Starting phenix.real_space_refine on Mon May 12 06:21:01 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9b4l_44184/05_2025/9b4l_44184.cif Found real_map, /net/cci-nas-00/data/ceres_data/9b4l_44184/05_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_44184/05_2025/9b4l_44184.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9b4l_44184/05_2025/9b4l_44184.map" model { file = "/net/cci-nas-00/data/ceres_data/9b4l_44184/05_2025/9b4l_44184.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9b4l_44184/05_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-5687/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: 7.47, per 1000 atoms: 0.86 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: 2.08 Conformation dependent library (CDL) restraints added in 779.5 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: 1.37 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: 2.52 Time building geometry restraints manager: 2.28 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: 4.290 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.390 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 24.180 Find NCS groups from input model: 0.700 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.550 ------------------------------------------------------------------------------- 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 : 0.830 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: 0.2746 time to fit residues: 156.7437 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 : 0.948 ------------------------------------------------------------------------------- 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 = 46)----------------| | r_work = 0.4083 r_free = 0.4083 target = 0.132739 restraints weight = 9399.274| |-----------------------------------------------------------------------------| r_work (start): 0.4037 rms_B_bonded: 2.89 r_work: 0.3897 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.3777 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3777 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8285 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 : 0.847 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: 0.8569 (ptpt) REVERT: A 324 SER cc_start: 0.8900 (t) cc_final: 0.8634 (m) REVERT: A 331 LYS cc_start: 0.9296 (mttt) cc_final: 0.9026 (mtpt) REVERT: A 344 LEU cc_start: 0.9417 (mp) cc_final: 0.9214 (mp) REVERT: A 353 LYS cc_start: 0.9264 (tttt) cc_final: 0.8852 (tttt) REVERT: B 321 LYS cc_start: 0.9396 (mttt) cc_final: 0.9174 (mttm) REVERT: B 331 LYS cc_start: 0.9383 (mttt) cc_final: 0.9076 (mtmt) REVERT: B 343 LYS cc_start: 0.8806 (mtpp) cc_final: 0.8568 (mtpp) REVERT: C 314 ASP cc_start: 0.8798 (t0) cc_final: 0.8402 (t0) REVERT: C 321 LYS cc_start: 0.9286 (mttt) cc_final: 0.9066 (mttp) REVERT: C 331 LYS cc_start: 0.9391 (mttt) cc_final: 0.9190 (mttm) REVERT: C 343 LYS cc_start: 0.8893 (mmtm) cc_final: 0.8356 (mptt) REVERT: C 347 LYS cc_start: 0.8480 (ptpt) cc_final: 0.8268 (ptpt) REVERT: C 349 ARG cc_start: 0.8022 (mtm-85) cc_final: 0.7744 (mtm-85) REVERT: C 375 LYS cc_start: 0.8986 (tttt) cc_final: 0.8758 (tttt) REVERT: D 327 ASN cc_start: 0.9222 (t0) cc_final: 0.9009 (t0) REVERT: D 343 LYS cc_start: 0.8913 (mmtm) cc_final: 0.8687 (mptt) REVERT: M 325 LEU cc_start: 0.9345 (tp) cc_final: 0.9077 (tp) REVERT: M 331 LYS cc_start: 0.9365 (mttt) cc_final: 0.9133 (mtmt) REVERT: M 343 LYS cc_start: 0.8613 (mmtm) cc_final: 0.8272 (mmtm) REVERT: N 317 LYS cc_start: 0.8288 (ptpp) cc_final: 0.8003 (ptmt) REVERT: N 331 LYS cc_start: 0.9374 (mttt) cc_final: 0.9160 (mtpt) REVERT: N 343 LYS cc_start: 0.8380 (mmtm) cc_final: 0.8025 (mtpp) REVERT: N 349 ARG cc_start: 0.7913 (mtm-85) cc_final: 0.7666 (mtm-85) REVERT: O 321 LYS cc_start: 0.9405 (mttt) cc_final: 0.9100 (mttp) REVERT: O 342 GLU cc_start: 0.6969 (OUTLIER) cc_final: 0.6593 (pt0) REVERT: O 375 LYS cc_start: 0.8864 (tttt) cc_final: 0.8593 (tttt) REVERT: P 313 VAL cc_start: 0.9176 (t) cc_final: 0.8763 (p) REVERT: P 331 LYS cc_start: 0.9367 (mttt) cc_final: 0.7719 (tmtt) REVERT: Y 314 ASP cc_start: 0.8967 (t0) cc_final: 0.8764 (t0) REVERT: Z 321 LYS cc_start: 0.9359 (mttt) cc_final: 0.9108 (mttp) REVERT: Z 331 LYS cc_start: 0.9334 (mttt) cc_final: 0.8915 (mtpt) REVERT: Z 353 LYS cc_start: 0.9291 (tttt) cc_final: 0.8978 (tttm) REVERT: Z 356 SER cc_start: 0.9416 (p) cc_final: 0.9073 (p) REVERT: Z 375 LYS cc_start: 0.9079 (tttt) cc_final: 0.8691 (ttmm) REVERT: 0 310 TYR cc_start: 0.8800 (t80) cc_final: 0.8210 (t80) REVERT: 0 343 LYS cc_start: 0.8761 (mtpp) cc_final: 0.8521 (mttp) REVERT: 0 375 LYS cc_start: 0.8967 (tttt) cc_final: 0.8684 (tttm) REVERT: 1 314 ASP cc_start: 0.9031 (t0) cc_final: 0.8749 (t0) REVERT: 1 343 LYS cc_start: 0.8996 (mmtm) cc_final: 0.8778 (mptt) outliers start: 24 outliers final: 14 residues processed: 424 average time/residue: 0.2677 time to fit residues: 143.3449 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 : 0.929 ------------------------------------------------------------------------------- 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: 0.7980 chunk 7 optimal weight: 10.0000 chunk 21 optimal weight: 0.2980 chunk 47 optimal weight: 2.9990 chunk 66 optimal weight: 6.9990 overall best weight: 2.0186 ------------------------------------------------------------------------------- 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 = 0.4846 r_free = 0.4846 target = 0.196656 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.126901 restraints weight = 9626.183| |-----------------------------------------------------------------------------| r_work (start): 0.3962 rms_B_bonded: 2.97 r_work: 0.3821 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.3701 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3701 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8325 moved from start: 0.2986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 8784 Z= 0.162 Angle : 0.645 6.746 11772 Z= 0.316 Chirality : 0.048 0.185 1356 Planarity : 0.003 0.025 1440 Dihedral : 11.652 65.461 1537 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.44 % Favored : 91.56 % Rotamer: Outliers : 4.10 % Allowed : 21.64 % Favored : 74.25 % 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 0.011 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 0.02824 ( 300) hydrogen bonds : angle 5.66525 ( 852) covalent geometry : bond 0.00387 ( 8778) covalent geometry : angle 0.64463 (11772) Misc. bond : bond 0.00018 ( 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 444 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 411 time to evaluate : 0.861 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 324 SER cc_start: 0.9131 (t) cc_final: 0.8855 (m) REVERT: A 344 LEU cc_start: 0.9417 (mp) cc_final: 0.9196 (mp) REVERT: B 331 LYS cc_start: 0.9316 (mttt) cc_final: 0.8966 (mtmt) REVERT: B 343 LYS cc_start: 0.8902 (mtpp) cc_final: 0.8636 (mtpp) REVERT: B 353 LYS cc_start: 0.9213 (tttm) cc_final: 0.8998 (tttm) REVERT: B 375 LYS cc_start: 0.9097 (tttt) cc_final: 0.8699 (ttmm) REVERT: C 308 ILE cc_start: 0.9104 (mt) cc_final: 0.8895 (mm) REVERT: C 314 ASP cc_start: 0.8927 (t0) cc_final: 0.8470 (t0) REVERT: C 331 LYS cc_start: 0.9322 (mttt) cc_final: 0.9085 (mttm) REVERT: C 343 LYS cc_start: 0.8987 (mmtm) cc_final: 0.8490 (mptt) REVERT: C 375 LYS cc_start: 0.8938 (tttt) cc_final: 0.8533 (tttt) REVERT: D 343 LYS cc_start: 0.9031 (mmtm) cc_final: 0.8791 (mmtp) REVERT: M 336 GLN cc_start: 0.9279 (tt0) cc_final: 0.9056 (tt0) REVERT: M 343 LYS cc_start: 0.8693 (mmtm) cc_final: 0.8066 (mtpp) REVERT: N 317 LYS cc_start: 0.8309 (ptpp) cc_final: 0.7994 (ptmm) REVERT: N 331 LYS cc_start: 0.9320 (mttt) cc_final: 0.9064 (mtpt) REVERT: N 343 LYS cc_start: 0.8598 (mmtm) cc_final: 0.8131 (mmmm) REVERT: N 345 ASP cc_start: 0.8913 (m-30) cc_final: 0.8638 (m-30) REVERT: O 321 LYS cc_start: 0.9400 (mttt) cc_final: 0.9133 (mttp) REVERT: O 375 LYS cc_start: 0.8843 (tttt) cc_final: 0.8539 (tttt) REVERT: P 313 VAL cc_start: 0.9146 (t) cc_final: 0.8696 (p) REVERT: Z 311 LYS cc_start: 0.9248 (ptpt) cc_final: 0.8674 (pttp) REVERT: Z 321 LYS cc_start: 0.9327 (mttt) cc_final: 0.9079 (mttp) REVERT: Z 331 LYS cc_start: 0.9312 (mttt) cc_final: 0.8905 (mtpt) REVERT: Z 353 LYS cc_start: 0.9371 (tttt) cc_final: 0.9055 (tttm) REVERT: Z 356 SER cc_start: 0.9555 (p) cc_final: 0.9230 (p) REVERT: Z 375 LYS cc_start: 0.9059 (tttt) cc_final: 0.8693 (ttmm) REVERT: 0 310 TYR cc_start: 0.8833 (t80) cc_final: 0.8545 (t80) REVERT: 0 331 LYS cc_start: 0.9415 (mttt) cc_final: 0.9152 (mtmt) REVERT: 0 343 LYS cc_start: 0.8768 (mtpp) cc_final: 0.8518 (mptt) REVERT: 1 313 VAL cc_start: 0.9085 (t) cc_final: 0.8551 (p) REVERT: 1 327 ASN cc_start: 0.9261 (t0) cc_final: 0.9041 (t0) REVERT: 1 331 LYS cc_start: 0.9390 (mtmm) cc_final: 0.9142 (mtmt) REVERT: 1 356 SER cc_start: 0.9470 (p) cc_final: 0.9187 (p) REVERT: 1 375 LYS cc_start: 0.8587 (tttt) cc_final: 0.8185 (tttm) outliers start: 33 outliers final: 21 residues processed: 414 average time/residue: 0.2614 time to fit residues: 136.8912 Evaluate side-chains 423 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 402 time to evaluate : 0.949 ------------------------------------------------------------------------------- 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 0 residue 339 VAL 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: 0.9990 chunk 54 optimal weight: 2.9990 chunk 19 optimal weight: 4.9990 chunk 31 optimal weight: 5.9990 chunk 57 optimal weight: 6.9990 chunk 60 optimal weight: 3.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 307 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4801 r_free = 0.4801 target = 0.192004 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.121934 restraints weight = 9607.424| |-----------------------------------------------------------------------------| r_work (start): 0.3893 rms_B_bonded: 3.06 r_work: 0.3751 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.3633 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.3633 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8368 moved from start: 0.3445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 8784 Z= 0.258 Angle : 0.711 8.160 11772 Z= 0.350 Chirality : 0.049 0.145 1356 Planarity : 0.003 0.024 1440 Dihedral : 11.563 65.848 1524 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.33 % Favored : 91.67 % Rotamer: Outliers : 5.85 % Allowed : 22.14 % Favored : 72.01 % 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: -2.37 (0.23), residues: 900 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.80 (0.18), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS 0 329 PHE 0.013 0.003 PHE A 346 TYR 0.015 0.003 TYR M 310 ARG 0.006 0.001 ARG O 349 Details of bonding type rmsd hydrogen bonds : bond 0.03036 ( 300) hydrogen bonds : angle 5.49305 ( 852) covalent geometry : bond 0.00619 ( 8778) covalent geometry : angle 0.71130 (11772) Misc. bond : bond 0.00046 ( 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 433 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 386 time to evaluate : 0.918 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 324 SER cc_start: 0.9149 (t) cc_final: 0.8892 (m) REVERT: B 331 LYS cc_start: 0.9300 (mttt) cc_final: 0.8958 (mtmt) REVERT: B 336 GLN cc_start: 0.9333 (tt0) cc_final: 0.8717 (tt0) REVERT: B 343 LYS cc_start: 0.9107 (mtpp) cc_final: 0.8882 (mtpp) REVERT: B 375 LYS cc_start: 0.9052 (tttt) cc_final: 0.8668 (ttmm) REVERT: C 314 ASP cc_start: 0.8898 (t0) cc_final: 0.8464 (t0) REVERT: C 331 LYS cc_start: 0.9347 (mttt) cc_final: 0.9133 (mttm) REVERT: C 342 GLU cc_start: 0.8734 (mt-10) cc_final: 0.8401 (mt-10) REVERT: C 375 LYS cc_start: 0.8988 (tttt) cc_final: 0.8574 (tttt) REVERT: M 336 GLN cc_start: 0.9309 (tt0) cc_final: 0.9084 (tt0) REVERT: M 343 LYS cc_start: 0.8758 (mmtm) cc_final: 0.8190 (mtpp) REVERT: N 331 LYS cc_start: 0.9331 (mttt) cc_final: 0.9098 (mtpt) REVERT: N 343 LYS cc_start: 0.8739 (mmtm) cc_final: 0.8197 (mtpp) REVERT: N 345 ASP cc_start: 0.8891 (m-30) cc_final: 0.8631 (m-30) REVERT: O 321 LYS cc_start: 0.9422 (mttt) cc_final: 0.9172 (mttp) REVERT: O 375 LYS cc_start: 0.8812 (tttt) cc_final: 0.8527 (tttt) REVERT: P 313 VAL cc_start: 0.9217 (t) cc_final: 0.8814 (p) REVERT: P 315 LEU cc_start: 0.9282 (OUTLIER) cc_final: 0.9031 (mp) REVERT: Y 315 LEU cc_start: 0.9348 (OUTLIER) cc_final: 0.9117 (mp) REVERT: Z 321 LYS cc_start: 0.9342 (mttt) cc_final: 0.9070 (mttp) REVERT: Z 331 LYS cc_start: 0.9318 (mttt) cc_final: 0.8913 (mtpt) REVERT: Z 347 LYS cc_start: 0.8622 (ptpt) cc_final: 0.7933 (ptmm) REVERT: Z 353 LYS cc_start: 0.9319 (tttt) cc_final: 0.9003 (tttm) REVERT: Z 375 LYS cc_start: 0.9002 (tttt) cc_final: 0.8634 (ttmm) REVERT: 1 375 LYS cc_start: 0.8595 (tttt) cc_final: 0.8118 (tttm) outliers start: 47 outliers final: 37 residues processed: 395 average time/residue: 0.2567 time to fit residues: 128.8857 Evaluate side-chains 421 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 382 time to evaluate : 0.854 ------------------------------------------------------------------------------- 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 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 358 ASP Chi-restraints excluded: chain M residue 372 GLU 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 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 315 LEU 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: 0.0670 chunk 2 optimal weight: 3.9990 chunk 0 optimal weight: 8.9990 chunk 48 optimal weight: 6.9990 chunk 50 optimal weight: 9.9990 chunk 72 optimal weight: 2.9990 chunk 60 optimal weight: 3.9990 chunk 75 optimal weight: 1.9990 chunk 82 optimal weight: 2.9990 chunk 43 optimal weight: 3.9990 chunk 9 optimal weight: 0.9990 overall best weight: 1.8126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 307 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4838 r_free = 0.4838 target = 0.195533 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.125916 restraints weight = 9565.364| |-----------------------------------------------------------------------------| r_work (start): 0.3961 rms_B_bonded: 3.07 r_work: 0.3818 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.3698 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3698 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8343 moved from start: 0.3613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 8784 Z= 0.149 Angle : 0.642 7.383 11772 Z= 0.314 Chirality : 0.048 0.135 1356 Planarity : 0.002 0.024 1440 Dihedral : 11.219 65.051 1521 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.22 % Favored : 92.78 % Rotamer: Outliers : 5.22 % Allowed : 25.75 % 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 : -1.77 (0.18), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS 1 374 PHE 0.011 0.002 PHE Z 378 TYR 0.012 0.002 TYR M 310 ARG 0.005 0.001 ARG O 349 Details of bonding type rmsd hydrogen bonds : bond 0.02388 ( 300) hydrogen bonds : angle 5.08364 ( 852) covalent geometry : bond 0.00352 ( 8778) covalent geometry : angle 0.64245 (11772) Misc. bond : bond 0.00024 ( 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 433 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 391 time to evaluate : 0.916 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 324 SER cc_start: 0.9124 (t) cc_final: 0.8820 (m) REVERT: B 331 LYS cc_start: 0.9296 (mttt) cc_final: 0.8940 (mtmt) REVERT: B 336 GLN cc_start: 0.9249 (tt0) cc_final: 0.8656 (tp40) REVERT: B 343 LYS cc_start: 0.9020 (mtpp) cc_final: 0.8740 (mtpp) REVERT: B 375 LYS cc_start: 0.9059 (tttt) cc_final: 0.8625 (ttmm) REVERT: C 311 LYS cc_start: 0.9121 (ptmt) cc_final: 0.8893 (ptpt) REVERT: C 314 ASP cc_start: 0.8925 (t0) cc_final: 0.8581 (t0) REVERT: C 331 LYS cc_start: 0.9331 (mttt) cc_final: 0.9086 (mttm) REVERT: D 342 GLU cc_start: 0.8608 (pt0) cc_final: 0.8287 (pt0) REVERT: M 336 GLN cc_start: 0.9269 (tt0) cc_final: 0.8987 (tt0) REVERT: M 343 LYS cc_start: 0.8760 (mmtm) cc_final: 0.8206 (mtpp) REVERT: N 331 LYS cc_start: 0.9308 (mttt) cc_final: 0.9081 (mtpt) REVERT: N 343 LYS cc_start: 0.8740 (mmtm) cc_final: 0.8252 (mtpp) REVERT: N 345 ASP cc_start: 0.8892 (m-30) cc_final: 0.8615 (m-30) REVERT: N 347 LYS cc_start: 0.8564 (ptpt) cc_final: 0.7889 (ptmm) REVERT: O 321 LYS cc_start: 0.9391 (mttt) cc_final: 0.9144 (mttp) REVERT: O 343 LYS cc_start: 0.9111 (mtpp) cc_final: 0.8482 (mttt) REVERT: O 375 LYS cc_start: 0.8840 (tttt) cc_final: 0.8544 (tttt) REVERT: P 313 VAL cc_start: 0.9135 (t) cc_final: 0.8744 (p) REVERT: P 315 LEU cc_start: 0.9296 (OUTLIER) cc_final: 0.9050 (mp) REVERT: P 331 LYS cc_start: 0.9376 (mttt) cc_final: 0.7634 (tmtt) REVERT: Y 315 LEU cc_start: 0.9339 (OUTLIER) cc_final: 0.9107 (mp) REVERT: Z 311 LYS cc_start: 0.9297 (ptpt) cc_final: 0.8755 (pttt) REVERT: Z 321 LYS cc_start: 0.9363 (mttt) cc_final: 0.9111 (mttp) REVERT: Z 331 LYS cc_start: 0.9257 (mttt) cc_final: 0.8839 (mtpt) REVERT: Z 347 LYS cc_start: 0.8560 (ptpt) cc_final: 0.7886 (ptmm) REVERT: Z 353 LYS cc_start: 0.9356 (tttt) cc_final: 0.9039 (tttm) REVERT: Z 375 LYS cc_start: 0.9016 (tttt) cc_final: 0.8665 (ttmm) REVERT: 1 313 VAL cc_start: 0.9134 (t) cc_final: 0.8654 (p) outliers start: 42 outliers final: 35 residues processed: 397 average time/residue: 0.2629 time to fit residues: 132.4210 Evaluate side-chains 416 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 379 time to evaluate : 0.857 ------------------------------------------------------------------------------- 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 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 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 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 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: 2.9990 chunk 14 optimal weight: 10.0000 chunk 80 optimal weight: 5.9990 chunk 1 optimal weight: 1.9990 chunk 77 optimal weight: 7.9990 chunk 74 optimal weight: 4.9990 chunk 28 optimal weight: 7.9990 chunk 4 optimal weight: 7.9990 chunk 71 optimal weight: 5.9990 chunk 79 optimal weight: 5.9990 chunk 45 optimal weight: 5.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- 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 M 327 ASN 1 374 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4788 r_free = 0.4788 target = 0.190751 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.120831 restraints weight = 9554.785| |-----------------------------------------------------------------------------| r_work (start): 0.3886 rms_B_bonded: 2.98 r_work: 0.3748 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3629 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.3629 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8419 moved from start: 0.3856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.055 8784 Z= 0.314 Angle : 0.756 7.901 11772 Z= 0.372 Chirality : 0.050 0.222 1356 Planarity : 0.003 0.032 1440 Dihedral : 11.709 65.143 1521 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.22 % Favored : 90.78 % Rotamer: Outliers : 5.85 % Allowed : 24.75 % Favored : 69.40 % 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: -2.52 (0.22), residues: 900 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.91 (0.17), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS 0 329 PHE 0.013 0.003 PHE 1 346 TYR 0.017 0.003 TYR M 310 ARG 0.006 0.001 ARG O 349 Details of bonding type rmsd hydrogen bonds : bond 0.03190 ( 300) hydrogen bonds : angle 5.35469 ( 852) covalent geometry : bond 0.00750 ( 8778) covalent geometry : angle 0.75627 (11772) Misc. bond : bond 0.00064 ( 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 420 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 373 time to evaluate : 0.953 Fit side-chains revert: symmetry clash REVERT: B 331 LYS cc_start: 0.9325 (mttt) cc_final: 0.8995 (mtmt) REVERT: B 336 GLN cc_start: 0.9323 (tt0) cc_final: 0.8717 (tp40) REVERT: B 343 LYS cc_start: 0.9115 (mtpp) cc_final: 0.8864 (mtpp) REVERT: B 347 LYS cc_start: 0.8394 (ptpt) cc_final: 0.8182 (ptpt) REVERT: B 375 LYS cc_start: 0.9082 (tttt) cc_final: 0.8711 (ttmm) REVERT: C 311 LYS cc_start: 0.9143 (ptmt) cc_final: 0.8883 (ptpt) REVERT: C 314 ASP cc_start: 0.8929 (t0) cc_final: 0.8584 (t0) REVERT: C 375 LYS cc_start: 0.8989 (tttt) cc_final: 0.8572 (ttpt) REVERT: D 375 LYS cc_start: 0.8737 (tttp) cc_final: 0.8357 (tttt) REVERT: M 343 LYS cc_start: 0.8769 (mmtm) cc_final: 0.8166 (mtpp) REVERT: N 331 LYS cc_start: 0.9360 (mttt) cc_final: 0.9138 (mtpt) REVERT: N 343 LYS cc_start: 0.8778 (mmtm) cc_final: 0.8219 (mmmm) REVERT: N 345 ASP cc_start: 0.8913 (m-30) cc_final: 0.8510 (m-30) REVERT: N 347 LYS cc_start: 0.8625 (ptpt) cc_final: 0.7991 (ptmm) REVERT: O 321 LYS cc_start: 0.9373 (mttt) cc_final: 0.9144 (mttp) REVERT: O 375 LYS cc_start: 0.8841 (tttt) cc_final: 0.8334 (tttm) REVERT: P 313 VAL cc_start: 0.9305 (t) cc_final: 0.8905 (p) REVERT: P 315 LEU cc_start: 0.9310 (OUTLIER) cc_final: 0.9067 (mp) REVERT: Y 315 LEU cc_start: 0.9345 (OUTLIER) cc_final: 0.9130 (mp) REVERT: Z 311 LYS cc_start: 0.9327 (ptpt) cc_final: 0.8782 (pttt) REVERT: Z 321 LYS cc_start: 0.9387 (mttt) cc_final: 0.9120 (mttp) REVERT: Z 331 LYS cc_start: 0.9296 (mttt) cc_final: 0.8904 (mtpt) REVERT: Z 347 LYS cc_start: 0.8588 (ptpt) cc_final: 0.7946 (ptmm) REVERT: Z 353 LYS cc_start: 0.9409 (tttt) cc_final: 0.9036 (tttm) REVERT: Z 375 LYS cc_start: 0.9033 (tttt) cc_final: 0.8650 (ttmm) REVERT: 0 343 LYS cc_start: 0.9082 (mtpp) cc_final: 0.8574 (mttm) REVERT: 0 378 PHE cc_start: 0.8870 (t80) cc_final: 0.8457 (t80) outliers start: 47 outliers final: 39 residues processed: 384 average time/residue: 0.2637 time to fit residues: 129.5109 Evaluate side-chains 407 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 366 time to evaluate : 0.966 ------------------------------------------------------------------------------- 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 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 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 O residue 372 GLU Chi-restraints excluded: chain P residue 315 LEU Chi-restraints excluded: chain P residue 319 THR Chi-restraints excluded: chain P residue 339 VAL 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 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: 3.9990 chunk 54 optimal weight: 0.9990 chunk 64 optimal weight: 2.9990 chunk 79 optimal weight: 3.9990 chunk 22 optimal weight: 10.0000 chunk 33 optimal weight: 0.7980 chunk 60 optimal weight: 0.8980 chunk 23 optimal weight: 3.9990 chunk 19 optimal weight: 0.9990 chunk 75 optimal weight: 2.9990 chunk 44 optimal weight: 0.9990 overall best weight: 0.9386 ------------------------------------------------------------------------------- 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 0 327 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4856 r_free = 0.4856 target = 0.197312 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4021 r_free = 0.4021 target = 0.128181 restraints weight = 9594.100| |-----------------------------------------------------------------------------| r_work (start): 0.3989 rms_B_bonded: 3.06 r_work: 0.3853 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.3726 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3726 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8320 moved from start: 0.3988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 8784 Z= 0.106 Angle : 0.640 8.061 11772 Z= 0.307 Chirality : 0.047 0.133 1356 Planarity : 0.003 0.031 1440 Dihedral : 11.247 64.180 1521 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.78 % Favored : 94.22 % Rotamer: Outliers : 3.98 % Allowed : 27.11 % Favored : 68.91 % 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: -2.38 (0.23), residues: 900 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.80 (0.17), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS C 374 PHE 0.015 0.002 PHE C 378 TYR 0.014 0.002 TYR O 310 ARG 0.006 0.001 ARG O 349 Details of bonding type rmsd hydrogen bonds : bond 0.02017 ( 300) hydrogen bonds : angle 4.85425 ( 852) covalent geometry : bond 0.00242 ( 8778) covalent geometry : angle 0.64007 (11772) Misc. bond : bond 0.00019 ( 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 418 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 386 time to evaluate : 0.853 Fit side-chains revert: symmetry clash REVERT: B 331 LYS cc_start: 0.9293 (mttt) cc_final: 0.9026 (mtmt) REVERT: B 336 GLN cc_start: 0.9230 (tt0) cc_final: 0.8582 (tp40) REVERT: B 343 LYS cc_start: 0.9038 (mtpp) cc_final: 0.8754 (mtpp) REVERT: B 353 LYS cc_start: 0.9275 (tttm) cc_final: 0.8969 (tttm) REVERT: B 375 LYS cc_start: 0.9027 (tttt) cc_final: 0.8670 (ttmm) REVERT: C 314 ASP cc_start: 0.8930 (t0) cc_final: 0.8594 (t0) REVERT: M 331 LYS cc_start: 0.9400 (mttt) cc_final: 0.9184 (mtmt) REVERT: M 343 LYS cc_start: 0.8790 (mmtm) cc_final: 0.8184 (mtpp) REVERT: N 331 LYS cc_start: 0.9328 (mttt) cc_final: 0.8950 (mtpt) REVERT: N 343 LYS cc_start: 0.8642 (mmtm) cc_final: 0.8259 (mmmm) REVERT: N 345 ASP cc_start: 0.8870 (m-30) cc_final: 0.8665 (m-30) REVERT: O 321 LYS cc_start: 0.9396 (mttt) cc_final: 0.9129 (mttp) REVERT: O 343 LYS cc_start: 0.9105 (mtpp) cc_final: 0.8457 (mmtt) REVERT: O 375 LYS cc_start: 0.8791 (tttt) cc_final: 0.8501 (tttt) REVERT: P 313 VAL cc_start: 0.9145 (t) cc_final: 0.8747 (p) REVERT: P 315 LEU cc_start: 0.9287 (OUTLIER) cc_final: 0.9042 (mp) REVERT: P 331 LYS cc_start: 0.9376 (mttt) cc_final: 0.7670 (tmtt) REVERT: Y 315 LEU cc_start: 0.9314 (OUTLIER) cc_final: 0.9079 (mp) REVERT: Z 311 LYS cc_start: 0.9297 (ptpt) cc_final: 0.8729 (pttt) REVERT: Z 317 LYS cc_start: 0.8378 (ptpt) cc_final: 0.8046 (ptmm) REVERT: Z 321 LYS cc_start: 0.9377 (mttt) cc_final: 0.9150 (mttp) REVERT: Z 331 LYS cc_start: 0.9210 (mttt) cc_final: 0.8906 (mtpt) REVERT: Z 347 LYS cc_start: 0.8545 (ptpt) cc_final: 0.7872 (ptmm) REVERT: Z 353 LYS cc_start: 0.9323 (tttt) cc_final: 0.9010 (tttm) REVERT: Z 375 LYS cc_start: 0.8997 (tttt) cc_final: 0.8619 (ttmm) REVERT: 0 343 LYS cc_start: 0.8946 (mtpp) cc_final: 0.8502 (mttp) REVERT: 1 310 TYR cc_start: 0.9240 (t80) cc_final: 0.9021 (t80) REVERT: 1 313 VAL cc_start: 0.9044 (t) cc_final: 0.8560 (p) outliers start: 32 outliers final: 27 residues processed: 389 average time/residue: 0.2577 time to fit residues: 127.8460 Evaluate side-chains 411 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 382 time to evaluate : 0.836 ------------------------------------------------------------------------------- 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 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 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 358 ASP Chi-restraints excluded: chain M residue 373 THR 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 Y residue 373 THR Chi-restraints excluded: chain Z residue 319 THR Chi-restraints excluded: chain Z residue 351 GLN 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: 9.9990 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: 10.0000 chunk 15 optimal weight: 5.9990 chunk 9 optimal weight: 0.6980 chunk 13 optimal weight: 3.9990 overall best weight: 3.2986 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4769 r_free = 0.4769 target = 0.188742 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.119114 restraints weight = 10115.991| |-----------------------------------------------------------------------------| r_work (start): 0.3950 rms_B_bonded: 3.15 r_work: 0.3813 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.3707 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.3707 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8262 moved from start: 0.4030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.070 8784 Z= 0.244 Angle : 0.720 9.351 11772 Z= 0.348 Chirality : 0.049 0.244 1356 Planarity : 0.003 0.041 1440 Dihedral : 11.419 64.186 1521 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.00 % Favored : 91.00 % Rotamer: Outliers : 4.73 % Allowed : 27.11 % 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: -2.45 (0.23), residues: 900 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.86 (0.17), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS M 374 PHE 0.013 0.002 PHE N 378 TYR 0.016 0.003 TYR O 310 ARG 0.007 0.001 ARG O 349 Details of bonding type rmsd hydrogen bonds : bond 0.02775 ( 300) hydrogen bonds : angle 5.09082 ( 852) covalent geometry : bond 0.00591 ( 8778) covalent geometry : angle 0.71972 (11772) Misc. bond : bond 0.00050 ( 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 412 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 374 time to evaluate : 0.838 Fit side-chains revert: symmetry clash REVERT: B 331 LYS cc_start: 0.9233 (mttt) cc_final: 0.8946 (mtmt) REVERT: B 336 GLN cc_start: 0.9269 (tt0) cc_final: 0.8612 (tp40) REVERT: B 343 LYS cc_start: 0.9051 (mtpp) cc_final: 0.8760 (mtpp) REVERT: B 353 LYS cc_start: 0.9237 (tttm) cc_final: 0.8871 (tttp) REVERT: B 375 LYS cc_start: 0.8976 (tttt) cc_final: 0.8595 (ttmm) REVERT: C 314 ASP cc_start: 0.8957 (t0) cc_final: 0.8608 (t0) REVERT: C 375 LYS cc_start: 0.8885 (tttt) cc_final: 0.8606 (ttpt) REVERT: D 375 LYS cc_start: 0.8521 (tttp) cc_final: 0.8272 (tttt) REVERT: M 343 LYS cc_start: 0.8742 (mmtm) cc_final: 0.8407 (ttmm) REVERT: N 331 LYS cc_start: 0.9286 (mttt) cc_final: 0.9045 (mtpt) REVERT: N 343 LYS cc_start: 0.8613 (mmtm) cc_final: 0.8070 (mmmm) REVERT: N 345 ASP cc_start: 0.8789 (m-30) cc_final: 0.8414 (m-30) REVERT: N 347 LYS cc_start: 0.8626 (ptpt) cc_final: 0.7892 (ptmm) REVERT: O 321 LYS cc_start: 0.9366 (mttt) cc_final: 0.9074 (mttp) REVERT: O 343 LYS cc_start: 0.9061 (mtpp) cc_final: 0.8442 (mttt) REVERT: O 375 LYS cc_start: 0.8808 (tttt) cc_final: 0.8301 (tttm) REVERT: P 313 VAL cc_start: 0.9162 (t) cc_final: 0.8744 (p) REVERT: P 315 LEU cc_start: 0.9209 (OUTLIER) cc_final: 0.8941 (mp) REVERT: P 378 PHE cc_start: 0.8361 (t80) cc_final: 0.7190 (p90) REVERT: Y 315 LEU cc_start: 0.9306 (OUTLIER) cc_final: 0.9090 (mp) REVERT: Z 311 LYS cc_start: 0.9346 (ptpt) cc_final: 0.8679 (pttt) REVERT: Z 321 LYS cc_start: 0.9314 (mttt) cc_final: 0.9031 (mttp) REVERT: Z 331 LYS cc_start: 0.9215 (mttt) cc_final: 0.8759 (mtpt) REVERT: Z 347 LYS cc_start: 0.8588 (ptpt) cc_final: 0.7840 (ptmm) REVERT: Z 353 LYS cc_start: 0.9263 (tttt) cc_final: 0.8892 (tttm) REVERT: Z 375 LYS cc_start: 0.8923 (tttt) cc_final: 0.8534 (ttmm) REVERT: 0 343 LYS cc_start: 0.8954 (mtpp) cc_final: 0.8439 (mttm) REVERT: 1 310 TYR cc_start: 0.9324 (t80) cc_final: 0.9112 (t80) outliers start: 38 outliers final: 33 residues processed: 383 average time/residue: 0.2649 time to fit residues: 130.0088 Evaluate side-chains 401 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 366 time to evaluate : 0.954 ------------------------------------------------------------------------------- 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 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 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 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 Y residue 373 THR 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 43 optimal weight: 8.9990 chunk 54 optimal weight: 0.9990 chunk 47 optimal weight: 1.9990 chunk 4 optimal weight: 4.9990 chunk 21 optimal weight: 7.9990 chunk 8 optimal weight: 5.9990 chunk 83 optimal weight: 6.9990 chunk 35 optimal weight: 5.9990 chunk 37 optimal weight: 2.9990 chunk 44 optimal weight: 7.9990 chunk 64 optimal weight: 8.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 307 GLN ** A 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 374 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4773 r_free = 0.4773 target = 0.189311 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.121282 restraints weight = 9832.693| |-----------------------------------------------------------------------------| r_work (start): 0.3947 rms_B_bonded: 2.98 r_work: 0.3810 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3706 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3706 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8265 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 0.064 8784 Z= 0.249 Angle : 0.737 9.565 11772 Z= 0.358 Chirality : 0.049 0.187 1356 Planarity : 0.003 0.046 1440 Dihedral : 11.478 64.200 1521 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.67 % Favored : 92.33 % Rotamer: Outliers : 4.85 % Allowed : 26.87 % 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: -2.53 (0.22), residues: 900 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.92 (0.17), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS M 374 PHE 0.015 0.003 PHE C 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 0.02821 ( 300) hydrogen bonds : angle 5.12307 ( 852) covalent geometry : bond 0.00601 ( 8778) covalent geometry : angle 0.73734 (11772) Misc. bond : bond 0.00053 ( 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 418 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 379 time to evaluate : 0.856 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 353 LYS cc_start: 0.9288 (tttt) cc_final: 0.8892 (tttt) REVERT: B 331 LYS cc_start: 0.9244 (mttt) cc_final: 0.8957 (mtmt) REVERT: B 336 GLN cc_start: 0.9242 (tt0) cc_final: 0.8619 (tp40) REVERT: B 343 LYS cc_start: 0.9058 (mtpp) cc_final: 0.8766 (mtpp) REVERT: B 353 LYS cc_start: 0.9233 (tttm) cc_final: 0.8875 (tttp) REVERT: B 375 LYS cc_start: 0.8991 (tttt) cc_final: 0.8605 (ttmm) REVERT: C 314 ASP cc_start: 0.8961 (t0) cc_final: 0.8644 (t0) REVERT: D 375 LYS cc_start: 0.8584 (tttp) cc_final: 0.8293 (tttt) REVERT: M 343 LYS cc_start: 0.8823 (mmtm) cc_final: 0.8469 (ttmm) REVERT: N 331 LYS cc_start: 0.9282 (mttt) cc_final: 0.9025 (mtpt) REVERT: N 343 LYS cc_start: 0.8587 (mmtm) cc_final: 0.8075 (mmmm) REVERT: N 345 ASP cc_start: 0.8814 (m-30) cc_final: 0.8422 (m-30) REVERT: N 347 LYS cc_start: 0.8606 (ptpt) cc_final: 0.7885 (ptmm) REVERT: O 321 LYS cc_start: 0.9375 (mttt) cc_final: 0.9086 (mttp) REVERT: O 343 LYS cc_start: 0.9099 (mtpp) cc_final: 0.8415 (mmtt) REVERT: O 375 LYS cc_start: 0.8792 (tttt) cc_final: 0.8271 (tttm) REVERT: P 313 VAL cc_start: 0.9173 (t) cc_final: 0.8744 (p) REVERT: P 315 LEU cc_start: 0.9224 (OUTLIER) cc_final: 0.8980 (mp) REVERT: Y 315 LEU cc_start: 0.9318 (OUTLIER) cc_final: 0.9095 (mp) REVERT: Z 311 LYS cc_start: 0.9354 (ptpt) cc_final: 0.8667 (pttt) REVERT: Z 321 LYS cc_start: 0.9324 (mttt) cc_final: 0.9091 (mttp) REVERT: Z 331 LYS cc_start: 0.9198 (mttt) cc_final: 0.8730 (mtpt) REVERT: Z 347 LYS cc_start: 0.8587 (ptpt) cc_final: 0.7842 (ptmm) REVERT: Z 353 LYS cc_start: 0.9264 (tttt) cc_final: 0.8888 (tttm) REVERT: Z 375 LYS cc_start: 0.8939 (tttt) cc_final: 0.8526 (ttmm) REVERT: Z 379 ARG cc_start: 0.7883 (ptt90) cc_final: 0.7362 (ptt90) REVERT: 0 343 LYS cc_start: 0.8980 (mtpp) cc_final: 0.8530 (mttm) REVERT: 0 378 PHE cc_start: 0.8862 (t80) cc_final: 0.8475 (t80) REVERT: 1 331 LYS cc_start: 0.9358 (mtmm) cc_final: 0.9106 (mtmt) outliers start: 39 outliers final: 36 residues processed: 389 average time/residue: 0.2641 time to fit residues: 130.1449 Evaluate side-chains 417 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 379 time to evaluate : 0.827 ------------------------------------------------------------------------------- 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 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 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 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 Y residue 373 THR 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 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: 8.9990 chunk 35 optimal weight: 5.9990 chunk 79 optimal weight: 1.9990 chunk 45 optimal weight: 6.9990 chunk 44 optimal weight: 7.9990 chunk 38 optimal weight: 0.9990 chunk 49 optimal weight: 5.9990 chunk 41 optimal weight: 0.9980 chunk 11 optimal weight: 0.5980 chunk 59 optimal weight: 0.1980 chunk 54 optimal weight: 1.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4830 r_free = 0.4830 target = 0.194518 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4054 r_free = 0.4054 target = 0.128225 restraints weight = 9715.702| |-----------------------------------------------------------------------------| r_work (start): 0.4056 rms_B_bonded: 2.95 r_work: 0.3918 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3816 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3816 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8223 moved from start: 0.4305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8784 Z= 0.109 Angle : 0.643 8.666 11772 Z= 0.311 Chirality : 0.047 0.134 1356 Planarity : 0.003 0.043 1440 Dihedral : 11.084 63.552 1521 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.89 % Favored : 93.11 % Rotamer: Outliers : 2.86 % Allowed : 29.73 % Favored : 67.41 % 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: -2.38 (0.23), residues: 900 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.80 (0.18), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS A 329 PHE 0.017 0.002 PHE N 378 TYR 0.009 0.002 TYR M 310 ARG 0.007 0.001 ARG O 349 Details of bonding type rmsd hydrogen bonds : bond 0.02016 ( 300) hydrogen bonds : angle 4.70771 ( 852) covalent geometry : bond 0.00254 ( 8778) covalent geometry : angle 0.64318 (11772) Misc. bond : bond 0.00022 ( 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 415 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 392 time to evaluate : 0.956 Fit side-chains revert: symmetry clash REVERT: A 353 LYS cc_start: 0.9261 (tttt) cc_final: 0.8917 (tttt) REVERT: B 331 LYS cc_start: 0.9204 (mttt) cc_final: 0.8923 (mtmt) REVERT: B 336 GLN cc_start: 0.9155 (tt0) cc_final: 0.8419 (tp40) REVERT: B 343 LYS cc_start: 0.8966 (mtpp) cc_final: 0.8686 (mtpp) REVERT: B 353 LYS cc_start: 0.9220 (tttm) cc_final: 0.8805 (tttp) REVERT: B 375 LYS cc_start: 0.8953 (tttt) cc_final: 0.8573 (ttmm) REVERT: C 314 ASP cc_start: 0.8854 (t0) cc_final: 0.8547 (t0) REVERT: C 342 GLU cc_start: 0.8806 (mt-10) cc_final: 0.8439 (mt-10) REVERT: D 375 LYS cc_start: 0.8633 (tttp) cc_final: 0.8332 (tttt) REVERT: M 331 LYS cc_start: 0.9358 (mttt) cc_final: 0.9108 (mtmt) REVERT: M 343 LYS cc_start: 0.8788 (mmtm) cc_final: 0.8492 (mmtt) REVERT: N 331 LYS cc_start: 0.9284 (mttt) cc_final: 0.8892 (mtpt) REVERT: N 343 LYS cc_start: 0.8588 (mmtm) cc_final: 0.8271 (mmmt) REVERT: O 321 LYS cc_start: 0.9403 (mttt) cc_final: 0.9116 (mttp) REVERT: O 343 LYS cc_start: 0.9098 (mtpp) cc_final: 0.8500 (mmtt) REVERT: O 375 LYS cc_start: 0.8790 (tttt) cc_final: 0.8282 (tttm) REVERT: P 313 VAL cc_start: 0.9034 (t) cc_final: 0.8577 (p) REVERT: P 315 LEU cc_start: 0.9199 (OUTLIER) cc_final: 0.8936 (mp) REVERT: P 331 LYS cc_start: 0.9263 (mttt) cc_final: 0.7556 (tmtt) REVERT: Y 315 LEU cc_start: 0.9284 (OUTLIER) cc_final: 0.9040 (mp) REVERT: Z 311 LYS cc_start: 0.9305 (ptpt) cc_final: 0.8669 (pttt) REVERT: Z 317 LYS cc_start: 0.8200 (ptpt) cc_final: 0.7837 (ptmm) REVERT: Z 321 LYS cc_start: 0.9309 (mttt) cc_final: 0.9084 (mttp) REVERT: Z 331 LYS cc_start: 0.9136 (mttt) cc_final: 0.8800 (mtpt) REVERT: Z 347 LYS cc_start: 0.8532 (ptpt) cc_final: 0.7854 (ptmm) REVERT: Z 353 LYS cc_start: 0.9261 (tttt) cc_final: 0.8922 (tttm) REVERT: Z 375 LYS cc_start: 0.8906 (tttt) cc_final: 0.8535 (ttmm) REVERT: 0 314 ASP cc_start: 0.8573 (t0) cc_final: 0.8367 (t0) REVERT: 0 343 LYS cc_start: 0.8855 (mtpp) cc_final: 0.8391 (mttm) REVERT: 0 378 PHE cc_start: 0.8856 (t80) cc_final: 0.8437 (t80) REVERT: 1 313 VAL cc_start: 0.8934 (t) cc_final: 0.8459 (p) REVERT: 1 375 LYS cc_start: 0.8440 (tttt) cc_final: 0.8140 (tttt) outliers start: 23 outliers final: 20 residues processed: 394 average time/residue: 0.2624 time to fit residues: 132.0426 Evaluate side-chains 413 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 391 time to evaluate : 0.859 ------------------------------------------------------------------------------- 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 B residue 339 VAL 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 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 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 48 optimal weight: 6.9990 chunk 75 optimal weight: 3.9990 chunk 72 optimal weight: 6.9990 chunk 20 optimal weight: 8.9990 chunk 65 optimal weight: 6.9990 chunk 41 optimal weight: 2.9990 chunk 68 optimal weight: 2.9990 chunk 30 optimal weight: 6.9990 chunk 17 optimal weight: 3.9990 chunk 43 optimal weight: 5.9990 chunk 81 optimal weight: 5.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- 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 ** 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 = 0.4755 r_free = 0.4755 target = 0.187525 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.118444 restraints weight = 10014.962| |-----------------------------------------------------------------------------| r_work (start): 0.3892 rms_B_bonded: 3.06 r_work: 0.3755 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3647 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3647 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8271 moved from start: 0.4254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.072 8784 Z= 0.288 Angle : 0.759 9.055 11772 Z= 0.371 Chirality : 0.050 0.167 1356 Planarity : 0.003 0.050 1440 Dihedral : 11.361 63.707 1521 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.00 % Favored : 91.00 % Rotamer: Outliers : 4.35 % Allowed : 27.74 % 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 0.005 0.001 HIS O 374 PHE 0.016 0.002 PHE N 378 TYR 0.016 0.002 TYR M 310 ARG 0.008 0.001 ARG O 349 Details of bonding type rmsd hydrogen bonds : bond 0.03005 ( 300) hydrogen bonds : angle 5.11382 ( 852) covalent geometry : bond 0.00696 ( 8778) covalent geometry : angle 0.75893 (11772) Misc. bond : bond 0.00059 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6385.35 seconds wall clock time: 111 minutes 41.67 seconds (6701.67 seconds total)