc_final: 0.8978 (mtmt) REVERT: B 336 GLN cc_start: 0.9320 (tt0) cc_final: 0.8731 (tp40) REVERT: B 343 LYS cc_start: 0.9063 (mtpp) cc_final: 0.8807 (mtpp) REVERT: B 375 LYS cc_start: 0.9080 (tttt) cc_final: 0.8643 (ttmm) REVERT: C 314 ASP cc_start: 0.8920 (t0) cc_final: 0.8683 (t0) REVERT: C 342 GLU cc_start: 0.8988 (mt-10) cc_final: 0.8530 (mt-10) REVERT: C 375 LYS cc_start: 0.8954 (tttt) cc_final: 0.8687 (ttpt) REVERT: D 343 LYS cc_start: 0.9160 (mmtm) cc_final: 0.8820 (mmtp) REVERT: M 336 GLN cc_start: 0.9287 (tt0) cc_final: 0.9058 (tt0) REVERT: M 343 LYS cc_start: 0.8805 (mmtm) cc_final: 0.8212 (mtpp) REVERT: N 317 LYS cc_start: 0.8445 (ptpp) cc_final: 0.8131 (ptmm) REVERT: N 343 LYS cc_start: 0.8730 (mmtm) cc_final: 0.8260 (mmmm) REVERT: N 345 ASP cc_start: 0.8905 (m-30) cc_final: 0.8532 (m-30) REVERT: N 347 LYS cc_start: 0.8558 (ptpt) cc_final: 0.7959 (ptmm) REVERT: O 321 LYS cc_start: 0.9380 (mttt) cc_final: 0.9116 (mttp) REVERT: O 343 LYS cc_start: 0.9169 (mtpp) cc_final: 0.8417 (mttm) REVERT: O 375 LYS cc_start: 0.8889 (tttt) cc_final: 0.8435 (tttm) REVERT: P 313 VAL cc_start: 0.9214 (t) cc_final: 0.8808 (p) REVERT: P 315 LEU cc_start: 0.9313 (OUTLIER) cc_final: 0.9072 (mp) REVERT: Y 315 LEU cc_start: 0.9341 (OUTLIER) cc_final: 0.9110 (mp) REVERT: Z 311 LYS cc_start: 0.9332 (ptpt) cc_final: 0.8725 (pttt) REVERT: Z 331 LYS cc_start: 0.9270 (mttt) cc_final: 0.8887 (mtpt) REVERT: Z 347 LYS cc_start: 0.8552 (ptpt) cc_final: 0.7939 (ptmm) REVERT: Z 353 LYS cc_start: 0.9408 (tttt) cc_final: 0.9077 (tttm) REVERT: Z 375 LYS cc_start: 0.9010 (tttt) cc_final: 0.8648 (ttmm) REVERT: 0 343 LYS cc_start: 0.9011 (mtpp) cc_final: 0.8610 (mttm) outliers start: 45 outliers final: 39 residues processed: 388 average time/residue: 0.2623 time to fit residues: 129.4316 Evaluate side-chains 418 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 377 time to evaluate : 0.945 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 352 SER Chi-restraints excluded: chain A residue 358 ASP Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain B residue 352 SER Chi-restraints excluded: chain B residue 358 ASP Chi-restraints excluded: chain B residue 379 ARG Chi-restraints excluded: chain C residue 309 VAL Chi-restraints excluded: chain C residue 339 VAL Chi-restraints excluded: chain C residue 358 ASP Chi-restraints excluded: chain D residue 319 THR Chi-restraints excluded: chain M residue 306 VAL Chi-restraints excluded: chain M residue 315 LEU Chi-restraints excluded: chain M residue 352 SER Chi-restraints excluded: chain M residue 358 ASP Chi-restraints excluded: chain M residue 372 GLU Chi-restraints excluded: chain M residue 373 THR Chi-restraints excluded: chain N residue 306 VAL Chi-restraints excluded: chain N residue 339 VAL Chi-restraints excluded: chain O residue 339 VAL Chi-restraints excluded: chain P residue 315 LEU Chi-restraints excluded: chain P residue 319 THR Chi-restraints excluded: chain Y residue 306 VAL Chi-restraints excluded: chain Y residue 315 LEU Chi-restraints excluded: chain Y residue 339 VAL Chi-restraints excluded: chain Y residue 373 THR Chi-restraints excluded: chain Z residue 306 VAL Chi-restraints excluded: chain Z residue 319 THR Chi-restraints excluded: chain Z residue 320 SER Chi-restraints excluded: chain Z residue 351 GLN Chi-restraints excluded: chain Z residue 358 ASP Chi-restraints excluded: chain Z residue 373 THR Chi-restraints excluded: chain 0 residue 315 LEU Chi-restraints excluded: chain 0 residue 339 VAL Chi-restraints excluded: chain 0 residue 358 ASP Chi-restraints excluded: chain 0 residue 376 LEU Chi-restraints excluded: chain 1 residue 315 LEU Chi-restraints excluded: chain 1 residue 319 THR Chi-restraints excluded: chain 1 residue 358 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 48 optimal weight: 0.9990 chunk 54 optimal weight: 2.9990 chunk 64 optimal weight: 6.9990 chunk 79 optimal weight: 1.9990 chunk 22 optimal weight: 10.0000 chunk 33 optimal weight: 5.9990 chunk 60 optimal weight: 0.0570 chunk 23 optimal weight: 7.9990 chunk 19 optimal weight: 0.6980 chunk 75 optimal weight: 3.9990 chunk 44 optimal weight: 1.9990 overall best weight: 1.1504 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 307 GLN A 327 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4814 r_free = 0.4814 target = 0.193977 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4021 r_free = 0.4021 target = 0.126885 restraints weight = 9746.780| |-----------------------------------------------------------------------------| r_work (start): 0.4007 rms_B_bonded: 2.97 r_work: 0.3873 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3767 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3767 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8209 moved from start: 0.4018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8784 Z= 0.114 Angle : 0.634 7.907 11772 Z= 0.309 Chirality : 0.047 0.136 1356 Planarity : 0.002 0.034 1440 Dihedral : 11.258 64.094 1520 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.00 % Favored : 94.00 % Rotamer: Outliers : 4.98 % Allowed : 26.87 % Favored : 68.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.35 (0.23), residues: 900 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.78 (0.17), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS N 374 PHE 0.016 0.002 PHE N 378 TYR 0.009 0.001 TYR M 310 ARG 0.006 0.001 ARG O 349 Details of bonding type rmsd hydrogen bonds : bond 0.02072 ( 300) hydrogen bonds : angle 4.87832 ( 852) covalent geometry : bond 0.00266 ( 8778) covalent geometry : angle 0.63366 (11772) Misc. bond : bond 0.00021 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 436 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 396 time to evaluate : 0.974 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 344 LEU cc_start: 0.9378 (mp) cc_final: 0.9138 (mp) REVERT: A 353 LYS cc_start: 0.9239 (tttt) cc_final: 0.8753 (tttt) REVERT: B 331 LYS cc_start: 0.9173 (mttt) cc_final: 0.8872 (mtmt) REVERT: B 336 GLN cc_start: 0.9210 (tt0) cc_final: 0.8518 (tp40) REVERT: B 343 LYS cc_start: 0.8953 (mtpp) cc_final: 0.8673 (mtpp) REVERT: B 353 LYS cc_start: 0.9196 (tttm) cc_final: 0.8783 (tttp) REVERT: B 375 LYS cc_start: 0.8950 (tttt) cc_final: 0.8567 (ttmm) REVERT: C 314 ASP cc_start: 0.8902 (t0) cc_final: 0.8589 (t0) REVERT: C 342 GLU cc_start: 0.8912 (mt-10) cc_final: 0.8489 (mt-10) REVERT: C 375 LYS cc_start: 0.8881 (tttt) cc_final: 0.8430 (ttpt) REVERT: D 343 LYS cc_start: 0.9021 (mmtm) cc_final: 0.8697 (mmtp) REVERT: M 331 LYS cc_start: 0.9348 (mttt) cc_final: 0.9086 (mtmt) REVERT: M 336 GLN cc_start: 0.9264 (tt0) cc_final: 0.8918 (tt0) REVERT: M 343 LYS cc_start: 0.8751 (mmtm) cc_final: 0.8407 (ttmm) REVERT: N 343 LYS cc_start: 0.8598 (mmtm) cc_final: 0.8115 (mmmm) REVERT: N 345 ASP cc_start: 0.8807 (m-30) cc_final: 0.8600 (m-30) REVERT: O 321 LYS cc_start: 0.9405 (mttt) cc_final: 0.9128 (mttp) REVERT: O 343 LYS cc_start: 0.9135 (mtpp) cc_final: 0.8258 (mttm) REVERT: O 375 LYS cc_start: 0.8849 (tttt) cc_final: 0.8365 (tttm) REVERT: P 313 VAL cc_start: 0.9062 (t) cc_final: 0.8588 (p) REVERT: P 315 LEU cc_start: 0.9240 (OUTLIER) cc_final: 0.8973 (mp) REVERT: P 331 LYS cc_start: 0.9296 (mttt) cc_final: 0.7513 (tmtt) REVERT: Y 315 LEU cc_start: 0.9316 (OUTLIER) cc_final: 0.9062 (mp) REVERT: Z 311 LYS cc_start: 0.9319 (ptpt) cc_final: 0.8673 (pttt) REVERT: Z 317 LYS cc_start: 0.8180 (ptpt) cc_final: 0.7830 (ptmm) REVERT: Z 331 LYS cc_start: 0.9159 (mttt) cc_final: 0.8677 (mtpt) REVERT: Z 347 LYS cc_start: 0.8531 (ptpt) cc_final: 0.7839 (ptmm) REVERT: Z 353 LYS cc_start: 0.9258 (tttt) cc_final: 0.8899 (tttm) REVERT: Z 375 LYS cc_start: 0.8895 (tttt) cc_final: 0.8528 (ttmm) REVERT: 0 314 ASP cc_start: 0.8568 (t0) cc_final: 0.8167 (t0) REVERT: 0 343 LYS cc_start: 0.8930 (mtpp) cc_final: 0.8347 (mttm) REVERT: 1 313 VAL cc_start: 0.8998 (t) cc_final: 0.8504 (p) outliers start: 40 outliers final: 32 residues processed: 400 average time/residue: 0.2686 time to fit residues: 136.1996 Evaluate side-chains 427 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 393 time to evaluate : 0.899 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 351 GLN Chi-restraints excluded: chain A residue 352 SER Chi-restraints excluded: chain A residue 358 ASP Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain B residue 358 ASP Chi-restraints excluded: chain B residue 379 ARG Chi-restraints excluded: chain C residue 309 VAL Chi-restraints excluded: chain C residue 339 VAL Chi-restraints excluded: chain C residue 358 ASP Chi-restraints excluded: chain D residue 319 THR Chi-restraints excluded: chain M residue 306 VAL Chi-restraints excluded: chain M residue 352 SER Chi-restraints excluded: chain M residue 358 ASP Chi-restraints excluded: chain N residue 339 VAL Chi-restraints excluded: chain O residue 339 VAL Chi-restraints excluded: chain O residue 342 GLU Chi-restraints excluded: chain P residue 315 LEU Chi-restraints excluded: chain P residue 319 THR Chi-restraints excluded: chain P residue 358 ASP Chi-restraints excluded: chain Y residue 315 LEU Chi-restraints excluded: chain Y residue 339 VAL Chi-restraints excluded: chain Z residue 306 VAL Chi-restraints excluded: chain Z residue 319 THR Chi-restraints excluded: chain Z residue 320 SER Chi-restraints excluded: chain Z residue 351 GLN Chi-restraints excluded: chain Z residue 358 ASP Chi-restraints excluded: chain Z residue 373 THR Chi-restraints excluded: chain 0 residue 339 VAL Chi-restraints excluded: chain 0 residue 358 ASP Chi-restraints excluded: chain 0 residue 376 LEU Chi-restraints excluded: chain 1 residue 319 THR Chi-restraints excluded: chain 1 residue 358 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 27 optimal weight: 8.9990 chunk 29 optimal weight: 7.9990 chunk 16 optimal weight: 7.9990 chunk 23 optimal weight: 0.7980 chunk 30 optimal weight: 4.9990 chunk 3 optimal weight: 7.9990 chunk 33 optimal weight: 6.9990 chunk 64 optimal weight: 9.9990 chunk 15 optimal weight: 5.9990 chunk 9 optimal weight: 0.9990 chunk 13 optimal weight: 0.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 307 GLN ** A 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 327 ASN ** 0 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4778 r_free = 0.4778 target = 0.190416 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.123446 restraints weight = 9919.528| |-----------------------------------------------------------------------------| r_work (start): 0.3963 rms_B_bonded: 2.95 r_work: 0.3827 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3721 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.3721 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8261 moved from start: 0.4063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 8784 Z= 0.207 Angle : 0.693 8.148 11772 Z= 0.337 Chirality : 0.048 0.160 1356 Planarity : 0.003 0.042 1440 Dihedral : 11.355 64.044 1520 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 8.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.56 % Favored : 91.44 % Rotamer: Outliers : 4.98 % Allowed : 26.74 % Favored : 68.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.41 (0.23), residues: 900 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.83 (0.17), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS M 374 PHE 0.014 0.003 PHE C 378 TYR 0.013 0.002 TYR M 310 ARG 0.007 0.001 ARG O 349 Details of bonding type rmsd hydrogen bonds : bond 0.02617 ( 300) hydrogen bonds : angle 5.01979 ( 852) covalent geometry : bond 0.00496 ( 8778) covalent geometry : angle 0.69259 (11772) Misc. bond : bond 0.00043 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 430 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 390 time to evaluate : 0.921 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 344 LEU cc_start: 0.9381 (mp) cc_final: 0.9106 (mp) REVERT: A 353 LYS cc_start: 0.9277 (tttt) cc_final: 0.8893 (tttt) REVERT: B 331 LYS cc_start: 0.9219 (mttt) cc_final: 0.8902 (mtmt) REVERT: B 336 GLN cc_start: 0.9253 (tt0) cc_final: 0.8576 (tp40) REVERT: B 343 LYS cc_start: 0.9031 (mtpp) cc_final: 0.8756 (mtpp) REVERT: B 353 LYS cc_start: 0.9242 (tttm) cc_final: 0.8912 (tttp) REVERT: B 375 LYS cc_start: 0.8981 (tttt) cc_final: 0.8608 (ttmm) REVERT: C 314 ASP cc_start: 0.8945 (t0) cc_final: 0.8663 (t0) REVERT: C 342 GLU cc_start: 0.8928 (mt-10) cc_final: 0.8523 (mt-10) REVERT: D 343 LYS cc_start: 0.9095 (mmtm) cc_final: 0.8709 (mmtp) REVERT: M 336 GLN cc_start: 0.9286 (tt0) cc_final: 0.8994 (tt0) REVERT: M 343 LYS cc_start: 0.8745 (mmtm) cc_final: 0.8403 (ttmm) REVERT: N 343 LYS cc_start: 0.8578 (mmtm) cc_final: 0.8086 (mmmt) REVERT: N 345 ASP cc_start: 0.8792 (m-30) cc_final: 0.8412 (m-30) REVERT: N 347 LYS cc_start: 0.8675 (ptpt) cc_final: 0.7921 (ptmm) REVERT: O 321 LYS cc_start: 0.9371 (mttt) cc_final: 0.9082 (mttp) REVERT: O 343 LYS cc_start: 0.9114 (mtpp) cc_final: 0.8265 (mttm) REVERT: O 375 LYS cc_start: 0.8885 (tttt) cc_final: 0.8370 (tttm) REVERT: P 313 VAL cc_start: 0.9127 (t) cc_final: 0.8673 (p) REVERT: P 315 LEU cc_start: 0.9241 (OUTLIER) cc_final: 0.8952 (mp) REVERT: Y 315 LEU cc_start: 0.9312 (OUTLIER) cc_final: 0.9087 (mp) REVERT: Z 311 LYS cc_start: 0.9337 (ptpt) cc_final: 0.8664 (pttt) REVERT: Z 331 LYS cc_start: 0.9188 (mttt) cc_final: 0.8732 (mtpt) REVERT: Z 347 LYS cc_start: 0.8610 (ptpt) cc_final: 0.7923 (ptmm) REVERT: Z 353 LYS cc_start: 0.9305 (tttt) cc_final: 0.8922 (tttm) REVERT: Z 375 LYS cc_start: 0.8921 (tttt) cc_final: 0.8557 (ttmm) REVERT: Z 379 ARG cc_start: 0.7865 (ptt90) cc_final: 0.7322 (ptt90) REVERT: 0 314 ASP cc_start: 0.8609 (t0) cc_final: 0.8122 (t0) REVERT: 0 343 LYS cc_start: 0.8956 (mtpp) cc_final: 0.8509 (mttm) REVERT: 1 313 VAL cc_start: 0.9104 (t) cc_final: 0.8637 (p) outliers start: 40 outliers final: 37 residues processed: 400 average time/residue: 0.2742 time to fit residues: 138.7798 Evaluate side-chains 429 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 390 time to evaluate : 1.066 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 351 GLN Chi-restraints excluded: chain A residue 352 SER Chi-restraints excluded: chain A residue 358 ASP Chi-restraints excluded: chain B residue 320 SER Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain B residue 352 SER Chi-restraints excluded: chain B residue 358 ASP Chi-restraints excluded: chain B residue 379 ARG Chi-restraints excluded: chain C residue 309 VAL Chi-restraints excluded: chain C residue 339 VAL Chi-restraints excluded: chain D residue 319 THR Chi-restraints excluded: chain M residue 306 VAL Chi-restraints excluded: chain M residue 315 LEU Chi-restraints excluded: chain M residue 352 SER Chi-restraints excluded: chain M residue 358 ASP Chi-restraints excluded: chain M residue 372 GLU Chi-restraints excluded: chain M residue 373 THR Chi-restraints excluded: chain N residue 306 VAL Chi-restraints excluded: chain N residue 339 VAL Chi-restraints excluded: chain O residue 339 VAL Chi-restraints excluded: chain P residue 315 LEU Chi-restraints excluded: chain P residue 319 THR Chi-restraints excluded: chain P residue 358 ASP Chi-restraints excluded: chain Y residue 315 LEU Chi-restraints excluded: chain Y residue 339 VAL Chi-restraints excluded: chain Z residue 306 VAL Chi-restraints excluded: chain Z residue 315 LEU Chi-restraints excluded: chain Z residue 319 THR Chi-restraints excluded: chain Z residue 320 SER Chi-restraints excluded: chain Z residue 358 ASP Chi-restraints excluded: chain Z residue 373 THR Chi-restraints excluded: chain 0 residue 339 VAL Chi-restraints excluded: chain 0 residue 358 ASP Chi-restraints excluded: chain 0 residue 376 LEU Chi-restraints excluded: chain 1 residue 315 LEU Chi-restraints excluded: chain 1 residue 319 THR Chi-restraints excluded: chain 1 residue 358 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 43 optimal weight: 10.0000 chunk 54 optimal weight: 4.9990 chunk 47 optimal weight: 0.9980 chunk 4 optimal weight: 4.9990 chunk 21 optimal weight: 3.9990 chunk 8 optimal weight: 9.9990 chunk 83 optimal weight: 2.9990 chunk 35 optimal weight: 5.9990 chunk 37 optimal weight: 5.9990 chunk 44 optimal weight: 7.9990 chunk 64 optimal weight: 4.9990 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 307 GLN ** B 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4765 r_free = 0.4765 target = 0.188828 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.121316 restraints weight = 9833.425| |-----------------------------------------------------------------------------| r_work (start): 0.3926 rms_B_bonded: 2.97 r_work: 0.3790 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3684 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3684 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8289 moved from start: 0.4158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.065 8784 Z= 0.262 Angle : 0.750 8.944 11772 Z= 0.364 Chirality : 0.050 0.173 1356 Planarity : 0.003 0.047 1440 Dihedral : 11.464 64.221 1520 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.33 % Favored : 91.67 % Rotamer: Outliers : 5.60 % Allowed : 26.49 % Favored : 67.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.50 (0.23), residues: 900 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.90 (0.17), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS 0 329 PHE 0.017 0.003 PHE N 378 TYR 0.015 0.002 TYR M 310 ARG 0.007 0.001 ARG O 349 Details of bonding type rmsd hydrogen bonds : bond 0.02904 ( 300) hydrogen bonds : angle 5.14079 ( 852) covalent geometry : bond 0.00631 ( 8778) covalent geometry : angle 0.74955 (11772) Misc. bond : bond 0.00057 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 428 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 383 time to evaluate : 0.976 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 344 LEU cc_start: 0.9369 (mp) cc_final: 0.9081 (mp) REVERT: A 353 LYS cc_start: 0.9298 (tttt) cc_final: 0.8907 (tttt) REVERT: B 331 LYS cc_start: 0.9227 (mttt) cc_final: 0.8943 (mtmt) REVERT: B 336 GLN cc_start: 0.9245 (tt0) cc_final: 0.8631 (tp40) REVERT: B 343 LYS cc_start: 0.9042 (mtpp) cc_final: 0.8770 (mtpp) REVERT: B 353 LYS cc_start: 0.9252 (tttm) cc_final: 0.8882 (tttp) REVERT: B 375 LYS cc_start: 0.8997 (tttt) cc_final: 0.8619 (ttmm) REVERT: C 314 ASP cc_start: 0.8943 (t0) cc_final: 0.8688 (t0) REVERT: C 342 GLU cc_start: 0.8972 (mt-10) cc_final: 0.8555 (mt-10) REVERT: D 343 LYS cc_start: 0.9138 (mmtm) cc_final: 0.8865 (mmtp) REVERT: M 336 GLN cc_start: 0.9287 (tt0) cc_final: 0.9000 (tt0) REVERT: M 343 LYS cc_start: 0.8771 (mmtm) cc_final: 0.8424 (ttmm) REVERT: N 343 LYS cc_start: 0.8655 (mmtm) cc_final: 0.8173 (mmmm) REVERT: N 345 ASP cc_start: 0.8823 (m-30) cc_final: 0.8451 (m-30) REVERT: N 347 LYS cc_start: 0.8687 (ptpt) cc_final: 0.7968 (ptmm) REVERT: O 321 LYS cc_start: 0.9377 (mttt) cc_final: 0.9095 (mttp) REVERT: O 343 LYS cc_start: 0.9099 (mtpp) cc_final: 0.8332 (mttm) REVERT: O 375 LYS cc_start: 0.8854 (tttt) cc_final: 0.8337 (tttm) REVERT: P 313 VAL cc_start: 0.9178 (t) cc_final: 0.8758 (p) REVERT: P 315 LEU cc_start: 0.9236 (OUTLIER) cc_final: 0.8995 (mp) REVERT: Y 315 LEU cc_start: 0.9300 (OUTLIER) cc_final: 0.9073 (mp) REVERT: Z 311 LYS cc_start: 0.9355 (ptpt) cc_final: 0.8690 (pttt) REVERT: Z 331 LYS cc_start: 0.9224 (mttt) cc_final: 0.8765 (mtpt) REVERT: Z 347 LYS cc_start: 0.8605 (ptpt) cc_final: 0.7896 (ptmm) REVERT: Z 353 LYS cc_start: 0.9332 (tttt) cc_final: 0.8964 (tttm) REVERT: Z 375 LYS cc_start: 0.8952 (tttt) cc_final: 0.8539 (ttmm) REVERT: Z 379 ARG cc_start: 0.7864 (ptt90) cc_final: 0.7291 (ptt90) REVERT: 0 343 LYS cc_start: 0.8990 (mtpp) cc_final: 0.8607 (mttm) REVERT: 0 378 PHE cc_start: 0.8867 (t80) cc_final: 0.8450 (t80) REVERT: 1 331 LYS cc_start: 0.9407 (mtmm) cc_final: 0.9165 (mtmt) outliers start: 45 outliers final: 40 residues processed: 393 average time/residue: 0.2678 time to fit residues: 133.4179 Evaluate side-chains 419 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 377 time to evaluate : 0.944 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 351 GLN Chi-restraints excluded: chain A residue 352 SER Chi-restraints excluded: chain A residue 358 ASP Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain B residue 320 SER Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain B residue 352 SER Chi-restraints excluded: chain B residue 358 ASP Chi-restraints excluded: chain B residue 379 ARG Chi-restraints excluded: chain C residue 309 VAL Chi-restraints excluded: chain C residue 339 VAL Chi-restraints excluded: chain D residue 319 THR Chi-restraints excluded: chain M residue 306 VAL Chi-restraints excluded: chain M residue 315 LEU Chi-restraints excluded: chain M residue 352 SER Chi-restraints excluded: chain M residue 358 ASP Chi-restraints excluded: chain M residue 372 GLU Chi-restraints excluded: chain M residue 373 THR Chi-restraints excluded: chain N residue 306 VAL Chi-restraints excluded: chain N residue 319 THR Chi-restraints excluded: chain N residue 339 VAL Chi-restraints excluded: chain O residue 339 VAL Chi-restraints excluded: chain O residue 340 LYS Chi-restraints excluded: chain O residue 342 GLU Chi-restraints excluded: chain P residue 315 LEU Chi-restraints excluded: chain P residue 319 THR Chi-restraints excluded: chain Y residue 315 LEU Chi-restraints excluded: chain Y residue 339 VAL Chi-restraints excluded: chain Z residue 306 VAL Chi-restraints excluded: chain Z residue 315 LEU Chi-restraints excluded: chain Z residue 319 THR Chi-restraints excluded: chain Z residue 320 SER Chi-restraints excluded: chain Z residue 351 GLN Chi-restraints excluded: chain Z residue 358 ASP Chi-restraints excluded: chain Z residue 373 THR Chi-restraints excluded: chain 0 residue 339 VAL Chi-restraints excluded: chain 0 residue 358 ASP Chi-restraints excluded: chain 0 residue 376 LEU Chi-restraints excluded: chain 1 residue 319 THR Chi-restraints excluded: chain 1 residue 358 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 78 optimal weight: 7.9990 chunk 35 optimal weight: 0.0980 chunk 79 optimal weight: 0.9980 chunk 45 optimal weight: 4.9990 chunk 44 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 chunk 49 optimal weight: 8.9990 chunk 41 optimal weight: 0.7980 chunk 11 optimal weight: 8.9990 chunk 59 optimal weight: 0.0570 chunk 54 optimal weight: 2.9990 overall best weight: 0.7900 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 307 GLN 0 362 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4828 r_free = 0.4828 target = 0.194883 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4045 r_free = 0.4045 target = 0.128324 restraints weight = 9715.016| |-----------------------------------------------------------------------------| r_work (start): 0.4059 rms_B_bonded: 2.94 r_work: 0.3923 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3820 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.3820 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8213 moved from start: 0.4348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 8784 Z= 0.103 Angle : 0.663 8.622 11772 Z= 0.317 Chirality : 0.047 0.134 1356 Planarity : 0.003 0.043 1440 Dihedral : 11.044 63.571 1520 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.44 % Favored : 93.56 % Rotamer: Outliers : 3.73 % Allowed : 28.61 % Favored : 67.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.36 (0.23), residues: 900 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.79 (0.17), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS C 374 PHE 0.013 0.002 PHE Z 378 TYR 0.012 0.002 TYR P 310 ARG 0.007 0.001 ARG O 349 Details of bonding type rmsd hydrogen bonds : bond 0.01969 ( 300) hydrogen bonds : angle 4.78131 ( 852) covalent geometry : bond 0.00233 ( 8778) covalent geometry : angle 0.66268 (11772) Misc. bond : bond 0.00023 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 420 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 390 time to evaluate : 1.007 Fit side-chains revert: symmetry clash REVERT: A 344 LEU cc_start: 0.9435 (mp) cc_final: 0.9185 (mp) REVERT: A 353 LYS cc_start: 0.9260 (tttt) cc_final: 0.8788 (tttt) REVERT: B 311 LYS cc_start: 0.9236 (ptpt) cc_final: 0.8683 (pttt) REVERT: B 331 LYS cc_start: 0.9179 (mttt) cc_final: 0.8928 (mtmt) REVERT: B 336 GLN cc_start: 0.9139 (tt0) cc_final: 0.8478 (tp40) REVERT: B 343 LYS cc_start: 0.8990 (mtpp) cc_final: 0.8731 (mtpp) REVERT: B 353 LYS cc_start: 0.9233 (tttm) cc_final: 0.8830 (tttp) REVERT: B 375 LYS cc_start: 0.8958 (tttt) cc_final: 0.8585 (ttmm) REVERT: C 314 ASP cc_start: 0.8830 (t0) cc_final: 0.8568 (t0) REVERT: C 342 GLU cc_start: 0.8837 (mt-10) cc_final: 0.8606 (mt-10) REVERT: D 343 LYS cc_start: 0.9021 (mmtm) cc_final: 0.8643 (mmtp) REVERT: M 331 LYS cc_start: 0.9345 (mttt) cc_final: 0.9106 (mtmt) REVERT: M 336 GLN cc_start: 0.9253 (tt0) cc_final: 0.8869 (tt0) REVERT: M 343 LYS cc_start: 0.8787 (mmtm) cc_final: 0.8463 (mmtt) REVERT: N 343 LYS cc_start: 0.8605 (mmtm) cc_final: 0.8274 (mmmt) REVERT: O 321 LYS cc_start: 0.9390 (mttt) cc_final: 0.9114 (mttp) REVERT: O 343 LYS cc_start: 0.9063 (mtpp) cc_final: 0.8238 (mttm) REVERT: O 344 LEU cc_start: 0.9541 (mp) cc_final: 0.9323 (mp) REVERT: O 375 LYS cc_start: 0.8841 (tttt) cc_final: 0.8323 (tttm) REVERT: P 315 LEU cc_start: 0.9202 (OUTLIER) cc_final: 0.8933 (mp) REVERT: P 331 LYS cc_start: 0.9262 (mttt) cc_final: 0.7560 (tmtt) REVERT: Y 315 LEU cc_start: 0.9285 (OUTLIER) cc_final: 0.9019 (mp) REVERT: Z 311 LYS cc_start: 0.9294 (ptpt) cc_final: 0.8648 (pttt) REVERT: Z 317 LYS cc_start: 0.8216 (ptpt) cc_final: 0.7858 (ptmm) REVERT: Z 331 LYS cc_start: 0.9160 (mttt) cc_final: 0.8788 (mtpt) REVERT: Z 347 LYS cc_start: 0.8537 (ptpt) cc_final: 0.7878 (ptmm) REVERT: Z 353 LYS cc_start: 0.9290 (tttt) cc_final: 0.8952 (tttm) REVERT: Z 375 LYS cc_start: 0.8908 (tttt) cc_final: 0.8538 (ttmm) REVERT: 0 314 ASP cc_start: 0.8539 (t0) cc_final: 0.8155 (t0) REVERT: 0 343 LYS cc_start: 0.8885 (mtpp) cc_final: 0.8432 (mttm) REVERT: 0 378 PHE cc_start: 0.8839 (t80) cc_final: 0.8424 (t80) REVERT: 1 313 VAL cc_start: 0.8940 (t) cc_final: 0.8462 (p) REVERT: 1 331 LYS cc_start: 0.9351 (mtmm) cc_final: 0.8969 (mtmt) REVERT: 1 375 LYS cc_start: 0.8375 (tttt) cc_final: 0.8060 (tttt) outliers start: 30 outliers final: 26 residues processed: 397 average time/residue: 0.2744 time to fit residues: 137.8770 Evaluate side-chains 416 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 388 time to evaluate : 1.020 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 351 GLN Chi-restraints excluded: chain A residue 352 SER Chi-restraints excluded: chain A residue 358 ASP Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain B residue 352 SER Chi-restraints excluded: chain B residue 358 ASP Chi-restraints excluded: chain B residue 379 ARG Chi-restraints excluded: chain C residue 309 VAL Chi-restraints excluded: chain C residue 339 VAL Chi-restraints excluded: chain D residue 319 THR Chi-restraints excluded: chain M residue 352 SER Chi-restraints excluded: chain M residue 358 ASP Chi-restraints excluded: chain N residue 339 VAL Chi-restraints excluded: chain O residue 339 VAL Chi-restraints excluded: chain P residue 315 LEU Chi-restraints excluded: chain P residue 319 THR Chi-restraints excluded: chain Y residue 315 LEU Chi-restraints excluded: chain Y residue 339 VAL Chi-restraints excluded: chain Z residue 320 SER Chi-restraints excluded: chain Z residue 351 GLN Chi-restraints excluded: chain Z residue 358 ASP Chi-restraints excluded: chain Z residue 373 THR Chi-restraints excluded: chain 0 residue 339 VAL Chi-restraints excluded: chain 0 residue 358 ASP Chi-restraints excluded: chain 0 residue 376 LEU Chi-restraints excluded: chain 1 residue 358 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 48 optimal weight: 8.9990 chunk 75 optimal weight: 5.9990 chunk 72 optimal weight: 5.9990 chunk 20 optimal weight: 9.9990 chunk 65 optimal weight: 6.9990 chunk 41 optimal weight: 1.9990 chunk 68 optimal weight: 4.9990 chunk 30 optimal weight: 6.9990 chunk 17 optimal weight: 6.9990 chunk 43 optimal weight: 10.0000 chunk 81 optimal weight: 9.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 307 GLN C 336 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4749 r_free = 0.4749 target = 0.186775 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.118750 restraints weight = 9964.232| |-----------------------------------------------------------------------------| r_work (start): 0.3914 rms_B_bonded: 2.99 r_work: 0.3779 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3674 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3674 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8314 moved from start: 0.4265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.081 8784 Z= 0.368 Angle : 0.820 8.851 11772 Z= 0.402 Chirality : 0.051 0.150 1356 Planarity : 0.003 0.049 1440 Dihedral : 11.535 64.286 1520 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 9.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.56 % Favored : 90.44 % Rotamer: Outliers : 4.48 % Allowed : 27.24 % Favored : 68.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.55 (0.22), residues: 900 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.94 (0.17), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS 0 329 PHE 0.014 0.003 PHE Z 378 TYR 0.017 0.002 TYR M 310 ARG 0.007 0.001 ARG O 349 Details of bonding type rmsd hydrogen bonds : bond 0.03399 ( 300) hydrogen bonds : angle 5.33893 ( 852) covalent geometry : bond 0.00888 ( 8778) covalent geometry : angle 0.81988 (11772) Misc. bond : bond 0.00076 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6788.29 seconds wall clock time: 118 minutes 29.78 seconds (7109.78 seconds total)