Starting phenix.real_space_refine on Tue Feb 13 22:31:31 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6sdz_10150/02_2024/6sdz_10150.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6sdz_10150/02_2024/6sdz_10150.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.97 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6sdz_10150/02_2024/6sdz_10150.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6sdz_10150/02_2024/6sdz_10150.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6sdz_10150/02_2024/6sdz_10150.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6sdz_10150/02_2024/6sdz_10150.pdb" } resolution = 2.97 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= 0.001 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 22 5.16 5 C 5115 2.51 5 N 1298 2.21 5 O 1474 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 21": "NH1" <-> "NH2" Residue "A GLU 61": "OE1" <-> "OE2" Residue "B ARG 21": "NH1" <-> "NH2" Residue "B GLU 61": "OE1" <-> "OE2" Residue "C ARG 21": "NH1" <-> "NH2" Residue "C GLU 61": "OE1" <-> "OE2" Residue "D ARG 21": "NH1" <-> "NH2" Residue "D GLU 61": "OE1" <-> "OE2" Residue "E ARG 21": "NH1" <-> "NH2" Residue "E GLU 61": "OE1" <-> "OE2" Residue "E PHE 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 21": "NH1" <-> "NH2" Residue "G ARG 21": "NH1" <-> "NH2" Residue "G GLU 61": "OE1" <-> "OE2" Residue "H ARG 21": "NH1" <-> "NH2" Residue "H GLU 61": "OE1" <-> "OE2" Residue "I ARG 21": "NH1" <-> "NH2" Residue "I GLU 61": "OE1" <-> "OE2" Residue "J ARG 21": "NH1" <-> "NH2" Residue "J GLU 61": "OE1" <-> "OE2" Residue "K ARG 21": "NH1" <-> "NH2" Residue "K GLU 61": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 7909 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 719 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 719 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 4, 'TRANS': 87} Chain breaks: 1 Chain: "B" Number of atoms: 719 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 719 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 4, 'TRANS': 87} Chain breaks: 1 Chain: "C" Number of atoms: 719 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 719 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 4, 'TRANS': 87} Chain breaks: 1 Chain: "D" Number of atoms: 719 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 719 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 4, 'TRANS': 87} Chain breaks: 1 Chain: "E" Number of atoms: 719 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 719 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 4, 'TRANS': 87} Chain breaks: 1 Chain: "F" Number of atoms: 719 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 719 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 4, 'TRANS': 87} Chain breaks: 1 Chain: "G" Number of atoms: 719 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 719 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 4, 'TRANS': 87} Chain breaks: 1 Chain: "H" Number of atoms: 719 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 719 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 4, 'TRANS': 87} Chain breaks: 1 Chain: "I" Number of atoms: 719 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 719 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 4, 'TRANS': 87} Chain breaks: 1 Chain: "J" Number of atoms: 719 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 719 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 4, 'TRANS': 87} Chain breaks: 1 Chain: "K" Number of atoms: 719 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 719 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 4, 'TRANS': 87} Chain breaks: 1 Time building chain proxies: 4.41, per 1000 atoms: 0.56 Number of scatterers: 7909 At special positions: 0 Unit cell: (82.16, 75.92, 68.64, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 22 16.00 O 1474 8.00 N 1298 7.00 C 5115 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: 3.15 Conformation dependent library (CDL) restraints added in 1.3 seconds 1936 Ramachandran restraints generated. 968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1914 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 12 sheets defined 0.0% alpha, 39.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.14 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 13 through 16 removed outlier: 6.222A pdb=" N VAL B 14 " --> pdb=" O LYS C 15 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N VAL C 14 " --> pdb=" O LYS D 15 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N VAL D 14 " --> pdb=" O LYS E 15 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N VAL I 14 " --> pdb=" O LYS J 15 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 19 through 21 removed outlier: 6.125A pdb=" N VAL B 20 " --> pdb=" O ARG C 21 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N VAL C 20 " --> pdb=" O ARG D 21 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N VAL D 20 " --> pdb=" O ARG E 21 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N VAL E 20 " --> pdb=" O ARG F 21 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N VAL F 20 " --> pdb=" O ARG G 21 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N VAL G 20 " --> pdb=" O ARG H 21 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N VAL H 20 " --> pdb=" O ARG I 21 " (cutoff:3.500A) removed outlier: 6.195A pdb=" N VAL I 20 " --> pdb=" O ARG J 21 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 25 through 34 removed outlier: 6.308A pdb=" N ILE A 26 " --> pdb=" O ASN B 27 " (cutoff:3.500A) removed outlier: 7.793A pdb=" N ALA B 29 " --> pdb=" O ILE A 26 " (cutoff:3.500A) removed outlier: 6.064A pdb=" N VAL A 28 " --> pdb=" O ALA B 29 " (cutoff:3.500A) removed outlier: 7.520A pdb=" N HIS B 31 " --> pdb=" O VAL A 28 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N MET A 30 " --> pdb=" O HIS B 31 " (cutoff:3.500A) removed outlier: 7.786A pdb=" N PHE B 33 " --> pdb=" O MET A 30 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N VAL A 32 " --> pdb=" O PHE B 33 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N ILE C 26 " --> pdb=" O ASN D 27 " (cutoff:3.500A) removed outlier: 7.948A pdb=" N ALA D 29 " --> pdb=" O ILE C 26 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N VAL C 28 " --> pdb=" O ALA D 29 " (cutoff:3.500A) removed outlier: 7.650A pdb=" N HIS D 31 " --> pdb=" O VAL C 28 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N MET C 30 " --> pdb=" O HIS D 31 " (cutoff:3.500A) removed outlier: 7.928A pdb=" N PHE D 33 " --> pdb=" O MET C 30 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N VAL C 32 " --> pdb=" O PHE D 33 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N ILE D 26 " --> pdb=" O ASN E 27 " (cutoff:3.500A) removed outlier: 7.870A pdb=" N ALA E 29 " --> pdb=" O ILE D 26 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N VAL D 28 " --> pdb=" O ALA E 29 " (cutoff:3.500A) removed outlier: 7.807A pdb=" N HIS E 31 " --> pdb=" O VAL D 28 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N MET D 30 " --> pdb=" O HIS E 31 " (cutoff:3.500A) removed outlier: 7.935A pdb=" N PHE E 33 " --> pdb=" O MET D 30 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N VAL D 32 " --> pdb=" O PHE E 33 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N ILE F 26 " --> pdb=" O ASN G 27 " (cutoff:3.500A) removed outlier: 7.862A pdb=" N ALA G 29 " --> pdb=" O ILE F 26 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N VAL F 28 " --> pdb=" O ALA G 29 " (cutoff:3.500A) removed outlier: 7.698A pdb=" N HIS G 31 " --> pdb=" O VAL F 28 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N MET F 30 " --> pdb=" O HIS G 31 " (cutoff:3.500A) removed outlier: 8.009A pdb=" N PHE G 33 " --> pdb=" O MET F 30 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N VAL F 32 " --> pdb=" O PHE G 33 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N ILE H 26 " --> pdb=" O ASN I 27 " (cutoff:3.500A) removed outlier: 7.821A pdb=" N ALA I 29 " --> pdb=" O ILE H 26 " (cutoff:3.500A) removed outlier: 6.054A pdb=" N VAL H 28 " --> pdb=" O ALA I 29 " (cutoff:3.500A) removed outlier: 7.567A pdb=" N HIS I 31 " --> pdb=" O VAL H 28 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N MET H 30 " --> pdb=" O HIS I 31 " (cutoff:3.500A) removed outlier: 7.903A pdb=" N PHE I 33 " --> pdb=" O MET H 30 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N VAL H 32 " --> pdb=" O PHE I 33 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N ILE I 26 " --> pdb=" O ASN J 27 " (cutoff:3.500A) removed outlier: 7.957A pdb=" N ALA J 29 " --> pdb=" O ILE I 26 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N VAL I 28 " --> pdb=" O ALA J 29 " (cutoff:3.500A) removed outlier: 7.696A pdb=" N HIS J 31 " --> pdb=" O VAL I 28 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N MET I 30 " --> pdb=" O HIS J 31 " (cutoff:3.500A) removed outlier: 7.980A pdb=" N PHE J 33 " --> pdb=" O MET I 30 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N VAL I 32 " --> pdb=" O PHE J 33 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 59 through 62 removed outlier: 6.306A pdb=" N THR A 59 " --> pdb=" O THR B 60 " (cutoff:3.500A) removed outlier: 8.104A pdb=" N GLU B 62 " --> pdb=" O THR A 59 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N GLU A 61 " --> pdb=" O GLU B 62 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N THR B 59 " --> pdb=" O THR C 60 " (cutoff:3.500A) removed outlier: 7.999A pdb=" N GLU C 62 " --> pdb=" O THR B 59 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N GLU B 61 " --> pdb=" O GLU C 62 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N THR C 59 " --> pdb=" O THR D 60 " (cutoff:3.500A) removed outlier: 8.012A pdb=" N GLU D 62 " --> pdb=" O THR C 59 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N GLU C 61 " --> pdb=" O GLU D 62 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N THR D 59 " --> pdb=" O THR E 60 " (cutoff:3.500A) removed outlier: 7.986A pdb=" N GLU E 62 " --> pdb=" O THR D 59 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N GLU D 61 " --> pdb=" O GLU E 62 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N THR E 59 " --> pdb=" O THR F 60 " (cutoff:3.500A) removed outlier: 8.075A pdb=" N GLU F 62 " --> pdb=" O THR E 59 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N GLU E 61 " --> pdb=" O GLU F 62 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N THR F 59 " --> pdb=" O THR G 60 " (cutoff:3.500A) removed outlier: 8.033A pdb=" N GLU G 62 " --> pdb=" O THR F 59 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N GLU F 61 " --> pdb=" O GLU G 62 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N THR G 59 " --> pdb=" O THR H 60 " (cutoff:3.500A) removed outlier: 8.082A pdb=" N GLU H 62 " --> pdb=" O THR G 59 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N GLU G 61 " --> pdb=" O GLU H 62 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N THR H 59 " --> pdb=" O THR I 60 " (cutoff:3.500A) removed outlier: 8.019A pdb=" N GLU I 62 " --> pdb=" O THR H 59 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N GLU H 61 " --> pdb=" O GLU I 62 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N THR I 59 " --> pdb=" O THR J 60 " (cutoff:3.500A) removed outlier: 8.044A pdb=" N GLU J 62 " --> pdb=" O THR I 59 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N GLU I 61 " --> pdb=" O GLU J 62 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N THR J 59 " --> pdb=" O THR K 60 " (cutoff:3.500A) removed outlier: 8.164A pdb=" N GLU K 62 " --> pdb=" O THR J 59 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N GLU J 61 " --> pdb=" O GLU K 62 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 65 through 66 Processing sheet with id=AA6, first strand: chain 'A' and resid 71 through 73 removed outlier: 6.438A pdb=" N GLU H 72 " --> pdb=" O ILE I 73 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 76 through 80 removed outlier: 9.165A pdb=" N LYS A 76 " --> pdb=" O SER B 77 " (cutoff:3.500A) removed outlier: 9.561A pdb=" N TRP B 79 " --> pdb=" O LYS A 76 " (cutoff:3.500A) removed outlier: 5.724A pdb=" N TYR A 78 " --> pdb=" O TRP B 79 " (cutoff:3.500A) removed outlier: 9.271A pdb=" N LYS B 76 " --> pdb=" O SER C 77 " (cutoff:3.500A) removed outlier: 9.651A pdb=" N TRP C 79 " --> pdb=" O LYS B 76 " (cutoff:3.500A) removed outlier: 5.777A pdb=" N TYR B 78 " --> pdb=" O TRP C 79 " (cutoff:3.500A) removed outlier: 9.307A pdb=" N LYS C 76 " --> pdb=" O SER D 77 " (cutoff:3.500A) removed outlier: 9.674A pdb=" N TRP D 79 " --> pdb=" O LYS C 76 " (cutoff:3.500A) removed outlier: 5.833A pdb=" N TYR C 78 " --> pdb=" O TRP D 79 " (cutoff:3.500A) removed outlier: 9.229A pdb=" N LYS D 76 " --> pdb=" O SER E 77 " (cutoff:3.500A) removed outlier: 9.615A pdb=" N TRP E 79 " --> pdb=" O LYS D 76 " (cutoff:3.500A) removed outlier: 5.709A pdb=" N TYR D 78 " --> pdb=" O TRP E 79 " (cutoff:3.500A) removed outlier: 9.306A pdb=" N LYS E 76 " --> pdb=" O SER F 77 " (cutoff:3.500A) removed outlier: 9.692A pdb=" N TRP F 79 " --> pdb=" O LYS E 76 " (cutoff:3.500A) removed outlier: 5.886A pdb=" N TYR E 78 " --> pdb=" O TRP F 79 " (cutoff:3.500A) removed outlier: 9.319A pdb=" N LYS F 76 " --> pdb=" O SER G 77 " (cutoff:3.500A) removed outlier: 9.697A pdb=" N TRP G 79 " --> pdb=" O LYS F 76 " (cutoff:3.500A) removed outlier: 5.805A pdb=" N TYR F 78 " --> pdb=" O TRP G 79 " (cutoff:3.500A) removed outlier: 9.280A pdb=" N LYS G 76 " --> pdb=" O SER H 77 " (cutoff:3.500A) removed outlier: 9.659A pdb=" N TRP H 79 " --> pdb=" O LYS G 76 " (cutoff:3.500A) removed outlier: 5.777A pdb=" N TYR G 78 " --> pdb=" O TRP H 79 " (cutoff:3.500A) removed outlier: 9.283A pdb=" N LYS H 76 " --> pdb=" O SER I 77 " (cutoff:3.500A) removed outlier: 9.652A pdb=" N TRP I 79 " --> pdb=" O LYS H 76 " (cutoff:3.500A) removed outlier: 5.793A pdb=" N TYR H 78 " --> pdb=" O TRP I 79 " (cutoff:3.500A) removed outlier: 9.248A pdb=" N LYS I 76 " --> pdb=" O SER J 77 " (cutoff:3.500A) removed outlier: 9.624A pdb=" N TRP J 79 " --> pdb=" O LYS I 76 " (cutoff:3.500A) removed outlier: 5.758A pdb=" N TYR I 78 " --> pdb=" O TRP J 79 " (cutoff:3.500A) removed outlier: 9.152A pdb=" N LYS J 76 " --> pdb=" O SER K 77 " (cutoff:3.500A) removed outlier: 9.542A pdb=" N TRP K 79 " --> pdb=" O LYS J 76 " (cutoff:3.500A) removed outlier: 5.709A pdb=" N TYR J 78 " --> pdb=" O TRP K 79 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'A' and resid 92 through 98 Processing sheet with id=AA9, first strand: chain 'A' and resid 103 through 104 Processing sheet with id=AB1, first strand: chain 'A' and resid 114 through 115 removed outlier: 6.877A pdb=" N TYR A 114 " --> pdb=" O SER B 115 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N TYR B 114 " --> pdb=" O SER C 115 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N TYR C 114 " --> pdb=" O SER D 115 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N TYR D 114 " --> pdb=" O SER E 115 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N TYR E 114 " --> pdb=" O SER F 115 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N TYR F 114 " --> pdb=" O SER G 115 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N TYR G 114 " --> pdb=" O SER H 115 " (cutoff:3.500A) removed outlier: 6.977A pdb=" N TYR H 114 " --> pdb=" O SER I 115 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N TYR I 114 " --> pdb=" O SER J 115 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N TYR J 114 " --> pdb=" O SER K 115 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'A' and resid 118 through 122 removed outlier: 6.589A pdb=" N THR E 119 " --> pdb=" O ALA F 120 " (cutoff:3.500A) removed outlier: 7.631A pdb=" N VAL F 122 " --> pdb=" O THR E 119 " (cutoff:3.500A) removed outlier: 6.068A pdb=" N VAL E 121 " --> pdb=" O VAL F 122 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 83 through 84 removed outlier: 3.501A pdb=" N ILE E 84 " --> pdb=" O GLY F 83 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 192 hydrogen bonds defined for protein. 576 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.32 Time building geometry restraints manager: 3.40 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1351 1.32 - 1.44: 2140 1.44 - 1.57: 4559 1.57 - 1.69: 2 1.69 - 1.81: 44 Bond restraints: 8096 Sorted by residual: bond pdb=" CE1 HIS A 31 " pdb=" NE2 HIS A 31 " ideal model delta sigma weight residual 1.321 1.375 -0.054 1.00e-02 1.00e+04 2.97e+01 bond pdb=" CA SER B 112 " pdb=" CB SER B 112 " ideal model delta sigma weight residual 1.529 1.491 0.038 1.20e-02 6.94e+03 1.01e+01 bond pdb=" CA SER D 112 " pdb=" CB SER D 112 " ideal model delta sigma weight residual 1.529 1.491 0.038 1.20e-02 6.94e+03 1.00e+01 bond pdb=" CA SER G 112 " pdb=" CB SER G 112 " ideal model delta sigma weight residual 1.529 1.492 0.037 1.20e-02 6.94e+03 9.62e+00 bond pdb=" CA SER H 112 " pdb=" CB SER H 112 " ideal model delta sigma weight residual 1.529 1.492 0.037 1.20e-02 6.94e+03 9.47e+00 ... (remaining 8091 not shown) Histogram of bond angle deviations from ideal: 95.61 - 103.33: 79 103.33 - 111.04: 2747 111.04 - 118.75: 3843 118.75 - 126.47: 4242 126.47 - 134.18: 89 Bond angle restraints: 11000 Sorted by residual: angle pdb=" CD1 LEU G 58 " pdb=" CG LEU G 58 " pdb=" CD2 LEU G 58 " ideal model delta sigma weight residual 110.80 101.03 9.77 2.20e+00 2.07e-01 1.97e+01 angle pdb=" CD1 LEU I 58 " pdb=" CG LEU I 58 " pdb=" CD2 LEU I 58 " ideal model delta sigma weight residual 110.80 102.17 8.63 2.20e+00 2.07e-01 1.54e+01 angle pdb=" O ILE C 68 " pdb=" C ILE C 68 " pdb=" N TYR C 69 " ideal model delta sigma weight residual 121.83 125.46 -3.63 1.03e+00 9.43e-01 1.24e+01 angle pdb=" CA GLU G 62 " pdb=" C GLU G 62 " pdb=" O GLU G 62 " ideal model delta sigma weight residual 121.40 117.46 3.94 1.13e+00 7.83e-01 1.22e+01 angle pdb=" CB GLU H 61 " pdb=" CG GLU H 61 " pdb=" CD GLU H 61 " ideal model delta sigma weight residual 112.60 118.47 -5.87 1.70e+00 3.46e-01 1.19e+01 ... (remaining 10995 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 11.00: 4047 11.00 - 21.99: 486 21.99 - 32.99: 172 32.99 - 43.98: 70 43.98 - 54.98: 10 Dihedral angle restraints: 4785 sinusoidal: 1826 harmonic: 2959 Sorted by residual: dihedral pdb=" C GLU E 63 " pdb=" N GLU E 63 " pdb=" CA GLU E 63 " pdb=" CB GLU E 63 " ideal model delta harmonic sigma weight residual -122.60 -131.36 8.76 0 2.50e+00 1.60e-01 1.23e+01 dihedral pdb=" CA ILE K 26 " pdb=" C ILE K 26 " pdb=" N ASN K 27 " pdb=" CA ASN K 27 " ideal model delta harmonic sigma weight residual 180.00 162.54 17.46 0 5.00e+00 4.00e-02 1.22e+01 dihedral pdb=" CA ILE H 26 " pdb=" C ILE H 26 " pdb=" N ASN H 27 " pdb=" CA ASN H 27 " ideal model delta harmonic sigma weight residual 180.00 162.57 17.43 0 5.00e+00 4.00e-02 1.21e+01 ... (remaining 4782 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.076: 846 0.076 - 0.151: 364 0.151 - 0.227: 52 0.227 - 0.303: 20 0.303 - 0.379: 5 Chirality restraints: 1287 Sorted by residual: chirality pdb=" CG LEU G 58 " pdb=" CB LEU G 58 " pdb=" CD1 LEU G 58 " pdb=" CD2 LEU G 58 " both_signs ideal model delta sigma weight residual False -2.59 -2.97 0.38 2.00e-01 2.50e+01 3.58e+00 chirality pdb=" CB VAL K 16 " pdb=" CA VAL K 16 " pdb=" CG1 VAL K 16 " pdb=" CG2 VAL K 16 " both_signs ideal model delta sigma weight residual False -2.63 -2.28 -0.35 2.00e-01 2.50e+01 3.12e+00 chirality pdb=" CG LEU C 58 " pdb=" CB LEU C 58 " pdb=" CD1 LEU C 58 " pdb=" CD2 LEU C 58 " both_signs ideal model delta sigma weight residual False -2.59 -2.26 -0.33 2.00e-01 2.50e+01 2.75e+00 ... (remaining 1284 not shown) Planarity restraints: 1353 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE K 64 " 0.013 2.00e-02 2.50e+03 4.88e-02 4.16e+01 pdb=" CG PHE K 64 " -0.039 2.00e-02 2.50e+03 pdb=" CD1 PHE K 64 " 0.075 2.00e-02 2.50e+03 pdb=" CD2 PHE K 64 " -0.044 2.00e-02 2.50e+03 pdb=" CE1 PHE K 64 " -0.067 2.00e-02 2.50e+03 pdb=" CE2 PHE K 64 " 0.053 2.00e-02 2.50e+03 pdb=" CZ PHE K 64 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 114 " -0.022 2.00e-02 2.50e+03 4.16e-02 3.47e+01 pdb=" CG TYR A 114 " 0.011 2.00e-02 2.50e+03 pdb=" CD1 TYR A 114 " 0.025 2.00e-02 2.50e+03 pdb=" CD2 TYR A 114 " 0.042 2.00e-02 2.50e+03 pdb=" CE1 TYR A 114 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR A 114 " -0.014 2.00e-02 2.50e+03 pdb=" CZ TYR A 114 " -0.091 2.00e-02 2.50e+03 pdb=" OH TYR A 114 " 0.048 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR J 114 " -0.019 2.00e-02 2.50e+03 2.81e-02 1.58e+01 pdb=" CG TYR J 114 " 0.009 2.00e-02 2.50e+03 pdb=" CD1 TYR J 114 " -0.015 2.00e-02 2.50e+03 pdb=" CD2 TYR J 114 " 0.006 2.00e-02 2.50e+03 pdb=" CE1 TYR J 114 " 0.017 2.00e-02 2.50e+03 pdb=" CE2 TYR J 114 " -0.005 2.00e-02 2.50e+03 pdb=" CZ TYR J 114 " 0.055 2.00e-02 2.50e+03 pdb=" OH TYR J 114 " -0.048 2.00e-02 2.50e+03 ... (remaining 1350 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 1654 2.79 - 3.32: 7696 3.32 - 3.85: 14998 3.85 - 4.37: 17613 4.37 - 4.90: 32309 Nonbonded interactions: 74270 Sorted by model distance: nonbonded pdb=" N SER J 112 " pdb=" OG SER K 112 " model vdw 2.263 2.520 nonbonded pdb=" N SER A 112 " pdb=" OG SER B 112 " model vdw 2.271 2.520 nonbonded pdb=" N SER I 112 " pdb=" OG SER J 112 " model vdw 2.274 2.520 nonbonded pdb=" N SER E 112 " pdb=" OG SER F 112 " model vdw 2.280 2.520 nonbonded pdb=" N SER B 112 " pdb=" OG SER C 112 " model vdw 2.312 2.520 ... (remaining 74265 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' } 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: 0.420 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 2.110 Check model and map are aligned: 0.120 Set scattering table: 0.070 Process input model: 25.190 Find NCS groups from input model: 0.520 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: 0.010 Load rotamer database and sin/cos tables:13.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.500 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8638 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 : 0.009 0.065 8096 Z= 0.601 Angle : 1.132 9.773 11000 Z= 0.727 Chirality : 0.084 0.379 1287 Planarity : 0.006 0.049 1353 Dihedral : 12.171 54.980 2871 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 27.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer: Outliers : 0.12 % Allowed : 3.73 % Favored : 96.15 % 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: -3.05 (0.22), residues: 968 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.32 (0.16), residues: 968 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.005 TRP E 79 HIS 0.037 0.004 HIS G 31 PHE 0.075 0.006 PHE K 64 TYR 0.091 0.009 TYR A 114 ARG 0.010 0.001 ARG A 34 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1936 Ramachandran restraints generated. 968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1936 Ramachandran restraints generated. 968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 393 residues out of total 858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 392 time to evaluate : 0.935 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 15 LYS cc_start: 0.9068 (mttt) cc_final: 0.8484 (mtpm) REVERT: A 34 ARG cc_start: 0.8632 (ttt180) cc_final: 0.8153 (tpp80) REVERT: A 63 GLU cc_start: 0.8662 (pt0) cc_final: 0.8199 (pp20) REVERT: A 70 LYS cc_start: 0.9197 (tttt) cc_final: 0.8978 (tppp) REVERT: A 90 HIS cc_start: 0.8324 (m90) cc_final: 0.8116 (m90) REVERT: A 104 ARG cc_start: 0.8021 (mtm-85) cc_final: 0.7536 (mtm-85) REVERT: B 15 LYS cc_start: 0.8779 (mttt) cc_final: 0.8126 (mtpp) REVERT: B 34 ARG cc_start: 0.8540 (ttt180) cc_final: 0.8034 (tpp80) REVERT: B 90 HIS cc_start: 0.8469 (m90) cc_final: 0.8046 (m90) REVERT: C 15 LYS cc_start: 0.8955 (mttt) cc_final: 0.8266 (mtpp) REVERT: C 72 GLU cc_start: 0.8358 (mt-10) cc_final: 0.8093 (mt-10) REVERT: C 90 HIS cc_start: 0.8443 (m90) cc_final: 0.8112 (m90) REVERT: D 15 LYS cc_start: 0.8720 (mttt) cc_final: 0.8294 (ttmm) REVERT: D 34 ARG cc_start: 0.8782 (ttt180) cc_final: 0.8443 (tpp80) REVERT: D 72 GLU cc_start: 0.7525 (mt-10) cc_final: 0.7017 (mt-10) REVERT: D 80 LYS cc_start: 0.9076 (tttt) cc_final: 0.8859 (tttp) REVERT: D 90 HIS cc_start: 0.8505 (m90) cc_final: 0.8126 (m90) REVERT: E 15 LYS cc_start: 0.8968 (mttt) cc_final: 0.8308 (mtpp) REVERT: E 21 ARG cc_start: 0.8390 (tpt-90) cc_final: 0.8146 (tpp80) REVERT: E 34 ARG cc_start: 0.8650 (ttt180) cc_final: 0.8433 (tpp80) REVERT: E 69 TYR cc_start: 0.8737 (m-80) cc_final: 0.8423 (m-80) REVERT: F 15 LYS cc_start: 0.8659 (mttt) cc_final: 0.8115 (ttmm) REVERT: F 21 ARG cc_start: 0.8401 (tpt-90) cc_final: 0.8152 (tpp80) REVERT: F 34 ARG cc_start: 0.8642 (ttt180) cc_final: 0.8352 (tpp80) REVERT: F 80 LYS cc_start: 0.9055 (tttt) cc_final: 0.8833 (tttm) REVERT: G 15 LYS cc_start: 0.9048 (mttt) cc_final: 0.8449 (ttmm) REVERT: G 18 ASP cc_start: 0.8566 (m-30) cc_final: 0.8320 (m-30) REVERT: G 34 ARG cc_start: 0.8628 (ttt180) cc_final: 0.8339 (tpp80) REVERT: G 63 GLU cc_start: 0.8441 (pt0) cc_final: 0.7899 (pm20) REVERT: G 90 HIS cc_start: 0.8552 (m90) cc_final: 0.8232 (m170) REVERT: G 99 ASP cc_start: 0.8518 (t0) cc_final: 0.8237 (t70) REVERT: H 15 LYS cc_start: 0.8885 (mttt) cc_final: 0.8233 (ttmm) REVERT: H 34 ARG cc_start: 0.8720 (ttt180) cc_final: 0.8378 (tpp80) REVERT: H 63 GLU cc_start: 0.8684 (pt0) cc_final: 0.8083 (pm20) REVERT: H 70 LYS cc_start: 0.9256 (tttt) cc_final: 0.8896 (tppp) REVERT: H 90 HIS cc_start: 0.8457 (m90) cc_final: 0.8120 (m90) REVERT: I 15 LYS cc_start: 0.8880 (mttt) cc_final: 0.8356 (ttmm) REVERT: I 34 ARG cc_start: 0.8620 (ttt180) cc_final: 0.8247 (tpp80) REVERT: I 80 LYS cc_start: 0.9178 (tttt) cc_final: 0.8944 (tttm) REVERT: I 100 SER cc_start: 0.8866 (t) cc_final: 0.8632 (p) REVERT: J 15 LYS cc_start: 0.8921 (mttt) cc_final: 0.8381 (ttmm) REVERT: J 34 ARG cc_start: 0.8652 (ttt180) cc_final: 0.8160 (tpp80) REVERT: J 63 GLU cc_start: 0.8685 (pt0) cc_final: 0.8435 (pt0) REVERT: J 84 ILE cc_start: 0.9426 (mt) cc_final: 0.9050 (pp) REVERT: J 100 SER cc_start: 0.8953 (t) cc_final: 0.8749 (p) REVERT: K 15 LYS cc_start: 0.8656 (mttt) cc_final: 0.8114 (ttmm) REVERT: K 27 ASN cc_start: 0.8796 (m-40) cc_final: 0.8539 (m-40) REVERT: K 80 LYS cc_start: 0.9062 (tttt) cc_final: 0.8836 (tttm) REVERT: K 84 ILE cc_start: 0.9476 (mt) cc_final: 0.9259 (pp) REVERT: K 90 HIS cc_start: 0.8669 (m90) cc_final: 0.8234 (m90) REVERT: K 100 SER cc_start: 0.8985 (t) cc_final: 0.8768 (p) outliers start: 1 outliers final: 1 residues processed: 393 average time/residue: 1.2328 time to fit residues: 510.1616 Evaluate side-chains 336 residues out of total 858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 335 time to evaluate : 0.943 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 110 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 83 optimal weight: 1.9990 chunk 75 optimal weight: 0.7980 chunk 41 optimal weight: 5.9990 chunk 25 optimal weight: 1.9990 chunk 50 optimal weight: 0.7980 chunk 40 optimal weight: 0.7980 chunk 77 optimal weight: 4.9990 chunk 30 optimal weight: 0.8980 chunk 47 optimal weight: 0.9990 chunk 57 optimal weight: 0.9980 chunk 89 optimal weight: 0.8980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8683 moved from start: 0.2726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8096 Z= 0.235 Angle : 0.763 8.473 11000 Z= 0.393 Chirality : 0.053 0.147 1287 Planarity : 0.005 0.040 1353 Dihedral : 5.870 23.836 1091 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 22.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 5.71 % Allowed : 18.76 % Favored : 75.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.84 (0.22), residues: 968 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.15 (0.17), residues: 968 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 79 HIS 0.005 0.001 HIS J 88 PHE 0.017 0.001 PHE K 64 TYR 0.021 0.002 TYR K 114 ARG 0.011 0.001 ARG K 104 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1936 Ramachandran restraints generated. 968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1936 Ramachandran restraints generated. 968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 411 residues out of total 858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 362 time to evaluate : 0.969 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 15 LYS cc_start: 0.8970 (mttt) cc_final: 0.8437 (mtpm) REVERT: A 34 ARG cc_start: 0.8642 (ttt180) cc_final: 0.8174 (tpp80) REVERT: A 63 GLU cc_start: 0.8698 (pt0) cc_final: 0.8202 (pp20) REVERT: A 66 GLU cc_start: 0.7950 (tm-30) cc_final: 0.7735 (tm-30) REVERT: A 88 HIS cc_start: 0.8982 (t-90) cc_final: 0.8750 (t-90) REVERT: A 104 ARG cc_start: 0.8242 (mtm-85) cc_final: 0.8022 (mtt-85) REVERT: A 106 THR cc_start: 0.9281 (m) cc_final: 0.9066 (p) REVERT: B 13 MET cc_start: 0.8361 (tmm) cc_final: 0.8031 (tmm) REVERT: B 15 LYS cc_start: 0.8898 (mttt) cc_final: 0.8388 (mtpp) REVERT: B 21 ARG cc_start: 0.8157 (mtp85) cc_final: 0.7755 (tpp80) REVERT: B 34 ARG cc_start: 0.8491 (ttt180) cc_final: 0.8156 (tpp80) REVERT: B 66 GLU cc_start: 0.7773 (tm-30) cc_final: 0.7522 (tm-30) REVERT: B 80 LYS cc_start: 0.9240 (ttpt) cc_final: 0.9014 (ttpt) REVERT: B 90 HIS cc_start: 0.8360 (m90) cc_final: 0.8100 (m90) REVERT: C 63 GLU cc_start: 0.8242 (OUTLIER) cc_final: 0.7786 (pm20) REVERT: C 66 GLU cc_start: 0.8086 (OUTLIER) cc_final: 0.7638 (tm-30) REVERT: D 13 MET cc_start: 0.8354 (tmm) cc_final: 0.7898 (tmm) REVERT: D 15 LYS cc_start: 0.8729 (mttt) cc_final: 0.8114 (mtpm) REVERT: D 18 ASP cc_start: 0.8519 (m-30) cc_final: 0.8256 (m-30) REVERT: D 34 ARG cc_start: 0.8734 (ttt180) cc_final: 0.8304 (tpp80) REVERT: D 63 GLU cc_start: 0.8349 (pm20) cc_final: 0.8139 (pm20) REVERT: D 69 TYR cc_start: 0.8178 (m-80) cc_final: 0.7931 (m-80) REVERT: D 70 LYS cc_start: 0.9050 (ttpp) cc_final: 0.8827 (tttp) REVERT: D 80 LYS cc_start: 0.9034 (tttt) cc_final: 0.8833 (tttp) REVERT: E 13 MET cc_start: 0.8547 (tmm) cc_final: 0.8011 (tmm) REVERT: E 15 LYS cc_start: 0.8969 (mttt) cc_final: 0.8458 (mttm) REVERT: E 34 ARG cc_start: 0.8708 (ttt180) cc_final: 0.8417 (tpp80) REVERT: E 70 LYS cc_start: 0.9008 (tttt) cc_final: 0.8581 (ptmm) REVERT: E 72 GLU cc_start: 0.8040 (mp0) cc_final: 0.7698 (mp0) REVERT: E 104 ARG cc_start: 0.8352 (ttm110) cc_final: 0.7875 (mtm-85) REVERT: F 15 LYS cc_start: 0.8783 (mttt) cc_final: 0.8302 (mtpp) REVERT: F 63 GLU cc_start: 0.8178 (pm20) cc_final: 0.7554 (pm20) REVERT: G 13 MET cc_start: 0.8601 (tmm) cc_final: 0.7878 (tmm) REVERT: G 15 LYS cc_start: 0.8956 (mttt) cc_final: 0.8490 (mttm) REVERT: G 34 ARG cc_start: 0.8707 (ttt180) cc_final: 0.8343 (tpp80) REVERT: G 63 GLU cc_start: 0.8422 (pt0) cc_final: 0.8105 (pm20) REVERT: G 104 ARG cc_start: 0.8321 (mtm-85) cc_final: 0.8116 (ttm110) REVERT: H 15 LYS cc_start: 0.9011 (mttt) cc_final: 0.8500 (ttmm) REVERT: H 34 ARG cc_start: 0.8701 (ttt180) cc_final: 0.8422 (tpp80) REVERT: H 62 GLU cc_start: 0.8342 (mp0) cc_final: 0.8114 (mp0) REVERT: H 63 GLU cc_start: 0.8684 (pt0) cc_final: 0.8286 (pm20) REVERT: H 90 HIS cc_start: 0.8535 (m90) cc_final: 0.8253 (m90) REVERT: I 13 MET cc_start: 0.8319 (tmm) cc_final: 0.7851 (tmm) REVERT: I 15 LYS cc_start: 0.8916 (mttt) cc_final: 0.8434 (ttmm) REVERT: I 21 ARG cc_start: 0.8364 (mtp-110) cc_final: 0.8019 (tpp80) REVERT: I 80 LYS cc_start: 0.9125 (tttt) cc_final: 0.8906 (tttm) REVERT: I 104 ARG cc_start: 0.8163 (mtm-85) cc_final: 0.7908 (ttm110) REVERT: J 15 LYS cc_start: 0.8793 (mttt) cc_final: 0.8321 (ttmm) REVERT: J 34 ARG cc_start: 0.8505 (ttt180) cc_final: 0.8047 (tpp80) REVERT: J 63 GLU cc_start: 0.8648 (pt0) cc_final: 0.8175 (pt0) REVERT: J 84 ILE cc_start: 0.9443 (mt) cc_final: 0.9031 (pp) REVERT: K 15 LYS cc_start: 0.9055 (mttt) cc_final: 0.8537 (mtpm) REVERT: K 62 GLU cc_start: 0.8647 (mm-30) cc_final: 0.8364 (mp0) REVERT: K 80 LYS cc_start: 0.9006 (tttt) cc_final: 0.8767 (tttm) REVERT: K 90 HIS cc_start: 0.8623 (m90) cc_final: 0.8272 (m90) REVERT: K 99 ASP cc_start: 0.8236 (t0) cc_final: 0.8004 (t70) REVERT: K 100 SER cc_start: 0.8513 (t) cc_final: 0.8236 (p) REVERT: K 118 THR cc_start: 0.9237 (m) cc_final: 0.9013 (p) outliers start: 49 outliers final: 13 residues processed: 372 average time/residue: 1.3011 time to fit residues: 508.7850 Evaluate side-chains 353 residues out of total 858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 338 time to evaluate : 0.853 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 ASP Chi-restraints excluded: chain A residue 98 ASN Chi-restraints excluded: chain A residue 117 SER Chi-restraints excluded: chain B residue 58 LEU Chi-restraints excluded: chain B residue 98 ASN Chi-restraints excluded: chain B residue 100 SER Chi-restraints excluded: chain C residue 63 GLU Chi-restraints excluded: chain C residue 66 GLU Chi-restraints excluded: chain C residue 80 LYS Chi-restraints excluded: chain C residue 98 ASN Chi-restraints excluded: chain D residue 98 ASN Chi-restraints excluded: chain G residue 98 ASN Chi-restraints excluded: chain H residue 18 ASP Chi-restraints excluded: chain I residue 18 ASP Chi-restraints excluded: chain J residue 98 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 49 optimal weight: 4.9990 chunk 27 optimal weight: 5.9990 chunk 74 optimal weight: 10.0000 chunk 61 optimal weight: 5.9990 chunk 24 optimal weight: 0.9990 chunk 90 optimal weight: 0.1980 chunk 97 optimal weight: 7.9990 chunk 80 optimal weight: 5.9990 chunk 89 optimal weight: 0.7980 chunk 30 optimal weight: 1.9990 chunk 72 optimal weight: 8.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 98 ASN D 90 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8725 moved from start: 0.3316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 8096 Z= 0.280 Angle : 0.758 8.666 11000 Z= 0.387 Chirality : 0.051 0.147 1287 Planarity : 0.005 0.056 1353 Dihedral : 5.759 23.398 1089 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 20.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 5.36 % Allowed : 23.89 % Favored : 70.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.82 (0.23), residues: 968 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.14 (0.17), residues: 968 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 79 HIS 0.003 0.001 HIS C 88 PHE 0.026 0.002 PHE K 64 TYR 0.020 0.002 TYR K 114 ARG 0.014 0.002 ARG F 104 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1936 Ramachandran restraints generated. 968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1936 Ramachandran restraints generated. 968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 391 residues out of total 858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 345 time to evaluate : 0.930 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 15 LYS cc_start: 0.8880 (mttt) cc_final: 0.8373 (mtpm) REVERT: A 34 ARG cc_start: 0.8637 (ttt180) cc_final: 0.8113 (tpp80) REVERT: A 63 GLU cc_start: 0.8703 (pt0) cc_final: 0.8176 (pp20) REVERT: A 66 GLU cc_start: 0.8233 (tm-30) cc_final: 0.7982 (tm-30) REVERT: A 89 GLU cc_start: 0.8055 (pm20) cc_final: 0.7418 (pm20) REVERT: A 106 THR cc_start: 0.9303 (m) cc_final: 0.9090 (p) REVERT: B 13 MET cc_start: 0.8427 (tmm) cc_final: 0.8151 (tmm) REVERT: B 15 LYS cc_start: 0.8956 (mttt) cc_final: 0.8507 (mtpm) REVERT: B 34 ARG cc_start: 0.8565 (ttt180) cc_final: 0.8136 (tpp80) REVERT: B 62 GLU cc_start: 0.8392 (mp0) cc_final: 0.8153 (mp0) REVERT: B 80 LYS cc_start: 0.9256 (ttpt) cc_final: 0.9035 (ttpt) REVERT: B 104 ARG cc_start: 0.8441 (ttm110) cc_final: 0.8217 (mtm-85) REVERT: C 63 GLU cc_start: 0.8219 (OUTLIER) cc_final: 0.7791 (pm20) REVERT: C 89 GLU cc_start: 0.8092 (mp0) cc_final: 0.7490 (pm20) REVERT: C 104 ARG cc_start: 0.8392 (mtm-85) cc_final: 0.8103 (ttm110) REVERT: D 13 MET cc_start: 0.8368 (tmm) cc_final: 0.8027 (tmm) REVERT: D 15 LYS cc_start: 0.8722 (mttt) cc_final: 0.8129 (mtpm) REVERT: D 18 ASP cc_start: 0.8466 (m-30) cc_final: 0.8159 (m-30) REVERT: D 34 ARG cc_start: 0.8752 (ttt180) cc_final: 0.8323 (tpp80) REVERT: D 66 GLU cc_start: 0.8088 (tm-30) cc_final: 0.7837 (tm-30) REVERT: D 80 LYS cc_start: 0.9075 (tttt) cc_final: 0.8854 (tttm) REVERT: D 89 GLU cc_start: 0.8422 (mp0) cc_final: 0.7739 (mp0) REVERT: E 34 ARG cc_start: 0.8681 (ttt180) cc_final: 0.8375 (tpp80) REVERT: F 13 MET cc_start: 0.8450 (tmm) cc_final: 0.7647 (tmm) REVERT: F 15 LYS cc_start: 0.8833 (mttt) cc_final: 0.8409 (mtpm) REVERT: F 63 GLU cc_start: 0.8236 (pm20) cc_final: 0.7703 (pm20) REVERT: G 13 MET cc_start: 0.8617 (tmm) cc_final: 0.8263 (tmm) REVERT: G 15 LYS cc_start: 0.9015 (mttt) cc_final: 0.8413 (mttp) REVERT: G 34 ARG cc_start: 0.8668 (ttt180) cc_final: 0.8334 (tpp80) REVERT: G 63 GLU cc_start: 0.8516 (pt0) cc_final: 0.8104 (pm20) REVERT: G 70 LYS cc_start: 0.9289 (OUTLIER) cc_final: 0.9057 (ttpp) REVERT: H 15 LYS cc_start: 0.8942 (mttt) cc_final: 0.8607 (mtpp) REVERT: H 34 ARG cc_start: 0.8697 (ttt180) cc_final: 0.8358 (tpp80) REVERT: H 63 GLU cc_start: 0.8676 (pt0) cc_final: 0.8345 (pm20) REVERT: I 63 GLU cc_start: 0.8595 (pt0) cc_final: 0.8300 (pt0) REVERT: I 80 LYS cc_start: 0.9165 (tttt) cc_final: 0.8952 (tttm) REVERT: I 104 ARG cc_start: 0.8201 (mtm-85) cc_final: 0.7921 (ttm110) REVERT: J 13 MET cc_start: 0.8784 (tmm) cc_final: 0.8553 (tmm) REVERT: J 15 LYS cc_start: 0.8808 (mttt) cc_final: 0.8363 (ttmm) REVERT: J 34 ARG cc_start: 0.8523 (ttt180) cc_final: 0.8087 (tpp80) REVERT: J 61 GLU cc_start: 0.8635 (OUTLIER) cc_final: 0.8292 (mt-10) REVERT: J 63 GLU cc_start: 0.8719 (pt0) cc_final: 0.8324 (pt0) REVERT: J 72 GLU cc_start: 0.8579 (OUTLIER) cc_final: 0.8237 (mm-30) REVERT: J 84 ILE cc_start: 0.9457 (mt) cc_final: 0.9107 (pp) REVERT: K 15 LYS cc_start: 0.9045 (mttt) cc_final: 0.8677 (mtpm) REVERT: K 80 LYS cc_start: 0.8951 (tttt) cc_final: 0.8717 (tttm) REVERT: K 90 HIS cc_start: 0.8701 (m90) cc_final: 0.8479 (m90) REVERT: K 100 SER cc_start: 0.8295 (t) cc_final: 0.8027 (p) REVERT: K 118 THR cc_start: 0.9253 (m) cc_final: 0.9047 (p) outliers start: 46 outliers final: 17 residues processed: 359 average time/residue: 1.3492 time to fit residues: 508.1098 Evaluate side-chains 350 residues out of total 858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 329 time to evaluate : 0.917 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 ASP Chi-restraints excluded: chain A residue 98 ASN Chi-restraints excluded: chain A residue 117 SER Chi-restraints excluded: chain B residue 26 ILE Chi-restraints excluded: chain B residue 100 SER Chi-restraints excluded: chain C residue 18 ASP Chi-restraints excluded: chain C residue 63 GLU Chi-restraints excluded: chain C residue 98 ASN Chi-restraints excluded: chain D residue 98 ASN Chi-restraints excluded: chain F residue 12 LEU Chi-restraints excluded: chain F residue 82 LEU Chi-restraints excluded: chain G residue 70 LYS Chi-restraints excluded: chain H residue 115 SER Chi-restraints excluded: chain I residue 82 LEU Chi-restraints excluded: chain I residue 98 ASN Chi-restraints excluded: chain J residue 26 ILE Chi-restraints excluded: chain J residue 61 GLU Chi-restraints excluded: chain J residue 72 GLU Chi-restraints excluded: chain J residue 98 ASN Chi-restraints excluded: chain K residue 58 LEU Chi-restraints excluded: chain K residue 96 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 88 optimal weight: 6.9990 chunk 67 optimal weight: 4.9990 chunk 46 optimal weight: 0.6980 chunk 9 optimal weight: 10.0000 chunk 42 optimal weight: 0.7980 chunk 60 optimal weight: 10.0000 chunk 90 optimal weight: 0.0970 chunk 95 optimal weight: 9.9990 chunk 47 optimal weight: 10.0000 chunk 85 optimal weight: 7.9990 chunk 25 optimal weight: 8.9990 overall best weight: 2.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 98 ASN D 90 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8759 moved from start: 0.3573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 8096 Z= 0.371 Angle : 0.796 9.179 11000 Z= 0.406 Chirality : 0.051 0.155 1287 Planarity : 0.005 0.067 1353 Dihedral : 5.809 23.249 1089 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 21.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 6.41 % Allowed : 23.89 % Favored : 69.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.80 (0.23), residues: 968 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.12 (0.18), residues: 968 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 79 HIS 0.006 0.001 HIS H 90 PHE 0.027 0.002 PHE K 64 TYR 0.019 0.002 TYR K 114 ARG 0.013 0.002 ARG F 104 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1936 Ramachandran restraints generated. 968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1936 Ramachandran restraints generated. 968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 399 residues out of total 858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 344 time to evaluate : 0.962 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 15 LYS cc_start: 0.8829 (mttt) cc_final: 0.8412 (mtpm) REVERT: A 34 ARG cc_start: 0.8630 (ttt180) cc_final: 0.8208 (tpp80) REVERT: A 62 GLU cc_start: 0.8124 (mp0) cc_final: 0.7832 (mp0) REVERT: A 63 GLU cc_start: 0.8730 (pt0) cc_final: 0.8190 (pp20) REVERT: A 66 GLU cc_start: 0.8425 (tm-30) cc_final: 0.8105 (tm-30) REVERT: A 89 GLU cc_start: 0.8065 (pm20) cc_final: 0.7628 (pm20) REVERT: A 104 ARG cc_start: 0.8314 (mtm-85) cc_final: 0.7882 (mtm-85) REVERT: A 106 THR cc_start: 0.9332 (m) cc_final: 0.9069 (p) REVERT: B 13 MET cc_start: 0.8471 (tmm) cc_final: 0.8237 (tmm) REVERT: B 15 LYS cc_start: 0.8998 (mttt) cc_final: 0.8551 (mtpm) REVERT: B 34 ARG cc_start: 0.8606 (ttt180) cc_final: 0.8121 (tpp80) REVERT: B 35 LYS cc_start: 0.9111 (ttmt) cc_final: 0.8897 (mtpp) REVERT: B 62 GLU cc_start: 0.8455 (mp0) cc_final: 0.8019 (mp0) REVERT: B 80 LYS cc_start: 0.9271 (ttpt) cc_final: 0.9051 (ttpt) REVERT: B 104 ARG cc_start: 0.8460 (ttm110) cc_final: 0.7890 (mtm-85) REVERT: C 63 GLU cc_start: 0.8271 (OUTLIER) cc_final: 0.7870 (pm20) REVERT: C 66 GLU cc_start: 0.8310 (OUTLIER) cc_final: 0.8058 (tm-30) REVERT: C 89 GLU cc_start: 0.8101 (mp0) cc_final: 0.7811 (mp0) REVERT: D 13 MET cc_start: 0.8462 (tmm) cc_final: 0.8100 (tmm) REVERT: D 15 LYS cc_start: 0.8808 (mttt) cc_final: 0.8208 (mtpm) REVERT: D 18 ASP cc_start: 0.8487 (m-30) cc_final: 0.8181 (m-30) REVERT: D 34 ARG cc_start: 0.8776 (ttt180) cc_final: 0.8375 (tpp80) REVERT: D 80 LYS cc_start: 0.9104 (tttt) cc_final: 0.8873 (tttm) REVERT: E 34 ARG cc_start: 0.8686 (ttt180) cc_final: 0.8398 (tpp80) REVERT: F 13 MET cc_start: 0.8583 (tmm) cc_final: 0.8005 (tmm) REVERT: F 15 LYS cc_start: 0.8896 (mttt) cc_final: 0.8495 (mtpm) REVERT: F 18 ASP cc_start: 0.8756 (m-30) cc_final: 0.8546 (m-30) REVERT: F 63 GLU cc_start: 0.8212 (pm20) cc_final: 0.7622 (pm20) REVERT: G 13 MET cc_start: 0.8641 (tmm) cc_final: 0.8238 (tmm) REVERT: G 15 LYS cc_start: 0.9040 (mttt) cc_final: 0.8443 (mttp) REVERT: G 30 MET cc_start: 0.7319 (tmm) cc_final: 0.5645 (tmm) REVERT: G 34 ARG cc_start: 0.8688 (ttt180) cc_final: 0.8345 (tpp80) REVERT: G 63 GLU cc_start: 0.8558 (pt0) cc_final: 0.8116 (pm20) REVERT: G 70 LYS cc_start: 0.9297 (OUTLIER) cc_final: 0.9007 (ttpp) REVERT: G 72 GLU cc_start: 0.8481 (mt-10) cc_final: 0.8178 (mt-10) REVERT: H 15 LYS cc_start: 0.8969 (mttt) cc_final: 0.8462 (mtpp) REVERT: H 18 ASP cc_start: 0.8816 (OUTLIER) cc_final: 0.8569 (m-30) REVERT: H 34 ARG cc_start: 0.8694 (ttt180) cc_final: 0.8357 (tpp80) REVERT: H 63 GLU cc_start: 0.8691 (pt0) cc_final: 0.8333 (pm20) REVERT: I 15 LYS cc_start: 0.8923 (mttt) cc_final: 0.8485 (mtpp) REVERT: I 18 ASP cc_start: 0.8892 (OUTLIER) cc_final: 0.8558 (m-30) REVERT: I 62 GLU cc_start: 0.8618 (mp0) cc_final: 0.8317 (mp0) REVERT: I 80 LYS cc_start: 0.9165 (tttt) cc_final: 0.8949 (tttm) REVERT: I 104 ARG cc_start: 0.8235 (mtm-85) cc_final: 0.7979 (ttm110) REVERT: J 13 MET cc_start: 0.8823 (tmm) cc_final: 0.8546 (tmm) REVERT: J 15 LYS cc_start: 0.8836 (mttt) cc_final: 0.8370 (ttmm) REVERT: J 34 ARG cc_start: 0.8566 (ttt180) cc_final: 0.8122 (tpp80) REVERT: J 63 GLU cc_start: 0.8736 (pt0) cc_final: 0.8357 (pt0) REVERT: J 84 ILE cc_start: 0.9463 (mt) cc_final: 0.9115 (pp) REVERT: K 13 MET cc_start: 0.8699 (tmm) cc_final: 0.8289 (tmt) REVERT: K 15 LYS cc_start: 0.9025 (mttt) cc_final: 0.8642 (mtpm) REVERT: K 35 LYS cc_start: 0.8966 (ttmt) cc_final: 0.8528 (mtmt) REVERT: K 73 ILE cc_start: 0.9115 (mt) cc_final: 0.8836 (mp) REVERT: K 80 LYS cc_start: 0.8949 (tttt) cc_final: 0.8708 (tttm) REVERT: K 90 HIS cc_start: 0.8731 (m90) cc_final: 0.8516 (m90) REVERT: K 100 SER cc_start: 0.8253 (t) cc_final: 0.8001 (p) REVERT: K 118 THR cc_start: 0.9300 (m) cc_final: 0.9059 (p) outliers start: 55 outliers final: 26 residues processed: 365 average time/residue: 1.3950 time to fit residues: 533.6658 Evaluate side-chains 360 residues out of total 858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 329 time to evaluate : 0.896 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 ASN Chi-restraints excluded: chain A residue 117 SER Chi-restraints excluded: chain B residue 26 ILE Chi-restraints excluded: chain B residue 100 SER Chi-restraints excluded: chain C residue 63 GLU Chi-restraints excluded: chain C residue 66 GLU Chi-restraints excluded: chain C residue 68 ILE Chi-restraints excluded: chain C residue 80 LYS Chi-restraints excluded: chain C residue 98 ASN Chi-restraints excluded: chain D residue 61 GLU Chi-restraints excluded: chain D residue 98 ASN Chi-restraints excluded: chain E residue 110 LEU Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 68 ILE Chi-restraints excluded: chain G residue 70 LYS Chi-restraints excluded: chain G residue 98 ASN Chi-restraints excluded: chain H residue 18 ASP Chi-restraints excluded: chain H residue 82 LEU Chi-restraints excluded: chain H residue 96 THR Chi-restraints excluded: chain H residue 115 SER Chi-restraints excluded: chain I residue 18 ASP Chi-restraints excluded: chain I residue 82 LEU Chi-restraints excluded: chain I residue 96 THR Chi-restraints excluded: chain I residue 98 ASN Chi-restraints excluded: chain J residue 18 ASP Chi-restraints excluded: chain J residue 26 ILE Chi-restraints excluded: chain J residue 98 ASN Chi-restraints excluded: chain K residue 58 LEU Chi-restraints excluded: chain K residue 59 THR Chi-restraints excluded: chain K residue 96 THR Chi-restraints excluded: chain K residue 117 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 79 optimal weight: 4.9990 chunk 54 optimal weight: 8.9990 chunk 1 optimal weight: 4.9990 chunk 71 optimal weight: 6.9990 chunk 39 optimal weight: 2.9990 chunk 81 optimal weight: 6.9990 chunk 66 optimal weight: 1.9990 chunk 0 optimal weight: 9.9990 chunk 48 optimal weight: 0.8980 chunk 85 optimal weight: 8.9990 chunk 24 optimal weight: 5.9990 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 98 ASN H 88 HIS H 90 HIS K 27 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8775 moved from start: 0.3792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 8096 Z= 0.416 Angle : 0.835 10.311 11000 Z= 0.423 Chirality : 0.052 0.192 1287 Planarity : 0.006 0.079 1353 Dihedral : 5.864 25.106 1089 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 23.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer: Outliers : 6.18 % Allowed : 24.94 % Favored : 68.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.80 (0.23), residues: 968 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.12 (0.18), residues: 968 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 79 HIS 0.004 0.001 HIS I 90 PHE 0.028 0.002 PHE K 64 TYR 0.021 0.002 TYR K 114 ARG 0.014 0.002 ARG F 104 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1936 Ramachandran restraints generated. 968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1936 Ramachandran restraints generated. 968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 388 residues out of total 858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 335 time to evaluate : 0.972 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 15 LYS cc_start: 0.8841 (mttt) cc_final: 0.8488 (mtpm) REVERT: A 18 ASP cc_start: 0.8673 (OUTLIER) cc_final: 0.8158 (m-30) REVERT: A 34 ARG cc_start: 0.8627 (ttt180) cc_final: 0.8292 (tpp80) REVERT: A 62 GLU cc_start: 0.8059 (mp0) cc_final: 0.7746 (mp0) REVERT: A 63 GLU cc_start: 0.8724 (pt0) cc_final: 0.8154 (pp20) REVERT: A 66 GLU cc_start: 0.8497 (tm-30) cc_final: 0.8103 (tm-30) REVERT: A 106 THR cc_start: 0.9349 (m) cc_final: 0.9066 (p) REVERT: B 13 MET cc_start: 0.8522 (tmm) cc_final: 0.8248 (tmm) REVERT: B 15 LYS cc_start: 0.8997 (mttt) cc_final: 0.8630 (mtpm) REVERT: B 18 ASP cc_start: 0.8646 (m-30) cc_final: 0.8250 (m-30) REVERT: B 21 ARG cc_start: 0.8187 (mmm160) cc_final: 0.7964 (mmm-85) REVERT: B 34 ARG cc_start: 0.8628 (ttt180) cc_final: 0.8193 (tpp80) REVERT: B 62 GLU cc_start: 0.8366 (mp0) cc_final: 0.7832 (mp0) REVERT: B 80 LYS cc_start: 0.9283 (ttpt) cc_final: 0.9062 (ttpt) REVERT: B 104 ARG cc_start: 0.8470 (ttm110) cc_final: 0.8251 (mtm-85) REVERT: C 62 GLU cc_start: 0.8446 (mp0) cc_final: 0.8246 (mp0) REVERT: C 63 GLU cc_start: 0.8284 (OUTLIER) cc_final: 0.7843 (pm20) REVERT: C 66 GLU cc_start: 0.8404 (OUTLIER) cc_final: 0.8137 (tm-30) REVERT: D 13 MET cc_start: 0.8458 (tmm) cc_final: 0.8096 (tmm) REVERT: D 15 LYS cc_start: 0.8890 (mttt) cc_final: 0.8304 (mtpm) REVERT: D 18 ASP cc_start: 0.8524 (m-30) cc_final: 0.8215 (m-30) REVERT: D 34 ARG cc_start: 0.8791 (ttt180) cc_final: 0.8378 (tpp80) REVERT: D 63 GLU cc_start: 0.8361 (pm20) cc_final: 0.8153 (pm20) REVERT: D 70 LYS cc_start: 0.9193 (OUTLIER) cc_final: 0.8696 (ttmm) REVERT: D 80 LYS cc_start: 0.9115 (tttt) cc_final: 0.8881 (tttm) REVERT: E 15 LYS cc_start: 0.9025 (mttt) cc_final: 0.8703 (mtpm) REVERT: E 34 ARG cc_start: 0.8707 (ttt180) cc_final: 0.8344 (tpp80) REVERT: E 62 GLU cc_start: 0.8716 (pm20) cc_final: 0.8140 (mp0) REVERT: F 13 MET cc_start: 0.8583 (tmm) cc_final: 0.8040 (tmm) REVERT: F 15 LYS cc_start: 0.8952 (mttt) cc_final: 0.8532 (mtpm) REVERT: F 18 ASP cc_start: 0.8715 (m-30) cc_final: 0.8388 (m-30) REVERT: F 62 GLU cc_start: 0.8647 (pm20) cc_final: 0.8340 (pm20) REVERT: F 63 GLU cc_start: 0.8266 (pm20) cc_final: 0.7637 (pm20) REVERT: G 13 MET cc_start: 0.8648 (tmm) cc_final: 0.8250 (tmm) REVERT: G 15 LYS cc_start: 0.9036 (mttt) cc_final: 0.8520 (mttp) REVERT: G 34 ARG cc_start: 0.8734 (ttt180) cc_final: 0.8402 (tpp80) REVERT: G 63 GLU cc_start: 0.8568 (pt0) cc_final: 0.8053 (pm20) REVERT: G 70 LYS cc_start: 0.9284 (OUTLIER) cc_final: 0.9071 (ttpp) REVERT: H 15 LYS cc_start: 0.9033 (mttt) cc_final: 0.8633 (mtpp) REVERT: H 34 ARG cc_start: 0.8660 (ttt180) cc_final: 0.8346 (tpp80) REVERT: H 63 GLU cc_start: 0.8704 (pt0) cc_final: 0.8308 (pm20) REVERT: H 84 ILE cc_start: 0.9435 (mt) cc_final: 0.9118 (pp) REVERT: I 15 LYS cc_start: 0.8892 (mttt) cc_final: 0.8569 (mtmm) REVERT: I 18 ASP cc_start: 0.8859 (OUTLIER) cc_final: 0.8474 (m-30) REVERT: I 62 GLU cc_start: 0.8594 (mp0) cc_final: 0.8261 (mp0) REVERT: I 80 LYS cc_start: 0.9178 (tttt) cc_final: 0.8960 (tttm) REVERT: I 89 GLU cc_start: 0.7971 (OUTLIER) cc_final: 0.7525 (pm20) REVERT: I 104 ARG cc_start: 0.8210 (mtm-85) cc_final: 0.8004 (ttm110) REVERT: J 13 MET cc_start: 0.8771 (tmm) cc_final: 0.8558 (tmm) REVERT: J 15 LYS cc_start: 0.8846 (mttt) cc_final: 0.8377 (ttmm) REVERT: J 34 ARG cc_start: 0.8571 (ttt180) cc_final: 0.8185 (tpp80) REVERT: J 63 GLU cc_start: 0.8749 (pt0) cc_final: 0.8432 (pt0) REVERT: J 72 GLU cc_start: 0.8598 (OUTLIER) cc_final: 0.8327 (mp0) REVERT: J 84 ILE cc_start: 0.9469 (mt) cc_final: 0.9143 (pp) REVERT: K 13 MET cc_start: 0.8689 (tmm) cc_final: 0.8468 (tmm) REVERT: K 15 LYS cc_start: 0.9055 (mttt) cc_final: 0.8627 (mtpm) REVERT: K 62 GLU cc_start: 0.8329 (mp0) cc_final: 0.8001 (mp0) REVERT: K 80 LYS cc_start: 0.8980 (tttt) cc_final: 0.8741 (tttm) REVERT: K 100 SER cc_start: 0.8212 (t) cc_final: 0.7960 (p) REVERT: K 106 THR cc_start: 0.9122 (m) cc_final: 0.8853 (p) REVERT: K 118 THR cc_start: 0.9283 (m) cc_final: 0.8999 (p) outliers start: 53 outliers final: 24 residues processed: 355 average time/residue: 1.3779 time to fit residues: 512.9510 Evaluate side-chains 353 residues out of total 858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 321 time to evaluate : 0.860 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 ASP Chi-restraints excluded: chain A residue 98 ASN Chi-restraints excluded: chain A residue 112 SER Chi-restraints excluded: chain A residue 117 SER Chi-restraints excluded: chain B residue 100 SER Chi-restraints excluded: chain C residue 18 ASP Chi-restraints excluded: chain C residue 63 GLU Chi-restraints excluded: chain C residue 66 GLU Chi-restraints excluded: chain C residue 96 THR Chi-restraints excluded: chain D residue 70 LYS Chi-restraints excluded: chain D residue 98 ASN Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 65 VAL Chi-restraints excluded: chain G residue 68 ILE Chi-restraints excluded: chain G residue 70 LYS Chi-restraints excluded: chain H residue 18 ASP Chi-restraints excluded: chain H residue 82 LEU Chi-restraints excluded: chain H residue 96 THR Chi-restraints excluded: chain H residue 98 ASN Chi-restraints excluded: chain H residue 115 SER Chi-restraints excluded: chain I residue 18 ASP Chi-restraints excluded: chain I residue 82 LEU Chi-restraints excluded: chain I residue 89 GLU Chi-restraints excluded: chain I residue 96 THR Chi-restraints excluded: chain I residue 98 ASN Chi-restraints excluded: chain J residue 18 ASP Chi-restraints excluded: chain J residue 26 ILE Chi-restraints excluded: chain J residue 72 GLU Chi-restraints excluded: chain J residue 98 ASN Chi-restraints excluded: chain K residue 59 THR Chi-restraints excluded: chain K residue 96 THR Chi-restraints excluded: chain K residue 117 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 32 optimal weight: 0.6980 chunk 86 optimal weight: 5.9990 chunk 18 optimal weight: 6.9990 chunk 56 optimal weight: 10.0000 chunk 23 optimal weight: 0.5980 chunk 95 optimal weight: 0.0670 chunk 79 optimal weight: 5.9990 chunk 44 optimal weight: 0.1980 chunk 7 optimal weight: 4.9990 chunk 31 optimal weight: 6.9990 chunk 50 optimal weight: 10.0000 overall best weight: 1.3120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 98 ASN H 90 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8741 moved from start: 0.3991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 8096 Z= 0.269 Angle : 0.826 9.923 11000 Z= 0.412 Chirality : 0.051 0.148 1287 Planarity : 0.006 0.074 1353 Dihedral : 5.748 24.471 1089 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 22.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.37 % Favored : 94.63 % Rotamer: Outliers : 5.83 % Allowed : 27.86 % Favored : 66.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.80 (0.23), residues: 968 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.13 (0.18), residues: 968 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP A 79 HIS 0.003 0.001 HIS B 31 PHE 0.026 0.001 PHE K 64 TYR 0.021 0.002 TYR K 114 ARG 0.017 0.002 ARG F 104 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1936 Ramachandran restraints generated. 968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1936 Ramachandran restraints generated. 968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 401 residues out of total 858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 351 time to evaluate : 0.995 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 15 LYS cc_start: 0.8743 (mttt) cc_final: 0.8448 (mtpm) REVERT: A 18 ASP cc_start: 0.8616 (OUTLIER) cc_final: 0.8174 (m-30) REVERT: A 34 ARG cc_start: 0.8608 (ttt180) cc_final: 0.8179 (tpp80) REVERT: A 61 GLU cc_start: 0.8307 (mt-10) cc_final: 0.8056 (mt-10) REVERT: A 62 GLU cc_start: 0.8000 (mp0) cc_final: 0.7657 (mp0) REVERT: A 63 GLU cc_start: 0.8735 (pt0) cc_final: 0.8120 (pp20) REVERT: A 66 GLU cc_start: 0.8490 (tm-30) cc_final: 0.8129 (tm-30) REVERT: A 96 THR cc_start: 0.9119 (OUTLIER) cc_final: 0.8912 (p) REVERT: A 106 THR cc_start: 0.9309 (m) cc_final: 0.9082 (p) REVERT: B 13 MET cc_start: 0.8628 (tmm) cc_final: 0.8291 (tmm) REVERT: B 15 LYS cc_start: 0.9033 (mttt) cc_final: 0.8658 (mtpm) REVERT: B 18 ASP cc_start: 0.8639 (m-30) cc_final: 0.8215 (m-30) REVERT: B 34 ARG cc_start: 0.8575 (ttt180) cc_final: 0.8079 (tpp80) REVERT: B 62 GLU cc_start: 0.8386 (mp0) cc_final: 0.7784 (mp0) REVERT: B 80 LYS cc_start: 0.9262 (ttpt) cc_final: 0.9040 (ttpt) REVERT: C 63 GLU cc_start: 0.8278 (OUTLIER) cc_final: 0.7800 (pm20) REVERT: C 66 GLU cc_start: 0.8414 (OUTLIER) cc_final: 0.8048 (tm-30) REVERT: C 70 LYS cc_start: 0.9463 (ptmm) cc_final: 0.9078 (ptmm) REVERT: D 13 MET cc_start: 0.8439 (tmm) cc_final: 0.8181 (tmm) REVERT: D 15 LYS cc_start: 0.8788 (mttt) cc_final: 0.8202 (mtpm) REVERT: D 18 ASP cc_start: 0.8489 (m-30) cc_final: 0.8177 (m-30) REVERT: D 34 ARG cc_start: 0.8768 (ttt180) cc_final: 0.8441 (tpp80) REVERT: D 70 LYS cc_start: 0.9179 (OUTLIER) cc_final: 0.8518 (ttmm) REVERT: D 80 LYS cc_start: 0.9077 (tttt) cc_final: 0.8844 (tttm) REVERT: E 15 LYS cc_start: 0.9017 (mttt) cc_final: 0.8697 (mtpm) REVERT: E 34 ARG cc_start: 0.8645 (ttt180) cc_final: 0.8376 (tpp80) REVERT: E 62 GLU cc_start: 0.8685 (pm20) cc_final: 0.8110 (mp0) REVERT: E 84 ILE cc_start: 0.9377 (mt) cc_final: 0.8963 (pp) REVERT: F 13 MET cc_start: 0.8615 (tmm) cc_final: 0.7997 (tmm) REVERT: F 15 LYS cc_start: 0.8937 (mttt) cc_final: 0.8523 (mtpm) REVERT: F 18 ASP cc_start: 0.8673 (m-30) cc_final: 0.8298 (m-30) REVERT: F 62 GLU cc_start: 0.8637 (pm20) cc_final: 0.8331 (pm20) REVERT: F 63 GLU cc_start: 0.8237 (pm20) cc_final: 0.7458 (pm20) REVERT: G 13 MET cc_start: 0.8629 (tmm) cc_final: 0.8197 (tmm) REVERT: G 15 LYS cc_start: 0.9038 (mttt) cc_final: 0.8463 (mttp) REVERT: G 34 ARG cc_start: 0.8716 (ttt180) cc_final: 0.8372 (tpp80) REVERT: G 63 GLU cc_start: 0.8545 (pt0) cc_final: 0.7890 (pm20) REVERT: G 70 LYS cc_start: 0.9272 (OUTLIER) cc_final: 0.9039 (ttpp) REVERT: H 15 LYS cc_start: 0.8924 (mttt) cc_final: 0.8339 (mtpp) REVERT: H 18 ASP cc_start: 0.8792 (OUTLIER) cc_final: 0.8255 (m-30) REVERT: H 34 ARG cc_start: 0.8633 (ttt180) cc_final: 0.8353 (tpp80) REVERT: H 35 LYS cc_start: 0.8985 (ttmt) cc_final: 0.8604 (mttt) REVERT: H 62 GLU cc_start: 0.8643 (mp0) cc_final: 0.8407 (mp0) REVERT: H 63 GLU cc_start: 0.8701 (pt0) cc_final: 0.8340 (pm20) REVERT: H 84 ILE cc_start: 0.9389 (mt) cc_final: 0.9079 (pp) REVERT: I 15 LYS cc_start: 0.8847 (mttt) cc_final: 0.8568 (mtpm) REVERT: I 18 ASP cc_start: 0.8727 (m-30) cc_final: 0.8171 (m-30) REVERT: I 62 GLU cc_start: 0.8548 (mp0) cc_final: 0.8142 (mp0) REVERT: I 80 LYS cc_start: 0.9166 (tttt) cc_final: 0.8943 (tttm) REVERT: I 104 ARG cc_start: 0.8176 (mtm-85) cc_final: 0.7932 (ttm110) REVERT: J 13 MET cc_start: 0.8766 (tmm) cc_final: 0.8487 (tmm) REVERT: J 15 LYS cc_start: 0.8799 (mttt) cc_final: 0.8234 (mtpp) REVERT: J 18 ASP cc_start: 0.8759 (OUTLIER) cc_final: 0.8226 (m-30) REVERT: J 34 ARG cc_start: 0.8551 (ttt180) cc_final: 0.8300 (ttt-90) REVERT: J 35 LYS cc_start: 0.8973 (ttmm) cc_final: 0.8556 (mttm) REVERT: J 63 GLU cc_start: 0.8810 (pt0) cc_final: 0.8372 (pt0) REVERT: J 72 GLU cc_start: 0.8502 (mm-30) cc_final: 0.8298 (mp0) REVERT: J 84 ILE cc_start: 0.9448 (mt) cc_final: 0.9151 (pp) REVERT: K 13 MET cc_start: 0.8715 (tmm) cc_final: 0.8283 (tmt) REVERT: K 15 LYS cc_start: 0.9064 (mttt) cc_final: 0.8604 (mtpm) REVERT: K 26 ILE cc_start: 0.9394 (OUTLIER) cc_final: 0.9133 (mp) REVERT: K 80 LYS cc_start: 0.8918 (tttt) cc_final: 0.8693 (tttp) REVERT: K 106 THR cc_start: 0.9084 (m) cc_final: 0.8825 (p) REVERT: K 118 THR cc_start: 0.9259 (m) cc_final: 0.8950 (p) outliers start: 50 outliers final: 21 residues processed: 366 average time/residue: 1.3643 time to fit residues: 523.5041 Evaluate side-chains 364 residues out of total 858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 334 time to evaluate : 0.868 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 ASP Chi-restraints excluded: chain A residue 96 THR Chi-restraints excluded: chain A residue 98 ASN Chi-restraints excluded: chain A residue 112 SER Chi-restraints excluded: chain A residue 117 SER Chi-restraints excluded: chain B residue 100 SER Chi-restraints excluded: chain C residue 63 GLU Chi-restraints excluded: chain C residue 66 GLU Chi-restraints excluded: chain C residue 96 THR Chi-restraints excluded: chain D residue 58 LEU Chi-restraints excluded: chain D residue 61 GLU Chi-restraints excluded: chain D residue 70 LYS Chi-restraints excluded: chain D residue 98 ASN Chi-restraints excluded: chain F residue 68 ILE Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 70 LYS Chi-restraints excluded: chain H residue 18 ASP Chi-restraints excluded: chain H residue 82 LEU Chi-restraints excluded: chain H residue 96 THR Chi-restraints excluded: chain H residue 98 ASN Chi-restraints excluded: chain H residue 115 SER Chi-restraints excluded: chain I residue 96 THR Chi-restraints excluded: chain I residue 98 ASN Chi-restraints excluded: chain J residue 18 ASP Chi-restraints excluded: chain J residue 26 ILE Chi-restraints excluded: chain J residue 61 GLU Chi-restraints excluded: chain K residue 26 ILE Chi-restraints excluded: chain K residue 30 MET Chi-restraints excluded: chain K residue 59 THR Chi-restraints excluded: chain K residue 96 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 92 optimal weight: 10.0000 chunk 10 optimal weight: 0.8980 chunk 54 optimal weight: 8.9990 chunk 69 optimal weight: 0.9980 chunk 80 optimal weight: 0.8980 chunk 53 optimal weight: 6.9990 chunk 95 optimal weight: 2.9990 chunk 59 optimal weight: 7.9990 chunk 58 optimal weight: 6.9990 chunk 44 optimal weight: 0.7980 chunk 38 optimal weight: 10.0000 overall best weight: 1.3182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 98 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8733 moved from start: 0.4200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 8096 Z= 0.265 Angle : 0.857 9.625 11000 Z= 0.424 Chirality : 0.051 0.165 1287 Planarity : 0.006 0.074 1353 Dihedral : 5.688 23.625 1089 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 21.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.10 % Favored : 93.90 % Rotamer: Outliers : 5.83 % Allowed : 28.67 % Favored : 65.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.82 (0.23), residues: 968 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.14 (0.18), residues: 968 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP A 79 HIS 0.003 0.001 HIS B 31 PHE 0.027 0.002 PHE K 64 TYR 0.020 0.002 TYR K 114 ARG 0.018 0.002 ARG H 104 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1936 Ramachandran restraints generated. 968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1936 Ramachandran restraints generated. 968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 401 residues out of total 858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 351 time to evaluate : 0.880 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 15 LYS cc_start: 0.8717 (mttt) cc_final: 0.8471 (mtpm) REVERT: A 18 ASP cc_start: 0.8657 (OUTLIER) cc_final: 0.8222 (m-30) REVERT: A 34 ARG cc_start: 0.8592 (ttt180) cc_final: 0.8162 (tpp80) REVERT: A 61 GLU cc_start: 0.8299 (mt-10) cc_final: 0.8080 (mt-10) REVERT: A 62 GLU cc_start: 0.7927 (mp0) cc_final: 0.7534 (mp0) REVERT: A 63 GLU cc_start: 0.8719 (pt0) cc_final: 0.8098 (pp20) REVERT: A 66 GLU cc_start: 0.8524 (tm-30) cc_final: 0.8211 (tm-30) REVERT: A 96 THR cc_start: 0.9131 (OUTLIER) cc_final: 0.8888 (p) REVERT: A 104 ARG cc_start: 0.8268 (mtm-85) cc_final: 0.7712 (mtm-85) REVERT: B 13 MET cc_start: 0.8660 (tmm) cc_final: 0.8131 (tmm) REVERT: B 15 LYS cc_start: 0.9006 (mttt) cc_final: 0.8555 (mtpm) REVERT: B 18 ASP cc_start: 0.8640 (m-30) cc_final: 0.8084 (m-30) REVERT: B 34 ARG cc_start: 0.8570 (ttt180) cc_final: 0.8116 (tpp80) REVERT: B 62 GLU cc_start: 0.8339 (mp0) cc_final: 0.7778 (mp0) REVERT: B 80 LYS cc_start: 0.9257 (ttpt) cc_final: 0.9029 (ttpt) REVERT: C 15 LYS cc_start: 0.8954 (mttt) cc_final: 0.8649 (mtpm) REVERT: C 18 ASP cc_start: 0.8649 (m-30) cc_final: 0.8303 (m-30) REVERT: C 63 GLU cc_start: 0.8224 (OUTLIER) cc_final: 0.7798 (pm20) REVERT: C 66 GLU cc_start: 0.8438 (OUTLIER) cc_final: 0.8016 (tm-30) REVERT: C 84 ILE cc_start: 0.9482 (mm) cc_final: 0.9188 (pp) REVERT: C 104 ARG cc_start: 0.8314 (mtm-85) cc_final: 0.8095 (ttm110) REVERT: D 13 MET cc_start: 0.8448 (tmm) cc_final: 0.8126 (tmm) REVERT: D 15 LYS cc_start: 0.8764 (mttt) cc_final: 0.8214 (mtpm) REVERT: D 18 ASP cc_start: 0.8468 (m-30) cc_final: 0.8150 (m-30) REVERT: D 34 ARG cc_start: 0.8746 (ttt180) cc_final: 0.8411 (tpp80) REVERT: D 80 LYS cc_start: 0.9074 (tttt) cc_final: 0.8841 (tttm) REVERT: E 15 LYS cc_start: 0.8995 (mttt) cc_final: 0.8751 (mtpm) REVERT: E 34 ARG cc_start: 0.8667 (ttt180) cc_final: 0.8403 (tpp80) REVERT: E 62 GLU cc_start: 0.8662 (pm20) cc_final: 0.7999 (mp0) REVERT: E 84 ILE cc_start: 0.9379 (mt) cc_final: 0.8990 (pp) REVERT: F 13 MET cc_start: 0.8628 (tmm) cc_final: 0.7930 (tmm) REVERT: F 18 ASP cc_start: 0.8670 (m-30) cc_final: 0.8386 (m-30) REVERT: F 62 GLU cc_start: 0.8609 (pm20) cc_final: 0.8278 (pm20) REVERT: F 63 GLU cc_start: 0.8174 (pm20) cc_final: 0.7963 (pm20) REVERT: G 13 MET cc_start: 0.8648 (tmm) cc_final: 0.8214 (tmm) REVERT: G 15 LYS cc_start: 0.9028 (mttt) cc_final: 0.8466 (mttp) REVERT: G 34 ARG cc_start: 0.8720 (ttt180) cc_final: 0.8353 (tpp80) REVERT: G 63 GLU cc_start: 0.8516 (pt0) cc_final: 0.8048 (pm20) REVERT: H 15 LYS cc_start: 0.8973 (mttt) cc_final: 0.8654 (mtpp) REVERT: H 34 ARG cc_start: 0.8595 (ttt180) cc_final: 0.8364 (tpp80) REVERT: H 35 LYS cc_start: 0.9032 (ttmt) cc_final: 0.8759 (mttt) REVERT: H 63 GLU cc_start: 0.8746 (pt0) cc_final: 0.8426 (pm20) REVERT: H 84 ILE cc_start: 0.9389 (mt) cc_final: 0.9069 (pp) REVERT: I 13 MET cc_start: 0.8509 (tmm) cc_final: 0.8289 (tpt) REVERT: I 18 ASP cc_start: 0.8723 (OUTLIER) cc_final: 0.8450 (m-30) REVERT: I 21 ARG cc_start: 0.8395 (mtp-110) cc_final: 0.8192 (mtp85) REVERT: I 62 GLU cc_start: 0.8523 (mp0) cc_final: 0.8133 (mp0) REVERT: I 80 LYS cc_start: 0.9150 (tttt) cc_final: 0.8925 (tttm) REVERT: I 104 ARG cc_start: 0.8150 (mtm-85) cc_final: 0.7917 (ttm110) REVERT: J 13 MET cc_start: 0.8751 (tmm) cc_final: 0.8359 (tmm) REVERT: J 15 LYS cc_start: 0.8811 (mttt) cc_final: 0.8189 (mtpp) REVERT: J 18 ASP cc_start: 0.8763 (OUTLIER) cc_final: 0.8206 (m-30) REVERT: J 34 ARG cc_start: 0.8572 (ttt180) cc_final: 0.8205 (tpp80) REVERT: J 35 LYS cc_start: 0.9002 (ttmm) cc_final: 0.8642 (mttm) REVERT: J 63 GLU cc_start: 0.8813 (pt0) cc_final: 0.8397 (pt0) REVERT: J 72 GLU cc_start: 0.8473 (mm-30) cc_final: 0.7920 (mp0) REVERT: J 84 ILE cc_start: 0.9445 (mt) cc_final: 0.9156 (pp) REVERT: K 13 MET cc_start: 0.8700 (tmm) cc_final: 0.8499 (tmm) REVERT: K 15 LYS cc_start: 0.9064 (mttt) cc_final: 0.8642 (mtpm) REVERT: K 26 ILE cc_start: 0.9386 (OUTLIER) cc_final: 0.9130 (mp) REVERT: K 80 LYS cc_start: 0.8887 (tttt) cc_final: 0.8662 (tttm) REVERT: K 106 THR cc_start: 0.9093 (m) cc_final: 0.8834 (p) REVERT: K 118 THR cc_start: 0.9257 (m) cc_final: 0.8952 (p) outliers start: 50 outliers final: 22 residues processed: 368 average time/residue: 1.2843 time to fit residues: 496.6274 Evaluate side-chains 362 residues out of total 858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 333 time to evaluate : 0.878 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 ASP Chi-restraints excluded: chain A residue 96 THR Chi-restraints excluded: chain A residue 98 ASN Chi-restraints excluded: chain A residue 117 SER Chi-restraints excluded: chain C residue 63 GLU Chi-restraints excluded: chain C residue 66 GLU Chi-restraints excluded: chain C residue 96 THR Chi-restraints excluded: chain D residue 98 ASN Chi-restraints excluded: chain F residue 58 LEU Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 61 GLU Chi-restraints excluded: chain G residue 98 ASN Chi-restraints excluded: chain H residue 18 ASP Chi-restraints excluded: chain H residue 82 LEU Chi-restraints excluded: chain H residue 96 THR Chi-restraints excluded: chain H residue 98 ASN Chi-restraints excluded: chain H residue 115 SER Chi-restraints excluded: chain I residue 18 ASP Chi-restraints excluded: chain I residue 82 LEU Chi-restraints excluded: chain I residue 96 THR Chi-restraints excluded: chain J residue 18 ASP Chi-restraints excluded: chain J residue 26 ILE Chi-restraints excluded: chain J residue 98 ASN Chi-restraints excluded: chain K residue 26 ILE Chi-restraints excluded: chain K residue 30 MET Chi-restraints excluded: chain K residue 59 THR Chi-restraints excluded: chain K residue 70 LYS Chi-restraints excluded: chain K residue 96 THR Chi-restraints excluded: chain K residue 117 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 56 optimal weight: 9.9990 chunk 28 optimal weight: 0.9990 chunk 18 optimal weight: 9.9990 chunk 60 optimal weight: 7.9990 chunk 65 optimal weight: 5.9990 chunk 47 optimal weight: 2.9990 chunk 8 optimal weight: 0.4980 chunk 75 optimal weight: 3.9990 chunk 86 optimal weight: 5.9990 chunk 91 optimal weight: 5.9990 chunk 83 optimal weight: 9.9990 overall best weight: 2.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 98 ASN H 90 HIS K 27 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8766 moved from start: 0.4206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 8096 Z= 0.403 Angle : 0.901 13.239 11000 Z= 0.447 Chirality : 0.053 0.179 1287 Planarity : 0.007 0.070 1353 Dihedral : 5.798 24.941 1089 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 25.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.10 % Favored : 93.90 % Rotamer: Outliers : 4.90 % Allowed : 32.40 % Favored : 62.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.84 (0.23), residues: 968 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.16 (0.18), residues: 968 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP I 79 HIS 0.003 0.001 HIS H 90 PHE 0.028 0.002 PHE K 64 TYR 0.018 0.002 TYR E 116 ARG 0.019 0.003 ARG F 104 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1936 Ramachandran restraints generated. 968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1936 Ramachandran restraints generated. 968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 371 residues out of total 858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 329 time to evaluate : 0.947 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 15 LYS cc_start: 0.8811 (mttt) cc_final: 0.8511 (mtpm) REVERT: A 18 ASP cc_start: 0.8679 (OUTLIER) cc_final: 0.8072 (m-30) REVERT: A 34 ARG cc_start: 0.8606 (ttt180) cc_final: 0.8249 (tpp80) REVERT: A 61 GLU cc_start: 0.8214 (mt-10) cc_final: 0.7849 (mt-10) REVERT: A 62 GLU cc_start: 0.7930 (mp0) cc_final: 0.7565 (mp0) REVERT: A 63 GLU cc_start: 0.8733 (pt0) cc_final: 0.7965 (pp20) REVERT: A 66 GLU cc_start: 0.8565 (tm-30) cc_final: 0.8141 (tm-30) REVERT: A 96 THR cc_start: 0.9122 (OUTLIER) cc_final: 0.8908 (p) REVERT: A 104 ARG cc_start: 0.8316 (mtm-85) cc_final: 0.7888 (mtm-85) REVERT: B 15 LYS cc_start: 0.8998 (mttt) cc_final: 0.8571 (mtpm) REVERT: B 18 ASP cc_start: 0.8667 (m-30) cc_final: 0.8038 (m-30) REVERT: B 34 ARG cc_start: 0.8637 (ttt180) cc_final: 0.8293 (tpp80) REVERT: B 62 GLU cc_start: 0.8323 (mp0) cc_final: 0.7590 (mp0) REVERT: B 63 GLU cc_start: 0.8305 (pm20) cc_final: 0.7905 (pm20) REVERT: B 80 LYS cc_start: 0.9264 (ttpt) cc_final: 0.9039 (ttpt) REVERT: C 15 LYS cc_start: 0.8999 (mttt) cc_final: 0.8710 (mtpm) REVERT: C 63 GLU cc_start: 0.8251 (OUTLIER) cc_final: 0.7889 (pm20) REVERT: C 66 GLU cc_start: 0.8513 (OUTLIER) cc_final: 0.8152 (tm-30) REVERT: C 104 ARG cc_start: 0.8353 (mtm-85) cc_final: 0.8118 (ttm110) REVERT: D 13 MET cc_start: 0.8478 (tmm) cc_final: 0.8102 (tmm) REVERT: D 15 LYS cc_start: 0.8856 (mttt) cc_final: 0.8364 (mtpp) REVERT: D 34 ARG cc_start: 0.8762 (ttt180) cc_final: 0.8447 (tpp80) REVERT: D 58 LEU cc_start: 0.9154 (OUTLIER) cc_final: 0.8943 (tp) REVERT: D 80 LYS cc_start: 0.9093 (tttt) cc_final: 0.8855 (tttm) REVERT: E 13 MET cc_start: 0.8711 (tmm) cc_final: 0.7871 (tmm) REVERT: E 15 LYS cc_start: 0.9006 (mttt) cc_final: 0.8790 (mtmm) REVERT: E 34 ARG cc_start: 0.8706 (ttt180) cc_final: 0.8374 (tpp80) REVERT: E 62 GLU cc_start: 0.8705 (pm20) cc_final: 0.8112 (mp0) REVERT: E 84 ILE cc_start: 0.9418 (mt) cc_final: 0.9058 (pp) REVERT: F 13 MET cc_start: 0.8772 (tmm) cc_final: 0.8120 (tmm) REVERT: F 18 ASP cc_start: 0.8700 (m-30) cc_final: 0.8416 (m-30) REVERT: F 62 GLU cc_start: 0.8614 (pm20) cc_final: 0.8282 (pm20) REVERT: F 63 GLU cc_start: 0.8268 (pm20) cc_final: 0.7990 (pm20) REVERT: G 13 MET cc_start: 0.8700 (tmm) cc_final: 0.8121 (tmm) REVERT: G 15 LYS cc_start: 0.9014 (mttt) cc_final: 0.8438 (mttp) REVERT: G 34 ARG cc_start: 0.8720 (ttt180) cc_final: 0.8378 (tpp80) REVERT: G 63 GLU cc_start: 0.8521 (pt0) cc_final: 0.8118 (pm20) REVERT: H 15 LYS cc_start: 0.8999 (mttt) cc_final: 0.8462 (mtpp) REVERT: H 18 ASP cc_start: 0.8814 (OUTLIER) cc_final: 0.8416 (m-30) REVERT: H 34 ARG cc_start: 0.8666 (ttt180) cc_final: 0.8373 (tpp80) REVERT: H 35 LYS cc_start: 0.9091 (ttmt) cc_final: 0.8786 (mttt) REVERT: H 63 GLU cc_start: 0.8760 (pt0) cc_final: 0.8456 (pm20) REVERT: H 84 ILE cc_start: 0.9430 (mt) cc_final: 0.9112 (pp) REVERT: H 89 GLU cc_start: 0.8926 (pm20) cc_final: 0.8691 (pm20) REVERT: I 15 LYS cc_start: 0.8881 (OUTLIER) cc_final: 0.8469 (ttmm) REVERT: I 18 ASP cc_start: 0.8583 (OUTLIER) cc_final: 0.8240 (m-30) REVERT: I 30 MET cc_start: 0.8171 (tmm) cc_final: 0.7967 (tmm) REVERT: I 62 GLU cc_start: 0.8556 (mp0) cc_final: 0.8217 (mp0) REVERT: I 80 LYS cc_start: 0.9165 (tttt) cc_final: 0.8941 (tttm) REVERT: I 104 ARG cc_start: 0.8175 (mtm-85) cc_final: 0.7960 (ttm110) REVERT: J 15 LYS cc_start: 0.8836 (mttt) cc_final: 0.8430 (ttmm) REVERT: J 34 ARG cc_start: 0.8583 (ttt180) cc_final: 0.8221 (tpp80) REVERT: J 35 LYS cc_start: 0.9004 (ttmm) cc_final: 0.8374 (mttm) REVERT: J 63 GLU cc_start: 0.8841 (pt0) cc_final: 0.8529 (pt0) REVERT: J 72 GLU cc_start: 0.8567 (mm-30) cc_final: 0.8200 (mp0) REVERT: J 84 ILE cc_start: 0.9463 (mt) cc_final: 0.9171 (pp) REVERT: K 13 MET cc_start: 0.8681 (tmm) cc_final: 0.8475 (tmm) REVERT: K 15 LYS cc_start: 0.9083 (mttt) cc_final: 0.8638 (mtpm) REVERT: K 26 ILE cc_start: 0.9421 (OUTLIER) cc_final: 0.9161 (mp) REVERT: K 80 LYS cc_start: 0.8910 (tttt) cc_final: 0.8682 (tttm) REVERT: K 106 THR cc_start: 0.9106 (m) cc_final: 0.8836 (p) REVERT: K 118 THR cc_start: 0.9265 (m) cc_final: 0.8899 (p) outliers start: 42 outliers final: 23 residues processed: 343 average time/residue: 1.3957 time to fit residues: 501.5175 Evaluate side-chains 351 residues out of total 858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 319 time to evaluate : 0.842 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 ASP Chi-restraints excluded: chain A residue 96 THR Chi-restraints excluded: chain A residue 98 ASN Chi-restraints excluded: chain A residue 117 SER Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain C residue 63 GLU Chi-restraints excluded: chain C residue 66 GLU Chi-restraints excluded: chain C residue 96 THR Chi-restraints excluded: chain D residue 58 LEU Chi-restraints excluded: chain D residue 98 ASN Chi-restraints excluded: chain E residue 110 LEU Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain H residue 18 ASP Chi-restraints excluded: chain H residue 82 LEU Chi-restraints excluded: chain H residue 96 THR Chi-restraints excluded: chain H residue 98 ASN Chi-restraints excluded: chain H residue 115 SER Chi-restraints excluded: chain I residue 15 LYS Chi-restraints excluded: chain I residue 18 ASP Chi-restraints excluded: chain I residue 34 ARG Chi-restraints excluded: chain I residue 82 LEU Chi-restraints excluded: chain I residue 96 THR Chi-restraints excluded: chain I residue 98 ASN Chi-restraints excluded: chain J residue 18 ASP Chi-restraints excluded: chain J residue 26 ILE Chi-restraints excluded: chain J residue 98 ASN Chi-restraints excluded: chain K residue 26 ILE Chi-restraints excluded: chain K residue 30 MET Chi-restraints excluded: chain K residue 59 THR Chi-restraints excluded: chain K residue 70 LYS Chi-restraints excluded: chain K residue 96 THR Chi-restraints excluded: chain K residue 117 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 88 optimal weight: 2.9990 chunk 91 optimal weight: 0.6980 chunk 53 optimal weight: 5.9990 chunk 38 optimal weight: 9.9990 chunk 69 optimal weight: 9.9990 chunk 27 optimal weight: 5.9990 chunk 80 optimal weight: 0.9980 chunk 84 optimal weight: 3.9990 chunk 58 optimal weight: 3.9990 chunk 94 optimal weight: 10.0000 chunk 57 optimal weight: 0.5980 overall best weight: 1.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 88 HIS B 98 ASN H 90 HIS K 27 ASN K 90 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8749 moved from start: 0.4301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 8096 Z= 0.320 Angle : 0.937 14.681 11000 Z= 0.460 Chirality : 0.052 0.180 1287 Planarity : 0.007 0.077 1353 Dihedral : 5.805 25.007 1089 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 24.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.20 % Favored : 93.80 % Rotamer: Outliers : 4.90 % Allowed : 32.75 % Favored : 62.35 % 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: -2.88 (0.23), residues: 968 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.19 (0.18), residues: 968 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 79 HIS 0.004 0.001 HIS I 88 PHE 0.030 0.002 PHE K 64 TYR 0.023 0.002 TYR E 116 ARG 0.019 0.003 ARG F 104 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1936 Ramachandran restraints generated. 968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1936 Ramachandran restraints generated. 968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 380 residues out of total 858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 338 time to evaluate : 0.954 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 15 LYS cc_start: 0.8778 (mttt) cc_final: 0.8480 (mtpm) REVERT: A 18 ASP cc_start: 0.8706 (OUTLIER) cc_final: 0.8167 (m-30) REVERT: A 34 ARG cc_start: 0.8600 (ttt180) cc_final: 0.8221 (tpp80) REVERT: A 62 GLU cc_start: 0.7872 (mp0) cc_final: 0.7458 (mp0) REVERT: A 63 GLU cc_start: 0.8717 (pt0) cc_final: 0.8107 (pp20) REVERT: A 66 GLU cc_start: 0.8577 (tm-30) cc_final: 0.8128 (tm-30) REVERT: A 96 THR cc_start: 0.9133 (OUTLIER) cc_final: 0.8877 (p) REVERT: A 104 ARG cc_start: 0.8333 (mtm-85) cc_final: 0.7880 (mtm-85) REVERT: B 34 ARG cc_start: 0.8657 (ttt180) cc_final: 0.8264 (tpp80) REVERT: B 61 GLU cc_start: 0.8601 (mt-10) cc_final: 0.8071 (mp0) REVERT: B 62 GLU cc_start: 0.8296 (mp0) cc_final: 0.7664 (mp0) REVERT: B 80 LYS cc_start: 0.9251 (ttpt) cc_final: 0.9024 (ttpt) REVERT: C 15 LYS cc_start: 0.9008 (mttt) cc_final: 0.8702 (mtpm) REVERT: C 63 GLU cc_start: 0.8189 (OUTLIER) cc_final: 0.7939 (pm20) REVERT: C 66 GLU cc_start: 0.8505 (OUTLIER) cc_final: 0.8171 (tm-30) REVERT: D 13 MET cc_start: 0.8487 (tmm) cc_final: 0.8073 (tmm) REVERT: D 15 LYS cc_start: 0.8839 (mttt) cc_final: 0.8182 (mtpp) REVERT: D 18 ASP cc_start: 0.8502 (m-30) cc_final: 0.7999 (m-30) REVERT: D 34 ARG cc_start: 0.8749 (ttt180) cc_final: 0.8428 (tpp80) REVERT: D 58 LEU cc_start: 0.9162 (OUTLIER) cc_final: 0.8944 (tp) REVERT: D 80 LYS cc_start: 0.9081 (tttt) cc_final: 0.8842 (tttm) REVERT: E 13 MET cc_start: 0.8668 (tmm) cc_final: 0.7845 (tmm) REVERT: E 15 LYS cc_start: 0.8997 (mttt) cc_final: 0.8691 (mtmm) REVERT: E 34 ARG cc_start: 0.8682 (ttt180) cc_final: 0.8400 (tpp80) REVERT: E 62 GLU cc_start: 0.8701 (pm20) cc_final: 0.8073 (mp0) REVERT: E 84 ILE cc_start: 0.9416 (mt) cc_final: 0.9054 (pp) REVERT: F 13 MET cc_start: 0.8843 (tmm) cc_final: 0.7899 (tmm) REVERT: F 15 LYS cc_start: 0.8890 (mtpp) cc_final: 0.8385 (mptp) REVERT: F 18 ASP cc_start: 0.8703 (m-30) cc_final: 0.8346 (m-30) REVERT: F 35 LYS cc_start: 0.8991 (OUTLIER) cc_final: 0.8762 (mttp) REVERT: F 62 GLU cc_start: 0.8590 (pm20) cc_final: 0.8254 (pm20) REVERT: G 13 MET cc_start: 0.8652 (tmm) cc_final: 0.8103 (tmm) REVERT: G 15 LYS cc_start: 0.8972 (mttt) cc_final: 0.8474 (mttp) REVERT: G 34 ARG cc_start: 0.8696 (ttt180) cc_final: 0.8349 (tpp80) REVERT: H 15 LYS cc_start: 0.9011 (mttt) cc_final: 0.8606 (mtpp) REVERT: H 34 ARG cc_start: 0.8641 (ttt180) cc_final: 0.8351 (tpp80) REVERT: H 35 LYS cc_start: 0.9098 (ttmt) cc_final: 0.8458 (mttt) REVERT: H 63 GLU cc_start: 0.8766 (pt0) cc_final: 0.8483 (pt0) REVERT: H 84 ILE cc_start: 0.9402 (mt) cc_final: 0.9085 (pp) REVERT: I 13 MET cc_start: 0.8439 (tmm) cc_final: 0.7930 (tpt) REVERT: I 15 LYS cc_start: 0.8862 (OUTLIER) cc_final: 0.8433 (ttmm) REVERT: I 18 ASP cc_start: 0.8534 (OUTLIER) cc_final: 0.7654 (m-30) REVERT: I 21 ARG cc_start: 0.8408 (mtp-110) cc_final: 0.8191 (mtp85) REVERT: I 62 GLU cc_start: 0.8556 (mp0) cc_final: 0.8190 (mp0) REVERT: I 80 LYS cc_start: 0.9152 (tttt) cc_final: 0.8927 (tttp) REVERT: I 104 ARG cc_start: 0.8154 (mtm-85) cc_final: 0.7943 (ttm110) REVERT: J 13 MET cc_start: 0.8741 (tmm) cc_final: 0.8004 (tmt) REVERT: J 21 ARG cc_start: 0.8362 (mmm160) cc_final: 0.7811 (mmm-85) REVERT: J 34 ARG cc_start: 0.8576 (ttt180) cc_final: 0.8214 (tpp80) REVERT: J 35 LYS cc_start: 0.8997 (ttmm) cc_final: 0.8600 (mttm) REVERT: J 63 GLU cc_start: 0.8791 (pt0) cc_final: 0.8389 (pt0) REVERT: J 72 GLU cc_start: 0.8558 (mm-30) cc_final: 0.8194 (mp0) REVERT: J 84 ILE cc_start: 0.9454 (mt) cc_final: 0.9168 (pp) REVERT: K 15 LYS cc_start: 0.9088 (mttt) cc_final: 0.8608 (mtpm) REVERT: K 63 GLU cc_start: 0.8550 (pt0) cc_final: 0.8336 (pt0) REVERT: K 80 LYS cc_start: 0.8885 (tttt) cc_final: 0.8656 (tttm) REVERT: K 106 THR cc_start: 0.9111 (m) cc_final: 0.8861 (p) REVERT: K 118 THR cc_start: 0.9256 (m) cc_final: 0.8881 (p) outliers start: 42 outliers final: 24 residues processed: 352 average time/residue: 1.3655 time to fit residues: 504.6464 Evaluate side-chains 356 residues out of total 858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 324 time to evaluate : 0.977 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 ASP Chi-restraints excluded: chain A residue 96 THR Chi-restraints excluded: chain A residue 98 ASN Chi-restraints excluded: chain A residue 112 SER Chi-restraints excluded: chain A residue 117 SER Chi-restraints excluded: chain C residue 63 GLU Chi-restraints excluded: chain C residue 66 GLU Chi-restraints excluded: chain C residue 96 THR Chi-restraints excluded: chain D residue 58 LEU Chi-restraints excluded: chain D residue 61 GLU Chi-restraints excluded: chain D residue 98 ASN Chi-restraints excluded: chain E residue 110 LEU Chi-restraints excluded: chain F residue 35 LYS Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain H residue 18 ASP Chi-restraints excluded: chain H residue 82 LEU Chi-restraints excluded: chain H residue 96 THR Chi-restraints excluded: chain H residue 98 ASN Chi-restraints excluded: chain H residue 115 SER Chi-restraints excluded: chain I residue 15 LYS Chi-restraints excluded: chain I residue 18 ASP Chi-restraints excluded: chain I residue 34 ARG Chi-restraints excluded: chain I residue 82 LEU Chi-restraints excluded: chain I residue 96 THR Chi-restraints excluded: chain I residue 98 ASN Chi-restraints excluded: chain J residue 26 ILE Chi-restraints excluded: chain J residue 98 ASN Chi-restraints excluded: chain K residue 30 MET Chi-restraints excluded: chain K residue 59 THR Chi-restraints excluded: chain K residue 70 LYS Chi-restraints excluded: chain K residue 96 THR Chi-restraints excluded: chain K residue 117 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 44 optimal weight: 0.0970 chunk 65 optimal weight: 9.9990 chunk 98 optimal weight: 0.3980 chunk 90 optimal weight: 0.0370 chunk 78 optimal weight: 10.0000 chunk 8 optimal weight: 0.9990 chunk 60 optimal weight: 9.9990 chunk 48 optimal weight: 5.9990 chunk 62 optimal weight: 0.6980 chunk 83 optimal weight: 9.9990 chunk 24 optimal weight: 10.0000 overall best weight: 0.4458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 88 HIS B 98 ASN H 90 HIS K 27 ASN K 90 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8704 moved from start: 0.4552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 8096 Z= 0.272 Angle : 0.971 14.659 11000 Z= 0.475 Chirality : 0.053 0.226 1287 Planarity : 0.008 0.084 1353 Dihedral : 5.838 21.707 1089 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 23.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.20 % Favored : 93.80 % Rotamer: Outliers : 3.96 % Allowed : 34.50 % Favored : 61.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.96 (0.23), residues: 968 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.25 (0.18), residues: 968 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP F 79 HIS 0.005 0.001 HIS B 31 PHE 0.026 0.002 PHE K 64 TYR 0.027 0.002 TYR E 116 ARG 0.020 0.003 ARG F 104 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1936 Ramachandran restraints generated. 968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1936 Ramachandran restraints generated. 968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 386 residues out of total 858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 352 time to evaluate : 1.168 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 15 LYS cc_start: 0.8714 (mttt) cc_final: 0.8397 (mtpm) REVERT: A 18 ASP cc_start: 0.8669 (m-30) cc_final: 0.8151 (m-30) REVERT: A 34 ARG cc_start: 0.8583 (ttt180) cc_final: 0.8217 (tpp80) REVERT: A 62 GLU cc_start: 0.7834 (mp0) cc_final: 0.7435 (mp0) REVERT: A 63 GLU cc_start: 0.8659 (pt0) cc_final: 0.7882 (pp20) REVERT: A 66 GLU cc_start: 0.8460 (tm-30) cc_final: 0.8258 (tm-30) REVERT: A 96 THR cc_start: 0.9098 (OUTLIER) cc_final: 0.8817 (p) REVERT: A 104 ARG cc_start: 0.8293 (mtm-85) cc_final: 0.7882 (mtm-85) REVERT: B 15 LYS cc_start: 0.8954 (mttt) cc_final: 0.8433 (mtpp) REVERT: B 18 ASP cc_start: 0.8559 (m-30) cc_final: 0.7635 (m-30) REVERT: B 34 ARG cc_start: 0.8706 (ttt180) cc_final: 0.8357 (tpp80) REVERT: B 61 GLU cc_start: 0.8615 (mt-10) cc_final: 0.8170 (mp0) REVERT: B 62 GLU cc_start: 0.8300 (mp0) cc_final: 0.7540 (mp0) REVERT: B 63 GLU cc_start: 0.8289 (pm20) cc_final: 0.7567 (pm20) REVERT: B 80 LYS cc_start: 0.9211 (ttpt) cc_final: 0.8975 (ttpt) REVERT: C 15 LYS cc_start: 0.8974 (mttt) cc_final: 0.8692 (mtpm) REVERT: C 18 ASP cc_start: 0.8581 (m-30) cc_final: 0.7786 (m-30) REVERT: C 34 ARG cc_start: 0.8555 (tpp80) cc_final: 0.8332 (tpp80) REVERT: C 62 GLU cc_start: 0.8370 (mp0) cc_final: 0.8167 (mp0) REVERT: C 63 GLU cc_start: 0.8340 (OUTLIER) cc_final: 0.8004 (pm20) REVERT: C 66 GLU cc_start: 0.8414 (OUTLIER) cc_final: 0.8072 (tm-30) REVERT: C 106 THR cc_start: 0.9259 (m) cc_final: 0.9058 (p) REVERT: D 13 MET cc_start: 0.8461 (tmm) cc_final: 0.8153 (tmm) REVERT: D 15 LYS cc_start: 0.8756 (mttt) cc_final: 0.8263 (mtpp) REVERT: D 34 ARG cc_start: 0.8736 (ttt180) cc_final: 0.8405 (tpp80) REVERT: D 58 LEU cc_start: 0.9070 (OUTLIER) cc_final: 0.8817 (tp) REVERT: D 80 LYS cc_start: 0.9043 (tttt) cc_final: 0.8796 (tttp) REVERT: D 106 THR cc_start: 0.9199 (m) cc_final: 0.8938 (m) REVERT: E 13 MET cc_start: 0.8650 (tmm) cc_final: 0.8416 (tmm) REVERT: E 15 LYS cc_start: 0.8918 (mttt) cc_final: 0.8607 (mtpm) REVERT: E 34 ARG cc_start: 0.8665 (ttt180) cc_final: 0.8340 (tpp80) REVERT: E 62 GLU cc_start: 0.8635 (pm20) cc_final: 0.8182 (mp0) REVERT: E 84 ILE cc_start: 0.9382 (mt) cc_final: 0.9036 (pp) REVERT: E 89 GLU cc_start: 0.7963 (mp0) cc_final: 0.7728 (mp0) REVERT: F 13 MET cc_start: 0.8833 (tmm) cc_final: 0.8607 (tmm) REVERT: F 15 LYS cc_start: 0.8934 (mtpp) cc_final: 0.8624 (mtpm) REVERT: F 18 ASP cc_start: 0.8643 (m-30) cc_final: 0.8236 (m-30) REVERT: G 15 LYS cc_start: 0.8903 (mttt) cc_final: 0.8444 (mtpp) REVERT: G 34 ARG cc_start: 0.8661 (ttt180) cc_final: 0.8317 (tpp80) REVERT: G 104 ARG cc_start: 0.8395 (ttm-80) cc_final: 0.8065 (mtm-85) REVERT: H 15 LYS cc_start: 0.8924 (mttt) cc_final: 0.8399 (mtpp) REVERT: H 18 ASP cc_start: 0.8836 (OUTLIER) cc_final: 0.8276 (m-30) REVERT: H 34 ARG cc_start: 0.8607 (ttt180) cc_final: 0.8306 (tpp80) REVERT: H 35 LYS cc_start: 0.9046 (ttmt) cc_final: 0.8427 (mttt) REVERT: H 63 GLU cc_start: 0.8713 (pt0) cc_final: 0.8413 (pt0) REVERT: H 84 ILE cc_start: 0.9347 (mt) cc_final: 0.9006 (pp) REVERT: I 13 MET cc_start: 0.8425 (tmm) cc_final: 0.7960 (tpt) REVERT: I 15 LYS cc_start: 0.8803 (OUTLIER) cc_final: 0.8109 (ttmm) REVERT: I 21 ARG cc_start: 0.8395 (mtp-110) cc_final: 0.8140 (mtp85) REVERT: I 62 GLU cc_start: 0.8518 (mp0) cc_final: 0.8176 (mp0) REVERT: I 72 GLU cc_start: 0.8453 (mt-10) cc_final: 0.8220 (mp0) REVERT: I 80 LYS cc_start: 0.9126 (tttt) cc_final: 0.8906 (tttm) REVERT: I 104 ARG cc_start: 0.8166 (mtm-85) cc_final: 0.7872 (ttm110) REVERT: J 13 MET cc_start: 0.8740 (tmm) cc_final: 0.7684 (tmt) REVERT: J 15 LYS cc_start: 0.8803 (mttt) cc_final: 0.8484 (mtmt) REVERT: J 18 ASP cc_start: 0.8860 (m-30) cc_final: 0.8600 (m-30) REVERT: J 34 ARG cc_start: 0.8543 (ttt180) cc_final: 0.8182 (tpp80) REVERT: J 35 LYS cc_start: 0.9021 (ttmm) cc_final: 0.8655 (mttm) REVERT: J 63 GLU cc_start: 0.8801 (pt0) cc_final: 0.8390 (pt0) REVERT: J 72 GLU cc_start: 0.8484 (mm-30) cc_final: 0.8122 (mp0) REVERT: J 84 ILE cc_start: 0.9424 (mt) cc_final: 0.9137 (pp) REVERT: K 13 MET cc_start: 0.8735 (tmm) cc_final: 0.8477 (tmt) REVERT: K 15 LYS cc_start: 0.9080 (mttt) cc_final: 0.8754 (mtpm) REVERT: K 80 LYS cc_start: 0.8822 (tttt) cc_final: 0.8600 (tttp) REVERT: K 106 THR cc_start: 0.9059 (m) cc_final: 0.8818 (p) REVERT: K 118 THR cc_start: 0.9231 (m) cc_final: 0.8932 (p) outliers start: 34 outliers final: 17 residues processed: 361 average time/residue: 1.3053 time to fit residues: 496.5441 Evaluate side-chains 358 residues out of total 858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 335 time to evaluate : 0.951 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 ILE Chi-restraints excluded: chain A residue 96 THR Chi-restraints excluded: chain A residue 98 ASN Chi-restraints excluded: chain A residue 112 SER Chi-restraints excluded: chain A residue 117 SER Chi-restraints excluded: chain C residue 63 GLU Chi-restraints excluded: chain C residue 66 GLU Chi-restraints excluded: chain D residue 58 LEU Chi-restraints excluded: chain D residue 98 ASN Chi-restraints excluded: chain E residue 110 LEU Chi-restraints excluded: chain F residue 58 LEU Chi-restraints excluded: chain F residue 60 THR Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain H residue 18 ASP Chi-restraints excluded: chain H residue 96 THR Chi-restraints excluded: chain H residue 98 ASN Chi-restraints excluded: chain I residue 15 LYS Chi-restraints excluded: chain I residue 34 ARG Chi-restraints excluded: chain I residue 96 THR Chi-restraints excluded: chain I residue 98 ASN Chi-restraints excluded: chain J residue 26 ILE Chi-restraints excluded: chain K residue 30 MET Chi-restraints excluded: chain K residue 70 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 72 optimal weight: 10.0000 chunk 11 optimal weight: 9.9990 chunk 21 optimal weight: 0.9980 chunk 78 optimal weight: 0.9990 chunk 32 optimal weight: 5.9990 chunk 80 optimal weight: 6.9990 chunk 9 optimal weight: 9.9990 chunk 14 optimal weight: 3.9990 chunk 69 optimal weight: 3.9990 chunk 4 optimal weight: 4.9990 chunk 56 optimal weight: 8.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 98 ASN H 90 HIS K 27 ASN K 90 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.070965 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.051924 restraints weight = 17318.643| |-----------------------------------------------------------------------------| r_work (start): 0.3456 rms_B_bonded: 3.69 r_work: 0.3317 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.3317 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8474 moved from start: 0.4544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 8096 Z= 0.428 Angle : 1.007 14.067 11000 Z= 0.500 Chirality : 0.055 0.223 1287 Planarity : 0.007 0.080 1353 Dihedral : 5.953 22.014 1089 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 25.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.20 % Favored : 93.80 % Rotamer: Outliers : 3.15 % Allowed : 35.78 % Favored : 61.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.94 (0.23), residues: 968 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.24 (0.18), residues: 968 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 79 HIS 0.003 0.001 HIS H 88 PHE 0.027 0.002 PHE K 64 TYR 0.028 0.003 TYR E 116 ARG 0.019 0.003 ARG F 104 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6496.70 seconds wall clock time: 114 minutes 35.35 seconds (6875.35 seconds total)