Starting phenix.real_space_refine on Mon Sep 14 21:44:19 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7o5h_12736/09_2026/7o5h_12736.cif Found real_map, /net/cci-nas-00/data/ceres_data/7o5h_12736/09_2026/7o5h_12736.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7o5h_12736/09_2026/7o5h_12736.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7o5h_12736/09_2026/7o5h_12736.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7o5h_12736/09_2026/7o5h_12736.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7o5h_12736/09_2026/7o5h_12736.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7o5h_12736/09_2026/7o5h_12736.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7o5h_12736/09_2026/7o5h_12736.map" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.006 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 964 5.49 5 Mg 167 5.21 5 S 59 5.16 5 C 17729 2.51 5 N 6377 2.21 5 O 9140 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.01s 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: 34436 Number of models: 1 Model: "" Number of chains: 22 Chain: "V" Number of atoms: 1955 Number of conformers: 1 Conformer: "" Number of residues, atoms: 251, 1955 Classifications: {'peptide': 251} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 231} Chain: "A" Number of atoms: 20726 Number of conformers: 1 Conformer: "" Number of residues, atoms: 964, 20726 Classifications: {'RNAv2': 964} Modifications used: {'rna2p_pur': 78, 'rna2p_pyr': 44, 'rna3p_pur': 485, 'rna3p_pyr': 357} Link IDs: {'rna2p': 121, 'rna3p': 842} Chain breaks: 7 Chain: "B" Number of atoms: 1760 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1760 Classifications: {'peptide': 225} Link IDs: {'PTRANS': 7, 'TRANS': 217} 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: 1165 Number of conformers: 1 Conformer: "" Number of residues, atoms: 158, 1165 Classifications: {'peptide': 158} Link IDs: {'PTRANS': 5, 'TRANS': 152} Chain: "F" Number of atoms: 839 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 839 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 5, 'TRANS': 97} Chain: "H" Number of atoms: 979 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 979 Classifications: {'peptide': 129} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 123} Chain: "K" Number of atoms: 877 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 877 Classifications: {'peptide': 117} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 109} Chain: "L" Number of atoms: 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: 702 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 702 Classifications: {'peptide': 87} Link IDs: {'TRANS': 86} Chain: "P" Number of atoms: 649 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 649 Classifications: {'peptide': 82} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 79} Chain: "Q" Number of atoms: 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: 456 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 456 Classifications: {'peptide': 55} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 52} Chain: "T" Number of atoms: 670 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 670 Classifications: {'peptide': 86} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 84} Chain: "U" Number of atoms: 252 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 252 Classifications: {'peptide': 30} Link IDs: {'PTRANS': 1, 'TRANS': 28} Chain: "A" Number of atoms: 161 Number of conformers: 1 Conformer: "" Number of residues, atoms: 161, 161 Unusual residues: {' MG': 161} Classifications: {'undetermined': 161} Link IDs: {None: 160} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "K" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "U" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 29871 SG CYS K 121 97.455 45.225 110.621 1.00 55.55 S Time building chain proxies: 6.65, per 1000 atoms: 0.19 Number of scatterers: 34436 At special positions: 0 Unit cell: (168.19, 191.82, 159.85, 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 59 16.00 P 964 15.00 Mg 167 11.99 O 9140 8.00 N 6377 7.00 C 17729 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.69 Conformation dependent library (CDL) restraints added in 735.1 milliseconds 3404 Ramachandran restraints generated. 1702 Oldfield, 0 Emsley, 1702 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3214 Finding SS restraints... Secondary structure from input PDB file: 69 helices and 15 sheets defined 46.6% alpha, 18.9% beta 317 base pairs and 590 stacking pairs defined. Time for finding SS restraints: 4.94 Creating SS restraints... Processing helix chain 'V' and resid 22 through 34 Processing helix chain 'V' and resid 51 through 56 removed outlier: 3.846A pdb=" N VAL V 55 " --> pdb=" O LEU V 51 " (cutoff:3.500A) Processing helix chain 'V' and resid 68 through 77 Processing helix chain 'V' and resid 96 through 105 removed outlier: 4.495A pdb=" N LEU V 100 " --> pdb=" O ASN V 96 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ALA V 101 " --> pdb=" O PHE V 97 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N GLU V 102 " --> pdb=" O GLY V 98 " (cutoff:3.500A) Processing helix chain 'V' and resid 115 through 128 removed outlier: 4.439A pdb=" N THR V 120 " --> pdb=" O TYR V 116 " (cutoff:3.500A) Proline residue: V 121 - end of helix Processing helix chain 'V' and resid 141 through 150 Processing helix chain 'V' and resid 158 through 167 removed outlier: 4.308A pdb=" N TYR V 167 " --> pdb=" O MET V 163 " (cutoff:3.500A) Processing helix chain 'V' and resid 177 through 179 No H-bonds generated for 'chain 'V' and resid 177 through 179' Processing helix chain 'V' and resid 206 through 218 Processing helix chain 'V' and resid 219 through 221 No H-bonds generated for 'chain 'V' and resid 219 through 221' Processing helix chain 'V' and resid 224 through 229 Processing helix chain 'V' and resid 234 through 241 Processing helix chain 'V' and resid 248 through 252 Processing helix chain 'V' and resid 253 through 268 Processing helix chain 'B' and resid 5 through 13 Processing helix chain 'B' and resid 24 through 29 Proline residue: B 29 - end of helix Processing helix chain 'B' and resid 42 through 63 removed outlier: 3.587A pdb=" N THR B 46 " --> pdb=" O ASN B 42 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N VAL B 47 " --> pdb=" O LEU B 43 " (cutoff:3.500A) Proline residue: B 48 - end of helix Processing helix chain 'B' and resid 73 through 87 removed outlier: 4.359A pdb=" N GLU B 78 " --> pdb=" O ARG B 74 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N LYS B 81 " --> pdb=" O SER B 77 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LEU B 85 " --> pdb=" O LYS B 81 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N SER B 86 " --> pdb=" O ASP B 82 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N CYS B 87 " --> pdb=" O ALA B 83 " (cutoff:3.500A) Processing helix chain 'B' and resid 103 through 123 removed outlier: 3.621A pdb=" N SER B 121 " --> pdb=" O LEU B 117 " (cutoff:3.500A) Processing helix chain 'B' and resid 132 through 149 Processing helix chain 'B' and resid 150 through 152 No H-bonds generated for 'chain 'B' and resid 150 through 152' Processing helix chain 'B' and resid 169 through 180 Processing helix chain 'B' and resid 192 through 196 removed outlier: 3.626A pdb=" N GLY B 195 " --> pdb=" O ASP B 192 " (cutoff:3.500A) Processing helix chain 'B' and resid 206 through 227 removed outlier: 3.762A pdb=" N THR B 220 " --> pdb=" O ALA B 216 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N GLN B 227 " --> pdb=" O GLU B 223 " (cutoff:3.500A) Processing helix chain 'D' and resid 7 through 16 removed outlier: 4.207A pdb=" N LEU D 11 " --> pdb=" O PRO D 7 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N SER D 12 " --> pdb=" O LYS D 8 " (cutoff:3.500A) Processing helix chain 'D' and resid 27 through 32 removed outlier: 3.778A pdb=" N LYS D 31 " --> pdb=" O ALA D 27 " (cutoff:3.500A) Processing helix chain 'D' and resid 39 through 43 removed outlier: 4.456A pdb=" N ALA D 43 " --> pdb=" O GLN D 40 " (cutoff:3.500A) Processing helix chain 'D' and resid 49 through 66 Processing helix chain 'D' and resid 68 through 82 Processing helix chain 'D' and resid 85 through 96 Processing helix chain 'D' and resid 97 through 105 Processing helix chain 'D' and resid 110 through 120 Processing helix chain 'D' and resid 147 through 150 Processing helix chain 'D' and resid 152 through 165 removed outlier: 3.752A pdb=" N LYS D 156 " --> pdb=" O GLN D 152 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N GLU D 160 " --> pdb=" O LYS D 156 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N LEU D 161 " --> pdb=" O ALA D 157 " (cutoff:3.500A) Processing helix chain 'D' and resid 197 through 206 Processing helix chain 'E' and resid 55 through 69 removed outlier: 3.597A pdb=" N ARG E 69 " --> pdb=" O GLU E 65 " (cutoff:3.500A) Processing helix chain 'E' and resid 108 through 119 removed outlier: 3.676A pdb=" N ALA E 113 " --> pdb=" O GLY E 109 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N VAL E 114 " --> pdb=" O ALA E 110 " (cutoff:3.500A) Processing helix chain 'E' and resid 132 through 146 removed outlier: 3.712A pdb=" N ASN E 146 " --> pdb=" O ASP E 142 " (cutoff:3.500A) Processing helix chain 'E' and resid 149 through 157 Processing helix chain 'E' and resid 160 through 165 Processing helix chain 'F' and resid 12 through 16 removed outlier: 4.934A pdb=" N GLU F 16 " --> pdb=" O ASP F 13 " (cutoff:3.500A) Processing helix chain 'F' and resid 17 through 32 removed outlier: 3.518A pdb=" N ARG F 24 " --> pdb=" O GLY F 20 " (cutoff:3.500A) Processing helix chain 'F' and resid 67 through 80 removed outlier: 3.551A pdb=" N ILE F 71 " --> pdb=" O PRO F 67 " (cutoff:3.500A) Processing helix chain 'H' and resid 5 through 20 removed outlier: 3.524A pdb=" N ASP H 9 " --> pdb=" O ASP H 5 " (cutoff:3.500A) Processing helix chain 'H' and resid 30 through 44 Processing helix chain 'H' and resid 88 through 92 Processing helix chain 'H' and resid 94 through 99 removed outlier: 3.679A pdb=" N ALA H 97 " --> pdb=" O LYS H 94 " (cutoff:3.500A) Processing helix chain 'H' and resid 113 through 120 Processing helix chain 'K' and resid 48 through 51 removed outlier: 3.879A pdb=" N GLY K 51 " --> pdb=" O GLY K 48 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 48 through 51' Processing helix chain 'K' and resid 59 through 75 removed outlier: 3.615A pdb=" N ALA K 63 " --> pdb=" O THR K 59 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N GLU K 68 " --> pdb=" O GLN K 64 " (cutoff:3.500A) Processing helix chain 'K' and resid 76 through 78 No H-bonds generated for 'chain 'K' and resid 76 through 78' Processing helix chain 'K' and resid 92 through 103 removed outlier: 3.574A pdb=" N THR K 96 " --> pdb=" O GLY K 92 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N ILE K 97 " --> pdb=" O ARG K 93 " (cutoff:3.500A) Processing helix chain 'L' and resid 3 through 10 Processing helix chain 'L' and resid 113 through 117 Processing helix chain 'O' and resid 4 through 16 Processing helix chain 'O' and resid 24 through 46 removed outlier: 4.263A pdb=" N GLY O 41 " --> pdb=" O ASN O 37 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N HIS O 42 " --> pdb=" O HIS O 38 " (cutoff:3.500A) Processing helix chain 'O' and resid 49 through 74 removed outlier: 3.750A pdb=" N GLY O 55 " --> pdb=" O HIS O 51 " (cutoff:3.500A) Processing helix chain 'O' and resid 74 through 86 Processing helix chain 'P' and resid 53 through 63 Processing helix chain 'P' and resid 68 through 82 Processing helix chain 'Q' and resid 49 through 52 removed outlier: 3.929A pdb=" N GLU Q 52 " --> pdb=" O GLU Q 49 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 49 through 52' Processing helix chain 'R' and resid 25 through 31 removed outlier: 3.805A pdb=" N ASN R 31 " --> pdb=" O ALA R 27 " (cutoff:3.500A) Processing helix chain 'R' and resid 41 through 46 removed outlier: 3.587A pdb=" N THR R 45 " --> pdb=" O PRO R 41 " (cutoff:3.500A) Processing helix chain 'R' and resid 48 through 65 Processing helix chain 'T' and resid 4 through 42 removed outlier: 3.506A pdb=" N ARG T 24 " --> pdb=" O HIS T 20 " (cutoff:3.500A) Processing helix chain 'T' and resid 43 through 64 removed outlier: 3.622A pdb=" N ALA T 47 " --> pdb=" O ASP T 43 " (cutoff:3.500A) Proline residue: T 56 - end of helix Processing helix chain 'T' and resid 68 through 87 Processing helix chain 'U' and resid 29 through 36 removed outlier: 3.578A pdb=" N ARG U 33 " --> pdb=" O LEU U 29 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ARG U 34 " --> pdb=" O ALA U 30 " (cutoff:3.500A) Processing helix chain 'U' and resid 40 through 55 Processing sheet with id=AA1, first strand: chain 'V' and resid 19 through 20 Processing sheet with id=AA2, first strand: chain 'V' and resid 85 through 89 removed outlier: 3.546A pdb=" N PHE V 111 " --> pdb=" O VAL V 42 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N ILE V 44 " --> pdb=" O PHE V 111 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N LEU V 108 " --> pdb=" O ASP V 135 " (cutoff:3.500A) removed outlier: 8.242A pdb=" N HIS V 137 " --> pdb=" O LEU V 108 " (cutoff:3.500A) removed outlier: 6.215A pdb=" N VAL V 110 " --> pdb=" O HIS V 137 " (cutoff:3.500A) removed outlier: 8.390A pdb=" N MET V 139 " --> pdb=" O VAL V 110 " (cutoff:3.500A) removed outlier: 7.328A pdb=" N ALA V 134 " --> pdb=" O PRO V 196 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N ARG V 193 " --> pdb=" O PRO V 172 " (cutoff:3.500A) removed outlier: 7.237A pdb=" N VAL V 195 " --> pdb=" O VAL V 170 " (cutoff:3.500A) removed outlier: 5.599A pdb=" N VAL V 170 " --> pdb=" O VAL V 195 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 16 through 19 removed outlier: 5.552A pdb=" N PHE B 16 " --> pdb=" O ILE B 41 " (cutoff:3.500A) removed outlier: 4.946A pdb=" N ILE B 41 " --> pdb=" O PHE B 16 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N HIS B 18 " --> pdb=" O HIS B 39 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 90 through 92 removed outlier: 6.268A pdb=" N LEU B 68 " --> pdb=" O PHE B 162 " (cutoff:3.500A) removed outlier: 7.903A pdb=" N ILE B 164 " --> pdb=" O LEU B 68 " (cutoff:3.500A) removed outlier: 6.977A pdb=" N VAL B 70 " --> pdb=" O ILE B 164 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N VAL B 183 " --> pdb=" O PHE B 198 " (cutoff:3.500A) removed outlier: 7.415A pdb=" N ILE B 200 " --> pdb=" O VAL B 183 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N ALA B 185 " --> pdb=" O ILE B 200 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 128 through 129 removed outlier: 3.849A pdb=" N ASP D 141 " --> pdb=" O PHE D 182 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 12 through 24 removed outlier: 5.001A pdb=" N GLU E 13 " --> pdb=" O GLY E 40 " (cutoff:3.500A) removed outlier: 7.286A pdb=" N GLY E 40 " --> pdb=" O GLU E 13 " (cutoff:3.500A) removed outlier: 5.240A pdb=" N LEU E 15 " --> pdb=" O VAL E 38 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N VAL E 38 " --> pdb=" O LEU E 15 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 85 through 88 removed outlier: 6.465A pdb=" N ILE E 106 " --> pdb=" O ALA E 125 " (cutoff:3.500A) removed outlier: 7.675A pdb=" N ALA E 127 " --> pdb=" O ILE E 106 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'F' and resid 35 through 51 removed outlier: 5.000A pdb=" N ILE F 36 " --> pdb=" O GLU F 65 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N GLU F 65 " --> pdb=" O ILE F 36 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ARG F 38 " --> pdb=" O ASN F 63 " (cutoff:3.500A) removed outlier: 5.488A pdb=" N TYR F 59 " --> pdb=" O TRP F 42 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N ARG F 44 " --> pdb=" O ALA F 57 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N ALA F 57 " --> pdb=" O ARG F 44 " (cutoff:3.500A) removed outlier: 4.827A pdb=" N GLN F 46 " --> pdb=" O HIS F 55 " (cutoff:3.500A) removed outlier: 8.496A pdb=" N HIS F 55 " --> pdb=" O GLN F 46 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N HIS F 3 " --> pdb=" O THR F 92 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N ARG F 86 " --> pdb=" O MET F 9 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'H' and resid 24 through 28 Processing sheet with id=AB1, first strand: chain 'H' and resid 74 through 77 Processing sheet with id=AB2, first strand: chain 'H' and resid 74 through 77 removed outlier: 6.845A pdb=" N VAL H 103 " --> pdb=" O ILE H 126 " (cutoff:3.500A) removed outlier: 4.983A pdb=" N TYR H 128 " --> pdb=" O ILE H 101 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N ILE H 101 " --> pdb=" O TYR H 128 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'K' and resid 41 through 46 removed outlier: 6.681A pdb=" N ILE K 34 " --> pdb=" O LEU K 42 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N TRP K 44 " --> pdb=" O VAL K 32 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N VAL K 32 " --> pdb=" O TRP K 44 " (cutoff:3.500A) removed outlier: 4.671A pdb=" N THR K 46 " --> pdb=" O THR K 30 " (cutoff:3.500A) removed outlier: 6.959A pdb=" N THR K 30 " --> pdb=" O THR K 46 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N LEU K 82 " --> pdb=" O ILE K 107 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N ASN K 109 " --> pdb=" O LEU K 82 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'L' and resid 62 through 66 removed outlier: 3.545A pdb=" N ARG L 36 " --> pdb=" O ARG L 54 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N ARG L 56 " --> pdb=" O CYS L 34 " (cutoff:3.500A) removed outlier: 5.864A pdb=" N CYS L 34 " --> pdb=" O ARG L 56 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N LYS L 30 " --> pdb=" O ILE L 82 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N SER L 78 " --> pdb=" O CYS L 34 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'P' and resid 50 through 52 removed outlier: 6.638A pdb=" N VAL P 19 " --> pdb=" O VAL P 36 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N PHE P 38 " --> pdb=" O TYR P 17 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N TYR P 17 " --> pdb=" O PHE P 38 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'Q' and resid 8 through 14 removed outlier: 7.521A pdb=" N GLN Q 9 " --> pdb=" O GLU Q 26 " (cutoff:3.500A) removed outlier: 5.019A pdb=" N GLU Q 26 " --> pdb=" O GLN Q 9 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N VAL Q 22 " --> pdb=" O VAL Q 13 " (cutoff:3.500A) removed outlier: 9.476A pdb=" N LYS Q 71 " --> pdb=" O LYS Q 43 " (cutoff:3.500A) removed outlier: 7.628A pdb=" N HIS Q 45 " --> pdb=" O LYS Q 71 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N TRP Q 73 " --> pdb=" O HIS Q 45 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LEU Q 75 " --> pdb=" O HIS Q 47 " (cutoff:3.500A) removed outlier: 5.283A pdb=" N LEU Q 75 " --> pdb=" O ARG Q 62 " (cutoff:3.500A) removed outlier: 5.921A pdb=" N ARG Q 62 " --> pdb=" O LEU Q 75 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ARG Q 77 " --> pdb=" O GLU Q 60 " (cutoff:3.500A) 666 hydrogen bonds defined for protein. 1899 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 778 hydrogen bonds 1242 hydrogen bond angles 0 basepair planarities 317 basepair parallelities 590 stacking parallelities Total time for adding SS restraints: 14.10 Time building geometry restraints manager: 3.66 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 6692 1.33 - 1.45: 13488 1.45 - 1.57: 14758 1.57 - 1.69: 1920 1.69 - 1.81: 105 Bond restraints: 36963 Sorted by residual: bond pdb=" C3' A A 411 " pdb=" O3' A A 411 " ideal model delta sigma weight residual 1.415 1.445 -0.030 2.00e-02 2.50e+03 2.19e+00 bond pdb=" CA VAL F 18 " pdb=" CB VAL F 18 " ideal model delta sigma weight residual 1.539 1.545 -0.006 5.40e-03 3.43e+04 1.21e+00 bond pdb=" CA VAL B 47 " pdb=" CB VAL B 47 " ideal model delta sigma weight residual 1.539 1.544 -0.005 5.40e-03 3.43e+04 1.03e+00 bond pdb=" C VAL V 110 " pdb=" N PHE V 111 " ideal model delta sigma weight residual 1.333 1.345 -0.012 1.30e-02 5.92e+03 8.83e-01 bond pdb=" C1' A A 71 " pdb=" N9 A A 71 " ideal model delta sigma weight residual 1.478 1.459 0.019 2.00e-02 2.50e+03 8.76e-01 ... (remaining 36958 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.13: 51012 1.13 - 2.27: 1230 2.27 - 3.40: 2039 3.40 - 4.53: 257 4.53 - 5.67: 169 Bond angle restraints: 54707 Sorted by residual: angle pdb=" C3' A A 411 " pdb=" O3' A A 411 " pdb=" P A A 412 " ideal model delta sigma weight residual 119.70 125.15 -5.45 1.20e+00 6.94e-01 2.06e+01 angle pdb=" C3' C A1107 " pdb=" O3' C A1107 " pdb=" P G A1108 " ideal model delta sigma weight residual 119.70 123.42 -3.72 1.20e+00 6.94e-01 9.60e+00 angle pdb=" C3' A A 71 " pdb=" C2' A A 71 " pdb=" O2' A A 71 " ideal model delta sigma weight residual 109.80 115.47 -5.67 2.00e+00 2.50e-01 8.03e+00 angle pdb=" O3' A A 499 " pdb=" C3' A A 499 " pdb=" C2' A A 499 " ideal model delta sigma weight residual 113.80 108.24 5.56 2.00e+00 2.50e-01 7.74e+00 angle pdb=" O3' A A 913 " pdb=" C3' A A 913 " pdb=" C2' A A 913 " ideal model delta sigma weight residual 113.80 108.27 5.53 2.00e+00 2.50e-01 7.63e+00 ... (remaining 54702 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.67: 18364 33.67 - 67.34: 1554 67.34 - 101.01: 131 101.01 - 134.69: 0 134.69 - 168.36: 2 Dihedral angle restraints: 20051 sinusoidal: 15078 harmonic: 4973 Sorted by residual: 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 36.34 -38.21 74.56 1 3.10e+00 1.04e-01 7.33e+02 dihedral pdb=" C4' G A1392 " pdb=" C3' G A1392 " pdb=" C2' G A1392 " pdb=" C1' G A1392 " ideal model delta sinusoidal sigma weight residual 36.34 -37.47 73.82 1 3.10e+00 1.04e-01 7.21e+02 dihedral pdb=" C4' U A 820 " pdb=" C3' U A 820 " pdb=" C2' U A 820 " pdb=" C1' U A 820 " ideal model delta sinusoidal sigma weight residual 36.34 -37.32 73.67 1 3.10e+00 1.04e-01 7.18e+02 ... (remaining 20048 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.064: 5441 0.064 - 0.128: 244 0.128 - 0.192: 9 0.192 - 0.256: 1029 0.256 - 0.320: 176 Chirality restraints: 6899 Sorted by residual: chirality pdb=" P A A 412 " pdb=" OP1 A A 412 " pdb=" OP2 A A 412 " pdb=" O5' A A 412 " both_signs ideal model delta sigma weight residual True 2.17 -2.49 -0.32 2.00e-01 2.50e+01 2.56e+00 chirality pdb=" C2' A A 71 " pdb=" C3' A A 71 " pdb=" O2' A A 71 " pdb=" C1' A A 71 " both_signs ideal model delta sigma weight residual False -2.79 -2.48 -0.31 2.00e-01 2.50e+01 2.47e+00 chirality pdb=" C2' U A 593 " pdb=" C3' U A 593 " pdb=" O2' U A 593 " pdb=" C1' U A 593 " both_signs ideal model delta sigma weight residual False -2.79 -2.48 -0.31 2.00e-01 2.50e+01 2.40e+00 ... (remaining 6896 not shown) Planarity restraints: 3369 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS L 44 " -0.020 5.00e-02 4.00e+02 3.00e-02 1.44e+00 pdb=" N PRO L 45 " 0.052 5.00e-02 4.00e+02 pdb=" CA PRO L 45 " -0.015 5.00e-02 4.00e+02 pdb=" CD PRO L 45 " -0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER D 138 " -0.020 5.00e-02 4.00e+02 2.97e-02 1.41e+00 pdb=" N PRO D 139 " 0.051 5.00e-02 4.00e+02 pdb=" CA PRO D 139 " -0.015 5.00e-02 4.00e+02 pdb=" CD PRO D 139 " -0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG H 80 " 0.019 5.00e-02 4.00e+02 2.92e-02 1.37e+00 pdb=" N PRO H 81 " -0.051 5.00e-02 4.00e+02 pdb=" CA PRO H 81 " 0.015 5.00e-02 4.00e+02 pdb=" CD PRO H 81 " 0.016 5.00e-02 4.00e+02 ... (remaining 3366 not shown) Histogram of nonbonded interaction distances: 1.26 - 1.99: 4 1.99 - 2.72: 2835 2.72 - 3.44: 46149 3.44 - 4.17: 112281 4.17 - 4.90: 155292 Nonbonded interactions: 316561 Sorted by model distance: nonbonded pdb="MG MG A1632 " pdb="MG MG A1696 " model vdw 1.262 1.300 nonbonded pdb=" OP1 C A 504 " pdb="MG MG A1725 " model vdw 1.933 2.170 nonbonded pdb=" OP2 A A 195 " pdb="MG MG A1642 " model vdw 1.976 2.170 nonbonded pdb=" OP1 A A 59 " pdb="MG MG A1621 " model vdw 1.983 2.170 nonbonded pdb=" O4' G A 713 " pdb="MG MG A1708 " model vdw 2.009 2.170 ... (remaining 316556 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.230 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: 0.020 Extract box with map and model: 0.590 Check model and map are aligned: 0.110 Set scattering table: 0.090 Process input model: 39.120 Find NCS groups from input model: 0.170 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:1.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8305 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 : 0.003 0.035 36963 Z= 0.130 Angle : 0.760 5.667 54707 Z= 0.312 Chirality : 0.103 0.320 6899 Planarity : 0.003 0.030 3369 Dihedral : 18.210 168.358 16837 Min Nonbonded Distance : 1.262 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 0.98 % Allowed : 3.07 % Favored : 95.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.09 (0.21), residues: 1702 helix: 1.77 (0.20), residues: 682 sheet: 0.14 (0.31), residues: 301 loop : 0.07 (0.24), residues: 719 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG R 63 TYR 0.007 0.001 TYR L 95 PHE 0.008 0.001 PHE V 111 TRP 0.007 0.001 TRP B 23 HIS 0.003 0.001 HIS E 89 Details of bonding type rmsd/Z covalent geometry : bond 0.00259 / 0.13 (36963) covalent geometry : angle 0.76003 / 0.31 (54707) hydrogen bonds : bond 0.22658 / 15.16 ( 1440) hydrogen bonds : angle 8.55959 / 5.62 ( 3141) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3404 Ramachandran restraints generated. 1702 Oldfield, 0 Emsley, 1702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3404 Ramachandran restraints generated. 1702 Oldfield, 0 Emsley, 1702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 427 residues out of total 1432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 413 time to evaluate : 0.762 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: V 23 GLN cc_start: 0.6955 (tp40) cc_final: 0.6617 (tp-100) REVERT: V 44 ILE cc_start: 0.6889 (mm) cc_final: 0.6495 (mt) REVERT: V 48 LEU cc_start: 0.8249 (tp) cc_final: 0.7819 (tt) REVERT: V 170 VAL cc_start: 0.8201 (t) cc_final: 0.7934 (p) REVERT: V 257 TYR cc_start: 0.8370 (m-80) cc_final: 0.8024 (m-80) REVERT: B 147 SER cc_start: 0.8068 (m) cc_final: 0.7784 (p) REVERT: B 168 HIS cc_start: 0.7716 (t-90) cc_final: 0.6926 (t-90) REVERT: B 170 HIS cc_start: 0.8659 (p-80) cc_final: 0.8294 (p-80) REVERT: D 47 ARG cc_start: 0.6536 (mtt180) cc_final: 0.6311 (mtm-85) REVERT: E 116 GLU cc_start: 0.6870 (tt0) cc_final: 0.6591 (tt0) REVERT: E 145 GLU cc_start: 0.7349 (pp20) cc_final: 0.7081 (pp20) REVERT: F 96 VAL cc_start: 0.8140 (m) cc_final: 0.7508 (m) REVERT: H 114 ARG cc_start: 0.7947 (ttm-80) cc_final: 0.7674 (ttm170) REVERT: O 6 GLU cc_start: 0.8143 (mp0) cc_final: 0.7850 (mp0) REVERT: O 72 ARG cc_start: 0.6869 (ttp-110) cc_final: 0.6655 (ttm110) REVERT: Q 9 GLN cc_start: 0.8117 (mt0) cc_final: 0.7849 (mt0) REVERT: Q 43 LYS cc_start: 0.7529 (mtmt) cc_final: 0.7290 (mtpp) REVERT: R 50 LYS cc_start: 0.8749 (tttt) cc_final: 0.8200 (ttmm) REVERT: R 54 GLN cc_start: 0.7912 (mt0) cc_final: 0.7653 (mt0) REVERT: T 28 MET cc_start: 0.8072 (ttp) cc_final: 0.7750 (ptm) outliers start: 14 outliers final: 4 residues processed: 427 average time/residue: 0.2523 time to fit residues: 162.6356 Evaluate side-chains 299 residues out of total 1432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 295 time to evaluate : 0.765 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 9 LEU Chi-restraints excluded: chain D residue 142 VAL Chi-restraints excluded: chain D residue 143 VAL Chi-restraints excluded: chain F residue 36 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 197 optimal weight: 2.9990 chunk 215 optimal weight: 7.9990 chunk 20 optimal weight: 5.9990 chunk 132 optimal weight: 0.9990 chunk 261 optimal weight: 0.9990 chunk 248 optimal weight: 3.9990 chunk 207 optimal weight: 0.9990 chunk 155 optimal weight: 7.9990 chunk 244 optimal weight: 0.9980 chunk 183 optimal weight: 7.9990 chunk 111 optimal weight: 4.9990 overall best weight: 1.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... V 78 HIS V 90 GLN ** V 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 202 HIS B 19 GLN B 36 ASN ** B 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 52 ASN K 15 GLN K 64 GLN L 5 ASN O 62 GLN P 18 GLN ** R 74 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 3 ASN T 20 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.065944 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.053033 restraints weight = 141428.565| |-----------------------------------------------------------------------------| r_work (start): 0.3111 rms_B_bonded: 1.45 r_work: 0.2999 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.2903 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.2903 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8448 moved from start: 0.2279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 36963 Z= 0.231 Angle : 1.291 20.935 54707 Z= 0.518 Chirality : 0.115 1.401 6899 Planarity : 0.005 0.040 3369 Dihedral : 17.960 170.837 13464 Min Nonbonded Distance : 1.175 Molprobity Statistics. All-atom Clashscore : 11.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 2.30 % Allowed : 9.78 % Favored : 87.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.03 (0.21), residues: 1702 helix: 1.66 (0.20), residues: 694 sheet: 0.30 (0.32), residues: 296 loop : -0.03 (0.24), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG K 69 TYR 0.013 0.001 TYR O 78 PHE 0.018 0.001 PHE K 61 TRP 0.009 0.001 TRP P 60 HIS 0.005 0.001 HIS D 41 Details of bonding type rmsd/Z covalent geometry : bond 0.00464 / 0.23 (36963) covalent geometry : angle 1.29055 / 0.52 (54707) hydrogen bonds : bond 0.06497 / 4.26 ( 1440) hydrogen bonds : angle 4.10042 / 2.83 ( 3141) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3404 Ramachandran restraints generated. 1702 Oldfield, 0 Emsley, 1702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3404 Ramachandran restraints generated. 1702 Oldfield, 0 Emsley, 1702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 365 residues out of total 1432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 332 time to evaluate : 0.756 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: V 23 GLN cc_start: 0.7219 (tp40) cc_final: 0.6998 (tp-100) REVERT: V 44 ILE cc_start: 0.6744 (mm) cc_final: 0.6338 (mt) REVERT: V 48 LEU cc_start: 0.8165 (tp) cc_final: 0.7841 (tt) REVERT: V 142 LYS cc_start: 0.7697 (tppt) cc_final: 0.7466 (tppt) REVERT: V 170 VAL cc_start: 0.8316 (t) cc_final: 0.8036 (p) REVERT: V 257 TYR cc_start: 0.8618 (m-80) cc_final: 0.8399 (m-80) REVERT: B 113 ARG cc_start: 0.8096 (tpp80) cc_final: 0.7669 (tpt170) REVERT: B 168 HIS cc_start: 0.7726 (t-90) cc_final: 0.6966 (t-90) REVERT: E 116 GLU cc_start: 0.7896 (tt0) cc_final: 0.7681 (tt0) REVERT: E 142 ASP cc_start: 0.7457 (m-30) cc_final: 0.7170 (m-30) REVERT: F 13 ASP cc_start: 0.7767 (m-30) cc_final: 0.7171 (t0) REVERT: F 75 GLU cc_start: 0.8224 (pp20) cc_final: 0.8005 (pp20) REVERT: F 81 ASN cc_start: 0.8003 (t0) cc_final: 0.7792 (t0) REVERT: Q 9 GLN cc_start: 0.8659 (mt0) cc_final: 0.8357 (mt0) REVERT: Q 48 ASP cc_start: 0.8192 (t0) cc_final: 0.7873 (t70) REVERT: R 50 LYS cc_start: 0.8860 (tttt) cc_final: 0.8417 (ttmm) REVERT: T 39 ILE cc_start: 0.9042 (tp) cc_final: 0.8581 (mm) REVERT: T 54 MET cc_start: 0.8391 (ttp) cc_final: 0.8065 (ttp) REVERT: T 79 LEU cc_start: 0.8062 (mt) cc_final: 0.7591 (mt) outliers start: 33 outliers final: 19 residues processed: 350 average time/residue: 0.2515 time to fit residues: 133.8343 Evaluate side-chains 306 residues out of total 1432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 287 time to evaluate : 0.497 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain V residue 199 THR Chi-restraints excluded: chain V residue 204 VAL Chi-restraints excluded: chain D residue 9 LEU Chi-restraints excluded: chain D residue 142 VAL Chi-restraints excluded: chain D residue 143 VAL Chi-restraints excluded: chain E residue 131 THR Chi-restraints excluded: chain F residue 36 ILE Chi-restraints excluded: chain F residue 51 ILE Chi-restraints excluded: chain F residue 85 ILE Chi-restraints excluded: chain F residue 87 SER Chi-restraints excluded: chain H residue 74 SER Chi-restraints excluded: chain K residue 20 VAL Chi-restraints excluded: chain K residue 32 VAL Chi-restraints excluded: chain K residue 59 THR Chi-restraints excluded: chain K residue 111 THR Chi-restraints excluded: chain L residue 4 VAL Chi-restraints excluded: chain L residue 10 LYS Chi-restraints excluded: chain O residue 18 ASP Chi-restraints excluded: chain R residue 42 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 227 optimal weight: 0.7980 chunk 105 optimal weight: 3.9990 chunk 53 optimal weight: 3.9990 chunk 141 optimal weight: 9.9990 chunk 160 optimal weight: 4.9990 chunk 80 optimal weight: 3.9990 chunk 85 optimal weight: 4.9990 chunk 9 optimal weight: 6.9990 chunk 144 optimal weight: 7.9990 chunk 223 optimal weight: 0.8980 chunk 103 optimal weight: 4.9990 overall best weight: 2.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** V 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 141 GLN V 202 HIS B 36 ASN ** B 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 22 HIS K 109 ASN ** R 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 74 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 61 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.064593 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.051554 restraints weight = 141713.772| |-----------------------------------------------------------------------------| r_work (start): 0.3067 rms_B_bonded: 1.37 r_work: 0.2955 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2858 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.2858 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8493 moved from start: 0.2688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 36963 Z= 0.307 Angle : 1.149 16.135 54707 Z= 0.467 Chirality : 0.094 1.061 6899 Planarity : 0.005 0.045 3369 Dihedral : 18.391 175.246 13464 Min Nonbonded Distance : 1.082 Molprobity Statistics. All-atom Clashscore : 11.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 3.28 % Allowed : 11.45 % Favored : 85.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.60 (0.20), residues: 1702 helix: 1.33 (0.20), residues: 696 sheet: 0.06 (0.32), residues: 285 loop : -0.28 (0.23), residues: 721 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 63 TYR 0.018 0.002 TYR V 157 PHE 0.011 0.002 PHE V 111 TRP 0.017 0.002 TRP B 23 HIS 0.007 0.001 HIS D 41 Details of bonding type rmsd/Z covalent geometry : bond 0.00626 / 0.31 (36963) covalent geometry : angle 1.14901 / 0.47 (54707) hydrogen bonds : bond 0.06296 / 4.03 ( 1440) hydrogen bonds : angle 4.02413 / 2.76 ( 3141) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3404 Ramachandran restraints generated. 1702 Oldfield, 0 Emsley, 1702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3404 Ramachandran restraints generated. 1702 Oldfield, 0 Emsley, 1702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 340 residues out of total 1432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 293 time to evaluate : 0.737 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: V 44 ILE cc_start: 0.6760 (mm) cc_final: 0.6353 (mt) REVERT: V 48 LEU cc_start: 0.8166 (tp) cc_final: 0.7856 (tt) REVERT: V 170 VAL cc_start: 0.8416 (t) cc_final: 0.8211 (p) REVERT: B 96 TRP cc_start: 0.8392 (t-100) cc_final: 0.7999 (t-100) REVERT: B 168 HIS cc_start: 0.7738 (t-90) cc_final: 0.7290 (t-90) REVERT: E 116 GLU cc_start: 0.8218 (tt0) cc_final: 0.8014 (tt0) REVERT: E 142 ASP cc_start: 0.7420 (m-30) cc_final: 0.7078 (m-30) REVERT: E 152 MET cc_start: 0.7877 (mtp) cc_final: 0.7588 (mtp) REVERT: F 75 GLU cc_start: 0.8196 (pp20) cc_final: 0.7975 (pp20) REVERT: F 81 ASN cc_start: 0.8360 (t0) cc_final: 0.7989 (t0) REVERT: H 3 MET cc_start: 0.8664 (tpp) cc_final: 0.8441 (tpp) REVERT: K 31 ILE cc_start: 0.8874 (mp) cc_final: 0.8656 (mt) REVERT: O 48 LYS cc_start: 0.8716 (mmtm) cc_final: 0.8477 (mtmm) REVERT: Q 5 ILE cc_start: 0.8844 (pt) cc_final: 0.8409 (pt) REVERT: Q 18 GLU cc_start: 0.7869 (mt-10) cc_final: 0.7561 (mt-10) REVERT: Q 48 ASP cc_start: 0.8274 (t0) cc_final: 0.8044 (t70) REVERT: T 39 ILE cc_start: 0.9014 (tp) cc_final: 0.8661 (mm) REVERT: T 79 LEU cc_start: 0.8163 (mt) cc_final: 0.7813 (mt) outliers start: 47 outliers final: 41 residues processed: 318 average time/residue: 0.2331 time to fit residues: 114.5629 Evaluate side-chains 306 residues out of total 1432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 265 time to evaluate : 0.743 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain V residue 25 VAL Chi-restraints excluded: chain V residue 161 SER Chi-restraints excluded: chain V residue 199 THR Chi-restraints excluded: chain V residue 204 VAL Chi-restraints excluded: chain B residue 77 SER Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain D residue 9 LEU Chi-restraints excluded: chain D residue 28 ILE Chi-restraints excluded: chain D residue 142 VAL Chi-restraints excluded: chain D residue 143 VAL Chi-restraints excluded: chain D residue 169 THR Chi-restraints excluded: chain E residue 25 VAL Chi-restraints excluded: chain E residue 34 THR Chi-restraints excluded: chain E residue 36 LEU Chi-restraints excluded: chain E residue 97 GLN Chi-restraints excluded: chain E residue 131 THR Chi-restraints excluded: chain E residue 165 LEU Chi-restraints excluded: chain F residue 36 ILE Chi-restraints excluded: chain F residue 51 ILE Chi-restraints excluded: chain F residue 78 PHE Chi-restraints excluded: chain F residue 85 ILE Chi-restraints excluded: chain F residue 87 SER Chi-restraints excluded: chain H residue 10 MET Chi-restraints excluded: chain H residue 74 SER Chi-restraints excluded: chain H residue 76 GLN Chi-restraints excluded: chain K residue 20 VAL Chi-restraints excluded: chain K residue 32 VAL Chi-restraints excluded: chain K residue 59 THR Chi-restraints excluded: chain K residue 111 THR Chi-restraints excluded: chain L residue 4 VAL Chi-restraints excluded: chain L residue 10 LYS Chi-restraints excluded: chain O residue 18 ASP Chi-restraints excluded: chain P residue 66 THR Chi-restraints excluded: chain Q residue 8 LEU Chi-restraints excluded: chain Q residue 33 ILE Chi-restraints excluded: chain R residue 42 SER Chi-restraints excluded: chain R residue 44 ILE Chi-restraints excluded: chain T residue 28 MET Chi-restraints excluded: chain T residue 66 LEU Chi-restraints excluded: chain T residue 75 HIS Chi-restraints excluded: chain T residue 83 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 250 optimal weight: 2.9990 chunk 62 optimal weight: 3.9990 chunk 51 optimal weight: 5.9990 chunk 255 optimal weight: 0.0170 chunk 94 optimal weight: 6.9990 chunk 81 optimal weight: 3.9990 chunk 20 optimal weight: 2.9990 chunk 17 optimal weight: 9.9990 chunk 260 optimal weight: 0.6980 chunk 203 optimal weight: 9.9990 chunk 202 optimal weight: 3.9990 overall best weight: 2.1424 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** V 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 202 HIS B 36 ASN B 120 GLN D 131 ASN ** R 74 HIS ** 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 = 0.3489 r_free = 0.3489 target = 0.065322 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.052357 restraints weight = 140739.490| |-----------------------------------------------------------------------------| r_work (start): 0.3092 rms_B_bonded: 1.37 r_work: 0.2979 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.2884 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.2884 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8468 moved from start: 0.2930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 36963 Z= 0.247 Angle : 1.071 15.923 54707 Z= 0.436 Chirality : 0.088 1.011 6899 Planarity : 0.005 0.043 3369 Dihedral : 18.446 178.506 13464 Min Nonbonded Distance : 1.105 Molprobity Statistics. All-atom Clashscore : 11.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 3.91 % Allowed : 12.71 % Favored : 83.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.61 (0.20), residues: 1702 helix: 1.43 (0.20), residues: 696 sheet: -0.03 (0.31), residues: 291 loop : -0.35 (0.23), residues: 715 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 108 TYR 0.032 0.002 TYR V 157 PHE 0.015 0.002 PHE E 95 TRP 0.011 0.002 TRP B 23 HIS 0.005 0.001 HIS E 89 Details of bonding type rmsd/Z covalent geometry : bond 0.00503 / 0.25 (36963) covalent geometry : angle 1.07113 / 0.44 (54707) hydrogen bonds : bond 0.05574 / 3.59 ( 1440) hydrogen bonds : angle 3.87156 / 2.66 ( 3141) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3404 Ramachandran restraints generated. 1702 Oldfield, 0 Emsley, 1702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3404 Ramachandran restraints generated. 1702 Oldfield, 0 Emsley, 1702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 349 residues out of total 1432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 293 time to evaluate : 0.762 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: V 44 ILE cc_start: 0.6730 (mm) cc_final: 0.6308 (mt) REVERT: V 48 LEU cc_start: 0.8185 (tp) cc_final: 0.7856 (tt) REVERT: V 142 LYS cc_start: 0.7773 (tppt) cc_final: 0.7535 (tppt) REVERT: V 157 TYR cc_start: 0.8065 (t80) cc_final: 0.7715 (t80) REVERT: V 170 VAL cc_start: 0.8418 (t) cc_final: 0.8195 (p) REVERT: B 90 PHE cc_start: 0.6406 (OUTLIER) cc_final: 0.5969 (m-10) REVERT: B 113 ARG cc_start: 0.8068 (tpp80) cc_final: 0.7235 (tpm170) REVERT: B 168 HIS cc_start: 0.7716 (t-90) cc_final: 0.7149 (t-90) REVERT: E 32 SER cc_start: 0.7037 (OUTLIER) cc_final: 0.6585 (m) REVERT: E 142 ASP cc_start: 0.7446 (m-30) cc_final: 0.7067 (m-30) REVERT: E 163 GLU cc_start: 0.8145 (mt-10) cc_final: 0.7854 (mt-10) REVERT: F 13 ASP cc_start: 0.7786 (m-30) cc_final: 0.7225 (t0) REVERT: F 17 GLN cc_start: 0.8577 (pm20) cc_final: 0.8265 (pm20) REVERT: F 81 ASN cc_start: 0.8407 (t0) cc_final: 0.8152 (t0) REVERT: K 31 ILE cc_start: 0.8870 (mp) cc_final: 0.8658 (mt) REVERT: Q 18 GLU cc_start: 0.7894 (mt-10) cc_final: 0.7652 (mt-10) REVERT: Q 48 ASP cc_start: 0.8175 (t0) cc_final: 0.7935 (t70) REVERT: T 54 MET cc_start: 0.8270 (ttp) cc_final: 0.8034 (ttp) REVERT: T 61 GLN cc_start: 0.8665 (OUTLIER) cc_final: 0.8325 (mp-120) REVERT: T 79 LEU cc_start: 0.8031 (mt) cc_final: 0.7550 (mt) outliers start: 56 outliers final: 47 residues processed: 328 average time/residue: 0.2410 time to fit residues: 122.2004 Evaluate side-chains 318 residues out of total 1432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 268 time to evaluate : 0.664 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain V residue 25 VAL Chi-restraints excluded: chain V residue 161 SER Chi-restraints excluded: chain V residue 199 THR Chi-restraints excluded: chain V residue 204 VAL Chi-restraints excluded: chain B residue 77 SER Chi-restraints excluded: chain B residue 90 PHE Chi-restraints excluded: chain B residue 120 GLN Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain D residue 9 LEU Chi-restraints excluded: chain D residue 28 ILE Chi-restraints excluded: chain D residue 142 VAL Chi-restraints excluded: chain D residue 143 VAL Chi-restraints excluded: chain D residue 169 THR Chi-restraints excluded: chain E residue 25 VAL Chi-restraints excluded: chain E residue 32 SER Chi-restraints excluded: chain E residue 34 THR Chi-restraints excluded: chain E residue 97 GLN Chi-restraints excluded: chain E residue 131 THR Chi-restraints excluded: chain E residue 165 LEU Chi-restraints excluded: chain F residue 36 ILE Chi-restraints excluded: chain F residue 51 ILE Chi-restraints excluded: chain F residue 54 LEU Chi-restraints excluded: chain F residue 64 VAL Chi-restraints excluded: chain F residue 78 PHE Chi-restraints excluded: chain F residue 85 ILE Chi-restraints excluded: chain F residue 87 SER Chi-restraints excluded: chain H residue 10 MET Chi-restraints excluded: chain H residue 26 THR Chi-restraints excluded: chain H residue 62 THR Chi-restraints excluded: chain H residue 74 SER Chi-restraints excluded: chain H residue 76 GLN Chi-restraints excluded: chain K residue 20 VAL Chi-restraints excluded: chain K residue 32 VAL Chi-restraints excluded: chain K residue 111 THR Chi-restraints excluded: chain L residue 4 VAL Chi-restraints excluded: chain L residue 10 LYS Chi-restraints excluded: chain L residue 56 ARG Chi-restraints excluded: chain L residue 109 ASP Chi-restraints excluded: chain O residue 18 ASP Chi-restraints excluded: chain P residue 45 GLU Chi-restraints excluded: chain P residue 53 ASP Chi-restraints excluded: chain P residue 66 THR Chi-restraints excluded: chain Q residue 33 ILE Chi-restraints excluded: chain Q residue 81 LYS Chi-restraints excluded: chain R residue 33 ILE Chi-restraints excluded: chain R residue 42 SER Chi-restraints excluded: chain T residue 40 GLU Chi-restraints excluded: chain T residue 61 GLN Chi-restraints excluded: chain T residue 66 LEU Chi-restraints excluded: chain T residue 75 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 72 optimal weight: 5.9990 chunk 231 optimal weight: 0.9980 chunk 147 optimal weight: 0.2980 chunk 64 optimal weight: 6.9990 chunk 38 optimal weight: 6.9990 chunk 137 optimal weight: 0.9980 chunk 51 optimal weight: 6.9990 chunk 199 optimal weight: 2.9990 chunk 83 optimal weight: 4.9990 chunk 96 optimal weight: 3.9990 chunk 228 optimal weight: 3.9990 overall best weight: 1.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** V 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 202 HIS B 36 ASN K 64 GLN ** R 74 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.065621 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.052687 restraints weight = 141513.401| |-----------------------------------------------------------------------------| r_work (start): 0.3102 rms_B_bonded: 1.36 r_work: 0.2988 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2892 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.2892 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8461 moved from start: 0.3070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 36963 Z= 0.226 Angle : 1.043 15.947 54707 Z= 0.425 Chirality : 0.085 0.985 6899 Planarity : 0.004 0.042 3369 Dihedral : 18.458 176.926 13464 Min Nonbonded Distance : 1.112 Molprobity Statistics. All-atom Clashscore : 10.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 3.77 % Allowed : 14.04 % Favored : 82.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.60 (0.20), residues: 1702 helix: 1.44 (0.20), residues: 696 sheet: -0.06 (0.31), residues: 291 loop : -0.36 (0.23), residues: 715 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG V 208 TYR 0.026 0.002 TYR V 157 PHE 0.015 0.001 PHE E 95 TRP 0.011 0.002 TRP B 23 HIS 0.005 0.001 HIS E 89 Details of bonding type rmsd/Z covalent geometry : bond 0.00459 / 0.23 (36963) covalent geometry : angle 1.04308 / 0.43 (54707) hydrogen bonds : bond 0.05455 / 3.53 ( 1440) hydrogen bonds : angle 3.80459 / 2.61 ( 3141) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3404 Ramachandran restraints generated. 1702 Oldfield, 0 Emsley, 1702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3404 Ramachandran restraints generated. 1702 Oldfield, 0 Emsley, 1702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 337 residues out of total 1432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 283 time to evaluate : 0.757 Fit side-chains revert: symmetry clash REVERT: V 44 ILE cc_start: 0.6846 (mm) cc_final: 0.6453 (mt) REVERT: V 48 LEU cc_start: 0.8251 (tp) cc_final: 0.7872 (tt) REVERT: V 142 LYS cc_start: 0.7834 (tppt) cc_final: 0.7606 (tppt) REVERT: V 157 TYR cc_start: 0.8070 (t80) cc_final: 0.7716 (t80) REVERT: V 170 VAL cc_start: 0.8404 (t) cc_final: 0.8180 (p) REVERT: B 90 PHE cc_start: 0.6401 (OUTLIER) cc_final: 0.5969 (m-10) REVERT: B 94 HIS cc_start: 0.6443 (m90) cc_final: 0.6172 (m170) REVERT: B 168 HIS cc_start: 0.7725 (t-90) cc_final: 0.7125 (t-90) REVERT: E 32 SER cc_start: 0.7074 (OUTLIER) cc_final: 0.6668 (m) REVERT: E 142 ASP cc_start: 0.7466 (m-30) cc_final: 0.7078 (m-30) REVERT: E 163 GLU cc_start: 0.8133 (mt-10) cc_final: 0.7881 (mt-10) REVERT: F 13 ASP cc_start: 0.7824 (m-30) cc_final: 0.7284 (t0) REVERT: F 65 GLU cc_start: 0.8001 (tm-30) cc_final: 0.7692 (tp30) REVERT: F 81 ASN cc_start: 0.8361 (t0) cc_final: 0.8072 (t0) REVERT: K 31 ILE cc_start: 0.8888 (mp) cc_final: 0.8675 (mt) REVERT: K 74 VAL cc_start: 0.8844 (t) cc_final: 0.8616 (m) REVERT: O 88 ARG cc_start: 0.7319 (mmm160) cc_final: 0.6415 (mmp80) REVERT: Q 18 GLU cc_start: 0.7892 (mt-10) cc_final: 0.7657 (mt-10) REVERT: Q 48 ASP cc_start: 0.8246 (t0) cc_final: 0.7995 (t70) REVERT: T 39 ILE cc_start: 0.9012 (tp) cc_final: 0.8764 (mm) REVERT: T 79 LEU cc_start: 0.8022 (mt) cc_final: 0.7534 (mt) outliers start: 54 outliers final: 48 residues processed: 315 average time/residue: 0.2377 time to fit residues: 116.5160 Evaluate side-chains 323 residues out of total 1432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 273 time to evaluate : 0.781 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain V residue 25 VAL Chi-restraints excluded: chain V residue 161 SER Chi-restraints excluded: chain V residue 199 THR Chi-restraints excluded: chain V residue 204 VAL Chi-restraints excluded: chain B residue 77 SER Chi-restraints excluded: chain B residue 90 PHE Chi-restraints excluded: chain B residue 110 SER Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 148 LEU Chi-restraints excluded: chain D residue 9 LEU Chi-restraints excluded: chain D residue 28 ILE Chi-restraints excluded: chain D residue 142 VAL Chi-restraints excluded: chain D residue 143 VAL Chi-restraints excluded: chain D residue 169 THR Chi-restraints excluded: chain E residue 25 VAL Chi-restraints excluded: chain E residue 32 SER Chi-restraints excluded: chain E residue 34 THR Chi-restraints excluded: chain E residue 36 LEU Chi-restraints excluded: chain E residue 97 GLN Chi-restraints excluded: chain E residue 131 THR Chi-restraints excluded: chain E residue 165 LEU Chi-restraints excluded: chain F residue 36 ILE Chi-restraints excluded: chain F residue 51 ILE Chi-restraints excluded: chain F residue 54 LEU Chi-restraints excluded: chain F residue 64 VAL Chi-restraints excluded: chain F residue 78 PHE Chi-restraints excluded: chain F residue 85 ILE Chi-restraints excluded: chain F residue 87 SER Chi-restraints excluded: chain H residue 10 MET Chi-restraints excluded: chain H residue 62 THR Chi-restraints excluded: chain H residue 74 SER Chi-restraints excluded: chain H residue 76 GLN Chi-restraints excluded: chain K residue 20 VAL Chi-restraints excluded: chain K residue 32 VAL Chi-restraints excluded: chain K residue 59 THR Chi-restraints excluded: chain K residue 111 THR Chi-restraints excluded: chain L residue 4 VAL Chi-restraints excluded: chain L residue 10 LYS Chi-restraints excluded: chain L residue 56 ARG Chi-restraints excluded: chain O residue 18 ASP Chi-restraints excluded: chain P residue 45 GLU Chi-restraints excluded: chain P residue 53 ASP Chi-restraints excluded: chain P residue 66 THR Chi-restraints excluded: chain Q residue 33 ILE Chi-restraints excluded: chain Q residue 38 ILE Chi-restraints excluded: chain R residue 33 ILE Chi-restraints excluded: chain R residue 42 SER Chi-restraints excluded: chain T residue 40 GLU Chi-restraints excluded: chain T residue 66 LEU Chi-restraints excluded: chain T residue 75 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 247 optimal weight: 0.8980 chunk 93 optimal weight: 8.9990 chunk 170 optimal weight: 2.9990 chunk 140 optimal weight: 3.9990 chunk 4 optimal weight: 0.9980 chunk 103 optimal weight: 4.9990 chunk 244 optimal weight: 0.9990 chunk 216 optimal weight: 7.9990 chunk 240 optimal weight: 6.9990 chunk 77 optimal weight: 4.9990 chunk 94 optimal weight: 6.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** V 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 202 HIS B 120 GLN ** Q 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 74 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.065609 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.052662 restraints weight = 140458.238| |-----------------------------------------------------------------------------| r_work (start): 0.3101 rms_B_bonded: 1.36 r_work: 0.2988 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.2892 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.2892 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8462 moved from start: 0.3179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 36963 Z= 0.234 Angle : 1.043 15.767 54707 Z= 0.426 Chirality : 0.084 0.979 6899 Planarity : 0.005 0.042 3369 Dihedral : 18.447 179.680 13464 Min Nonbonded Distance : 1.107 Molprobity Statistics. All-atom Clashscore : 11.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 4.61 % Allowed : 14.11 % Favored : 81.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.58 (0.20), residues: 1702 helix: 1.45 (0.20), residues: 696 sheet: -0.01 (0.31), residues: 284 loop : -0.44 (0.23), residues: 722 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG V 208 TYR 0.022 0.002 TYR V 157 PHE 0.015 0.001 PHE E 95 TRP 0.012 0.002 TRP B 23 HIS 0.004 0.001 HIS E 89 Details of bonding type rmsd/Z covalent geometry : bond 0.00477 / 0.23 (36963) covalent geometry : angle 1.04312 / 0.43 (54707) hydrogen bonds : bond 0.05426 / 3.50 ( 1440) hydrogen bonds : angle 3.80810 / 2.61 ( 3141) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3404 Ramachandran restraints generated. 1702 Oldfield, 0 Emsley, 1702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3404 Ramachandran restraints generated. 1702 Oldfield, 0 Emsley, 1702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 347 residues out of total 1432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 281 time to evaluate : 0.686 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: V 44 ILE cc_start: 0.6854 (mm) cc_final: 0.6460 (mt) REVERT: V 48 LEU cc_start: 0.8221 (tp) cc_final: 0.7874 (tt) REVERT: V 142 LYS cc_start: 0.7909 (tppt) cc_final: 0.7676 (tppt) REVERT: V 157 TYR cc_start: 0.8135 (t80) cc_final: 0.7758 (t80) REVERT: V 170 VAL cc_start: 0.8408 (t) cc_final: 0.8187 (p) REVERT: V 241 MET cc_start: 0.7330 (ttm) cc_final: 0.7088 (mtt) REVERT: B 90 PHE cc_start: 0.6425 (OUTLIER) cc_final: 0.6139 (m-10) REVERT: B 94 HIS cc_start: 0.6322 (m90) cc_final: 0.6015 (m170) REVERT: B 118 GLU cc_start: 0.7032 (pp20) cc_final: 0.6666 (mt-10) REVERT: B 120 GLN cc_start: 0.6159 (OUTLIER) cc_final: 0.5939 (pp30) REVERT: B 168 HIS cc_start: 0.7744 (t-90) cc_final: 0.7086 (t-90) REVERT: E 14 LYS cc_start: 0.8054 (mttt) cc_final: 0.7838 (mttt) REVERT: E 32 SER cc_start: 0.7087 (OUTLIER) cc_final: 0.6674 (m) REVERT: E 142 ASP cc_start: 0.7429 (m-30) cc_final: 0.7032 (m-30) REVERT: E 163 GLU cc_start: 0.8136 (mt-10) cc_final: 0.7876 (mt-10) REVERT: F 13 ASP cc_start: 0.7922 (m-30) cc_final: 0.7379 (t0) REVERT: F 65 GLU cc_start: 0.8004 (tm-30) cc_final: 0.7732 (tm-30) REVERT: F 68 GLN cc_start: 0.7400 (mp10) cc_final: 0.7165 (mp10) REVERT: F 81 ASN cc_start: 0.8416 (t0) cc_final: 0.8045 (t0) REVERT: K 31 ILE cc_start: 0.8832 (mp) cc_final: 0.8612 (mt) REVERT: K 74 VAL cc_start: 0.8916 (t) cc_final: 0.8682 (m) REVERT: O 88 ARG cc_start: 0.7261 (mmm160) cc_final: 0.6379 (mmp80) REVERT: Q 18 GLU cc_start: 0.7899 (mt-10) cc_final: 0.7690 (mt-10) REVERT: Q 48 ASP cc_start: 0.8246 (t0) cc_final: 0.8001 (t70) REVERT: T 39 ILE cc_start: 0.9032 (tp) cc_final: 0.8712 (mm) REVERT: T 61 GLN cc_start: 0.8659 (OUTLIER) cc_final: 0.8342 (mp-120) REVERT: T 79 LEU cc_start: 0.8398 (mt) cc_final: 0.8090 (mt) outliers start: 66 outliers final: 53 residues processed: 319 average time/residue: 0.2302 time to fit residues: 114.7775 Evaluate side-chains 327 residues out of total 1432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 270 time to evaluate : 0.714 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain V residue 25 VAL Chi-restraints excluded: chain V residue 161 SER Chi-restraints excluded: chain V residue 199 THR Chi-restraints excluded: chain V residue 204 VAL Chi-restraints excluded: chain B residue 77 SER Chi-restraints excluded: chain B residue 90 PHE Chi-restraints excluded: chain B residue 110 SER Chi-restraints excluded: chain B residue 120 GLN Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 148 LEU Chi-restraints excluded: chain D residue 5 LEU Chi-restraints excluded: chain D residue 9 LEU Chi-restraints excluded: chain D residue 142 VAL Chi-restraints excluded: chain D residue 143 VAL Chi-restraints excluded: chain D residue 169 THR Chi-restraints excluded: chain E residue 25 VAL Chi-restraints excluded: chain E residue 32 SER Chi-restraints excluded: chain E residue 34 THR Chi-restraints excluded: chain E residue 36 LEU Chi-restraints excluded: chain E residue 97 GLN Chi-restraints excluded: chain E residue 131 THR Chi-restraints excluded: chain E residue 165 LEU Chi-restraints excluded: chain F residue 36 ILE Chi-restraints excluded: chain F residue 51 ILE Chi-restraints excluded: chain F residue 54 LEU Chi-restraints excluded: chain F residue 64 VAL Chi-restraints excluded: chain F residue 78 PHE Chi-restraints excluded: chain F residue 85 ILE Chi-restraints excluded: chain F residue 87 SER Chi-restraints excluded: chain H residue 10 MET Chi-restraints excluded: chain H residue 26 THR Chi-restraints excluded: chain H residue 62 THR Chi-restraints excluded: chain H residue 74 SER Chi-restraints excluded: chain H residue 76 GLN Chi-restraints excluded: chain K residue 32 VAL Chi-restraints excluded: chain K residue 59 THR Chi-restraints excluded: chain K residue 111 THR Chi-restraints excluded: chain L residue 4 VAL Chi-restraints excluded: chain L residue 10 LYS Chi-restraints excluded: chain L residue 56 ARG Chi-restraints excluded: chain L residue 109 ASP Chi-restraints excluded: chain O residue 18 ASP Chi-restraints excluded: chain P residue 45 GLU Chi-restraints excluded: chain P residue 53 ASP Chi-restraints excluded: chain P residue 66 THR Chi-restraints excluded: chain Q residue 28 PHE Chi-restraints excluded: chain Q residue 33 ILE Chi-restraints excluded: chain Q residue 38 ILE Chi-restraints excluded: chain Q residue 61 ILE Chi-restraints excluded: chain R residue 33 ILE Chi-restraints excluded: chain R residue 42 SER Chi-restraints excluded: chain R residue 44 ILE Chi-restraints excluded: chain T residue 40 GLU Chi-restraints excluded: chain T residue 61 GLN Chi-restraints excluded: chain T residue 66 LEU Chi-restraints excluded: chain T residue 75 HIS Chi-restraints excluded: chain T residue 86 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 248 optimal weight: 0.6980 chunk 110 optimal weight: 3.9990 chunk 151 optimal weight: 0.9980 chunk 22 optimal weight: 0.8980 chunk 21 optimal weight: 0.8980 chunk 5 optimal weight: 9.9990 chunk 247 optimal weight: 0.8980 chunk 166 optimal weight: 6.9990 chunk 34 optimal weight: 4.9990 chunk 201 optimal weight: 9.9990 chunk 68 optimal weight: 5.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... V 202 HIS B 120 GLN F 94 HIS ** R 74 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.066780 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.053946 restraints weight = 141457.877| |-----------------------------------------------------------------------------| r_work (start): 0.3140 rms_B_bonded: 1.37 r_work: 0.3028 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.2931 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.2931 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8427 moved from start: 0.3286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 36963 Z= 0.162 Angle : 0.995 15.652 54707 Z= 0.407 Chirality : 0.080 0.931 6899 Planarity : 0.004 0.059 3369 Dihedral : 18.440 178.955 13464 Min Nonbonded Distance : 1.133 Molprobity Statistics. All-atom Clashscore : 10.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 3.28 % Allowed : 16.27 % Favored : 80.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.68 (0.21), residues: 1702 helix: 1.51 (0.20), residues: 696 sheet: 0.07 (0.31), residues: 284 loop : -0.35 (0.23), residues: 722 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG K 69 TYR 0.022 0.001 TYR V 157 PHE 0.015 0.001 PHE E 95 TRP 0.008 0.001 TRP P 60 HIS 0.003 0.001 HIS V 202 Details of bonding type rmsd/Z covalent geometry : bond 0.00328 / 0.16 (36963) covalent geometry : angle 0.99500 / 0.41 (54707) hydrogen bonds : bond 0.05155 / 3.36 ( 1440) hydrogen bonds : angle 3.70400 / 2.53 ( 3141) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3404 Ramachandran restraints generated. 1702 Oldfield, 0 Emsley, 1702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3404 Ramachandran restraints generated. 1702 Oldfield, 0 Emsley, 1702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 332 residues out of total 1432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 285 time to evaluate : 0.653 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: V 44 ILE cc_start: 0.6841 (mm) cc_final: 0.6436 (mt) REVERT: V 48 LEU cc_start: 0.8218 (tp) cc_final: 0.7868 (tt) REVERT: V 142 LYS cc_start: 0.7883 (tppt) cc_final: 0.7646 (tppt) REVERT: V 157 TYR cc_start: 0.8083 (t80) cc_final: 0.7723 (t80) REVERT: V 170 VAL cc_start: 0.8390 (t) cc_final: 0.8151 (p) REVERT: B 90 PHE cc_start: 0.6372 (OUTLIER) cc_final: 0.5999 (m-10) REVERT: B 94 HIS cc_start: 0.6302 (m90) cc_final: 0.5994 (m170) REVERT: B 113 ARG cc_start: 0.7989 (tpp80) cc_final: 0.7137 (tpm170) REVERT: B 168 HIS cc_start: 0.7684 (t-90) cc_final: 0.7041 (t-90) REVERT: E 32 SER cc_start: 0.6689 (OUTLIER) cc_final: 0.6452 (m) REVERT: E 142 ASP cc_start: 0.7482 (m-30) cc_final: 0.7052 (m-30) REVERT: F 13 ASP cc_start: 0.7884 (m-30) cc_final: 0.7295 (t0) REVERT: F 14 GLN cc_start: 0.8952 (mt0) cc_final: 0.8657 (pt0) REVERT: F 65 GLU cc_start: 0.7914 (tm-30) cc_final: 0.7700 (tm-30) REVERT: F 81 ASN cc_start: 0.8384 (t0) cc_final: 0.8006 (t0) REVERT: K 31 ILE cc_start: 0.8870 (mp) cc_final: 0.8663 (mt) REVERT: K 74 VAL cc_start: 0.8891 (t) cc_final: 0.8655 (m) REVERT: K 127 ARG cc_start: 0.5061 (ptt180) cc_final: 0.4567 (ptm-80) REVERT: O 88 ARG cc_start: 0.7264 (mmm160) cc_final: 0.6372 (mmp80) REVERT: Q 18 GLU cc_start: 0.7859 (mt-10) cc_final: 0.7631 (mt-10) REVERT: Q 48 ASP cc_start: 0.8115 (t0) cc_final: 0.7852 (t70) REVERT: T 39 ILE cc_start: 0.8961 (tp) cc_final: 0.8723 (mm) REVERT: T 61 GLN cc_start: 0.8644 (OUTLIER) cc_final: 0.8311 (mp-120) REVERT: T 79 LEU cc_start: 0.8155 (mt) cc_final: 0.7795 (mt) outliers start: 47 outliers final: 34 residues processed: 316 average time/residue: 0.2260 time to fit residues: 111.7302 Evaluate side-chains 298 residues out of total 1432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 261 time to evaluate : 0.660 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain V residue 161 SER Chi-restraints excluded: chain V residue 199 THR Chi-restraints excluded: chain V residue 204 VAL Chi-restraints excluded: chain B residue 90 PHE Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 148 LEU Chi-restraints excluded: chain D residue 9 LEU Chi-restraints excluded: chain D residue 142 VAL Chi-restraints excluded: chain D residue 143 VAL Chi-restraints excluded: chain D residue 169 THR Chi-restraints excluded: chain E residue 25 VAL Chi-restraints excluded: chain E residue 32 SER Chi-restraints excluded: chain E residue 34 THR Chi-restraints excluded: chain E residue 97 GLN Chi-restraints excluded: chain E residue 131 THR Chi-restraints excluded: chain E residue 165 LEU Chi-restraints excluded: chain F residue 36 ILE Chi-restraints excluded: chain F residue 51 ILE Chi-restraints excluded: chain F residue 85 ILE Chi-restraints excluded: chain F residue 87 SER Chi-restraints excluded: chain H residue 74 SER Chi-restraints excluded: chain H residue 76 GLN Chi-restraints excluded: chain K residue 32 VAL Chi-restraints excluded: chain K residue 59 THR Chi-restraints excluded: chain K residue 111 THR Chi-restraints excluded: chain L residue 4 VAL Chi-restraints excluded: chain L residue 109 ASP Chi-restraints excluded: chain P residue 45 GLU Chi-restraints excluded: chain P residue 53 ASP Chi-restraints excluded: chain Q residue 28 PHE Chi-restraints excluded: chain Q residue 33 ILE Chi-restraints excluded: chain Q residue 38 ILE Chi-restraints excluded: chain R residue 33 ILE Chi-restraints excluded: chain R residue 42 SER Chi-restraints excluded: chain T residue 40 GLU Chi-restraints excluded: chain T residue 61 GLN Chi-restraints excluded: chain T residue 66 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 121 optimal weight: 2.9990 chunk 129 optimal weight: 1.9990 chunk 168 optimal weight: 0.9990 chunk 68 optimal weight: 6.9990 chunk 93 optimal weight: 8.9990 chunk 259 optimal weight: 5.9990 chunk 56 optimal weight: 5.9990 chunk 62 optimal weight: 4.9990 chunk 10 optimal weight: 0.5980 chunk 256 optimal weight: 0.9980 chunk 99 optimal weight: 4.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... V 202 HIS ** B 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 94 HIS ** R 74 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.066502 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.053604 restraints weight = 141122.192| |-----------------------------------------------------------------------------| r_work (start): 0.3128 rms_B_bonded: 1.38 r_work: 0.3016 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2918 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.2918 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8438 moved from start: 0.3331 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 36963 Z= 0.199 Angle : 1.005 16.017 54707 Z= 0.412 Chirality : 0.081 0.958 6899 Planarity : 0.004 0.040 3369 Dihedral : 18.396 178.453 13464 Min Nonbonded Distance : 1.125 Molprobity Statistics. All-atom Clashscore : 11.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 3.28 % Allowed : 16.97 % Favored : 79.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.65 (0.21), residues: 1702 helix: 1.49 (0.20), residues: 695 sheet: -0.04 (0.31), residues: 291 loop : -0.34 (0.23), residues: 716 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG K 69 TYR 0.019 0.001 TYR V 157 PHE 0.014 0.001 PHE E 95 TRP 0.021 0.002 TRP F 42 HIS 0.004 0.001 HIS E 89 Details of bonding type rmsd/Z covalent geometry : bond 0.00406 / 0.20 (36963) covalent geometry : angle 1.00514 / 0.41 (54707) hydrogen bonds : bond 0.05224 / 3.39 ( 1440) hydrogen bonds : angle 3.74974 / 2.56 ( 3141) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3404 Ramachandran restraints generated. 1702 Oldfield, 0 Emsley, 1702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3404 Ramachandran restraints generated. 1702 Oldfield, 0 Emsley, 1702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 318 residues out of total 1432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 271 time to evaluate : 0.737 Fit side-chains revert: symmetry clash REVERT: V 44 ILE cc_start: 0.6848 (mm) cc_final: 0.6445 (mt) REVERT: V 157 TYR cc_start: 0.8214 (t80) cc_final: 0.7840 (t80) REVERT: V 170 VAL cc_start: 0.8392 (t) cc_final: 0.8160 (p) REVERT: B 90 PHE cc_start: 0.6210 (OUTLIER) cc_final: 0.5885 (m-10) REVERT: B 118 GLU cc_start: 0.7045 (pp20) cc_final: 0.6817 (mt-10) REVERT: B 168 HIS cc_start: 0.7696 (t-90) cc_final: 0.7036 (t-90) REVERT: E 32 SER cc_start: 0.6817 (OUTLIER) cc_final: 0.6521 (m) REVERT: E 64 MET cc_start: 0.8491 (tpp) cc_final: 0.8141 (mmt) REVERT: E 96 MET cc_start: 0.8141 (OUTLIER) cc_final: 0.7749 (mtm) REVERT: E 142 ASP cc_start: 0.7470 (m-30) cc_final: 0.7067 (m-30) REVERT: F 13 ASP cc_start: 0.7900 (m-30) cc_final: 0.7302 (t0) REVERT: F 14 GLN cc_start: 0.9025 (mt0) cc_final: 0.8752 (pt0) REVERT: F 75 GLU cc_start: 0.8118 (pp20) cc_final: 0.7875 (pp20) REVERT: F 81 ASN cc_start: 0.8419 (t0) cc_final: 0.8033 (t0) REVERT: K 74 VAL cc_start: 0.8869 (t) cc_final: 0.8594 (m) REVERT: O 26 GLU cc_start: 0.8830 (mp0) cc_final: 0.8481 (mp0) REVERT: O 88 ARG cc_start: 0.7249 (mmm160) cc_final: 0.6364 (mmp80) REVERT: Q 48 ASP cc_start: 0.8169 (t0) cc_final: 0.7906 (t70) REVERT: T 39 ILE cc_start: 0.8993 (tp) cc_final: 0.8713 (mm) REVERT: T 61 GLN cc_start: 0.8676 (OUTLIER) cc_final: 0.8340 (mp-120) REVERT: T 79 LEU cc_start: 0.8127 (mt) cc_final: 0.7761 (mt) outliers start: 47 outliers final: 38 residues processed: 302 average time/residue: 0.2254 time to fit residues: 106.8014 Evaluate side-chains 304 residues out of total 1432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 262 time to evaluate : 0.518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain V residue 161 SER Chi-restraints excluded: chain V residue 199 THR Chi-restraints excluded: chain V residue 204 VAL Chi-restraints excluded: chain B residue 90 PHE Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 148 LEU Chi-restraints excluded: chain D residue 5 LEU Chi-restraints excluded: chain D residue 9 LEU Chi-restraints excluded: chain D residue 142 VAL Chi-restraints excluded: chain D residue 143 VAL Chi-restraints excluded: chain D residue 169 THR Chi-restraints excluded: chain E residue 25 VAL Chi-restraints excluded: chain E residue 32 SER Chi-restraints excluded: chain E residue 34 THR Chi-restraints excluded: chain E residue 96 MET Chi-restraints excluded: chain E residue 97 GLN Chi-restraints excluded: chain E residue 131 THR Chi-restraints excluded: chain E residue 165 LEU Chi-restraints excluded: chain F residue 36 ILE Chi-restraints excluded: chain F residue 51 ILE Chi-restraints excluded: chain F residue 64 VAL Chi-restraints excluded: chain F residue 85 ILE Chi-restraints excluded: chain F residue 87 SER Chi-restraints excluded: chain H residue 62 THR Chi-restraints excluded: chain H residue 74 SER Chi-restraints excluded: chain H residue 76 GLN Chi-restraints excluded: chain K residue 32 VAL Chi-restraints excluded: chain K residue 59 THR Chi-restraints excluded: chain K residue 111 THR Chi-restraints excluded: chain L residue 4 VAL Chi-restraints excluded: chain L residue 109 ASP Chi-restraints excluded: chain P residue 45 GLU Chi-restraints excluded: chain P residue 53 ASP Chi-restraints excluded: chain Q residue 28 PHE Chi-restraints excluded: chain Q residue 33 ILE Chi-restraints excluded: chain Q residue 38 ILE Chi-restraints excluded: chain R residue 33 ILE Chi-restraints excluded: chain R residue 42 SER Chi-restraints excluded: chain T residue 40 GLU Chi-restraints excluded: chain T residue 61 GLN Chi-restraints excluded: chain T residue 66 LEU Chi-restraints excluded: chain T residue 75 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 200 optimal weight: 9.9990 chunk 210 optimal weight: 5.9990 chunk 36 optimal weight: 5.9990 chunk 160 optimal weight: 3.9990 chunk 57 optimal weight: 7.9990 chunk 194 optimal weight: 2.9990 chunk 166 optimal weight: 6.9990 chunk 141 optimal weight: 6.9990 chunk 211 optimal weight: 0.8980 chunk 152 optimal weight: 2.9990 chunk 230 optimal weight: 4.9990 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... V 202 HIS B 19 GLN ** B 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 82 GLN F 94 HIS K 15 GLN ** Q 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 74 HIS ** 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 = 0.3468 r_free = 0.3468 target = 0.064532 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.051550 restraints weight = 140918.221| |-----------------------------------------------------------------------------| r_work (start): 0.3066 rms_B_bonded: 1.37 r_work: 0.2954 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2859 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.2859 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8493 moved from start: 0.3291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.056 36963 Z= 0.341 Angle : 1.146 15.753 54707 Z= 0.470 Chirality : 0.090 1.077 6899 Planarity : 0.005 0.043 3369 Dihedral : 18.478 179.933 13464 Min Nonbonded Distance : 1.059 Molprobity Statistics. All-atom Clashscore : 12.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 3.56 % Allowed : 17.32 % Favored : 79.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.25 (0.20), residues: 1702 helix: 1.15 (0.20), residues: 693 sheet: -0.15 (0.31), residues: 285 loop : -0.59 (0.23), residues: 724 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG K 69 TYR 0.022 0.002 TYR V 157 PHE 0.013 0.002 PHE V 124 TRP 0.019 0.002 TRP B 23 HIS 0.006 0.001 HIS O 46 Details of bonding type rmsd/Z covalent geometry : bond 0.00695 / 0.34 (36963) covalent geometry : angle 1.14636 / 0.47 (54707) hydrogen bonds : bond 0.06093 / 3.88 ( 1440) hydrogen bonds : angle 4.07711 / 2.78 ( 3141) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3404 Ramachandran restraints generated. 1702 Oldfield, 0 Emsley, 1702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3404 Ramachandran restraints generated. 1702 Oldfield, 0 Emsley, 1702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 321 residues out of total 1432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 270 time to evaluate : 0.704 Fit side-chains revert: symmetry clash REVERT: V 157 TYR cc_start: 0.8293 (t80) cc_final: 0.7926 (t80) REVERT: V 170 VAL cc_start: 0.8433 (t) cc_final: 0.8233 (p) REVERT: B 168 HIS cc_start: 0.7817 (t-90) cc_final: 0.7110 (t-90) REVERT: E 14 LYS cc_start: 0.8122 (mttt) cc_final: 0.7790 (mmtt) REVERT: E 64 MET cc_start: 0.8521 (tpp) cc_final: 0.8182 (mmt) REVERT: E 96 MET cc_start: 0.8239 (OUTLIER) cc_final: 0.7950 (mtm) REVERT: E 142 ASP cc_start: 0.7403 (m-30) cc_final: 0.7092 (m-30) REVERT: E 145 GLU cc_start: 0.7758 (pp20) cc_final: 0.7518 (pp20) REVERT: E 163 GLU cc_start: 0.7916 (OUTLIER) cc_final: 0.7414 (pt0) REVERT: F 13 ASP cc_start: 0.7916 (m-30) cc_final: 0.7311 (t0) REVERT: F 14 GLN cc_start: 0.9008 (mt0) cc_final: 0.8714 (pt0) REVERT: F 75 GLU cc_start: 0.8119 (pp20) cc_final: 0.7878 (pp20) REVERT: F 81 ASN cc_start: 0.8380 (t0) cc_final: 0.7935 (t0) REVERT: K 74 VAL cc_start: 0.8899 (t) cc_final: 0.8626 (m) REVERT: O 88 ARG cc_start: 0.7381 (mmm160) cc_final: 0.6430 (mmp80) REVERT: Q 48 ASP cc_start: 0.8350 (t0) cc_final: 0.8125 (t70) REVERT: T 61 GLN cc_start: 0.8737 (OUTLIER) cc_final: 0.8371 (mp-120) REVERT: T 79 LEU cc_start: 0.8258 (mt) cc_final: 0.7949 (mt) outliers start: 51 outliers final: 43 residues processed: 298 average time/residue: 0.2289 time to fit residues: 106.6473 Evaluate side-chains 306 residues out of total 1432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 260 time to evaluate : 0.735 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain V residue 161 SER Chi-restraints excluded: chain V residue 199 THR Chi-restraints excluded: chain V residue 204 VAL Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 148 LEU Chi-restraints excluded: chain D residue 5 LEU Chi-restraints excluded: chain D residue 9 LEU Chi-restraints excluded: chain D residue 142 VAL Chi-restraints excluded: chain D residue 143 VAL Chi-restraints excluded: chain D residue 169 THR Chi-restraints excluded: chain E residue 25 VAL Chi-restraints excluded: chain E residue 32 SER Chi-restraints excluded: chain E residue 34 THR Chi-restraints excluded: chain E residue 36 LEU Chi-restraints excluded: chain E residue 96 MET Chi-restraints excluded: chain E residue 97 GLN Chi-restraints excluded: chain E residue 131 THR Chi-restraints excluded: chain E residue 163 GLU Chi-restraints excluded: chain E residue 165 LEU Chi-restraints excluded: chain F residue 36 ILE Chi-restraints excluded: chain F residue 51 ILE Chi-restraints excluded: chain F residue 54 LEU Chi-restraints excluded: chain F residue 64 VAL Chi-restraints excluded: chain F residue 85 ILE Chi-restraints excluded: chain F residue 87 SER Chi-restraints excluded: chain H residue 62 THR Chi-restraints excluded: chain H residue 74 SER Chi-restraints excluded: chain H residue 76 GLN Chi-restraints excluded: chain K residue 32 VAL Chi-restraints excluded: chain K residue 59 THR Chi-restraints excluded: chain K residue 111 THR Chi-restraints excluded: chain L residue 4 VAL Chi-restraints excluded: chain L residue 56 ARG Chi-restraints excluded: chain L residue 109 ASP Chi-restraints excluded: chain P residue 45 GLU Chi-restraints excluded: chain P residue 53 ASP Chi-restraints excluded: chain Q residue 28 PHE Chi-restraints excluded: chain Q residue 33 ILE Chi-restraints excluded: chain Q residue 38 ILE Chi-restraints excluded: chain R residue 33 ILE Chi-restraints excluded: chain R residue 42 SER Chi-restraints excluded: chain T residue 40 GLU Chi-restraints excluded: chain T residue 61 GLN Chi-restraints excluded: chain T residue 66 LEU Chi-restraints excluded: chain T residue 75 HIS Chi-restraints excluded: chain T residue 86 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 193 optimal weight: 0.0030 chunk 18 optimal weight: 2.9990 chunk 155 optimal weight: 0.0270 chunk 44 optimal weight: 9.9990 chunk 48 optimal weight: 5.9990 chunk 169 optimal weight: 0.9990 chunk 134 optimal weight: 4.9990 chunk 233 optimal weight: 1.9990 chunk 110 optimal weight: 2.9990 chunk 13 optimal weight: 0.0770 chunk 49 optimal weight: 4.9990 overall best weight: 0.6210 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... V 202 HIS B 89 GLN ** B 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 36 GLN F 94 HIS L 20 ASN ** R 74 HIS ** 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 = 0.3550 r_free = 0.3550 target = 0.067699 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.054961 restraints weight = 141214.446| |-----------------------------------------------------------------------------| r_work (start): 0.3172 rms_B_bonded: 1.36 r_work: 0.3060 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2965 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.2965 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8394 moved from start: 0.3553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 36963 Z= 0.147 Angle : 0.983 15.530 54707 Z= 0.405 Chirality : 0.078 0.894 6899 Planarity : 0.004 0.039 3369 Dihedral : 18.482 178.696 13464 Min Nonbonded Distance : 1.154 Molprobity Statistics. All-atom Clashscore : 11.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 2.65 % Allowed : 18.72 % Favored : 78.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.67 (0.21), residues: 1702 helix: 1.49 (0.20), residues: 696 sheet: 0.07 (0.31), residues: 281 loop : -0.34 (0.23), residues: 725 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG H 88 TYR 0.022 0.001 TYR V 157 PHE 0.023 0.001 PHE B 90 TRP 0.008 0.001 TRP P 60 HIS 0.003 0.000 HIS E 89 Details of bonding type rmsd/Z covalent geometry : bond 0.00297 / 0.15 (36963) covalent geometry : angle 0.98344 / 0.40 (54707) hydrogen bonds : bond 0.05122 / 3.37 ( 1440) hydrogen bonds : angle 3.79404 / 2.57 ( 3141) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3404 Ramachandran restraints generated. 1702 Oldfield, 0 Emsley, 1702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3404 Ramachandran restraints generated. 1702 Oldfield, 0 Emsley, 1702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 324 residues out of total 1432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 286 time to evaluate : 0.607 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: V 170 VAL cc_start: 0.8384 (t) cc_final: 0.8147 (p) REVERT: B 159 ASP cc_start: 0.7547 (m-30) cc_final: 0.7275 (t0) REVERT: B 168 HIS cc_start: 0.7739 (t-90) cc_final: 0.6991 (t-90) REVERT: B 191 SER cc_start: 0.8891 (m) cc_final: 0.8580 (m) REVERT: E 142 ASP cc_start: 0.7603 (m-30) cc_final: 0.7307 (m-30) REVERT: E 145 GLU cc_start: 0.7687 (pp20) cc_final: 0.7399 (pp20) REVERT: F 13 ASP cc_start: 0.8016 (m-30) cc_final: 0.7216 (t0) REVERT: F 75 GLU cc_start: 0.7979 (pp20) cc_final: 0.7761 (pp20) REVERT: F 81 ASN cc_start: 0.8298 (t0) cc_final: 0.8023 (t0) REVERT: H 91 GLU cc_start: 0.7584 (pt0) cc_final: 0.7373 (pt0) REVERT: K 74 VAL cc_start: 0.8779 (t) cc_final: 0.8414 (m) REVERT: K 77 TYR cc_start: 0.6723 (m-80) cc_final: 0.6462 (m-80) REVERT: K 106 ARG cc_start: 0.6796 (ttt-90) cc_final: 0.6560 (ttt90) REVERT: L 62 GLU cc_start: 0.7529 (tp30) cc_final: 0.7287 (tm-30) REVERT: O 6 GLU cc_start: 0.8876 (mp0) cc_final: 0.8498 (mp0) REVERT: O 88 ARG cc_start: 0.7212 (mmm160) cc_final: 0.6360 (mmp80) REVERT: Q 48 ASP cc_start: 0.8004 (t0) cc_final: 0.7726 (t70) REVERT: T 39 ILE cc_start: 0.9294 (tp) cc_final: 0.8910 (mm) REVERT: T 61 GLN cc_start: 0.8676 (OUTLIER) cc_final: 0.8307 (mp-120) REVERT: T 79 LEU cc_start: 0.8158 (mt) cc_final: 0.7823 (mt) outliers start: 38 outliers final: 29 residues processed: 310 average time/residue: 0.2394 time to fit residues: 116.3387 Evaluate side-chains 300 residues out of total 1432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 270 time to evaluate : 0.745 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain V residue 161 SER Chi-restraints excluded: chain V residue 199 THR Chi-restraints excluded: chain V residue 204 VAL Chi-restraints excluded: chain B residue 148 LEU Chi-restraints excluded: chain D residue 5 LEU Chi-restraints excluded: chain D residue 9 LEU Chi-restraints excluded: chain D residue 142 VAL Chi-restraints excluded: chain D residue 143 VAL Chi-restraints excluded: chain D residue 169 THR Chi-restraints excluded: chain E residue 25 VAL Chi-restraints excluded: chain E residue 131 THR Chi-restraints excluded: chain E residue 165 LEU Chi-restraints excluded: chain F residue 21 MET Chi-restraints excluded: chain F residue 51 ILE Chi-restraints excluded: chain F residue 85 ILE Chi-restraints excluded: chain F residue 87 SER Chi-restraints excluded: chain H residue 62 THR Chi-restraints excluded: chain H residue 76 GLN Chi-restraints excluded: chain K residue 32 VAL Chi-restraints excluded: chain K residue 59 THR Chi-restraints excluded: chain K residue 111 THR Chi-restraints excluded: chain L residue 4 VAL Chi-restraints excluded: chain L residue 56 ARG Chi-restraints excluded: chain Q residue 28 PHE Chi-restraints excluded: chain Q residue 33 ILE Chi-restraints excluded: chain Q residue 38 ILE Chi-restraints excluded: chain R residue 33 ILE Chi-restraints excluded: chain R residue 42 SER Chi-restraints excluded: chain T residue 40 GLU Chi-restraints excluded: chain T residue 61 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 252 optimal weight: 0.7980 chunk 110 optimal weight: 4.9990 chunk 19 optimal weight: 2.9990 chunk 191 optimal weight: 0.0970 chunk 85 optimal weight: 4.9990 chunk 37 optimal weight: 5.9990 chunk 33 optimal weight: 7.9990 chunk 167 optimal weight: 0.9980 chunk 216 optimal weight: 1.9990 chunk 40 optimal weight: 7.9990 chunk 83 optimal weight: 5.9990 overall best weight: 1.3782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... V 202 HIS ** B 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 94 HIS O 35 GLN ** R 74 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.066912 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.054057 restraints weight = 140761.592| |-----------------------------------------------------------------------------| r_work (start): 0.3141 rms_B_bonded: 1.36 r_work: 0.3029 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2932 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.2932 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8422 moved from start: 0.3532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 36963 Z= 0.191 Angle : 1.001 15.971 54707 Z= 0.411 Chirality : 0.079 0.951 6899 Planarity : 0.004 0.050 3369 Dihedral : 18.396 178.821 13462 Min Nonbonded Distance : 1.133 Molprobity Statistics. All-atom Clashscore : 11.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 2.23 % Allowed : 19.20 % Favored : 78.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.63 (0.21), residues: 1702 helix: 1.44 (0.20), residues: 696 sheet: 0.08 (0.32), residues: 273 loop : -0.35 (0.23), residues: 733 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG F 24 TYR 0.017 0.001 TYR F 59 PHE 0.027 0.001 PHE B 90 TRP 0.007 0.001 TRP P 60 HIS 0.004 0.001 HIS E 89 Details of bonding type rmsd/Z covalent geometry : bond 0.00390 / 0.19 (36963) covalent geometry : angle 1.00064 / 0.41 (54707) hydrogen bonds : bond 0.05188 / 3.39 ( 1440) hydrogen bonds : angle 3.84098 / 2.61 ( 3141) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10175.43 seconds wall clock time: 174 minutes 27.36 seconds (10467.36 seconds total)