Starting phenix.real_space_refine on Tue Sep 15 16:14:20 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6nqb_0482/09_2026/6nqb_0482.cif Found real_map, /net/cci-nas-00/data/ceres_data/6nqb_0482/09_2026/6nqb_0482.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6nqb_0482/09_2026/6nqb_0482.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6nqb_0482/09_2026/6nqb_0482.map" restraint_files = "/net/cci-nas-00/data/ceres_data/6nqb_0482/09_2026/6nqb_0482.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6nqb_0482/09_2026/6nqb_0482.cif" model { file = "/net/cci-nas-00/data/ceres_data/6nqb_0482/09_2026/6nqb_0482.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6nqb_0482/09_2026/6nqb_0482.cif" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 1.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 1341 5.49 5 Mg 1 5.21 5 S 49 5.16 5 C 21496 2.51 5 N 7902 2.21 5 O 11781 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 42570 Number of models: 1 Model: "" Number of chains: 17 Chain: "C" Number of atoms: 1624 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1624 Classifications: {'peptide': 206} Link IDs: {'PTRANS': 7, 'TRANS': 198} Chain: "J" Number of atoms: 786 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 786 Classifications: {'peptide': 98} Link IDs: {'CIS': 1, 'PTRANS': 5, 'TRANS': 91} Chain: "N" Number of atoms: 774 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 774 Classifications: {'peptide': 96} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 91} Chain breaks: 1 Chain: "S" Number of atoms: 594 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 594 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 5, 'TRANS': 68} Chain: "A" Number of atoms: 28767 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1341, 28767 Classifications: {'RNAv2': 1341} Modifications used: {'rna2p_pur': 98, 'rna2p_pyr': 68, 'rna3p_pur': 663, 'rna3p_pyr': 512} Link IDs: {'rna2p': 165, 'rna3p': 1175} Chain breaks: 2 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: 1089 Number of conformers: 1 Conformer: "" Number of residues, atoms: 149, 1089 Classifications: {'peptide': 149} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 143} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "F" Number of atoms: 630 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 630 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 4, 'TRANS': 72} Chain breaks: 1 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: "L" Number of atoms: 955 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 955 Classifications: {'peptide': 123} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 115} Chain: "O" Number of atoms: 698 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 698 Classifications: {'peptide': 86} Link IDs: {'TRANS': 85} Chain: "P" Number of atoms: 629 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 629 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 2, 'TRANS': 76} Chain: "Q" Number of atoms: 641 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 641 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 2, 'TRANS': 76} Chain: "R" Number of atoms: 405 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 405 Classifications: {'peptide': 49} Link IDs: {'PTRANS': 2, 'TRANS': 46} Chain breaks: 1 Chain: "T" Number of atoms: 659 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 659 Classifications: {'peptide': 85} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 83} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "B" Number of atoms: 1696 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1696 Classifications: {'peptide': 217} Link IDs: {'PTRANS': 7, 'TRANS': 209} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Time building chain proxies: 9.06, per 1000 atoms: 0.21 Number of scatterers: 42570 At special positions: 0 Unit cell: (204.943, 215.673, 154.512, 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 49 16.00 P 1341 15.00 Mg 1 11.99 O 11781 8.00 N 7902 7.00 C 21496 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: 3.55 Conformation dependent library (CDL) restraints added in 873.3 milliseconds 3432 Ramachandran restraints generated. 1716 Oldfield, 0 Emsley, 1716 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3256 Finding SS restraints... Secondary structure from input PDB file: 59 helices and 18 sheets defined 33.4% alpha, 9.4% beta 250 base pairs and 620 stacking pairs defined. Time for finding SS restraints: 6.01 Creating SS restraints... Processing helix chain 'C' and resid 27 through 40 removed outlier: 4.580A pdb=" N LEU C 32 " --> pdb=" O PHE C 28 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ASP C 33 " --> pdb=" O ALA C 29 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LYS C 37 " --> pdb=" O ASP C 33 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N VAL C 38 " --> pdb=" O SER C 34 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ARG C 39 " --> pdb=" O ASP C 35 " (cutoff:3.500A) Processing helix chain 'C' and resid 71 through 76 removed outlier: 3.889A pdb=" N VAL C 75 " --> pdb=" O ARG C 71 " (cutoff:3.500A) Processing helix chain 'C' and resid 84 through 93 removed outlier: 3.760A pdb=" N VAL C 89 " --> pdb=" O LYS C 85 " (cutoff:3.500A) removed outlier: 4.953A pdb=" N VAL C 90 " --> pdb=" O LEU C 86 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ALA C 91 " --> pdb=" O ARG C 87 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N ASP C 92 " --> pdb=" O LYS C 88 " (cutoff:3.500A) Processing helix chain 'C' and resid 111 through 125 removed outlier: 3.796A pdb=" N ILE C 119 " --> pdb=" O VAL C 115 " (cutoff:3.500A) Processing helix chain 'C' and resid 128 through 143 removed outlier: 4.367A pdb=" N LYS C 134 " --> pdb=" O ARG C 130 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N ARG C 135 " --> pdb=" O ARG C 131 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N GLN C 138 " --> pdb=" O LYS C 134 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N ALA C 140 " --> pdb=" O ALA C 136 " (cutoff:3.500A) Processing helix chain 'J' and resid 18 through 21 Processing helix chain 'J' and resid 22 through 27 removed outlier: 4.352A pdb=" N GLU J 27 " --> pdb=" O ALA J 23 " (cutoff:3.500A) Processing helix chain 'N' and resid 4 through 18 removed outlier: 4.596A pdb=" N VAL N 10 " --> pdb=" O LYS N 6 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N LYS N 11 " --> pdb=" O ALA N 7 " (cutoff:3.500A) removed outlier: 4.991A pdb=" N LEU N 15 " --> pdb=" O LYS N 11 " (cutoff:3.500A) removed outlier: 4.745A pdb=" N ALA N 16 " --> pdb=" O ARG N 12 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N ASP N 17 " --> pdb=" O VAL N 13 " (cutoff:3.500A) Processing helix chain 'N' and resid 24 through 28 removed outlier: 3.536A pdb=" N LYS N 27 " --> pdb=" O ALA N 24 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ALA N 28 " --> pdb=" O GLU N 25 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 24 through 28' Processing helix chain 'N' and resid 41 through 49 removed outlier: 3.918A pdb=" N LEU N 45 " --> pdb=" O TRP N 41 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N THR N 49 " --> pdb=" O LEU N 45 " (cutoff:3.500A) Processing helix chain 'N' and resid 79 through 89 removed outlier: 3.867A pdb=" N ARG N 84 " --> pdb=" O ARG N 80 " (cutoff:3.500A) Processing helix chain 'S' and resid 11 through 16 Processing helix chain 'S' and resid 40 through 44 removed outlier: 3.851A pdb=" N ILE S 44 " --> pdb=" O PRO S 41 " (cutoff:3.500A) Processing helix chain 'S' and resid 69 through 73 removed outlier: 4.139A pdb=" N GLU S 72 " --> pdb=" O LYS S 69 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N PHE S 73 " --> pdb=" O LEU S 70 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 69 through 73' Processing helix chain 'D' and resid 8 through 14 Processing helix chain 'D' and resid 24 through 28 removed outlier: 3.564A pdb=" N ILE D 27 " --> pdb=" O VAL D 24 " (cutoff:3.500A) Processing helix chain 'D' and resid 48 through 61 removed outlier: 4.056A pdb=" N VAL D 52 " --> pdb=" O SER D 48 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N GLN D 53 " --> pdb=" O ASP D 49 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N GLU D 56 " --> pdb=" O VAL D 52 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N VAL D 60 " --> pdb=" O GLU D 56 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ARG D 61 " --> pdb=" O LYS D 57 " (cutoff:3.500A) Processing helix chain 'D' and resid 67 through 81 removed outlier: 3.738A pdb=" N ASN D 73 " --> pdb=" O ARG D 69 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ALA D 79 " --> pdb=" O TYR D 75 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N ARG D 80 " --> pdb=" O LYS D 76 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N LEU D 81 " --> pdb=" O GLU D 77 " (cutoff:3.500A) Processing helix chain 'D' and resid 84 through 95 Processing helix chain 'D' and resid 96 through 104 removed outlier: 3.573A pdb=" N ARG D 103 " --> pdb=" O ASN D 99 " (cutoff:3.500A) Processing helix chain 'D' and resid 109 through 119 Processing helix chain 'D' and resid 146 through 149 Processing helix chain 'D' and resid 157 through 164 removed outlier: 3.619A pdb=" N ALA D 161 " --> pdb=" O ALA D 157 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N GLN D 163 " --> pdb=" O GLU D 159 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ARG D 164 " --> pdb=" O LEU D 160 " (cutoff:3.500A) Processing helix chain 'D' and resid 196 through 204 removed outlier: 3.609A pdb=" N VAL D 200 " --> pdb=" O GLU D 196 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N LEU D 202 " --> pdb=" O LEU D 198 " (cutoff:3.500A) Processing helix chain 'E' and resid 55 through 67 removed outlier: 4.051A pdb=" N ILE E 59 " --> pdb=" O VAL E 55 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N GLN E 60 " --> pdb=" O PRO E 56 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N GLU E 64 " --> pdb=" O GLN E 60 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N LYS E 65 " --> pdb=" O LYS E 61 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ALA E 66 " --> pdb=" O ALA E 62 " (cutoff:3.500A) Processing helix chain 'E' and resid 108 through 118 removed outlier: 4.159A pdb=" N ALA E 112 " --> pdb=" O GLY E 108 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N VAL E 113 " --> pdb=" O ALA E 109 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N VAL E 116 " --> pdb=" O ALA E 112 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N GLY E 118 " --> pdb=" O LEU E 114 " (cutoff:3.500A) Processing helix chain 'E' and resid 131 through 145 removed outlier: 3.990A pdb=" N VAL E 136 " --> pdb=" O PRO E 132 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N ARG E 137 " --> pdb=" O ILE E 133 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ALA E 138 " --> pdb=" O ASN E 134 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N THR E 139 " --> pdb=" O VAL E 135 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N ILE E 140 " --> pdb=" O VAL E 136 " (cutoff:3.500A) Processing helix chain 'E' and resid 148 through 157 removed outlier: 3.835A pdb=" N LYS E 155 " --> pdb=" O MET E 151 " (cutoff:3.500A) Processing helix chain 'F' and resid 14 through 16 No H-bonds generated for 'chain 'F' and resid 14 through 16' Processing helix chain 'F' and resid 17 through 25 removed outlier: 3.588A pdb=" N MET F 21 " --> pdb=" O GLN F 17 " (cutoff:3.500A) Processing helix chain 'F' and resid 26 through 31 Processing helix chain 'F' and resid 71 through 76 removed outlier: 3.694A pdb=" N GLU F 75 " --> pdb=" O ILE F 71 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N THR F 76 " --> pdb=" O ASP F 72 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 71 through 76' Processing helix chain 'H' and resid 6 through 15 removed outlier: 3.745A pdb=" N ARG H 12 " --> pdb=" O ASP H 8 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N ARG H 14 " --> pdb=" O LEU H 10 " (cutoff:3.500A) Processing helix chain 'H' and resid 29 through 40 removed outlier: 3.783A pdb=" N ALA H 34 " --> pdb=" O LYS H 30 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ALA H 36 " --> pdb=" O LYS H 32 " (cutoff:3.500A) removed outlier: 4.744A pdb=" N VAL H 38 " --> pdb=" O ALA H 34 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N LEU H 39 " --> pdb=" O ILE H 35 " (cutoff:3.500A) Processing helix chain 'H' and resid 87 through 91 Processing helix chain 'H' and resid 112 through 116 removed outlier: 4.409A pdb=" N ALA H 115 " --> pdb=" O ASP H 112 " (cutoff:3.500A) Processing helix chain 'L' and resid 2 through 7 removed outlier: 3.596A pdb=" N LEU L 6 " --> pdb=" O THR L 2 " (cutoff:3.500A) Processing helix chain 'O' and resid 4 through 9 removed outlier: 3.642A pdb=" N LYS O 9 " --> pdb=" O GLU O 5 " (cutoff:3.500A) Processing helix chain 'O' and resid 23 through 42 removed outlier: 3.525A pdb=" N ALA O 33 " --> pdb=" O ALA O 29 " (cutoff:3.500A) removed outlier: 4.661A pdb=" N LEU O 38 " --> pdb=" O GLN O 34 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N HIS O 41 " --> pdb=" O HIS O 37 " (cutoff:3.500A) Processing helix chain 'O' and resid 51 through 73 removed outlier: 3.587A pdb=" N MET O 58 " --> pdb=" O GLY O 54 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N SER O 60 " --> pdb=" O LEU O 56 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LEU O 66 " --> pdb=" O ARG O 62 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N TYR O 68 " --> pdb=" O LYS O 64 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N LYS O 72 " --> pdb=" O TYR O 68 " (cutoff:3.500A) Processing helix chain 'O' and resid 73 through 85 Processing helix chain 'P' and resid 53 through 64 removed outlier: 4.107A pdb=" N ILE P 57 " --> pdb=" O ASP P 53 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N GLY P 62 " --> pdb=" O ALA P 58 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLY P 64 " --> pdb=" O TRP P 60 " (cutoff:3.500A) Processing helix chain 'P' and resid 68 through 78 removed outlier: 4.322A pdb=" N LYS P 76 " --> pdb=" O ALA P 72 " (cutoff:3.500A) Processing helix chain 'R' and resid 24 through 30 removed outlier: 3.557A pdb=" N LEU R 28 " --> pdb=" O ASP R 24 " (cutoff:3.500A) Processing helix chain 'R' and resid 40 through 45 Processing helix chain 'R' and resid 51 through 60 removed outlier: 3.958A pdb=" N ARG R 56 " --> pdb=" O ARG R 52 " (cutoff:3.500A) Processing helix chain 'R' and resid 61 through 64 removed outlier: 3.596A pdb=" N LEU R 64 " --> pdb=" O ALA R 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 61 through 64' Processing helix chain 'T' and resid 6 through 41 removed outlier: 3.889A pdb=" N GLN T 12 " --> pdb=" O LYS T 8 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N ASN T 20 " --> pdb=" O ALA T 16 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ARG T 23 " --> pdb=" O HIS T 19 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N SER T 25 " --> pdb=" O ALA T 21 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N MET T 26 " --> pdb=" O SER T 22 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N PHE T 30 " --> pdb=" O MET T 26 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N VAL T 34 " --> pdb=" O PHE T 30 " (cutoff:3.500A) Processing helix chain 'T' and resid 43 through 60 removed outlier: 3.619A pdb=" N PHE T 50 " --> pdb=" O ALA T 46 " (cutoff:3.500A) Proline residue: T 55 - end of helix removed outlier: 3.725A pdb=" N ASP T 58 " --> pdb=" O GLN T 54 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N GLN T 60 " --> pdb=" O ILE T 56 " (cutoff:3.500A) Processing helix chain 'T' and resid 73 through 86 removed outlier: 3.904A pdb=" N THR T 79 " --> pdb=" O LYS T 75 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N LYS T 84 " --> pdb=" O ALA T 80 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N ALA T 86 " --> pdb=" O ILE T 82 " (cutoff:3.500A) Processing helix chain 'B' and resid 52 through 61 removed outlier: 4.320A pdb=" N ASN B 57 " --> pdb=" O LEU B 53 " (cutoff:3.500A) removed outlier: 4.931A pdb=" N LYS B 58 " --> pdb=" O ALA B 54 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ILE B 59 " --> pdb=" O GLU B 55 " (cutoff:3.500A) Processing helix chain 'B' and resid 102 through 112 Processing helix chain 'B' and resid 117 through 122 Processing helix chain 'B' and resid 131 through 136 removed outlier: 4.290A pdb=" N MET B 135 " --> pdb=" O LYS B 131 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ARG B 136 " --> pdb=" O GLU B 132 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 131 through 136' Processing helix chain 'B' and resid 136 through 147 removed outlier: 3.827A pdb=" N LEU B 140 " --> pdb=" O ARG B 136 " (cutoff:3.500A) removed outlier: 4.863A pdb=" N GLU B 144 " --> pdb=" O LEU B 140 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N ASN B 145 " --> pdb=" O GLU B 141 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N SER B 146 " --> pdb=" O LYS B 142 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LEU B 147 " --> pdb=" O LEU B 143 " (cutoff:3.500A) Processing helix chain 'B' and resid 148 through 151 removed outlier: 4.019A pdb=" N LYS B 151 " --> pdb=" O GLY B 148 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 148 through 151' Processing helix chain 'B' and resid 168 through 176 Processing helix chain 'B' and resid 177 through 179 No H-bonds generated for 'chain 'B' and resid 177 through 179' Processing helix chain 'B' and resid 205 through 217 removed outlier: 3.592A pdb=" N VAL B 209 " --> pdb=" O ALA B 205 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N THR B 210 " --> pdb=" O ILE B 206 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N LEU B 211 " --> pdb=" O ARG B 207 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N TYR B 212 " --> pdb=" O ALA B 208 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N LEU B 213 " --> pdb=" O VAL B 209 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N ALA B 215 " --> pdb=" O LEU B 211 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 51 through 55 removed outlier: 3.511A pdb=" N ARG C 53 " --> pdb=" O HIS C 68 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N HIS C 68 " --> pdb=" O ARG C 53 " (cutoff:3.500A) removed outlier: 5.775A pdb=" N VAL C 65 " --> pdb=" O ASN C 101 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N ALA C 103 " --> pdb=" O VAL C 65 " (cutoff:3.500A) removed outlier: 5.895A pdb=" N ILE C 67 " --> pdb=" O ALA C 103 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 168 through 169 Processing sheet with id=AA3, first strand: chain 'J' and resid 6 through 12 removed outlier: 3.707A pdb=" N LEU J 10 " --> pdb=" O ARG J 72 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N THR J 69 " --> pdb=" O ARG J 45 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'J' and resid 65 through 66 removed outlier: 3.747A pdb=" N LYS N 96 " --> pdb=" O GLU J 66 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'S' and resid 50 through 51 Processing sheet with id=AA6, first strand: chain 'D' and resid 127 through 128 Processing sheet with id=AA7, first strand: chain 'D' and resid 170 through 172 Processing sheet with id=AA8, first strand: chain 'E' and resid 12 through 14 removed outlier: 3.967A pdb=" N THR E 36 " --> pdb=" O GLY E 48 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 85 through 87 removed outlier: 3.748A pdb=" N LEU E 123 " --> pdb=" O GLN E 96 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'F' and resid 5 through 8 Processing sheet with id=AB2, first strand: chain 'H' and resid 23 through 24 removed outlier: 3.988A pdb=" N ASP H 47 " --> pdb=" O THR H 61 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'H' and resid 100 through 104 removed outlier: 7.386A pdb=" N ILE H 100 " --> pdb=" O TYR H 127 " (cutoff:3.500A) removed outlier: 5.607A pdb=" N TYR H 127 " --> pdb=" O ILE H 100 " (cutoff:3.500A) removed outlier: 7.287A pdb=" N VAL H 102 " --> pdb=" O ILE H 125 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N GLU H 123 " --> pdb=" O SER H 104 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'L' and resid 30 through 31 removed outlier: 3.597A pdb=" N GLY L 31 " --> pdb=" O ILE L 79 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'L' and resid 51 through 55 Processing sheet with id=AB6, first strand: chain 'P' and resid 18 through 21 removed outlier: 4.345A pdb=" N GLY P 37 " --> pdb=" O VAL P 19 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N VAL P 21 " --> pdb=" O ARG P 35 " (cutoff:3.500A) removed outlier: 5.378A pdb=" N ARG P 35 " --> pdb=" O VAL P 21 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ARG P 51 " --> pdb=" O PHE P 38 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'Q' and resid 7 through 10 removed outlier: 4.025A pdb=" N ARG Q 76 " --> pdb=" O GLU Q 59 " (cutoff:3.500A) removed outlier: 6.068A pdb=" N ARG Q 61 " --> pdb=" O LEU Q 74 " (cutoff:3.500A) removed outlier: 5.323A pdb=" N LEU Q 74 " --> pdb=" O ARG Q 61 " (cutoff:3.500A) removed outlier: 8.963A pdb=" N LYS Q 70 " --> pdb=" O LYS Q 42 " (cutoff:3.500A) removed outlier: 7.385A pdb=" N HIS Q 44 " --> pdb=" O LYS Q 70 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N TRP Q 72 " --> pdb=" O HIS Q 44 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N THR Q 41 " --> pdb=" O ILE Q 24 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ILE Q 24 " --> pdb=" O THR Q 41 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 30 through 33 removed outlier: 4.303A pdb=" N GLY B 32 " --> pdb=" O ILE B 39 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 89 through 91 removed outlier: 6.165A pdb=" N PHE B 68 " --> pdb=" O VAL B 91 " (cutoff:3.500A) 321 hydrogen bonds defined for protein. 903 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 594 hydrogen bonds 890 hydrogen bond angles 0 basepair planarities 250 basepair parallelities 620 stacking parallelities Total time for adding SS restraints: 14.43 Time building geometry restraints manager: 4.96 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 5140 1.32 - 1.45: 19614 1.45 - 1.57: 18690 1.57 - 1.69: 2681 1.69 - 1.81: 88 Bond restraints: 46213 Sorted by residual: bond pdb=" C VAL B 46 " pdb=" N PRO B 47 " ideal model delta sigma weight residual 1.335 1.383 -0.047 1.30e-02 5.92e+03 1.33e+01 bond pdb=" CA ARG R 62 " pdb=" C ARG R 62 " ideal model delta sigma weight residual 1.522 1.569 -0.046 1.37e-02 5.33e+03 1.14e+01 bond pdb=" CA THR B 71 " pdb=" C THR B 71 " ideal model delta sigma weight residual 1.518 1.629 -0.111 4.01e-02 6.22e+02 7.62e+00 bond pdb=" C SER H 78 " pdb=" N ARG H 79 " ideal model delta sigma weight residual 1.339 1.202 0.137 5.57e-02 3.22e+02 6.09e+00 bond pdb=" C3' A A1201 " pdb=" O3' A A1201 " ideal model delta sigma weight residual 1.415 1.455 -0.040 2.00e-02 2.50e+03 3.92e+00 ... (remaining 46208 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.63: 67714 3.63 - 7.27: 1267 7.27 - 10.90: 60 10.90 - 14.53: 10 14.53 - 18.17: 1 Bond angle restraints: 69052 Sorted by residual: angle pdb=" C THR B 19 " pdb=" N ARG B 20 " pdb=" CA ARG B 20 " ideal model delta sigma weight residual 120.38 130.91 -10.53 1.37e+00 5.33e-01 5.90e+01 angle pdb=" C3' C A 372 " pdb=" O3' C A 372 " pdb=" P A A 373 " ideal model delta sigma weight residual 119.70 128.51 -8.81 1.20e+00 6.94e-01 5.39e+01 angle pdb=" C3' U A1065 " pdb=" O3' U A1065 " pdb=" P C A1066 " ideal model delta sigma weight residual 119.70 127.94 -8.24 1.20e+00 6.94e-01 4.72e+01 angle pdb=" C3' A A1201 " pdb=" O3' A A1201 " pdb=" P U A1202 " ideal model delta sigma weight residual 119.70 127.82 -8.12 1.20e+00 6.94e-01 4.58e+01 angle pdb=" C3' G A 484 " pdb=" O3' G A 484 " pdb=" P U A 485 " ideal model delta sigma weight residual 119.70 127.61 -7.91 1.20e+00 6.94e-01 4.35e+01 ... (remaining 69047 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.81: 21883 35.81 - 71.62: 2752 71.62 - 107.43: 109 107.43 - 143.24: 4 143.24 - 179.05: 7 Dihedral angle restraints: 24755 sinusoidal: 19726 harmonic: 5029 Sorted by residual: dihedral pdb=" C4' A A 495 " pdb=" C3' A A 495 " pdb=" C2' A A 495 " pdb=" C1' A A 495 " ideal model delta sinusoidal sigma weight residual 36.34 -40.00 76.35 1 3.10e+00 1.04e-01 7.63e+02 dihedral pdb=" C4' A A 71 " pdb=" C3' A A 71 " pdb=" C2' A A 71 " pdb=" C1' A A 71 " ideal model delta sinusoidal sigma weight residual 36.35 -39.84 76.18 1 3.10e+00 1.04e-01 7.60e+02 dihedral pdb=" C4' C A1226 " pdb=" C3' C A1226 " pdb=" C2' C A1226 " pdb=" C1' C A1226 " ideal model delta sinusoidal sigma weight residual 36.34 -39.81 76.16 1 3.10e+00 1.04e-01 7.60e+02 ... (remaining 24752 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.093: 6744 0.093 - 0.187: 509 0.187 - 0.280: 1411 0.280 - 0.374: 153 0.374 - 0.467: 7 Chirality restraints: 8824 Sorted by residual: chirality pdb=" P A A 373 " pdb=" OP1 A A 373 " pdb=" OP2 A A 373 " pdb=" O5' A A 373 " both_signs ideal model delta sigma weight residual True 2.17 -2.64 -0.47 2.00e-01 2.50e+01 5.45e+00 chirality pdb=" P A A 329 " pdb=" OP1 A A 329 " pdb=" OP2 A A 329 " pdb=" O5' A A 329 " both_signs ideal model delta sigma weight residual True 2.17 -2.64 -0.47 2.00e-01 2.50e+01 5.43e+00 chirality pdb=" P C A1243 " pdb=" OP1 C A1243 " pdb=" OP2 C A1243 " pdb=" O5' C A1243 " both_signs ideal model delta sigma weight residual True 2.17 -2.62 -0.45 2.00e-01 2.50e+01 5.00e+00 ... (remaining 8821 not shown) Planarity restraints: 3762 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN B 23 " 0.053 5.00e-02 4.00e+02 8.03e-02 1.03e+01 pdb=" N PRO B 24 " -0.139 5.00e-02 4.00e+02 pdb=" CA PRO B 24 " 0.042 5.00e-02 4.00e+02 pdb=" CD PRO B 24 " 0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C CYS L 26 " 0.046 5.00e-02 4.00e+02 6.98e-02 7.78e+00 pdb=" N PRO L 27 " -0.121 5.00e-02 4.00e+02 pdb=" CA PRO L 27 " 0.036 5.00e-02 4.00e+02 pdb=" CD PRO L 27 " 0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN P 40 " -0.046 5.00e-02 4.00e+02 6.97e-02 7.77e+00 pdb=" N PRO P 41 " 0.120 5.00e-02 4.00e+02 pdb=" CA PRO P 41 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO P 41 " -0.038 5.00e-02 4.00e+02 ... (remaining 3759 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 7047 2.75 - 3.29: 37901 3.29 - 3.83: 89123 3.83 - 4.36: 101178 4.36 - 4.90: 137572 Nonbonded interactions: 372821 Sorted by model distance: nonbonded pdb=" O2' U A 662 " pdb=" OP1 G A 836 " model vdw 2.216 3.040 nonbonded pdb=" O SER N 99 " pdb=" O2' C A1114 " model vdw 2.227 3.040 nonbonded pdb=" O2' U A 343 " pdb=" O6 G A 346 " model vdw 2.239 3.040 nonbonded pdb=" OP2 C A 522 " pdb=" OH TYR L 65 " model vdw 2.260 3.040 nonbonded pdb=" OP1 U A 62 " pdb=" O2' C A 385 " model vdw 2.263 3.040 ... (remaining 372816 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.720 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: 0.060 Extract box with map and model: 0.760 Check model and map are aligned: 0.160 Set scattering table: 0.080 Process input model: 46.440 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.830 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7888 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 : 0.006 0.137 46213 Z= 0.298 Angle : 1.210 18.166 69052 Z= 0.535 Chirality : 0.113 0.467 8824 Planarity : 0.006 0.080 3762 Dihedral : 22.066 179.055 21499 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.06 % Allowed : 13.64 % Favored : 86.31 % Rotamer: Outliers : 0.41 % Allowed : 5.01 % Favored : 94.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.54 % 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: -5.36 (0.15), residues: 1716 helix: -4.19 (0.12), residues: 487 sheet: -3.39 (0.28), residues: 231 loop : -3.37 (0.16), residues: 998 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG D 13 TYR 0.029 0.003 TYR L 65 PHE 0.028 0.003 PHE B 49 TRP 0.042 0.003 TRP B 22 HIS 0.020 0.002 HIS J 15 Details of bonding type rmsd/Z covalent geometry : bond 0.00598 / 0.30 (46213) covalent geometry : angle 1.21047 / 0.54 (69052) hydrogen bonds : bond 0.31374 / 20.98 ( 915) hydrogen bonds : angle 12.00358 / 8.43 ( 1793) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3432 Ramachandran restraints generated. 1716 Oldfield, 0 Emsley, 1716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3432 Ramachandran restraints generated. 1716 Oldfield, 0 Emsley, 1716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 548 residues out of total 1458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 542 time to evaluate : 0.898 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: C 32 LEU cc_start: 0.8512 (pt) cc_final: 0.8058 (tp) REVERT: C 36 PHE cc_start: 0.9092 (t80) cc_final: 0.8795 (t80) REVERT: C 42 LEU cc_start: 0.8055 (mt) cc_final: 0.7803 (mt) REVERT: C 108 PRO cc_start: 0.6733 (Cg_endo) cc_final: 0.6221 (Cg_exo) REVERT: C 182 ASP cc_start: 0.7466 (t0) cc_final: 0.6987 (t0) REVERT: C 186 SER cc_start: 0.8401 (t) cc_final: 0.8035 (t) REVERT: J 52 LEU cc_start: 0.9090 (mp) cc_final: 0.8604 (tp) REVERT: J 69 THR cc_start: 0.7293 (m) cc_final: 0.6945 (p) REVERT: J 88 MET cc_start: 0.6361 (mpp) cc_final: 0.6076 (ptp) REVERT: N 57 SER cc_start: 0.7049 (m) cc_final: 0.6169 (t) REVERT: N 81 ILE cc_start: 0.7382 (OUTLIER) cc_final: 0.7181 (pp) REVERT: N 82 LYS cc_start: 0.8129 (mmpt) cc_final: 0.7751 (mmtm) REVERT: N 83 VAL cc_start: 0.9056 (t) cc_final: 0.8845 (t) REVERT: N 92 ILE cc_start: 0.8438 (mt) cc_final: 0.8115 (pt) REVERT: D 69 ARG cc_start: 0.8708 (mmp-170) cc_final: 0.7764 (ptt180) REVERT: D 147 LYS cc_start: 0.7851 (mttt) cc_final: 0.7563 (mmmt) REVERT: D 195 ASN cc_start: 0.8263 (m-40) cc_final: 0.7839 (t0) REVERT: E 93 VAL cc_start: 0.9586 (t) cc_final: 0.9368 (m) REVERT: E 94 PHE cc_start: 0.8663 (t80) cc_final: 0.8253 (t80) REVERT: F 4 TYR cc_start: 0.5743 (m-80) cc_final: 0.4908 (m-80) REVERT: F 17 GLN cc_start: 0.8004 (tt0) cc_final: 0.7798 (tp40) REVERT: F 68 GLN cc_start: 0.6458 (pm20) cc_final: 0.4736 (mm-40) REVERT: F 89 VAL cc_start: 0.7443 (t) cc_final: 0.6487 (m) REVERT: H 30 LYS cc_start: 0.8473 (mmpt) cc_final: 0.7802 (mttt) REVERT: H 37 ASN cc_start: 0.8116 (t0) cc_final: 0.7108 (t0) REVERT: H 87 ARG cc_start: 0.7385 (ttm170) cc_final: 0.7020 (ttt-90) REVERT: L 63 THR cc_start: 0.6556 (t) cc_final: 0.6126 (t) REVERT: L 69 GLU cc_start: 0.7089 (tt0) cc_final: 0.6315 (mm-30) REVERT: O 16 ARG cc_start: 0.8055 (ptp-170) cc_final: 0.7350 (mtm-85) REVERT: O 38 LEU cc_start: 0.8516 (mt) cc_final: 0.8089 (tt) REVERT: P 5 ARG cc_start: 0.8456 (pmt100) cc_final: 0.8255 (ptt90) REVERT: P 35 ARG cc_start: 0.8844 (tmm160) cc_final: 0.8638 (tmm-80) REVERT: Q 59 GLU cc_start: 0.7849 (mm-30) cc_final: 0.6304 (mm-30) REVERT: T 31 ILE cc_start: 0.9434 (mt) cc_final: 0.9118 (mt) REVERT: T 53 MET cc_start: 0.8431 (ptm) cc_final: 0.8075 (ppp) REVERT: T 56 ILE cc_start: 0.8880 (mt) cc_final: 0.8507 (mm) REVERT: B 29 PHE cc_start: 0.8392 (m-80) cc_final: 0.8012 (m-80) REVERT: B 112 ARG cc_start: 0.4519 (ttt90) cc_final: 0.1826 (ttm110) REVERT: B 136 ARG cc_start: 0.6514 (mtp180) cc_final: 0.6005 (mtm110) REVERT: B 191 ASP cc_start: 0.6505 (t0) cc_final: 0.6286 (t70) outliers start: 6 outliers final: 1 residues processed: 545 average time/residue: 0.3140 time to fit residues: 261.5515 Evaluate side-chains 320 residues out of total 1458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 318 time to evaluate : 0.897 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 81 ILE Chi-restraints excluded: chain O residue 11 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 299 random chunks: chunk 197 optimal weight: 6.9990 chunk 215 optimal weight: 5.9990 chunk 20 optimal weight: 20.0000 chunk 132 optimal weight: 20.0000 chunk 261 optimal weight: 4.9990 chunk 248 optimal weight: 9.9990 chunk 207 optimal weight: 8.9990 chunk 155 optimal weight: 20.0000 chunk 244 optimal weight: 0.7980 chunk 183 optimal weight: 2.9990 chunk 298 optimal weight: 8.9990 overall best weight: 4.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 5 HIS C 24 ASN C 175 HIS ** J 15 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 59 GLN ** D 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 55 HIS F 63 ASN H 15 ASN H 17 GLN ** H 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 72 ASN ** P 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 73 HIS T 20 ASN ** T 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 74 HIS B 38 HIS B 121 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4144 r_free = 0.4144 target = 0.101749 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.075837 restraints weight = 194418.520| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.078037 restraints weight = 65775.881| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 62)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.079338 restraints weight = 34995.546| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 53)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.080071 restraints weight = 24752.248| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.080393 restraints weight = 20665.859| |-----------------------------------------------------------------------------| r_work (final): 0.3690 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7842 moved from start: 0.3086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.108 46213 Z= 0.279 Angle : 1.434 18.899 69052 Z= 0.577 Chirality : 0.111 1.113 8824 Planarity : 0.006 0.072 3762 Dihedral : 20.694 179.918 18027 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 19.08 Ramachandran Plot: Outliers : 0.06 % Allowed : 13.34 % Favored : 86.60 % Rotamer: Outliers : 4.46 % Allowed : 15.04 % Favored : 80.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -4.52 (0.17), residues: 1716 helix: -2.95 (0.17), residues: 522 sheet: -3.10 (0.31), residues: 221 loop : -3.08 (0.18), residues: 973 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG F 91 TYR 0.015 0.002 TYR H 64 PHE 0.023 0.002 PHE D 106 TRP 0.025 0.002 TRP Q 72 HIS 0.011 0.002 HIS R 73 Details of bonding type rmsd/Z covalent geometry : bond 0.00566 / 0.28 (46213) covalent geometry : angle 1.43447 / 0.58 (69052) hydrogen bonds : bond 0.10823 / 6.63 ( 915) hydrogen bonds : angle 5.32828 / 3.77 ( 1793) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3432 Ramachandran restraints generated. 1716 Oldfield, 0 Emsley, 1716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3432 Ramachandran restraints generated. 1716 Oldfield, 0 Emsley, 1716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 428 residues out of total 1458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 363 time to evaluate : 0.919 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: C 36 PHE cc_start: 0.9047 (t80) cc_final: 0.8743 (t80) REVERT: C 111 ASP cc_start: 0.8321 (t70) cc_final: 0.8044 (t70) REVERT: C 143 LEU cc_start: 0.6840 (OUTLIER) cc_final: 0.6181 (mp) REVERT: C 182 ASP cc_start: 0.7276 (t0) cc_final: 0.6804 (t0) REVERT: J 52 LEU cc_start: 0.9025 (mp) cc_final: 0.8419 (tp) REVERT: N 5 MET cc_start: 0.5698 (tpt) cc_final: 0.4992 (tpp) REVERT: N 27 LYS cc_start: -0.1330 (pptt) cc_final: -0.1751 (ptpt) REVERT: N 57 SER cc_start: 0.6714 (m) cc_final: 0.6218 (t) REVERT: N 75 LYS cc_start: 0.8973 (tptt) cc_final: 0.8767 (tppt) REVERT: N 92 ILE cc_start: 0.8201 (mt) cc_final: 0.7901 (pt) REVERT: S 78 THR cc_start: 0.6733 (m) cc_final: 0.6502 (p) REVERT: D 69 ARG cc_start: 0.8863 (mmp-170) cc_final: 0.7699 (ptt180) REVERT: D 123 MET cc_start: 0.8447 (ttt) cc_final: 0.8098 (ttt) REVERT: D 195 ASN cc_start: 0.8388 (m-40) cc_final: 0.7922 (t0) REVERT: E 47 PHE cc_start: 0.6742 (p90) cc_final: 0.6019 (p90) REVERT: E 67 ARG cc_start: 0.8692 (ttm110) cc_final: 0.8154 (mtm-85) REVERT: E 94 PHE cc_start: 0.8681 (t80) cc_final: 0.8274 (t80) REVERT: F 9 MET cc_start: 0.5879 (mtt) cc_final: 0.5277 (ppp) REVERT: F 14 GLN cc_start: 0.8738 (tp-100) cc_final: 0.8083 (tp-100) REVERT: F 62 MET cc_start: 0.3190 (mmm) cc_final: 0.2464 (mmm) REVERT: F 68 GLN cc_start: 0.6654 (pm20) cc_final: 0.5310 (mm-40) REVERT: H 9 MET cc_start: 0.8066 (ttp) cc_final: 0.7616 (tmm) REVERT: H 37 ASN cc_start: 0.8401 (t0) cc_final: 0.7862 (t0) REVERT: H 63 LYS cc_start: 0.5947 (tttt) cc_final: 0.5448 (tppt) REVERT: H 87 ARG cc_start: 0.7006 (ttm170) cc_final: 0.6683 (ttt-90) REVERT: L 69 GLU cc_start: 0.7052 (tt0) cc_final: 0.6241 (mm-30) REVERT: O 16 ARG cc_start: 0.7830 (ptp-170) cc_final: 0.7015 (ptt-90) REVERT: O 38 LEU cc_start: 0.8610 (mt) cc_final: 0.8214 (tp) REVERT: R 51 GLN cc_start: 0.7657 (pm20) cc_final: 0.6711 (tp40) REVERT: R 69 TYR cc_start: 0.2365 (OUTLIER) cc_final: -0.1222 (m-10) REVERT: T 65 LEU cc_start: 0.6305 (OUTLIER) cc_final: 0.5824 (mt) REVERT: B 26 MET cc_start: 0.3208 (tpp) cc_final: 0.2392 (tpp) REVERT: B 56 LEU cc_start: 0.6738 (OUTLIER) cc_final: 0.6466 (mp) REVERT: B 125 PHE cc_start: 0.3636 (t80) cc_final: 0.3175 (t80) REVERT: B 153 MET cc_start: 0.5151 (ttm) cc_final: 0.3578 (mtp) REVERT: B 183 PHE cc_start: 0.1847 (m-10) cc_final: 0.1429 (m-10) REVERT: B 196 ASP cc_start: 0.6149 (p0) cc_final: 0.5923 (p0) outliers start: 65 outliers final: 32 residues processed: 401 average time/residue: 0.2802 time to fit residues: 178.4881 Evaluate side-chains 328 residues out of total 1458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 292 time to evaluate : 0.898 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 20 THR Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 143 LEU Chi-restraints excluded: chain C residue 149 LYS Chi-restraints excluded: chain J residue 42 LEU Chi-restraints excluded: chain N residue 44 VAL Chi-restraints excluded: chain D residue 100 VAL Chi-restraints excluded: chain D residue 109 THR Chi-restraints excluded: chain D residue 158 LEU Chi-restraints excluded: chain D residue 199 ILE Chi-restraints excluded: chain E residue 29 ILE Chi-restraints excluded: chain E residue 36 THR Chi-restraints excluded: chain E residue 79 THR Chi-restraints excluded: chain F residue 7 VAL Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 80 PHE Chi-restraints excluded: chain H residue 84 ILE Chi-restraints excluded: chain L residue 2 THR Chi-restraints excluded: chain L residue 32 VAL Chi-restraints excluded: chain L residue 46 SER Chi-restraints excluded: chain L residue 97 VAL Chi-restraints excluded: chain O residue 9 LYS Chi-restraints excluded: chain O residue 11 VAL Chi-restraints excluded: chain P residue 71 VAL Chi-restraints excluded: chain Q residue 6 THR Chi-restraints excluded: chain Q residue 27 PHE Chi-restraints excluded: chain R residue 46 THR Chi-restraints excluded: chain R residue 53 GLN Chi-restraints excluded: chain R residue 69 TYR Chi-restraints excluded: chain T residue 19 HIS Chi-restraints excluded: chain T residue 25 SER Chi-restraints excluded: chain T residue 42 ASP Chi-restraints excluded: chain T residue 65 LEU Chi-restraints excluded: chain B residue 56 LEU Chi-restraints excluded: chain B residue 93 HIS Chi-restraints excluded: chain B residue 113 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 299 random chunks: chunk 238 optimal weight: 6.9990 chunk 282 optimal weight: 20.0000 chunk 19 optimal weight: 10.0000 chunk 138 optimal weight: 30.0000 chunk 145 optimal weight: 9.9990 chunk 235 optimal weight: 1.9990 chunk 102 optimal weight: 8.9990 chunk 264 optimal weight: 7.9990 chunk 117 optimal weight: 6.9990 chunk 184 optimal weight: 5.9990 chunk 245 optimal weight: 10.0000 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 15 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 34 ASN ** D 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 139 ASN ** E 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 120 HIS F 17 GLN L 4 ASN O 37 HIS ** P 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 20 ASN ** T 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 74 HIS B 121 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4113 r_free = 0.4113 target = 0.100080 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.074960 restraints weight = 197644.350| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.077181 restraints weight = 72314.578| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.077411 restraints weight = 39567.648| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.077502 restraints weight = 31079.814| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.077742 restraints weight = 31625.553| |-----------------------------------------------------------------------------| r_work (final): 0.3629 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7898 moved from start: 0.4108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.114 46213 Z= 0.321 Angle : 1.334 18.672 69052 Z= 0.538 Chirality : 0.099 1.295 8824 Planarity : 0.006 0.073 3762 Dihedral : 20.677 179.632 18025 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 22.43 Ramachandran Plot: Outliers : 0.06 % Allowed : 14.92 % Favored : 85.02 % Rotamer: Outliers : 5.08 % Allowed : 17.58 % Favored : 77.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: -4.12 (0.18), residues: 1716 helix: -2.32 (0.20), residues: 525 sheet: -2.95 (0.31), residues: 219 loop : -3.01 (0.18), residues: 972 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG E 137 TYR 0.021 0.003 TYR C 167 PHE 0.033 0.003 PHE N 20 TRP 0.026 0.002 TRP Q 72 HIS 0.012 0.002 HIS O 45 Details of bonding type rmsd/Z covalent geometry : bond 0.00656 / 0.32 (46213) covalent geometry : angle 1.33416 / 0.54 (69052) hydrogen bonds : bond 0.10488 / 6.35 ( 915) hydrogen bonds : angle 5.00000 / 3.55 ( 1793) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3432 Ramachandran restraints generated. 1716 Oldfield, 0 Emsley, 1716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3432 Ramachandran restraints generated. 1716 Oldfield, 0 Emsley, 1716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 399 residues out of total 1458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 325 time to evaluate : 0.895 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: C 36 PHE cc_start: 0.9085 (t80) cc_final: 0.8778 (t80) REVERT: C 111 ASP cc_start: 0.8351 (t70) cc_final: 0.8080 (t70) REVERT: C 141 MET cc_start: 0.8492 (mmm) cc_final: 0.7815 (tpt) REVERT: C 143 LEU cc_start: 0.7011 (OUTLIER) cc_final: 0.6371 (mp) REVERT: C 151 GLU cc_start: 0.7092 (tt0) cc_final: 0.6670 (tm-30) REVERT: C 182 ASP cc_start: 0.7350 (t0) cc_final: 0.6916 (t0) REVERT: J 52 LEU cc_start: 0.9050 (mp) cc_final: 0.8478 (tp) REVERT: N 5 MET cc_start: 0.5975 (tpt) cc_final: 0.5432 (tpp) REVERT: S 78 THR cc_start: 0.6877 (m) cc_final: 0.6629 (p) REVERT: D 69 ARG cc_start: 0.8944 (mmp-170) cc_final: 0.7691 (ptt180) REVERT: D 74 TYR cc_start: 0.7856 (m-80) cc_final: 0.7464 (m-80) REVERT: D 123 MET cc_start: 0.8521 (ttt) cc_final: 0.8096 (ttt) REVERT: D 195 ASN cc_start: 0.8520 (m-40) cc_final: 0.8246 (t0) REVERT: E 18 ASN cc_start: 0.8553 (m110) cc_final: 0.8284 (m-40) REVERT: E 47 PHE cc_start: 0.6904 (p90) cc_final: 0.6591 (p90) REVERT: E 64 GLU cc_start: 0.8459 (tm-30) cc_final: 0.8247 (tm-30) REVERT: E 120 HIS cc_start: 0.7813 (OUTLIER) cc_final: 0.7391 (m-70) REVERT: F 18 VAL cc_start: 0.8600 (t) cc_final: 0.8151 (t) REVERT: F 62 MET cc_start: 0.3036 (mmm) cc_final: 0.2505 (mmm) REVERT: F 68 GLN cc_start: 0.6481 (pm20) cc_final: 0.5559 (mm110) REVERT: F 88 MET cc_start: 0.7716 (mtt) cc_final: 0.7101 (mpp) REVERT: H 9 MET cc_start: 0.7941 (OUTLIER) cc_final: 0.7613 (tmm) REVERT: H 15 ASN cc_start: 0.5846 (OUTLIER) cc_final: 0.5407 (t0) REVERT: H 37 ASN cc_start: 0.8481 (t0) cc_final: 0.7884 (t0) REVERT: H 63 LYS cc_start: 0.6065 (tttt) cc_final: 0.5426 (tppt) REVERT: H 64 TYR cc_start: 0.7394 (OUTLIER) cc_final: 0.6649 (p90) REVERT: H 87 ARG cc_start: 0.7186 (ttm170) cc_final: 0.6723 (ttt-90) REVERT: L 77 SER cc_start: 0.8173 (m) cc_final: 0.7874 (t) REVERT: O 38 LEU cc_start: 0.8677 (mt) cc_final: 0.8321 (tp) REVERT: O 42 PHE cc_start: 0.8335 (OUTLIER) cc_final: 0.7961 (t80) REVERT: P 28 ARG cc_start: 0.7477 (mmp80) cc_final: 0.7180 (mpp-170) REVERT: Q 8 GLN cc_start: 0.8336 (tp40) cc_final: 0.8044 (mm-40) REVERT: R 51 GLN cc_start: 0.7850 (pm20) cc_final: 0.6693 (tp-100) REVERT: R 69 TYR cc_start: 0.1548 (OUTLIER) cc_final: -0.1862 (m-10) REVERT: B 44 LYS cc_start: 0.8896 (mmtt) cc_final: 0.8670 (mmmm) REVERT: B 56 LEU cc_start: 0.6668 (OUTLIER) cc_final: 0.6460 (mp) REVERT: B 183 PHE cc_start: 0.1321 (m-10) cc_final: 0.0795 (m-10) outliers start: 74 outliers final: 44 residues processed: 364 average time/residue: 0.2740 time to fit residues: 161.1638 Evaluate side-chains 325 residues out of total 1458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 273 time to evaluate : 0.816 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 20 THR Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 143 LEU Chi-restraints excluded: chain C residue 197 VAL Chi-restraints excluded: chain J residue 42 LEU Chi-restraints excluded: chain J residue 69 THR Chi-restraints excluded: chain N residue 44 VAL Chi-restraints excluded: chain N residue 54 SER Chi-restraints excluded: chain S residue 57 VAL Chi-restraints excluded: chain D residue 27 ILE Chi-restraints excluded: chain D residue 100 VAL Chi-restraints excluded: chain E residue 29 ILE Chi-restraints excluded: chain E residue 35 LEU Chi-restraints excluded: chain E residue 36 THR Chi-restraints excluded: chain E residue 79 THR Chi-restraints excluded: chain E residue 120 HIS Chi-restraints excluded: chain F residue 7 VAL Chi-restraints excluded: chain F residue 80 PHE Chi-restraints excluded: chain H residue 9 MET Chi-restraints excluded: chain H residue 15 ASN Chi-restraints excluded: chain H residue 64 TYR Chi-restraints excluded: chain H residue 65 PHE Chi-restraints excluded: chain H residue 74 ILE Chi-restraints excluded: chain H residue 84 ILE Chi-restraints excluded: chain H residue 105 THR Chi-restraints excluded: chain L residue 2 THR Chi-restraints excluded: chain L residue 18 SER Chi-restraints excluded: chain L residue 46 SER Chi-restraints excluded: chain L residue 103 CYS Chi-restraints excluded: chain O residue 9 LYS Chi-restraints excluded: chain O residue 11 VAL Chi-restraints excluded: chain O residue 37 HIS Chi-restraints excluded: chain O residue 42 PHE Chi-restraints excluded: chain O residue 55 LEU Chi-restraints excluded: chain O residue 80 LEU Chi-restraints excluded: chain O residue 86 LEU Chi-restraints excluded: chain P residue 20 VAL Chi-restraints excluded: chain Q residue 6 THR Chi-restraints excluded: chain R residue 42 ARG Chi-restraints excluded: chain R residue 46 THR Chi-restraints excluded: chain R residue 53 GLN Chi-restraints excluded: chain R residue 69 TYR Chi-restraints excluded: chain T residue 19 HIS Chi-restraints excluded: chain T residue 25 SER Chi-restraints excluded: chain T residue 31 ILE Chi-restraints excluded: chain T residue 38 ILE Chi-restraints excluded: chain T residue 42 ASP Chi-restraints excluded: chain B residue 56 LEU Chi-restraints excluded: chain B residue 93 HIS Chi-restraints excluded: chain B residue 106 VAL Chi-restraints excluded: chain B residue 113 LEU Chi-restraints excluded: chain B residue 220 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 299 random chunks: chunk 229 optimal weight: 0.7980 chunk 273 optimal weight: 10.0000 chunk 89 optimal weight: 8.9990 chunk 160 optimal weight: 30.0000 chunk 68 optimal weight: 5.9990 chunk 192 optimal weight: 0.0870 chunk 251 optimal weight: 4.9990 chunk 283 optimal weight: 30.0000 chunk 166 optimal weight: 40.0000 chunk 275 optimal weight: 6.9990 chunk 247 optimal weight: 3.9990 overall best weight: 3.1764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 15 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 40 HIS D 70 GLN ** D 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 120 HIS E 147 ASN O 37 HIS P 26 ASN ** T 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4167 r_free = 0.4167 target = 0.103048 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.078347 restraints weight = 195159.438| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.080861 restraints weight = 69767.409| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.080980 restraints weight = 37139.755| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.081041 restraints weight = 29770.970| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.081333 restraints weight = 30532.036| |-----------------------------------------------------------------------------| r_work (final): 0.3708 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7830 moved from start: 0.4643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.080 46213 Z= 0.208 Angle : 1.154 17.734 69052 Z= 0.466 Chirality : 0.087 1.018 8824 Planarity : 0.005 0.063 3762 Dihedral : 20.182 179.847 18025 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 16.41 Ramachandran Plot: Outliers : 0.06 % Allowed : 12.06 % Favored : 87.88 % Rotamer: Outliers : 4.53 % Allowed : 20.54 % Favored : 74.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -3.60 (0.19), residues: 1716 helix: -1.75 (0.21), residues: 521 sheet: -2.62 (0.31), residues: 245 loop : -2.76 (0.19), residues: 950 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG F 24 TYR 0.017 0.002 TYR C 167 PHE 0.025 0.002 PHE C 129 TRP 0.024 0.002 TRP C 166 HIS 0.025 0.002 HIS O 37 Details of bonding type rmsd/Z covalent geometry : bond 0.00423 / 0.21 (46213) covalent geometry : angle 1.15360 / 0.47 (69052) hydrogen bonds : bond 0.09208 / 5.29 ( 915) hydrogen bonds : angle 4.47693 / 3.18 ( 1793) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3432 Ramachandran restraints generated. 1716 Oldfield, 0 Emsley, 1716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3432 Ramachandran restraints generated. 1716 Oldfield, 0 Emsley, 1716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 386 residues out of total 1458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 320 time to evaluate : 0.910 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: C 36 PHE cc_start: 0.9058 (t80) cc_final: 0.8758 (t80) REVERT: C 111 ASP cc_start: 0.8428 (t70) cc_final: 0.8117 (t70) REVERT: C 143 LEU cc_start: 0.6916 (OUTLIER) cc_final: 0.6606 (tt) REVERT: C 169 GLU cc_start: 0.7543 (tp30) cc_final: 0.7013 (mp0) REVERT: C 182 ASP cc_start: 0.7622 (t0) cc_final: 0.7216 (t0) REVERT: J 52 LEU cc_start: 0.9073 (mp) cc_final: 0.8509 (tp) REVERT: N 5 MET cc_start: 0.5948 (tpt) cc_final: 0.5537 (tpp) REVERT: N 92 ILE cc_start: 0.8620 (OUTLIER) cc_final: 0.8412 (pt) REVERT: S 78 THR cc_start: 0.7004 (m) cc_final: 0.6731 (p) REVERT: D 3 TYR cc_start: 0.7838 (t80) cc_final: 0.7236 (t80) REVERT: D 69 ARG cc_start: 0.8855 (mmp-170) cc_final: 0.7660 (ptt180) REVERT: E 12 GLU cc_start: 0.7259 (mp0) cc_final: 0.7027 (mp0) REVERT: E 18 ASN cc_start: 0.8463 (m110) cc_final: 0.8121 (m-40) REVERT: E 94 PHE cc_start: 0.8468 (t80) cc_final: 0.7930 (t80) REVERT: E 120 HIS cc_start: 0.7605 (OUTLIER) cc_final: 0.6984 (m-70) REVERT: F 24 ARG cc_start: 0.8215 (ttm110) cc_final: 0.7497 (mtm110) REVERT: F 62 MET cc_start: 0.2981 (mmm) cc_final: 0.2520 (mmm) REVERT: F 68 GLN cc_start: 0.6752 (pm20) cc_final: 0.5852 (mm-40) REVERT: F 88 MET cc_start: 0.7738 (mtt) cc_final: 0.7268 (mpp) REVERT: H 30 LYS cc_start: 0.8039 (mmpt) cc_final: 0.7415 (mptt) REVERT: H 37 ASN cc_start: 0.8403 (t0) cc_final: 0.8164 (t0) REVERT: H 63 LYS cc_start: 0.6239 (tttt) cc_final: 0.5661 (tppt) REVERT: H 64 TYR cc_start: 0.7698 (OUTLIER) cc_final: 0.6745 (p90) REVERT: H 87 ARG cc_start: 0.6903 (ttm170) cc_final: 0.6603 (ttt-90) REVERT: O 38 LEU cc_start: 0.8611 (mt) cc_final: 0.8326 (tp) REVERT: O 42 PHE cc_start: 0.8329 (OUTLIER) cc_final: 0.7981 (t80) REVERT: Q 8 GLN cc_start: 0.8226 (tp40) cc_final: 0.7938 (mm-40) REVERT: R 51 GLN cc_start: 0.7799 (pm20) cc_final: 0.6740 (tp-100) REVERT: T 26 MET cc_start: 0.8923 (ttp) cc_final: 0.8702 (tmm) REVERT: B 44 LYS cc_start: 0.8946 (mmtt) cc_final: 0.8571 (mmmm) REVERT: B 132 GLU cc_start: 0.7166 (mp0) cc_final: 0.6881 (pm20) REVERT: B 150 ILE cc_start: 0.3420 (OUTLIER) cc_final: 0.3189 (tp) REVERT: B 183 PHE cc_start: 0.1447 (m-10) cc_final: 0.1008 (m-10) REVERT: B 196 ASP cc_start: 0.6239 (p0) cc_final: 0.6014 (p0) outliers start: 66 outliers final: 40 residues processed: 361 average time/residue: 0.2720 time to fit residues: 159.1384 Evaluate side-chains 329 residues out of total 1458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 283 time to evaluate : 0.880 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 20 THR Chi-restraints excluded: chain C residue 133 MET Chi-restraints excluded: chain C residue 143 LEU Chi-restraints excluded: chain C residue 174 LEU Chi-restraints excluded: chain J residue 17 LEU Chi-restraints excluded: chain J residue 42 LEU Chi-restraints excluded: chain J residue 69 THR Chi-restraints excluded: chain N residue 44 VAL Chi-restraints excluded: chain N residue 92 ILE Chi-restraints excluded: chain D residue 100 VAL Chi-restraints excluded: chain E residue 29 ILE Chi-restraints excluded: chain E residue 35 LEU Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 79 THR Chi-restraints excluded: chain E residue 80 LEU Chi-restraints excluded: chain E residue 104 ILE Chi-restraints excluded: chain E residue 120 HIS Chi-restraints excluded: chain F residue 7 VAL Chi-restraints excluded: chain F residue 26 THR Chi-restraints excluded: chain F residue 80 PHE Chi-restraints excluded: chain H residue 64 TYR Chi-restraints excluded: chain H residue 65 PHE Chi-restraints excluded: chain H residue 84 ILE Chi-restraints excluded: chain L residue 32 VAL Chi-restraints excluded: chain L residue 46 SER Chi-restraints excluded: chain L residue 78 VAL Chi-restraints excluded: chain O residue 9 LYS Chi-restraints excluded: chain O residue 11 VAL Chi-restraints excluded: chain O residue 26 VAL Chi-restraints excluded: chain O residue 42 PHE Chi-restraints excluded: chain O residue 80 LEU Chi-restraints excluded: chain O residue 86 LEU Chi-restraints excluded: chain P residue 20 VAL Chi-restraints excluded: chain Q residue 4 ILE Chi-restraints excluded: chain Q residue 6 THR Chi-restraints excluded: chain Q residue 27 PHE Chi-restraints excluded: chain R residue 42 ARG Chi-restraints excluded: chain R residue 53 GLN Chi-restraints excluded: chain T residue 19 HIS Chi-restraints excluded: chain T residue 22 SER Chi-restraints excluded: chain T residue 25 SER Chi-restraints excluded: chain T residue 42 ASP Chi-restraints excluded: chain B residue 93 HIS Chi-restraints excluded: chain B residue 113 LEU Chi-restraints excluded: chain B residue 150 ILE Chi-restraints excluded: chain B residue 220 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 299 random chunks: chunk 256 optimal weight: 4.9990 chunk 105 optimal weight: 6.9990 chunk 167 optimal weight: 30.0000 chunk 73 optimal weight: 5.9990 chunk 103 optimal weight: 8.9990 chunk 106 optimal weight: 6.9990 chunk 132 optimal weight: 20.0000 chunk 56 optimal weight: 4.9990 chunk 67 optimal weight: 8.9990 chunk 164 optimal weight: 20.0000 chunk 13 optimal weight: 0.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 15 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 73 ASN ** D 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 37 HIS ** O 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 20 ASN ** T 60 GLN ** 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 = 0.4139 r_free = 0.4139 target = 0.101538 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.076682 restraints weight = 195698.684| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.078931 restraints weight = 71291.987| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.079100 restraints weight = 39393.744| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.079324 restraints weight = 31134.553| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.079501 restraints weight = 30390.523| |-----------------------------------------------------------------------------| r_work (final): 0.3667 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7857 moved from start: 0.4803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.105 46213 Z= 0.264 Angle : 1.207 17.539 69052 Z= 0.486 Chirality : 0.089 1.088 8824 Planarity : 0.005 0.064 3762 Dihedral : 20.220 179.274 18025 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 19.16 Ramachandran Plot: Outliers : 0.06 % Allowed : 14.16 % Favored : 85.78 % Rotamer: Outliers : 4.81 % Allowed : 22.32 % Favored : 72.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % 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: -3.56 (0.19), residues: 1716 helix: -1.76 (0.21), residues: 524 sheet: -2.46 (0.33), residues: 236 loop : -2.76 (0.19), residues: 956 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG E 137 TYR 0.022 0.002 TYR C 167 PHE 0.024 0.002 PHE C 129 TRP 0.014 0.002 TRP Q 72 HIS 0.010 0.002 HIS O 37 Details of bonding type rmsd/Z covalent geometry : bond 0.00538 / 0.26 (46213) covalent geometry : angle 1.20691 / 0.49 (69052) hydrogen bonds : bond 0.09493 / 5.57 ( 915) hydrogen bonds : angle 4.58734 / 3.25 ( 1793) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3432 Ramachandran restraints generated. 1716 Oldfield, 0 Emsley, 1716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3432 Ramachandran restraints generated. 1716 Oldfield, 0 Emsley, 1716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 355 residues out of total 1458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 285 time to evaluate : 0.872 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: C 36 PHE cc_start: 0.9054 (t80) cc_final: 0.8815 (t80) REVERT: C 111 ASP cc_start: 0.8474 (t70) cc_final: 0.8134 (t70) REVERT: C 130 ARG cc_start: 0.7007 (tmm-80) cc_final: 0.5934 (tmt170) REVERT: C 141 MET cc_start: 0.8373 (mmm) cc_final: 0.6745 (tpt) REVERT: C 182 ASP cc_start: 0.7587 (t0) cc_final: 0.7159 (t0) REVERT: J 52 LEU cc_start: 0.9063 (mp) cc_final: 0.8516 (tp) REVERT: N 5 MET cc_start: 0.6057 (tpt) cc_final: 0.5566 (tpp) REVERT: N 92 ILE cc_start: 0.8661 (mt) cc_final: 0.8417 (pt) REVERT: S 78 THR cc_start: 0.7070 (m) cc_final: 0.6790 (p) REVERT: D 69 ARG cc_start: 0.8940 (mmp-170) cc_final: 0.7688 (ptt180) REVERT: D 194 ILE cc_start: 0.8381 (mp) cc_final: 0.8180 (mm) REVERT: E 12 GLU cc_start: 0.7386 (mp0) cc_final: 0.7149 (mp0) REVERT: E 18 ASN cc_start: 0.8543 (m110) cc_final: 0.8098 (m-40) REVERT: E 94 PHE cc_start: 0.8537 (t80) cc_final: 0.7937 (t80) REVERT: E 151 MET cc_start: 0.8192 (tpp) cc_final: 0.7927 (tpp) REVERT: F 24 ARG cc_start: 0.8030 (ttm110) cc_final: 0.7535 (mtm110) REVERT: F 62 MET cc_start: 0.2862 (mmm) cc_final: 0.2265 (mmm) REVERT: F 68 GLN cc_start: 0.6756 (pm20) cc_final: 0.5765 (mm-40) REVERT: F 88 MET cc_start: 0.7822 (mtt) cc_final: 0.7214 (mpp) REVERT: H 15 ASN cc_start: 0.5916 (OUTLIER) cc_final: 0.5373 (t0) REVERT: H 26 MET cc_start: 0.8757 (pmm) cc_final: 0.8420 (ptp) REVERT: H 30 LYS cc_start: 0.8051 (mmpt) cc_final: 0.7423 (mptt) REVERT: H 37 ASN cc_start: 0.8346 (t0) cc_final: 0.8084 (t0) REVERT: H 63 LYS cc_start: 0.6298 (tttt) cc_final: 0.5641 (tppt) REVERT: H 64 TYR cc_start: 0.7436 (OUTLIER) cc_final: 0.6434 (p90) REVERT: H 87 ARG cc_start: 0.7078 (ttm170) cc_final: 0.6654 (ttt-90) REVERT: L 75 GLU cc_start: 0.8195 (OUTLIER) cc_final: 0.6833 (mp0) REVERT: O 38 LEU cc_start: 0.8639 (mt) cc_final: 0.8267 (tp) REVERT: O 42 PHE cc_start: 0.8371 (OUTLIER) cc_final: 0.8018 (t80) REVERT: O 58 MET cc_start: 0.8416 (ptp) cc_final: 0.8192 (ptp) REVERT: Q 8 GLN cc_start: 0.8245 (tp40) cc_final: 0.7884 (mm-40) REVERT: R 51 GLN cc_start: 0.7817 (pm20) cc_final: 0.6798 (tp-100) REVERT: R 59 LYS cc_start: 0.8573 (mttp) cc_final: 0.8364 (ptpp) REVERT: T 26 MET cc_start: 0.8937 (ttp) cc_final: 0.8727 (tmm) REVERT: T 65 LEU cc_start: 0.6867 (mt) cc_final: 0.6573 (mt) REVERT: B 44 LYS cc_start: 0.8913 (mmtt) cc_final: 0.8675 (mmmm) REVERT: B 196 ASP cc_start: 0.6170 (p0) cc_final: 0.5966 (p0) outliers start: 70 outliers final: 51 residues processed: 330 average time/residue: 0.2713 time to fit residues: 145.0697 Evaluate side-chains 322 residues out of total 1458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 267 time to evaluate : 0.875 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 20 THR Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 93 ILE Chi-restraints excluded: chain C residue 174 LEU Chi-restraints excluded: chain C residue 197 VAL Chi-restraints excluded: chain J residue 42 LEU Chi-restraints excluded: chain J residue 44 THR Chi-restraints excluded: chain J residue 69 THR Chi-restraints excluded: chain N residue 44 VAL Chi-restraints excluded: chain N residue 54 SER Chi-restraints excluded: chain S residue 57 VAL Chi-restraints excluded: chain D residue 10 LEU Chi-restraints excluded: chain D residue 100 VAL Chi-restraints excluded: chain E residue 29 ILE Chi-restraints excluded: chain E residue 35 LEU Chi-restraints excluded: chain E residue 36 THR Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 79 THR Chi-restraints excluded: chain E residue 104 ILE Chi-restraints excluded: chain E residue 123 LEU Chi-restraints excluded: chain F residue 7 VAL Chi-restraints excluded: chain F residue 26 THR Chi-restraints excluded: chain F residue 80 PHE Chi-restraints excluded: chain H residue 15 ASN Chi-restraints excluded: chain H residue 45 ILE Chi-restraints excluded: chain H residue 54 THR Chi-restraints excluded: chain H residue 64 TYR Chi-restraints excluded: chain H residue 65 PHE Chi-restraints excluded: chain H residue 84 ILE Chi-restraints excluded: chain L residue 2 THR Chi-restraints excluded: chain L residue 46 SER Chi-restraints excluded: chain L residue 75 GLU Chi-restraints excluded: chain L residue 103 CYS Chi-restraints excluded: chain O residue 9 LYS Chi-restraints excluded: chain O residue 11 VAL Chi-restraints excluded: chain O residue 37 HIS Chi-restraints excluded: chain O residue 42 PHE Chi-restraints excluded: chain O residue 55 LEU Chi-restraints excluded: chain O residue 80 LEU Chi-restraints excluded: chain O residue 86 LEU Chi-restraints excluded: chain P residue 20 VAL Chi-restraints excluded: chain Q residue 4 ILE Chi-restraints excluded: chain Q residue 6 THR Chi-restraints excluded: chain Q residue 15 LYS Chi-restraints excluded: chain R residue 42 ARG Chi-restraints excluded: chain R residue 46 THR Chi-restraints excluded: chain T residue 19 HIS Chi-restraints excluded: chain T residue 25 SER Chi-restraints excluded: chain T residue 42 ASP Chi-restraints excluded: chain B residue 93 HIS Chi-restraints excluded: chain B residue 106 VAL Chi-restraints excluded: chain B residue 111 LYS Chi-restraints excluded: chain B residue 113 LEU Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain B residue 220 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 299 random chunks: chunk 91 optimal weight: 10.0000 chunk 191 optimal weight: 3.9990 chunk 257 optimal weight: 5.9990 chunk 289 optimal weight: 20.0000 chunk 71 optimal weight: 8.9990 chunk 194 optimal weight: 3.9990 chunk 123 optimal weight: 20.0000 chunk 292 optimal weight: 10.0000 chunk 221 optimal weight: 6.9990 chunk 59 optimal weight: 10.0000 chunk 268 optimal weight: 4.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 15 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 39 GLN ** D 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 120 HIS O 37 HIS R 73 HIS ** T 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4129 r_free = 0.4129 target = 0.101028 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.076061 restraints weight = 194838.411| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.078354 restraints weight = 69466.011| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.078505 restraints weight = 38645.709| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.078733 restraints weight = 30465.554| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.078849 restraints weight = 30524.937| |-----------------------------------------------------------------------------| r_work (final): 0.3653 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7880 moved from start: 0.4950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.109 46213 Z= 0.281 Angle : 1.227 17.178 69052 Z= 0.494 Chirality : 0.090 1.143 8824 Planarity : 0.006 0.080 3762 Dihedral : 20.225 179.773 18025 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 19.60 Ramachandran Plot: Outliers : 0.06 % Allowed : 14.22 % Favored : 85.72 % Rotamer: Outliers : 5.70 % Allowed : 22.87 % Favored : 71.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % 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: -3.49 (0.19), residues: 1716 helix: -1.67 (0.21), residues: 523 sheet: -2.55 (0.31), residues: 249 loop : -2.69 (0.19), residues: 944 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E 137 TYR 0.016 0.002 TYR F 25 PHE 0.026 0.002 PHE B 15 TRP 0.016 0.002 TRP Q 72 HIS 0.013 0.002 HIS O 37 Details of bonding type rmsd/Z covalent geometry : bond 0.00574 / 0.28 (46213) covalent geometry : angle 1.22655 / 0.49 (69052) hydrogen bonds : bond 0.09540 / 5.56 ( 915) hydrogen bonds : angle 4.66895 / 3.30 ( 1793) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3432 Ramachandran restraints generated. 1716 Oldfield, 0 Emsley, 1716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3432 Ramachandran restraints generated. 1716 Oldfield, 0 Emsley, 1716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 364 residues out of total 1458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 281 time to evaluate : 0.888 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: C 36 PHE cc_start: 0.9059 (t80) cc_final: 0.8813 (t80) REVERT: C 111 ASP cc_start: 0.8492 (t70) cc_final: 0.8146 (t70) REVERT: C 130 ARG cc_start: 0.7218 (tmm-80) cc_final: 0.6145 (tmt170) REVERT: C 182 ASP cc_start: 0.7722 (t0) cc_final: 0.7315 (t0) REVERT: J 52 LEU cc_start: 0.9070 (mp) cc_final: 0.8500 (tp) REVERT: N 5 MET cc_start: 0.6079 (tpt) cc_final: 0.5651 (tpp) REVERT: S 28 LYS cc_start: 0.4957 (OUTLIER) cc_final: 0.4674 (pmmt) REVERT: S 78 THR cc_start: 0.7124 (m) cc_final: 0.6869 (t) REVERT: D 194 ILE cc_start: 0.8404 (mp) cc_final: 0.8187 (mm) REVERT: E 12 GLU cc_start: 0.7407 (mp0) cc_final: 0.7131 (mp0) REVERT: E 45 VAL cc_start: 0.8821 (OUTLIER) cc_final: 0.8603 (m) REVERT: E 94 PHE cc_start: 0.8553 (t80) cc_final: 0.8040 (t80) REVERT: E 151 MET cc_start: 0.8121 (tpp) cc_final: 0.7817 (tpp) REVERT: F 24 ARG cc_start: 0.8079 (ttm110) cc_final: 0.7610 (mtm110) REVERT: F 62 MET cc_start: 0.2954 (mmm) cc_final: 0.2399 (mmm) REVERT: F 68 GLN cc_start: 0.6790 (pm20) cc_final: 0.5779 (mm-40) REVERT: F 88 MET cc_start: 0.7803 (mtt) cc_final: 0.7277 (mpp) REVERT: H 15 ASN cc_start: 0.5989 (OUTLIER) cc_final: 0.5532 (t0) REVERT: H 30 LYS cc_start: 0.8116 (mmpt) cc_final: 0.7876 (ttpt) REVERT: H 37 ASN cc_start: 0.8330 (t0) cc_final: 0.7778 (t0) REVERT: H 63 LYS cc_start: 0.6128 (tttt) cc_final: 0.5429 (tppt) REVERT: H 64 TYR cc_start: 0.7362 (OUTLIER) cc_final: 0.6367 (p90) REVERT: H 87 ARG cc_start: 0.7161 (ttm170) cc_final: 0.6814 (ttt-90) REVERT: O 37 HIS cc_start: 0.8859 (t70) cc_final: 0.8512 (t-170) REVERT: O 38 LEU cc_start: 0.8475 (mt) cc_final: 0.8093 (tt) REVERT: O 42 PHE cc_start: 0.8406 (OUTLIER) cc_final: 0.8003 (t80) REVERT: O 58 MET cc_start: 0.8271 (ptp) cc_final: 0.8039 (ptp) REVERT: R 51 GLN cc_start: 0.7829 (pm20) cc_final: 0.6763 (tp-100) REVERT: B 44 LYS cc_start: 0.8914 (mmtt) cc_final: 0.8655 (mmmm) REVERT: B 196 ASP cc_start: 0.6225 (p0) cc_final: 0.5991 (p0) outliers start: 83 outliers final: 57 residues processed: 335 average time/residue: 0.2740 time to fit residues: 149.2281 Evaluate side-chains 336 residues out of total 1458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 274 time to evaluate : 0.903 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 20 THR Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 93 ILE Chi-restraints excluded: chain C residue 174 LEU Chi-restraints excluded: chain C residue 175 HIS Chi-restraints excluded: chain J residue 42 LEU Chi-restraints excluded: chain J residue 69 THR Chi-restraints excluded: chain J residue 71 LEU Chi-restraints excluded: chain N residue 15 LEU Chi-restraints excluded: chain N residue 54 SER Chi-restraints excluded: chain S residue 28 LYS Chi-restraints excluded: chain S residue 62 THR Chi-restraints excluded: chain D residue 10 LEU Chi-restraints excluded: chain D residue 39 GLN Chi-restraints excluded: chain D residue 100 VAL Chi-restraints excluded: chain E residue 29 ILE Chi-restraints excluded: chain E residue 35 LEU Chi-restraints excluded: chain E residue 36 THR Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain E residue 79 THR Chi-restraints excluded: chain E residue 104 ILE Chi-restraints excluded: chain E residue 123 LEU Chi-restraints excluded: chain E residue 141 ASP Chi-restraints excluded: chain F residue 7 VAL Chi-restraints excluded: chain F residue 26 THR Chi-restraints excluded: chain F residue 80 PHE Chi-restraints excluded: chain H residue 15 ASN Chi-restraints excluded: chain H residue 64 TYR Chi-restraints excluded: chain H residue 65 PHE Chi-restraints excluded: chain H residue 84 ILE Chi-restraints excluded: chain L residue 2 THR Chi-restraints excluded: chain L residue 34 THR Chi-restraints excluded: chain L residue 46 SER Chi-restraints excluded: chain L residue 103 CYS Chi-restraints excluded: chain O residue 9 LYS Chi-restraints excluded: chain O residue 11 VAL Chi-restraints excluded: chain O residue 42 PHE Chi-restraints excluded: chain O residue 53 ARG Chi-restraints excluded: chain O residue 55 LEU Chi-restraints excluded: chain O residue 80 LEU Chi-restraints excluded: chain O residue 86 LEU Chi-restraints excluded: chain P residue 20 VAL Chi-restraints excluded: chain P residue 78 VAL Chi-restraints excluded: chain Q residue 4 ILE Chi-restraints excluded: chain Q residue 6 THR Chi-restraints excluded: chain Q residue 15 LYS Chi-restraints excluded: chain Q residue 27 PHE Chi-restraints excluded: chain Q residue 75 VAL Chi-restraints excluded: chain R residue 42 ARG Chi-restraints excluded: chain R residue 46 THR Chi-restraints excluded: chain R residue 53 GLN Chi-restraints excluded: chain T residue 19 HIS Chi-restraints excluded: chain T residue 22 SER Chi-restraints excluded: chain T residue 25 SER Chi-restraints excluded: chain T residue 42 ASP Chi-restraints excluded: chain B residue 93 HIS Chi-restraints excluded: chain B residue 106 VAL Chi-restraints excluded: chain B residue 111 LYS Chi-restraints excluded: chain B residue 113 LEU Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain B residue 220 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 299 random chunks: chunk 236 optimal weight: 7.9990 chunk 167 optimal weight: 30.0000 chunk 120 optimal weight: 9.9990 chunk 65 optimal weight: 20.0000 chunk 126 optimal weight: 7.9990 chunk 258 optimal weight: 3.9990 chunk 7 optimal weight: 20.0000 chunk 154 optimal weight: 30.0000 chunk 283 optimal weight: 5.9990 chunk 284 optimal weight: 0.7980 chunk 47 optimal weight: 5.9990 overall best weight: 4.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 15 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 39 GLN D 70 GLN ** D 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 72 ASN Q 49 ASN R 73 HIS ** T 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4173 r_free = 0.4173 target = 0.102291 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.077255 restraints weight = 195993.043| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.079299 restraints weight = 70229.783| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.080501 restraints weight = 38362.653| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 53)----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.081168 restraints weight = 27452.580| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 48)----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.081491 restraints weight = 23056.636| |-----------------------------------------------------------------------------| r_work (final): 0.3735 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7855 moved from start: 0.5168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.102 46213 Z= 0.272 Angle : 1.217 16.486 69052 Z= 0.490 Chirality : 0.090 1.133 8824 Planarity : 0.005 0.071 3762 Dihedral : 20.209 179.407 18025 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 19.68 Ramachandran Plot: Outliers : 0.06 % Allowed : 14.22 % Favored : 85.72 % Rotamer: Outliers : 5.43 % Allowed : 23.49 % Favored : 71.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -3.39 (0.19), residues: 1716 helix: -1.57 (0.22), residues: 524 sheet: -2.53 (0.32), residues: 249 loop : -2.62 (0.19), residues: 943 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG N 64 TYR 0.015 0.002 TYR C 167 PHE 0.026 0.002 PHE B 89 TRP 0.017 0.002 TRP Q 72 HIS 0.008 0.002 HIS D 40 Details of bonding type rmsd/Z covalent geometry : bond 0.00554 / 0.27 (46213) covalent geometry : angle 1.21676 / 0.49 (69052) hydrogen bonds : bond 0.09559 / 5.50 ( 915) hydrogen bonds : angle 4.63604 / 3.28 ( 1793) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3432 Ramachandran restraints generated. 1716 Oldfield, 0 Emsley, 1716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3432 Ramachandran restraints generated. 1716 Oldfield, 0 Emsley, 1716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 360 residues out of total 1458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 281 time to evaluate : 0.864 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: C 36 PHE cc_start: 0.9037 (t80) cc_final: 0.8806 (t80) REVERT: C 111 ASP cc_start: 0.8613 (t70) cc_final: 0.8174 (t70) REVERT: C 130 ARG cc_start: 0.7231 (tmm-80) cc_final: 0.6166 (tmt170) REVERT: C 182 ASP cc_start: 0.7701 (t0) cc_final: 0.7195 (t0) REVERT: J 52 LEU cc_start: 0.9050 (mp) cc_final: 0.8451 (tp) REVERT: N 5 MET cc_start: 0.5995 (tpt) cc_final: 0.5609 (tpp) REVERT: N 19 TYR cc_start: 0.8066 (OUTLIER) cc_final: 0.7851 (m-10) REVERT: S 28 LYS cc_start: 0.5116 (OUTLIER) cc_final: 0.4870 (pmmt) REVERT: S 78 THR cc_start: 0.7123 (m) cc_final: 0.6883 (t) REVERT: D 3 TYR cc_start: 0.7950 (t80) cc_final: 0.7639 (t80) REVERT: D 123 MET cc_start: 0.8385 (tpp) cc_final: 0.7398 (tpp) REVERT: D 194 ILE cc_start: 0.8373 (mp) cc_final: 0.8136 (mm) REVERT: E 12 GLU cc_start: 0.7338 (mp0) cc_final: 0.7098 (mp0) REVERT: E 18 ASN cc_start: 0.8424 (m110) cc_final: 0.8084 (m-40) REVERT: E 70 MET cc_start: 0.6836 (mmp) cc_final: 0.5125 (ptp) REVERT: E 94 PHE cc_start: 0.8562 (t80) cc_final: 0.8095 (t80) REVERT: E 140 ILE cc_start: 0.8318 (mt) cc_final: 0.8067 (tp) REVERT: E 144 GLU cc_start: 0.7739 (mm-30) cc_final: 0.7520 (mm-30) REVERT: E 151 MET cc_start: 0.7807 (tpp) cc_final: 0.7607 (tpp) REVERT: F 62 MET cc_start: 0.3000 (mmm) cc_final: 0.2423 (mmm) REVERT: F 68 GLN cc_start: 0.6921 (pm20) cc_final: 0.5894 (mm-40) REVERT: F 73 GLU cc_start: 0.9264 (pm20) cc_final: 0.9042 (pm20) REVERT: F 88 MET cc_start: 0.7792 (mtt) cc_final: 0.7307 (mpp) REVERT: H 15 ASN cc_start: 0.6041 (OUTLIER) cc_final: 0.5590 (t0) REVERT: H 26 MET cc_start: 0.8526 (pmm) cc_final: 0.8137 (ptp) REVERT: H 30 LYS cc_start: 0.8145 (mmpt) cc_final: 0.7850 (ttpt) REVERT: H 37 ASN cc_start: 0.8222 (t0) cc_final: 0.8002 (t0) REVERT: H 63 LYS cc_start: 0.5940 (tttt) cc_final: 0.5395 (tppt) REVERT: H 64 TYR cc_start: 0.6923 (OUTLIER) cc_final: 0.5620 (p90) REVERT: H 87 ARG cc_start: 0.7166 (ttm170) cc_final: 0.6877 (ttt-90) REVERT: O 38 LEU cc_start: 0.8493 (mt) cc_final: 0.8051 (tt) REVERT: O 58 MET cc_start: 0.8171 (ptp) cc_final: 0.7945 (ptp) REVERT: O 70 LYS cc_start: 0.9058 (mmmt) cc_final: 0.8650 (mmmm) REVERT: B 44 LYS cc_start: 0.8899 (mmtt) cc_final: 0.8651 (mmmm) REVERT: B 126 ASP cc_start: 0.8406 (t0) cc_final: 0.7844 (p0) REVERT: B 196 ASP cc_start: 0.6122 (p0) cc_final: 0.5891 (p0) outliers start: 79 outliers final: 61 residues processed: 334 average time/residue: 0.2630 time to fit residues: 143.2288 Evaluate side-chains 328 residues out of total 1458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 263 time to evaluate : 0.854 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 20 THR Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 93 ILE Chi-restraints excluded: chain C residue 174 LEU Chi-restraints excluded: chain C residue 175 HIS Chi-restraints excluded: chain C residue 197 VAL Chi-restraints excluded: chain J residue 42 LEU Chi-restraints excluded: chain J residue 44 THR Chi-restraints excluded: chain J residue 69 THR Chi-restraints excluded: chain J residue 71 LEU Chi-restraints excluded: chain N residue 15 LEU Chi-restraints excluded: chain N residue 19 TYR Chi-restraints excluded: chain N residue 44 VAL Chi-restraints excluded: chain N residue 54 SER Chi-restraints excluded: chain N residue 95 LEU Chi-restraints excluded: chain S residue 28 LYS Chi-restraints excluded: chain D residue 39 GLN Chi-restraints excluded: chain D residue 100 VAL Chi-restraints excluded: chain D residue 172 VAL Chi-restraints excluded: chain E residue 29 ILE Chi-restraints excluded: chain E residue 35 LEU Chi-restraints excluded: chain E residue 36 THR Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 79 THR Chi-restraints excluded: chain E residue 104 ILE Chi-restraints excluded: chain F residue 7 VAL Chi-restraints excluded: chain F residue 26 THR Chi-restraints excluded: chain F residue 80 PHE Chi-restraints excluded: chain H residue 11 THR Chi-restraints excluded: chain H residue 15 ASN Chi-restraints excluded: chain H residue 45 ILE Chi-restraints excluded: chain H residue 64 TYR Chi-restraints excluded: chain H residue 84 ILE Chi-restraints excluded: chain H residue 94 VAL Chi-restraints excluded: chain H residue 110 MET Chi-restraints excluded: chain L residue 2 THR Chi-restraints excluded: chain L residue 34 THR Chi-restraints excluded: chain L residue 46 SER Chi-restraints excluded: chain L residue 103 CYS Chi-restraints excluded: chain O residue 9 LYS Chi-restraints excluded: chain O residue 11 VAL Chi-restraints excluded: chain O residue 42 PHE Chi-restraints excluded: chain O residue 53 ARG Chi-restraints excluded: chain O residue 55 LEU Chi-restraints excluded: chain O residue 80 LEU Chi-restraints excluded: chain O residue 83 ARG Chi-restraints excluded: chain O residue 86 LEU Chi-restraints excluded: chain P residue 20 VAL Chi-restraints excluded: chain P residue 71 VAL Chi-restraints excluded: chain Q residue 4 ILE Chi-restraints excluded: chain Q residue 6 THR Chi-restraints excluded: chain Q residue 27 PHE Chi-restraints excluded: chain R residue 42 ARG Chi-restraints excluded: chain R residue 46 THR Chi-restraints excluded: chain R residue 72 ARG Chi-restraints excluded: chain T residue 19 HIS Chi-restraints excluded: chain T residue 22 SER Chi-restraints excluded: chain T residue 25 SER Chi-restraints excluded: chain T residue 42 ASP Chi-restraints excluded: chain B residue 93 HIS Chi-restraints excluded: chain B residue 106 VAL Chi-restraints excluded: chain B residue 111 LYS Chi-restraints excluded: chain B residue 113 LEU Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain B residue 220 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 299 random chunks: chunk 288 optimal weight: 7.9990 chunk 295 optimal weight: 20.0000 chunk 247 optimal weight: 0.0970 chunk 131 optimal weight: 8.9990 chunk 35 optimal weight: 0.7980 chunk 217 optimal weight: 10.0000 chunk 253 optimal weight: 1.9990 chunk 290 optimal weight: 0.9980 chunk 118 optimal weight: 10.0000 chunk 97 optimal weight: 9.9990 chunk 46 optimal weight: 6.9990 overall best weight: 2.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 15 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 70 GLN ** D 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 17 GLN H 66 GLN R 73 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4204 r_free = 0.4204 target = 0.105096 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.079883 restraints weight = 191505.302| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.082106 restraints weight = 64774.022| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.083445 restraints weight = 34036.353| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 55)----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.084208 restraints weight = 23749.158| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 70)----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.084607 restraints weight = 19610.513| |-----------------------------------------------------------------------------| r_work (final): 0.3779 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7732 moved from start: 0.5648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 46213 Z= 0.171 Angle : 1.077 16.617 69052 Z= 0.436 Chirality : 0.081 0.782 8824 Planarity : 0.005 0.066 3762 Dihedral : 19.845 179.829 18025 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 14.52 Ramachandran Plot: Outliers : 0.06 % Allowed : 11.31 % Favored : 88.64 % Rotamer: Outliers : 4.19 % Allowed : 24.93 % Favored : 70.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % 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 (0.20), residues: 1716 helix: -1.12 (0.23), residues: 524 sheet: -2.19 (0.33), residues: 234 loop : -2.44 (0.19), residues: 958 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG P 28 TYR 0.015 0.002 TYR D 3 PHE 0.032 0.002 PHE H 65 TRP 0.011 0.002 TRP Q 72 HIS 0.024 0.001 HIS D 40 Details of bonding type rmsd/Z covalent geometry : bond 0.00348 / 0.17 (46213) covalent geometry : angle 1.07741 / 0.44 (69052) hydrogen bonds : bond 0.09479 / 5.24 ( 915) hydrogen bonds : angle 4.23874 / 2.97 ( 1793) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3432 Ramachandran restraints generated. 1716 Oldfield, 0 Emsley, 1716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3432 Ramachandran restraints generated. 1716 Oldfield, 0 Emsley, 1716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 368 residues out of total 1458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 307 time to evaluate : 0.890 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: C 21 TRP cc_start: 0.6184 (p-90) cc_final: 0.5980 (p-90) REVERT: C 36 PHE cc_start: 0.9048 (t80) cc_final: 0.8744 (t80) REVERT: C 111 ASP cc_start: 0.8570 (t70) cc_final: 0.8158 (t70) REVERT: C 117 ASP cc_start: 0.8628 (t0) cc_final: 0.8427 (m-30) REVERT: C 130 ARG cc_start: 0.7039 (tmm-80) cc_final: 0.6768 (mmt180) REVERT: C 182 ASP cc_start: 0.7913 (t0) cc_final: 0.7437 (t0) REVERT: J 52 LEU cc_start: 0.8901 (mp) cc_final: 0.8308 (tp) REVERT: N 5 MET cc_start: 0.6015 (tpt) cc_final: 0.5599 (tpp) REVERT: N 78 LEU cc_start: 0.7447 (mm) cc_final: 0.7156 (mm) REVERT: N 91 GLU cc_start: 0.7707 (mt-10) cc_final: 0.6949 (mt-10) REVERT: N 92 ILE cc_start: 0.8474 (mt) cc_final: 0.8111 (pt) REVERT: S 28 LYS cc_start: 0.5024 (OUTLIER) cc_final: 0.4770 (pmmt) REVERT: S 78 THR cc_start: 0.6980 (m) cc_final: 0.6712 (t) REVERT: D 30 LYS cc_start: 0.8035 (mmtt) cc_final: 0.7432 (pttt) REVERT: D 46 ARG cc_start: 0.7258 (OUTLIER) cc_final: 0.6171 (ptt90) REVERT: D 123 MET cc_start: 0.8091 (tpp) cc_final: 0.7113 (tpp) REVERT: E 12 GLU cc_start: 0.7361 (mp0) cc_final: 0.7103 (mp0) REVERT: E 18 ASN cc_start: 0.8525 (m110) cc_final: 0.8175 (m-40) REVERT: E 70 MET cc_start: 0.6513 (mmp) cc_final: 0.4644 (ppp) REVERT: E 94 PHE cc_start: 0.8488 (t80) cc_final: 0.7768 (t80) REVERT: E 151 MET cc_start: 0.8180 (tpp) cc_final: 0.7843 (tpp) REVERT: F 24 ARG cc_start: 0.8526 (ttm110) cc_final: 0.7979 (mtm-85) REVERT: F 62 MET cc_start: 0.2824 (mmm) cc_final: 0.2350 (mmm) REVERT: F 68 GLN cc_start: 0.7057 (pm20) cc_final: 0.6175 (mt0) REVERT: F 73 GLU cc_start: 0.9252 (pm20) cc_final: 0.9049 (pm20) REVERT: H 15 ASN cc_start: 0.5671 (OUTLIER) cc_final: 0.5145 (t0) REVERT: H 30 LYS cc_start: 0.8003 (mmpt) cc_final: 0.7710 (ttpt) REVERT: H 37 ASN cc_start: 0.8274 (t0) cc_final: 0.7936 (t0) REVERT: H 63 LYS cc_start: 0.5842 (tttt) cc_final: 0.5391 (tppt) REVERT: H 64 TYR cc_start: 0.7559 (OUTLIER) cc_final: 0.6407 (p90) REVERT: H 87 ARG cc_start: 0.6778 (ttm170) cc_final: 0.6484 (ttt-90) REVERT: O 19 ASN cc_start: 0.6945 (t0) cc_final: 0.6730 (t0) REVERT: Q 79 GLU cc_start: 0.9019 (mm-30) cc_final: 0.8686 (mp0) REVERT: B 26 MET cc_start: 0.1801 (tmm) cc_final: 0.1447 (ttp) REVERT: B 29 PHE cc_start: 0.8299 (m-80) cc_final: 0.7949 (t80) REVERT: B 44 LYS cc_start: 0.8933 (mmtt) cc_final: 0.8570 (mmmm) REVERT: B 126 ASP cc_start: 0.8484 (t0) cc_final: 0.7977 (p0) outliers start: 61 outliers final: 40 residues processed: 345 average time/residue: 0.2671 time to fit residues: 148.5321 Evaluate side-chains 323 residues out of total 1458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 279 time to evaluate : 0.780 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 20 THR Chi-restraints excluded: chain C residue 93 ILE Chi-restraints excluded: chain C residue 175 HIS Chi-restraints excluded: chain J residue 42 LEU Chi-restraints excluded: chain J residue 69 THR Chi-restraints excluded: chain N residue 15 LEU Chi-restraints excluded: chain N residue 44 VAL Chi-restraints excluded: chain N residue 54 SER Chi-restraints excluded: chain S residue 28 LYS Chi-restraints excluded: chain D residue 46 ARG Chi-restraints excluded: chain D residue 172 VAL Chi-restraints excluded: chain E residue 29 ILE Chi-restraints excluded: chain E residue 35 LEU Chi-restraints excluded: chain E residue 36 THR Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 79 THR Chi-restraints excluded: chain F residue 26 THR Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 80 PHE Chi-restraints excluded: chain H residue 11 THR Chi-restraints excluded: chain H residue 15 ASN Chi-restraints excluded: chain H residue 64 TYR Chi-restraints excluded: chain H residue 84 ILE Chi-restraints excluded: chain H residue 94 VAL Chi-restraints excluded: chain L residue 2 THR Chi-restraints excluded: chain L residue 46 SER Chi-restraints excluded: chain L residue 103 CYS Chi-restraints excluded: chain O residue 9 LYS Chi-restraints excluded: chain O residue 11 VAL Chi-restraints excluded: chain O residue 42 PHE Chi-restraints excluded: chain O residue 53 ARG Chi-restraints excluded: chain O residue 80 LEU Chi-restraints excluded: chain O residue 83 ARG Chi-restraints excluded: chain O residue 86 LEU Chi-restraints excluded: chain Q residue 4 ILE Chi-restraints excluded: chain Q residue 27 PHE Chi-restraints excluded: chain R residue 53 GLN Chi-restraints excluded: chain T residue 25 SER Chi-restraints excluded: chain T residue 42 ASP Chi-restraints excluded: chain B residue 45 THR Chi-restraints excluded: chain B residue 93 HIS Chi-restraints excluded: chain B residue 111 LYS Chi-restraints excluded: chain B residue 113 LEU Chi-restraints excluded: chain B residue 220 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 299 random chunks: chunk 126 optimal weight: 8.9990 chunk 202 optimal weight: 9.9990 chunk 106 optimal weight: 7.9990 chunk 30 optimal weight: 5.9990 chunk 236 optimal weight: 0.0980 chunk 29 optimal weight: 8.9990 chunk 219 optimal weight: 9.9990 chunk 231 optimal weight: 0.0980 chunk 55 optimal weight: 6.9990 chunk 56 optimal weight: 6.9990 chunk 72 optimal weight: 10.0000 overall best weight: 4.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 2 GLN ** C 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 15 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 73 HIS T 51 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4209 r_free = 0.4209 target = 0.104269 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.079318 restraints weight = 195476.844| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.081400 restraints weight = 70246.036| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.082639 restraints weight = 38272.355| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 70)----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.083338 restraints weight = 27324.136| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 57)----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.083708 restraints weight = 22776.719| |-----------------------------------------------------------------------------| r_work (final): 0.3784 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7798 moved from start: 0.5683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.083 46213 Z= 0.232 Angle : 1.137 14.853 69052 Z= 0.460 Chirality : 0.083 0.862 8824 Planarity : 0.005 0.066 3762 Dihedral : 19.915 179.572 18025 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 16.98 Ramachandran Plot: Outliers : 0.06 % Allowed : 12.76 % Favored : 87.18 % Rotamer: Outliers : 4.67 % Allowed : 25.48 % Favored : 69.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -3.07 (0.19), residues: 1716 helix: -1.18 (0.22), residues: 538 sheet: -2.27 (0.32), residues: 242 loop : -2.55 (0.19), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG F 24 TYR 0.025 0.002 TYR C 167 PHE 0.043 0.002 PHE H 65 TRP 0.025 0.002 TRP C 166 HIS 0.006 0.001 HIS P 59 Details of bonding type rmsd/Z covalent geometry : bond 0.00476 / 0.23 (46213) covalent geometry : angle 1.13697 / 0.46 (69052) hydrogen bonds : bond 0.09565 / 5.39 ( 915) hydrogen bonds : angle 4.34943 / 3.06 ( 1793) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3432 Ramachandran restraints generated. 1716 Oldfield, 0 Emsley, 1716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3432 Ramachandran restraints generated. 1716 Oldfield, 0 Emsley, 1716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 341 residues out of total 1458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 273 time to evaluate : 0.820 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: C 36 PHE cc_start: 0.9031 (t80) cc_final: 0.8731 (t80) REVERT: C 111 ASP cc_start: 0.8526 (t70) cc_final: 0.8107 (t70) REVERT: C 130 ARG cc_start: 0.7011 (tmm-80) cc_final: 0.6761 (mmt180) REVERT: C 182 ASP cc_start: 0.7874 (t0) cc_final: 0.7411 (t0) REVERT: J 52 LEU cc_start: 0.8950 (mp) cc_final: 0.8353 (tp) REVERT: N 5 MET cc_start: 0.6062 (tpt) cc_final: 0.5615 (tpp) REVERT: N 91 GLU cc_start: 0.7705 (mt-10) cc_final: 0.6967 (mt-10) REVERT: N 95 LEU cc_start: 0.6720 (tp) cc_final: 0.6397 (tp) REVERT: S 28 LYS cc_start: 0.4987 (OUTLIER) cc_final: 0.4735 (pmmt) REVERT: S 65 MET cc_start: -0.0572 (mtt) cc_final: -0.0824 (mtt) REVERT: S 78 THR cc_start: 0.6776 (m) cc_final: 0.6523 (t) REVERT: D 123 MET cc_start: 0.8086 (tpp) cc_final: 0.7143 (tpp) REVERT: D 194 ILE cc_start: 0.8365 (mp) cc_final: 0.8127 (mm) REVERT: E 12 GLU cc_start: 0.7332 (mp0) cc_final: 0.7106 (mp0) REVERT: E 18 ASN cc_start: 0.8506 (m110) cc_final: 0.8065 (m-40) REVERT: E 70 MET cc_start: 0.6711 (mmp) cc_final: 0.5073 (ptp) REVERT: E 94 PHE cc_start: 0.8488 (t80) cc_final: 0.7770 (t80) REVERT: F 62 MET cc_start: 0.2879 (mmm) cc_final: 0.2412 (mmm) REVERT: F 68 GLN cc_start: 0.7032 (pm20) cc_final: 0.6119 (mt0) REVERT: H 15 ASN cc_start: 0.5810 (OUTLIER) cc_final: 0.5359 (t0) REVERT: H 26 MET cc_start: 0.8548 (pmm) cc_final: 0.8151 (ptp) REVERT: H 30 LYS cc_start: 0.8065 (mmpt) cc_final: 0.7739 (ttpt) REVERT: H 37 ASN cc_start: 0.8209 (t0) cc_final: 0.7853 (t0) REVERT: H 63 LYS cc_start: 0.5734 (tttt) cc_final: 0.5266 (tppt) REVERT: H 64 TYR cc_start: 0.7181 (OUTLIER) cc_final: 0.6214 (p90) REVERT: H 87 ARG cc_start: 0.6886 (ttm170) cc_final: 0.6605 (ttt-90) REVERT: Q 48 GLU cc_start: 0.8477 (mm-30) cc_final: 0.7940 (mm-30) REVERT: Q 79 GLU cc_start: 0.8997 (mm-30) cc_final: 0.8694 (mp0) REVERT: B 26 MET cc_start: 0.2039 (tmm) cc_final: 0.1585 (ttp) REVERT: B 29 PHE cc_start: 0.8328 (m-80) cc_final: 0.7855 (t80) REVERT: B 44 LYS cc_start: 0.8937 (mmtt) cc_final: 0.8736 (mmmm) REVERT: B 126 ASP cc_start: 0.8474 (t0) cc_final: 0.7976 (p0) outliers start: 68 outliers final: 57 residues processed: 320 average time/residue: 0.2702 time to fit residues: 140.7272 Evaluate side-chains 321 residues out of total 1458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 261 time to evaluate : 0.803 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 20 THR Chi-restraints excluded: chain C residue 93 ILE Chi-restraints excluded: chain C residue 174 LEU Chi-restraints excluded: chain C residue 175 HIS Chi-restraints excluded: chain J residue 42 LEU Chi-restraints excluded: chain J residue 69 THR Chi-restraints excluded: chain N residue 15 LEU Chi-restraints excluded: chain N residue 54 SER Chi-restraints excluded: chain S residue 28 LYS Chi-restraints excluded: chain S residue 62 THR Chi-restraints excluded: chain D residue 46 ARG Chi-restraints excluded: chain D residue 172 VAL Chi-restraints excluded: chain E residue 29 ILE Chi-restraints excluded: chain E residue 35 LEU Chi-restraints excluded: chain E residue 36 THR Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 79 THR Chi-restraints excluded: chain E residue 104 ILE Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 7 VAL Chi-restraints excluded: chain F residue 26 THR Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 80 PHE Chi-restraints excluded: chain F residue 85 ILE Chi-restraints excluded: chain H residue 11 THR Chi-restraints excluded: chain H residue 15 ASN Chi-restraints excluded: chain H residue 45 ILE Chi-restraints excluded: chain H residue 64 TYR Chi-restraints excluded: chain H residue 84 ILE Chi-restraints excluded: chain H residue 94 VAL Chi-restraints excluded: chain H residue 110 MET Chi-restraints excluded: chain L residue 2 THR Chi-restraints excluded: chain L residue 15 VAL Chi-restraints excluded: chain L residue 46 SER Chi-restraints excluded: chain L residue 103 CYS Chi-restraints excluded: chain O residue 9 LYS Chi-restraints excluded: chain O residue 11 VAL Chi-restraints excluded: chain O residue 42 PHE Chi-restraints excluded: chain O residue 53 ARG Chi-restraints excluded: chain O residue 55 LEU Chi-restraints excluded: chain O residue 80 LEU Chi-restraints excluded: chain O residue 83 ARG Chi-restraints excluded: chain O residue 86 LEU Chi-restraints excluded: chain P residue 20 VAL Chi-restraints excluded: chain P residue 78 VAL Chi-restraints excluded: chain Q residue 4 ILE Chi-restraints excluded: chain Q residue 27 PHE Chi-restraints excluded: chain Q residue 58 VAL Chi-restraints excluded: chain Q residue 75 VAL Chi-restraints excluded: chain R residue 46 THR Chi-restraints excluded: chain R residue 53 GLN Chi-restraints excluded: chain R residue 72 ARG Chi-restraints excluded: chain T residue 25 SER Chi-restraints excluded: chain T residue 42 ASP Chi-restraints excluded: chain B residue 45 THR Chi-restraints excluded: chain B residue 93 HIS Chi-restraints excluded: chain B residue 111 LYS Chi-restraints excluded: chain B residue 113 LEU Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain B residue 220 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 299 random chunks: chunk 241 optimal weight: 3.9990 chunk 138 optimal weight: 30.0000 chunk 167 optimal weight: 30.0000 chunk 121 optimal weight: 10.0000 chunk 79 optimal weight: 10.0000 chunk 243 optimal weight: 5.9990 chunk 61 optimal weight: 10.0000 chunk 86 optimal weight: 9.9990 chunk 13 optimal weight: 5.9990 chunk 135 optimal weight: 20.0000 chunk 111 optimal weight: 10.0000 overall best weight: 7.1992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 15 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 59 GLN ** D 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 19 ASN R 73 HIS ** T 60 GLN ** 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 = 0.4142 r_free = 0.4142 target = 0.100555 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.076108 restraints weight = 199054.442| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.078310 restraints weight = 79451.921| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.078326 restraints weight = 44978.322| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.078198 restraints weight = 37377.464| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.078449 restraints weight = 37546.842| |-----------------------------------------------------------------------------| r_work (final): 0.3667 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7934 moved from start: 0.5714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.122 46213 Z= 0.371 Angle : 1.349 17.543 69052 Z= 0.543 Chirality : 0.095 1.172 8824 Planarity : 0.006 0.089 3762 Dihedral : 20.302 179.457 18025 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 23.94 Ramachandran Plot: Outliers : 0.06 % Allowed : 15.03 % Favored : 84.91 % Rotamer: Outliers : 4.53 % Allowed : 26.17 % Favored : 69.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.18 % 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: -3.24 (0.19), residues: 1716 helix: -1.39 (0.22), residues: 521 sheet: -2.35 (0.32), residues: 245 loop : -2.60 (0.19), residues: 950 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 13 TYR 0.030 0.002 TYR C 167 PHE 0.049 0.003 PHE H 65 TRP 0.026 0.003 TRP C 166 HIS 0.009 0.002 HIS B 167 Details of bonding type rmsd/Z covalent geometry : bond 0.00756 / 0.37 (46213) covalent geometry : angle 1.34914 / 0.54 (69052) hydrogen bonds : bond 0.10816 / 6.24 ( 915) hydrogen bonds : angle 4.81422 / 3.41 ( 1793) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3432 Ramachandran restraints generated. 1716 Oldfield, 0 Emsley, 1716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3432 Ramachandran restraints generated. 1716 Oldfield, 0 Emsley, 1716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 324 residues out of total 1458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 258 time to evaluate : 0.933 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: C 36 PHE cc_start: 0.9038 (t80) cc_final: 0.8761 (t80) REVERT: C 111 ASP cc_start: 0.8354 (t70) cc_final: 0.7987 (t70) REVERT: C 130 ARG cc_start: 0.7189 (tmm-80) cc_final: 0.6006 (tmt170) REVERT: C 182 ASP cc_start: 0.7973 (t0) cc_final: 0.7668 (t0) REVERT: J 42 LEU cc_start: 0.7763 (OUTLIER) cc_final: 0.6869 (mt) REVERT: J 52 LEU cc_start: 0.8983 (mp) cc_final: 0.8440 (tp) REVERT: J 73 LEU cc_start: 0.6189 (mt) cc_final: 0.5935 (tt) REVERT: N 5 MET cc_start: 0.6486 (tpt) cc_final: 0.6083 (tpp) REVERT: N 91 GLU cc_start: 0.7995 (mt-10) cc_final: 0.7537 (mt-10) REVERT: N 95 LEU cc_start: 0.6673 (tp) cc_final: 0.6278 (tp) REVERT: S 28 LYS cc_start: 0.4907 (OUTLIER) cc_final: 0.4611 (pmmt) REVERT: S 65 MET cc_start: -0.1232 (mtt) cc_final: -0.1477 (mtt) REVERT: S 78 THR cc_start: 0.6595 (m) cc_final: 0.6309 (t) REVERT: D 3 TYR cc_start: 0.8055 (t80) cc_final: 0.7846 (t80) REVERT: D 123 MET cc_start: 0.8263 (tpp) cc_final: 0.7201 (tpp) REVERT: E 45 VAL cc_start: 0.8763 (OUTLIER) cc_final: 0.8152 (m) REVERT: E 67 ARG cc_start: 0.8824 (mmm-85) cc_final: 0.8590 (tpp80) REVERT: E 70 MET cc_start: 0.7058 (mmp) cc_final: 0.5803 (ptp) REVERT: E 94 PHE cc_start: 0.8510 (t80) cc_final: 0.8089 (t80) REVERT: F 62 MET cc_start: 0.3123 (mmm) cc_final: 0.2555 (mmm) REVERT: F 68 GLN cc_start: 0.7141 (pm20) cc_final: 0.6200 (mt0) REVERT: F 73 GLU cc_start: 0.9320 (pm20) cc_final: 0.9084 (pm20) REVERT: F 90 MET cc_start: 0.5586 (mmm) cc_final: 0.5136 (mmt) REVERT: H 15 ASN cc_start: 0.5903 (OUTLIER) cc_final: 0.5426 (t0) REVERT: H 30 LYS cc_start: 0.8084 (mmpt) cc_final: 0.7780 (ttpt) REVERT: H 37 ASN cc_start: 0.8308 (t0) cc_final: 0.8049 (t0) REVERT: H 63 LYS cc_start: 0.5880 (tttt) cc_final: 0.5231 (tppt) REVERT: H 64 TYR cc_start: 0.7294 (OUTLIER) cc_final: 0.6496 (p90) REVERT: H 87 ARG cc_start: 0.7221 (ttm170) cc_final: 0.6923 (ttt-90) REVERT: O 3 SER cc_start: 0.8480 (m) cc_final: 0.8018 (p) REVERT: O 80 LEU cc_start: 0.8339 (OUTLIER) cc_final: 0.8025 (tt) REVERT: Q 48 GLU cc_start: 0.8347 (mm-30) cc_final: 0.8012 (mm-30) REVERT: B 44 LYS cc_start: 0.8889 (mmtt) cc_final: 0.8628 (mmmm) REVERT: B 126 ASP cc_start: 0.8555 (t0) cc_final: 0.8030 (p0) outliers start: 66 outliers final: 50 residues processed: 302 average time/residue: 0.2662 time to fit residues: 131.5761 Evaluate side-chains 302 residues out of total 1458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 246 time to evaluate : 0.886 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 20 THR Chi-restraints excluded: chain C residue 93 ILE Chi-restraints excluded: chain C residue 174 LEU Chi-restraints excluded: chain C residue 175 HIS Chi-restraints excluded: chain J residue 42 LEU Chi-restraints excluded: chain J residue 69 THR Chi-restraints excluded: chain N residue 54 SER Chi-restraints excluded: chain S residue 28 LYS Chi-restraints excluded: chain D residue 27 ILE Chi-restraints excluded: chain D residue 46 ARG Chi-restraints excluded: chain D residue 172 VAL Chi-restraints excluded: chain E residue 29 ILE Chi-restraints excluded: chain E residue 35 LEU Chi-restraints excluded: chain E residue 36 THR Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain E residue 79 THR Chi-restraints excluded: chain E residue 104 ILE Chi-restraints excluded: chain E residue 113 VAL Chi-restraints excluded: chain E residue 139 THR Chi-restraints excluded: chain F residue 7 VAL Chi-restraints excluded: chain F residue 26 THR Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 80 PHE Chi-restraints excluded: chain F residue 85 ILE Chi-restraints excluded: chain H residue 11 THR Chi-restraints excluded: chain H residue 15 ASN Chi-restraints excluded: chain H residue 64 TYR Chi-restraints excluded: chain H residue 84 ILE Chi-restraints excluded: chain H residue 94 VAL Chi-restraints excluded: chain H residue 110 MET Chi-restraints excluded: chain L residue 2 THR Chi-restraints excluded: chain L residue 15 VAL Chi-restraints excluded: chain L residue 34 THR Chi-restraints excluded: chain L residue 103 CYS Chi-restraints excluded: chain O residue 9 LYS Chi-restraints excluded: chain O residue 11 VAL Chi-restraints excluded: chain O residue 42 PHE Chi-restraints excluded: chain O residue 53 ARG Chi-restraints excluded: chain O residue 55 LEU Chi-restraints excluded: chain O residue 80 LEU Chi-restraints excluded: chain O residue 83 ARG Chi-restraints excluded: chain O residue 86 LEU Chi-restraints excluded: chain P residue 20 VAL Chi-restraints excluded: chain P residue 78 VAL Chi-restraints excluded: chain Q residue 4 ILE Chi-restraints excluded: chain Q residue 27 PHE Chi-restraints excluded: chain Q residue 58 VAL Chi-restraints excluded: chain R residue 46 THR Chi-restraints excluded: chain R residue 53 GLN Chi-restraints excluded: chain T residue 25 SER Chi-restraints excluded: chain T residue 42 ASP Chi-restraints excluded: chain T residue 57 VAL Chi-restraints excluded: chain B residue 93 HIS Chi-restraints excluded: chain B residue 113 LEU Chi-restraints excluded: chain B residue 220 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 299 random chunks: chunk 129 optimal weight: 9.9990 chunk 35 optimal weight: 10.0000 chunk 14 optimal weight: 5.9990 chunk 258 optimal weight: 3.9990 chunk 98 optimal weight: 7.9990 chunk 198 optimal weight: 3.9990 chunk 39 optimal weight: 2.9990 chunk 18 optimal weight: 6.9990 chunk 75 optimal weight: 1.9990 chunk 216 optimal weight: 9.9990 chunk 8 optimal weight: 5.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 15 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 81 GLN ** F 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 73 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4158 r_free = 0.4158 target = 0.102693 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.078130 restraints weight = 196546.345| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.080274 restraints weight = 73275.133| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.080458 restraints weight = 41690.545| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.080663 restraints weight = 32666.253| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.080831 restraints weight = 31806.611| |-----------------------------------------------------------------------------| r_work (final): 0.3688 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7830 moved from start: 0.5949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.075 46213 Z= 0.229 Angle : 1.160 15.407 69052 Z= 0.470 Chirality : 0.085 0.894 8824 Planarity : 0.005 0.063 3762 Dihedral : 20.037 179.626 18025 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 17.96 Ramachandran Plot: Outliers : 0.06 % Allowed : 12.76 % Favored : 87.18 % Rotamer: Outliers : 4.19 % Allowed : 26.92 % Favored : 68.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: -3.04 (0.19), residues: 1716 helix: -1.18 (0.22), residues: 533 sheet: -2.17 (0.34), residues: 230 loop : -2.54 (0.19), residues: 953 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG F 91 TYR 0.023 0.002 TYR C 167 PHE 0.050 0.002 PHE H 65 TRP 0.023 0.002 TRP B 103 HIS 0.007 0.001 HIS O 45 Details of bonding type rmsd/Z covalent geometry : bond 0.00468 / 0.23 (46213) covalent geometry : angle 1.16034 / 0.47 (69052) hydrogen bonds : bond 0.10002 / 5.61 ( 915) hydrogen bonds : angle 4.50750 / 3.18 ( 1793) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8361.46 seconds wall clock time: 145 minutes 21.14 seconds (8721.14 seconds total)