Starting phenix.real_space_refine on Fri Mar 22 04:37:38 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nas_12246/03_2024/7nas_12246_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nas_12246/03_2024/7nas_12246.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nas_12246/03_2024/7nas_12246_neut_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.31 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nas_12246/03_2024/7nas_12246_neut_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nas_12246/03_2024/7nas_12246_neut_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nas_12246/03_2024/7nas_12246.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nas_12246/03_2024/7nas_12246.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nas_12246/03_2024/7nas_12246_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nas_12246/03_2024/7nas_12246_neut_updated.pdb" } resolution = 3.31 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= 0.004 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: 6 Type Number sf(0) Gaussians P 974 5.49 5 Mg 43 5.21 5 S 46 5.16 5 C 16464 2.51 5 N 6037 2.21 5 O 8826 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "D TYR 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 15": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q PHE 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T TYR 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T PHE 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X PHE 21": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X PHE 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X TYR 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X PHE 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X PHE 150": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 32390 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 20936 Number of conformers: 1 Conformer: "" Number of residues, atoms: 974, 20936 Classifications: {'RNA': 974} Modifications used: {'rna2p_pur': 77, 'rna2p_pyr': 50, 'rna3p': 5, 'rna3p_pur': 484, 'rna3p_pyr': 358} Link IDs: {'rna2p': 126, 'rna3p': 847} Chain breaks: 2 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 1 Chain: "D" Number of atoms: 1643 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1643 Classifications: {'peptide': 205} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 198} Chain: "E" Number of atoms: 1152 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1152 Classifications: {'peptide': 156} Link IDs: {'PTRANS': 5, 'TRANS': 150} Chain: "F" Number of atoms: 862 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 862 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 5, 'TRANS': 100} Chain: "H" Number of atoms: 979 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 979 Classifications: {'peptide': 129} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 123} Chain: "K" Number of atoms: 877 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 877 Classifications: {'peptide': 117} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 109} Chain: "L" Number of atoms: 957 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 957 Classifications: {'peptide': 123} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 115} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'D2T:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "O" Number of atoms: 714 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 714 Classifications: {'peptide': 88} Modifications used: {'COO': 1} Link IDs: {'TRANS': 87} Chain: "P" Number of atoms: 649 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 649 Classifications: {'peptide': 82} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 79} Chain: "Q" Number of atoms: 648 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 648 Classifications: {'peptide': 80} Link IDs: {'PTRANS': 2, 'TRANS': 77} Chain: "R" Number of atoms: 535 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 535 Classifications: {'peptide': 65} Link IDs: {'PTRANS': 2, 'TRANS': 62} Chain: "T" Number of atoms: 670 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 670 Classifications: {'peptide': 86} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 84} Chain: "U" Number of atoms: 551 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 551 Classifications: {'peptide': 66} Link IDs: {'PTRANS': 2, 'TRANS': 63} Chain: "X" Number of atoms: 1174 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1174 Classifications: {'peptide': 151} Link IDs: {'PTRANS': 5, 'TRANS': 145} Chain: "A" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 43 Unusual residues: {' MG': 43} Classifications: {'undetermined': 43} Link IDs: {None: 42} Time building chain proxies: 17.51, per 1000 atoms: 0.54 Number of scatterers: 32390 At special positions: 0 Unit cell: (146.475, 214.83, 138.88, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 46 16.00 P 974 15.00 Mg 43 11.99 O 8826 8.00 N 6037 7.00 C 16464 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: 21.60 Conformation dependent library (CDL) restraints added in 2.6 seconds 2850 Ramachandran restraints generated. 1425 Oldfield, 0 Emsley, 1425 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2702 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 52 helices and 15 sheets defined 36.9% alpha, 16.2% beta 299 base pairs and 491 stacking pairs defined. Time for finding SS restraints: 20.08 Creating SS restraints... Processing helix chain 'D' and resid 9 through 15 Processing helix chain 'D' and resid 28 through 31 No H-bonds generated for 'chain 'D' and resid 28 through 31' Processing helix chain 'D' and resid 40 through 43 removed outlier: 4.036A pdb=" N ALA D 43 " --> pdb=" O GLN D 40 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 40 through 43' Processing helix chain 'D' and resid 50 through 65 Processing helix chain 'D' and resid 69 through 79 Processing helix chain 'D' and resid 86 through 96 removed outlier: 3.534A pdb=" N LEU D 91 " --> pdb=" O GLY D 87 " (cutoff:3.500A) Processing helix chain 'D' and resid 98 through 104 Processing helix chain 'D' and resid 111 through 119 Processing helix chain 'D' and resid 125 through 127 No H-bonds generated for 'chain 'D' and resid 125 through 127' Processing helix chain 'D' and resid 147 through 150 No H-bonds generated for 'chain 'D' and resid 147 through 150' Processing helix chain 'D' and resid 153 through 162 Processing helix chain 'D' and resid 197 through 204 removed outlier: 3.586A pdb=" N TYR D 204 " --> pdb=" O ILE D 200 " (cutoff:3.500A) Processing helix chain 'E' and resid 56 through 68 removed outlier: 3.689A pdb=" N ARG E 68 " --> pdb=" O MET E 64 " (cutoff:3.500A) Processing helix chain 'E' and resid 109 through 118 removed outlier: 3.898A pdb=" N ALA E 113 " --> pdb=" O GLY E 109 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N VAL E 114 " --> pdb=" O ALA E 110 " (cutoff:3.500A) Processing helix chain 'E' and resid 133 through 138 Processing helix chain 'E' and resid 141 through 145 Processing helix chain 'E' and resid 152 through 156 Processing helix chain 'E' and resid 161 through 164 No H-bonds generated for 'chain 'E' and resid 161 through 164' Processing helix chain 'F' and resid 12 through 31 removed outlier: 4.934A pdb=" N GLU F 16 " --> pdb=" O ASP F 13 " (cutoff:3.500A) Proline residue: F 19 - end of helix removed outlier: 4.913A pdb=" N GLU F 23 " --> pdb=" O GLY F 20 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N TYR F 25 " --> pdb=" O ILE F 22 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ALA F 28 " --> pdb=" O TYR F 25 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ILE F 29 " --> pdb=" O THR F 26 " (cutoff:3.500A) Processing helix chain 'F' and resid 68 through 80 Processing helix chain 'F' and resid 103 through 105 No H-bonds generated for 'chain 'F' and resid 103 through 105' Processing helix chain 'H' and resid 6 through 20 Processing helix chain 'H' and resid 31 through 42 removed outlier: 3.507A pdb=" N ALA H 35 " --> pdb=" O LYS H 31 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LEU H 40 " --> pdb=" O ILE H 36 " (cutoff:3.500A) Processing helix chain 'H' and resid 113 through 119 Processing helix chain 'K' and resid 48 through 50 No H-bonds generated for 'chain 'K' and resid 48 through 50' Processing helix chain 'K' and resid 54 through 56 No H-bonds generated for 'chain 'K' and resid 54 through 56' Processing helix chain 'K' and resid 60 through 74 removed outlier: 3.593A pdb=" N ALA K 66 " --> pdb=" O ALA K 62 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N GLU K 68 " --> pdb=" O GLN K 64 " (cutoff:3.500A) removed outlier: 4.740A pdb=" N ALA K 73 " --> pdb=" O ARG K 69 " (cutoff:3.500A) Processing helix chain 'K' and resid 93 through 101 Processing helix chain 'L' and resid 4 through 9 removed outlier: 3.748A pdb=" N ARG L 9 " --> pdb=" O ASN L 5 " (cutoff:3.500A) Processing helix chain 'L' and resid 22 through 24 No H-bonds generated for 'chain 'L' and resid 22 through 24' Processing helix chain 'L' and resid 114 through 117 Processing helix chain 'O' and resid 5 through 15 Processing helix chain 'O' and resid 25 through 43 removed outlier: 4.092A pdb=" N GLY O 41 " --> pdb=" O ASN O 37 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N HIS O 42 " --> pdb=" O HIS O 38 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N PHE O 43 " --> pdb=" O LEU O 39 " (cutoff:3.500A) Processing helix chain 'O' and resid 50 through 73 Processing helix chain 'O' and resid 75 through 85 Processing helix chain 'P' and resid 54 through 63 Processing helix chain 'P' and resid 69 through 81 Processing helix chain 'Q' and resid 49 through 51 No H-bonds generated for 'chain 'Q' and resid 49 through 51' Processing helix chain 'R' and resid 12 through 16 Processing helix chain 'R' and resid 26 through 32 Processing helix chain 'R' and resid 42 through 45 No H-bonds generated for 'chain 'R' and resid 42 through 45' Processing helix chain 'R' and resid 49 through 64 Processing helix chain 'T' and resid 5 through 41 removed outlier: 3.517A pdb=" N SER T 14 " --> pdb=" O ARG T 10 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N GLU T 15 " --> pdb=" O ALA T 11 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N LYS T 16 " --> pdb=" O ILE T 12 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N MET T 28 " --> pdb=" O ARG T 24 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N PHE T 31 " --> pdb=" O MET T 27 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LYS T 34 " --> pdb=" O THR T 30 " (cutoff:3.500A) Processing helix chain 'T' and resid 45 through 63 Proline residue: T 56 - end of helix Processing helix chain 'T' and resid 69 through 86 Processing helix chain 'U' and resid 12 through 24 Processing helix chain 'U' and resid 28 through 36 removed outlier: 4.110A pdb=" N ARG U 34 " --> pdb=" O ALA U 30 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ARG U 35 " --> pdb=" O GLU U 31 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N GLU U 36 " --> pdb=" O VAL U 32 " (cutoff:3.500A) Processing helix chain 'U' and resid 41 through 66 removed outlier: 3.682A pdb=" N ARG U 47 " --> pdb=" O THR U 43 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N GLU U 63 " --> pdb=" O LYS U 59 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ASN U 64 " --> pdb=" O LEU U 60 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ALA U 65 " --> pdb=" O ALA U 61 " (cutoff:3.500A) Processing helix chain 'X' and resid 5 through 19 Proline residue: X 15 - end of helix Processing helix chain 'X' and resid 48 through 64 removed outlier: 3.650A pdb=" N VAL X 64 " --> pdb=" O ALA X 60 " (cutoff:3.500A) Processing helix chain 'X' and resid 88 through 93 Processing helix chain 'X' and resid 138 through 140 No H-bonds generated for 'chain 'X' and resid 138 through 140' Processing sheet with id= A, first strand: chain 'D' and resid 123 through 125 removed outlier: 4.718A pdb=" N ILE D 123 " --> pdb=" O VAL D 130 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'D' and resid 141 through 144 removed outlier: 3.693A pdb=" N ASP D 141 " --> pdb=" O PHE D 182 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'E' and resid 12 through 15 Processing sheet with id= D, first strand: chain 'E' and resid 19 through 21 Processing sheet with id= E, first strand: chain 'E' and resid 85 through 89 Processing sheet with id= F, first strand: chain 'F' and resid 84 through 88 removed outlier: 6.666A pdb=" N MET F 9 " --> pdb=" O ILE F 85 " (cutoff:3.500A) removed outlier: 4.659A pdb=" N SER F 87 " --> pdb=" O VAL F 7 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N VAL F 7 " --> pdb=" O SER F 87 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N PHE F 8 " --> pdb=" O VAL F 60 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLY F 43 " --> pdb=" O TYR F 59 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N LEU F 61 " --> pdb=" O ASP F 41 " (cutoff:3.500A) removed outlier: 5.436A pdb=" N ASP F 41 " --> pdb=" O LEU F 61 " (cutoff:3.500A) removed outlier: 7.335A pdb=" N ASN F 63 " --> pdb=" O LEU F 39 " (cutoff:3.500A) removed outlier: 5.718A pdb=" N LEU F 39 " --> pdb=" O ASN F 63 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'H' and resid 24 through 28 removed outlier: 4.202A pdb=" N ASP H 48 " --> pdb=" O THR H 62 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'H' and resid 74 through 77 removed outlier: 6.848A pdb=" N VAL H 103 " --> pdb=" O ILE H 126 " (cutoff:3.500A) removed outlier: 4.661A pdb=" N TYR H 128 " --> pdb=" O ILE H 101 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N ILE H 101 " --> pdb=" O TYR H 128 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'K' and resid 106 through 112 removed outlier: 3.523A pdb=" N LEU K 82 " --> pdb=" O ARG K 106 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N VAL K 84 " --> pdb=" O THR K 108 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N ILE K 110 " --> pdb=" O VAL K 84 " (cutoff:3.500A) removed outlier: 7.547A pdb=" N VAL K 86 " --> pdb=" O ILE K 110 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N ASP K 112 " --> pdb=" O VAL K 86 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'L' and resid 79 through 82 removed outlier: 6.214A pdb=" N ARG L 54 " --> pdb=" O THR L 35 " (cutoff:3.500A) removed outlier: 5.114A pdb=" N VAL L 37 " --> pdb=" O VAL L 52 " (cutoff:3.500A) removed outlier: 7.438A pdb=" N VAL L 52 " --> pdb=" O VAL L 37 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N THR L 39 " --> pdb=" O ARG L 50 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N ARG L 50 " --> pdb=" O THR L 39 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'P' and resid 2 through 11 removed outlier: 3.619A pdb=" N ARG P 51 " --> pdb=" O PHE P 38 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'Q' and resid 24 through 30 Processing sheet with id= M, first strand: chain 'Q' and resid 59 through 63 removed outlier: 3.557A pdb=" N ARG Q 77 " --> pdb=" O GLU Q 60 " (cutoff:3.500A) removed outlier: 5.629A pdb=" N ARG Q 62 " --> pdb=" O LEU Q 75 " (cutoff:3.500A) removed outlier: 5.155A pdb=" N LEU Q 75 " --> pdb=" O ARG Q 62 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'X' and resid 75 through 78 removed outlier: 3.514A pdb=" N ILE X 40 " --> pdb=" O SER X 77 " (cutoff:3.500A) removed outlier: 5.802A pdb=" N ASP X 41 " --> pdb=" O LEU X 23 " (cutoff:3.500A) removed outlier: 5.425A pdb=" N LEU X 23 " --> pdb=" O ASP X 41 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'X' and resid 141 through 146 removed outlier: 6.955A pdb=" N VAL X 102 " --> pdb=" O GLN X 142 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N ALA X 144 " --> pdb=" O THR X 100 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N THR X 100 " --> pdb=" O ALA X 144 " (cutoff:3.500A) removed outlier: 4.940A pdb=" N LEU X 146 " --> pdb=" O GLU X 98 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N GLU X 98 " --> pdb=" O LEU X 146 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N VAL X 116 " --> pdb=" O THR X 128 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N THR X 126 " --> pdb=" O LYS X 118 " (cutoff:3.500A) removed outlier: 5.414A pdb=" N VAL X 120 " --> pdb=" O MET X 124 " (cutoff:3.500A) removed outlier: 7.275A pdb=" N MET X 124 " --> pdb=" O VAL X 120 " (cutoff:3.500A) 431 hydrogen bonds defined for protein. 1197 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 702 hydrogen bonds 954 hydrogen bond angles 0 basepair planarities 299 basepair parallelities 491 stacking parallelities Total time for adding SS restraints: 20.60 Time building geometry restraints manager: 22.31 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 5774 1.33 - 1.45: 13876 1.45 - 1.57: 13344 1.57 - 1.70: 1945 1.70 - 1.82: 79 Bond restraints: 35018 Sorted by residual: bond pdb=" N3 2MG A1516 " pdb=" C4 2MG A1516 " ideal model delta sigma weight residual 1.496 1.338 0.158 2.00e-02 2.50e+03 6.22e+01 bond pdb=" C2 G7M A 527 " pdb=" N3 G7M A 527 " ideal model delta sigma weight residual 1.462 1.312 0.150 2.00e-02 2.50e+03 5.63e+01 bond pdb=" N3 G7M A 527 " pdb=" C4 G7M A 527 " ideal model delta sigma weight residual 1.492 1.355 0.137 2.00e-02 2.50e+03 4.67e+01 bond pdb=" C2 2MG A1516 " pdb=" N2 2MG A1516 " ideal model delta sigma weight residual 1.475 1.340 0.135 2.00e-02 2.50e+03 4.57e+01 bond pdb=" C5 MA6 A1518 " pdb=" C4 MA6 A1518 " ideal model delta sigma weight residual 1.342 1.472 -0.130 2.00e-02 2.50e+03 4.22e+01 ... (remaining 35013 not shown) Histogram of bond angle deviations from ideal: 97.23 - 105.27: 4763 105.27 - 113.30: 22142 113.30 - 121.33: 16605 121.33 - 129.37: 7750 129.37 - 137.40: 862 Bond angle restraints: 52122 Sorted by residual: angle pdb=" N ASN U 9 " pdb=" CA ASN U 9 " pdb=" C ASN U 9 " ideal model delta sigma weight residual 114.12 101.73 12.39 1.39e+00 5.18e-01 7.95e+01 angle pdb=" C VAL X 24 " pdb=" N GLY X 25 " pdb=" CA GLY X 25 " ideal model delta sigma weight residual 121.65 115.87 5.78 6.80e-01 2.16e+00 7.22e+01 angle pdb=" C1' 2MG A1516 " pdb=" N9 2MG A1516 " pdb=" C8 2MG A1516 " ideal model delta sigma weight residual 110.07 128.74 -18.67 3.00e+00 1.11e-01 3.87e+01 angle pdb=" C TYR X 39 " pdb=" N ILE X 40 " pdb=" CA ILE X 40 " ideal model delta sigma weight residual 122.68 131.75 -9.07 1.58e+00 4.01e-01 3.29e+01 angle pdb=" C1' G7M A 527 " pdb=" N9 G7M A 527 " pdb=" C8 G7M A 527 " ideal model delta sigma weight residual 112.61 129.41 -16.80 3.00e+00 1.11e-01 3.14e+01 ... (remaining 52117 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.85: 19679 35.85 - 71.71: 2427 71.71 - 107.56: 284 107.56 - 143.41: 6 143.41 - 179.26: 7 Dihedral angle restraints: 22403 sinusoidal: 18224 harmonic: 4179 Sorted by residual: dihedral pdb=" O4' U A 365 " pdb=" C1' U A 365 " pdb=" N1 U A 365 " pdb=" C2 U A 365 " ideal model delta sinusoidal sigma weight residual 200.00 52.16 147.84 1 1.50e+01 4.44e-03 7.88e+01 dihedral pdb=" O4' C A 754 " pdb=" C1' C A 754 " pdb=" N1 C A 754 " pdb=" C2 C A 754 " ideal model delta sinusoidal sigma weight residual 200.00 55.88 144.12 1 1.50e+01 4.44e-03 7.72e+01 dihedral pdb=" O4' U A1540 " pdb=" C1' U A1540 " pdb=" N1 U A1540 " pdb=" C2 U A1540 " ideal model delta sinusoidal sigma weight residual -128.00 51.26 -179.26 1 1.70e+01 3.46e-03 6.64e+01 ... (remaining 22400 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.104: 6389 0.104 - 0.209: 195 0.209 - 0.313: 21 0.313 - 0.417: 2 0.417 - 0.522: 2 Chirality restraints: 6609 Sorted by residual: chirality pdb=" CA D2T L 89 " pdb=" N D2T L 89 " pdb=" C D2T L 89 " pdb=" CB D2T L 89 " both_signs ideal model delta sigma weight residual False 2.51 1.99 0.52 2.00e-01 2.50e+01 6.81e+00 chirality pdb=" C3' A A 523 " pdb=" C4' A A 523 " pdb=" O3' A A 523 " pdb=" C2' A A 523 " both_signs ideal model delta sigma weight residual False -2.48 -2.05 -0.43 2.00e-01 2.50e+01 4.63e+00 chirality pdb=" CB VAL X 147 " pdb=" CA VAL X 147 " pdb=" CG1 VAL X 147 " pdb=" CG2 VAL X 147 " both_signs ideal model delta sigma weight residual False -2.63 -2.30 -0.33 2.00e-01 2.50e+01 2.67e+00 ... (remaining 6606 not shown) Planarity restraints: 2993 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C5' 2MG A1516 " -0.015 2.00e-02 2.50e+03 4.42e-01 4.40e+03 pdb=" C4' 2MG A1516 " 0.403 2.00e-02 2.50e+03 pdb=" O4' 2MG A1516 " 0.392 2.00e-02 2.50e+03 pdb=" C3' 2MG A1516 " -0.541 2.00e-02 2.50e+03 pdb=" O3' 2MG A1516 " -0.336 2.00e-02 2.50e+03 pdb=" C2' 2MG A1516 " -0.286 2.00e-02 2.50e+03 pdb=" O2' 2MG A1516 " 0.720 2.00e-02 2.50e+03 pdb=" C1' 2MG A1516 " 0.269 2.00e-02 2.50e+03 pdb=" N9 2MG A1516 " -0.606 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C6 MA6 A1519 " -0.123 2.00e-02 2.50e+03 2.03e-01 4.14e+02 pdb=" N6 MA6 A1519 " 0.352 2.00e-02 2.50e+03 pdb=" C10 MA6 A1519 " -0.117 2.00e-02 2.50e+03 pdb=" C9 MA6 A1519 " -0.112 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C6 MA6 A1518 " -0.123 2.00e-02 2.50e+03 2.00e-01 4.02e+02 pdb=" N6 MA6 A1518 " 0.347 2.00e-02 2.50e+03 pdb=" C10 MA6 A1518 " -0.115 2.00e-02 2.50e+03 pdb=" C9 MA6 A1518 " -0.110 2.00e-02 2.50e+03 ... (remaining 2990 not shown) Histogram of nonbonded interaction distances: 1.63 - 2.28: 194 2.28 - 2.94: 15454 2.94 - 3.59: 62765 3.59 - 4.25: 101343 4.25 - 4.90: 134645 Nonbonded interactions: 314401 Sorted by model distance: nonbonded pdb=" OP2 C A 175 " pdb="MG MG A1631 " model vdw 1.629 2.170 nonbonded pdb=" OP1 A A 572 " pdb="MG MG A1626 " model vdw 1.678 2.170 nonbonded pdb=" OP1 U A 387 " pdb="MG MG A1604 " model vdw 1.682 2.170 nonbonded pdb=" CB LEU X 36 " pdb=" CD2 LEU X 74 " model vdw 1.724 3.860 nonbonded pdb=" OP1 C A 578 " pdb="MG MG A1642 " model vdw 1.728 2.170 ... (remaining 314396 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 2.870 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 13.860 Check model and map are aligned: 0.440 Set scattering table: 0.260 Process input model: 112.420 Find NCS groups from input model: 0.680 Set up NCS constraints: 0.090 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:3.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 133.860 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8920 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 0.158 35018 Z= 0.527 Angle : 0.799 18.673 52122 Z= 0.460 Chirality : 0.046 0.522 6609 Planarity : 0.011 0.442 2993 Dihedral : 23.493 179.264 19701 Min Nonbonded Distance : 1.629 Molprobity Statistics. All-atom Clashscore : 25.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.14 % Favored : 91.86 % Rotamer: Outliers : 0.00 % Allowed : 10.66 % Favored : 89.34 % Cbeta Deviations : 0.22 % 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: -3.73 (0.19), residues: 1425 helix: -2.64 (0.18), residues: 528 sheet: -2.28 (0.30), residues: 280 loop : -2.22 (0.22), residues: 617 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP Q 73 HIS 0.009 0.001 HIS F 11 PHE 0.015 0.002 PHE X 94 TYR 0.012 0.002 TYR K 77 ARG 0.010 0.001 ARG T 74 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2850 Ramachandran restraints generated. 1425 Oldfield, 0 Emsley, 1425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2850 Ramachandran restraints generated. 1425 Oldfield, 0 Emsley, 1425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 391 residues out of total 1201 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 391 time to evaluate : 2.016 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: symmetry clash 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: symmetry clash 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 74 ASN cc_start: 0.9471 (m110) cc_final: 0.9208 (m110) REVERT: D 124 MET cc_start: 0.8676 (mtm) cc_final: 0.8299 (mtm) REVERT: D 164 GLN cc_start: 0.8997 (mp10) cc_final: 0.8750 (mp10) REVERT: D 206 LYS cc_start: 0.9308 (ptmt) cc_final: 0.9048 (ttmm) REVERT: E 10 GLU cc_start: 0.8429 (pp20) cc_final: 0.7957 (pp20) REVERT: E 12 GLN cc_start: 0.9032 (tt0) cc_final: 0.8628 (mp10) REVERT: E 13 GLU cc_start: 0.8768 (mp0) cc_final: 0.8480 (mp0) REVERT: E 45 ARG cc_start: 0.8718 (ttt90) cc_final: 0.7921 (ttt90) REVERT: E 60 ILE cc_start: 0.9549 (tt) cc_final: 0.9224 (pt) REVERT: E 71 MET cc_start: 0.7950 (mtp) cc_final: 0.7679 (ttp) REVERT: E 116 GLU cc_start: 0.9263 (tp30) cc_final: 0.9001 (tm-30) REVERT: F 6 ILE cc_start: 0.9232 (mp) cc_final: 0.8997 (mp) REVERT: F 9 MET cc_start: 0.8655 (mtm) cc_final: 0.8430 (mtm) REVERT: F 56 LYS cc_start: 0.9027 (tptp) cc_final: 0.8764 (tppt) REVERT: F 72 ASP cc_start: 0.9233 (m-30) cc_final: 0.8984 (m-30) REVERT: F 74 LEU cc_start: 0.9545 (tp) cc_final: 0.9294 (tp) REVERT: F 82 ASP cc_start: 0.9185 (p0) cc_final: 0.8956 (p0) REVERT: F 88 MET cc_start: 0.8298 (tmm) cc_final: 0.8071 (tmm) REVERT: H 43 GLU cc_start: 0.9151 (mm-30) cc_final: 0.8807 (mm-30) REVERT: H 60 GLU cc_start: 0.8796 (tm-30) cc_final: 0.8583 (tm-30) REVERT: H 111 MET cc_start: 0.8661 (pmm) cc_final: 0.8106 (pmm) REVERT: K 31 ILE cc_start: 0.9643 (mt) cc_final: 0.9377 (tp) REVERT: L 49 LEU cc_start: 0.8537 (mt) cc_final: 0.7926 (mm) REVERT: L 81 LEU cc_start: 0.9636 (tp) cc_final: 0.9379 (tp) REVERT: O 58 ARG cc_start: 0.8930 (mtp180) cc_final: 0.8646 (ttt180) REVERT: Q 34 TYR cc_start: 0.9212 (m-80) cc_final: 0.8655 (m-10) REVERT: Q 80 GLU cc_start: 0.8219 (tm-30) cc_final: 0.7910 (tm-30) REVERT: R 42 SER cc_start: 0.9430 (p) cc_final: 0.9106 (p) REVERT: T 12 ILE cc_start: 0.9686 (mt) cc_final: 0.9470 (mt) REVERT: U 10 GLU cc_start: 0.6931 (pt0) cc_final: 0.6494 (pm20) REVERT: U 12 PHE cc_start: 0.6597 (t80) cc_final: 0.6163 (t80) REVERT: U 20 LYS cc_start: 0.9323 (ttmt) cc_final: 0.9027 (ttpp) REVERT: U 46 LYS cc_start: 0.9749 (ptmt) cc_final: 0.9442 (mmtm) REVERT: U 54 LYS cc_start: 0.9505 (ttpp) cc_final: 0.9290 (ttpp) REVERT: X 41 ASP cc_start: 0.8249 (t0) cc_final: 0.7935 (t70) outliers start: 0 outliers final: 0 residues processed: 391 average time/residue: 0.5494 time to fit residues: 316.1885 Evaluate side-chains 303 residues out of total 1201 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 303 time to evaluate : 1.753 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 199 optimal weight: 8.9990 chunk 178 optimal weight: 7.9990 chunk 99 optimal weight: 0.9990 chunk 61 optimal weight: 8.9990 chunk 120 optimal weight: 0.9980 chunk 95 optimal weight: 9.9990 chunk 184 optimal weight: 2.9990 chunk 71 optimal weight: 10.0000 chunk 112 optimal weight: 4.9990 chunk 137 optimal weight: 5.9990 chunk 214 optimal weight: 1.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 146 ASN O 38 HIS P 29 ASN ** R 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 3 ASN ** T 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 70 ASN T 78 ASN ** U 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8861 moved from start: 0.2128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 35018 Z= 0.203 Angle : 0.580 11.914 52122 Z= 0.307 Chirality : 0.034 0.252 6609 Planarity : 0.005 0.119 2993 Dihedral : 23.972 178.964 16843 Min Nonbonded Distance : 1.861 Molprobity Statistics. All-atom Clashscore : 20.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 2.50 % Allowed : 20.07 % Favored : 77.44 % 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: -2.05 (0.21), residues: 1425 helix: -0.75 (0.21), residues: 536 sheet: -1.86 (0.30), residues: 272 loop : -1.53 (0.24), residues: 617 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP X 113 HIS 0.006 0.001 HIS F 11 PHE 0.016 0.001 PHE F 8 TYR 0.011 0.001 TYR R 70 ARG 0.006 0.000 ARG O 88 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2850 Ramachandran restraints generated. 1425 Oldfield, 0 Emsley, 1425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2850 Ramachandran restraints generated. 1425 Oldfield, 0 Emsley, 1425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 382 residues out of total 1201 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 352 time to evaluate : 1.920 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: symmetry clash 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 73 ARG cc_start: 0.9263 (ptm-80) cc_final: 0.8837 (ttp80) REVERT: D 74 ASN cc_start: 0.9310 (m110) cc_final: 0.9089 (m110) REVERT: D 105 MET cc_start: 0.9255 (mtt) cc_final: 0.9051 (mtt) REVERT: D 124 MET cc_start: 0.8591 (mtm) cc_final: 0.8348 (mtm) REVERT: D 164 GLN cc_start: 0.9040 (mp10) cc_final: 0.8732 (mp10) REVERT: D 206 LYS cc_start: 0.9171 (ptmt) cc_final: 0.8941 (ttmm) REVERT: E 12 GLN cc_start: 0.9044 (tt0) cc_final: 0.8672 (mp10) REVERT: E 13 GLU cc_start: 0.8729 (mp0) cc_final: 0.8407 (mp0) REVERT: E 36 LEU cc_start: 0.9256 (tp) cc_final: 0.9052 (tt) REVERT: E 45 ARG cc_start: 0.8651 (ttt90) cc_final: 0.8117 (ttt90) REVERT: E 64 MET cc_start: 0.9372 (OUTLIER) cc_final: 0.9124 (tpp) REVERT: E 97 GLN cc_start: 0.8957 (pt0) cc_final: 0.8607 (pt0) REVERT: F 82 ASP cc_start: 0.9139 (p0) cc_final: 0.8933 (p0) REVERT: F 88 MET cc_start: 0.8380 (tmm) cc_final: 0.8096 (tmm) REVERT: H 43 GLU cc_start: 0.9030 (mm-30) cc_final: 0.8689 (mm-30) REVERT: H 59 LEU cc_start: 0.9429 (tp) cc_final: 0.9186 (tp) REVERT: H 101 ILE cc_start: 0.9541 (mm) cc_final: 0.9229 (mm) REVERT: H 111 MET cc_start: 0.8517 (pmm) cc_final: 0.8254 (pmm) REVERT: L 62 GLU cc_start: 0.8624 (tt0) cc_final: 0.8148 (tp30) REVERT: Q 34 TYR cc_start: 0.9151 (m-80) cc_final: 0.8627 (m-10) REVERT: Q 80 GLU cc_start: 0.8283 (tm-30) cc_final: 0.8038 (tm-30) REVERT: T 12 ILE cc_start: 0.9624 (mt) cc_final: 0.9376 (mm) REVERT: T 18 ARG cc_start: 0.9252 (ttp80) cc_final: 0.8975 (ttp80) REVERT: T 29 ARG cc_start: 0.9018 (ptp-110) cc_final: 0.7925 (ptp-110) REVERT: U 12 PHE cc_start: 0.6642 (t80) cc_final: 0.6145 (t80) REVERT: U 19 PHE cc_start: 0.9044 (t80) cc_final: 0.8824 (t80) REVERT: U 20 LYS cc_start: 0.9484 (ttmt) cc_final: 0.9151 (ttpp) REVERT: X 41 ASP cc_start: 0.8156 (t0) cc_final: 0.7815 (t0) outliers start: 30 outliers final: 17 residues processed: 362 average time/residue: 0.5406 time to fit residues: 297.4602 Evaluate side-chains 323 residues out of total 1201 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 305 time to evaluate : 1.629 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 17 THR Chi-restraints excluded: chain D residue 29 ASP Chi-restraints excluded: chain D residue 142 VAL Chi-restraints excluded: chain E residue 64 MET Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain H residue 9 ASP Chi-restraints excluded: chain H residue 74 SER Chi-restraints excluded: chain K residue 16 VAL Chi-restraints excluded: chain K residue 96 THR Chi-restraints excluded: chain L residue 16 VAL Chi-restraints excluded: chain L residue 97 THR Chi-restraints excluded: chain P residue 69 ASP Chi-restraints excluded: chain Q residue 38 ILE Chi-restraints excluded: chain X residue 83 ARG Chi-restraints excluded: chain X residue 121 ASP Chi-restraints excluded: chain X residue 135 VAL Chi-restraints excluded: chain X residue 149 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 119 optimal weight: 5.9990 chunk 66 optimal weight: 10.0000 chunk 178 optimal weight: 6.9990 chunk 145 optimal weight: 0.7980 chunk 59 optimal weight: 10.0000 chunk 214 optimal weight: 4.9990 chunk 231 optimal weight: 5.9990 chunk 191 optimal weight: 0.9990 chunk 212 optimal weight: 0.9990 chunk 73 optimal weight: 10.0000 chunk 172 optimal weight: 8.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 71 GLN D 74 ASN P 29 ASN ** R 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 54 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8852 moved from start: 0.2589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 35018 Z= 0.207 Angle : 0.553 11.768 52122 Z= 0.295 Chirality : 0.032 0.252 6609 Planarity : 0.005 0.117 2993 Dihedral : 23.799 178.704 16843 Min Nonbonded Distance : 1.849 Molprobity Statistics. All-atom Clashscore : 20.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 3.25 % Allowed : 23.23 % Favored : 73.52 % 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: -1.36 (0.22), residues: 1425 helix: 0.02 (0.22), residues: 542 sheet: -1.52 (0.31), residues: 262 loop : -1.36 (0.24), residues: 621 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.003 TRP F 42 HIS 0.005 0.001 HIS F 11 PHE 0.017 0.001 PHE X 150 TYR 0.011 0.001 TYR R 32 ARG 0.007 0.001 ARG L 94 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2850 Ramachandran restraints generated. 1425 Oldfield, 0 Emsley, 1425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2850 Ramachandran restraints generated. 1425 Oldfield, 0 Emsley, 1425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 371 residues out of total 1201 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 332 time to evaluate : 2.196 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: symmetry clash 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 73 ARG cc_start: 0.9288 (ptm-80) cc_final: 0.9032 (ttp80) REVERT: D 74 ASN cc_start: 0.9398 (m-40) cc_final: 0.9137 (m110) REVERT: D 124 MET cc_start: 0.8660 (mtm) cc_final: 0.8411 (mtm) REVERT: D 164 GLN cc_start: 0.9048 (mp10) cc_final: 0.8727 (mp10) REVERT: D 206 LYS cc_start: 0.9170 (ptmt) cc_final: 0.8955 (ttmm) REVERT: E 26 LYS cc_start: 0.9463 (tptp) cc_final: 0.8950 (mmmm) REVERT: E 45 ARG cc_start: 0.8626 (ttt90) cc_final: 0.8116 (ttt90) REVERT: E 64 MET cc_start: 0.9384 (OUTLIER) cc_final: 0.9028 (tpp) REVERT: E 66 LYS cc_start: 0.8990 (mtmm) cc_final: 0.8678 (mtmm) REVERT: E 71 MET cc_start: 0.7555 (mtp) cc_final: 0.7172 (ttt) REVERT: E 97 GLN cc_start: 0.8983 (pt0) cc_final: 0.8622 (pt0) REVERT: E 116 GLU cc_start: 0.8422 (tm-30) cc_final: 0.7940 (tm-30) REVERT: F 5 GLU cc_start: 0.8643 (mm-30) cc_final: 0.8194 (mm-30) REVERT: F 9 MET cc_start: 0.8608 (mtm) cc_final: 0.8378 (mtm) REVERT: F 82 ASP cc_start: 0.9146 (p0) cc_final: 0.8926 (p0) REVERT: F 88 MET cc_start: 0.8443 (tmm) cc_final: 0.8061 (tmm) REVERT: H 43 GLU cc_start: 0.8946 (mm-30) cc_final: 0.8584 (mm-30) REVERT: H 101 ILE cc_start: 0.9565 (mm) cc_final: 0.9245 (mm) REVERT: H 111 MET cc_start: 0.8512 (pmm) cc_final: 0.8265 (pmm) REVERT: K 38 GLN cc_start: 0.9370 (mp10) cc_final: 0.9072 (mp10) REVERT: L 62 GLU cc_start: 0.8635 (tt0) cc_final: 0.8172 (tp30) REVERT: O 28 GLN cc_start: 0.9315 (OUTLIER) cc_final: 0.8368 (mp10) REVERT: Q 30 LYS cc_start: 0.9253 (ttpp) cc_final: 0.8888 (ttpp) REVERT: Q 34 TYR cc_start: 0.9166 (m-80) cc_final: 0.8588 (m-10) REVERT: R 16 GLU cc_start: 0.9297 (mm-30) cc_final: 0.9081 (mp0) REVERT: T 18 ARG cc_start: 0.9256 (ttp80) cc_final: 0.8966 (ttp80) REVERT: U 12 PHE cc_start: 0.6799 (t80) cc_final: 0.6163 (t80) REVERT: U 54 LYS cc_start: 0.9432 (ptmt) cc_final: 0.9113 (pttp) REVERT: X 37 ARG cc_start: 0.8055 (mtm-85) cc_final: 0.7839 (mtm-85) REVERT: X 41 ASP cc_start: 0.8240 (t0) cc_final: 0.7940 (t0) REVERT: X 53 ASP cc_start: 0.9411 (m-30) cc_final: 0.9062 (p0) REVERT: X 74 LEU cc_start: 0.9002 (OUTLIER) cc_final: 0.8754 (pp) REVERT: X 114 GLN cc_start: 0.8315 (tt0) cc_final: 0.8106 (tm-30) outliers start: 39 outliers final: 33 residues processed: 348 average time/residue: 0.5037 time to fit residues: 266.8722 Evaluate side-chains 341 residues out of total 1201 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 305 time to evaluate : 1.907 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 17 THR Chi-restraints excluded: chain D residue 29 ASP Chi-restraints excluded: chain D residue 142 VAL Chi-restraints excluded: chain E residue 64 MET Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 130 SER Chi-restraints excluded: chain F residue 10 VAL Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain H residue 9 ASP Chi-restraints excluded: chain H residue 61 LEU Chi-restraints excluded: chain H residue 74 SER Chi-restraints excluded: chain H residue 103 VAL Chi-restraints excluded: chain H residue 129 VAL Chi-restraints excluded: chain K residue 96 THR Chi-restraints excluded: chain L residue 16 VAL Chi-restraints excluded: chain L residue 79 VAL Chi-restraints excluded: chain L residue 97 THR Chi-restraints excluded: chain O residue 28 GLN Chi-restraints excluded: chain P residue 19 VAL Chi-restraints excluded: chain P residue 69 ASP Chi-restraints excluded: chain Q residue 17 MET Chi-restraints excluded: chain Q residue 38 ILE Chi-restraints excluded: chain Q residue 42 THR Chi-restraints excluded: chain Q residue 57 ASP Chi-restraints excluded: chain Q residue 58 VAL Chi-restraints excluded: chain R residue 42 SER Chi-restraints excluded: chain R residue 68 LEU Chi-restraints excluded: chain R residue 71 THR Chi-restraints excluded: chain U residue 32 VAL Chi-restraints excluded: chain X residue 40 ILE Chi-restraints excluded: chain X residue 47 ASN Chi-restraints excluded: chain X residue 74 LEU Chi-restraints excluded: chain X residue 83 ARG Chi-restraints excluded: chain X residue 121 ASP Chi-restraints excluded: chain X residue 135 VAL Chi-restraints excluded: chain X residue 149 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 212 optimal weight: 4.9990 chunk 161 optimal weight: 5.9990 chunk 111 optimal weight: 0.4980 chunk 23 optimal weight: 10.0000 chunk 102 optimal weight: 0.9990 chunk 144 optimal weight: 2.9990 chunk 215 optimal weight: 20.0000 chunk 228 optimal weight: 8.9990 chunk 112 optimal weight: 1.9990 chunk 204 optimal weight: 8.9990 chunk 61 optimal weight: 10.0000 overall best weight: 2.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 70 ASN ** R 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 54 GLN T 78 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8834 moved from start: 0.2968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 35018 Z= 0.182 Angle : 0.538 11.870 52122 Z= 0.286 Chirality : 0.031 0.238 6609 Planarity : 0.004 0.116 2993 Dihedral : 23.704 178.473 16843 Min Nonbonded Distance : 1.867 Molprobity Statistics. All-atom Clashscore : 18.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 3.50 % Allowed : 24.81 % Favored : 71.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.09 (0.22), residues: 1425 helix: 0.24 (0.22), residues: 535 sheet: -1.36 (0.31), residues: 257 loop : -1.19 (0.24), residues: 633 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.003 TRP F 42 HIS 0.005 0.001 HIS X 56 PHE 0.017 0.001 PHE E 33 TYR 0.018 0.001 TYR D 135 ARG 0.008 0.000 ARG F 45 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2850 Ramachandran restraints generated. 1425 Oldfield, 0 Emsley, 1425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2850 Ramachandran restraints generated. 1425 Oldfield, 0 Emsley, 1425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 369 residues out of total 1201 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 327 time to evaluate : 2.090 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: symmetry clash 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 73 ARG cc_start: 0.9275 (ptm-80) cc_final: 0.8986 (ttp80) REVERT: D 74 ASN cc_start: 0.9393 (m-40) cc_final: 0.8983 (m110) REVERT: D 124 MET cc_start: 0.8668 (mtm) cc_final: 0.8407 (mtm) REVERT: D 164 GLN cc_start: 0.9013 (mp10) cc_final: 0.8706 (mp10) REVERT: D 206 LYS cc_start: 0.9144 (ptmt) cc_final: 0.8941 (ttmm) REVERT: E 64 MET cc_start: 0.9390 (OUTLIER) cc_final: 0.9165 (mmm) REVERT: E 97 GLN cc_start: 0.8958 (pt0) cc_final: 0.8589 (pt0) REVERT: F 9 MET cc_start: 0.8589 (mtm) cc_final: 0.8330 (mtm) REVERT: F 82 ASP cc_start: 0.9175 (p0) cc_final: 0.8963 (p0) REVERT: F 88 MET cc_start: 0.8453 (tmm) cc_final: 0.8052 (tmm) REVERT: H 43 GLU cc_start: 0.9007 (mm-30) cc_final: 0.8605 (mm-30) REVERT: H 101 ILE cc_start: 0.9566 (mm) cc_final: 0.9232 (mm) REVERT: H 111 MET cc_start: 0.8553 (pmm) cc_final: 0.8323 (pmm) REVERT: K 38 GLN cc_start: 0.9346 (mp10) cc_final: 0.9049 (mp10) REVERT: L 62 GLU cc_start: 0.8610 (tt0) cc_final: 0.8180 (tp30) REVERT: O 28 GLN cc_start: 0.9305 (OUTLIER) cc_final: 0.8323 (mp10) REVERT: P 75 ILE cc_start: 0.9453 (mt) cc_final: 0.9252 (mp) REVERT: Q 30 LYS cc_start: 0.9268 (ttpp) cc_final: 0.8885 (ttpp) REVERT: Q 34 TYR cc_start: 0.9111 (m-80) cc_final: 0.8629 (m-10) REVERT: T 18 ARG cc_start: 0.9252 (ttp80) cc_final: 0.8954 (ttp80) REVERT: T 31 PHE cc_start: 0.9112 (m-80) cc_final: 0.8733 (m-10) REVERT: U 12 PHE cc_start: 0.6739 (t80) cc_final: 0.6126 (t80) REVERT: U 54 LYS cc_start: 0.9449 (ptmt) cc_final: 0.9112 (pttp) REVERT: X 41 ASP cc_start: 0.8237 (t0) cc_final: 0.7918 (t0) REVERT: X 114 GLN cc_start: 0.8231 (tt0) cc_final: 0.7984 (tm-30) outliers start: 42 outliers final: 34 residues processed: 349 average time/residue: 0.4928 time to fit residues: 262.5102 Evaluate side-chains 337 residues out of total 1201 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 301 time to evaluate : 1.947 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 29 ASP Chi-restraints excluded: chain E residue 64 MET Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 134 ILE Chi-restraints excluded: chain F residue 10 VAL Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain H residue 9 ASP Chi-restraints excluded: chain H residue 61 LEU Chi-restraints excluded: chain H residue 74 SER Chi-restraints excluded: chain H residue 103 VAL Chi-restraints excluded: chain H residue 104 VAL Chi-restraints excluded: chain H residue 129 VAL Chi-restraints excluded: chain K residue 16 VAL Chi-restraints excluded: chain K residue 96 THR Chi-restraints excluded: chain K residue 110 ILE Chi-restraints excluded: chain K residue 119 ASN Chi-restraints excluded: chain L residue 16 VAL Chi-restraints excluded: chain L residue 79 VAL Chi-restraints excluded: chain L residue 97 THR Chi-restraints excluded: chain O residue 28 GLN Chi-restraints excluded: chain P residue 19 VAL Chi-restraints excluded: chain P residue 55 ASP Chi-restraints excluded: chain P residue 59 HIS Chi-restraints excluded: chain Q residue 29 VAL Chi-restraints excluded: chain Q residue 38 ILE Chi-restraints excluded: chain Q residue 42 THR Chi-restraints excluded: chain Q residue 57 ASP Chi-restraints excluded: chain Q residue 58 VAL Chi-restraints excluded: chain R residue 42 SER Chi-restraints excluded: chain R residue 68 LEU Chi-restraints excluded: chain U residue 3 VAL Chi-restraints excluded: chain X residue 40 ILE Chi-restraints excluded: chain X residue 83 ARG Chi-restraints excluded: chain X residue 121 ASP Chi-restraints excluded: chain X residue 135 VAL Chi-restraints excluded: chain X residue 149 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 189 optimal weight: 3.9990 chunk 129 optimal weight: 7.9990 chunk 3 optimal weight: 10.0000 chunk 169 optimal weight: 50.0000 chunk 94 optimal weight: 10.0000 chunk 194 optimal weight: 0.6980 chunk 157 optimal weight: 20.0000 chunk 0 optimal weight: 10.0000 chunk 116 optimal weight: 7.9990 chunk 204 optimal weight: 7.9990 chunk 57 optimal weight: 10.0000 overall best weight: 5.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 71 GLN K 64 GLN R 52 GLN R 54 GLN ** T 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 70 ASN ** X 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8882 moved from start: 0.2704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.060 35018 Z= 0.366 Angle : 0.637 11.875 52122 Z= 0.335 Chirality : 0.036 0.237 6609 Planarity : 0.005 0.117 2993 Dihedral : 23.785 178.687 16843 Min Nonbonded Distance : 1.786 Molprobity Statistics. All-atom Clashscore : 24.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.40 % Favored : 94.60 % Rotamer: Outliers : 4.75 % Allowed : 25.40 % Favored : 69.86 % 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: -1.24 (0.22), residues: 1425 helix: 0.04 (0.22), residues: 536 sheet: -1.49 (0.30), residues: 267 loop : -1.15 (0.24), residues: 622 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.059 0.004 TRP F 42 HIS 0.006 0.001 HIS F 11 PHE 0.019 0.002 PHE E 33 TYR 0.013 0.002 TYR D 51 ARG 0.005 0.001 ARG R 43 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2850 Ramachandran restraints generated. 1425 Oldfield, 0 Emsley, 1425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2850 Ramachandran restraints generated. 1425 Oldfield, 0 Emsley, 1425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 361 residues out of total 1201 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 304 time to evaluate : 1.900 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: symmetry clash 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: symmetry clash revert: symmetry clash REVERT: D 73 ARG cc_start: 0.9357 (ptm-80) cc_final: 0.9055 (ttp80) REVERT: D 74 ASN cc_start: 0.9443 (m-40) cc_final: 0.9019 (m110) REVERT: D 124 MET cc_start: 0.8739 (mtm) cc_final: 0.8427 (mtm) REVERT: D 164 GLN cc_start: 0.9001 (mp10) cc_final: 0.8711 (mp10) REVERT: D 206 LYS cc_start: 0.9276 (ptmt) cc_final: 0.9051 (ttmm) REVERT: E 26 LYS cc_start: 0.9433 (mmmt) cc_final: 0.8896 (mmmm) REVERT: E 64 MET cc_start: 0.9431 (tpt) cc_final: 0.9140 (mmm) REVERT: E 97 GLN cc_start: 0.9059 (pt0) cc_final: 0.8833 (pt0) REVERT: F 82 ASP cc_start: 0.9197 (p0) cc_final: 0.8975 (p0) REVERT: F 88 MET cc_start: 0.8424 (tmm) cc_final: 0.7988 (tmm) REVERT: H 43 GLU cc_start: 0.8922 (mm-30) cc_final: 0.8579 (mm-30) REVERT: H 101 ILE cc_start: 0.9568 (mm) cc_final: 0.9241 (mm) REVERT: H 111 MET cc_start: 0.8620 (pmm) cc_final: 0.8267 (pmm) REVERT: K 38 GLN cc_start: 0.9358 (mp10) cc_final: 0.9026 (mp10) REVERT: O 28 GLN cc_start: 0.9353 (OUTLIER) cc_final: 0.8373 (mp10) REVERT: Q 52 GLU cc_start: 0.9154 (pm20) cc_final: 0.8938 (pm20) REVERT: T 40 GLU cc_start: 0.9181 (tm-30) cc_final: 0.8976 (tm-30) REVERT: U 12 PHE cc_start: 0.6901 (t80) cc_final: 0.6162 (t80) REVERT: U 54 LYS cc_start: 0.9454 (ptmt) cc_final: 0.9124 (pttp) REVERT: X 37 ARG cc_start: 0.8085 (mtm-85) cc_final: 0.7870 (mtm-85) REVERT: X 41 ASP cc_start: 0.8377 (t0) cc_final: 0.8033 (t0) REVERT: X 53 ASP cc_start: 0.9442 (m-30) cc_final: 0.9096 (p0) outliers start: 57 outliers final: 44 residues processed: 334 average time/residue: 0.4952 time to fit residues: 250.4820 Evaluate side-chains 329 residues out of total 1201 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 284 time to evaluate : 1.985 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 17 THR Chi-restraints excluded: chain D residue 29 ASP Chi-restraints excluded: chain E residue 34 THR Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 130 SER Chi-restraints excluded: chain E residue 134 ILE Chi-restraints excluded: chain F residue 47 LEU Chi-restraints excluded: chain F residue 59 TYR Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 89 VAL Chi-restraints excluded: chain F residue 92 THR Chi-restraints excluded: chain H residue 9 ASP Chi-restraints excluded: chain H residue 61 LEU Chi-restraints excluded: chain H residue 74 SER Chi-restraints excluded: chain H residue 103 VAL Chi-restraints excluded: chain H residue 129 VAL Chi-restraints excluded: chain K residue 16 VAL Chi-restraints excluded: chain K residue 64 GLN Chi-restraints excluded: chain K residue 96 THR Chi-restraints excluded: chain K residue 110 ILE Chi-restraints excluded: chain K residue 119 ASN Chi-restraints excluded: chain L residue 16 VAL Chi-restraints excluded: chain L residue 79 VAL Chi-restraints excluded: chain L residue 97 THR Chi-restraints excluded: chain O residue 28 GLN Chi-restraints excluded: chain O residue 59 MET Chi-restraints excluded: chain P residue 19 VAL Chi-restraints excluded: chain P residue 69 ASP Chi-restraints excluded: chain P residue 71 VAL Chi-restraints excluded: chain Q residue 17 MET Chi-restraints excluded: chain Q residue 29 VAL Chi-restraints excluded: chain Q residue 38 ILE Chi-restraints excluded: chain Q residue 42 THR Chi-restraints excluded: chain Q residue 57 ASP Chi-restraints excluded: chain Q residue 58 VAL Chi-restraints excluded: chain R residue 68 LEU Chi-restraints excluded: chain R residue 71 THR Chi-restraints excluded: chain U residue 3 VAL Chi-restraints excluded: chain X residue 40 ILE Chi-restraints excluded: chain X residue 47 ASN Chi-restraints excluded: chain X residue 50 ASP Chi-restraints excluded: chain X residue 83 ARG Chi-restraints excluded: chain X residue 105 MET Chi-restraints excluded: chain X residue 121 ASP Chi-restraints excluded: chain X residue 135 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 76 optimal weight: 10.0000 chunk 205 optimal weight: 7.9990 chunk 45 optimal weight: 10.0000 chunk 133 optimal weight: 5.9990 chunk 56 optimal weight: 10.0000 chunk 228 optimal weight: 8.9990 chunk 189 optimal weight: 8.9990 chunk 105 optimal weight: 9.9990 chunk 18 optimal weight: 10.0000 chunk 75 optimal weight: 10.0000 chunk 119 optimal weight: 7.9990 overall best weight: 7.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 71 GLN K 64 GLN ** K 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 70 ASN ** U 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8908 moved from start: 0.2621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.065 35018 Z= 0.491 Angle : 0.736 12.438 52122 Z= 0.384 Chirality : 0.040 0.253 6609 Planarity : 0.006 0.118 2993 Dihedral : 23.915 179.259 16843 Min Nonbonded Distance : 1.746 Molprobity Statistics. All-atom Clashscore : 29.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.04 % Favored : 93.96 % Rotamer: Outliers : 5.41 % Allowed : 27.31 % Favored : 67.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.59 (0.21), residues: 1425 helix: -0.38 (0.22), residues: 540 sheet: -1.69 (0.29), residues: 278 loop : -1.20 (0.25), residues: 607 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.068 0.004 TRP F 42 HIS 0.007 0.002 HIS F 11 PHE 0.018 0.002 PHE E 33 TYR 0.015 0.002 TYR D 51 ARG 0.008 0.001 ARG X 30 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2850 Ramachandran restraints generated. 1425 Oldfield, 0 Emsley, 1425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2850 Ramachandran restraints generated. 1425 Oldfield, 0 Emsley, 1425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 352 residues out of total 1201 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 287 time to evaluate : 2.032 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: symmetry clash 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 73 ARG cc_start: 0.9377 (ptm-80) cc_final: 0.9100 (ttp80) REVERT: D 74 ASN cc_start: 0.9458 (m-40) cc_final: 0.9035 (m110) REVERT: D 164 GLN cc_start: 0.9001 (mp10) cc_final: 0.8720 (mp10) REVERT: E 12 GLN cc_start: 0.8508 (tm-30) cc_final: 0.8196 (pp30) REVERT: E 64 MET cc_start: 0.9395 (OUTLIER) cc_final: 0.9038 (mmm) REVERT: F 9 MET cc_start: 0.8646 (mtm) cc_final: 0.8396 (mtm) REVERT: F 45 ARG cc_start: 0.8071 (ttm110) cc_final: 0.7728 (ttm110) REVERT: F 82 ASP cc_start: 0.9233 (p0) cc_final: 0.8993 (p0) REVERT: H 43 GLU cc_start: 0.9107 (mm-30) cc_final: 0.8646 (mm-30) REVERT: H 111 MET cc_start: 0.8613 (pmm) cc_final: 0.8272 (pmm) REVERT: O 28 GLN cc_start: 0.9341 (OUTLIER) cc_final: 0.8396 (mp10) REVERT: R 18 VAL cc_start: 0.8185 (OUTLIER) cc_final: 0.7937 (p) REVERT: T 18 ARG cc_start: 0.9277 (ttp80) cc_final: 0.9058 (ttp80) REVERT: U 39 GLU cc_start: 0.8423 (tt0) cc_final: 0.8204 (tt0) REVERT: U 54 LYS cc_start: 0.9471 (ptmt) cc_final: 0.9155 (pttp) outliers start: 65 outliers final: 53 residues processed: 325 average time/residue: 0.4980 time to fit residues: 246.0446 Evaluate side-chains 333 residues out of total 1201 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 277 time to evaluate : 2.064 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 17 THR Chi-restraints excluded: chain D residue 29 ASP Chi-restraints excluded: chain D residue 143 VAL Chi-restraints excluded: chain E residue 30 ILE Chi-restraints excluded: chain E residue 34 THR Chi-restraints excluded: chain E residue 64 MET Chi-restraints excluded: chain E residue 68 ARG Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 96 MET Chi-restraints excluded: chain E residue 130 SER Chi-restraints excluded: chain F residue 47 LEU Chi-restraints excluded: chain F residue 59 TYR Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 89 VAL Chi-restraints excluded: chain F residue 92 THR Chi-restraints excluded: chain H residue 9 ASP Chi-restraints excluded: chain H residue 61 LEU Chi-restraints excluded: chain H residue 74 SER Chi-restraints excluded: chain H residue 99 LEU Chi-restraints excluded: chain H residue 103 VAL Chi-restraints excluded: chain H residue 104 VAL Chi-restraints excluded: chain H residue 129 VAL Chi-restraints excluded: chain K residue 16 VAL Chi-restraints excluded: chain K residue 64 GLN Chi-restraints excluded: chain K residue 96 THR Chi-restraints excluded: chain K residue 110 ILE Chi-restraints excluded: chain K residue 119 ASN Chi-restraints excluded: chain L residue 16 VAL Chi-restraints excluded: chain L residue 55 VAL Chi-restraints excluded: chain L residue 97 THR Chi-restraints excluded: chain O residue 28 GLN Chi-restraints excluded: chain O residue 59 MET Chi-restraints excluded: chain P residue 19 VAL Chi-restraints excluded: chain P residue 69 ASP Chi-restraints excluded: chain P residue 71 VAL Chi-restraints excluded: chain Q residue 17 MET Chi-restraints excluded: chain Q residue 29 VAL Chi-restraints excluded: chain Q residue 38 ILE Chi-restraints excluded: chain Q residue 42 THR Chi-restraints excluded: chain Q residue 57 ASP Chi-restraints excluded: chain Q residue 79 VAL Chi-restraints excluded: chain R residue 18 VAL Chi-restraints excluded: chain R residue 68 LEU Chi-restraints excluded: chain R residue 71 THR Chi-restraints excluded: chain U residue 3 VAL Chi-restraints excluded: chain U residue 4 ILE Chi-restraints excluded: chain X residue 33 THR Chi-restraints excluded: chain X residue 40 ILE Chi-restraints excluded: chain X residue 47 ASN Chi-restraints excluded: chain X residue 50 ASP Chi-restraints excluded: chain X residue 74 LEU Chi-restraints excluded: chain X residue 83 ARG Chi-restraints excluded: chain X residue 105 MET Chi-restraints excluded: chain X residue 116 VAL Chi-restraints excluded: chain X residue 121 ASP Chi-restraints excluded: chain X residue 135 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 220 optimal weight: 2.9990 chunk 25 optimal weight: 10.0000 chunk 130 optimal weight: 1.9990 chunk 166 optimal weight: 8.9990 chunk 129 optimal weight: 5.9990 chunk 192 optimal weight: 0.9980 chunk 127 optimal weight: 4.9990 chunk 227 optimal weight: 5.9990 chunk 142 optimal weight: 0.9990 chunk 138 optimal weight: 6.9990 chunk 105 optimal weight: 0.8980 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 71 GLN K 101 ASN P 29 ASN R 54 GLN ** X 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8826 moved from start: 0.3364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 35018 Z= 0.165 Angle : 0.579 13.596 52122 Z= 0.301 Chirality : 0.032 0.221 6609 Planarity : 0.005 0.115 2993 Dihedral : 23.699 178.739 16843 Min Nonbonded Distance : 1.862 Molprobity Statistics. All-atom Clashscore : 18.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 3.83 % Allowed : 29.56 % Favored : 66.61 % 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: -1.02 (0.22), residues: 1425 helix: 0.16 (0.22), residues: 542 sheet: -1.42 (0.30), residues: 262 loop : -0.95 (0.26), residues: 621 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.003 TRP F 42 HIS 0.004 0.001 HIS F 11 PHE 0.018 0.001 PHE K 61 TYR 0.023 0.001 TYR L 38 ARG 0.006 0.001 ARG O 88 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2850 Ramachandran restraints generated. 1425 Oldfield, 0 Emsley, 1425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2850 Ramachandran restraints generated. 1425 Oldfield, 0 Emsley, 1425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 374 residues out of total 1201 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 328 time to evaluate : 1.777 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: symmetry clash 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: D 73 ARG cc_start: 0.9317 (ptm-80) cc_final: 0.8996 (ttp80) REVERT: D 74 ASN cc_start: 0.9396 (m-40) cc_final: 0.8982 (m110) REVERT: D 124 MET cc_start: 0.8760 (mtm) cc_final: 0.8450 (mtm) REVERT: D 164 GLN cc_start: 0.8991 (mp10) cc_final: 0.8695 (mp10) REVERT: E 64 MET cc_start: 0.9345 (OUTLIER) cc_final: 0.9039 (mmm) REVERT: F 9 MET cc_start: 0.8646 (mtm) cc_final: 0.8366 (mtm) REVERT: F 41 ASP cc_start: 0.8894 (t70) cc_final: 0.8675 (t0) REVERT: F 88 MET cc_start: 0.8543 (tmm) cc_final: 0.8040 (tmm) REVERT: H 43 GLU cc_start: 0.8885 (mm-30) cc_final: 0.8517 (mm-30) REVERT: H 101 ILE cc_start: 0.9565 (mm) cc_final: 0.9239 (mm) REVERT: H 111 MET cc_start: 0.8589 (pmm) cc_final: 0.8341 (pmm) REVERT: H 128 TYR cc_start: 0.8909 (m-80) cc_final: 0.8631 (m-80) REVERT: L 38 TYR cc_start: 0.9323 (p90) cc_final: 0.8989 (p90) REVERT: L 62 GLU cc_start: 0.8643 (tt0) cc_final: 0.8161 (tp30) REVERT: Q 27 ARG cc_start: 0.8674 (ptt-90) cc_final: 0.8451 (ptt-90) REVERT: R 16 GLU cc_start: 0.9239 (mm-30) cc_final: 0.9033 (mp0) REVERT: T 18 ARG cc_start: 0.9206 (ttp80) cc_final: 0.8964 (ttp80) REVERT: T 28 MET cc_start: 0.8920 (ppp) cc_final: 0.8603 (ppp) REVERT: T 31 PHE cc_start: 0.9064 (m-80) cc_final: 0.8701 (m-10) REVERT: U 54 LYS cc_start: 0.9470 (ptmt) cc_final: 0.9123 (pttp) REVERT: X 37 ARG cc_start: 0.8191 (mtm-85) cc_final: 0.7965 (mtm-85) REVERT: X 53 ASP cc_start: 0.9390 (m-30) cc_final: 0.9014 (p0) outliers start: 46 outliers final: 32 residues processed: 349 average time/residue: 0.5034 time to fit residues: 267.2438 Evaluate side-chains 329 residues out of total 1201 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 296 time to evaluate : 1.937 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 29 ASP Chi-restraints excluded: chain E residue 34 THR Chi-restraints excluded: chain E residue 64 MET Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 130 SER Chi-restraints excluded: chain E residue 142 ASP Chi-restraints excluded: chain F residue 59 TYR Chi-restraints excluded: chain F residue 89 VAL Chi-restraints excluded: chain F residue 92 THR Chi-restraints excluded: chain H residue 61 LEU Chi-restraints excluded: chain H residue 74 SER Chi-restraints excluded: chain H residue 103 VAL Chi-restraints excluded: chain H residue 104 VAL Chi-restraints excluded: chain K residue 96 THR Chi-restraints excluded: chain K residue 119 ASN Chi-restraints excluded: chain L residue 16 VAL Chi-restraints excluded: chain L residue 72 HIS Chi-restraints excluded: chain P residue 19 VAL Chi-restraints excluded: chain P residue 59 HIS Chi-restraints excluded: chain P residue 69 ASP Chi-restraints excluded: chain Q residue 12 VAL Chi-restraints excluded: chain Q residue 42 THR Chi-restraints excluded: chain Q residue 57 ASP Chi-restraints excluded: chain Q residue 58 VAL Chi-restraints excluded: chain R residue 71 THR Chi-restraints excluded: chain U residue 3 VAL Chi-restraints excluded: chain X residue 1 MET Chi-restraints excluded: chain X residue 40 ILE Chi-restraints excluded: chain X residue 74 LEU Chi-restraints excluded: chain X residue 83 ARG Chi-restraints excluded: chain X residue 105 MET Chi-restraints excluded: chain X residue 135 VAL Chi-restraints excluded: chain X residue 149 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 140 optimal weight: 10.0000 chunk 90 optimal weight: 10.0000 chunk 135 optimal weight: 4.9990 chunk 68 optimal weight: 10.0000 chunk 44 optimal weight: 10.0000 chunk 144 optimal weight: 4.9990 chunk 154 optimal weight: 9.9990 chunk 112 optimal weight: 0.9980 chunk 21 optimal weight: 10.0000 chunk 178 optimal weight: 0.9980 chunk 206 optimal weight: 5.9990 overall best weight: 3.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 71 GLN K 64 GLN P 29 ASN P 59 HIS ** U 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8856 moved from start: 0.3264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 35018 Z= 0.257 Angle : 0.601 12.001 52122 Z= 0.315 Chirality : 0.033 0.205 6609 Planarity : 0.005 0.116 2993 Dihedral : 23.684 178.509 16843 Min Nonbonded Distance : 1.840 Molprobity Statistics. All-atom Clashscore : 21.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer: Outliers : 4.00 % Allowed : 30.14 % Favored : 65.86 % 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: -0.97 (0.22), residues: 1425 helix: 0.12 (0.22), residues: 541 sheet: -1.26 (0.31), residues: 274 loop : -0.90 (0.26), residues: 610 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.003 TRP F 42 HIS 0.005 0.001 HIS F 11 PHE 0.015 0.001 PHE U 19 TYR 0.026 0.002 TYR D 51 ARG 0.013 0.001 ARG Q 11 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2850 Ramachandran restraints generated. 1425 Oldfield, 0 Emsley, 1425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2850 Ramachandran restraints generated. 1425 Oldfield, 0 Emsley, 1425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 352 residues out of total 1201 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 304 time to evaluate : 2.023 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: symmetry clash 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: D 73 ARG cc_start: 0.9341 (ptm-80) cc_final: 0.9025 (ttp80) REVERT: D 74 ASN cc_start: 0.9422 (m-40) cc_final: 0.8994 (m110) REVERT: D 103 TYR cc_start: 0.9391 (t80) cc_final: 0.9071 (t80) REVERT: D 124 MET cc_start: 0.8779 (mtm) cc_final: 0.8493 (mtm) REVERT: D 164 GLN cc_start: 0.8975 (mp10) cc_final: 0.8697 (mp10) REVERT: E 26 LYS cc_start: 0.9389 (mmmt) cc_final: 0.8903 (mmmm) REVERT: E 64 MET cc_start: 0.9381 (OUTLIER) cc_final: 0.9027 (mmm) REVERT: F 9 MET cc_start: 0.8605 (mtm) cc_final: 0.8366 (mtm) REVERT: F 41 ASP cc_start: 0.8929 (t70) cc_final: 0.8595 (t0) REVERT: F 88 MET cc_start: 0.8446 (tmm) cc_final: 0.8051 (tmm) REVERT: H 43 GLU cc_start: 0.8957 (mm-30) cc_final: 0.8468 (mm-30) REVERT: H 101 ILE cc_start: 0.9565 (mm) cc_final: 0.9245 (mm) REVERT: H 111 MET cc_start: 0.8522 (pmm) cc_final: 0.8275 (pmm) REVERT: K 97 ILE cc_start: 0.9728 (tt) cc_final: 0.9522 (pt) REVERT: L 38 TYR cc_start: 0.9349 (p90) cc_final: 0.8850 (p90) REVERT: L 62 GLU cc_start: 0.8677 (tt0) cc_final: 0.8188 (tp30) REVERT: O 28 GLN cc_start: 0.9322 (OUTLIER) cc_final: 0.8381 (mp10) REVERT: P 80 LYS cc_start: 0.9442 (pttm) cc_final: 0.9175 (pttm) REVERT: R 70 TYR cc_start: 0.8524 (m-10) cc_final: 0.8243 (m-10) REVERT: T 28 MET cc_start: 0.8964 (ppp) cc_final: 0.8730 (ppp) REVERT: T 31 PHE cc_start: 0.9123 (m-80) cc_final: 0.8748 (m-10) REVERT: T 39 ILE cc_start: 0.9562 (OUTLIER) cc_final: 0.9284 (tt) REVERT: U 54 LYS cc_start: 0.9499 (ptmt) cc_final: 0.9181 (pttp) REVERT: X 37 ARG cc_start: 0.8159 (mtm-85) cc_final: 0.7881 (mtm-85) REVERT: X 53 ASP cc_start: 0.9422 (m-30) cc_final: 0.9061 (p0) outliers start: 48 outliers final: 42 residues processed: 333 average time/residue: 0.5113 time to fit residues: 259.1061 Evaluate side-chains 338 residues out of total 1201 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 293 time to evaluate : 1.816 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 17 THR Chi-restraints excluded: chain D residue 29 ASP Chi-restraints excluded: chain E residue 34 THR Chi-restraints excluded: chain E residue 64 MET Chi-restraints excluded: chain E residue 94 VAL Chi-restraints excluded: chain E residue 130 SER Chi-restraints excluded: chain E residue 142 ASP Chi-restraints excluded: chain F residue 47 LEU Chi-restraints excluded: chain F residue 59 TYR Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 89 VAL Chi-restraints excluded: chain F residue 92 THR Chi-restraints excluded: chain H residue 61 LEU Chi-restraints excluded: chain H residue 74 SER Chi-restraints excluded: chain H residue 103 VAL Chi-restraints excluded: chain H residue 129 VAL Chi-restraints excluded: chain K residue 64 GLN Chi-restraints excluded: chain K residue 96 THR Chi-restraints excluded: chain K residue 110 ILE Chi-restraints excluded: chain K residue 119 ASN Chi-restraints excluded: chain L residue 16 VAL Chi-restraints excluded: chain L residue 39 THR Chi-restraints excluded: chain L residue 72 HIS Chi-restraints excluded: chain O residue 28 GLN Chi-restraints excluded: chain O residue 59 MET Chi-restraints excluded: chain P residue 19 VAL Chi-restraints excluded: chain P residue 59 HIS Chi-restraints excluded: chain P residue 69 ASP Chi-restraints excluded: chain Q residue 12 VAL Chi-restraints excluded: chain Q residue 42 THR Chi-restraints excluded: chain Q residue 57 ASP Chi-restraints excluded: chain Q residue 58 VAL Chi-restraints excluded: chain R residue 18 VAL Chi-restraints excluded: chain R residue 31 ASN Chi-restraints excluded: chain R residue 71 THR Chi-restraints excluded: chain T residue 39 ILE Chi-restraints excluded: chain T residue 59 ASP Chi-restraints excluded: chain U residue 3 VAL Chi-restraints excluded: chain X residue 3 THR Chi-restraints excluded: chain X residue 40 ILE Chi-restraints excluded: chain X residue 74 LEU Chi-restraints excluded: chain X residue 83 ARG Chi-restraints excluded: chain X residue 105 MET Chi-restraints excluded: chain X residue 121 ASP Chi-restraints excluded: chain X residue 135 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 217 optimal weight: 7.9990 chunk 198 optimal weight: 1.9990 chunk 211 optimal weight: 5.9990 chunk 127 optimal weight: 3.9990 chunk 92 optimal weight: 10.0000 chunk 166 optimal weight: 0.8980 chunk 65 optimal weight: 10.0000 chunk 191 optimal weight: 7.9990 chunk 200 optimal weight: 0.8980 chunk 139 optimal weight: 0.9990 chunk 224 optimal weight: 20.0000 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 64 GLN P 29 ASN ** U 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8821 moved from start: 0.3608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 35018 Z= 0.173 Angle : 0.577 15.977 52122 Z= 0.301 Chirality : 0.031 0.193 6609 Planarity : 0.005 0.115 2993 Dihedral : 23.620 178.202 16843 Min Nonbonded Distance : 1.886 Molprobity Statistics. All-atom Clashscore : 18.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 3.41 % Allowed : 31.22 % Favored : 65.36 % 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: -0.85 (0.22), residues: 1425 helix: 0.19 (0.22), residues: 542 sheet: -1.10 (0.32), residues: 269 loop : -0.87 (0.26), residues: 614 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.052 0.004 TRP F 42 HIS 0.013 0.001 HIS P 59 PHE 0.016 0.001 PHE U 19 TYR 0.023 0.001 TYR L 38 ARG 0.013 0.001 ARG F 45 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2850 Ramachandran restraints generated. 1425 Oldfield, 0 Emsley, 1425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2850 Ramachandran restraints generated. 1425 Oldfield, 0 Emsley, 1425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 362 residues out of total 1201 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 321 time to evaluate : 1.658 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: symmetry clash 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 73 ARG cc_start: 0.9308 (ptm-80) cc_final: 0.8980 (ttp80) REVERT: D 74 ASN cc_start: 0.9386 (m-40) cc_final: 0.8966 (m110) REVERT: D 103 TYR cc_start: 0.9355 (t80) cc_final: 0.9086 (t80) REVERT: D 124 MET cc_start: 0.8775 (mtm) cc_final: 0.8474 (mtm) REVERT: D 164 GLN cc_start: 0.8959 (mp10) cc_final: 0.8682 (mp10) REVERT: E 26 LYS cc_start: 0.9368 (mmmt) cc_final: 0.8841 (mmmm) REVERT: E 64 MET cc_start: 0.9340 (OUTLIER) cc_final: 0.9049 (mmm) REVERT: F 5 GLU cc_start: 0.8539 (mm-30) cc_final: 0.8053 (mm-30) REVERT: F 41 ASP cc_start: 0.8792 (t70) cc_final: 0.8461 (t0) REVERT: F 88 MET cc_start: 0.8420 (tmm) cc_final: 0.8061 (tmm) REVERT: H 42 GLU cc_start: 0.8474 (pp20) cc_final: 0.8243 (pp20) REVERT: H 43 GLU cc_start: 0.8800 (mm-30) cc_final: 0.8507 (mm-30) REVERT: H 101 ILE cc_start: 0.9519 (mm) cc_final: 0.9215 (mm) REVERT: H 111 MET cc_start: 0.8523 (pmm) cc_final: 0.8318 (pmm) REVERT: K 97 ILE cc_start: 0.9673 (tt) cc_final: 0.9456 (pt) REVERT: L 38 TYR cc_start: 0.9292 (p90) cc_final: 0.8696 (p90) REVERT: L 62 GLU cc_start: 0.8672 (tt0) cc_final: 0.8192 (tp30) REVERT: O 28 GLN cc_start: 0.9264 (OUTLIER) cc_final: 0.8296 (mp10) REVERT: P 48 GLU cc_start: 0.8187 (tm-30) cc_final: 0.7782 (pp20) REVERT: P 80 LYS cc_start: 0.9407 (pttm) cc_final: 0.9149 (pttm) REVERT: R 70 TYR cc_start: 0.8493 (m-10) cc_final: 0.8227 (m-10) REVERT: T 31 PHE cc_start: 0.9035 (m-80) cc_final: 0.8696 (m-10) REVERT: T 39 ILE cc_start: 0.9510 (OUTLIER) cc_final: 0.9228 (tt) REVERT: U 54 LYS cc_start: 0.9494 (ptmt) cc_final: 0.9177 (pttp) REVERT: X 26 ILE cc_start: 0.8684 (mm) cc_final: 0.8413 (mt) REVERT: X 37 ARG cc_start: 0.8180 (mtm-85) cc_final: 0.7950 (mtm-85) REVERT: X 53 ASP cc_start: 0.9358 (m-30) cc_final: 0.8968 (p0) outliers start: 41 outliers final: 37 residues processed: 347 average time/residue: 0.5107 time to fit residues: 266.7965 Evaluate side-chains 343 residues out of total 1201 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 303 time to evaluate : 1.994 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 17 THR Chi-restraints excluded: chain D residue 29 ASP Chi-restraints excluded: chain E residue 34 THR Chi-restraints excluded: chain E residue 64 MET Chi-restraints excluded: chain E residue 94 VAL Chi-restraints excluded: chain F residue 59 TYR Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 89 VAL Chi-restraints excluded: chain F residue 92 THR Chi-restraints excluded: chain H residue 61 LEU Chi-restraints excluded: chain H residue 74 SER Chi-restraints excluded: chain H residue 129 VAL Chi-restraints excluded: chain K residue 64 GLN Chi-restraints excluded: chain K residue 96 THR Chi-restraints excluded: chain K residue 110 ILE Chi-restraints excluded: chain K residue 119 ASN Chi-restraints excluded: chain L residue 16 VAL Chi-restraints excluded: chain L residue 55 VAL Chi-restraints excluded: chain L residue 72 HIS Chi-restraints excluded: chain L residue 97 THR Chi-restraints excluded: chain O residue 28 GLN Chi-restraints excluded: chain P residue 19 VAL Chi-restraints excluded: chain P residue 69 ASP Chi-restraints excluded: chain Q residue 12 VAL Chi-restraints excluded: chain Q residue 42 THR Chi-restraints excluded: chain Q residue 57 ASP Chi-restraints excluded: chain Q residue 58 VAL Chi-restraints excluded: chain R residue 18 VAL Chi-restraints excluded: chain R residue 71 THR Chi-restraints excluded: chain T residue 39 ILE Chi-restraints excluded: chain T residue 59 ASP Chi-restraints excluded: chain U residue 42 THR Chi-restraints excluded: chain X residue 3 THR Chi-restraints excluded: chain X residue 40 ILE Chi-restraints excluded: chain X residue 74 LEU Chi-restraints excluded: chain X residue 83 ARG Chi-restraints excluded: chain X residue 105 MET Chi-restraints excluded: chain X residue 121 ASP Chi-restraints excluded: chain X residue 135 VAL Chi-restraints excluded: chain X residue 149 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 136 optimal weight: 6.9990 chunk 106 optimal weight: 2.9990 chunk 155 optimal weight: 10.0000 chunk 235 optimal weight: 8.9990 chunk 216 optimal weight: 8.9990 chunk 187 optimal weight: 0.8980 chunk 19 optimal weight: 10.0000 chunk 144 optimal weight: 6.9990 chunk 114 optimal weight: 10.0000 chunk 148 optimal weight: 2.9990 chunk 199 optimal weight: 0.9980 overall best weight: 2.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 64 GLN P 59 HIS ** U 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8839 moved from start: 0.3559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 35018 Z= 0.226 Angle : 0.591 15.060 52122 Z= 0.310 Chirality : 0.032 0.276 6609 Planarity : 0.005 0.116 2993 Dihedral : 23.605 178.145 16843 Min Nonbonded Distance : 1.860 Molprobity Statistics. All-atom Clashscore : 20.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 4.08 % Allowed : 30.97 % Favored : 64.95 % 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: -0.86 (0.22), residues: 1425 helix: 0.12 (0.22), residues: 535 sheet: -1.02 (0.32), residues: 269 loop : -0.83 (0.26), residues: 621 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.059 0.004 TRP F 42 HIS 0.004 0.001 HIS F 11 PHE 0.015 0.001 PHE U 19 TYR 0.030 0.002 TYR D 51 ARG 0.009 0.001 ARG T 18 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2850 Ramachandran restraints generated. 1425 Oldfield, 0 Emsley, 1425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2850 Ramachandran restraints generated. 1425 Oldfield, 0 Emsley, 1425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 353 residues out of total 1201 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 304 time to evaluate : 2.238 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: symmetry clash 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: D 73 ARG cc_start: 0.9322 (ptm-80) cc_final: 0.9008 (ttp80) REVERT: D 74 ASN cc_start: 0.9402 (m-40) cc_final: 0.8972 (m110) REVERT: D 103 TYR cc_start: 0.9350 (t80) cc_final: 0.9066 (t80) REVERT: D 124 MET cc_start: 0.8758 (mtm) cc_final: 0.8474 (mtm) REVERT: D 164 GLN cc_start: 0.8944 (mp10) cc_final: 0.8658 (mp10) REVERT: E 26 LYS cc_start: 0.9386 (mmmt) cc_final: 0.8859 (mmmm) REVERT: E 36 LEU cc_start: 0.9596 (OUTLIER) cc_final: 0.9387 (pt) REVERT: E 71 MET cc_start: 0.8243 (tmm) cc_final: 0.7309 (tmm) REVERT: F 1 MET cc_start: 0.7775 (ttm) cc_final: 0.6835 (tmm) REVERT: F 9 MET cc_start: 0.8599 (mtm) cc_final: 0.8347 (mtm) REVERT: F 41 ASP cc_start: 0.8801 (t70) cc_final: 0.8501 (t0) REVERT: F 88 MET cc_start: 0.8415 (tmm) cc_final: 0.8046 (tmm) REVERT: H 42 GLU cc_start: 0.8387 (pp20) cc_final: 0.8127 (pp20) REVERT: H 43 GLU cc_start: 0.8793 (mm-30) cc_final: 0.8575 (mm-30) REVERT: H 61 LEU cc_start: 0.9383 (OUTLIER) cc_final: 0.9115 (mt) REVERT: H 101 ILE cc_start: 0.9525 (mm) cc_final: 0.9220 (mm) REVERT: H 111 MET cc_start: 0.8511 (pmm) cc_final: 0.8294 (pmm) REVERT: K 97 ILE cc_start: 0.9710 (tt) cc_final: 0.9497 (pt) REVERT: L 62 GLU cc_start: 0.8630 (tt0) cc_final: 0.8176 (tp30) REVERT: O 28 GLN cc_start: 0.9305 (OUTLIER) cc_final: 0.8361 (mp10) REVERT: P 48 GLU cc_start: 0.8101 (tm-30) cc_final: 0.7796 (pp20) REVERT: P 80 LYS cc_start: 0.9438 (pttm) cc_final: 0.9146 (pttm) REVERT: Q 77 ARG cc_start: 0.8280 (ptm160) cc_final: 0.7771 (ptm160) REVERT: T 31 PHE cc_start: 0.9060 (m-80) cc_final: 0.8699 (m-10) REVERT: T 39 ILE cc_start: 0.9516 (OUTLIER) cc_final: 0.9251 (tt) REVERT: U 19 PHE cc_start: 0.8645 (t80) cc_final: 0.8380 (t80) REVERT: U 54 LYS cc_start: 0.9518 (ptmt) cc_final: 0.9219 (pttp) REVERT: X 26 ILE cc_start: 0.8697 (mm) cc_final: 0.8440 (mt) REVERT: X 37 ARG cc_start: 0.8117 (mtm-85) cc_final: 0.7912 (mtm-85) REVERT: X 47 ASN cc_start: 0.8542 (OUTLIER) cc_final: 0.8210 (t0) REVERT: X 53 ASP cc_start: 0.9370 (m-30) cc_final: 0.8984 (p0) outliers start: 49 outliers final: 41 residues processed: 335 average time/residue: 0.5065 time to fit residues: 258.2029 Evaluate side-chains 346 residues out of total 1201 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 300 time to evaluate : 1.940 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 17 THR Chi-restraints excluded: chain D residue 29 ASP Chi-restraints excluded: chain D residue 143 VAL Chi-restraints excluded: chain E residue 34 THR Chi-restraints excluded: chain E residue 36 LEU Chi-restraints excluded: chain E residue 70 ASN Chi-restraints excluded: chain E residue 94 VAL Chi-restraints excluded: chain F residue 47 LEU Chi-restraints excluded: chain F residue 59 TYR Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 89 VAL Chi-restraints excluded: chain F residue 92 THR Chi-restraints excluded: chain H residue 61 LEU Chi-restraints excluded: chain H residue 74 SER Chi-restraints excluded: chain H residue 129 VAL Chi-restraints excluded: chain K residue 16 VAL Chi-restraints excluded: chain K residue 64 GLN Chi-restraints excluded: chain K residue 96 THR Chi-restraints excluded: chain K residue 110 ILE Chi-restraints excluded: chain K residue 119 ASN Chi-restraints excluded: chain L residue 16 VAL Chi-restraints excluded: chain L residue 20 ASN Chi-restraints excluded: chain L residue 72 HIS Chi-restraints excluded: chain L residue 97 THR Chi-restraints excluded: chain O residue 28 GLN Chi-restraints excluded: chain P residue 19 VAL Chi-restraints excluded: chain P residue 59 HIS Chi-restraints excluded: chain P residue 69 ASP Chi-restraints excluded: chain Q residue 12 VAL Chi-restraints excluded: chain Q residue 42 THR Chi-restraints excluded: chain Q residue 57 ASP Chi-restraints excluded: chain Q residue 58 VAL Chi-restraints excluded: chain R residue 18 VAL Chi-restraints excluded: chain R residue 65 LEU Chi-restraints excluded: chain R residue 71 THR Chi-restraints excluded: chain T residue 39 ILE Chi-restraints excluded: chain T residue 59 ASP Chi-restraints excluded: chain U residue 3 VAL Chi-restraints excluded: chain X residue 3 THR Chi-restraints excluded: chain X residue 40 ILE Chi-restraints excluded: chain X residue 47 ASN Chi-restraints excluded: chain X residue 74 LEU Chi-restraints excluded: chain X residue 83 ARG Chi-restraints excluded: chain X residue 105 MET Chi-restraints excluded: chain X residue 121 ASP Chi-restraints excluded: chain X residue 135 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 57 optimal weight: 10.0000 chunk 172 optimal weight: 5.9990 chunk 27 optimal weight: 10.0000 chunk 52 optimal weight: 10.0000 chunk 187 optimal weight: 0.9990 chunk 78 optimal weight: 10.0000 chunk 192 optimal weight: 0.9990 chunk 23 optimal weight: 10.0000 chunk 34 optimal weight: 10.0000 chunk 164 optimal weight: 0.5980 chunk 10 optimal weight: 10.0000 overall best weight: 3.7190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 71 GLN K 64 GLN ** U 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2959 r_free = 0.2959 target = 0.029879 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2645 r_free = 0.2645 target = 0.023473 restraints weight = 299590.195| |-----------------------------------------------------------------------------| r_work (start): 0.2630 rms_B_bonded: 2.50 r_work: 0.2503 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.2503 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8989 moved from start: 0.3508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 35018 Z= 0.262 Angle : 0.613 12.771 52122 Z= 0.322 Chirality : 0.033 0.324 6609 Planarity : 0.005 0.116 2993 Dihedral : 23.619 178.124 16843 Min Nonbonded Distance : 1.836 Molprobity Statistics. All-atom Clashscore : 21.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % Rotamer: Outliers : 4.58 % Allowed : 30.72 % Favored : 64.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -0.94 (0.22), residues: 1425 helix: 0.01 (0.22), residues: 537 sheet: -1.06 (0.32), residues: 271 loop : -0.84 (0.26), residues: 617 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.053 0.004 TRP F 42 HIS 0.005 0.001 HIS F 11 PHE 0.016 0.001 PHE U 19 TYR 0.034 0.002 TYR D 51 ARG 0.013 0.001 ARG K 69 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5934.66 seconds wall clock time: 109 minutes 31.27 seconds (6571.27 seconds total)