Starting phenix.real_space_refine on Mon Mar 11 02:08:37 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ovt_13089/03_2024/7ovt_13089.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ovt_13089/03_2024/7ovt_13089.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.69 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ovt_13089/03_2024/7ovt_13089.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ovt_13089/03_2024/7ovt_13089.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ovt_13089/03_2024/7ovt_13089.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ovt_13089/03_2024/7ovt_13089.pdb" } resolution = 2.69 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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 24 5.16 5 C 4212 2.51 5 N 1128 2.21 5 O 1224 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 2": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 18": "NH1" <-> "NH2" Residue "A ASP 22": "OD1" <-> "OD2" Residue "A TYR 34": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 2": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 18": "NH1" <-> "NH2" Residue "B ASP 22": "OD1" <-> "OD2" Residue "B TYR 34": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 2": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 18": "NH1" <-> "NH2" Residue "C ASP 22": "OD1" <-> "OD2" Residue "C TYR 34": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 2": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 18": "NH1" <-> "NH2" Residue "D ASP 22": "OD1" <-> "OD2" Residue "D TYR 34": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 2": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 18": "NH1" <-> "NH2" Residue "E ASP 22": "OD1" <-> "OD2" Residue "E TYR 34": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 2": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 18": "NH1" <-> "NH2" Residue "F ASP 22": "OD1" <-> "OD2" Residue "F TYR 34": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 2": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 18": "NH1" <-> "NH2" Residue "G ASP 22": "OD1" <-> "OD2" Residue "G TYR 34": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 2": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 18": "NH1" <-> "NH2" Residue "H ASP 22": "OD1" <-> "OD2" Residue "H TYR 34": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 2": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 18": "NH1" <-> "NH2" Residue "I ASP 22": "OD1" <-> "OD2" Residue "I TYR 34": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 2": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 18": "NH1" <-> "NH2" Residue "J ASP 22": "OD1" <-> "OD2" Residue "J TYR 34": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 2": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ARG 18": "NH1" <-> "NH2" Residue "K ASP 22": "OD1" <-> "OD2" Residue "K TYR 34": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 2": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 18": "NH1" <-> "NH2" Residue "L ASP 22": "OD1" <-> "OD2" Residue "L TYR 34": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 6588 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 549 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 549 Classifications: {'peptide': 69} Link IDs: {'PTRANS': 1, 'TRANS': 67} Chain: "B" Number of atoms: 549 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 549 Classifications: {'peptide': 69} Link IDs: {'PTRANS': 1, 'TRANS': 67} Chain: "C" Number of atoms: 549 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 549 Classifications: {'peptide': 69} Link IDs: {'PTRANS': 1, 'TRANS': 67} Chain: "D" Number of atoms: 549 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 549 Classifications: {'peptide': 69} Link IDs: {'PTRANS': 1, 'TRANS': 67} Chain: "E" Number of atoms: 549 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 549 Classifications: {'peptide': 69} Link IDs: {'PTRANS': 1, 'TRANS': 67} Chain: "F" Number of atoms: 549 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 549 Classifications: {'peptide': 69} Link IDs: {'PTRANS': 1, 'TRANS': 67} Chain: "G" Number of atoms: 549 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 549 Classifications: {'peptide': 69} Link IDs: {'PTRANS': 1, 'TRANS': 67} Chain: "H" Number of atoms: 549 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 549 Classifications: {'peptide': 69} Link IDs: {'PTRANS': 1, 'TRANS': 67} Chain: "I" Number of atoms: 549 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 549 Classifications: {'peptide': 69} Link IDs: {'PTRANS': 1, 'TRANS': 67} Chain: "J" Number of atoms: 549 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 549 Classifications: {'peptide': 69} Link IDs: {'PTRANS': 1, 'TRANS': 67} Chain: "K" Number of atoms: 549 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 549 Classifications: {'peptide': 69} Link IDs: {'PTRANS': 1, 'TRANS': 67} Chain: "L" Number of atoms: 549 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 549 Classifications: {'peptide': 69} Link IDs: {'PTRANS': 1, 'TRANS': 67} Time building chain proxies: 3.87, per 1000 atoms: 0.59 Number of scatterers: 6588 At special positions: 0 Unit cell: (105.04, 127.92, 54.08, 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 24 16.00 O 1224 8.00 N 1128 7.00 C 4212 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.26 Conformation dependent library (CDL) restraints added in 1.3 seconds 1608 Ramachandran restraints generated. 804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1392 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 12 sheets defined 0.0% alpha, 58.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.75 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 2 through 21 removed outlier: 6.752A pdb=" N PHE A 10 " --> pdb=" O ALA C 9 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N GLN C 11 " --> pdb=" O PHE A 10 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N GLY A 12 " --> pdb=" O GLN C 11 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N ALA C 13 " --> pdb=" O GLY A 12 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N MET A 16 " --> pdb=" O ASP C 15 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N TRP C 17 " --> pdb=" O MET A 16 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N PHE C 10 " --> pdb=" O ALA E 9 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N GLN E 11 " --> pdb=" O PHE C 10 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N GLY C 12 " --> pdb=" O GLN E 11 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N ALA E 13 " --> pdb=" O GLY C 12 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N MET C 16 " --> pdb=" O ASP E 15 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N TRP E 17 " --> pdb=" O MET C 16 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N PHE E 10 " --> pdb=" O ALA G 9 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N GLN G 11 " --> pdb=" O PHE E 10 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N GLY E 12 " --> pdb=" O GLN G 11 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N ALA G 13 " --> pdb=" O GLY E 12 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N MET E 16 " --> pdb=" O ASP G 15 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N TRP G 17 " --> pdb=" O MET E 16 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N PHE G 10 " --> pdb=" O ALA I 9 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N GLN I 11 " --> pdb=" O PHE G 10 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N GLY G 12 " --> pdb=" O GLN I 11 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N ALA I 13 " --> pdb=" O GLY G 12 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N MET G 16 " --> pdb=" O ASP I 15 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N TRP I 17 " --> pdb=" O MET G 16 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N PHE I 10 " --> pdb=" O ALA K 9 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N GLN K 11 " --> pdb=" O PHE I 10 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N GLY I 12 " --> pdb=" O GLN K 11 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N ALA K 13 " --> pdb=" O GLY I 12 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N MET I 16 " --> pdb=" O ASP K 15 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N TRP K 17 " --> pdb=" O MET I 16 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 27 through 29 Processing sheet with id=AA3, first strand: chain 'A' and resid 33 through 38 removed outlier: 6.533A pdb=" N LYS A 33 " --> pdb=" O TYR C 34 " (cutoff:3.500A) removed outlier: 7.939A pdb=" N HIS C 36 " --> pdb=" O LYS A 33 " (cutoff:3.500A) removed outlier: 6.185A pdb=" N PHE A 35 " --> pdb=" O HIS C 36 " (cutoff:3.500A) removed outlier: 7.907A pdb=" N ARG C 38 " --> pdb=" O PHE A 35 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N ALA A 37 " --> pdb=" O ARG C 38 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N LYS C 33 " --> pdb=" O TYR E 34 " (cutoff:3.500A) removed outlier: 7.939A pdb=" N HIS E 36 " --> pdb=" O LYS C 33 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N PHE C 35 " --> pdb=" O HIS E 36 " (cutoff:3.500A) removed outlier: 7.907A pdb=" N ARG E 38 " --> pdb=" O PHE C 35 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N ALA C 37 " --> pdb=" O ARG E 38 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N LYS E 33 " --> pdb=" O TYR G 34 " (cutoff:3.500A) removed outlier: 7.939A pdb=" N HIS G 36 " --> pdb=" O LYS E 33 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N PHE E 35 " --> pdb=" O HIS G 36 " (cutoff:3.500A) removed outlier: 7.907A pdb=" N ARG G 38 " --> pdb=" O PHE E 35 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N ALA E 37 " --> pdb=" O ARG G 38 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N LYS G 33 " --> pdb=" O TYR I 34 " (cutoff:3.500A) removed outlier: 7.938A pdb=" N HIS I 36 " --> pdb=" O LYS G 33 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N PHE G 35 " --> pdb=" O HIS I 36 " (cutoff:3.500A) removed outlier: 7.907A pdb=" N ARG I 38 " --> pdb=" O PHE G 35 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N ALA G 37 " --> pdb=" O ARG I 38 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N LYS I 33 " --> pdb=" O TYR K 34 " (cutoff:3.500A) removed outlier: 7.939A pdb=" N HIS K 36 " --> pdb=" O LYS I 33 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N PHE I 35 " --> pdb=" O HIS K 36 " (cutoff:3.500A) removed outlier: 7.907A pdb=" N ARG K 38 " --> pdb=" O PHE I 35 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N ALA I 37 " --> pdb=" O ARG K 38 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 41 through 46 removed outlier: 6.879A pdb=" N ALA C 43 " --> pdb=" O ASP A 42 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N ALA A 44 " --> pdb=" O ALA C 43 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N ALA E 43 " --> pdb=" O ASP C 42 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N ALA C 44 " --> pdb=" O ALA E 43 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N ALA G 43 " --> pdb=" O ASP E 42 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N ALA E 44 " --> pdb=" O ALA G 43 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N ALA I 43 " --> pdb=" O ASP G 42 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N ALA G 44 " --> pdb=" O ALA I 43 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N ALA K 43 " --> pdb=" O ASP I 42 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N ALA I 44 " --> pdb=" O ALA K 43 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 51 through 58 removed outlier: 6.214A pdb=" N VAL A 51 " --> pdb=" O TRP C 52 " (cutoff:3.500A) removed outlier: 7.550A pdb=" N ALA C 54 " --> pdb=" O VAL A 51 " (cutoff:3.500A) removed outlier: 5.759A pdb=" N ALA A 53 " --> pdb=" O ALA C 54 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N LYS C 56 " --> pdb=" O ALA A 53 " (cutoff:3.500A) removed outlier: 7.071A pdb=" N GLU A 55 " --> pdb=" O LYS C 56 " (cutoff:3.500A) removed outlier: 9.966A pdb=" N SER C 58 " --> pdb=" O GLU A 55 " (cutoff:3.500A) removed outlier: 8.745A pdb=" N ILE A 57 " --> pdb=" O SER C 58 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N VAL C 51 " --> pdb=" O TRP E 52 " (cutoff:3.500A) removed outlier: 7.549A pdb=" N ALA E 54 " --> pdb=" O VAL C 51 " (cutoff:3.500A) removed outlier: 5.759A pdb=" N ALA C 53 " --> pdb=" O ALA E 54 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N LYS E 56 " --> pdb=" O ALA C 53 " (cutoff:3.500A) removed outlier: 7.071A pdb=" N GLU C 55 " --> pdb=" O LYS E 56 " (cutoff:3.500A) removed outlier: 9.965A pdb=" N SER E 58 " --> pdb=" O GLU C 55 " (cutoff:3.500A) removed outlier: 8.745A pdb=" N ILE C 57 " --> pdb=" O SER E 58 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N VAL E 51 " --> pdb=" O TRP G 52 " (cutoff:3.500A) removed outlier: 7.550A pdb=" N ALA G 54 " --> pdb=" O VAL E 51 " (cutoff:3.500A) removed outlier: 5.759A pdb=" N ALA E 53 " --> pdb=" O ALA G 54 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N LYS G 56 " --> pdb=" O ALA E 53 " (cutoff:3.500A) removed outlier: 7.071A pdb=" N GLU E 55 " --> pdb=" O LYS G 56 " (cutoff:3.500A) removed outlier: 9.966A pdb=" N SER G 58 " --> pdb=" O GLU E 55 " (cutoff:3.500A) removed outlier: 8.745A pdb=" N ILE E 57 " --> pdb=" O SER G 58 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N VAL G 51 " --> pdb=" O TRP I 52 " (cutoff:3.500A) removed outlier: 7.550A pdb=" N ALA I 54 " --> pdb=" O VAL G 51 " (cutoff:3.500A) removed outlier: 5.759A pdb=" N ALA G 53 " --> pdb=" O ALA I 54 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N LYS I 56 " --> pdb=" O ALA G 53 " (cutoff:3.500A) removed outlier: 7.071A pdb=" N GLU G 55 " --> pdb=" O LYS I 56 " (cutoff:3.500A) removed outlier: 9.966A pdb=" N SER I 58 " --> pdb=" O GLU G 55 " (cutoff:3.500A) removed outlier: 8.745A pdb=" N ILE G 57 " --> pdb=" O SER I 58 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N VAL I 51 " --> pdb=" O TRP K 52 " (cutoff:3.500A) removed outlier: 7.550A pdb=" N ALA K 54 " --> pdb=" O VAL I 51 " (cutoff:3.500A) removed outlier: 5.759A pdb=" N ALA I 53 " --> pdb=" O ALA K 54 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N LYS K 56 " --> pdb=" O ALA I 53 " (cutoff:3.500A) removed outlier: 7.072A pdb=" N GLU I 55 " --> pdb=" O LYS K 56 " (cutoff:3.500A) removed outlier: 9.965A pdb=" N SER K 58 " --> pdb=" O GLU I 55 " (cutoff:3.500A) removed outlier: 8.745A pdb=" N ILE I 57 " --> pdb=" O SER K 58 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 65 through 67 Processing sheet with id=AA7, first strand: chain 'B' and resid 2 through 21 removed outlier: 6.752A pdb=" N PHE B 10 " --> pdb=" O ALA D 9 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N GLN D 11 " --> pdb=" O PHE B 10 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N GLY B 12 " --> pdb=" O GLN D 11 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N ALA D 13 " --> pdb=" O GLY B 12 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N MET B 16 " --> pdb=" O ASP D 15 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N TRP D 17 " --> pdb=" O MET B 16 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N PHE D 10 " --> pdb=" O ALA F 9 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N GLN F 11 " --> pdb=" O PHE D 10 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N GLY D 12 " --> pdb=" O GLN F 11 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N ALA F 13 " --> pdb=" O GLY D 12 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N MET D 16 " --> pdb=" O ASP F 15 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N TRP F 17 " --> pdb=" O MET D 16 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N PHE F 10 " --> pdb=" O ALA H 9 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N GLN H 11 " --> pdb=" O PHE F 10 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N GLY F 12 " --> pdb=" O GLN H 11 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N ALA H 13 " --> pdb=" O GLY F 12 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N MET F 16 " --> pdb=" O ASP H 15 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N TRP H 17 " --> pdb=" O MET F 16 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N PHE H 10 " --> pdb=" O ALA J 9 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N GLN J 11 " --> pdb=" O PHE H 10 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N GLY H 12 " --> pdb=" O GLN J 11 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N ALA J 13 " --> pdb=" O GLY H 12 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N MET H 16 " --> pdb=" O ASP J 15 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N TRP J 17 " --> pdb=" O MET H 16 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N PHE J 10 " --> pdb=" O ALA L 9 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N GLN L 11 " --> pdb=" O PHE J 10 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N GLY J 12 " --> pdb=" O GLN L 11 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N ALA L 13 " --> pdb=" O GLY J 12 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N MET J 16 " --> pdb=" O ASP L 15 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N TRP L 17 " --> pdb=" O MET J 16 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 27 through 29 Processing sheet with id=AA9, first strand: chain 'B' and resid 33 through 38 removed outlier: 6.534A pdb=" N LYS B 33 " --> pdb=" O TYR D 34 " (cutoff:3.500A) removed outlier: 7.939A pdb=" N HIS D 36 " --> pdb=" O LYS B 33 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N PHE B 35 " --> pdb=" O HIS D 36 " (cutoff:3.500A) removed outlier: 7.907A pdb=" N ARG D 38 " --> pdb=" O PHE B 35 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N ALA B 37 " --> pdb=" O ARG D 38 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N LYS D 33 " --> pdb=" O TYR F 34 " (cutoff:3.500A) removed outlier: 7.939A pdb=" N HIS F 36 " --> pdb=" O LYS D 33 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N PHE D 35 " --> pdb=" O HIS F 36 " (cutoff:3.500A) removed outlier: 7.908A pdb=" N ARG F 38 " --> pdb=" O PHE D 35 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N ALA D 37 " --> pdb=" O ARG F 38 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N LYS F 33 " --> pdb=" O TYR H 34 " (cutoff:3.500A) removed outlier: 7.939A pdb=" N HIS H 36 " --> pdb=" O LYS F 33 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N PHE F 35 " --> pdb=" O HIS H 36 " (cutoff:3.500A) removed outlier: 7.907A pdb=" N ARG H 38 " --> pdb=" O PHE F 35 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N ALA F 37 " --> pdb=" O ARG H 38 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N LYS H 33 " --> pdb=" O TYR J 34 " (cutoff:3.500A) removed outlier: 7.939A pdb=" N HIS J 36 " --> pdb=" O LYS H 33 " (cutoff:3.500A) removed outlier: 6.185A pdb=" N PHE H 35 " --> pdb=" O HIS J 36 " (cutoff:3.500A) removed outlier: 7.907A pdb=" N ARG J 38 " --> pdb=" O PHE H 35 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N ALA H 37 " --> pdb=" O ARG J 38 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N LYS J 33 " --> pdb=" O TYR L 34 " (cutoff:3.500A) removed outlier: 7.939A pdb=" N HIS L 36 " --> pdb=" O LYS J 33 " (cutoff:3.500A) removed outlier: 6.185A pdb=" N PHE J 35 " --> pdb=" O HIS L 36 " (cutoff:3.500A) removed outlier: 7.907A pdb=" N ARG L 38 " --> pdb=" O PHE J 35 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N ALA J 37 " --> pdb=" O ARG L 38 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'B' and resid 41 through 46 removed outlier: 6.879A pdb=" N ALA D 43 " --> pdb=" O ASP B 42 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N ALA B 44 " --> pdb=" O ALA D 43 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N ALA F 43 " --> pdb=" O ASP D 42 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N ALA D 44 " --> pdb=" O ALA F 43 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N ALA H 43 " --> pdb=" O ASP F 42 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N ALA F 44 " --> pdb=" O ALA H 43 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N ALA J 43 " --> pdb=" O ASP H 42 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N ALA H 44 " --> pdb=" O ALA J 43 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N ALA L 43 " --> pdb=" O ASP J 42 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N ALA J 44 " --> pdb=" O ALA L 43 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 51 through 58 removed outlier: 6.214A pdb=" N VAL B 51 " --> pdb=" O TRP D 52 " (cutoff:3.500A) removed outlier: 7.551A pdb=" N ALA D 54 " --> pdb=" O VAL B 51 " (cutoff:3.500A) removed outlier: 5.759A pdb=" N ALA B 53 " --> pdb=" O ALA D 54 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N LYS D 56 " --> pdb=" O ALA B 53 " (cutoff:3.500A) removed outlier: 7.071A pdb=" N GLU B 55 " --> pdb=" O LYS D 56 " (cutoff:3.500A) removed outlier: 9.966A pdb=" N SER D 58 " --> pdb=" O GLU B 55 " (cutoff:3.500A) removed outlier: 8.745A pdb=" N ILE B 57 " --> pdb=" O SER D 58 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N VAL D 51 " --> pdb=" O TRP F 52 " (cutoff:3.500A) removed outlier: 7.550A pdb=" N ALA F 54 " --> pdb=" O VAL D 51 " (cutoff:3.500A) removed outlier: 5.759A pdb=" N ALA D 53 " --> pdb=" O ALA F 54 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N LYS F 56 " --> pdb=" O ALA D 53 " (cutoff:3.500A) removed outlier: 7.071A pdb=" N GLU D 55 " --> pdb=" O LYS F 56 " (cutoff:3.500A) removed outlier: 9.965A pdb=" N SER F 58 " --> pdb=" O GLU D 55 " (cutoff:3.500A) removed outlier: 8.745A pdb=" N ILE D 57 " --> pdb=" O SER F 58 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N VAL F 51 " --> pdb=" O TRP H 52 " (cutoff:3.500A) removed outlier: 7.551A pdb=" N ALA H 54 " --> pdb=" O VAL F 51 " (cutoff:3.500A) removed outlier: 5.760A pdb=" N ALA F 53 " --> pdb=" O ALA H 54 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N LYS H 56 " --> pdb=" O ALA F 53 " (cutoff:3.500A) removed outlier: 7.072A pdb=" N GLU F 55 " --> pdb=" O LYS H 56 " (cutoff:3.500A) removed outlier: 9.965A pdb=" N SER H 58 " --> pdb=" O GLU F 55 " (cutoff:3.500A) removed outlier: 8.745A pdb=" N ILE F 57 " --> pdb=" O SER H 58 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N VAL H 51 " --> pdb=" O TRP J 52 " (cutoff:3.500A) removed outlier: 7.550A pdb=" N ALA J 54 " --> pdb=" O VAL H 51 " (cutoff:3.500A) removed outlier: 5.758A pdb=" N ALA H 53 " --> pdb=" O ALA J 54 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N LYS J 56 " --> pdb=" O ALA H 53 " (cutoff:3.500A) removed outlier: 7.071A pdb=" N GLU H 55 " --> pdb=" O LYS J 56 " (cutoff:3.500A) removed outlier: 9.965A pdb=" N SER J 58 " --> pdb=" O GLU H 55 " (cutoff:3.500A) removed outlier: 8.745A pdb=" N ILE H 57 " --> pdb=" O SER J 58 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N VAL J 51 " --> pdb=" O TRP L 52 " (cutoff:3.500A) removed outlier: 7.549A pdb=" N ALA L 54 " --> pdb=" O VAL J 51 " (cutoff:3.500A) removed outlier: 5.759A pdb=" N ALA J 53 " --> pdb=" O ALA L 54 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N LYS L 56 " --> pdb=" O ALA J 53 " (cutoff:3.500A) removed outlier: 7.072A pdb=" N GLU J 55 " --> pdb=" O LYS L 56 " (cutoff:3.500A) removed outlier: 9.965A pdb=" N SER L 58 " --> pdb=" O GLU J 55 " (cutoff:3.500A) removed outlier: 8.745A pdb=" N ILE J 57 " --> pdb=" O SER L 58 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'B' and resid 65 through 67 200 hydrogen bonds defined for protein. 600 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: 1.83 Time building geometry restraints manager: 2.47 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.30: 1140 1.30 - 1.42: 2280 1.42 - 1.54: 3324 1.54 - 1.66: 12 1.66 - 1.79: 48 Bond restraints: 6804 Sorted by residual: bond pdb=" C ILE D 6 " pdb=" O ILE D 6 " ideal model delta sigma weight residual 1.236 1.180 0.056 1.04e-02 9.25e+03 2.91e+01 bond pdb=" C ILE L 6 " pdb=" O ILE L 6 " ideal model delta sigma weight residual 1.236 1.180 0.056 1.04e-02 9.25e+03 2.91e+01 bond pdb=" C ILE K 6 " pdb=" O ILE K 6 " ideal model delta sigma weight residual 1.236 1.180 0.056 1.04e-02 9.25e+03 2.91e+01 bond pdb=" C ILE H 6 " pdb=" O ILE H 6 " ideal model delta sigma weight residual 1.236 1.180 0.056 1.04e-02 9.25e+03 2.90e+01 bond pdb=" C ILE G 6 " pdb=" O ILE G 6 " ideal model delta sigma weight residual 1.236 1.180 0.056 1.04e-02 9.25e+03 2.90e+01 ... (remaining 6799 not shown) Histogram of bond angle deviations from ideal: 100.78 - 107.47: 416 107.47 - 114.16: 2834 114.16 - 120.85: 3747 120.85 - 127.54: 2027 127.54 - 134.22: 84 Bond angle restraints: 9108 Sorted by residual: angle pdb=" N GLY H 49 " pdb=" CA GLY H 49 " pdb=" C GLY H 49 " ideal model delta sigma weight residual 110.46 120.12 -9.66 1.43e+00 4.89e-01 4.56e+01 angle pdb=" N GLY B 49 " pdb=" CA GLY B 49 " pdb=" C GLY B 49 " ideal model delta sigma weight residual 110.46 120.11 -9.65 1.43e+00 4.89e-01 4.55e+01 angle pdb=" N GLY A 49 " pdb=" CA GLY A 49 " pdb=" C GLY A 49 " ideal model delta sigma weight residual 110.46 120.09 -9.63 1.43e+00 4.89e-01 4.54e+01 angle pdb=" N GLY G 49 " pdb=" CA GLY G 49 " pdb=" C GLY G 49 " ideal model delta sigma weight residual 110.46 120.08 -9.62 1.43e+00 4.89e-01 4.52e+01 angle pdb=" N GLY C 49 " pdb=" CA GLY C 49 " pdb=" C GLY C 49 " ideal model delta sigma weight residual 110.46 120.07 -9.61 1.43e+00 4.89e-01 4.52e+01 ... (remaining 9103 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 11.12: 3048 11.12 - 22.25: 384 22.25 - 33.37: 180 33.37 - 44.49: 60 44.49 - 55.62: 36 Dihedral angle restraints: 3708 sinusoidal: 1464 harmonic: 2244 Sorted by residual: dihedral pdb=" CA SER K 58 " pdb=" C SER K 58 " pdb=" N ASP K 59 " pdb=" CA ASP K 59 " ideal model delta harmonic sigma weight residual 180.00 166.03 13.97 0 5.00e+00 4.00e-02 7.80e+00 dihedral pdb=" CA SER L 58 " pdb=" C SER L 58 " pdb=" N ASP L 59 " pdb=" CA ASP L 59 " ideal model delta harmonic sigma weight residual 180.00 166.07 13.93 0 5.00e+00 4.00e-02 7.77e+00 dihedral pdb=" CA SER A 58 " pdb=" C SER A 58 " pdb=" N ASP A 59 " pdb=" CA ASP A 59 " ideal model delta harmonic sigma weight residual 180.00 166.09 13.91 0 5.00e+00 4.00e-02 7.74e+00 ... (remaining 3705 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 349 0.056 - 0.111: 191 0.111 - 0.167: 108 0.167 - 0.222: 84 0.222 - 0.278: 12 Chirality restraints: 744 Sorted by residual: chirality pdb=" CA ALA A 9 " pdb=" N ALA A 9 " pdb=" C ALA A 9 " pdb=" CB ALA A 9 " both_signs ideal model delta sigma weight residual False 2.48 2.21 0.28 2.00e-01 2.50e+01 1.93e+00 chirality pdb=" CA ALA E 9 " pdb=" N ALA E 9 " pdb=" C ALA E 9 " pdb=" CB ALA E 9 " both_signs ideal model delta sigma weight residual False 2.48 2.21 0.28 2.00e-01 2.50e+01 1.92e+00 chirality pdb=" CA ALA B 9 " pdb=" N ALA B 9 " pdb=" C ALA B 9 " pdb=" CB ALA B 9 " both_signs ideal model delta sigma weight residual False 2.48 2.21 0.28 2.00e-01 2.50e+01 1.90e+00 ... (remaining 741 not shown) Planarity restraints: 1236 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLN K 45 " 0.017 2.00e-02 2.50e+03 3.45e-02 1.19e+01 pdb=" C GLN K 45 " -0.060 2.00e-02 2.50e+03 pdb=" O GLN K 45 " 0.023 2.00e-02 2.50e+03 pdb=" N ARG K 46 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN B 45 " -0.017 2.00e-02 2.50e+03 3.45e-02 1.19e+01 pdb=" C GLN B 45 " 0.060 2.00e-02 2.50e+03 pdb=" O GLN B 45 " -0.023 2.00e-02 2.50e+03 pdb=" N ARG B 46 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN I 45 " 0.017 2.00e-02 2.50e+03 3.44e-02 1.19e+01 pdb=" C GLN I 45 " -0.060 2.00e-02 2.50e+03 pdb=" O GLN I 45 " 0.022 2.00e-02 2.50e+03 pdb=" N ARG I 46 " 0.020 2.00e-02 2.50e+03 ... (remaining 1233 not shown) Histogram of nonbonded interaction distances: 2.55 - 3.02: 3855 3.02 - 3.49: 5880 3.49 - 3.96: 11333 3.96 - 4.43: 13888 4.43 - 4.90: 25547 Nonbonded interactions: 60503 Sorted by model distance: nonbonded pdb=" O ASP L 22 " pdb=" OD1 ASP L 22 " model vdw 2.550 3.040 nonbonded pdb=" O ASP J 22 " pdb=" OD1 ASP J 22 " model vdw 2.550 3.040 nonbonded pdb=" O ASP H 22 " pdb=" OD1 ASP H 22 " model vdw 2.551 3.040 nonbonded pdb=" O ASP D 22 " pdb=" OD1 ASP D 22 " model vdw 2.551 3.040 nonbonded pdb=" O ASP F 22 " pdb=" OD1 ASP F 22 " model vdw 2.551 3.040 ... (remaining 60498 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' } 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: 1.320 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: 5.680 Check model and map are aligned: 0.100 Set scattering table: 0.060 Process input model: 21.120 Find NCS groups from input model: 0.430 Set up NCS constraints: 0.050 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:13.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.950 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7987 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 : 0.017 0.060 6804 Z= 1.115 Angle : 1.671 9.655 9108 Z= 1.121 Chirality : 0.100 0.278 744 Planarity : 0.008 0.040 1236 Dihedral : 13.711 55.616 2316 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 2.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.46 (0.17), residues: 804 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.63 (0.13), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.004 TRP L 17 HIS 0.001 0.001 HIS I 36 PHE 0.028 0.002 PHE F 2 TYR 0.043 0.007 TYR D 20 ARG 0.003 0.001 ARG C 46 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1608 Ramachandran restraints generated. 804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1608 Ramachandran restraints generated. 804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 212 time to evaluate : 0.723 Fit side-chains REVERT: A 65 GLN cc_start: 0.9123 (mt0) cc_final: 0.8892 (mt0) REVERT: B 38 ARG cc_start: 0.7783 (ttt180) cc_final: 0.7416 (tpp80) REVERT: B 45 GLN cc_start: 0.8993 (mt0) cc_final: 0.8778 (mt0) REVERT: B 56 LYS cc_start: 0.8497 (mtmt) cc_final: 0.8274 (mttt) REVERT: B 65 GLN cc_start: 0.9030 (mt0) cc_final: 0.8773 (mt0) REVERT: C 22 ASP cc_start: 0.7977 (t0) cc_final: 0.7696 (t0) REVERT: C 38 ARG cc_start: 0.7552 (ttt180) cc_final: 0.7254 (tpp-160) REVERT: C 65 GLN cc_start: 0.9045 (mt0) cc_final: 0.8822 (mt0) REVERT: D 25 GLU cc_start: 0.8247 (mt-10) cc_final: 0.7811 (mp0) REVERT: D 38 ARG cc_start: 0.7511 (ttt180) cc_final: 0.7252 (ttt90) REVERT: D 45 GLN cc_start: 0.9012 (mt0) cc_final: 0.8776 (mt0) REVERT: E 38 ARG cc_start: 0.7575 (ttt180) cc_final: 0.7168 (tpp80) REVERT: F 16 MET cc_start: 0.9173 (mtt) cc_final: 0.8970 (mtt) REVERT: F 25 GLU cc_start: 0.8382 (mt-10) cc_final: 0.7942 (mt-10) REVERT: F 38 ARG cc_start: 0.7597 (ttt180) cc_final: 0.7028 (tpp80) REVERT: F 66 GLU cc_start: 0.8808 (mt-10) cc_final: 0.8593 (mt-10) REVERT: G 22 ASP cc_start: 0.7943 (t0) cc_final: 0.7161 (t0) REVERT: G 25 GLU cc_start: 0.8356 (mt-10) cc_final: 0.8123 (mp0) REVERT: G 38 ARG cc_start: 0.7549 (ttt180) cc_final: 0.7081 (tpp80) REVERT: H 25 GLU cc_start: 0.8322 (mt-10) cc_final: 0.7740 (mp0) REVERT: H 38 ARG cc_start: 0.7526 (ttt180) cc_final: 0.7097 (tpp80) REVERT: I 22 ASP cc_start: 0.7958 (t0) cc_final: 0.7738 (t0) REVERT: I 25 GLU cc_start: 0.8388 (mt-10) cc_final: 0.7840 (mt-10) REVERT: I 38 ARG cc_start: 0.7795 (ttt180) cc_final: 0.7457 (tpp-160) REVERT: I 56 LYS cc_start: 0.8387 (mtmt) cc_final: 0.8115 (mttp) REVERT: I 66 GLU cc_start: 0.8802 (mt-10) cc_final: 0.8536 (mt-10) REVERT: J 16 MET cc_start: 0.9156 (mtt) cc_final: 0.8941 (mtt) REVERT: J 22 ASP cc_start: 0.7976 (t0) cc_final: 0.7461 (t0) REVERT: J 23 MET cc_start: 0.8768 (mtt) cc_final: 0.8469 (mtt) REVERT: J 25 GLU cc_start: 0.8232 (mt-10) cc_final: 0.7463 (mt-10) REVERT: J 38 ARG cc_start: 0.7535 (ttt180) cc_final: 0.7262 (ttt90) REVERT: J 65 GLN cc_start: 0.9189 (mt0) cc_final: 0.8983 (mt0) REVERT: K 63 SER cc_start: 0.8847 (m) cc_final: 0.8526 (p) REVERT: K 66 GLU cc_start: 0.8815 (mt-10) cc_final: 0.8585 (mt-10) REVERT: L 25 GLU cc_start: 0.8367 (mt-10) cc_final: 0.8157 (mp0) REVERT: L 29 LYS cc_start: 0.8468 (tttp) cc_final: 0.8173 (tttp) REVERT: L 38 ARG cc_start: 0.7834 (ttt180) cc_final: 0.7620 (ttt180) outliers start: 0 outliers final: 0 residues processed: 212 average time/residue: 1.7460 time to fit residues: 382.5650 Evaluate side-chains 201 residues out of total 576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 201 time to evaluate : 0.733 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 60 optimal weight: 0.9980 chunk 54 optimal weight: 0.5980 chunk 30 optimal weight: 0.8980 chunk 18 optimal weight: 0.7980 chunk 36 optimal weight: 0.6980 chunk 29 optimal weight: 0.7980 chunk 56 optimal weight: 0.8980 chunk 21 optimal weight: 0.8980 chunk 34 optimal weight: 0.7980 chunk 42 optimal weight: 0.5980 chunk 65 optimal weight: 1.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 65 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7894 moved from start: 0.2129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 6804 Z= 0.216 Angle : 0.540 4.546 9108 Z= 0.338 Chirality : 0.043 0.121 744 Planarity : 0.004 0.038 1236 Dihedral : 4.411 16.127 900 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 3.47 % Allowed : 14.58 % Favored : 81.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.74 (0.16), residues: 804 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.84 (0.13), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP G 28 HIS 0.001 0.000 HIS B 36 PHE 0.014 0.001 PHE E 2 TYR 0.007 0.001 TYR G 20 ARG 0.003 0.000 ARG J 18 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1608 Ramachandran restraints generated. 804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1608 Ramachandran restraints generated. 804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 157 time to evaluate : 0.738 Fit side-chains revert: symmetry clash REVERT: A 8 GLU cc_start: 0.8142 (OUTLIER) cc_final: 0.7782 (mt-10) REVERT: B 56 LYS cc_start: 0.8392 (mtmt) cc_final: 0.8171 (mttt) REVERT: C 38 ARG cc_start: 0.7478 (ttt180) cc_final: 0.7269 (tpp-160) REVERT: C 65 GLN cc_start: 0.8881 (mt0) cc_final: 0.8675 (mt0) REVERT: D 38 ARG cc_start: 0.7480 (ttt180) cc_final: 0.7211 (ttt90) REVERT: E 25 GLU cc_start: 0.8418 (mt-10) cc_final: 0.8074 (mp0) REVERT: E 29 LYS cc_start: 0.8453 (tttt) cc_final: 0.7739 (tptt) REVERT: E 38 ARG cc_start: 0.7481 (ttt180) cc_final: 0.7148 (tpp80) REVERT: F 38 ARG cc_start: 0.7495 (ttt180) cc_final: 0.7022 (tpp80) REVERT: G 38 ARG cc_start: 0.7487 (ttt180) cc_final: 0.7073 (tpp80) REVERT: H 25 GLU cc_start: 0.8261 (mt-10) cc_final: 0.8040 (mt-10) REVERT: H 38 ARG cc_start: 0.7512 (ttt180) cc_final: 0.6859 (tpp80) REVERT: H 46 ARG cc_start: 0.8633 (OUTLIER) cc_final: 0.8301 (tmt170) REVERT: I 22 ASP cc_start: 0.7903 (t0) cc_final: 0.7697 (t0) REVERT: I 25 GLU cc_start: 0.8391 (mt-10) cc_final: 0.8137 (mt-10) REVERT: I 38 ARG cc_start: 0.7821 (ttt180) cc_final: 0.7600 (tpp-160) REVERT: I 56 LYS cc_start: 0.8308 (mtmt) cc_final: 0.8038 (mttp) REVERT: I 62 GLU cc_start: 0.7504 (tp30) cc_final: 0.7169 (tp30) REVERT: J 25 GLU cc_start: 0.8154 (mt-10) cc_final: 0.7699 (mt-10) REVERT: J 38 ARG cc_start: 0.7587 (ttt180) cc_final: 0.7252 (tpp-160) REVERT: J 65 GLN cc_start: 0.9014 (mt0) cc_final: 0.8649 (mt0) REVERT: K 25 GLU cc_start: 0.8439 (mt-10) cc_final: 0.8019 (mt-10) REVERT: K 38 ARG cc_start: 0.7829 (ttt180) cc_final: 0.7172 (tpp80) REVERT: K 63 SER cc_start: 0.8967 (m) cc_final: 0.8647 (p) outliers start: 20 outliers final: 5 residues processed: 167 average time/residue: 1.8029 time to fit residues: 311.1244 Evaluate side-chains 160 residues out of total 576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 153 time to evaluate : 0.680 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 GLU Chi-restraints excluded: chain A residue 63 SER Chi-restraints excluded: chain B residue 63 SER Chi-restraints excluded: chain C residue 32 ASP Chi-restraints excluded: chain F residue 32 ASP Chi-restraints excluded: chain H residue 46 ARG Chi-restraints excluded: chain L residue 32 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 36 optimal weight: 1.9990 chunk 20 optimal weight: 2.9990 chunk 54 optimal weight: 2.9990 chunk 44 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 65 optimal weight: 2.9990 chunk 70 optimal weight: 2.9990 chunk 58 optimal weight: 0.9990 chunk 64 optimal weight: 0.6980 chunk 22 optimal weight: 2.9990 chunk 52 optimal weight: 1.9990 overall best weight: 1.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 45 GLN C 45 GLN D 45 GLN D 65 GLN E 45 GLN L 65 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7948 moved from start: 0.2378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.040 6804 Z= 0.422 Angle : 0.578 5.160 9108 Z= 0.353 Chirality : 0.044 0.128 744 Planarity : 0.003 0.026 1236 Dihedral : 4.807 20.289 900 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer: Outliers : 5.56 % Allowed : 14.93 % Favored : 79.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.81 (0.16), residues: 804 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.89 (0.12), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP J 28 HIS 0.001 0.000 HIS B 36 PHE 0.014 0.002 PHE I 2 TYR 0.012 0.001 TYR A 20 ARG 0.005 0.001 ARG B 18 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1608 Ramachandran restraints generated. 804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1608 Ramachandran restraints generated. 804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 154 time to evaluate : 0.634 Fit side-chains revert: symmetry clash REVERT: A 8 GLU cc_start: 0.8078 (OUTLIER) cc_final: 0.7460 (tt0) REVERT: A 32 ASP cc_start: 0.8513 (OUTLIER) cc_final: 0.7982 (m-30) REVERT: B 46 ARG cc_start: 0.8621 (ttt-90) cc_final: 0.8415 (ttt-90) REVERT: B 65 GLN cc_start: 0.8848 (mt0) cc_final: 0.8599 (mt0) REVERT: C 65 GLN cc_start: 0.8897 (mt0) cc_final: 0.8681 (mt0) REVERT: D 25 GLU cc_start: 0.8238 (mt-10) cc_final: 0.7675 (mp0) REVERT: D 38 ARG cc_start: 0.7527 (ttt180) cc_final: 0.6971 (ttm-80) REVERT: E 8 GLU cc_start: 0.8290 (OUTLIER) cc_final: 0.8079 (mt-10) REVERT: E 25 GLU cc_start: 0.8405 (mt-10) cc_final: 0.8162 (mp0) REVERT: E 29 LYS cc_start: 0.8455 (tttt) cc_final: 0.7692 (tptt) REVERT: E 38 ARG cc_start: 0.7459 (ttt180) cc_final: 0.7119 (tpp80) REVERT: F 38 ARG cc_start: 0.7511 (ttt180) cc_final: 0.7266 (tpp80) REVERT: G 8 GLU cc_start: 0.8272 (OUTLIER) cc_final: 0.7914 (mt-10) REVERT: G 38 ARG cc_start: 0.7509 (ttt180) cc_final: 0.7074 (tpp80) REVERT: H 38 ARG cc_start: 0.7471 (ttt180) cc_final: 0.6786 (tpp80) REVERT: I 25 GLU cc_start: 0.8380 (mt-10) cc_final: 0.8034 (mt-10) REVERT: I 38 ARG cc_start: 0.7880 (ttt180) cc_final: 0.7625 (tpp-160) REVERT: I 56 LYS cc_start: 0.8319 (OUTLIER) cc_final: 0.8060 (mttp) REVERT: J 38 ARG cc_start: 0.7579 (ttt180) cc_final: 0.7360 (tpp-160) REVERT: J 65 GLN cc_start: 0.9020 (mt0) cc_final: 0.8663 (mt0) REVERT: K 25 GLU cc_start: 0.8498 (mt-10) cc_final: 0.8024 (mt-10) REVERT: K 32 ASP cc_start: 0.8238 (OUTLIER) cc_final: 0.7894 (m-30) outliers start: 32 outliers final: 12 residues processed: 165 average time/residue: 1.7122 time to fit residues: 291.9504 Evaluate side-chains 171 residues out of total 576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 153 time to evaluate : 0.653 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 GLU Chi-restraints excluded: chain A residue 32 ASP Chi-restraints excluded: chain A residue 63 SER Chi-restraints excluded: chain B residue 32 ASP Chi-restraints excluded: chain B residue 63 SER Chi-restraints excluded: chain C residue 32 ASP Chi-restraints excluded: chain C residue 59 ASP Chi-restraints excluded: chain E residue 8 GLU Chi-restraints excluded: chain F residue 32 ASP Chi-restraints excluded: chain G residue 8 GLU Chi-restraints excluded: chain I residue 32 ASP Chi-restraints excluded: chain I residue 56 LYS Chi-restraints excluded: chain I residue 63 SER Chi-restraints excluded: chain J residue 32 ASP Chi-restraints excluded: chain J residue 46 ARG Chi-restraints excluded: chain K residue 32 ASP Chi-restraints excluded: chain L residue 32 ASP Chi-restraints excluded: chain L residue 63 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 64 optimal weight: 3.9990 chunk 49 optimal weight: 1.9990 chunk 33 optimal weight: 3.9990 chunk 7 optimal weight: 1.9990 chunk 31 optimal weight: 0.8980 chunk 43 optimal weight: 0.6980 chunk 65 optimal weight: 2.9990 chunk 69 optimal weight: 0.7980 chunk 34 optimal weight: 3.9990 chunk 62 optimal weight: 0.0870 chunk 18 optimal weight: 1.9990 overall best weight: 0.8960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 45 GLN ** D 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 45 GLN ** F 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 65 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7916 moved from start: 0.2547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 6804 Z= 0.256 Angle : 0.512 4.652 9108 Z= 0.313 Chirality : 0.042 0.126 744 Planarity : 0.003 0.021 1236 Dihedral : 4.630 19.016 900 Min Nonbonded Distance : 2.309 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.97 % Favored : 94.03 % Rotamer: Outliers : 4.34 % Allowed : 17.19 % Favored : 78.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.84 (0.16), residues: 804 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.92 (0.12), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP G 28 HIS 0.001 0.000 HIS F 36 PHE 0.012 0.001 PHE I 2 TYR 0.007 0.001 TYR A 20 ARG 0.003 0.000 ARG B 18 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1608 Ramachandran restraints generated. 804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1608 Ramachandran restraints generated. 804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 155 time to evaluate : 0.716 Fit side-chains REVERT: A 8 GLU cc_start: 0.8036 (OUTLIER) cc_final: 0.7445 (tt0) REVERT: B 56 LYS cc_start: 0.8311 (mttt) cc_final: 0.8109 (mttt) REVERT: B 65 GLN cc_start: 0.8852 (mt0) cc_final: 0.8595 (mt0) REVERT: D 25 GLU cc_start: 0.8221 (mt-10) cc_final: 0.7706 (mp0) REVERT: D 38 ARG cc_start: 0.7496 (ttt180) cc_final: 0.6949 (ttm-80) REVERT: E 8 GLU cc_start: 0.8261 (OUTLIER) cc_final: 0.8059 (mt-10) REVERT: E 25 GLU cc_start: 0.8387 (mt-10) cc_final: 0.8120 (mp0) REVERT: E 29 LYS cc_start: 0.8424 (tttt) cc_final: 0.7675 (tptt) REVERT: E 38 ARG cc_start: 0.7430 (ttt180) cc_final: 0.7135 (tpp80) REVERT: F 38 ARG cc_start: 0.7460 (ttt180) cc_final: 0.7246 (tpp80) REVERT: G 8 GLU cc_start: 0.8301 (OUTLIER) cc_final: 0.8020 (mt-10) REVERT: G 25 GLU cc_start: 0.8217 (mt-10) cc_final: 0.7723 (mp0) REVERT: G 38 ARG cc_start: 0.7495 (ttt180) cc_final: 0.7058 (tpp80) REVERT: G 46 ARG cc_start: 0.8557 (OUTLIER) cc_final: 0.6711 (tmt170) REVERT: H 38 ARG cc_start: 0.7478 (ttt180) cc_final: 0.6811 (tpp80) REVERT: I 25 GLU cc_start: 0.8403 (mt-10) cc_final: 0.8098 (mt-10) REVERT: I 38 ARG cc_start: 0.7855 (ttt180) cc_final: 0.7612 (tpp-160) REVERT: I 56 LYS cc_start: 0.8321 (mtmt) cc_final: 0.8055 (mttp) REVERT: I 62 GLU cc_start: 0.7887 (OUTLIER) cc_final: 0.7476 (tp30) REVERT: J 38 ARG cc_start: 0.7583 (ttt180) cc_final: 0.7363 (tpp-160) REVERT: J 65 GLN cc_start: 0.8998 (mt0) cc_final: 0.8676 (mt0) REVERT: K 25 GLU cc_start: 0.8531 (mt-10) cc_final: 0.8057 (mt-10) outliers start: 25 outliers final: 7 residues processed: 163 average time/residue: 1.7076 time to fit residues: 287.9641 Evaluate side-chains 166 residues out of total 576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 154 time to evaluate : 0.694 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 GLU Chi-restraints excluded: chain A residue 63 SER Chi-restraints excluded: chain B residue 32 ASP Chi-restraints excluded: chain C residue 32 ASP Chi-restraints excluded: chain E residue 8 GLU Chi-restraints excluded: chain F residue 32 ASP Chi-restraints excluded: chain G residue 8 GLU Chi-restraints excluded: chain G residue 46 ARG Chi-restraints excluded: chain I residue 32 ASP Chi-restraints excluded: chain I residue 62 GLU Chi-restraints excluded: chain J residue 32 ASP Chi-restraints excluded: chain L residue 32 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 57 optimal weight: 3.9990 chunk 39 optimal weight: 6.9990 chunk 1 optimal weight: 2.9990 chunk 51 optimal weight: 0.8980 chunk 28 optimal weight: 2.9990 chunk 59 optimal weight: 3.9990 chunk 48 optimal weight: 2.9990 chunk 0 optimal weight: 1.9990 chunk 35 optimal weight: 3.9990 chunk 62 optimal weight: 0.9980 chunk 17 optimal weight: 3.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 GLN C 45 GLN E 45 GLN H 45 GLN L 65 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7968 moved from start: 0.2578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.050 6804 Z= 0.527 Angle : 0.602 5.337 9108 Z= 0.364 Chirality : 0.044 0.131 744 Planarity : 0.003 0.023 1236 Dihedral : 5.036 20.491 900 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.97 % Favored : 93.03 % Rotamer: Outliers : 6.25 % Allowed : 15.45 % Favored : 78.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.90 (0.16), residues: 804 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.97 (0.12), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP J 28 HIS 0.002 0.001 HIS B 36 PHE 0.014 0.002 PHE A 5 TYR 0.011 0.002 TYR A 20 ARG 0.005 0.001 ARG B 18 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1608 Ramachandran restraints generated. 804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1608 Ramachandran restraints generated. 804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 161 time to evaluate : 0.685 Fit side-chains revert: symmetry clash REVERT: A 8 GLU cc_start: 0.8014 (OUTLIER) cc_final: 0.7484 (tt0) REVERT: A 32 ASP cc_start: 0.8537 (OUTLIER) cc_final: 0.7986 (m-30) REVERT: A 46 ARG cc_start: 0.8684 (OUTLIER) cc_final: 0.8020 (tmt170) REVERT: B 65 GLN cc_start: 0.8876 (mt0) cc_final: 0.8624 (mt0) REVERT: D 8 GLU cc_start: 0.8340 (OUTLIER) cc_final: 0.7939 (mt-10) REVERT: D 25 GLU cc_start: 0.8194 (mt-10) cc_final: 0.7725 (mp0) REVERT: D 38 ARG cc_start: 0.7363 (ttt180) cc_final: 0.6873 (ttt90) REVERT: E 8 GLU cc_start: 0.8268 (OUTLIER) cc_final: 0.8054 (mt-10) REVERT: E 23 MET cc_start: 0.8738 (OUTLIER) cc_final: 0.8449 (mtt) REVERT: E 29 LYS cc_start: 0.8414 (tttt) cc_final: 0.7596 (tptt) REVERT: E 38 ARG cc_start: 0.7475 (ttt180) cc_final: 0.7112 (tpp80) REVERT: F 38 ARG cc_start: 0.7464 (ttt180) cc_final: 0.7243 (tpp80) REVERT: F 56 LYS cc_start: 0.8404 (OUTLIER) cc_final: 0.8108 (mttp) REVERT: G 8 GLU cc_start: 0.8230 (OUTLIER) cc_final: 0.7939 (mt-10) REVERT: G 38 ARG cc_start: 0.7525 (ttt180) cc_final: 0.7147 (tpp80) REVERT: G 46 ARG cc_start: 0.8569 (OUTLIER) cc_final: 0.6745 (tmt170) REVERT: H 8 GLU cc_start: 0.8344 (OUTLIER) cc_final: 0.8117 (mt-10) REVERT: H 38 ARG cc_start: 0.7504 (ttt180) cc_final: 0.7276 (ttt180) REVERT: I 8 GLU cc_start: 0.8178 (OUTLIER) cc_final: 0.7643 (mt-10) REVERT: I 25 GLU cc_start: 0.8402 (mt-10) cc_final: 0.8117 (mt-10) REVERT: I 38 ARG cc_start: 0.7869 (ttt180) cc_final: 0.7619 (tpp-160) REVERT: J 38 ARG cc_start: 0.7594 (ttt180) cc_final: 0.7389 (tpp-160) REVERT: J 65 GLN cc_start: 0.9025 (mt0) cc_final: 0.8675 (mt0) REVERT: K 25 GLU cc_start: 0.8493 (mt-10) cc_final: 0.8024 (mt-10) REVERT: L 29 LYS cc_start: 0.8190 (tttp) cc_final: 0.7928 (tttp) outliers start: 36 outliers final: 15 residues processed: 169 average time/residue: 1.6693 time to fit residues: 291.7583 Evaluate side-chains 185 residues out of total 576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 159 time to evaluate : 0.714 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 GLU Chi-restraints excluded: chain A residue 32 ASP Chi-restraints excluded: chain A residue 46 ARG Chi-restraints excluded: chain A residue 63 SER Chi-restraints excluded: chain B residue 29 LYS Chi-restraints excluded: chain B residue 32 ASP Chi-restraints excluded: chain C residue 32 ASP Chi-restraints excluded: chain C residue 59 ASP Chi-restraints excluded: chain D residue 8 GLU Chi-restraints excluded: chain E residue 8 GLU Chi-restraints excluded: chain E residue 23 MET Chi-restraints excluded: chain F residue 32 ASP Chi-restraints excluded: chain F residue 56 LYS Chi-restraints excluded: chain F residue 59 ASP Chi-restraints excluded: chain G residue 8 GLU Chi-restraints excluded: chain G residue 32 ASP Chi-restraints excluded: chain G residue 46 ARG Chi-restraints excluded: chain H residue 8 GLU Chi-restraints excluded: chain I residue 8 GLU Chi-restraints excluded: chain I residue 32 ASP Chi-restraints excluded: chain I residue 63 SER Chi-restraints excluded: chain J residue 32 ASP Chi-restraints excluded: chain J residue 46 ARG Chi-restraints excluded: chain J residue 63 SER Chi-restraints excluded: chain L residue 32 ASP Chi-restraints excluded: chain L residue 63 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 23 optimal weight: 0.8980 chunk 62 optimal weight: 0.8980 chunk 13 optimal weight: 0.6980 chunk 40 optimal weight: 0.6980 chunk 17 optimal weight: 2.9990 chunk 69 optimal weight: 0.7980 chunk 57 optimal weight: 0.9990 chunk 32 optimal weight: 0.9990 chunk 5 optimal weight: 0.6980 chunk 36 optimal weight: 0.6980 chunk 67 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 GLN ** D 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 45 GLN ** F 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 65 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7907 moved from start: 0.2700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 6804 Z= 0.209 Angle : 0.496 4.529 9108 Z= 0.303 Chirality : 0.042 0.123 744 Planarity : 0.002 0.018 1236 Dihedral : 4.570 18.257 900 Min Nonbonded Distance : 2.308 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.22 % Favored : 93.78 % Rotamer: Outliers : 4.51 % Allowed : 17.71 % Favored : 77.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.89 (0.16), residues: 804 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.96 (0.12), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP G 28 HIS 0.001 0.000 HIS G 36 PHE 0.011 0.001 PHE I 2 TYR 0.005 0.001 TYR A 20 ARG 0.003 0.000 ARG B 18 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1608 Ramachandran restraints generated. 804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1608 Ramachandran restraints generated. 804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 156 time to evaluate : 0.715 Fit side-chains revert: symmetry clash REVERT: A 8 GLU cc_start: 0.8080 (OUTLIER) cc_final: 0.7512 (tt0) REVERT: A 32 ASP cc_start: 0.8444 (OUTLIER) cc_final: 0.7957 (m-30) REVERT: B 65 GLN cc_start: 0.8812 (mt0) cc_final: 0.8561 (mt0) REVERT: D 25 GLU cc_start: 0.8217 (mt-10) cc_final: 0.7728 (mp0) REVERT: D 38 ARG cc_start: 0.7449 (ttt180) cc_final: 0.6922 (ttt90) REVERT: E 25 GLU cc_start: 0.8421 (mt-10) cc_final: 0.8110 (mp0) REVERT: E 29 LYS cc_start: 0.8393 (tttt) cc_final: 0.7608 (tptt) REVERT: E 38 ARG cc_start: 0.7545 (ttt180) cc_final: 0.7250 (tpp80) REVERT: F 38 ARG cc_start: 0.7446 (ttt180) cc_final: 0.7236 (tpp80) REVERT: F 56 LYS cc_start: 0.8389 (OUTLIER) cc_final: 0.8162 (mttp) REVERT: G 8 GLU cc_start: 0.8276 (OUTLIER) cc_final: 0.7968 (mt-10) REVERT: G 25 GLU cc_start: 0.8233 (mt-10) cc_final: 0.7835 (mp0) REVERT: G 38 ARG cc_start: 0.7473 (ttt180) cc_final: 0.7031 (tpp80) REVERT: H 38 ARG cc_start: 0.7484 (ttt180) cc_final: 0.6998 (tpp80) REVERT: I 8 GLU cc_start: 0.8094 (OUTLIER) cc_final: 0.7623 (mt-10) REVERT: I 25 GLU cc_start: 0.8420 (mt-10) cc_final: 0.8075 (mt-10) REVERT: I 38 ARG cc_start: 0.7830 (ttt180) cc_final: 0.7605 (tpp-160) REVERT: J 38 ARG cc_start: 0.7580 (ttt180) cc_final: 0.7363 (tpp-160) REVERT: J 65 GLN cc_start: 0.8988 (mt0) cc_final: 0.8704 (mt0) REVERT: K 25 GLU cc_start: 0.8542 (mt-10) cc_final: 0.8065 (mt-10) outliers start: 26 outliers final: 12 residues processed: 166 average time/residue: 1.6393 time to fit residues: 281.7762 Evaluate side-chains 171 residues out of total 576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 154 time to evaluate : 0.737 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 GLU Chi-restraints excluded: chain A residue 32 ASP Chi-restraints excluded: chain A residue 63 SER Chi-restraints excluded: chain B residue 29 LYS Chi-restraints excluded: chain B residue 32 ASP Chi-restraints excluded: chain C residue 32 ASP Chi-restraints excluded: chain F residue 32 ASP Chi-restraints excluded: chain F residue 56 LYS Chi-restraints excluded: chain G residue 8 GLU Chi-restraints excluded: chain G residue 32 ASP Chi-restraints excluded: chain I residue 8 GLU Chi-restraints excluded: chain I residue 32 ASP Chi-restraints excluded: chain I residue 63 SER Chi-restraints excluded: chain J residue 32 ASP Chi-restraints excluded: chain J residue 46 ARG Chi-restraints excluded: chain K residue 63 SER Chi-restraints excluded: chain L residue 32 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 7 optimal weight: 1.9990 chunk 39 optimal weight: 5.9990 chunk 50 optimal weight: 0.9990 chunk 58 optimal weight: 1.9990 chunk 38 optimal weight: 0.9980 chunk 69 optimal weight: 0.3980 chunk 43 optimal weight: 2.9990 chunk 42 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 chunk 27 optimal weight: 0.9990 chunk 41 optimal weight: 0.9990 overall best weight: 0.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 45 GLN C 65 GLN ** D 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 45 GLN ** F 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7915 moved from start: 0.2735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 6804 Z= 0.252 Angle : 0.506 4.564 9108 Z= 0.307 Chirality : 0.042 0.124 744 Planarity : 0.002 0.016 1236 Dihedral : 4.588 18.593 900 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.47 % Favored : 93.53 % Rotamer: Outliers : 4.69 % Allowed : 17.19 % Favored : 78.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.89 (0.16), residues: 804 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.96 (0.12), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP J 28 HIS 0.001 0.000 HIS B 36 PHE 0.011 0.001 PHE D 2 TYR 0.006 0.001 TYR A 20 ARG 0.004 0.000 ARG B 18 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1608 Ramachandran restraints generated. 804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1608 Ramachandran restraints generated. 804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 153 time to evaluate : 0.695 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 8 GLU cc_start: 0.8065 (OUTLIER) cc_final: 0.7531 (tt0) REVERT: A 32 ASP cc_start: 0.8463 (OUTLIER) cc_final: 0.7993 (m-30) REVERT: A 46 ARG cc_start: 0.8654 (OUTLIER) cc_final: 0.7977 (tmt170) REVERT: B 65 GLN cc_start: 0.8851 (mt0) cc_final: 0.8595 (mt0) REVERT: D 25 GLU cc_start: 0.8181 (mt-10) cc_final: 0.7736 (mp0) REVERT: D 38 ARG cc_start: 0.7449 (ttt180) cc_final: 0.6921 (ttt90) REVERT: E 25 GLU cc_start: 0.8419 (mt-10) cc_final: 0.8121 (mp0) REVERT: E 29 LYS cc_start: 0.8404 (tttt) cc_final: 0.7598 (tptt) REVERT: E 38 ARG cc_start: 0.7549 (ttt180) cc_final: 0.7250 (tpp80) REVERT: G 8 GLU cc_start: 0.8256 (OUTLIER) cc_final: 0.7945 (mt-10) REVERT: G 25 GLU cc_start: 0.8239 (mt-10) cc_final: 0.7835 (mp0) REVERT: G 38 ARG cc_start: 0.7474 (ttt180) cc_final: 0.7029 (tpp80) REVERT: G 66 GLU cc_start: 0.8620 (OUTLIER) cc_final: 0.8230 (mt-10) REVERT: H 38 ARG cc_start: 0.7489 (ttt180) cc_final: 0.7004 (tpp80) REVERT: I 8 GLU cc_start: 0.8145 (OUTLIER) cc_final: 0.7680 (mt-10) REVERT: I 25 GLU cc_start: 0.8390 (mt-10) cc_final: 0.8109 (mt-10) REVERT: I 38 ARG cc_start: 0.7814 (ttt180) cc_final: 0.7580 (tpp-160) REVERT: I 62 GLU cc_start: 0.7927 (tp30) cc_final: 0.7485 (tp30) REVERT: J 38 ARG cc_start: 0.7583 (ttt180) cc_final: 0.7365 (tpp-160) REVERT: J 65 GLN cc_start: 0.8996 (mt0) cc_final: 0.8694 (mt0) REVERT: K 25 GLU cc_start: 0.8545 (mt-10) cc_final: 0.8072 (mt-10) outliers start: 27 outliers final: 14 residues processed: 161 average time/residue: 1.6904 time to fit residues: 281.4811 Evaluate side-chains 171 residues out of total 576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 151 time to evaluate : 0.598 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 GLU Chi-restraints excluded: chain A residue 32 ASP Chi-restraints excluded: chain A residue 46 ARG Chi-restraints excluded: chain A residue 63 SER Chi-restraints excluded: chain B residue 29 LYS Chi-restraints excluded: chain B residue 32 ASP Chi-restraints excluded: chain C residue 32 ASP Chi-restraints excluded: chain F residue 32 ASP Chi-restraints excluded: chain G residue 8 GLU Chi-restraints excluded: chain G residue 32 ASP Chi-restraints excluded: chain G residue 46 ARG Chi-restraints excluded: chain G residue 66 GLU Chi-restraints excluded: chain I residue 8 GLU Chi-restraints excluded: chain I residue 32 ASP Chi-restraints excluded: chain J residue 32 ASP Chi-restraints excluded: chain J residue 46 ARG Chi-restraints excluded: chain J residue 63 SER Chi-restraints excluded: chain K residue 63 SER Chi-restraints excluded: chain L residue 32 ASP Chi-restraints excluded: chain L residue 63 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 20 optimal weight: 2.9990 chunk 13 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 chunk 47 optimal weight: 2.9990 chunk 34 optimal weight: 3.9990 chunk 6 optimal weight: 2.9990 chunk 54 optimal weight: 0.9990 chunk 63 optimal weight: 0.9990 chunk 66 optimal weight: 0.0060 chunk 60 optimal weight: 0.3980 chunk 64 optimal weight: 2.9990 overall best weight: 0.8802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7914 moved from start: 0.2768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 6804 Z= 0.250 Angle : 0.503 4.547 9108 Z= 0.306 Chirality : 0.042 0.129 744 Planarity : 0.002 0.016 1236 Dihedral : 4.562 18.765 900 Min Nonbonded Distance : 2.292 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.47 % Favored : 93.53 % Rotamer: Outliers : 5.21 % Allowed : 17.71 % Favored : 77.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.88 (0.16), residues: 804 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.95 (0.12), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP G 28 HIS 0.001 0.000 HIS F 36 PHE 0.010 0.001 PHE D 2 TYR 0.006 0.001 TYR A 20 ARG 0.003 0.000 ARG B 18 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1608 Ramachandran restraints generated. 804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1608 Ramachandran restraints generated. 804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 156 time to evaluate : 0.652 Fit side-chains revert: symmetry clash REVERT: A 8 GLU cc_start: 0.8056 (OUTLIER) cc_final: 0.7528 (tt0) REVERT: A 32 ASP cc_start: 0.8463 (OUTLIER) cc_final: 0.7951 (m-30) REVERT: A 46 ARG cc_start: 0.8657 (OUTLIER) cc_final: 0.7984 (tmt170) REVERT: B 65 GLN cc_start: 0.8823 (mt0) cc_final: 0.8575 (mt0) REVERT: D 25 GLU cc_start: 0.8179 (mt-10) cc_final: 0.7739 (mp0) REVERT: D 38 ARG cc_start: 0.7464 (ttt180) cc_final: 0.6933 (ttt90) REVERT: E 25 GLU cc_start: 0.8401 (mt-10) cc_final: 0.8112 (mp0) REVERT: E 29 LYS cc_start: 0.8415 (tttt) cc_final: 0.7604 (tptt) REVERT: E 38 ARG cc_start: 0.7558 (ttt180) cc_final: 0.7234 (tpp80) REVERT: G 8 GLU cc_start: 0.8240 (OUTLIER) cc_final: 0.7989 (mt-10) REVERT: G 25 GLU cc_start: 0.8257 (mt-10) cc_final: 0.7833 (mp0) REVERT: G 38 ARG cc_start: 0.7476 (ttt180) cc_final: 0.7021 (tpp80) REVERT: G 46 ARG cc_start: 0.8546 (OUTLIER) cc_final: 0.6774 (tmt170) REVERT: G 66 GLU cc_start: 0.8618 (OUTLIER) cc_final: 0.8241 (mt-10) REVERT: H 38 ARG cc_start: 0.7447 (ttt180) cc_final: 0.7003 (tpp80) REVERT: I 8 GLU cc_start: 0.8130 (OUTLIER) cc_final: 0.7626 (mt-10) REVERT: I 25 GLU cc_start: 0.8384 (mt-10) cc_final: 0.8043 (mt-10) REVERT: I 38 ARG cc_start: 0.7781 (ttt180) cc_final: 0.7560 (tpp-160) REVERT: I 62 GLU cc_start: 0.7917 (OUTLIER) cc_final: 0.7472 (tp30) REVERT: J 38 ARG cc_start: 0.7616 (ttt180) cc_final: 0.7399 (tpp-160) REVERT: J 62 GLU cc_start: 0.7875 (tt0) cc_final: 0.7499 (tp30) REVERT: J 65 GLN cc_start: 0.8995 (mt0) cc_final: 0.8703 (mt0) REVERT: K 25 GLU cc_start: 0.8543 (mt-10) cc_final: 0.8096 (mt-10) outliers start: 30 outliers final: 15 residues processed: 165 average time/residue: 1.6880 time to fit residues: 288.0243 Evaluate side-chains 178 residues out of total 576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 155 time to evaluate : 0.702 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 GLU Chi-restraints excluded: chain A residue 32 ASP Chi-restraints excluded: chain A residue 46 ARG Chi-restraints excluded: chain A residue 63 SER Chi-restraints excluded: chain B residue 29 LYS Chi-restraints excluded: chain B residue 32 ASP Chi-restraints excluded: chain C residue 32 ASP Chi-restraints excluded: chain C residue 59 ASP Chi-restraints excluded: chain F residue 32 ASP Chi-restraints excluded: chain G residue 8 GLU Chi-restraints excluded: chain G residue 46 ARG Chi-restraints excluded: chain G residue 66 GLU Chi-restraints excluded: chain I residue 8 GLU Chi-restraints excluded: chain I residue 23 MET Chi-restraints excluded: chain I residue 32 ASP Chi-restraints excluded: chain I residue 62 GLU Chi-restraints excluded: chain I residue 63 SER Chi-restraints excluded: chain J residue 32 ASP Chi-restraints excluded: chain J residue 46 ARG Chi-restraints excluded: chain J residue 63 SER Chi-restraints excluded: chain K residue 63 SER Chi-restraints excluded: chain L residue 32 ASP Chi-restraints excluded: chain L residue 63 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 66 optimal weight: 0.9990 chunk 38 optimal weight: 0.9990 chunk 28 optimal weight: 0.2980 chunk 50 optimal weight: 0.5980 chunk 19 optimal weight: 1.9990 chunk 58 optimal weight: 0.8980 chunk 61 optimal weight: 1.9990 chunk 64 optimal weight: 0.6980 chunk 42 optimal weight: 2.9990 chunk 68 optimal weight: 0.6980 chunk 41 optimal weight: 3.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7897 moved from start: 0.2836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 6804 Z= 0.192 Angle : 0.487 4.380 9108 Z= 0.295 Chirality : 0.041 0.125 744 Planarity : 0.002 0.015 1236 Dihedral : 4.395 17.949 900 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.34 % Favored : 93.66 % Rotamer: Outliers : 4.17 % Allowed : 19.27 % Favored : 76.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.85 (0.16), residues: 804 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.92 (0.12), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP G 28 HIS 0.001 0.000 HIS G 36 PHE 0.010 0.001 PHE I 2 TYR 0.005 0.001 TYR A 20 ARG 0.002 0.000 ARG B 18 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1608 Ramachandran restraints generated. 804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1608 Ramachandran restraints generated. 804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 154 time to evaluate : 0.688 Fit side-chains revert: symmetry clash REVERT: A 8 GLU cc_start: 0.8058 (OUTLIER) cc_final: 0.7532 (tt0) REVERT: A 46 ARG cc_start: 0.8645 (OUTLIER) cc_final: 0.8103 (tmt170) REVERT: B 65 GLN cc_start: 0.8814 (mt0) cc_final: 0.8563 (mt0) REVERT: D 25 GLU cc_start: 0.8198 (mt-10) cc_final: 0.7752 (mp0) REVERT: D 38 ARG cc_start: 0.7503 (ttt180) cc_final: 0.6964 (ttt90) REVERT: E 25 GLU cc_start: 0.8385 (mt-10) cc_final: 0.8100 (mp0) REVERT: E 29 LYS cc_start: 0.8391 (tttt) cc_final: 0.7639 (tptt) REVERT: E 38 ARG cc_start: 0.7543 (ttt180) cc_final: 0.7248 (tpp80) REVERT: G 8 GLU cc_start: 0.8226 (OUTLIER) cc_final: 0.7923 (mt-10) REVERT: G 25 GLU cc_start: 0.8268 (mt-10) cc_final: 0.7856 (mp0) REVERT: G 38 ARG cc_start: 0.7465 (ttt180) cc_final: 0.7014 (tpp80) REVERT: G 66 GLU cc_start: 0.8600 (OUTLIER) cc_final: 0.8229 (mt-10) REVERT: H 38 ARG cc_start: 0.7479 (ttt180) cc_final: 0.7048 (tpp80) REVERT: I 8 GLU cc_start: 0.8133 (OUTLIER) cc_final: 0.7706 (mt-10) REVERT: I 25 GLU cc_start: 0.8391 (mt-10) cc_final: 0.8050 (mt-10) REVERT: I 38 ARG cc_start: 0.7785 (ttt180) cc_final: 0.7562 (tpp-160) REVERT: I 62 GLU cc_start: 0.7913 (OUTLIER) cc_final: 0.7477 (tp30) REVERT: J 38 ARG cc_start: 0.7562 (ttt180) cc_final: 0.7346 (tpp-160) REVERT: J 62 GLU cc_start: 0.7864 (tt0) cc_final: 0.7481 (tp30) REVERT: J 65 GLN cc_start: 0.8992 (mt0) cc_final: 0.8700 (mt0) REVERT: K 23 MET cc_start: 0.8839 (mtt) cc_final: 0.8537 (mtt) REVERT: K 25 GLU cc_start: 0.8564 (mt-10) cc_final: 0.8130 (mt-10) outliers start: 24 outliers final: 16 residues processed: 161 average time/residue: 1.7536 time to fit residues: 291.8840 Evaluate side-chains 174 residues out of total 576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 152 time to evaluate : 0.686 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 GLU Chi-restraints excluded: chain A residue 46 ARG Chi-restraints excluded: chain A residue 63 SER Chi-restraints excluded: chain B residue 29 LYS Chi-restraints excluded: chain B residue 32 ASP Chi-restraints excluded: chain C residue 32 ASP Chi-restraints excluded: chain D residue 32 ASP Chi-restraints excluded: chain F residue 32 ASP Chi-restraints excluded: chain G residue 8 GLU Chi-restraints excluded: chain G residue 66 GLU Chi-restraints excluded: chain H residue 63 SER Chi-restraints excluded: chain I residue 8 GLU Chi-restraints excluded: chain I residue 23 MET Chi-restraints excluded: chain I residue 32 ASP Chi-restraints excluded: chain I residue 62 GLU Chi-restraints excluded: chain I residue 63 SER Chi-restraints excluded: chain J residue 32 ASP Chi-restraints excluded: chain J residue 46 ARG Chi-restraints excluded: chain J residue 63 SER Chi-restraints excluded: chain K residue 63 SER Chi-restraints excluded: chain L residue 32 ASP Chi-restraints excluded: chain L residue 63 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 32 optimal weight: 0.7980 chunk 47 optimal weight: 4.9990 chunk 71 optimal weight: 1.9990 chunk 66 optimal weight: 0.5980 chunk 57 optimal weight: 6.9990 chunk 5 optimal weight: 0.0040 chunk 44 optimal weight: 1.9990 chunk 35 optimal weight: 0.6980 chunk 45 optimal weight: 1.9990 chunk 60 optimal weight: 0.9990 chunk 17 optimal weight: 0.4980 overall best weight: 0.5192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 65 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7887 moved from start: 0.2894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.018 6804 Z= 0.165 Angle : 0.475 4.294 9108 Z= 0.288 Chirality : 0.041 0.124 744 Planarity : 0.002 0.014 1236 Dihedral : 4.278 17.409 900 Min Nonbonded Distance : 2.310 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.34 % Favored : 93.66 % Rotamer: Outliers : 3.82 % Allowed : 20.83 % Favored : 75.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.84 (0.16), residues: 804 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.92 (0.12), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP G 28 HIS 0.001 0.000 HIS G 36 PHE 0.009 0.001 PHE E 2 TYR 0.010 0.001 TYR J 34 ARG 0.002 0.000 ARG B 18 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1608 Ramachandran restraints generated. 804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1608 Ramachandran restraints generated. 804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 153 time to evaluate : 0.711 Fit side-chains revert: symmetry clash REVERT: A 8 GLU cc_start: 0.8053 (OUTLIER) cc_final: 0.7570 (tt0) REVERT: A 46 ARG cc_start: 0.8641 (OUTLIER) cc_final: 0.8105 (tmt170) REVERT: B 65 GLN cc_start: 0.8788 (mt0) cc_final: 0.8536 (mt0) REVERT: C 25 GLU cc_start: 0.8161 (mt-10) cc_final: 0.7411 (tp30) REVERT: D 25 GLU cc_start: 0.8177 (mt-10) cc_final: 0.7749 (mp0) REVERT: D 38 ARG cc_start: 0.7481 (ttt180) cc_final: 0.6941 (ttt90) REVERT: E 25 GLU cc_start: 0.8388 (mt-10) cc_final: 0.7991 (mp0) REVERT: E 29 LYS cc_start: 0.8385 (tttt) cc_final: 0.7666 (tptt) REVERT: E 38 ARG cc_start: 0.7540 (ttt180) cc_final: 0.7248 (tpp80) REVERT: G 8 GLU cc_start: 0.8233 (OUTLIER) cc_final: 0.7960 (mt-10) REVERT: G 25 GLU cc_start: 0.8267 (mt-10) cc_final: 0.7848 (mp0) REVERT: G 38 ARG cc_start: 0.7456 (ttt180) cc_final: 0.7006 (tpp80) REVERT: G 46 ARG cc_start: 0.8545 (OUTLIER) cc_final: 0.6738 (tmt170) REVERT: G 66 GLU cc_start: 0.8589 (OUTLIER) cc_final: 0.8215 (mt-10) REVERT: H 38 ARG cc_start: 0.7503 (ttt180) cc_final: 0.7067 (tpp80) REVERT: I 8 GLU cc_start: 0.8145 (OUTLIER) cc_final: 0.7533 (mt-10) REVERT: I 25 GLU cc_start: 0.8381 (mt-10) cc_final: 0.8105 (mt-10) REVERT: I 38 ARG cc_start: 0.7791 (ttt180) cc_final: 0.7566 (tpp-160) REVERT: I 62 GLU cc_start: 0.7917 (OUTLIER) cc_final: 0.7622 (tp30) REVERT: J 38 ARG cc_start: 0.7587 (ttt180) cc_final: 0.7370 (tpp-160) REVERT: J 65 GLN cc_start: 0.8988 (mt0) cc_final: 0.8695 (mt0) REVERT: K 25 GLU cc_start: 0.8573 (mt-10) cc_final: 0.8131 (mt-10) outliers start: 22 outliers final: 12 residues processed: 160 average time/residue: 1.6888 time to fit residues: 279.5645 Evaluate side-chains 171 residues out of total 576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 152 time to evaluate : 0.695 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 GLU Chi-restraints excluded: chain A residue 46 ARG Chi-restraints excluded: chain A residue 63 SER Chi-restraints excluded: chain B residue 29 LYS Chi-restraints excluded: chain B residue 32 ASP Chi-restraints excluded: chain C residue 32 ASP Chi-restraints excluded: chain F residue 32 ASP Chi-restraints excluded: chain G residue 8 GLU Chi-restraints excluded: chain G residue 46 ARG Chi-restraints excluded: chain G residue 66 GLU Chi-restraints excluded: chain H residue 63 SER Chi-restraints excluded: chain I residue 8 GLU Chi-restraints excluded: chain I residue 23 MET Chi-restraints excluded: chain I residue 32 ASP Chi-restraints excluded: chain I residue 62 GLU Chi-restraints excluded: chain I residue 63 SER Chi-restraints excluded: chain J residue 32 ASP Chi-restraints excluded: chain J residue 46 ARG Chi-restraints excluded: chain K residue 63 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 52 optimal weight: 2.9990 chunk 8 optimal weight: 2.9990 chunk 15 optimal weight: 5.9990 chunk 57 optimal weight: 6.9990 chunk 23 optimal weight: 3.9990 chunk 58 optimal weight: 4.9990 chunk 7 optimal weight: 1.9990 chunk 10 optimal weight: 3.9990 chunk 50 optimal weight: 3.9990 chunk 3 optimal weight: 0.9980 chunk 41 optimal weight: 0.9980 overall best weight: 1.9986 ------------------------------------------------------------------------------- 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 = 0.3835 r_free = 0.3835 target = 0.117135 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.094578 restraints weight = 7799.156| |-----------------------------------------------------------------------------| r_work (start): 0.3544 rms_B_bonded: 2.50 r_work: 0.3394 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3256 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3256 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8373 moved from start: 0.2733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.050 6804 Z= 0.526 Angle : 0.598 5.266 9108 Z= 0.359 Chirality : 0.044 0.135 744 Planarity : 0.003 0.031 1236 Dihedral : 4.950 21.196 900 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.84 % Favored : 92.16 % Rotamer: Outliers : 3.82 % Allowed : 20.49 % Favored : 75.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.94 (0.16), residues: 804 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.00 (0.12), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP K 17 HIS 0.002 0.001 HIS B 36 PHE 0.015 0.002 PHE A 5 TYR 0.012 0.002 TYR J 34 ARG 0.005 0.001 ARG B 18 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4530.95 seconds wall clock time: 79 minutes 46.57 seconds (4786.57 seconds total)