Starting phenix.real_space_refine on Thu Oct 29 17:10:30 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7afi_11766/10_2026/7afi_11766.cif Found real_map, /net/cci-nas-00/data/ceres_data/7afi_11766/10_2026/7afi_11766.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.53 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7afi_11766/10_2026/7afi_11766.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7afi_11766/10_2026/7afi_11766.map" model { file = "/net/cci-nas-00/data/ceres_data/7afi_11766/10_2026/7afi_11766.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7afi_11766/10_2026/7afi_11766.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7afi_11766/10_2026/7afi_11766.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7afi_11766/10_2026/7afi_11766.cif" } resolution = 3.53 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 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 1066 5.49 5 Mg 46 5.21 5 S 45 5.16 5 C 16997 2.51 5 N 6274 2.21 5 O 9375 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 27 residue(s): 0.19s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 33803 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 22908 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1066, 22908 Classifications: {'RNA': 4, 'RNAv2': 1062} Modifications used: {'rna2p_pur': 81, 'rna2p_pyr': 58, 'rna3p': 5, 'rna3p_pur': 532, 'rna3p_pyr': 390} Link IDs: {'rna2p': 138, 'rna3p': 927} Chain breaks: 3 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 3 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: 866 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 866 Classifications: {'peptide': 116} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 108} 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: "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: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 46 Unusual residues: {' MG': 46} Classifications: {'undetermined': 46} Link IDs: {None: 45} Time building chain proxies: 6.20, per 1000 atoms: 0.18 Number of scatterers: 33803 At special positions: 0 Unit cell: (146.475, 214.83, 139.965, 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 45 16.00 P 1066 15.00 Mg 46 11.99 O 9375 8.00 N 6274 7.00 C 16997 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.98 Conformation dependent library (CDL) restraints added in 627.6 milliseconds 2720 Ramachandran restraints generated. 1360 Oldfield, 0 Emsley, 1360 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2570 Finding SS restraints... Secondary structure from input PDB file: 49 helices and 16 sheets defined 41.8% alpha, 22.4% beta 334 base pairs and 521 stacking pairs defined. Time for finding SS restraints: 6.00 Creating SS restraints... Processing helix chain 'D' and resid 7 through 15 removed outlier: 4.309A pdb=" N LEU D 11 " --> pdb=" O PRO D 7 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N SER D 12 " --> pdb=" O LYS D 8 " (cutoff:3.500A) Processing helix chain 'D' and resid 27 through 31 Processing helix chain 'D' and resid 39 through 43 removed outlier: 3.683A pdb=" N ALA D 43 " --> pdb=" O GLN D 40 " (cutoff:3.500A) Processing helix chain 'D' and resid 49 through 65 removed outlier: 3.541A pdb=" N GLN D 54 " --> pdb=" O ASP D 50 " (cutoff:3.500A) Processing helix chain 'D' and resid 68 through 82 Processing helix chain 'D' and resid 85 through 96 Processing helix chain 'D' and resid 97 through 105 Processing helix chain 'D' and resid 110 through 120 removed outlier: 3.522A pdb=" N LEU D 117 " --> pdb=" O GLU D 113 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N VAL D 118 " --> pdb=" O ALA D 114 " (cutoff:3.500A) Processing helix chain 'D' and resid 147 through 151 removed outlier: 3.774A pdb=" N LYS D 151 " --> pdb=" O LYS D 148 " (cutoff:3.500A) Processing helix chain 'D' and resid 152 through 163 removed outlier: 4.059A pdb=" N LYS D 156 " --> pdb=" O GLN D 152 " (cutoff:3.500A) Processing helix chain 'D' and resid 196 through 206 removed outlier: 4.411A pdb=" N ILE D 200 " --> pdb=" O ASN D 196 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N SER D 205 " --> pdb=" O VAL D 201 " (cutoff:3.500A) Processing helix chain 'E' and resid 55 through 67 Processing helix chain 'E' and resid 108 through 119 removed outlier: 3.858A pdb=" N VAL E 114 " --> pdb=" O ALA E 110 " (cutoff:3.500A) Processing helix chain 'E' and resid 132 through 147 Processing helix chain 'E' and resid 149 through 158 Processing helix chain 'E' and resid 160 through 165 Processing helix chain 'F' and resid 12 through 16 removed outlier: 4.522A pdb=" N GLU F 16 " --> pdb=" O ASP F 13 " (cutoff:3.500A) Processing helix chain 'F' and resid 17 through 32 removed outlier: 3.541A pdb=" N TYR F 25 " --> pdb=" O MET F 21 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ALA F 28 " --> pdb=" O ARG F 24 " (cutoff:3.500A) Processing helix chain 'F' and resid 67 through 81 removed outlier: 3.698A pdb=" N ILE F 71 " --> pdb=" O PRO F 67 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ASP F 72 " --> pdb=" O GLN F 68 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N GLU F 73 " --> pdb=" O GLU F 69 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N LEU F 74 " --> pdb=" O VAL F 70 " (cutoff:3.500A) Processing helix chain 'F' and resid 100 through 106 Processing helix chain 'H' and resid 5 through 20 removed outlier: 3.660A pdb=" N ASP H 9 " --> pdb=" O ASP H 5 " (cutoff:3.500A) Processing helix chain 'H' and resid 30 through 42 removed outlier: 3.688A pdb=" N VAL H 39 " --> pdb=" O ALA H 35 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N LEU H 40 " --> pdb=" O ILE H 36 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N LYS H 41 " --> pdb=" O ALA H 37 " (cutoff:3.500A) Processing helix chain 'H' and resid 88 through 92 Processing helix chain 'H' and resid 95 through 99 Processing helix chain 'H' and resid 113 through 120 Processing helix chain 'K' and resid 47 through 51 Processing helix chain 'K' and resid 55 through 58 Processing helix chain 'K' and resid 59 through 78 removed outlier: 3.630A pdb=" N LYS K 75 " --> pdb=" O ALA K 71 " (cutoff:3.500A) removed outlier: 5.752A pdb=" N GLU K 76 " --> pdb=" O ASP K 72 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N TYR K 77 " --> pdb=" O ALA K 73 " (cutoff:3.500A) Processing helix chain 'K' and resid 92 through 104 Processing helix chain 'L' and resid 3 through 10 Processing helix chain 'L' and resid 21 through 25 Processing helix chain 'L' and resid 113 through 117 Processing helix chain 'O' and resid 4 through 15 Processing helix chain 'O' and resid 24 through 46 removed outlier: 3.566A pdb=" N GLN O 40 " --> pdb=" O ILE O 36 " (cutoff:3.500A) removed outlier: 4.784A pdb=" N GLY O 41 " --> pdb=" O ASN O 37 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N HIS O 42 " --> pdb=" O HIS O 38 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N PHE O 43 " --> pdb=" O LEU O 39 " (cutoff:3.500A) Processing helix chain 'O' and resid 49 through 74 removed outlier: 3.552A pdb=" N GLY O 55 " --> pdb=" O HIS O 51 " (cutoff:3.500A) Processing helix chain 'O' and resid 76 through 86 removed outlier: 4.077A pdb=" N GLU O 83 " --> pdb=" O THR O 79 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N ARG O 84 " --> pdb=" O GLN O 80 " (cutoff:3.500A) Processing helix chain 'P' and resid 53 through 63 Processing helix chain 'P' and resid 68 through 81 Processing helix chain 'Q' and resid 49 through 52 Processing helix chain 'R' and resid 11 through 17 Processing helix chain 'R' and resid 25 through 32 removed outlier: 3.915A pdb=" N ASN R 31 " --> pdb=" O ALA R 27 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N TYR R 32 " --> pdb=" O THR R 28 " (cutoff:3.500A) Processing helix chain 'R' and resid 41 through 46 Processing helix chain 'R' and resid 48 through 65 removed outlier: 3.760A pdb=" N GLN R 54 " --> pdb=" O LYS R 50 " (cutoff:3.500A) Processing helix chain 'T' and resid 4 through 42 removed outlier: 3.506A pdb=" N ILE T 12 " --> pdb=" O LYS T 8 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N GLU T 15 " --> pdb=" O ALA T 11 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N HIS T 20 " --> pdb=" O LYS T 16 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ILE T 32 " --> pdb=" O MET T 28 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N VAL T 35 " --> pdb=" O PHE T 31 " (cutoff:3.500A) Processing helix chain 'T' and resid 43 through 64 Proline residue: T 56 - end of helix Processing helix chain 'T' and resid 68 through 85 Processing helix chain 'X' and resid 4 through 19 removed outlier: 3.578A pdb=" N ALA X 14 " --> pdb=" O GLU X 10 " (cutoff:3.500A) Proline residue: X 15 - end of helix Processing helix chain 'X' and resid 47 through 65 removed outlier: 4.293A pdb=" N VAL X 64 " --> pdb=" O ALA X 60 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLU X 65 " --> pdb=" O VAL X 61 " (cutoff:3.500A) Processing helix chain 'X' and resid 87 through 94 removed outlier: 3.831A pdb=" N TYR X 91 " --> pdb=" O THR X 87 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'D' and resid 129 through 130 removed outlier: 4.802A pdb=" N ILE D 123 " --> pdb=" O VAL D 130 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 171 through 174 Processing sheet with id=AA3, first strand: chain 'E' and resid 12 through 23 removed outlier: 4.748A pdb=" N GLU E 13 " --> pdb=" O GLY E 40 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N GLY E 40 " --> pdb=" O GLU E 13 " (cutoff:3.500A) removed outlier: 5.539A pdb=" N LEU E 15 " --> pdb=" O VAL E 38 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N VAL E 38 " --> pdb=" O LEU E 15 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ALA E 17 " --> pdb=" O LEU E 36 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'E' and resid 85 through 89 Processing sheet with id=AA5, first strand: chain 'F' and resid 35 through 44 removed outlier: 5.042A pdb=" N ILE F 36 " --> pdb=" O GLU F 65 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N GLU F 65 " --> pdb=" O ILE F 36 " (cutoff:3.500A) removed outlier: 6.028A pdb=" N TYR F 59 " --> pdb=" O TRP F 42 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N HIS F 58 " --> pdb=" O VAL F 10 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N VAL F 10 " --> pdb=" O HIS F 58 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N VAL F 64 " --> pdb=" O TYR F 4 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ARG F 2 " --> pdb=" O ALA F 66 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N MET F 9 " --> pdb=" O ILE F 85 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'F' and resid 35 through 44 removed outlier: 5.042A pdb=" N ILE F 36 " --> pdb=" O GLU F 65 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N GLU F 65 " --> pdb=" O ILE F 36 " (cutoff:3.500A) removed outlier: 6.028A pdb=" N TYR F 59 " --> pdb=" O TRP F 42 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N HIS F 58 " --> pdb=" O VAL F 10 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N VAL F 10 " --> pdb=" O HIS F 58 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N VAL F 64 " --> pdb=" O TYR F 4 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ARG F 2 " --> pdb=" O ALA F 66 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'H' and resid 24 through 27 removed outlier: 3.602A pdb=" N VAL H 25 " --> pdb=" O LEU H 61 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N LEU H 61 " --> pdb=" O VAL H 25 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 65 through 66 Processing sheet with id=AA9, first strand: chain 'H' and resid 75 through 77 Processing sheet with id=AB1, first strand: chain 'H' and resid 75 through 77 removed outlier: 6.859A pdb=" N VAL H 103 " --> pdb=" O ILE H 126 " (cutoff:3.500A) removed outlier: 5.213A pdb=" N TYR H 128 " --> pdb=" O ILE H 101 " (cutoff:3.500A) removed outlier: 7.081A pdb=" N ILE H 101 " --> pdb=" O TYR H 128 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'K' and resid 41 through 46 removed outlier: 7.972A pdb=" N LEU K 82 " --> pdb=" O THR K 108 " (cutoff:3.500A) removed outlier: 7.161A pdb=" N ILE K 110 " --> pdb=" O LEU K 82 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N VAL K 84 " --> pdb=" O ILE K 110 " (cutoff:3.500A) removed outlier: 5.113A pdb=" N ASP K 112 " --> pdb=" O VAL K 84 " (cutoff:3.500A) removed outlier: 5.802A pdb=" N VAL K 86 " --> pdb=" O ASP K 112 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'X' and resid 23 through 29 removed outlier: 4.791A pdb=" N GLY X 25 " --> pdb=" O TYR X 39 " (cutoff:3.500A) removed outlier: 7.244A pdb=" N LEU X 36 " --> pdb=" O GLU X 75 " (cutoff:3.500A) removed outlier: 7.681A pdb=" N SER X 77 " --> pdb=" O LEU X 36 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N ILE X 38 " --> pdb=" O SER X 77 " (cutoff:3.500A) removed outlier: 7.589A pdb=" N THR L 97 " --> pdb=" O THR L 64 " (cutoff:3.500A) removed outlier: 7.128A pdb=" N TYR L 66 " --> pdb=" O THR L 97 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N ARG L 50 " --> pdb=" O THR L 39 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N THR L 39 " --> pdb=" O ARG L 50 " (cutoff:3.500A) removed outlier: 7.365A pdb=" N VAL L 52 " --> pdb=" O VAL L 37 " (cutoff:3.500A) removed outlier: 5.165A pdb=" N VAL L 37 " --> pdb=" O VAL L 52 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N ARG L 54 " --> pdb=" O THR L 35 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'P' and resid 50 through 52 removed outlier: 5.497A pdb=" N ARG P 35 " --> pdb=" O VAL P 21 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N VAL P 21 " --> pdb=" O ARG P 35 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N VAL P 2 " --> pdb=" O THR P 66 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'Q' and resid 8 through 14 removed outlier: 15.316A pdb=" N LEU Q 8 " --> pdb=" O PHE Q 28 " (cutoff:3.500A) removed outlier: 13.638A pdb=" N PHE Q 28 " --> pdb=" O LEU Q 8 " (cutoff:3.500A) removed outlier: 7.645A pdb=" N GLY Q 10 " --> pdb=" O GLU Q 26 " (cutoff:3.500A) removed outlier: 7.717A pdb=" N GLU Q 26 " --> pdb=" O GLY Q 10 " (cutoff:3.500A) removed outlier: 5.500A pdb=" N VAL Q 12 " --> pdb=" O ALA Q 24 " (cutoff:3.500A) removed outlier: 6.026A pdb=" N ALA Q 24 " --> pdb=" O VAL Q 12 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ILE Q 25 " --> pdb=" O THR Q 42 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N THR Q 42 " --> pdb=" O ILE Q 25 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N VAL Q 29 " --> pdb=" O ILE Q 38 " (cutoff:3.500A) removed outlier: 8.628A pdb=" N LYS Q 71 " --> pdb=" O LYS Q 43 " (cutoff:3.500A) removed outlier: 7.761A pdb=" N HIS Q 45 " --> pdb=" O LYS Q 71 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N TRP Q 73 " --> pdb=" O HIS Q 45 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N VAL Q 76 " --> pdb=" O GLU Q 60 " (cutoff:3.500A) removed outlier: 7.435A pdb=" N GLU Q 60 " --> pdb=" O VAL Q 76 " (cutoff:3.500A) removed outlier: 5.706A pdb=" N VAL Q 78 " --> pdb=" O VAL Q 58 " (cutoff:3.500A) removed outlier: 8.072A pdb=" N VAL Q 58 " --> pdb=" O VAL Q 78 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'R' and resid 33 through 34 removed outlier: 3.528A pdb=" N LYS R 38 " --> pdb=" O THR R 34 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'X' and resid 132 through 137 removed outlier: 6.957A pdb=" N MET X 124 " --> pdb=" O VAL X 120 " (cutoff:3.500A) removed outlier: 5.351A pdb=" N VAL X 120 " --> pdb=" O MET X 124 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N THR X 126 " --> pdb=" O LYS X 118 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N VAL X 116 " --> pdb=" O THR X 128 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N GLU X 98 " --> pdb=" O VAL X 147 " (cutoff:3.500A) 500 hydrogen bonds defined for protein. 1404 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 775 hydrogen bonds 992 hydrogen bond angles 0 basepair planarities 334 basepair parallelities 521 stacking parallelities Total time for adding SS restraints: 14.52 Time building geometry restraints manager: 4.00 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 3733 1.32 - 1.44: 15878 1.44 - 1.57: 14839 1.57 - 1.69: 2128 1.69 - 1.82: 78 Bond restraints: 36656 Sorted by residual: bond pdb=" C HIS Q 31 " pdb=" N PRO Q 32 " ideal model delta sigma weight residual 1.335 1.413 -0.077 1.36e-02 5.41e+03 3.22e+01 bond pdb=" O3' C A 525 " pdb=" P C A 526 " ideal model delta sigma weight residual 1.607 1.667 -0.060 1.20e-02 6.94e+03 2.51e+01 bond pdb=" C5 2MG A1516 " pdb=" C4 2MG A1516 " ideal model delta sigma weight residual 1.382 1.468 -0.086 2.00e-02 2.50e+03 1.85e+01 bond pdb=" C PRO K 60 " pdb=" O PRO K 60 " ideal model delta sigma weight residual 1.238 1.190 0.047 1.24e-02 6.50e+03 1.46e+01 bond pdb=" C4 PSU A 516 " pdb=" C5 PSU A 516 " ideal model delta sigma weight residual 1.390 1.464 -0.074 2.00e-02 2.50e+03 1.37e+01 ... (remaining 36651 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.86: 52338 2.86 - 5.72: 2370 5.72 - 8.58: 72 8.58 - 11.43: 8 11.43 - 14.29: 3 Bond angle restraints: 54791 Sorted by residual: angle pdb=" CA PHE K 52 " pdb=" C PHE K 52 " pdb=" O PHE K 52 " ideal model delta sigma weight residual 121.05 111.12 9.93 1.14e+00 7.69e-01 7.59e+01 angle pdb=" C HIS Q 31 " pdb=" N PRO Q 32 " pdb=" CA PRO Q 32 " ideal model delta sigma weight residual 119.05 110.82 8.23 1.11e+00 8.12e-01 5.50e+01 angle pdb=" N ASN Q 51 " pdb=" CA ASN Q 51 " pdb=" C ASN Q 51 " ideal model delta sigma weight residual 111.39 101.78 9.61 1.38e+00 5.25e-01 4.85e+01 angle pdb=" CA PHE K 52 " pdb=" C PHE K 52 " pdb=" N ARG K 53 " ideal model delta sigma weight residual 115.86 123.18 -7.32 1.26e+00 6.30e-01 3.38e+01 angle pdb=" N PRO F 12 " pdb=" CA PRO F 12 " pdb=" C PRO F 12 " ideal model delta sigma weight residual 113.81 105.68 8.13 1.45e+00 4.76e-01 3.14e+01 ... (remaining 54786 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.18: 17241 34.18 - 68.36: 2193 68.36 - 102.53: 180 102.53 - 136.71: 0 136.71 - 170.89: 1 Dihedral angle restraints: 19615 sinusoidal: 15635 harmonic: 3980 Sorted by residual: dihedral pdb=" C4' A A 792 " pdb=" C3' A A 792 " pdb=" C2' A A 792 " pdb=" C1' A A 792 " ideal model delta sinusoidal sigma weight residual 36.35 -43.94 80.29 1 3.10e+00 1.04e-01 8.30e+02 dihedral pdb=" C4' U A1390 " pdb=" C3' U A1390 " pdb=" C2' U A1390 " pdb=" C1' U A1390 " ideal model delta sinusoidal sigma weight residual 36.34 -41.60 77.95 1 3.10e+00 1.04e-01 7.90e+02 dihedral pdb=" C4' C A 817 " pdb=" C3' C A 817 " pdb=" C2' C A 817 " pdb=" C1' C A 817 " ideal model delta sinusoidal sigma weight residual 36.34 -40.29 76.64 1 3.10e+00 1.04e-01 7.68e+02 ... (remaining 19612 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.121: 5330 0.121 - 0.243: 1386 0.243 - 0.364: 274 0.364 - 0.485: 3 0.485 - 0.607: 2 Chirality restraints: 6995 Sorted by residual: chirality pdb=" CA ARG K 69 " pdb=" N ARG K 69 " pdb=" C ARG K 69 " pdb=" CB ARG K 69 " both_signs ideal model delta sigma weight residual False 2.51 1.90 0.61 2.00e-01 2.50e+01 9.20e+00 chirality pdb=" CA ASP K 72 " pdb=" N ASP K 72 " pdb=" C ASP K 72 " pdb=" CB ASP K 72 " both_signs ideal model delta sigma weight residual False 2.51 2.02 0.49 2.00e-01 2.50e+01 6.06e+00 chirality pdb=" CA GLU K 68 " pdb=" N GLU K 68 " pdb=" C GLU K 68 " pdb=" CB GLU K 68 " both_signs ideal model delta sigma weight residual False 2.51 2.06 0.45 2.00e-01 2.50e+01 5.13e+00 ... (remaining 6992 not shown) Planarity restraints: 2986 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C6 MA6 A1519 " 0.121 2.00e-02 2.50e+03 2.00e-01 3.98e+02 pdb=" N6 MA6 A1519 " -0.346 2.00e-02 2.50e+03 pdb=" C10 MA6 A1519 " 0.116 2.00e-02 2.50e+03 pdb=" C9 MA6 A1519 " 0.109 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C6 MA6 A1518 " 0.121 2.00e-02 2.50e+03 1.97e-01 3.89e+02 pdb=" N6 MA6 A1518 " -0.341 2.00e-02 2.50e+03 pdb=" C10 MA6 A1518 " 0.114 2.00e-02 2.50e+03 pdb=" C9 MA6 A1518 " 0.106 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' 2MG A1516 " -0.006 2.00e-02 2.50e+03 2.68e-02 2.34e+01 pdb=" N9 2MG A1516 " -0.009 2.00e-02 2.50e+03 pdb=" C8 2MG A1516 " 0.011 2.00e-02 2.50e+03 pdb=" N7 2MG A1516 " 0.020 2.00e-02 2.50e+03 pdb=" C5 2MG A1516 " 0.006 2.00e-02 2.50e+03 pdb=" C6 2MG A1516 " 0.004 2.00e-02 2.50e+03 pdb=" O6 2MG A1516 " 0.016 2.00e-02 2.50e+03 pdb=" N1 2MG A1516 " -0.009 2.00e-02 2.50e+03 pdb=" C2 2MG A1516 " -0.030 2.00e-02 2.50e+03 pdb=" N2 2MG A1516 " -0.037 2.00e-02 2.50e+03 pdb=" N3 2MG A1516 " -0.022 2.00e-02 2.50e+03 pdb=" C4 2MG A1516 " -0.014 2.00e-02 2.50e+03 pdb=" CM2 2MG A1516 " 0.073 2.00e-02 2.50e+03 ... (remaining 2983 not shown) Histogram of nonbonded interaction distances: 1.84 - 2.45: 517 2.45 - 3.06: 24312 3.06 - 3.67: 74052 3.67 - 4.29: 99150 4.29 - 4.90: 132092 Nonbonded interactions: 330123 Sorted by model distance: nonbonded pdb=" OP2 A A 560 " pdb="MG MG A1603 " model vdw 1.836 2.170 nonbonded pdb=" OP2 C A 175 " pdb="MG MG A1623 " model vdw 1.845 2.170 nonbonded pdb=" OP2 G A 117 " pdb="MG MG A1644 " model vdw 1.846 2.170 nonbonded pdb=" N7 G A 362 " pdb="MG MG A1611 " model vdw 1.852 2.250 nonbonded pdb=" OP2 A A 53 " pdb="MG MG A1624 " model vdw 1.867 2.170 ... (remaining 330118 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.030 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 0.520 Check model and map are aligned: 0.110 Set scattering table: 0.080 Process input model: 40.620 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.950 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8945 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 : 0.011 0.086 36656 Z= 0.600 Angle : 1.204 14.293 54791 Z= 0.612 Chirality : 0.109 0.607 6995 Planarity : 0.007 0.200 2986 Dihedral : 21.950 170.891 17045 Min Nonbonded Distance : 1.836 Molprobity Statistics. All-atom Clashscore : 33.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.04 % Favored : 90.96 % Rotamer: Outliers : 0.00 % Allowed : 16.96 % Favored : 83.04 % Cbeta Deviations : 0.62 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.95 (0.21), residues: 1360 helix: -1.89 (0.23), residues: 473 sheet: -1.88 (0.32), residues: 236 loop : -1.95 (0.21), residues: 651 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG X 110 TYR 0.014 0.002 TYR O 69 PHE 0.020 0.002 PHE K 61 TRP 0.009 0.001 TRP Q 73 HIS 0.009 0.002 HIS X 56 Details of bonding type rmsd/Z covalent geometry : bond 0.01054 / 0.60 (36656) covalent geometry : angle 1.20404 / 0.61 (54791) hydrogen bonds : bond 0.33007 / 17.35 ( 1262) hydrogen bonds : angle 10.67565 / 4.34 ( 2396) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2720 Ramachandran restraints generated. 1360 Oldfield, 0 Emsley, 1360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2720 Ramachandran restraints generated. 1360 Oldfield, 0 Emsley, 1360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 399 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 399 time to evaluate : 0.658 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: 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 135 TYR cc_start: 0.9415 (t80) cc_final: 0.9049 (t80) REVERT: E 14 LYS cc_start: 0.9037 (mttm) cc_final: 0.8550 (mmtm) REVERT: E 30 ILE cc_start: 0.9000 (mm) cc_final: 0.8732 (mm) REVERT: E 68 ARG cc_start: 0.9342 (mtt-85) cc_final: 0.8815 (mmt90) REVERT: E 103 THR cc_start: 0.9431 (m) cc_final: 0.9173 (p) REVERT: E 116 GLU cc_start: 0.8564 (tm-30) cc_final: 0.8158 (tm-30) REVERT: F 5 GLU cc_start: 0.8805 (tt0) cc_final: 0.8602 (tm-30) REVERT: F 17 GLN cc_start: 0.9307 (tp-100) cc_final: 0.9089 (tp-100) REVERT: F 80 PHE cc_start: 0.9099 (t80) cc_final: 0.8779 (t80) REVERT: F 88 MET cc_start: 0.9061 (tpt) cc_final: 0.8808 (tpt) REVERT: H 3 MET cc_start: 0.8909 (tmm) cc_final: 0.8511 (tmm) REVERT: H 27 MET cc_start: 0.8665 (ptp) cc_final: 0.8437 (ptp) REVERT: H 80 ARG cc_start: 0.9536 (mtm110) cc_final: 0.9151 (mtp-110) REVERT: H 88 ARG cc_start: 0.8664 (mtp-110) cc_final: 0.8016 (mtp85) REVERT: K 42 LEU cc_start: 0.9065 (mm) cc_final: 0.8784 (mt) REVERT: K 70 CYS cc_start: 0.8854 (t) cc_final: 0.8462 (m) REVERT: L 41 THR cc_start: 0.8335 (p) cc_final: 0.8064 (p) REVERT: P 76 LYS cc_start: 0.9686 (ttmm) cc_final: 0.9479 (tptt) REVERT: Q 8 LEU cc_start: 0.9319 (tp) cc_final: 0.8795 (tt) REVERT: Q 60 GLU cc_start: 0.8680 (tt0) cc_final: 0.8333 (tp30) REVERT: Q 81 LYS cc_start: 0.8698 (tppt) cc_final: 0.8244 (tppt) REVERT: R 26 ILE cc_start: 0.9686 (pt) cc_final: 0.9301 (mt) REVERT: R 57 ARG cc_start: 0.9304 (mtm-85) cc_final: 0.9093 (mmm160) REVERT: T 24 ARG cc_start: 0.9222 (tpp-160) cc_final: 0.8914 (mmm-85) REVERT: T 59 ASP cc_start: 0.8608 (m-30) cc_final: 0.8392 (m-30) REVERT: X 40 ILE cc_start: 0.9485 (mp) cc_final: 0.9183 (pt) REVERT: X 136 PHE cc_start: 0.8165 (m-80) cc_final: 0.7899 (m-80) REVERT: X 143 LYS cc_start: 0.8853 (tptp) cc_final: 0.8613 (mtmm) outliers start: 0 outliers final: 0 residues processed: 399 average time/residue: 0.2601 time to fit residues: 154.5100 Evaluate side-chains 271 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 271 time to evaluate : 0.574 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 239 random chunks: [216, 98, 194, 227, 107, 10, 66, 130, 124, 103, 235] chunk 216 optimal weight: 6.9990 chunk 98 optimal weight: 10.0000 chunk 194 optimal weight: 4.9990 chunk 227 optimal weight: 8.9990 chunk 107 optimal weight: 6.9990 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 5.9990 chunk 130 optimal weight: 6.9990 chunk 124 optimal weight: 0.9990 chunk 103 optimal weight: 3.9990 chunk 235 optimal weight: 5.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 136 GLN ** E 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 135 ASN F 14 GLN ** F 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 15 GLN K 40 ASN K 119 ASN ** O 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 40 GLN Q 9 GLN Q 51 ASN R 19 GLN ** T 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 61 GLN T 70 ASN X 47 ASN ** X 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 109 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2940 r_free = 0.2940 target = 0.028830 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2635 r_free = 0.2635 target = 0.022529 restraints weight = 368658.763| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.2668 r_free = 0.2668 target = 0.023326 restraints weight = 138142.371| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2690 r_free = 0.2690 target = 0.023800 restraints weight = 78941.093| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.2703 r_free = 0.2703 target = 0.024080 restraints weight = 57041.884| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.2711 r_free = 0.2711 target = 0.024245 restraints weight = 47287.521| |-----------------------------------------------------------------------------| r_work (final): 0.2706 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8893 moved from start: 0.3195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 36656 Z= 0.284 Angle : 1.334 19.040 54791 Z= 0.536 Chirality : 0.103 1.469 6995 Planarity : 0.005 0.047 2986 Dihedral : 20.124 176.588 14347 Min Nonbonded Distance : 1.846 Molprobity Statistics. All-atom Clashscore : 22.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 4.55 % Allowed : 20.45 % Favored : 75.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.96 (0.21), residues: 1360 helix: -0.84 (0.20), residues: 515 sheet: -1.94 (0.28), residues: 280 loop : -1.19 (0.25), residues: 565 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG O 58 TYR 0.037 0.003 TYR K 77 PHE 0.023 0.002 PHE F 8 TRP 0.019 0.003 TRP K 44 HIS 0.011 0.002 HIS X 56 Details of bonding type rmsd/Z covalent geometry : bond 0.00568 / 0.28 (36656) covalent geometry : angle 1.33439 / 0.54 (54791) hydrogen bonds : bond 0.12511 / 6.49 ( 1262) hydrogen bonds : angle 4.96665 / 1.99 ( 2396) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2720 Ramachandran restraints generated. 1360 Oldfield, 0 Emsley, 1360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2720 Ramachandran restraints generated. 1360 Oldfield, 0 Emsley, 1360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 378 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 326 time to evaluate : 0.666 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: D 64 ILE cc_start: 0.9292 (tp) cc_final: 0.9053 (mt) REVERT: D 71 GLN cc_start: 0.9344 (tt0) cc_final: 0.9141 (tt0) REVERT: D 206 LYS cc_start: 0.9239 (ttpp) cc_final: 0.8754 (ttmm) REVERT: E 12 GLN cc_start: 0.8984 (mp10) cc_final: 0.8758 (mp10) REVERT: E 14 LYS cc_start: 0.9090 (mttm) cc_final: 0.8769 (mmtm) REVERT: E 54 ARG cc_start: 0.4301 (mtt180) cc_final: 0.3877 (mpt180) REVERT: E 71 MET cc_start: 0.8754 (tpp) cc_final: 0.8518 (tpp) REVERT: E 96 MET cc_start: 0.8939 (mpp) cc_final: 0.8628 (mpp) REVERT: E 116 GLU cc_start: 0.8677 (tm-30) cc_final: 0.8145 (tm-30) REVERT: F 5 GLU cc_start: 0.8653 (tt0) cc_final: 0.8410 (tm-30) REVERT: F 17 GLN cc_start: 0.9314 (tp-100) cc_final: 0.8916 (tm-30) REVERT: F 62 MET cc_start: 0.7986 (mpp) cc_final: 0.7756 (mpp) REVERT: F 69 GLU cc_start: 0.9321 (pm20) cc_final: 0.9049 (pm20) REVERT: F 80 PHE cc_start: 0.8919 (t80) cc_final: 0.8695 (t80) REVERT: F 88 MET cc_start: 0.9126 (tpt) cc_final: 0.8876 (tpp) REVERT: F 93 LYS cc_start: 0.9280 (mttt) cc_final: 0.9039 (tttt) REVERT: H 3 MET cc_start: 0.9062 (tmm) cc_final: 0.8706 (tmm) REVERT: H 58 GLU cc_start: 0.8002 (mm-30) cc_final: 0.7742 (mm-30) REVERT: H 80 ARG cc_start: 0.9380 (mtm110) cc_final: 0.9119 (mtp-110) REVERT: H 88 ARG cc_start: 0.8615 (mtp-110) cc_final: 0.8165 (mtp85) REVERT: H 96 MET cc_start: 0.9100 (mtp) cc_final: 0.8253 (ttm) REVERT: K 87 LYS cc_start: 0.8914 (OUTLIER) cc_final: 0.8543 (mtmt) REVERT: K 94 GLU cc_start: 0.9263 (tt0) cc_final: 0.8717 (tm-30) REVERT: O 53 ARG cc_start: 0.9401 (tpp80) cc_final: 0.8759 (tpp80) REVERT: O 59 MET cc_start: 0.9287 (mtm) cc_final: 0.8926 (mtm) REVERT: P 54 LEU cc_start: 0.9650 (mt) cc_final: 0.9409 (mt) REVERT: P 76 LYS cc_start: 0.9580 (ttmm) cc_final: 0.9363 (tptt) REVERT: Q 7 THR cc_start: 0.9331 (OUTLIER) cc_final: 0.9045 (m) REVERT: Q 8 LEU cc_start: 0.9346 (tp) cc_final: 0.8931 (tp) REVERT: Q 60 GLU cc_start: 0.8688 (tt0) cc_final: 0.8289 (mm-30) REVERT: Q 61 ILE cc_start: 0.9446 (mm) cc_final: 0.9011 (mm) REVERT: Q 75 LEU cc_start: 0.8796 (OUTLIER) cc_final: 0.8499 (pt) REVERT: Q 81 LYS cc_start: 0.8546 (tppt) cc_final: 0.8028 (tppt) REVERT: R 57 ARG cc_start: 0.9120 (mtm-85) cc_final: 0.8725 (mmm160) REVERT: T 24 ARG cc_start: 0.9219 (tpp-160) cc_final: 0.8871 (mmm-85) REVERT: X 37 ARG cc_start: 0.9087 (ttp80) cc_final: 0.8843 (ttp-110) REVERT: X 74 LEU cc_start: 0.9310 (OUTLIER) cc_final: 0.9098 (tp) REVERT: X 113 TRP cc_start: 0.8327 (m-90) cc_final: 0.7496 (m-90) REVERT: X 143 LYS cc_start: 0.8929 (tptp) cc_final: 0.8478 (mtmt) outliers start: 52 outliers final: 29 residues processed: 353 average time/residue: 0.2307 time to fit residues: 125.8436 Evaluate side-chains 298 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 265 time to evaluate : 0.718 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 17 THR Chi-restraints excluded: chain D residue 169 THR Chi-restraints excluded: chain D residue 195 ILE Chi-restraints excluded: chain D residue 196 ASN Chi-restraints excluded: chain D residue 200 ILE Chi-restraints excluded: chain E residue 34 THR Chi-restraints excluded: chain E residue 48 PHE Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 13 ASP Chi-restraints excluded: chain F residue 18 VAL Chi-restraints excluded: chain F residue 61 LEU Chi-restraints excluded: chain F residue 85 ILE Chi-restraints excluded: chain H residue 72 VAL Chi-restraints excluded: chain H residue 106 THR Chi-restraints excluded: chain H residue 129 VAL Chi-restraints excluded: chain K residue 23 ILE Chi-restraints excluded: chain K residue 31 ILE Chi-restraints excluded: chain K residue 55 SER Chi-restraints excluded: chain K residue 87 LYS Chi-restraints excluded: chain L residue 24 LEU Chi-restraints excluded: chain L residue 49 LEU Chi-restraints excluded: chain L residue 97 THR Chi-restraints excluded: chain P residue 2 VAL Chi-restraints excluded: chain P residue 3 THR Chi-restraints excluded: chain P residue 34 GLU Chi-restraints excluded: chain P residue 42 ILE Chi-restraints excluded: chain Q residue 7 THR Chi-restraints excluded: chain Q residue 55 ILE Chi-restraints excluded: chain Q residue 75 LEU Chi-restraints excluded: chain X residue 50 ASP Chi-restraints excluded: chain X residue 74 LEU Chi-restraints excluded: chain X residue 112 LYS Chi-restraints excluded: chain X residue 125 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 239 random chunks: [188, 157, 13, 211, 26, 232, 199, 46, 168, 112, 123] chunk 188 optimal weight: 6.9990 chunk 157 optimal weight: 6.9990 chunk 13 optimal weight: 8.9990 chunk 211 optimal weight: 5.9990 chunk 26 optimal weight: 8.9990 chunk 232 optimal weight: 8.9990 chunk 199 optimal weight: 10.0000 chunk 46 optimal weight: 9.9990 chunk 168 optimal weight: 50.0000 chunk 112 optimal weight: 0.9990 chunk 123 optimal weight: 2.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 126 ASN ** E 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 81 ASN L 46 ASN ** O 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 50 ASN ** T 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 109 ASN X 114 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2948 r_free = 0.2948 target = 0.029179 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2646 r_free = 0.2646 target = 0.022838 restraints weight = 369578.318| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.2677 r_free = 0.2677 target = 0.023643 restraints weight = 138629.655| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2698 r_free = 0.2698 target = 0.024134 restraints weight = 79626.594| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.2711 r_free = 0.2711 target = 0.024417 restraints weight = 57757.509| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2717 r_free = 0.2717 target = 0.024558 restraints weight = 47909.216| |-----------------------------------------------------------------------------| r_work (final): 0.2710 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8900 moved from start: 0.4056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.083 36656 Z= 0.293 Angle : 1.149 15.901 54791 Z= 0.466 Chirality : 0.082 1.019 6995 Planarity : 0.005 0.069 2986 Dihedral : 19.941 179.744 14347 Min Nonbonded Distance : 1.831 Molprobity Statistics. All-atom Clashscore : 22.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 5.59 % Allowed : 22.64 % Favored : 71.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.38 (0.22), residues: 1360 helix: -0.04 (0.21), residues: 520 sheet: -1.86 (0.29), residues: 268 loop : -1.10 (0.25), residues: 572 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG O 58 TYR 0.029 0.002 TYR X 72 PHE 0.020 0.002 PHE E 95 TRP 0.011 0.002 TRP X 113 HIS 0.007 0.001 HIS X 56 Details of bonding type rmsd/Z covalent geometry : bond 0.00592 / 0.29 (36656) covalent geometry : angle 1.14866 / 0.47 (54791) hydrogen bonds : bond 0.11643 / 6.04 ( 1262) hydrogen bonds : angle 4.56427 / 1.83 ( 2396) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2720 Ramachandran restraints generated. 1360 Oldfield, 0 Emsley, 1360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2720 Ramachandran restraints generated. 1360 Oldfield, 0 Emsley, 1360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 358 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 294 time to evaluate : 0.677 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: D 54 GLN cc_start: 0.9305 (OUTLIER) cc_final: 0.8766 (mp10) REVERT: D 71 GLN cc_start: 0.9339 (tt0) cc_final: 0.9058 (tt0) REVERT: D 75 TYR cc_start: 0.9197 (m-80) cc_final: 0.8841 (m-80) REVERT: D 105 MET cc_start: 0.9300 (mtp) cc_final: 0.8798 (mtp) REVERT: D 124 MET cc_start: 0.9222 (ttm) cc_final: 0.8938 (tpp) REVERT: D 132 ILE cc_start: 0.9281 (mm) cc_final: 0.8999 (mt) REVERT: D 206 LYS cc_start: 0.9241 (ttpp) cc_final: 0.8776 (ttmm) REVERT: E 14 LYS cc_start: 0.9065 (mttm) cc_final: 0.8761 (mmtm) REVERT: E 54 ARG cc_start: 0.2960 (mtt180) cc_final: 0.2675 (mpt180) REVERT: E 116 GLU cc_start: 0.8710 (tm-30) cc_final: 0.8210 (tm-30) REVERT: F 5 GLU cc_start: 0.8692 (tt0) cc_final: 0.8388 (tm-30) REVERT: F 17 GLN cc_start: 0.9349 (tp-100) cc_final: 0.8980 (tm-30) REVERT: F 35 LYS cc_start: 0.9373 (mptt) cc_final: 0.8935 (mmtt) REVERT: F 62 MET cc_start: 0.8401 (mpp) cc_final: 0.8073 (mpp) REVERT: F 88 MET cc_start: 0.9139 (tpt) cc_final: 0.8907 (tpp) REVERT: H 3 MET cc_start: 0.9230 (tmm) cc_final: 0.8790 (tmm) REVERT: H 58 GLU cc_start: 0.8418 (mm-30) cc_final: 0.8036 (mm-30) REVERT: H 80 ARG cc_start: 0.9250 (mtm110) cc_final: 0.8861 (mtp-110) REVERT: H 96 MET cc_start: 0.9153 (mtp) cc_final: 0.8420 (ttm) REVERT: H 126 ILE cc_start: 0.9662 (mp) cc_final: 0.8337 (mp) REVERT: K 24 HIS cc_start: 0.8647 (t70) cc_final: 0.8339 (t70) REVERT: K 70 CYS cc_start: 0.8750 (t) cc_final: 0.8397 (m) REVERT: K 75 LYS cc_start: 0.8863 (pptt) cc_final: 0.8492 (mmtt) REVERT: K 85 MET cc_start: 0.9047 (mtm) cc_final: 0.8704 (pmm) REVERT: K 94 GLU cc_start: 0.9312 (tt0) cc_final: 0.8764 (tm-30) REVERT: K 98 ARG cc_start: 0.8998 (tmm-80) cc_final: 0.8796 (tmm-80) REVERT: O 80 GLN cc_start: 0.9111 (tp-100) cc_final: 0.8729 (tp-100) REVERT: P 53 ASP cc_start: 0.9043 (t0) cc_final: 0.8808 (t0) REVERT: P 76 LYS cc_start: 0.9591 (ttmm) cc_final: 0.9353 (tptt) REVERT: Q 7 THR cc_start: 0.9358 (OUTLIER) cc_final: 0.8991 (m) REVERT: Q 8 LEU cc_start: 0.9336 (tp) cc_final: 0.8871 (tt) REVERT: Q 60 GLU cc_start: 0.8562 (tt0) cc_final: 0.8153 (mm-30) REVERT: Q 61 ILE cc_start: 0.9402 (mm) cc_final: 0.9037 (mm) REVERT: Q 75 LEU cc_start: 0.8760 (OUTLIER) cc_final: 0.8394 (pt) REVERT: Q 81 LYS cc_start: 0.8579 (tppt) cc_final: 0.8055 (tppt) REVERT: R 32 TYR cc_start: 0.8777 (m-80) cc_final: 0.8554 (m-80) REVERT: T 24 ARG cc_start: 0.9222 (tpp-160) cc_final: 0.8869 (mmm-85) REVERT: X 37 ARG cc_start: 0.9178 (ttp80) cc_final: 0.8915 (ttp80) REVERT: X 72 TYR cc_start: 0.7796 (t80) cc_final: 0.7588 (t80) outliers start: 64 outliers final: 34 residues processed: 335 average time/residue: 0.2310 time to fit residues: 119.3144 Evaluate side-chains 302 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 265 time to evaluate : 0.603 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 54 GLN Chi-restraints excluded: chain D residue 169 THR Chi-restraints excluded: chain D residue 187 GLU Chi-restraints excluded: chain D residue 195 ILE Chi-restraints excluded: chain D residue 196 ASN Chi-restraints excluded: chain D residue 200 ILE Chi-restraints excluded: chain E residue 34 THR Chi-restraints excluded: chain E residue 48 PHE Chi-restraints excluded: chain E residue 85 VAL Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 10 VAL Chi-restraints excluded: chain F residue 13 ASP Chi-restraints excluded: chain F residue 18 VAL Chi-restraints excluded: chain F residue 61 LEU Chi-restraints excluded: chain H residue 74 SER Chi-restraints excluded: chain H residue 112 THR Chi-restraints excluded: chain K residue 23 ILE Chi-restraints excluded: chain K residue 108 THR Chi-restraints excluded: chain L residue 49 LEU Chi-restraints excluded: chain L residue 97 THR Chi-restraints excluded: chain P residue 2 VAL Chi-restraints excluded: chain P residue 3 THR Chi-restraints excluded: chain P residue 42 ILE Chi-restraints excluded: chain P residue 57 ILE Chi-restraints excluded: chain Q residue 7 THR Chi-restraints excluded: chain Q residue 55 ILE Chi-restraints excluded: chain Q residue 75 LEU Chi-restraints excluded: chain R residue 39 ILE Chi-restraints excluded: chain X residue 11 MET Chi-restraints excluded: chain X residue 50 ASP Chi-restraints excluded: chain X residue 74 LEU Chi-restraints excluded: chain X residue 89 GLU Chi-restraints excluded: chain X residue 102 VAL Chi-restraints excluded: chain X residue 105 MET Chi-restraints excluded: chain X residue 109 ASN Chi-restraints excluded: chain X residue 110 ARG Chi-restraints excluded: chain X residue 146 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 239 random chunks: [60, 149, 138, 83, 50, 206, 157, 120, 136, 80, 228] chunk 60 optimal weight: 8.9990 chunk 149 optimal weight: 6.9990 chunk 138 optimal weight: 1.9990 chunk 83 optimal weight: 10.0000 chunk 50 optimal weight: 9.9990 chunk 206 optimal weight: 7.9990 chunk 157 optimal weight: 9.9990 chunk 120 optimal weight: 8.9990 chunk 136 optimal weight: 6.9990 chunk 80 optimal weight: 9.9990 chunk 228 optimal weight: 4.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 35 GLN ** Q 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2931 r_free = 0.2931 target = 0.028783 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2630 r_free = 0.2630 target = 0.022470 restraints weight = 373124.012| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2661 r_free = 0.2661 target = 0.023263 restraints weight = 140434.984| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.2682 r_free = 0.2682 target = 0.023746 restraints weight = 81245.179| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.2695 r_free = 0.2695 target = 0.024018 restraints weight = 59249.258| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.2701 r_free = 0.2701 target = 0.024167 restraints weight = 49669.802| |-----------------------------------------------------------------------------| r_work (final): 0.2695 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8910 moved from start: 0.4326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.056 36656 Z= 0.332 Angle : 1.168 12.944 54791 Z= 0.473 Chirality : 0.081 0.839 6995 Planarity : 0.005 0.076 2986 Dihedral : 19.928 179.561 14347 Min Nonbonded Distance : 1.834 Molprobity Statistics. All-atom Clashscore : 24.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 5.86 % Allowed : 23.95 % Favored : 70.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.16 (0.22), residues: 1360 helix: 0.19 (0.22), residues: 520 sheet: -1.72 (0.30), residues: 268 loop : -1.06 (0.25), residues: 572 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG Q 27 TYR 0.025 0.002 TYR R 70 PHE 0.018 0.002 PHE X 28 TRP 0.031 0.004 TRP X 113 HIS 0.007 0.001 HIS L 72 Details of bonding type rmsd/Z covalent geometry : bond 0.00667 / 0.33 (36656) covalent geometry : angle 1.16786 / 0.47 (54791) hydrogen bonds : bond 0.11707 / 6.08 ( 1262) hydrogen bonds : angle 4.57230 / 1.83 ( 2396) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2720 Ramachandran restraints generated. 1360 Oldfield, 0 Emsley, 1360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2720 Ramachandran restraints generated. 1360 Oldfield, 0 Emsley, 1360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 354 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 287 time to evaluate : 0.524 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 54 GLN cc_start: 0.9160 (OUTLIER) cc_final: 0.8943 (mp10) REVERT: D 105 MET cc_start: 0.9270 (mtp) cc_final: 0.8808 (mtp) REVERT: D 124 MET cc_start: 0.9258 (ttm) cc_final: 0.8873 (tpp) REVERT: E 14 LYS cc_start: 0.9022 (mttm) cc_final: 0.8759 (mmtm) REVERT: E 20 ARG cc_start: 0.8540 (tmm-80) cc_final: 0.8047 (ttt180) REVERT: E 66 LYS cc_start: 0.9694 (mtpp) cc_final: 0.9479 (mtpp) REVERT: E 71 MET cc_start: 0.8898 (tpp) cc_final: 0.8121 (tpp) REVERT: F 17 GLN cc_start: 0.9375 (tp-100) cc_final: 0.8995 (tm-30) REVERT: F 35 LYS cc_start: 0.9431 (mptt) cc_final: 0.8993 (mmtt) REVERT: F 42 TRP cc_start: 0.8282 (m-10) cc_final: 0.8061 (m-10) REVERT: F 62 MET cc_start: 0.8440 (mpp) cc_final: 0.8145 (mpp) REVERT: F 88 MET cc_start: 0.9148 (tpt) cc_final: 0.8254 (tpt) REVERT: H 3 MET cc_start: 0.9243 (tmm) cc_final: 0.9031 (tmm) REVERT: H 80 ARG cc_start: 0.9261 (mtm110) cc_final: 0.8819 (mtp-110) REVERT: H 121 LEU cc_start: 0.9292 (tp) cc_final: 0.9057 (tp) REVERT: K 24 HIS cc_start: 0.8576 (t70) cc_final: 0.8349 (t70) REVERT: K 70 CYS cc_start: 0.8842 (t) cc_final: 0.8498 (m) REVERT: K 75 LYS cc_start: 0.8757 (pptt) cc_final: 0.8366 (mmtt) REVERT: K 94 GLU cc_start: 0.9334 (tt0) cc_final: 0.8768 (tm-30) REVERT: O 59 MET cc_start: 0.9245 (mtm) cc_final: 0.8810 (mtp) REVERT: O 71 LYS cc_start: 0.9607 (ttpt) cc_final: 0.9205 (ttpt) REVERT: O 80 GLN cc_start: 0.9130 (tp-100) cc_final: 0.8743 (tp-100) REVERT: P 33 ILE cc_start: 0.9812 (mm) cc_final: 0.9216 (mm) REVERT: P 47 GLU cc_start: 0.8230 (tt0) cc_final: 0.7763 (mt-10) REVERT: P 53 ASP cc_start: 0.9029 (t0) cc_final: 0.8817 (t0) REVERT: P 76 LYS cc_start: 0.9583 (ttmm) cc_final: 0.9249 (tptt) REVERT: Q 7 THR cc_start: 0.9402 (OUTLIER) cc_final: 0.8952 (m) REVERT: Q 8 LEU cc_start: 0.9297 (tp) cc_final: 0.8759 (tt) REVERT: Q 60 GLU cc_start: 0.8469 (tt0) cc_final: 0.8191 (mm-30) REVERT: Q 61 ILE cc_start: 0.9391 (mm) cc_final: 0.9069 (mm) REVERT: Q 69 LYS cc_start: 0.8987 (ttmt) cc_final: 0.8681 (ttpp) REVERT: Q 81 LYS cc_start: 0.8495 (tppt) cc_final: 0.8038 (tppt) REVERT: R 32 TYR cc_start: 0.8770 (m-80) cc_final: 0.8497 (m-80) REVERT: R 67 LEU cc_start: 0.9683 (OUTLIER) cc_final: 0.9437 (mp) REVERT: T 24 ARG cc_start: 0.9230 (tpp-160) cc_final: 0.8871 (mmm-85) REVERT: T 85 LYS cc_start: 0.9319 (OUTLIER) cc_final: 0.8919 (mmmm) REVERT: X 37 ARG cc_start: 0.9201 (ttp80) cc_final: 0.8971 (ttp80) REVERT: X 56 HIS cc_start: 0.9127 (OUTLIER) cc_final: 0.8438 (p-80) REVERT: X 72 TYR cc_start: 0.8171 (t80) cc_final: 0.7840 (t80) REVERT: X 124 MET cc_start: 0.9117 (tmm) cc_final: 0.8833 (tmm) outliers start: 67 outliers final: 45 residues processed: 326 average time/residue: 0.2323 time to fit residues: 117.2392 Evaluate side-chains 313 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 263 time to evaluate : 0.656 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 54 GLN Chi-restraints excluded: chain D residue 169 THR Chi-restraints excluded: chain D residue 187 GLU Chi-restraints excluded: chain D residue 195 ILE Chi-restraints excluded: chain D residue 196 ASN Chi-restraints excluded: chain D residue 200 ILE Chi-restraints excluded: chain E residue 34 THR Chi-restraints excluded: chain E residue 48 PHE Chi-restraints excluded: chain E residue 61 GLN Chi-restraints excluded: chain E residue 72 ILE Chi-restraints excluded: chain E residue 85 VAL Chi-restraints excluded: chain E residue 140 THR Chi-restraints excluded: chain F residue 10 VAL Chi-restraints excluded: chain F residue 13 ASP Chi-restraints excluded: chain F residue 18 VAL Chi-restraints excluded: chain F residue 53 LYS Chi-restraints excluded: chain F residue 61 LEU Chi-restraints excluded: chain F residue 85 ILE Chi-restraints excluded: chain H residue 72 VAL Chi-restraints excluded: chain H residue 112 THR Chi-restraints excluded: chain K residue 23 ILE Chi-restraints excluded: chain K residue 55 SER Chi-restraints excluded: chain K residue 108 THR Chi-restraints excluded: chain L residue 49 LEU Chi-restraints excluded: chain L residue 80 ILE Chi-restraints excluded: chain L residue 90 LEU Chi-restraints excluded: chain L residue 97 THR Chi-restraints excluded: chain O residue 10 LYS Chi-restraints excluded: chain O residue 22 THR Chi-restraints excluded: chain O residue 25 THR Chi-restraints excluded: chain P residue 2 VAL Chi-restraints excluded: chain P residue 3 THR Chi-restraints excluded: chain P residue 42 ILE Chi-restraints excluded: chain P residue 59 HIS Chi-restraints excluded: chain Q residue 7 THR Chi-restraints excluded: chain Q residue 28 PHE Chi-restraints excluded: chain Q residue 42 THR Chi-restraints excluded: chain Q residue 55 ILE Chi-restraints excluded: chain R residue 26 ILE Chi-restraints excluded: chain R residue 33 ILE Chi-restraints excluded: chain R residue 39 ILE Chi-restraints excluded: chain R residue 67 LEU Chi-restraints excluded: chain T residue 85 LYS Chi-restraints excluded: chain X residue 42 SER Chi-restraints excluded: chain X residue 50 ASP Chi-restraints excluded: chain X residue 56 HIS Chi-restraints excluded: chain X residue 89 GLU Chi-restraints excluded: chain X residue 110 ARG Chi-restraints excluded: chain X residue 125 ILE Chi-restraints excluded: chain X residue 146 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 239 random chunks: [175, 194, 46, 4, 75, 35, 51, 174, 225, 164, 96] chunk 175 optimal weight: 10.0000 chunk 194 optimal weight: 1.9990 chunk 46 optimal weight: 10.0000 chunk 4 optimal weight: 8.9990 chunk 75 optimal weight: 10.0000 chunk 35 optimal weight: 8.9990 chunk 51 optimal weight: 10.0000 chunk 174 optimal weight: 6.9990 chunk 225 optimal weight: 6.9990 chunk 164 optimal weight: 9.9990 chunk 96 optimal weight: 9.9990 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 76 GLN ** T 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2921 r_free = 0.2921 target = 0.028526 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2620 r_free = 0.2620 target = 0.022240 restraints weight = 377744.047| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.2651 r_free = 0.2651 target = 0.023026 restraints weight = 140596.212| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2672 r_free = 0.2672 target = 0.023501 restraints weight = 80940.205| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.2684 r_free = 0.2684 target = 0.023778 restraints weight = 58998.420| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.2692 r_free = 0.2692 target = 0.023930 restraints weight = 49244.949| |-----------------------------------------------------------------------------| r_work (final): 0.2684 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8916 moved from start: 0.4487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.063 36656 Z= 0.376 Angle : 1.200 13.491 54791 Z= 0.486 Chirality : 0.081 0.838 6995 Planarity : 0.005 0.060 2986 Dihedral : 19.961 179.955 14347 Min Nonbonded Distance : 1.848 Molprobity Statistics. All-atom Clashscore : 26.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer: Outliers : 7.08 % Allowed : 25.00 % Favored : 67.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.13 (0.22), residues: 1360 helix: 0.15 (0.22), residues: 514 sheet: -1.59 (0.30), residues: 261 loop : -1.02 (0.26), residues: 585 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG L 14 TYR 0.026 0.002 TYR R 70 PHE 0.013 0.002 PHE E 95 TRP 0.041 0.004 TRP X 113 HIS 0.012 0.002 HIS O 46 Details of bonding type rmsd/Z covalent geometry : bond 0.00753 / 0.38 (36656) covalent geometry : angle 1.19994 / 0.49 (54791) hydrogen bonds : bond 0.11962 / 6.22 ( 1262) hydrogen bonds : angle 4.64164 / 1.85 ( 2396) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2720 Ramachandran restraints generated. 1360 Oldfield, 0 Emsley, 1360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2720 Ramachandran restraints generated. 1360 Oldfield, 0 Emsley, 1360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 355 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 274 time to evaluate : 0.659 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 54 GLN cc_start: 0.9149 (OUTLIER) cc_final: 0.8761 (mp10) REVERT: D 75 TYR cc_start: 0.9245 (m-80) cc_final: 0.8889 (m-80) REVERT: D 105 MET cc_start: 0.9287 (mtp) cc_final: 0.8817 (mtp) REVERT: D 124 MET cc_start: 0.9215 (ttm) cc_final: 0.8992 (tpp) REVERT: E 14 LYS cc_start: 0.9150 (mttm) cc_final: 0.8730 (mmtm) REVERT: E 66 LYS cc_start: 0.9708 (mtpp) cc_final: 0.9466 (mtpp) REVERT: E 165 LEU cc_start: 0.9244 (mt) cc_final: 0.8891 (pp) REVERT: F 62 MET cc_start: 0.8359 (mpp) cc_final: 0.8036 (mpp) REVERT: F 88 MET cc_start: 0.9076 (tpt) cc_final: 0.8186 (tpt) REVERT: H 3 MET cc_start: 0.9149 (tmm) cc_final: 0.8939 (tmm) REVERT: H 75 ILE cc_start: 0.8650 (OUTLIER) cc_final: 0.8353 (pp) REVERT: H 80 ARG cc_start: 0.9238 (mtm110) cc_final: 0.8794 (mtp-110) REVERT: H 96 MET cc_start: 0.9194 (mtp) cc_final: 0.8432 (ttm) REVERT: H 121 LEU cc_start: 0.9365 (tp) cc_final: 0.9132 (tp) REVERT: K 70 CYS cc_start: 0.8833 (t) cc_final: 0.8481 (m) REVERT: K 75 LYS cc_start: 0.8890 (pptt) cc_final: 0.8439 (mmtt) REVERT: K 85 MET cc_start: 0.9153 (mtm) cc_final: 0.8919 (pmm) REVERT: K 94 GLU cc_start: 0.9324 (tt0) cc_final: 0.8617 (tm-30) REVERT: K 98 ARG cc_start: 0.9036 (tmm-80) cc_final: 0.8797 (ptt-90) REVERT: O 59 MET cc_start: 0.9307 (mtm) cc_final: 0.8803 (mtp) REVERT: O 72 ARG cc_start: 0.8366 (ptt90) cc_final: 0.8138 (ppt170) REVERT: O 80 GLN cc_start: 0.9147 (tp-100) cc_final: 0.8790 (tp-100) REVERT: P 34 GLU cc_start: 0.8977 (pm20) cc_final: 0.8724 (pm20) REVERT: P 47 GLU cc_start: 0.8325 (tt0) cc_final: 0.7942 (mt-10) REVERT: P 76 LYS cc_start: 0.9524 (ttmm) cc_final: 0.9238 (tptt) REVERT: P 80 LYS cc_start: 0.9287 (mtpp) cc_final: 0.9062 (mttt) REVERT: Q 7 THR cc_start: 0.9407 (OUTLIER) cc_final: 0.8963 (m) REVERT: Q 8 LEU cc_start: 0.9323 (tp) cc_final: 0.8771 (tp) REVERT: Q 60 GLU cc_start: 0.8487 (tt0) cc_final: 0.8052 (mm-30) REVERT: Q 61 ILE cc_start: 0.9401 (mm) cc_final: 0.9118 (mm) REVERT: Q 69 LYS cc_start: 0.8968 (ttmt) cc_final: 0.8729 (ttmt) REVERT: Q 75 LEU cc_start: 0.8812 (OUTLIER) cc_final: 0.8346 (pt) REVERT: R 67 LEU cc_start: 0.9704 (OUTLIER) cc_final: 0.9455 (mp) REVERT: T 24 ARG cc_start: 0.9186 (tpp-160) cc_final: 0.8907 (mmm-85) REVERT: T 60 ARG cc_start: 0.9366 (OUTLIER) cc_final: 0.8984 (mtm-85) REVERT: T 85 LYS cc_start: 0.9305 (OUTLIER) cc_final: 0.8906 (mmmm) REVERT: X 37 ARG cc_start: 0.9189 (ttp80) cc_final: 0.8924 (ttp80) REVERT: X 46 ILE cc_start: 0.9000 (OUTLIER) cc_final: 0.8680 (mp) REVERT: X 56 HIS cc_start: 0.9134 (OUTLIER) cc_final: 0.8424 (p-80) REVERT: X 72 TYR cc_start: 0.8507 (t80) cc_final: 0.8291 (t80) REVERT: X 124 MET cc_start: 0.9080 (tmm) cc_final: 0.8842 (tmm) outliers start: 81 outliers final: 56 residues processed: 321 average time/residue: 0.2370 time to fit residues: 117.2277 Evaluate side-chains 316 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 251 time to evaluate : 0.680 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 54 GLN Chi-restraints excluded: chain D residue 145 ILE Chi-restraints excluded: chain D residue 169 THR Chi-restraints excluded: chain D residue 187 GLU Chi-restraints excluded: chain D residue 195 ILE Chi-restraints excluded: chain D residue 196 ASN Chi-restraints excluded: chain D residue 200 ILE Chi-restraints excluded: chain E residue 29 ARG Chi-restraints excluded: chain E residue 34 THR Chi-restraints excluded: chain E residue 48 PHE Chi-restraints excluded: chain E residue 55 GLU Chi-restraints excluded: chain E residue 61 GLN Chi-restraints excluded: chain E residue 85 VAL Chi-restraints excluded: chain E residue 101 GLU Chi-restraints excluded: chain E residue 140 THR Chi-restraints excluded: chain F residue 10 VAL Chi-restraints excluded: chain F residue 13 ASP Chi-restraints excluded: chain F residue 18 VAL Chi-restraints excluded: chain F residue 47 LEU Chi-restraints excluded: chain F residue 53 LYS Chi-restraints excluded: chain F residue 61 LEU Chi-restraints excluded: chain F residue 81 ASN Chi-restraints excluded: chain F residue 87 SER Chi-restraints excluded: chain H residue 75 ILE Chi-restraints excluded: chain H residue 99 LEU Chi-restraints excluded: chain H residue 112 THR Chi-restraints excluded: chain H residue 125 ILE Chi-restraints excluded: chain K residue 23 ILE Chi-restraints excluded: chain K residue 31 ILE Chi-restraints excluded: chain K residue 55 SER Chi-restraints excluded: chain K residue 108 THR Chi-restraints excluded: chain L residue 49 LEU Chi-restraints excluded: chain L residue 80 ILE Chi-restraints excluded: chain L residue 90 LEU Chi-restraints excluded: chain L residue 97 THR Chi-restraints excluded: chain O residue 10 LYS Chi-restraints excluded: chain O residue 22 THR Chi-restraints excluded: chain O residue 25 THR Chi-restraints excluded: chain P residue 2 VAL Chi-restraints excluded: chain P residue 3 THR Chi-restraints excluded: chain P residue 59 HIS Chi-restraints excluded: chain Q residue 7 THR Chi-restraints excluded: chain Q residue 28 PHE Chi-restraints excluded: chain Q residue 33 ILE Chi-restraints excluded: chain Q residue 42 THR Chi-restraints excluded: chain Q residue 50 ASN Chi-restraints excluded: chain Q residue 53 CYS Chi-restraints excluded: chain Q residue 55 ILE Chi-restraints excluded: chain Q residue 75 LEU Chi-restraints excluded: chain R residue 18 VAL Chi-restraints excluded: chain R residue 26 ILE Chi-restraints excluded: chain R residue 33 ILE Chi-restraints excluded: chain R residue 39 ILE Chi-restraints excluded: chain R residue 67 LEU Chi-restraints excluded: chain T residue 60 ARG Chi-restraints excluded: chain T residue 85 LYS Chi-restraints excluded: chain X residue 42 SER Chi-restraints excluded: chain X residue 46 ILE Chi-restraints excluded: chain X residue 50 ASP Chi-restraints excluded: chain X residue 56 HIS Chi-restraints excluded: chain X residue 89 GLU Chi-restraints excluded: chain X residue 110 ARG Chi-restraints excluded: chain X residue 120 VAL Chi-restraints excluded: chain X residue 125 ILE Chi-restraints excluded: chain X residue 146 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 239 random chunks: [81, 58, 72, 158, 93, 134, 55, 195, 152, 160, 142] chunk 81 optimal weight: 7.9990 chunk 58 optimal weight: 7.9990 chunk 72 optimal weight: 8.9990 chunk 158 optimal weight: 6.9990 chunk 93 optimal weight: 20.0000 chunk 134 optimal weight: 5.9990 chunk 55 optimal weight: 7.9990 chunk 195 optimal weight: 2.9990 chunk 152 optimal weight: 6.9990 chunk 160 optimal weight: 0.9980 chunk 142 optimal weight: 3.9990 overall best weight: 4.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2958 r_free = 0.2958 target = 0.029514 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2661 r_free = 0.2661 target = 0.023181 restraints weight = 365989.816| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.2692 r_free = 0.2692 target = 0.023987 restraints weight = 137609.129| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.2713 r_free = 0.2713 target = 0.024481 restraints weight = 79313.330| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.2726 r_free = 0.2726 target = 0.024761 restraints weight = 57665.646| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.2733 r_free = 0.2733 target = 0.024918 restraints weight = 48253.616| |-----------------------------------------------------------------------------| r_work (final): 0.2726 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8890 moved from start: 0.4858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 36656 Z= 0.260 Angle : 1.090 12.718 54791 Z= 0.443 Chirality : 0.077 0.795 6995 Planarity : 0.005 0.054 2986 Dihedral : 19.779 179.373 14347 Min Nonbonded Distance : 1.880 Molprobity Statistics. All-atom Clashscore : 20.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 6.03 % Allowed : 26.05 % Favored : 67.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.00 (0.23), residues: 1360 helix: 0.32 (0.23), residues: 516 sheet: -1.68 (0.29), residues: 282 loop : -0.89 (0.27), residues: 562 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG L 14 TYR 0.020 0.002 TYR R 70 PHE 0.014 0.002 PHE E 95 TRP 0.034 0.004 TRP X 113 HIS 0.006 0.001 HIS X 56 Details of bonding type rmsd/Z covalent geometry : bond 0.00522 / 0.26 (36656) covalent geometry : angle 1.08955 / 0.44 (54791) hydrogen bonds : bond 0.11179 / 5.81 ( 1262) hydrogen bonds : angle 4.42924 / 1.77 ( 2396) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2720 Ramachandran restraints generated. 1360 Oldfield, 0 Emsley, 1360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2720 Ramachandran restraints generated. 1360 Oldfield, 0 Emsley, 1360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 353 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 284 time to evaluate : 0.639 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: D 54 GLN cc_start: 0.9127 (OUTLIER) cc_final: 0.8923 (mp10) REVERT: D 105 MET cc_start: 0.9267 (mtp) cc_final: 0.8824 (mtp) REVERT: D 124 MET cc_start: 0.9205 (ttm) cc_final: 0.8942 (tpp) REVERT: E 12 GLN cc_start: 0.8589 (mp10) cc_final: 0.8354 (pm20) REVERT: E 14 LYS cc_start: 0.9154 (mttm) cc_final: 0.8661 (mmtm) REVERT: E 29 ARG cc_start: 0.6732 (OUTLIER) cc_final: 0.6505 (ptp-110) REVERT: E 61 GLN cc_start: 0.9514 (OUTLIER) cc_final: 0.9256 (tp-100) REVERT: E 64 MET cc_start: 0.8929 (mmm) cc_final: 0.8661 (mmm) REVERT: E 66 LYS cc_start: 0.9704 (mtpp) cc_final: 0.9462 (mtpp) REVERT: E 71 MET cc_start: 0.8887 (tpp) cc_final: 0.8071 (tpp) REVERT: E 116 GLU cc_start: 0.8719 (tp30) cc_final: 0.8483 (tp30) REVERT: E 131 THR cc_start: 0.9108 (p) cc_final: 0.8863 (m) REVERT: E 165 LEU cc_start: 0.9265 (mt) cc_final: 0.8986 (pp) REVERT: F 1 MET cc_start: 0.9207 (ptp) cc_final: 0.8923 (ttp) REVERT: F 17 GLN cc_start: 0.9143 (tm-30) cc_final: 0.8899 (tm-30) REVERT: F 35 LYS cc_start: 0.9373 (mptt) cc_final: 0.8955 (mmtt) REVERT: F 42 TRP cc_start: 0.8146 (m-10) cc_final: 0.7834 (m-10) REVERT: F 62 MET cc_start: 0.8413 (mpp) cc_final: 0.8148 (mpp) REVERT: F 88 MET cc_start: 0.9092 (tpt) cc_final: 0.8221 (tpt) REVERT: H 42 GLU cc_start: 0.9096 (mt-10) cc_final: 0.8642 (mp0) REVERT: H 80 ARG cc_start: 0.9234 (mtm110) cc_final: 0.8801 (mtm110) REVERT: H 96 MET cc_start: 0.9205 (mtp) cc_final: 0.8429 (ttm) REVERT: H 121 LEU cc_start: 0.9397 (tp) cc_final: 0.9157 (tp) REVERT: K 70 CYS cc_start: 0.8734 (t) cc_final: 0.8492 (m) REVERT: K 75 LYS cc_start: 0.8950 (pptt) cc_final: 0.8416 (mmtt) REVERT: K 85 MET cc_start: 0.9017 (mtm) cc_final: 0.8791 (pmm) REVERT: K 98 ARG cc_start: 0.8947 (tmm-80) cc_final: 0.8619 (ptt90) REVERT: O 59 MET cc_start: 0.9282 (mtm) cc_final: 0.8888 (mtp) REVERT: O 80 GLN cc_start: 0.9139 (tp-100) cc_final: 0.8803 (tp-100) REVERT: P 34 GLU cc_start: 0.9160 (pm20) cc_final: 0.8886 (pm20) REVERT: P 47 GLU cc_start: 0.8383 (tt0) cc_final: 0.8036 (mt-10) REVERT: P 76 LYS cc_start: 0.9534 (ttmm) cc_final: 0.9289 (tptt) REVERT: Q 8 LEU cc_start: 0.9326 (tp) cc_final: 0.8727 (tp) REVERT: Q 60 GLU cc_start: 0.8565 (tt0) cc_final: 0.8095 (mm-30) REVERT: Q 61 ILE cc_start: 0.9405 (mm) cc_final: 0.9090 (mm) REVERT: Q 69 LYS cc_start: 0.8970 (ttmt) cc_final: 0.8683 (ttpp) REVERT: Q 75 LEU cc_start: 0.8704 (OUTLIER) cc_final: 0.8208 (pt) REVERT: R 61 ARG cc_start: 0.9285 (mtt180) cc_final: 0.8484 (mtt90) REVERT: R 67 LEU cc_start: 0.9685 (OUTLIER) cc_final: 0.9423 (mp) REVERT: T 24 ARG cc_start: 0.9179 (tpp-160) cc_final: 0.8866 (mmm-85) REVERT: T 60 ARG cc_start: 0.9348 (OUTLIER) cc_final: 0.8986 (mtm-85) REVERT: T 85 LYS cc_start: 0.9314 (OUTLIER) cc_final: 0.8972 (mmmm) REVERT: X 56 HIS cc_start: 0.9135 (OUTLIER) cc_final: 0.8302 (p-80) outliers start: 69 outliers final: 48 residues processed: 326 average time/residue: 0.2279 time to fit residues: 115.3618 Evaluate side-chains 321 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 265 time to evaluate : 0.691 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 54 GLN Chi-restraints excluded: chain D residue 169 THR Chi-restraints excluded: chain D residue 187 GLU Chi-restraints excluded: chain D residue 195 ILE Chi-restraints excluded: chain D residue 196 ASN Chi-restraints excluded: chain D residue 200 ILE Chi-restraints excluded: chain E residue 29 ARG Chi-restraints excluded: chain E residue 34 THR Chi-restraints excluded: chain E residue 48 PHE Chi-restraints excluded: chain E residue 61 GLN Chi-restraints excluded: chain E residue 72 ILE Chi-restraints excluded: chain E residue 85 VAL Chi-restraints excluded: chain E residue 140 THR Chi-restraints excluded: chain F residue 10 VAL Chi-restraints excluded: chain F residue 13 ASP Chi-restraints excluded: chain F residue 18 VAL Chi-restraints excluded: chain F residue 53 LYS Chi-restraints excluded: chain F residue 61 LEU Chi-restraints excluded: chain F residue 85 ILE Chi-restraints excluded: chain F residue 87 SER Chi-restraints excluded: chain H residue 112 THR Chi-restraints excluded: chain K residue 23 ILE Chi-restraints excluded: chain K residue 31 ILE Chi-restraints excluded: chain K residue 55 SER Chi-restraints excluded: chain K residue 108 THR Chi-restraints excluded: chain L residue 49 LEU Chi-restraints excluded: chain L residue 80 ILE Chi-restraints excluded: chain L residue 90 LEU Chi-restraints excluded: chain L residue 97 THR Chi-restraints excluded: chain O residue 22 THR Chi-restraints excluded: chain O residue 25 THR Chi-restraints excluded: chain P residue 2 VAL Chi-restraints excluded: chain P residue 3 THR Chi-restraints excluded: chain P residue 59 HIS Chi-restraints excluded: chain P residue 74 LEU Chi-restraints excluded: chain Q residue 28 PHE Chi-restraints excluded: chain Q residue 42 THR Chi-restraints excluded: chain Q residue 55 ILE Chi-restraints excluded: chain Q residue 75 LEU Chi-restraints excluded: chain R residue 18 VAL Chi-restraints excluded: chain R residue 26 ILE Chi-restraints excluded: chain R residue 33 ILE Chi-restraints excluded: chain R residue 39 ILE Chi-restraints excluded: chain R residue 67 LEU Chi-restraints excluded: chain T residue 60 ARG Chi-restraints excluded: chain T residue 79 LEU Chi-restraints excluded: chain T residue 85 LYS Chi-restraints excluded: chain X residue 42 SER Chi-restraints excluded: chain X residue 56 HIS Chi-restraints excluded: chain X residue 89 GLU Chi-restraints excluded: chain X residue 102 VAL Chi-restraints excluded: chain X residue 110 ARG Chi-restraints excluded: chain X residue 120 VAL Chi-restraints excluded: chain X residue 125 ILE Chi-restraints excluded: chain X residue 129 VAL Chi-restraints excluded: chain X residue 146 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 239 random chunks: [92, 126, 58, 149, 216, 20, 198, 116, 44, 211, 55] chunk 92 optimal weight: 10.0000 chunk 126 optimal weight: 5.9990 chunk 58 optimal weight: 8.9990 chunk 149 optimal weight: 8.9990 chunk 216 optimal weight: 6.9990 chunk 20 optimal weight: 9.9990 chunk 198 optimal weight: 10.0000 chunk 116 optimal weight: 8.9990 chunk 44 optimal weight: 10.0000 chunk 211 optimal weight: 0.9990 chunk 55 optimal weight: 8.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 76 GLN ** T 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2930 r_free = 0.2930 target = 0.028737 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2630 r_free = 0.2630 target = 0.022477 restraints weight = 371660.937| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.2662 r_free = 0.2662 target = 0.023269 restraints weight = 137635.293| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2683 r_free = 0.2683 target = 0.023752 restraints weight = 78669.489| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.2696 r_free = 0.2696 target = 0.024034 restraints weight = 56978.010| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.2703 r_free = 0.2703 target = 0.024188 restraints weight = 47280.773| |-----------------------------------------------------------------------------| r_work (final): 0.2696 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8909 moved from start: 0.4796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.058 36656 Z= 0.355 Angle : 1.172 13.175 54791 Z= 0.476 Chirality : 0.079 0.776 6995 Planarity : 0.005 0.077 2986 Dihedral : 19.862 179.197 14347 Min Nonbonded Distance : 1.845 Molprobity Statistics. All-atom Clashscore : 25.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.37 % Favored : 94.63 % Rotamer: Outliers : 6.12 % Allowed : 26.14 % Favored : 67.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.08 (0.23), residues: 1360 helix: 0.20 (0.23), residues: 512 sheet: -1.68 (0.30), residues: 274 loop : -0.91 (0.27), residues: 574 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG L 14 TYR 0.036 0.003 TYR X 72 PHE 0.015 0.002 PHE E 31 TRP 0.040 0.004 TRP F 42 HIS 0.016 0.002 HIS O 46 Details of bonding type rmsd/Z covalent geometry : bond 0.00713 / 0.36 (36656) covalent geometry : angle 1.17233 / 0.48 (54791) hydrogen bonds : bond 0.11695 / 6.09 ( 1262) hydrogen bonds : angle 4.55310 / 1.81 ( 2396) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2720 Ramachandran restraints generated. 1360 Oldfield, 0 Emsley, 1360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2720 Ramachandran restraints generated. 1360 Oldfield, 0 Emsley, 1360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 334 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 264 time to evaluate : 0.615 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 54 GLN cc_start: 0.9122 (OUTLIER) cc_final: 0.8911 (mp10) REVERT: D 62 ARG cc_start: 0.8551 (OUTLIER) cc_final: 0.8226 (ttp-170) REVERT: D 75 TYR cc_start: 0.9230 (m-80) cc_final: 0.8841 (m-80) REVERT: D 105 MET cc_start: 0.9280 (mtp) cc_final: 0.8840 (mtp) REVERT: D 124 MET cc_start: 0.9212 (ttm) cc_final: 0.8959 (tpp) REVERT: D 132 ILE cc_start: 0.9390 (OUTLIER) cc_final: 0.9120 (mt) REVERT: E 14 LYS cc_start: 0.9122 (mttm) cc_final: 0.8706 (mmtm) REVERT: E 29 ARG cc_start: 0.6703 (OUTLIER) cc_final: 0.6422 (ptp-110) REVERT: E 61 GLN cc_start: 0.9532 (OUTLIER) cc_final: 0.9284 (tp-100) REVERT: E 66 LYS cc_start: 0.9703 (mtpp) cc_final: 0.9447 (mtpp) REVERT: E 71 MET cc_start: 0.8863 (tpp) cc_final: 0.8033 (tpp) REVERT: E 165 LEU cc_start: 0.9231 (mt) cc_final: 0.8947 (pp) REVERT: F 1 MET cc_start: 0.9221 (ptp) cc_final: 0.8762 (ttp) REVERT: F 17 GLN cc_start: 0.9107 (tm-30) cc_final: 0.7935 (tm-30) REVERT: F 21 MET cc_start: 0.9388 (tpp) cc_final: 0.8893 (tpp) REVERT: F 35 LYS cc_start: 0.9378 (mptt) cc_final: 0.8988 (mmtm) REVERT: F 42 TRP cc_start: 0.8370 (m-10) cc_final: 0.8168 (m-10) REVERT: F 62 MET cc_start: 0.8404 (mpp) cc_final: 0.8153 (mpp) REVERT: F 88 MET cc_start: 0.9114 (tpt) cc_final: 0.8250 (tpt) REVERT: H 3 MET cc_start: 0.8896 (tmm) cc_final: 0.8618 (tmm) REVERT: H 42 GLU cc_start: 0.9055 (mt-10) cc_final: 0.8620 (mp0) REVERT: H 80 ARG cc_start: 0.9260 (mtm110) cc_final: 0.8834 (mtm110) REVERT: H 96 MET cc_start: 0.9183 (mtp) cc_final: 0.8373 (ttm) REVERT: H 121 LEU cc_start: 0.9413 (tp) cc_final: 0.9177 (tp) REVERT: K 70 CYS cc_start: 0.8779 (t) cc_final: 0.8487 (m) REVERT: K 75 LYS cc_start: 0.8930 (pptt) cc_final: 0.8419 (mmtt) REVERT: K 85 MET cc_start: 0.9153 (mtm) cc_final: 0.8878 (pmm) REVERT: O 59 MET cc_start: 0.9370 (mtm) cc_final: 0.8870 (mtm) REVERT: O 80 GLN cc_start: 0.9143 (tp-100) cc_final: 0.8832 (tp-100) REVERT: P 34 GLU cc_start: 0.9313 (pm20) cc_final: 0.8946 (pm20) REVERT: P 47 GLU cc_start: 0.8453 (tt0) cc_final: 0.8092 (mt-10) REVERT: P 76 LYS cc_start: 0.9532 (ttmm) cc_final: 0.9284 (tptt) REVERT: Q 8 LEU cc_start: 0.9355 (tp) cc_final: 0.8840 (tt) REVERT: Q 39 LYS cc_start: 0.9145 (mtmm) cc_final: 0.8938 (mtmm) REVERT: Q 60 GLU cc_start: 0.8642 (tt0) cc_final: 0.8207 (tp30) REVERT: Q 69 LYS cc_start: 0.8972 (ttmt) cc_final: 0.8634 (ttpp) REVERT: Q 75 LEU cc_start: 0.8684 (OUTLIER) cc_final: 0.8201 (pt) REVERT: R 61 ARG cc_start: 0.9337 (mtt180) cc_final: 0.8648 (mtm180) REVERT: R 67 LEU cc_start: 0.9723 (OUTLIER) cc_final: 0.9446 (mp) REVERT: T 24 ARG cc_start: 0.9185 (tpp-160) cc_final: 0.8867 (mmm-85) REVERT: T 60 ARG cc_start: 0.9361 (OUTLIER) cc_final: 0.9009 (mtm-85) REVERT: T 85 LYS cc_start: 0.9286 (OUTLIER) cc_final: 0.8902 (mmmm) REVERT: X 46 ILE cc_start: 0.9002 (OUTLIER) cc_final: 0.8652 (mp) REVERT: X 56 HIS cc_start: 0.9191 (OUTLIER) cc_final: 0.8366 (p-80) REVERT: X 118 LYS cc_start: 0.9115 (mmmt) cc_final: 0.8897 (mmmt) outliers start: 70 outliers final: 52 residues processed: 311 average time/residue: 0.2296 time to fit residues: 110.4553 Evaluate side-chains 317 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 254 time to evaluate : 0.579 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 54 GLN Chi-restraints excluded: chain D residue 62 ARG Chi-restraints excluded: chain D residue 132 ILE Chi-restraints excluded: chain D residue 169 THR Chi-restraints excluded: chain D residue 187 GLU Chi-restraints excluded: chain D residue 195 ILE Chi-restraints excluded: chain D residue 196 ASN Chi-restraints excluded: chain D residue 200 ILE Chi-restraints excluded: chain E residue 29 ARG Chi-restraints excluded: chain E residue 34 THR Chi-restraints excluded: chain E residue 48 PHE Chi-restraints excluded: chain E residue 61 GLN Chi-restraints excluded: chain E residue 85 VAL Chi-restraints excluded: chain E residue 121 HIS Chi-restraints excluded: chain E residue 140 THR Chi-restraints excluded: chain F residue 10 VAL Chi-restraints excluded: chain F residue 13 ASP Chi-restraints excluded: chain F residue 18 VAL Chi-restraints excluded: chain F residue 47 LEU Chi-restraints excluded: chain F residue 53 LYS Chi-restraints excluded: chain F residue 61 LEU Chi-restraints excluded: chain F residue 81 ASN Chi-restraints excluded: chain F residue 85 ILE Chi-restraints excluded: chain F residue 87 SER Chi-restraints excluded: chain H residue 112 THR Chi-restraints excluded: chain K residue 23 ILE Chi-restraints excluded: chain K residue 31 ILE Chi-restraints excluded: chain K residue 55 SER Chi-restraints excluded: chain K residue 95 SER Chi-restraints excluded: chain K residue 108 THR Chi-restraints excluded: chain L residue 49 LEU Chi-restraints excluded: chain L residue 80 ILE Chi-restraints excluded: chain L residue 90 LEU Chi-restraints excluded: chain L residue 97 THR Chi-restraints excluded: chain O residue 10 LYS Chi-restraints excluded: chain O residue 22 THR Chi-restraints excluded: chain O residue 25 THR Chi-restraints excluded: chain P residue 2 VAL Chi-restraints excluded: chain P residue 3 THR Chi-restraints excluded: chain P residue 59 HIS Chi-restraints excluded: chain P residue 74 LEU Chi-restraints excluded: chain Q residue 28 PHE Chi-restraints excluded: chain Q residue 42 THR Chi-restraints excluded: chain Q residue 55 ILE Chi-restraints excluded: chain Q residue 75 LEU Chi-restraints excluded: chain R residue 18 VAL Chi-restraints excluded: chain R residue 26 ILE Chi-restraints excluded: chain R residue 33 ILE Chi-restraints excluded: chain R residue 39 ILE Chi-restraints excluded: chain R residue 67 LEU Chi-restraints excluded: chain T residue 60 ARG Chi-restraints excluded: chain T residue 79 LEU Chi-restraints excluded: chain T residue 85 LYS Chi-restraints excluded: chain X residue 42 SER Chi-restraints excluded: chain X residue 46 ILE Chi-restraints excluded: chain X residue 50 ASP Chi-restraints excluded: chain X residue 56 HIS Chi-restraints excluded: chain X residue 89 GLU Chi-restraints excluded: chain X residue 110 ARG Chi-restraints excluded: chain X residue 120 VAL Chi-restraints excluded: chain X residue 125 ILE Chi-restraints excluded: chain X residue 129 VAL Chi-restraints excluded: chain X residue 146 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 239 random chunks: [162, 125, 25, 29, 81, 34, 85, 3, 202, 22, 193] chunk 162 optimal weight: 4.9990 chunk 125 optimal weight: 5.9990 chunk 25 optimal weight: 10.0000 chunk 29 optimal weight: 7.9990 chunk 81 optimal weight: 7.9990 chunk 34 optimal weight: 10.0000 chunk 85 optimal weight: 10.0000 chunk 3 optimal weight: 8.9990 chunk 202 optimal weight: 7.9990 chunk 22 optimal weight: 7.9990 chunk 193 optimal weight: 6.9990 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 76 GLN ** T 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2923 r_free = 0.2923 target = 0.028558 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2622 r_free = 0.2622 target = 0.022294 restraints weight = 371479.670| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.2654 r_free = 0.2654 target = 0.023079 restraints weight = 138042.699| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.2675 r_free = 0.2675 target = 0.023552 restraints weight = 79315.342| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.2688 r_free = 0.2688 target = 0.023823 restraints weight = 57657.536| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.2695 r_free = 0.2695 target = 0.023976 restraints weight = 48233.826| |-----------------------------------------------------------------------------| r_work (final): 0.2687 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8915 moved from start: 0.4818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.084 36656 Z= 0.375 Angle : 1.199 13.473 54791 Z= 0.488 Chirality : 0.080 0.764 6995 Planarity : 0.006 0.083 2986 Dihedral : 19.905 179.895 14347 Min Nonbonded Distance : 1.841 Molprobity Statistics. All-atom Clashscore : 26.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.88 % Favored : 94.12 % Rotamer: Outliers : 6.56 % Allowed : 26.14 % Favored : 67.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.19 (0.23), residues: 1360 helix: 0.05 (0.22), residues: 511 sheet: -1.66 (0.30), residues: 269 loop : -0.96 (0.26), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG L 14 TYR 0.034 0.003 TYR X 72 PHE 0.014 0.002 PHE E 31 TRP 0.038 0.004 TRP F 42 HIS 0.012 0.002 HIS O 46 Details of bonding type rmsd/Z covalent geometry : bond 0.00754 / 0.38 (36656) covalent geometry : angle 1.19892 / 0.49 (54791) hydrogen bonds : bond 0.11896 / 6.21 ( 1262) hydrogen bonds : angle 4.64516 / 1.84 ( 2396) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2720 Ramachandran restraints generated. 1360 Oldfield, 0 Emsley, 1360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2720 Ramachandran restraints generated. 1360 Oldfield, 0 Emsley, 1360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 340 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 265 time to evaluate : 0.636 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 54 GLN cc_start: 0.9137 (OUTLIER) cc_final: 0.8934 (mp10) REVERT: D 62 ARG cc_start: 0.8566 (OUTLIER) cc_final: 0.8196 (ttp-170) REVERT: D 75 TYR cc_start: 0.9216 (m-80) cc_final: 0.8804 (m-80) REVERT: D 105 MET cc_start: 0.9291 (mtp) cc_final: 0.8885 (mtp) REVERT: D 124 MET cc_start: 0.9215 (ttm) cc_final: 0.8959 (tpp) REVERT: D 132 ILE cc_start: 0.9395 (OUTLIER) cc_final: 0.9118 (mt) REVERT: E 14 LYS cc_start: 0.9120 (mttm) cc_final: 0.8662 (mmtm) REVERT: E 29 ARG cc_start: 0.6526 (OUTLIER) cc_final: 0.6248 (ptp-110) REVERT: E 61 GLN cc_start: 0.9540 (OUTLIER) cc_final: 0.9121 (tp-100) REVERT: E 66 LYS cc_start: 0.9706 (mtpp) cc_final: 0.9437 (mtpp) REVERT: E 71 MET cc_start: 0.8840 (tpp) cc_final: 0.8098 (tpp) REVERT: E 165 LEU cc_start: 0.9224 (mt) cc_final: 0.8956 (pp) REVERT: F 1 MET cc_start: 0.9240 (ptp) cc_final: 0.8798 (ttp) REVERT: F 17 GLN cc_start: 0.9103 (tm-30) cc_final: 0.7753 (tm-30) REVERT: F 21 MET cc_start: 0.9406 (tpp) cc_final: 0.8845 (tpp) REVERT: F 35 LYS cc_start: 0.9364 (mptt) cc_final: 0.8985 (mmtm) REVERT: F 62 MET cc_start: 0.8408 (mpp) cc_final: 0.8158 (mpp) REVERT: F 88 MET cc_start: 0.9124 (tpt) cc_final: 0.8269 (tpt) REVERT: H 3 MET cc_start: 0.8848 (tmm) cc_final: 0.8614 (tmm) REVERT: H 42 GLU cc_start: 0.9030 (mt-10) cc_final: 0.8625 (mp0) REVERT: H 80 ARG cc_start: 0.9241 (mtm110) cc_final: 0.8828 (mtm110) REVERT: H 96 MET cc_start: 0.9193 (mtp) cc_final: 0.8413 (ttm) REVERT: H 121 LEU cc_start: 0.9402 (tp) cc_final: 0.9142 (tp) REVERT: K 70 CYS cc_start: 0.8791 (t) cc_final: 0.8439 (m) REVERT: K 75 LYS cc_start: 0.8951 (pptt) cc_final: 0.8412 (mmtt) REVERT: L 20 ASN cc_start: 0.9416 (p0) cc_final: 0.9075 (p0) REVERT: O 59 MET cc_start: 0.9347 (mtm) cc_final: 0.8725 (mtp) REVERT: O 80 GLN cc_start: 0.9149 (tp-100) cc_final: 0.8844 (tp-100) REVERT: P 47 GLU cc_start: 0.8385 (tt0) cc_final: 0.8100 (mt-10) REVERT: P 76 LYS cc_start: 0.9542 (ttmm) cc_final: 0.9218 (tptt) REVERT: P 80 LYS cc_start: 0.9295 (mttt) cc_final: 0.8788 (mtpp) REVERT: Q 8 LEU cc_start: 0.9341 (tp) cc_final: 0.8670 (tt) REVERT: Q 60 GLU cc_start: 0.8724 (tt0) cc_final: 0.8428 (tp30) REVERT: Q 61 ILE cc_start: 0.9565 (mm) cc_final: 0.9000 (tp) REVERT: Q 69 LYS cc_start: 0.8979 (ttmt) cc_final: 0.8775 (ttmm) REVERT: R 61 ARG cc_start: 0.9373 (mtt180) cc_final: 0.8652 (mtt90) REVERT: R 67 LEU cc_start: 0.9719 (OUTLIER) cc_final: 0.9464 (mp) REVERT: T 24 ARG cc_start: 0.9184 (tpp-160) cc_final: 0.8876 (mmm-85) REVERT: T 60 ARG cc_start: 0.9379 (OUTLIER) cc_final: 0.9016 (mtm-85) REVERT: T 85 LYS cc_start: 0.9283 (OUTLIER) cc_final: 0.8902 (mmmm) REVERT: X 46 ILE cc_start: 0.9030 (OUTLIER) cc_final: 0.8683 (mp) REVERT: X 56 HIS cc_start: 0.9227 (OUTLIER) cc_final: 0.8385 (p-80) REVERT: X 124 MET cc_start: 0.9030 (tmm) cc_final: 0.8678 (tmm) outliers start: 75 outliers final: 55 residues processed: 315 average time/residue: 0.2174 time to fit residues: 106.7601 Evaluate side-chains 320 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 255 time to evaluate : 0.472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 54 GLN Chi-restraints excluded: chain D residue 62 ARG Chi-restraints excluded: chain D residue 132 ILE Chi-restraints excluded: chain D residue 169 THR Chi-restraints excluded: chain D residue 187 GLU Chi-restraints excluded: chain D residue 195 ILE Chi-restraints excluded: chain D residue 196 ASN Chi-restraints excluded: chain D residue 200 ILE Chi-restraints excluded: chain E residue 29 ARG Chi-restraints excluded: chain E residue 34 THR Chi-restraints excluded: chain E residue 48 PHE Chi-restraints excluded: chain E residue 61 GLN Chi-restraints excluded: chain E residue 121 HIS Chi-restraints excluded: chain E residue 140 THR Chi-restraints excluded: chain F residue 10 VAL Chi-restraints excluded: chain F residue 13 ASP Chi-restraints excluded: chain F residue 18 VAL Chi-restraints excluded: chain F residue 47 LEU Chi-restraints excluded: chain F residue 53 LYS Chi-restraints excluded: chain F residue 61 LEU Chi-restraints excluded: chain F residue 81 ASN Chi-restraints excluded: chain F residue 84 VAL Chi-restraints excluded: chain F residue 87 SER Chi-restraints excluded: chain F residue 89 VAL Chi-restraints excluded: chain H residue 112 THR Chi-restraints excluded: chain K residue 23 ILE Chi-restraints excluded: chain K residue 31 ILE Chi-restraints excluded: chain K residue 55 SER Chi-restraints excluded: chain K residue 95 SER Chi-restraints excluded: chain K residue 108 THR Chi-restraints excluded: chain L residue 49 LEU Chi-restraints excluded: chain L residue 80 ILE Chi-restraints excluded: chain L residue 90 LEU Chi-restraints excluded: chain L residue 97 THR Chi-restraints excluded: chain O residue 10 LYS Chi-restraints excluded: chain O residue 22 THR Chi-restraints excluded: chain O residue 25 THR Chi-restraints excluded: chain P residue 2 VAL Chi-restraints excluded: chain P residue 3 THR Chi-restraints excluded: chain P residue 42 ILE Chi-restraints excluded: chain P residue 59 HIS Chi-restraints excluded: chain P residue 74 LEU Chi-restraints excluded: chain Q residue 28 PHE Chi-restraints excluded: chain Q residue 42 THR Chi-restraints excluded: chain Q residue 55 ILE Chi-restraints excluded: chain Q residue 63 GLU Chi-restraints excluded: chain Q residue 75 LEU Chi-restraints excluded: chain R residue 18 VAL Chi-restraints excluded: chain R residue 26 ILE Chi-restraints excluded: chain R residue 33 ILE Chi-restraints excluded: chain R residue 39 ILE Chi-restraints excluded: chain R residue 67 LEU Chi-restraints excluded: chain T residue 60 ARG Chi-restraints excluded: chain T residue 79 LEU Chi-restraints excluded: chain T residue 85 LYS Chi-restraints excluded: chain X residue 42 SER Chi-restraints excluded: chain X residue 46 ILE Chi-restraints excluded: chain X residue 50 ASP Chi-restraints excluded: chain X residue 56 HIS Chi-restraints excluded: chain X residue 89 GLU Chi-restraints excluded: chain X residue 110 ARG Chi-restraints excluded: chain X residue 120 VAL Chi-restraints excluded: chain X residue 125 ILE Chi-restraints excluded: chain X residue 129 VAL Chi-restraints excluded: chain X residue 146 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 239 random chunks: [188, 77, 232, 21, 99, 197, 166, 141, 0, 25, 97] chunk 188 optimal weight: 1.9990 chunk 77 optimal weight: 9.9990 chunk 232 optimal weight: 7.9990 chunk 21 optimal weight: 9.9990 chunk 99 optimal weight: 10.0000 chunk 197 optimal weight: 0.1980 chunk 166 optimal weight: 30.0000 chunk 141 optimal weight: 7.9990 chunk 0 optimal weight: 9.9990 chunk 25 optimal weight: 8.9990 chunk 97 optimal weight: 10.0000 overall best weight: 5.4388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 76 GLN H 118 GLN K 38 GLN ** Q 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2936 r_free = 0.2936 target = 0.028916 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2639 r_free = 0.2639 target = 0.022662 restraints weight = 365566.467| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.2670 r_free = 0.2670 target = 0.023448 restraints weight = 136801.609| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2691 r_free = 0.2691 target = 0.023926 restraints weight = 78665.912| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.2703 r_free = 0.2703 target = 0.024200 restraints weight = 57213.562| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.2710 r_free = 0.2710 target = 0.024358 restraints weight = 47797.176| |-----------------------------------------------------------------------------| r_work (final): 0.2703 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8900 moved from start: 0.4953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.091 36656 Z= 0.316 Angle : 1.150 12.861 54791 Z= 0.470 Chirality : 0.079 0.752 6995 Planarity : 0.005 0.070 2986 Dihedral : 19.849 179.882 14347 Min Nonbonded Distance : 1.854 Molprobity Statistics. All-atom Clashscore : 24.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.51 % Favored : 94.49 % Rotamer: Outliers : 5.86 % Allowed : 27.97 % Favored : 66.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.15 (0.23), residues: 1360 helix: 0.05 (0.22), residues: 521 sheet: -1.52 (0.31), residues: 264 loop : -1.00 (0.27), residues: 575 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG L 14 TYR 0.032 0.002 TYR X 72 PHE 0.029 0.002 PHE H 66 TRP 0.035 0.004 TRP F 42 HIS 0.011 0.001 HIS O 46 Details of bonding type rmsd/Z covalent geometry : bond 0.00636 / 0.32 (36656) covalent geometry : angle 1.15022 / 0.47 (54791) hydrogen bonds : bond 0.11541 / 6.02 ( 1262) hydrogen bonds : angle 4.56799 / 1.82 ( 2396) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2720 Ramachandran restraints generated. 1360 Oldfield, 0 Emsley, 1360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2720 Ramachandran restraints generated. 1360 Oldfield, 0 Emsley, 1360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 333 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 266 time to evaluate : 0.472 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 62 ARG cc_start: 0.8543 (OUTLIER) cc_final: 0.8327 (ttp-110) REVERT: D 75 TYR cc_start: 0.9204 (m-80) cc_final: 0.8828 (m-80) REVERT: D 105 MET cc_start: 0.9254 (mtp) cc_final: 0.8826 (mtp) REVERT: D 124 MET cc_start: 0.9198 (ttm) cc_final: 0.8969 (tpp) REVERT: D 132 ILE cc_start: 0.9389 (OUTLIER) cc_final: 0.9106 (mt) REVERT: E 14 LYS cc_start: 0.9097 (mttm) cc_final: 0.8838 (mmtm) REVERT: E 29 ARG cc_start: 0.6624 (OUTLIER) cc_final: 0.6331 (ptp-110) REVERT: E 66 LYS cc_start: 0.9701 (mtpp) cc_final: 0.9447 (mtpp) REVERT: E 71 MET cc_start: 0.8842 (tpp) cc_final: 0.8130 (tpp) REVERT: E 86 LYS cc_start: 0.9311 (ttmm) cc_final: 0.8979 (mmtt) REVERT: E 165 LEU cc_start: 0.9213 (mt) cc_final: 0.8949 (pp) REVERT: F 1 MET cc_start: 0.9198 (ptp) cc_final: 0.8890 (ttp) REVERT: F 17 GLN cc_start: 0.9072 (tm-30) cc_final: 0.7790 (tm-30) REVERT: F 21 MET cc_start: 0.9366 (tpp) cc_final: 0.8775 (tpp) REVERT: F 35 LYS cc_start: 0.9375 (mptt) cc_final: 0.8953 (mmtt) REVERT: F 42 TRP cc_start: 0.8253 (m-10) cc_final: 0.8037 (m-10) REVERT: F 62 MET cc_start: 0.8441 (mpp) cc_final: 0.8185 (mpp) REVERT: F 88 MET cc_start: 0.9107 (tpt) cc_final: 0.8236 (tpt) REVERT: H 42 GLU cc_start: 0.9041 (mt-10) cc_final: 0.8602 (mp0) REVERT: H 67 GLN cc_start: 0.9294 (mp10) cc_final: 0.8619 (pm20) REVERT: H 80 ARG cc_start: 0.9234 (mtm110) cc_final: 0.8824 (mtm110) REVERT: H 121 LEU cc_start: 0.9393 (tp) cc_final: 0.9129 (tp) REVERT: K 75 LYS cc_start: 0.8934 (pptt) cc_final: 0.8394 (mmtt) REVERT: K 85 MET cc_start: 0.9119 (mtm) cc_final: 0.8874 (pmm) REVERT: L 20 ASN cc_start: 0.9439 (p0) cc_final: 0.9108 (p0) REVERT: O 53 ARG cc_start: 0.9349 (tpp80) cc_final: 0.9093 (tpp80) REVERT: O 59 MET cc_start: 0.9280 (mtm) cc_final: 0.8961 (mtp) REVERT: O 71 LYS cc_start: 0.9578 (ttpt) cc_final: 0.9160 (ttpt) REVERT: O 80 GLN cc_start: 0.9100 (tp-100) cc_final: 0.8794 (tp-100) REVERT: P 47 GLU cc_start: 0.8354 (tt0) cc_final: 0.8095 (mt-10) REVERT: P 76 LYS cc_start: 0.9508 (ttmm) cc_final: 0.9233 (tptt) REVERT: P 80 LYS cc_start: 0.9266 (mttt) cc_final: 0.8899 (mttm) REVERT: Q 8 LEU cc_start: 0.9361 (tp) cc_final: 0.8705 (tt) REVERT: Q 60 GLU cc_start: 0.8683 (tt0) cc_final: 0.8378 (tp30) REVERT: Q 61 ILE cc_start: 0.9561 (mm) cc_final: 0.9032 (tp) REVERT: Q 69 LYS cc_start: 0.8968 (ttmt) cc_final: 0.8763 (ttmm) REVERT: R 61 ARG cc_start: 0.9377 (mtt180) cc_final: 0.8777 (mtm180) REVERT: R 67 LEU cc_start: 0.9719 (OUTLIER) cc_final: 0.9464 (mp) REVERT: T 24 ARG cc_start: 0.9160 (tpp-160) cc_final: 0.8868 (mmm-85) REVERT: T 60 ARG cc_start: 0.9366 (OUTLIER) cc_final: 0.8992 (mtm-85) REVERT: T 85 LYS cc_start: 0.9262 (OUTLIER) cc_final: 0.8890 (mmmm) REVERT: X 46 ILE cc_start: 0.9053 (OUTLIER) cc_final: 0.8749 (mp) REVERT: X 56 HIS cc_start: 0.9217 (OUTLIER) cc_final: 0.8372 (p-80) REVERT: X 103 LEU cc_start: 0.8209 (OUTLIER) cc_final: 0.7957 (pp) REVERT: X 110 ARG cc_start: 0.4966 (OUTLIER) cc_final: 0.3116 (ptp90) REVERT: X 124 MET cc_start: 0.9013 (tmm) cc_final: 0.8687 (tmm) outliers start: 67 outliers final: 50 residues processed: 312 average time/residue: 0.2262 time to fit residues: 108.9232 Evaluate side-chains 321 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 261 time to evaluate : 0.517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 62 ARG Chi-restraints excluded: chain D residue 132 ILE Chi-restraints excluded: chain D residue 169 THR Chi-restraints excluded: chain D residue 187 GLU Chi-restraints excluded: chain D residue 195 ILE Chi-restraints excluded: chain D residue 196 ASN Chi-restraints excluded: chain D residue 200 ILE Chi-restraints excluded: chain E residue 29 ARG Chi-restraints excluded: chain E residue 34 THR Chi-restraints excluded: chain E residue 48 PHE Chi-restraints excluded: chain E residue 121 HIS Chi-restraints excluded: chain E residue 140 THR Chi-restraints excluded: chain F residue 10 VAL Chi-restraints excluded: chain F residue 13 ASP Chi-restraints excluded: chain F residue 18 VAL Chi-restraints excluded: chain F residue 47 LEU Chi-restraints excluded: chain F residue 53 LYS Chi-restraints excluded: chain F residue 61 LEU Chi-restraints excluded: chain F residue 81 ASN Chi-restraints excluded: chain F residue 84 VAL Chi-restraints excluded: chain F residue 87 SER Chi-restraints excluded: chain H residue 112 THR Chi-restraints excluded: chain K residue 23 ILE Chi-restraints excluded: chain K residue 31 ILE Chi-restraints excluded: chain K residue 55 SER Chi-restraints excluded: chain K residue 95 SER Chi-restraints excluded: chain K residue 108 THR Chi-restraints excluded: chain L residue 49 LEU Chi-restraints excluded: chain L residue 80 ILE Chi-restraints excluded: chain L residue 90 LEU Chi-restraints excluded: chain L residue 97 THR Chi-restraints excluded: chain O residue 10 LYS Chi-restraints excluded: chain O residue 22 THR Chi-restraints excluded: chain O residue 25 THR Chi-restraints excluded: chain P residue 2 VAL Chi-restraints excluded: chain P residue 3 THR Chi-restraints excluded: chain P residue 59 HIS Chi-restraints excluded: chain P residue 74 LEU Chi-restraints excluded: chain Q residue 28 PHE Chi-restraints excluded: chain Q residue 42 THR Chi-restraints excluded: chain Q residue 55 ILE Chi-restraints excluded: chain R residue 18 VAL Chi-restraints excluded: chain R residue 26 ILE Chi-restraints excluded: chain R residue 33 ILE Chi-restraints excluded: chain R residue 39 ILE Chi-restraints excluded: chain R residue 67 LEU Chi-restraints excluded: chain T residue 60 ARG Chi-restraints excluded: chain T residue 79 LEU Chi-restraints excluded: chain T residue 85 LYS Chi-restraints excluded: chain X residue 42 SER Chi-restraints excluded: chain X residue 46 ILE Chi-restraints excluded: chain X residue 50 ASP Chi-restraints excluded: chain X residue 56 HIS Chi-restraints excluded: chain X residue 89 GLU Chi-restraints excluded: chain X residue 103 LEU Chi-restraints excluded: chain X residue 110 ARG Chi-restraints excluded: chain X residue 120 VAL Chi-restraints excluded: chain X residue 125 ILE Chi-restraints excluded: chain X residue 129 VAL Chi-restraints excluded: chain X residue 146 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 239 random chunks: [54, 172, 138, 91, 221, 47, 103, 87, 219, 43, 61] chunk 54 optimal weight: 8.9990 chunk 172 optimal weight: 9.9990 chunk 138 optimal weight: 0.9980 chunk 91 optimal weight: 10.0000 chunk 221 optimal weight: 9.9990 chunk 47 optimal weight: 9.9990 chunk 103 optimal weight: 10.0000 chunk 87 optimal weight: 8.9990 chunk 219 optimal weight: 6.9990 chunk 43 optimal weight: 9.9990 chunk 61 optimal weight: 8.9990 overall best weight: 6.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 76 GLN ** Q 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2918 r_free = 0.2918 target = 0.028466 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2619 r_free = 0.2619 target = 0.022229 restraints weight = 374677.998| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.2650 r_free = 0.2650 target = 0.023005 restraints weight = 138968.463| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.2671 r_free = 0.2671 target = 0.023481 restraints weight = 79733.390| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.2684 r_free = 0.2684 target = 0.023748 restraints weight = 57970.112| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.2691 r_free = 0.2691 target = 0.023896 restraints weight = 48555.022| |-----------------------------------------------------------------------------| r_work (final): 0.2684 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8917 moved from start: 0.4920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.070 36656 Z= 0.384 Angle : 1.214 13.653 54791 Z= 0.496 Chirality : 0.081 0.735 6995 Planarity : 0.006 0.072 2986 Dihedral : 19.936 178.722 14347 Min Nonbonded Distance : 1.842 Molprobity Statistics. All-atom Clashscore : 27.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.18 % Favored : 93.82 % Rotamer: Outliers : 5.86 % Allowed : 28.23 % Favored : 65.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.35 (0.22), residues: 1360 helix: -0.23 (0.22), residues: 520 sheet: -1.56 (0.31), residues: 264 loop : -1.03 (0.26), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG L 14 TYR 0.032 0.003 TYR X 72 PHE 0.035 0.002 PHE H 66 TRP 0.040 0.004 TRP F 42 HIS 0.024 0.002 HIS O 46 Details of bonding type rmsd/Z covalent geometry : bond 0.00771 / 0.38 (36656) covalent geometry : angle 1.21402 / 0.50 (54791) hydrogen bonds : bond 0.12053 / 6.30 ( 1262) hydrogen bonds : angle 4.68842 / 1.88 ( 2396) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2720 Ramachandran restraints generated. 1360 Oldfield, 0 Emsley, 1360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2720 Ramachandran restraints generated. 1360 Oldfield, 0 Emsley, 1360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 330 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 263 time to evaluate : 0.639 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 62 ARG cc_start: 0.8568 (OUTLIER) cc_final: 0.8200 (ttp-170) REVERT: D 75 TYR cc_start: 0.9191 (m-80) cc_final: 0.8766 (m-80) REVERT: D 105 MET cc_start: 0.9292 (mtp) cc_final: 0.8873 (mtp) REVERT: D 124 MET cc_start: 0.9205 (ttm) cc_final: 0.8950 (tpp) REVERT: D 132 ILE cc_start: 0.9406 (OUTLIER) cc_final: 0.9148 (mt) REVERT: E 14 LYS cc_start: 0.9227 (mttm) cc_final: 0.8837 (mmtm) REVERT: E 29 ARG cc_start: 0.6609 (OUTLIER) cc_final: 0.6342 (ptp-110) REVERT: E 66 LYS cc_start: 0.9721 (mtpp) cc_final: 0.9475 (mtpp) REVERT: E 71 MET cc_start: 0.8807 (tpp) cc_final: 0.8156 (tpp) REVERT: E 86 LYS cc_start: 0.9301 (ttmm) cc_final: 0.8883 (tppt) REVERT: E 165 LEU cc_start: 0.9238 (mt) cc_final: 0.8961 (pp) REVERT: F 1 MET cc_start: 0.9181 (ptp) cc_final: 0.8741 (ttp) REVERT: F 17 GLN cc_start: 0.9118 (tm-30) cc_final: 0.7888 (tm-30) REVERT: F 21 MET cc_start: 0.9414 (tpp) cc_final: 0.9005 (mpp) REVERT: F 35 LYS cc_start: 0.9375 (mptt) cc_final: 0.8987 (mmtm) REVERT: F 42 TRP cc_start: 0.8383 (m-10) cc_final: 0.8172 (m-10) REVERT: F 62 MET cc_start: 0.8450 (mpp) cc_final: 0.8180 (mpp) REVERT: F 88 MET cc_start: 0.9118 (tpt) cc_final: 0.8280 (tpt) REVERT: H 42 GLU cc_start: 0.9009 (mt-10) cc_final: 0.8599 (mp0) REVERT: H 80 ARG cc_start: 0.9233 (mtm110) cc_final: 0.8811 (mtm110) REVERT: H 96 MET cc_start: 0.9125 (mtp) cc_final: 0.8677 (ttm) REVERT: H 121 LEU cc_start: 0.9454 (tp) cc_final: 0.9188 (tp) REVERT: K 75 LYS cc_start: 0.9012 (pptt) cc_final: 0.8547 (mmtt) REVERT: K 85 MET cc_start: 0.9155 (mtm) cc_final: 0.8908 (pmm) REVERT: L 20 ASN cc_start: 0.9431 (p0) cc_final: 0.9093 (p0) REVERT: O 59 MET cc_start: 0.9356 (mtm) cc_final: 0.8856 (mtp) REVERT: O 80 GLN cc_start: 0.9140 (tp-100) cc_final: 0.8875 (tp-100) REVERT: P 76 LYS cc_start: 0.9551 (ttmm) cc_final: 0.9182 (tptt) REVERT: P 80 LYS cc_start: 0.9299 (mttt) cc_final: 0.8753 (mtpp) REVERT: Q 8 LEU cc_start: 0.9366 (tp) cc_final: 0.8649 (tt) REVERT: Q 60 GLU cc_start: 0.8651 (tt0) cc_final: 0.8318 (tp30) REVERT: Q 61 ILE cc_start: 0.9621 (mm) cc_final: 0.9271 (mm) REVERT: R 61 ARG cc_start: 0.9389 (mtt180) cc_final: 0.8779 (mtm-85) REVERT: R 67 LEU cc_start: 0.9724 (OUTLIER) cc_final: 0.9473 (mp) REVERT: T 24 ARG cc_start: 0.9176 (tpp-160) cc_final: 0.8884 (mmm-85) REVERT: T 85 LYS cc_start: 0.9277 (OUTLIER) cc_final: 0.8903 (mmmm) REVERT: X 46 ILE cc_start: 0.9064 (OUTLIER) cc_final: 0.8705 (mp) REVERT: X 56 HIS cc_start: 0.9253 (OUTLIER) cc_final: 0.8394 (p-80) REVERT: X 103 LEU cc_start: 0.8222 (OUTLIER) cc_final: 0.7975 (pp) REVERT: X 124 MET cc_start: 0.8985 (tmm) cc_final: 0.8740 (tmm) outliers start: 67 outliers final: 54 residues processed: 306 average time/residue: 0.2310 time to fit residues: 109.8205 Evaluate side-chains 317 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 255 time to evaluate : 0.623 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 62 ARG Chi-restraints excluded: chain D residue 132 ILE Chi-restraints excluded: chain D residue 169 THR Chi-restraints excluded: chain D residue 187 GLU Chi-restraints excluded: chain D residue 195 ILE Chi-restraints excluded: chain D residue 196 ASN Chi-restraints excluded: chain D residue 200 ILE Chi-restraints excluded: chain E residue 29 ARG Chi-restraints excluded: chain E residue 34 THR Chi-restraints excluded: chain E residue 48 PHE Chi-restraints excluded: chain E residue 121 HIS Chi-restraints excluded: chain E residue 140 THR Chi-restraints excluded: chain F residue 10 VAL Chi-restraints excluded: chain F residue 13 ASP Chi-restraints excluded: chain F residue 18 VAL Chi-restraints excluded: chain F residue 47 LEU Chi-restraints excluded: chain F residue 53 LYS Chi-restraints excluded: chain F residue 61 LEU Chi-restraints excluded: chain F residue 81 ASN Chi-restraints excluded: chain F residue 84 VAL Chi-restraints excluded: chain F residue 85 ILE Chi-restraints excluded: chain F residue 87 SER Chi-restraints excluded: chain F residue 89 VAL Chi-restraints excluded: chain H residue 112 THR Chi-restraints excluded: chain K residue 23 ILE Chi-restraints excluded: chain K residue 31 ILE Chi-restraints excluded: chain K residue 55 SER Chi-restraints excluded: chain K residue 95 SER Chi-restraints excluded: chain K residue 108 THR Chi-restraints excluded: chain L residue 49 LEU Chi-restraints excluded: chain L residue 80 ILE Chi-restraints excluded: chain L residue 90 LEU Chi-restraints excluded: chain L residue 97 THR Chi-restraints excluded: chain O residue 10 LYS Chi-restraints excluded: chain O residue 22 THR Chi-restraints excluded: chain O residue 25 THR Chi-restraints excluded: chain P residue 2 VAL Chi-restraints excluded: chain P residue 3 THR Chi-restraints excluded: chain P residue 59 HIS Chi-restraints excluded: chain P residue 74 LEU Chi-restraints excluded: chain Q residue 28 PHE Chi-restraints excluded: chain Q residue 42 THR Chi-restraints excluded: chain Q residue 55 ILE Chi-restraints excluded: chain Q residue 63 GLU Chi-restraints excluded: chain R residue 18 VAL Chi-restraints excluded: chain R residue 26 ILE Chi-restraints excluded: chain R residue 33 ILE Chi-restraints excluded: chain R residue 39 ILE Chi-restraints excluded: chain R residue 67 LEU Chi-restraints excluded: chain T residue 79 LEU Chi-restraints excluded: chain T residue 85 LYS Chi-restraints excluded: chain X residue 42 SER Chi-restraints excluded: chain X residue 46 ILE Chi-restraints excluded: chain X residue 50 ASP Chi-restraints excluded: chain X residue 56 HIS Chi-restraints excluded: chain X residue 89 GLU Chi-restraints excluded: chain X residue 103 LEU Chi-restraints excluded: chain X residue 110 ARG Chi-restraints excluded: chain X residue 120 VAL Chi-restraints excluded: chain X residue 125 ILE Chi-restraints excluded: chain X residue 129 VAL Chi-restraints excluded: chain X residue 146 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 239 random chunks: [91, 171, 204, 75, 208, 14, 220, 233, 214, 192, 65] chunk 91 optimal weight: 8.9990 chunk 171 optimal weight: 10.0000 chunk 204 optimal weight: 4.9990 chunk 75 optimal weight: 10.0000 chunk 208 optimal weight: 4.9990 chunk 14 optimal weight: 8.9990 chunk 220 optimal weight: 10.0000 chunk 233 optimal weight: 6.9990 chunk 214 optimal weight: 3.9990 chunk 192 optimal weight: 2.9990 chunk 65 optimal weight: 8.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 76 GLN Q 50 ASN ** T 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2945 r_free = 0.2945 target = 0.029170 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2650 r_free = 0.2650 target = 0.022910 restraints weight = 365349.989| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.2681 r_free = 0.2681 target = 0.023702 restraints weight = 136639.894| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2702 r_free = 0.2702 target = 0.024167 restraints weight = 78587.020| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.2714 r_free = 0.2714 target = 0.024450 restraints weight = 57548.478| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.2721 r_free = 0.2721 target = 0.024591 restraints weight = 48024.477| |-----------------------------------------------------------------------------| r_work (final): 0.2713 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8894 moved from start: 0.5132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.064 36656 Z= 0.288 Angle : 1.132 12.586 54791 Z= 0.466 Chirality : 0.078 0.715 6995 Planarity : 0.005 0.069 2986 Dihedral : 19.842 179.218 14347 Min Nonbonded Distance : 1.855 Molprobity Statistics. All-atom Clashscore : 23.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.15 % Favored : 94.85 % Rotamer: Outliers : 5.33 % Allowed : 28.76 % Favored : 65.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.25 (0.23), residues: 1360 helix: -0.13 (0.22), residues: 520 sheet: -1.64 (0.31), residues: 261 loop : -0.90 (0.27), residues: 579 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG L 14 TYR 0.029 0.002 TYR X 72 PHE 0.033 0.002 PHE H 66 TRP 0.030 0.003 TRP F 42 HIS 0.024 0.002 HIS O 46 Details of bonding type rmsd/Z covalent geometry : bond 0.00582 / 0.29 (36656) covalent geometry : angle 1.13215 / 0.47 (54791) hydrogen bonds : bond 0.11431 / 5.97 ( 1262) hydrogen bonds : angle 4.60871 / 1.84 ( 2396) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5831.01 seconds wall clock time: 101 minutes 57.01 seconds (6117.01 seconds total)