Starting phenix.real_space_refine on Wed Sep 17 13:00:05 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9b4l_44184/09_2025/9b4l_44184.cif Found real_map, /net/cci-nas-00/data/ceres_data/9b4l_44184/09_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_44184/09_2025/9b4l_44184.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9b4l_44184/09_2025/9b4l_44184.map" model { file = "/net/cci-nas-00/data/ceres_data/9b4l_44184/09_2025/9b4l_44184.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9b4l_44184/09_2025/9b4l_44184.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 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-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: 2.35, per 1000 atoms: 0.27 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: 0.73 Conformation dependent library (CDL) restraints added in 215.8 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 0.45 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: 1.38 Time building geometry restraints manager: 0.92 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1446 1.32 - 1.44: 2046 1.44 - 1.56: 5274 1.56 - 1.68: 0 1.68 - 1.80: 12 Bond restraints: 8778 Sorted by residual: bond pdb=" C LYS D 321 " pdb=" O LYS D 321 " ideal model delta sigma weight residual 1.235 1.199 0.036 1.14e-02 7.69e+03 9.98e+00 bond pdb=" C LYS 1 321 " pdb=" O LYS 1 321 " ideal model delta sigma weight residual 1.235 1.199 0.036 1.14e-02 7.69e+03 9.96e+00 bond pdb=" C LYS P 321 " pdb=" O LYS P 321 " ideal model delta sigma weight residual 1.235 1.199 0.036 1.14e-02 7.69e+03 9.92e+00 bond pdb=" C LYS O 321 " pdb=" O LYS O 321 " ideal model delta sigma weight residual 1.235 1.201 0.034 1.14e-02 7.69e+03 9.06e+00 bond pdb=" C LYS 0 321 " pdb=" O LYS 0 321 " ideal model delta sigma weight residual 1.235 1.201 0.034 1.14e-02 7.69e+03 9.02e+00 ... (remaining 8773 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.63: 10878 1.63 - 3.25: 745 3.25 - 4.88: 83 4.88 - 6.50: 42 6.50 - 8.13: 24 Bond angle restraints: 11772 Sorted by residual: angle pdb=" C LYS 0 321 " pdb=" CA LYS 0 321 " pdb=" CB LYS 0 321 " ideal model delta sigma weight residual 109.70 104.19 5.51 1.81e+00 3.05e-01 9.28e+00 angle pdb=" C LYS O 321 " pdb=" CA LYS O 321 " pdb=" CB LYS O 321 " ideal model delta sigma weight residual 109.70 104.19 5.51 1.81e+00 3.05e-01 9.27e+00 angle pdb=" C LYS C 321 " pdb=" CA LYS C 321 " pdb=" CB LYS C 321 " ideal model delta sigma weight residual 109.70 104.19 5.51 1.81e+00 3.05e-01 9.26e+00 angle pdb=" C SER C 320 " pdb=" N LYS C 321 " pdb=" CA LYS C 321 " ideal model delta sigma weight residual 122.74 118.54 4.20 1.54e+00 4.22e-01 7.43e+00 angle pdb=" C SER O 320 " pdb=" N LYS O 321 " pdb=" CA LYS O 321 " ideal model delta sigma weight residual 122.74 118.54 4.20 1.54e+00 4.22e-01 7.42e+00 ... (remaining 11767 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.49: 4188 13.49 - 26.98: 504 26.98 - 40.47: 108 40.47 - 53.96: 42 53.96 - 67.45: 84 Dihedral angle restraints: 4926 sinusoidal: 2250 harmonic: 2676 Sorted by residual: dihedral pdb=" C LYS 0 321 " pdb=" N LYS 0 321 " pdb=" CA LYS 0 321 " pdb=" CB LYS 0 321 " ideal model delta harmonic sigma weight residual -122.60 -113.10 -9.50 0 2.50e+00 1.60e-01 1.44e+01 dihedral pdb=" C LYS O 321 " pdb=" N LYS O 321 " pdb=" CA LYS O 321 " pdb=" CB LYS O 321 " ideal model delta harmonic sigma weight residual -122.60 -113.10 -9.50 0 2.50e+00 1.60e-01 1.44e+01 dihedral pdb=" C LYS C 321 " pdb=" N LYS C 321 " pdb=" CA LYS C 321 " pdb=" CB LYS C 321 " ideal model delta harmonic sigma weight residual -122.60 -113.10 -9.50 0 2.50e+00 1.60e-01 1.44e+01 ... (remaining 4923 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 795 0.036 - 0.071: 240 0.071 - 0.107: 166 0.107 - 0.142: 113 0.142 - 0.178: 42 Chirality restraints: 1356 Sorted by residual: chirality pdb=" CA LYS 0 321 " pdb=" N LYS 0 321 " pdb=" C LYS 0 321 " pdb=" CB LYS 0 321 " both_signs ideal model delta sigma weight residual False 2.51 2.69 -0.18 2.00e-01 2.50e+01 7.91e-01 chirality pdb=" CA LYS O 321 " pdb=" N LYS O 321 " pdb=" C LYS O 321 " pdb=" CB LYS O 321 " both_signs ideal model delta sigma weight residual False 2.51 2.69 -0.18 2.00e-01 2.50e+01 7.90e-01 chirality pdb=" CA LYS C 321 " pdb=" N LYS C 321 " pdb=" C LYS C 321 " pdb=" CB LYS C 321 " both_signs ideal model delta sigma weight residual False 2.51 2.69 -0.18 2.00e-01 2.50e+01 7.83e-01 ... (remaining 1353 not shown) Planarity restraints: 1440 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS N 343 " 0.010 2.00e-02 2.50e+03 2.08e-02 4.31e+00 pdb=" C LYS N 343 " -0.036 2.00e-02 2.50e+03 pdb=" O LYS N 343 " 0.014 2.00e-02 2.50e+03 pdb=" N LEU N 344 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS 1 343 " -0.010 2.00e-02 2.50e+03 2.08e-02 4.31e+00 pdb=" C LYS 1 343 " 0.036 2.00e-02 2.50e+03 pdb=" O LYS 1 343 " -0.014 2.00e-02 2.50e+03 pdb=" N LEU 1 344 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS D 343 " -0.010 2.00e-02 2.50e+03 2.07e-02 4.27e+00 pdb=" C LYS D 343 " 0.036 2.00e-02 2.50e+03 pdb=" O LYS D 343 " -0.013 2.00e-02 2.50e+03 pdb=" N LEU D 344 " -0.012 2.00e-02 2.50e+03 ... (remaining 1437 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 2064 2.81 - 3.34: 6564 3.34 - 3.86: 14647 3.86 - 4.38: 15223 4.38 - 4.90: 30376 Nonbonded interactions: 68874 Sorted by model distance: nonbonded pdb=" O DLE G 2 " pdb=" O DTR T 6 " model vdw 2.292 3.040 nonbonded pdb=" O DTR H 6 " pdb=" O DLE 4 2 " model vdw 2.293 3.040 nonbonded pdb=" NZ LYS M 343 " pdb=" OE2 GLU N 342 " model vdw 2.342 3.120 nonbonded pdb=" NZ LYS Y 343 " pdb=" OE2 GLU Z 342 " model vdw 2.343 3.120 nonbonded pdb=" NZ LYS A 343 " pdb=" OE2 GLU B 342 " model vdw 2.343 3.120 ... (remaining 68869 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain '0' and resid 304 through 380) selection = chain '1' selection = (chain 'A' and resid 304 through 380) selection = chain 'B' selection = (chain 'C' and resid 304 through 380) selection = chain 'D' selection = (chain 'M' and resid 304 through 380) selection = chain 'N' selection = (chain 'O' and resid 304 through 380) selection = chain 'P' selection = chain 'Y' selection = chain 'Z' } ncs_group { reference = chain '2' selection = chain '4' selection = chain '5' selection = chain '6' selection = chain '7' selection = chain '8' selection = chain '9' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.960 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.130 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 8.970 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.670 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -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 ARG 0.002 0.001 ARG M 379 TYR 0.011 0.003 TYR 0 310 PHE 0.008 0.002 PHE Y 346 HIS 0.002 0.001 HIS 1 362 Details of bonding type rmsd covalent geometry : bond 0.00798 ( 8778) covalent geometry : angle 0.95150 (11772) hydrogen bonds : bond 0.19442 ( 300) hydrogen bonds : angle 11.44775 ( 852) 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 : 0.337 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: 0.1323 time to fit residues: 75.4851 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 : 0.321 ------------------------------------------------------------------------------- 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 49 optimal weight: 0.5980 chunk 53 optimal weight: 0.6980 chunk 5 optimal weight: 3.9990 chunk 33 optimal weight: 3.9990 chunk 65 optimal weight: 3.9990 chunk 62 optimal weight: 0.8980 chunk 51 optimal weight: 0.6980 chunk 38 optimal weight: 2.9990 chunk 61 optimal weight: 2.9990 chunk 45 optimal weight: 0.9980 chunk 74 optimal weight: 0.4980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 351 GLN ** Y 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 0 327 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4913 r_free = 0.4913 target = 0.202941 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4116 r_free = 0.4116 target = 0.135346 restraints weight = 9469.080| |-----------------------------------------------------------------------------| r_work (start): 0.4072 rms_B_bonded: 2.93 r_work: 0.3931 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work: 0.3813 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.3813 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8257 moved from start: 0.2512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 8784 Z= 0.113 Angle : 0.647 8.070 11772 Z= 0.312 Chirality : 0.049 0.154 1356 Planarity : 0.003 0.021 1440 Dihedral : 12.729 66.705 1565 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.11 % Favored : 93.89 % Rotamer: Outliers : 2.61 % Allowed : 21.27 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -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 ARG 0.005 0.000 ARG O 349 TYR 0.012 0.002 TYR M 310 PHE 0.017 0.003 PHE 1 378 HIS 0.002 0.000 HIS P 374 Details of bonding type rmsd covalent geometry : bond 0.00246 ( 8778) covalent geometry : angle 0.64663 (11772) hydrogen bonds : bond 0.02750 ( 300) hydrogen bonds : angle 6.26729 ( 852) Misc. bond : bond 0.00047 ( 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 447 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 426 time to evaluate : 0.339 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 331 LYS cc_start: 0.9304 (mttt) cc_final: 0.9025 (mtpt) REVERT: A 353 LYS cc_start: 0.9177 (tttt) cc_final: 0.8909 (tttt) REVERT: B 321 LYS cc_start: 0.9365 (mttt) cc_final: 0.9146 (mttm) REVERT: B 331 LYS cc_start: 0.9385 (mttt) cc_final: 0.9078 (mtmt) REVERT: B 353 LYS cc_start: 0.9128 (tttt) cc_final: 0.8798 (tttt) REVERT: C 314 ASP cc_start: 0.8801 (t0) cc_final: 0.8399 (t0) REVERT: C 321 LYS cc_start: 0.9282 (mttt) cc_final: 0.9067 (mttp) REVERT: C 331 LYS cc_start: 0.9402 (mttt) cc_final: 0.9177 (mttm) REVERT: C 343 LYS cc_start: 0.8862 (mmtm) cc_final: 0.8540 (mptt) REVERT: C 349 ARG cc_start: 0.7967 (mtm-85) cc_final: 0.7707 (mtm-85) REVERT: C 375 LYS cc_start: 0.8984 (tttt) cc_final: 0.8619 (tttt) REVERT: D 327 ASN cc_start: 0.9182 (t0) cc_final: 0.8961 (t0) REVERT: D 331 LYS cc_start: 0.9394 (mtmm) cc_final: 0.9173 (mttt) REVERT: M 331 LYS cc_start: 0.9364 (mttt) cc_final: 0.9134 (mtmt) REVERT: N 317 LYS cc_start: 0.8277 (ptpp) cc_final: 0.7999 (ptmt) REVERT: N 331 LYS cc_start: 0.9365 (mttt) cc_final: 0.9014 (mtpt) REVERT: N 343 LYS cc_start: 0.8300 (mmtm) cc_final: 0.7849 (mtpp) REVERT: N 349 ARG cc_start: 0.7936 (mtm-85) cc_final: 0.7728 (mtm-85) REVERT: O 321 LYS cc_start: 0.9386 (mttt) cc_final: 0.9075 (mttp) REVERT: O 349 ARG cc_start: 0.7764 (mtm-85) cc_final: 0.7366 (mtm180) REVERT: P 313 VAL cc_start: 0.9170 (t) cc_final: 0.8752 (p) REVERT: P 331 LYS cc_start: 0.9361 (mttt) cc_final: 0.7723 (tmtt) REVERT: Y 314 ASP cc_start: 0.8946 (t0) cc_final: 0.8738 (t0) REVERT: Z 321 LYS cc_start: 0.9349 (mttt) cc_final: 0.9114 (mttp) REVERT: Z 331 LYS cc_start: 0.9335 (mttt) cc_final: 0.8917 (mtpt) REVERT: Z 353 LYS cc_start: 0.9231 (tttt) cc_final: 0.8926 (tttm) REVERT: Z 356 SER cc_start: 0.9366 (p) cc_final: 0.9036 (p) REVERT: Z 375 LYS cc_start: 0.9098 (tttt) cc_final: 0.8700 (ttmm) REVERT: 0 310 TYR cc_start: 0.8767 (t80) cc_final: 0.8112 (t80) REVERT: 0 375 LYS cc_start: 0.8992 (tttt) cc_final: 0.8716 (tttm) REVERT: 1 314 ASP cc_start: 0.9066 (t0) cc_final: 0.8767 (t0) REVERT: 1 347 LYS cc_start: 0.8381 (ptpt) cc_final: 0.8169 (ptpt) outliers start: 21 outliers final: 8 residues processed: 428 average time/residue: 0.1288 time to fit residues: 69.7982 Evaluate side-chains 403 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 395 time to evaluate : 0.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain C residue 339 VAL Chi-restraints excluded: chain O residue 339 VAL Chi-restraints excluded: chain Z residue 311 LYS 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 46 optimal weight: 7.9990 chunk 21 optimal weight: 2.9990 chunk 39 optimal weight: 5.9990 chunk 27 optimal weight: 6.9990 chunk 4 optimal weight: 9.9990 chunk 71 optimal weight: 10.0000 chunk 55 optimal weight: 5.9990 chunk 52 optimal weight: 1.9990 chunk 69 optimal weight: 7.9990 chunk 43 optimal weight: 9.9990 chunk 16 optimal weight: 6.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 307 GLN O 327 ASN P 327 ASN 1 368 ASN 1 374 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4792 r_free = 0.4792 target = 0.191221 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.121284 restraints weight = 9564.957| |-----------------------------------------------------------------------------| r_work (start): 0.3897 rms_B_bonded: 2.95 r_work: 0.3755 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.3635 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3635 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8414 moved from start: 0.3135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.058 8784 Z= 0.342 Angle : 0.752 6.856 11772 Z= 0.376 Chirality : 0.050 0.264 1356 Planarity : 0.003 0.026 1440 Dihedral : 12.015 66.791 1525 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.89 % Favored : 90.11 % Rotamer: Outliers : 4.73 % Allowed : 21.89 % Favored : 73.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.44 (0.23), residues: 900 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.85 (0.17), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG O 379 TYR 0.019 0.003 TYR A 310 PHE 0.012 0.002 PHE A 346 HIS 0.007 0.001 HIS 0 329 Details of bonding type rmsd covalent geometry : bond 0.00820 ( 8778) covalent geometry : angle 0.75238 (11772) hydrogen bonds : bond 0.03521 ( 300) hydrogen bonds : angle 6.04153 ( 852) Misc. bond : bond 0.00058 ( 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 427 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 389 time to evaluate : 0.315 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 347 LYS cc_start: 0.8467 (ptpt) cc_final: 0.8258 (ptpt) REVERT: B 331 LYS cc_start: 0.9365 (mttt) cc_final: 0.9046 (mtmt) REVERT: B 353 LYS cc_start: 0.9409 (tttt) cc_final: 0.9208 (tttm) REVERT: B 375 LYS cc_start: 0.9108 (tttt) cc_final: 0.8696 (ttmm) REVERT: C 314 ASP cc_start: 0.8883 (t0) cc_final: 0.8534 (t0) REVERT: C 331 LYS cc_start: 0.9355 (mttt) cc_final: 0.9096 (mttm) REVERT: C 343 LYS cc_start: 0.9043 (mmtm) cc_final: 0.8748 (mptt) REVERT: M 343 LYS cc_start: 0.8641 (mmtm) cc_final: 0.8040 (mtpp) REVERT: N 331 LYS cc_start: 0.9333 (mttt) cc_final: 0.9127 (mtpt) REVERT: N 343 LYS cc_start: 0.8838 (mmtm) cc_final: 0.8323 (mtpp) REVERT: N 345 ASP cc_start: 0.8965 (m-30) cc_final: 0.8716 (m-30) REVERT: N 347 LYS cc_start: 0.8503 (ptpt) cc_final: 0.7849 (ptmm) REVERT: O 321 LYS cc_start: 0.9441 (mttt) cc_final: 0.9139 (mttp) REVERT: O 343 LYS cc_start: 0.9148 (mtpp) cc_final: 0.8500 (mmtt) REVERT: O 375 LYS cc_start: 0.8925 (tttt) cc_final: 0.8681 (tttt) REVERT: P 313 VAL cc_start: 0.9253 (t) cc_final: 0.8841 (p) REVERT: Y 315 LEU cc_start: 0.9355 (OUTLIER) cc_final: 0.9118 (mp) REVERT: Z 331 LYS cc_start: 0.9347 (mttt) cc_final: 0.8960 (mtpt) REVERT: Z 344 LEU cc_start: 0.9624 (mp) cc_final: 0.9342 (mp) REVERT: Z 347 LYS cc_start: 0.8573 (ptpt) cc_final: 0.7848 (ptmm) REVERT: Z 353 LYS cc_start: 0.9358 (tttt) cc_final: 0.9026 (tttm) REVERT: Z 375 LYS cc_start: 0.9025 (tttt) cc_final: 0.8660 (ttmm) REVERT: 0 343 LYS cc_start: 0.9013 (mtpp) cc_final: 0.8676 (mptt) REVERT: 0 378 PHE cc_start: 0.8913 (t80) cc_final: 0.8552 (t80) REVERT: 1 343 LYS cc_start: 0.9230 (mptt) cc_final: 0.9012 (mptt) outliers start: 38 outliers final: 25 residues processed: 402 average time/residue: 0.1243 time to fit residues: 63.4259 Evaluate side-chains 403 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 377 time to evaluate : 0.326 ------------------------------------------------------------------------------- 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 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 339 VAL 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 O residue 339 VAL Chi-restraints excluded: chain O residue 352 SER Chi-restraints excluded: chain P residue 319 THR Chi-restraints excluded: chain Y residue 306 VAL Chi-restraints excluded: chain Y residue 315 LEU Chi-restraints excluded: chain Y residue 339 VAL Chi-restraints excluded: chain Y residue 373 THR Chi-restraints excluded: chain Z residue 306 VAL Chi-restraints excluded: chain Z residue 311 LYS Chi-restraints excluded: chain Z residue 319 THR Chi-restraints excluded: chain Z residue 320 SER Chi-restraints excluded: chain 0 residue 339 VAL Chi-restraints excluded: chain 1 residue 319 THR Chi-restraints excluded: chain 1 residue 342 GLU 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 36 optimal weight: 4.9990 chunk 81 optimal weight: 0.9990 chunk 15 optimal weight: 9.9990 chunk 41 optimal weight: 0.9990 chunk 73 optimal weight: 4.9990 chunk 45 optimal weight: 0.7980 chunk 11 optimal weight: 0.8980 chunk 25 optimal weight: 0.7980 chunk 64 optimal weight: 3.9990 chunk 31 optimal weight: 0.9990 chunk 32 optimal weight: 0.8980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4861 r_free = 0.4861 target = 0.197801 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4032 r_free = 0.4032 target = 0.129326 restraints weight = 9629.818| |-----------------------------------------------------------------------------| r_work (start): 0.4003 rms_B_bonded: 2.93 r_work: 0.3863 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.3743 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.3743 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8319 moved from start: 0.3453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 8784 Z= 0.104 Angle : 0.614 8.209 11772 Z= 0.296 Chirality : 0.047 0.133 1356 Planarity : 0.002 0.023 1440 Dihedral : 11.189 65.140 1525 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.78 % Favored : 94.22 % Rotamer: Outliers : 3.73 % Allowed : 26.74 % Favored : 69.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.25 (0.23), residues: 900 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.70 (0.18), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG P 349 TYR 0.009 0.002 TYR O 310 PHE 0.011 0.002 PHE N 378 HIS 0.002 0.000 HIS M 374 Details of bonding type rmsd covalent geometry : bond 0.00238 ( 8778) covalent geometry : angle 0.61359 (11772) hydrogen bonds : bond 0.02113 ( 300) hydrogen bonds : angle 5.22478 ( 852) Misc. bond : bond 0.00010 ( 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 426 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 396 time to evaluate : 0.277 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 331 LYS cc_start: 0.9305 (mttt) cc_final: 0.8957 (mtmt) REVERT: B 343 LYS cc_start: 0.8802 (mtpp) cc_final: 0.8506 (mtpp) REVERT: B 353 LYS cc_start: 0.9316 (tttt) cc_final: 0.9017 (tttm) REVERT: B 375 LYS cc_start: 0.9065 (tttt) cc_final: 0.8693 (ttmm) REVERT: C 314 ASP cc_start: 0.8922 (t0) cc_final: 0.8535 (t0) REVERT: C 343 LYS cc_start: 0.8967 (mmtm) cc_final: 0.8764 (mptt) REVERT: C 349 ARG cc_start: 0.8261 (mtm-85) cc_final: 0.8015 (mtm-85) REVERT: D 314 ASP cc_start: 0.9141 (t70) cc_final: 0.8936 (t0) REVERT: D 331 LYS cc_start: 0.9416 (mtmm) cc_final: 0.9190 (mtmt) REVERT: M 336 GLN cc_start: 0.9197 (tt0) cc_final: 0.8974 (tt0) REVERT: M 343 LYS cc_start: 0.8656 (mmtm) cc_final: 0.8015 (mtpp) REVERT: N 331 LYS cc_start: 0.9336 (mttt) cc_final: 0.9089 (mtpt) REVERT: N 343 LYS cc_start: 0.8722 (mmtm) cc_final: 0.8161 (mtpp) REVERT: N 345 ASP cc_start: 0.8954 (m-30) cc_final: 0.8628 (m-30) REVERT: O 321 LYS cc_start: 0.9416 (mttt) cc_final: 0.9147 (mttp) REVERT: O 343 LYS cc_start: 0.9140 (mtpp) cc_final: 0.8466 (mmtt) REVERT: P 313 VAL cc_start: 0.9127 (t) cc_final: 0.8678 (p) REVERT: P 315 LEU cc_start: 0.9279 (OUTLIER) cc_final: 0.9066 (mp) REVERT: P 331 LYS cc_start: 0.9384 (mttt) cc_final: 0.7596 (tmtt) REVERT: Z 311 LYS cc_start: 0.9291 (ptpp) cc_final: 0.8979 (pttt) REVERT: Z 331 LYS cc_start: 0.9231 (mttt) cc_final: 0.8813 (mtpt) REVERT: Z 347 LYS cc_start: 0.8523 (ptpt) cc_final: 0.7812 (ptmm) REVERT: Z 353 LYS cc_start: 0.9333 (tttt) cc_final: 0.9040 (tttm) REVERT: Z 375 LYS cc_start: 0.9039 (tttt) cc_final: 0.8699 (ttmm) REVERT: 0 343 LYS cc_start: 0.8864 (mtpp) cc_final: 0.8552 (mttp) REVERT: 1 313 VAL cc_start: 0.9045 (t) cc_final: 0.8515 (p) REVERT: 1 327 ASN cc_start: 0.9227 (t0) cc_final: 0.9013 (t0) REVERT: 1 331 LYS cc_start: 0.9380 (mtmm) cc_final: 0.8934 (mtmt) outliers start: 30 outliers final: 21 residues processed: 401 average time/residue: 0.1193 time to fit residues: 61.0748 Evaluate side-chains 407 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 385 time to evaluate : 0.321 ------------------------------------------------------------------------------- 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 358 ASP Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain B residue 352 SER Chi-restraints excluded: chain B residue 358 ASP Chi-restraints excluded: chain C residue 309 VAL Chi-restraints excluded: chain C residue 339 VAL Chi-restraints excluded: chain C residue 358 ASP Chi-restraints excluded: chain M residue 352 SER Chi-restraints excluded: chain M residue 358 ASP 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 Y residue 373 THR Chi-restraints excluded: chain Z residue 319 THR Chi-restraints excluded: chain Z residue 351 GLN Chi-restraints excluded: chain 0 residue 339 VAL Chi-restraints excluded: chain 0 residue 376 LEU Chi-restraints excluded: chain 1 residue 315 LEU 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 73 optimal weight: 5.9990 chunk 32 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 5 optimal weight: 6.9990 chunk 24 optimal weight: 7.9990 chunk 27 optimal weight: 9.9990 chunk 13 optimal weight: 6.9990 chunk 34 optimal weight: 0.9990 chunk 17 optimal weight: 0.9990 chunk 83 optimal weight: 6.9990 chunk 66 optimal weight: 6.9990 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 Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4786 r_free = 0.4786 target = 0.190858 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.121190 restraints weight = 9732.675| |-----------------------------------------------------------------------------| r_work (start): 0.3888 rms_B_bonded: 3.00 r_work: 0.3741 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.3618 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3618 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8406 moved from start: 0.3693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.055 8784 Z= 0.315 Angle : 0.740 8.045 11772 Z= 0.366 Chirality : 0.050 0.226 1356 Planarity : 0.003 0.033 1440 Dihedral : 11.668 65.595 1521 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.56 % Favored : 90.44 % Rotamer: Outliers : 5.10 % Allowed : 25.00 % Favored : 69.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.41 (0.23), residues: 900 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.83 (0.17), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG O 349 TYR 0.017 0.003 TYR A 310 PHE 0.013 0.003 PHE Y 346 HIS 0.005 0.001 HIS 0 329 Details of bonding type rmsd covalent geometry : bond 0.00755 ( 8778) covalent geometry : angle 0.74023 (11772) hydrogen bonds : bond 0.03148 ( 300) hydrogen bonds : angle 5.45805 ( 852) Misc. bond : bond 0.00059 ( 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 411 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 370 time to evaluate : 0.345 Fit side-chains REVERT: B 331 LYS cc_start: 0.9319 (mttt) cc_final: 0.8980 (mtmt) REVERT: B 343 LYS cc_start: 0.8953 (mtpp) cc_final: 0.8643 (mtpp) REVERT: B 353 LYS cc_start: 0.9389 (tttt) cc_final: 0.9186 (tttm) REVERT: B 375 LYS cc_start: 0.9070 (tttt) cc_final: 0.8680 (ttmm) REVERT: C 314 ASP cc_start: 0.8892 (t0) cc_final: 0.8577 (t0) REVERT: M 336 GLN cc_start: 0.9327 (tt0) cc_final: 0.9083 (tt0) REVERT: M 343 LYS cc_start: 0.8748 (mmtm) cc_final: 0.8105 (mtpp) REVERT: N 331 LYS cc_start: 0.9346 (mttt) cc_final: 0.9123 (mtpt) REVERT: N 343 LYS cc_start: 0.8913 (mmtm) cc_final: 0.8288 (mtpp) REVERT: N 345 ASP cc_start: 0.8893 (m-30) cc_final: 0.8519 (m-30) REVERT: N 347 LYS cc_start: 0.8581 (ptpt) cc_final: 0.7890 (ptmm) REVERT: O 321 LYS cc_start: 0.9387 (mttt) cc_final: 0.9163 (mttp) REVERT: O 343 LYS cc_start: 0.9162 (mtpp) cc_final: 0.8944 (mtpp) REVERT: O 375 LYS cc_start: 0.8855 (tttt) cc_final: 0.8516 (tttt) REVERT: P 313 VAL cc_start: 0.9289 (t) cc_final: 0.8890 (p) REVERT: P 315 LEU cc_start: 0.9251 (OUTLIER) cc_final: 0.9013 (mp) REVERT: Y 315 LEU cc_start: 0.9322 (OUTLIER) cc_final: 0.9101 (mp) REVERT: Z 311 LYS cc_start: 0.9376 (ptpp) cc_final: 0.8953 (pttt) REVERT: Z 331 LYS cc_start: 0.9295 (mttt) cc_final: 0.8887 (mtpt) REVERT: Z 347 LYS cc_start: 0.8593 (ptpt) cc_final: 0.7932 (ptmm) REVERT: Z 353 LYS cc_start: 0.9369 (tttt) cc_final: 0.9027 (tttm) REVERT: Z 375 LYS cc_start: 0.9019 (tttt) cc_final: 0.8645 (ttmm) REVERT: 0 343 LYS cc_start: 0.9008 (mtpp) cc_final: 0.8607 (mttm) REVERT: 0 378 PHE cc_start: 0.8863 (t80) cc_final: 0.8452 (t80) outliers start: 41 outliers final: 34 residues processed: 381 average time/residue: 0.1187 time to fit residues: 58.2462 Evaluate side-chains 406 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 370 time to evaluate : 0.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 352 SER Chi-restraints excluded: chain A residue 358 ASP Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain B residue 352 SER Chi-restraints excluded: chain B residue 358 ASP Chi-restraints excluded: chain 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 N residue 306 VAL Chi-restraints excluded: chain N residue 319 THR Chi-restraints excluded: chain O residue 306 VAL Chi-restraints excluded: chain O residue 339 VAL Chi-restraints excluded: chain O residue 352 SER Chi-restraints excluded: chain P residue 315 LEU Chi-restraints excluded: chain P residue 319 THR Chi-restraints excluded: chain Y residue 306 VAL Chi-restraints excluded: chain Y residue 315 LEU Chi-restraints excluded: chain Y residue 339 VAL Chi-restraints excluded: chain Y residue 373 THR Chi-restraints excluded: chain Z residue 306 VAL Chi-restraints excluded: chain Z residue 319 THR Chi-restraints excluded: chain Z residue 320 SER Chi-restraints excluded: chain Z residue 351 GLN Chi-restraints excluded: chain Z residue 373 THR Chi-restraints excluded: chain 0 residue 339 VAL 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 9 optimal weight: 0.8980 chunk 51 optimal weight: 0.7980 chunk 65 optimal weight: 0.8980 chunk 82 optimal weight: 1.9990 chunk 19 optimal weight: 0.7980 chunk 56 optimal weight: 6.9990 chunk 39 optimal weight: 4.9990 chunk 22 optimal weight: 10.0000 chunk 40 optimal weight: 0.6980 chunk 42 optimal weight: 6.9990 chunk 32 optimal weight: 1.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 = 0.4865 r_free = 0.4865 target = 0.198073 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.129504 restraints weight = 9622.867| |-----------------------------------------------------------------------------| r_work (start): 0.4008 rms_B_bonded: 3.05 r_work: 0.3864 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work: 0.3743 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3743 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8304 moved from start: 0.3929 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= 0.100 Angle : 0.621 7.806 11772 Z= 0.299 Chirality : 0.047 0.134 1356 Planarity : 0.002 0.034 1440 Dihedral : 11.177 64.472 1521 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 3.98 % Allowed : 26.74 % Favored : 69.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.29 (0.23), residues: 900 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.74 (0.18), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG O 349 TYR 0.011 0.002 TYR P 310 PHE 0.013 0.002 PHE N 378 HIS 0.001 0.000 HIS P 374 Details of bonding type rmsd covalent geometry : bond 0.00232 ( 8778) covalent geometry : angle 0.62145 (11772) hydrogen bonds : bond 0.01973 ( 300) hydrogen bonds : angle 4.85772 ( 852) Misc. bond : bond 0.00013 ( 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 428 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 396 time to evaluate : 0.389 Fit side-chains REVERT: B 331 LYS cc_start: 0.9271 (mttt) cc_final: 0.8921 (mtmt) REVERT: B 353 LYS cc_start: 0.9313 (tttt) cc_final: 0.9039 (tttm) REVERT: B 375 LYS cc_start: 0.9019 (tttt) cc_final: 0.8664 (ttmm) REVERT: C 314 ASP cc_start: 0.8960 (t70) cc_final: 0.8603 (t0) REVERT: M 331 LYS cc_start: 0.9404 (mttt) cc_final: 0.9184 (mtmt) REVERT: M 336 GLN cc_start: 0.9237 (tt0) cc_final: 0.8884 (tt0) REVERT: M 343 LYS cc_start: 0.8675 (mmtm) cc_final: 0.8041 (mtpp) REVERT: N 331 LYS cc_start: 0.9320 (mttt) cc_final: 0.9069 (mtpt) REVERT: N 343 LYS cc_start: 0.8810 (mmtm) cc_final: 0.8213 (mtpp) REVERT: N 345 ASP cc_start: 0.8910 (m-30) cc_final: 0.8602 (m-30) REVERT: O 321 LYS cc_start: 0.9409 (mttt) cc_final: 0.9158 (mttp) REVERT: O 369 LYS cc_start: 0.9203 (ttmm) cc_final: 0.9001 (ttmm) REVERT: O 375 LYS cc_start: 0.8849 (tttt) cc_final: 0.8536 (tttt) REVERT: P 313 VAL cc_start: 0.9099 (t) cc_final: 0.8709 (p) REVERT: P 315 LEU cc_start: 0.9194 (OUTLIER) cc_final: 0.8977 (mp) REVERT: P 331 LYS cc_start: 0.9377 (mttt) cc_final: 0.7638 (tmtt) REVERT: Y 315 LEU cc_start: 0.9323 (OUTLIER) cc_final: 0.9074 (mp) REVERT: Z 311 LYS cc_start: 0.9301 (ptpp) cc_final: 0.8944 (pttt) REVERT: Z 317 LYS cc_start: 0.8365 (ptpt) cc_final: 0.8036 (ptmm) REVERT: Z 331 LYS cc_start: 0.9216 (mttt) cc_final: 0.8778 (mtpt) REVERT: Z 347 LYS cc_start: 0.8520 (ptpt) cc_final: 0.7859 (ptmm) REVERT: Z 353 LYS cc_start: 0.9318 (tttt) cc_final: 0.9015 (tttm) REVERT: Z 375 LYS cc_start: 0.8988 (tttt) cc_final: 0.8637 (ttmm) REVERT: 0 314 ASP cc_start: 0.8516 (t0) cc_final: 0.8170 (t0) REVERT: 1 313 VAL cc_start: 0.8999 (t) cc_final: 0.8498 (p) outliers start: 32 outliers final: 24 residues processed: 400 average time/residue: 0.1173 time to fit residues: 60.5378 Evaluate side-chains 418 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 392 time to evaluate : 0.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 352 SER Chi-restraints excluded: chain A residue 358 ASP Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain B residue 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 M residue 352 SER Chi-restraints excluded: chain M residue 358 ASP Chi-restraints excluded: chain O residue 306 VAL Chi-restraints excluded: chain O residue 339 VAL Chi-restraints excluded: chain P residue 315 LEU 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 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 358 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 55 optimal weight: 0.0060 chunk 46 optimal weight: 5.9990 chunk 57 optimal weight: 4.9990 chunk 50 optimal weight: 5.9990 chunk 22 optimal weight: 10.0000 chunk 8 optimal weight: 6.9990 chunk 80 optimal weight: 4.9990 chunk 48 optimal weight: 5.9990 chunk 2 optimal weight: 7.9990 chunk 5 optimal weight: 6.9990 chunk 3 optimal weight: 5.9990 overall best weight: 4.4004 ------------------------------------------------------------------------------- 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 D 374 HIS M 327 ASN P 374 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4782 r_free = 0.4782 target = 0.190751 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.120800 restraints weight = 9757.267| |-----------------------------------------------------------------------------| r_work (start): 0.3886 rms_B_bonded: 3.02 r_work: 0.3741 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.3621 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3621 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8404 moved from start: 0.3948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.073 8784 Z= 0.315 Angle : 0.760 8.729 11772 Z= 0.369 Chirality : 0.050 0.306 1356 Planarity : 0.003 0.042 1440 Dihedral : 11.565 64.742 1521 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.44 % Favored : 90.56 % Rotamer: Outliers : 4.98 % Allowed : 25.37 % Favored : 69.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.44 (0.23), residues: 900 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.85 (0.17), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG O 349 TYR 0.016 0.003 TYR A 310 PHE 0.013 0.002 PHE C 346 HIS 0.005 0.001 HIS 0 329 Details of bonding type rmsd covalent geometry : bond 0.00761 ( 8778) covalent geometry : angle 0.76005 (11772) hydrogen bonds : bond 0.03149 ( 300) hydrogen bonds : angle 5.26484 ( 852) Misc. bond : bond 0.00060 ( 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 417 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 377 time to evaluate : 0.335 Fit side-chains revert: symmetry clash REVERT: A 353 LYS cc_start: 0.9398 (tttt) cc_final: 0.9030 (tttt) REVERT: B 331 LYS cc_start: 0.9329 (mttt) cc_final: 0.8986 (mtmt) REVERT: B 343 LYS cc_start: 0.8969 (mtpp) cc_final: 0.8560 (mtpp) REVERT: B 353 LYS cc_start: 0.9412 (tttt) cc_final: 0.9068 (tttm) REVERT: B 375 LYS cc_start: 0.9061 (tttt) cc_final: 0.8691 (ttmm) REVERT: C 314 ASP cc_start: 0.8900 (t70) cc_final: 0.8658 (t0) REVERT: D 343 LYS cc_start: 0.9150 (mmtt) cc_final: 0.8764 (mmtt) REVERT: M 336 GLN cc_start: 0.9332 (tt0) cc_final: 0.9048 (tt0) REVERT: M 343 LYS cc_start: 0.8814 (mmtm) cc_final: 0.8202 (mtpp) REVERT: N 331 LYS cc_start: 0.9351 (mttt) cc_final: 0.9134 (mtpt) REVERT: N 343 LYS cc_start: 0.8898 (mmtm) cc_final: 0.8259 (mtpp) REVERT: N 345 ASP cc_start: 0.8901 (m-30) cc_final: 0.8482 (m-30) REVERT: N 347 LYS cc_start: 0.8589 (ptpt) cc_final: 0.7951 (ptmm) REVERT: O 321 LYS cc_start: 0.9387 (mttt) cc_final: 0.9162 (mttp) REVERT: O 375 LYS cc_start: 0.8833 (tttt) cc_final: 0.8570 (tttt) REVERT: P 313 VAL cc_start: 0.9238 (t) cc_final: 0.8835 (p) REVERT: P 315 LEU cc_start: 0.9268 (OUTLIER) cc_final: 0.9005 (mp) REVERT: Y 315 LEU cc_start: 0.9318 (OUTLIER) cc_final: 0.9089 (mp) REVERT: Z 311 LYS cc_start: 0.9374 (ptpp) cc_final: 0.8970 (pttt) REVERT: Z 331 LYS cc_start: 0.9291 (mttt) cc_final: 0.8885 (mtpt) REVERT: Z 347 LYS cc_start: 0.8583 (ptpt) cc_final: 0.7930 (ptmm) REVERT: Z 353 LYS cc_start: 0.9379 (tttt) cc_final: 0.9031 (tttm) REVERT: Z 375 LYS cc_start: 0.9013 (tttt) cc_final: 0.8626 (ttmm) REVERT: 0 343 LYS cc_start: 0.9053 (mtpp) cc_final: 0.8546 (mttm) REVERT: 0 378 PHE cc_start: 0.8888 (t80) cc_final: 0.8508 (t80) outliers start: 40 outliers final: 33 residues processed: 388 average time/residue: 0.1256 time to fit residues: 62.3116 Evaluate side-chains 409 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 374 time to evaluate : 0.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 352 SER Chi-restraints excluded: chain A residue 358 ASP Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain B residue 352 SER Chi-restraints excluded: chain B residue 379 ARG Chi-restraints excluded: chain C residue 309 VAL Chi-restraints excluded: chain C residue 339 VAL Chi-restraints excluded: chain C residue 358 ASP Chi-restraints excluded: chain D residue 319 THR Chi-restraints excluded: chain M residue 306 VAL Chi-restraints excluded: chain M residue 352 SER Chi-restraints excluded: chain M residue 358 ASP Chi-restraints excluded: chain M residue 372 GLU Chi-restraints excluded: chain M residue 373 THR Chi-restraints excluded: chain N residue 306 VAL Chi-restraints excluded: chain O residue 306 VAL Chi-restraints excluded: chain O residue 339 VAL Chi-restraints excluded: chain O residue 352 SER 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 56 optimal weight: 6.9990 chunk 38 optimal weight: 0.7980 chunk 18 optimal weight: 7.9990 chunk 37 optimal weight: 0.7980 chunk 44 optimal weight: 2.9990 chunk 6 optimal weight: 0.8980 chunk 54 optimal weight: 0.6980 chunk 47 optimal weight: 0.6980 chunk 21 optimal weight: 8.9990 chunk 67 optimal weight: 4.9990 chunk 32 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 307 GLN B 327 ASN M 327 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4810 r_free = 0.4810 target = 0.194083 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3992 r_free = 0.3992 target = 0.125940 restraints weight = 9854.760| |-----------------------------------------------------------------------------| r_work (start): 0.4041 rms_B_bonded: 3.08 r_work: 0.3905 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3802 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.3802 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8160 moved from start: 0.4149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 8784 Z= 0.099 Angle : 0.632 8.630 11772 Z= 0.304 Chirality : 0.047 0.131 1356 Planarity : 0.003 0.040 1440 Dihedral : 11.127 63.885 1521 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 3.86 % Allowed : 26.62 % Favored : 69.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.33 (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 ARG 0.007 0.001 ARG O 349 TYR 0.011 0.002 TYR P 310 PHE 0.018 0.002 PHE N 378 HIS 0.002 0.000 HIS 1 330 Details of bonding type rmsd covalent geometry : bond 0.00228 ( 8778) covalent geometry : angle 0.63181 (11772) hydrogen bonds : bond 0.02007 ( 300) hydrogen bonds : angle 4.71910 ( 852) Misc. bond : bond 0.00013 ( 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 423 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 392 time to evaluate : 0.323 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 331 LYS cc_start: 0.9301 (mtpt) cc_final: 0.9076 (mtpt) REVERT: A 353 LYS cc_start: 0.9170 (tttt) cc_final: 0.8800 (tttt) REVERT: B 331 LYS cc_start: 0.9162 (mttt) cc_final: 0.8866 (mtmt) REVERT: B 343 LYS cc_start: 0.8769 (mtpp) cc_final: 0.8354 (mtpp) REVERT: B 353 LYS cc_start: 0.9220 (tttt) cc_final: 0.8911 (tttm) REVERT: B 375 LYS cc_start: 0.8917 (tttt) cc_final: 0.8537 (ttmm) REVERT: C 314 ASP cc_start: 0.8920 (t70) cc_final: 0.8576 (t0) REVERT: M 331 LYS cc_start: 0.9339 (mttt) cc_final: 0.9087 (mtmt) REVERT: M 336 GLN cc_start: 0.9242 (tt0) cc_final: 0.8862 (tt0) REVERT: M 343 LYS cc_start: 0.8595 (mmtm) cc_final: 0.7894 (mtpp) REVERT: N 331 LYS cc_start: 0.9246 (mttt) cc_final: 0.8832 (mtpt) REVERT: N 343 LYS cc_start: 0.8797 (mmtm) cc_final: 0.8184 (mtpp) REVERT: N 345 ASP cc_start: 0.8821 (m-30) cc_final: 0.8519 (m-30) REVERT: O 321 LYS cc_start: 0.9388 (mttt) cc_final: 0.9118 (mttp) REVERT: O 343 LYS cc_start: 0.9160 (mtpp) cc_final: 0.8488 (mptt) REVERT: O 375 LYS cc_start: 0.8772 (tttt) cc_final: 0.8481 (tttt) REVERT: P 313 VAL cc_start: 0.9041 (t) cc_final: 0.8628 (p) REVERT: P 315 LEU cc_start: 0.9071 (OUTLIER) cc_final: 0.8810 (mp) REVERT: P 331 LYS cc_start: 0.9238 (mttt) cc_final: 0.7474 (tmtt) REVERT: Y 315 LEU cc_start: 0.9276 (OUTLIER) cc_final: 0.9029 (mp) REVERT: Z 311 LYS cc_start: 0.9325 (ptpp) cc_final: 0.8873 (pttt) REVERT: Z 316 SER cc_start: 0.9365 (p) cc_final: 0.9095 (p) REVERT: Z 317 LYS cc_start: 0.8133 (ptpt) cc_final: 0.7800 (ptmm) REVERT: Z 331 LYS cc_start: 0.9151 (mttt) cc_final: 0.8769 (mtpt) REVERT: Z 347 LYS cc_start: 0.8519 (ptpt) cc_final: 0.7805 (ptmm) REVERT: Z 353 LYS cc_start: 0.9188 (tttt) cc_final: 0.8823 (tttm) REVERT: Z 375 LYS cc_start: 0.8855 (tttt) cc_final: 0.8480 (ttmm) REVERT: 0 314 ASP cc_start: 0.8484 (t0) cc_final: 0.8034 (t0) REVERT: 0 343 LYS cc_start: 0.8891 (mtpp) cc_final: 0.8397 (mttm) REVERT: 1 313 VAL cc_start: 0.8924 (t) cc_final: 0.8433 (p) REVERT: 1 331 LYS cc_start: 0.9336 (mtmm) cc_final: 0.8956 (mtmt) REVERT: 1 375 LYS cc_start: 0.8364 (tttt) cc_final: 0.8102 (tttt) outliers start: 31 outliers final: 26 residues processed: 397 average time/residue: 0.1168 time to fit residues: 59.4211 Evaluate side-chains 416 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 388 time to evaluate : 0.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 352 SER Chi-restraints excluded: chain A residue 358 ASP Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain B residue 352 SER Chi-restraints excluded: chain B residue 358 ASP Chi-restraints excluded: chain C residue 309 VAL Chi-restraints excluded: chain C residue 339 VAL Chi-restraints excluded: chain C residue 358 ASP 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 O residue 339 VAL Chi-restraints excluded: chain O residue 352 SER Chi-restraints excluded: chain P residue 315 LEU 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 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 358 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 49 optimal weight: 7.9990 chunk 64 optimal weight: 9.9990 chunk 20 optimal weight: 8.9990 chunk 47 optimal weight: 6.9990 chunk 28 optimal weight: 0.0470 chunk 13 optimal weight: 8.9990 chunk 80 optimal weight: 6.9990 chunk 5 optimal weight: 0.2980 chunk 59 optimal weight: 4.9990 chunk 17 optimal weight: 0.9980 chunk 21 optimal weight: 2.9990 overall best weight: 1.8682 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 307 GLN ** B 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4776 r_free = 0.4776 target = 0.191180 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.122566 restraints weight = 9893.878| |-----------------------------------------------------------------------------| r_work (start): 0.3965 rms_B_bonded: 3.06 r_work: 0.3831 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.3725 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3725 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8246 moved from start: 0.4138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 8784 Z= 0.154 Angle : 0.676 10.776 11772 Z= 0.319 Chirality : 0.048 0.135 1356 Planarity : 0.003 0.047 1440 Dihedral : 11.143 63.707 1521 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.22 % Favored : 91.78 % Rotamer: Outliers : 3.48 % Allowed : 27.86 % Favored : 68.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -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 ARG 0.007 0.001 ARG O 349 TYR 0.016 0.002 TYR Y 310 PHE 0.019 0.002 PHE N 378 HIS 0.003 0.001 HIS O 374 Details of bonding type rmsd covalent geometry : bond 0.00366 ( 8778) covalent geometry : angle 0.67567 (11772) hydrogen bonds : bond 0.02357 ( 300) hydrogen bonds : angle 4.82605 ( 852) Misc. bond : bond 0.00028 ( 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 413 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 385 time to evaluate : 0.339 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 331 LYS cc_start: 0.9334 (mtpt) cc_final: 0.9127 (mtpt) REVERT: A 353 LYS cc_start: 0.9256 (tttt) cc_final: 0.8867 (tttt) REVERT: B 331 LYS cc_start: 0.9229 (mttt) cc_final: 0.8923 (mtmt) REVERT: B 343 LYS cc_start: 0.8867 (mtpp) cc_final: 0.8472 (mtpp) REVERT: B 353 LYS cc_start: 0.9314 (tttt) cc_final: 0.8959 (tttm) REVERT: B 375 LYS cc_start: 0.8953 (tttt) cc_final: 0.8587 (ttmm) REVERT: C 314 ASP cc_start: 0.8918 (t70) cc_final: 0.8626 (t0) REVERT: M 336 GLN cc_start: 0.9270 (tt0) cc_final: 0.8876 (tt0) REVERT: M 343 LYS cc_start: 0.8680 (mmtm) cc_final: 0.8005 (mtpp) REVERT: N 331 LYS cc_start: 0.9273 (mttt) cc_final: 0.8865 (mtpt) REVERT: N 343 LYS cc_start: 0.8845 (mmtm) cc_final: 0.8233 (mtpp) REVERT: N 345 ASP cc_start: 0.8832 (m-30) cc_final: 0.8499 (m-30) REVERT: O 321 LYS cc_start: 0.9386 (mttt) cc_final: 0.9111 (mttp) REVERT: O 343 LYS cc_start: 0.9115 (mtpp) cc_final: 0.8522 (mmtt) REVERT: O 375 LYS cc_start: 0.8800 (tttt) cc_final: 0.8506 (tttt) REVERT: P 313 VAL cc_start: 0.9062 (t) cc_final: 0.8624 (p) REVERT: P 315 LEU cc_start: 0.9112 (OUTLIER) cc_final: 0.8864 (mp) REVERT: Y 315 LEU cc_start: 0.9302 (OUTLIER) cc_final: 0.9053 (mp) REVERT: Z 311 LYS cc_start: 0.9356 (ptpp) cc_final: 0.8901 (pttt) REVERT: Z 331 LYS cc_start: 0.9179 (mttt) cc_final: 0.8697 (mtpt) REVERT: Z 347 LYS cc_start: 0.8567 (ptpt) cc_final: 0.7870 (ptmm) REVERT: Z 353 LYS cc_start: 0.9240 (tttt) cc_final: 0.8890 (tttm) REVERT: Z 375 LYS cc_start: 0.8890 (tttt) cc_final: 0.8535 (ttmm) REVERT: 0 314 ASP cc_start: 0.8547 (t0) cc_final: 0.8110 (t0) REVERT: 0 343 LYS cc_start: 0.8955 (mtpp) cc_final: 0.8443 (mttm) REVERT: 1 313 VAL cc_start: 0.8976 (t) cc_final: 0.8472 (p) REVERT: 1 327 ASN cc_start: 0.9252 (t0) cc_final: 0.8958 (t0) REVERT: 1 375 LYS cc_start: 0.8453 (tttt) cc_final: 0.8166 (tttt) outliers start: 28 outliers final: 26 residues processed: 392 average time/residue: 0.1252 time to fit residues: 62.7574 Evaluate side-chains 411 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 383 time to evaluate : 0.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 352 SER Chi-restraints excluded: chain A residue 358 ASP Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain B residue 352 SER Chi-restraints excluded: chain B residue 358 ASP Chi-restraints excluded: chain C residue 309 VAL Chi-restraints excluded: chain C residue 339 VAL Chi-restraints excluded: chain D residue 342 GLU 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 O residue 339 VAL Chi-restraints excluded: chain O residue 352 SER Chi-restraints excluded: chain P residue 315 LEU Chi-restraints excluded: chain Y residue 315 LEU Chi-restraints excluded: chain Y residue 339 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 0 residue 325 LEU Chi-restraints excluded: chain 0 residue 338 GLU Chi-restraints excluded: chain 0 residue 339 VAL Chi-restraints excluded: chain 0 residue 358 ASP Chi-restraints excluded: chain 0 residue 376 LEU Chi-restraints excluded: chain 1 residue 358 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 24 optimal weight: 7.9990 chunk 75 optimal weight: 4.9990 chunk 18 optimal weight: 10.0000 chunk 56 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 65 optimal weight: 5.9990 chunk 20 optimal weight: 8.9990 chunk 17 optimal weight: 0.5980 chunk 49 optimal weight: 4.9990 chunk 67 optimal weight: 6.9990 chunk 29 optimal weight: 10.0000 overall best weight: 4.7188 ------------------------------------------------------------------------------- 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 ** 0 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4741 r_free = 0.4741 target = 0.187746 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.121125 restraints weight = 9835.518| |-----------------------------------------------------------------------------| r_work (start): 0.3913 rms_B_bonded: 2.87 r_work: 0.3776 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3671 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.3671 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8310 moved from start: 0.4194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.071 8784 Z= 0.336 Angle : 0.800 8.474 11772 Z= 0.387 Chirality : 0.051 0.155 1356 Planarity : 0.003 0.052 1440 Dihedral : 11.545 64.457 1521 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 9.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.44 % Favored : 91.56 % Rotamer: Outliers : 3.61 % Allowed : 28.11 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.52 (0.23), 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 ARG 0.007 0.001 ARG O 349 TYR 0.018 0.003 TYR Y 310 PHE 0.017 0.003 PHE N 378 HIS 0.005 0.001 HIS O 374 Details of bonding type rmsd covalent geometry : bond 0.00808 ( 8778) covalent geometry : angle 0.80010 (11772) hydrogen bonds : bond 0.03163 ( 300) hydrogen bonds : angle 5.27924 ( 852) Misc. bond : bond 0.00065 ( 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 403 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 374 time to evaluate : 0.251 Fit side-chains revert: symmetry clash REVERT: A 331 LYS cc_start: 0.9336 (mtpt) cc_final: 0.9108 (mtpt) REVERT: A 353 LYS cc_start: 0.9308 (tttt) cc_final: 0.8899 (tttt) REVERT: B 331 LYS cc_start: 0.9300 (mttt) cc_final: 0.9019 (mtmt) REVERT: B 343 LYS cc_start: 0.8930 (mtpp) cc_final: 0.8529 (mtpp) REVERT: B 353 LYS cc_start: 0.9319 (tttt) cc_final: 0.8934 (tttm) REVERT: B 375 LYS cc_start: 0.9004 (tttt) cc_final: 0.8625 (ttmm) REVERT: C 314 ASP cc_start: 0.8928 (t70) cc_final: 0.8654 (t0) REVERT: D 342 GLU cc_start: 0.9335 (tt0) cc_final: 0.8871 (mm-30) REVERT: M 336 GLN cc_start: 0.9303 (tt0) cc_final: 0.8973 (tt0) REVERT: M 343 LYS cc_start: 0.8748 (mmtm) cc_final: 0.8255 (ttmm) REVERT: N 331 LYS cc_start: 0.9311 (mttt) cc_final: 0.9047 (mtpt) REVERT: N 343 LYS cc_start: 0.8921 (mmtm) cc_final: 0.8294 (mtpp) REVERT: N 345 ASP cc_start: 0.8849 (m-30) cc_final: 0.8409 (m-30) REVERT: N 347 LYS cc_start: 0.8647 (ptpt) cc_final: 0.7929 (ptmm) REVERT: O 321 LYS cc_start: 0.9383 (mttt) cc_final: 0.9095 (mttp) REVERT: O 343 LYS cc_start: 0.9130 (mtpp) cc_final: 0.8541 (mptt) REVERT: O 375 LYS cc_start: 0.8823 (tttt) cc_final: 0.8536 (tttt) REVERT: P 313 VAL cc_start: 0.9247 (t) cc_final: 0.8837 (p) REVERT: P 315 LEU cc_start: 0.9150 (OUTLIER) cc_final: 0.8917 (mp) REVERT: P 331 LYS cc_start: 0.9278 (mttt) cc_final: 0.7490 (tmtt) REVERT: Y 315 LEU cc_start: 0.9293 (OUTLIER) cc_final: 0.9071 (mp) REVERT: Z 311 LYS cc_start: 0.9387 (ptpp) cc_final: 0.8915 (pttt) REVERT: Z 331 LYS cc_start: 0.9241 (mttt) cc_final: 0.8927 (mtpt) REVERT: Z 347 LYS cc_start: 0.8570 (ptpt) cc_final: 0.7894 (ptmm) REVERT: Z 353 LYS cc_start: 0.9268 (tttt) cc_final: 0.8887 (tttm) REVERT: Z 375 LYS cc_start: 0.8962 (tttt) cc_final: 0.8552 (ttmm) REVERT: Z 379 ARG cc_start: 0.7862 (ptt90) cc_final: 0.7404 (ptt90) REVERT: 0 343 LYS cc_start: 0.8989 (mtpp) cc_final: 0.8479 (mttm) REVERT: 0 378 PHE cc_start: 0.8888 (t80) cc_final: 0.8514 (t80) REVERT: 1 331 LYS cc_start: 0.9415 (mtmt) cc_final: 0.9013 (mtmt) REVERT: 1 375 LYS cc_start: 0.8513 (tttt) cc_final: 0.8229 (tttt) outliers start: 29 outliers final: 24 residues processed: 385 average time/residue: 0.1186 time to fit residues: 58.7006 Evaluate side-chains 399 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 373 time to evaluate : 0.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 352 SER Chi-restraints excluded: chain A residue 358 ASP Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain B residue 352 SER Chi-restraints excluded: chain B residue 379 ARG Chi-restraints excluded: chain C residue 309 VAL Chi-restraints excluded: chain C residue 339 VAL 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 O residue 339 VAL Chi-restraints excluded: chain O residue 352 SER Chi-restraints excluded: chain P residue 315 LEU 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 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 358 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 26 optimal weight: 0.9980 chunk 34 optimal weight: 0.9990 chunk 28 optimal weight: 3.9990 chunk 17 optimal weight: 1.9990 chunk 47 optimal weight: 0.5980 chunk 12 optimal weight: 0.9990 chunk 56 optimal weight: 6.9990 chunk 44 optimal weight: 4.9990 chunk 82 optimal weight: 0.9990 chunk 19 optimal weight: 0.9990 chunk 41 optimal weight: 2.9990 overall best weight: 0.9186 ------------------------------------------------------------------------------- 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 = 0.4806 r_free = 0.4806 target = 0.192858 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.124860 restraints weight = 9732.830| |-----------------------------------------------------------------------------| r_work (start): 0.4003 rms_B_bonded: 3.03 r_work: 0.3869 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3763 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3763 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8205 moved from start: 0.4334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 8784 Z= 0.108 Angle : 0.666 8.624 11772 Z= 0.317 Chirality : 0.048 0.137 1356 Planarity : 0.003 0.045 1440 Dihedral : 11.106 63.629 1521 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.00 % Favored : 94.00 % Rotamer: Outliers : 3.23 % Allowed : 28.73 % Favored : 68.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.34 (0.23), residues: 900 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.78 (0.18), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG O 349 TYR 0.015 0.002 TYR Y 310 PHE 0.020 0.002 PHE N 378 HIS 0.002 0.000 HIS N 374 Details of bonding type rmsd covalent geometry : bond 0.00247 ( 8778) covalent geometry : angle 0.66596 (11772) hydrogen bonds : bond 0.02021 ( 300) hydrogen bonds : angle 4.77920 ( 852) Misc. bond : bond 0.00017 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3276.37 seconds wall clock time: 57 minutes 3.68 seconds (3423.68 seconds total)