Starting phenix.real_space_refine on Sat Sep 12 01:34:06 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9sqv_55118/09_2026/9sqv_55118.cif Found real_map, /net/cci-nas-00/data/ceres_data/9sqv_55118/09_2026/9sqv_55118.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.21 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9sqv_55118/09_2026/9sqv_55118.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9sqv_55118/09_2026/9sqv_55118.map" model { file = "/net/cci-nas-00/data/ceres_data/9sqv_55118/09_2026/9sqv_55118.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9sqv_55118/09_2026/9sqv_55118.cif" } resolution = 3.21 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= 0.001 sd= 0.024 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: 5 Type Number sf(0) Gaussians Zn 2 6.06 5 S 64 5.16 5 C 7964 2.51 5 N 2159 2.21 5 O 2356 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 13 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: 12545 Number of models: 1 Model: "" Number of chains: 10 Chain: "G" Number of atoms: 602 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 602 Classifications: {'peptide': 76} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 72} Chain: "H" Number of atoms: 601 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 601 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 3, 'TRANS': 72} Chain: "C" Number of atoms: 1842 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1842 Classifications: {'peptide': 230} Link IDs: {'PTRANS': 4, 'TRANS': 225} Chain breaks: 1 Chain: "D" Number of atoms: 1835 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1835 Classifications: {'peptide': 229} Link IDs: {'PTRANS': 4, 'TRANS': 224} Chain breaks: 1 Chain: "A" Number of atoms: 2007 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 249, 2000 Classifications: {'peptide': 249} Link IDs: {'PTRANS': 8, 'TRANS': 240} Chain breaks: 2 Conformer: "B" Number of residues, atoms: 249, 2000 Classifications: {'peptide': 249} Link IDs: {'PTRANS': 8, 'TRANS': 240} Chain breaks: 2 bond proxies already assigned to first conformer: 2027 Chain: "B" Number of atoms: 1898 Number of conformers: 1 Conformer: "" Number of residues, atoms: 237, 1898 Classifications: {'peptide': 237} Link IDs: {'PTRANS': 8, 'TRANS': 228} Chain breaks: 2 Chain: "F" Number of atoms: 1856 Number of conformers: 1 Conformer: "" Number of residues, atoms: 235, 1856 Classifications: {'peptide': 235} Link IDs: {'PTRANS': 18, 'TRANS': 216} Chain breaks: 1 Chain: "E" Number of atoms: 1902 Number of conformers: 1 Conformer: "" Number of residues, atoms: 240, 1902 Classifications: {'peptide': 240} Link IDs: {'PTRANS': 19, 'TRANS': 220} Chain breaks: 1 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Residues with excluded nonbonded symmetry interactions: 4 residue: pdb=" N LEU G 73 " occ=0.86 ... (6 atoms not shown) pdb=" CD2 LEU G 73 " occ=0.86 residue: pdb=" N ARG G 74 " occ=0.63 ... (9 atoms not shown) pdb=" NH2 ARG G 74 " occ=0.63 residue: pdb=" N GLY G 75 " occ=0.47 ... (2 atoms not shown) pdb=" O GLY G 75 " occ=0.47 residue: pdb=" N GLY G 76 " occ=0.65 ... (3 atoms not shown) pdb=" OXT GLY G 76 " occ=0.65 Time building chain proxies: 3.19, per 1000 atoms: 0.25 Number of scatterers: 12545 At special positions: 0 Unit cell: (114.7, 113.96, 153.18, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 2 29.99 S 64 16.00 O 2356 8.00 N 2159 7.00 C 7964 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.98 Conformation dependent library (CDL) restraints added in 605.8 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 401 " pdb="ZN ZN A 401 " - pdb=" NE2 HIS A 124 " pdb="ZN ZN A 401 " - pdb=" NE2 HIS A 122 " pdb=" ZN B 401 " pdb="ZN ZN B 401 " - pdb=" NE2 HIS B 122 " pdb="ZN ZN B 401 " - pdb=" NE2 HIS B 124 " 3082 Ramachandran restraints generated. 1541 Oldfield, 0 Emsley, 1541 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2974 Finding SS restraints... Secondary structure from input PDB file: 51 helices and 11 sheets defined 41.7% alpha, 18.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.36 Creating SS restraints... Processing helix chain 'G' and resid 22 through 34 removed outlier: 3.621A pdb=" N LYS G 29 " --> pdb=" O ASN G 25 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N ILE G 30 " --> pdb=" O VAL G 26 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N GLN G 31 " --> pdb=" O LYS G 27 " (cutoff:3.500A) Processing helix chain 'H' and resid 22 through 32 removed outlier: 3.641A pdb=" N GLN H 31 " --> pdb=" O LYS H 27 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ASP H 32 " --> pdb=" O ALA H 28 " (cutoff:3.500A) Processing helix chain 'H' and resid 56 through 60 Processing helix chain 'C' and resid 12 through 25 removed outlier: 3.609A pdb=" N GLY C 16 " --> pdb=" O GLY C 12 " (cutoff:3.500A) Processing helix chain 'C' and resid 81 through 89 removed outlier: 3.788A pdb=" N LYS C 87 " --> pdb=" O GLN C 83 " (cutoff:3.500A) Processing helix chain 'C' and resid 111 through 124 removed outlier: 3.804A pdb=" N LYS C 119 " --> pdb=" O ARG C 115 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N HIS C 124 " --> pdb=" O ASN C 120 " (cutoff:3.500A) Processing helix chain 'C' and resid 155 through 159 Processing helix chain 'C' and resid 170 through 174 removed outlier: 3.832A pdb=" N MET C 173 " --> pdb=" O ASN C 170 " (cutoff:3.500A) Processing helix chain 'C' and resid 188 through 198 removed outlier: 3.627A pdb=" N HIS C 198 " --> pdb=" O ALA C 194 " (cutoff:3.500A) Processing helix chain 'C' and resid 198 through 203 removed outlier: 3.905A pdb=" N PHE C 202 " --> pdb=" O HIS C 198 " (cutoff:3.500A) Processing helix chain 'C' and resid 209 through 250 removed outlier: 3.708A pdb=" N LEU C 222 " --> pdb=" O MET C 218 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N GLU C 234 " --> pdb=" O CYS C 230 " (cutoff:3.500A) Processing helix chain 'D' and resid 12 through 23 Processing helix chain 'D' and resid 81 through 89 removed outlier: 3.569A pdb=" N LYS D 87 " --> pdb=" O GLN D 83 " (cutoff:3.500A) Processing helix chain 'D' and resid 111 through 126 removed outlier: 3.763A pdb=" N LYS D 119 " --> pdb=" O ARG D 115 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N GLU D 123 " --> pdb=" O LYS D 119 " (cutoff:3.500A) Processing helix chain 'D' and resid 188 through 198 removed outlier: 4.018A pdb=" N HIS D 198 " --> pdb=" O ALA D 194 " (cutoff:3.500A) Processing helix chain 'D' and resid 198 through 203 removed outlier: 3.642A pdb=" N PHE D 202 " --> pdb=" O HIS D 198 " (cutoff:3.500A) Processing helix chain 'D' and resid 209 through 251 removed outlier: 3.902A pdb=" N HIS D 213 " --> pdb=" O LEU D 209 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N MET D 218 " --> pdb=" O LYS D 214 " (cutoff:3.500A) Processing helix chain 'A' and resid 16 through 27 Processing helix chain 'A' and resid 93 through 112 removed outlier: 4.131A pdb=" N ALA A 99 " --> pdb=" O GLU A 95 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ALA A 100 " --> pdb=" O GLN A 96 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N SER A 101 " --> pdb=" O LEU A 97 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N THR A 102 " --> pdb=" O SER A 98 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ARG A 106 " --> pdb=" O THR A 102 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N GLU A 109 " --> pdb=" O GLU A 105 " (cutoff:3.500A) Processing helix chain 'A' and resid 134 through 142 removed outlier: 3.845A pdb=" N ALA A 140 " --> pdb=" O VAL A 136 " (cutoff:3.500A) Processing helix chain 'A' and resid 143 through 145 No H-bonds generated for 'chain 'A' and resid 143 through 145' Processing helix chain 'A' and resid 225 through 233 Processing helix chain 'A' and resid 234 through 253 removed outlier: 3.689A pdb=" N LEU A 253 " --> pdb=" O ARG A 249 " (cutoff:3.500A) Processing helix chain 'A' and resid 257 through 277 removed outlier: 3.740A pdb=" N SER A 277 " --> pdb=" O CYS A 273 " (cutoff:3.500A) Processing helix chain 'A' and resid 279 through 308 removed outlier: 3.536A pdb=" N LEU A 284 " --> pdb=" O SER A 280 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N GLU A 292 " --> pdb=" O GLU A 288 " (cutoff:3.500A) Processing helix chain 'B' and resid 16 through 27 Processing helix chain 'B' and resid 93 through 112 removed outlier: 3.569A pdb=" N THR B 102 " --> pdb=" O SER B 98 " (cutoff:3.500A) Processing helix chain 'B' and resid 132 through 144 Processing helix chain 'B' and resid 225 through 233 removed outlier: 3.609A pdb=" N SER B 231 " --> pdb=" O VAL B 227 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N VAL B 233 " --> pdb=" O LEU B 229 " (cutoff:3.500A) Processing helix chain 'B' and resid 233 through 253 removed outlier: 4.149A pdb=" N LYS B 237 " --> pdb=" O VAL B 233 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N LEU B 253 " --> pdb=" O ARG B 249 " (cutoff:3.500A) Processing helix chain 'B' and resid 257 through 279 removed outlier: 3.647A pdb=" N THR B 269 " --> pdb=" O GLY B 265 " (cutoff:3.500A) Processing helix chain 'B' and resid 279 through 308 removed outlier: 3.816A pdb=" N GLN B 303 " --> pdb=" O GLN B 299 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N GLU B 304 " --> pdb=" O GLU B 300 " (cutoff:3.500A) Processing helix chain 'F' and resid 6 through 10 removed outlier: 3.561A pdb=" N ILE F 10 " --> pdb=" O LEU F 7 " (cutoff:3.500A) Processing helix chain 'F' and resid 11 through 13 No H-bonds generated for 'chain 'F' and resid 11 through 13' Processing helix chain 'F' and resid 14 through 24 removed outlier: 3.632A pdb=" N SER F 19 " --> pdb=" O SER F 15 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N VAL F 21 " --> pdb=" O PHE F 17 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N ASN F 24 " --> pdb=" O SER F 20 " (cutoff:3.500A) Processing helix chain 'F' and resid 99 through 104 removed outlier: 3.622A pdb=" N ALA F 103 " --> pdb=" O LEU F 99 " (cutoff:3.500A) Processing helix chain 'F' and resid 111 through 129 removed outlier: 3.801A pdb=" N VAL F 116 " --> pdb=" O CYS F 112 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N VAL F 117 " --> pdb=" O LEU F 113 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N LEU F 120 " --> pdb=" O VAL F 116 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N GLN F 122 " --> pdb=" O LYS F 118 " (cutoff:3.500A) Processing helix chain 'F' and resid 130 through 133 removed outlier: 3.598A pdb=" N ARG F 133 " --> pdb=" O SER F 130 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 130 through 133' Processing helix chain 'F' and resid 137 through 139 No H-bonds generated for 'chain 'F' and resid 137 through 139' Processing helix chain 'F' and resid 140 through 148 removed outlier: 4.490A pdb=" N THR F 144 " --> pdb=" O PHE F 140 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N GLU F 148 " --> pdb=" O THR F 144 " (cutoff:3.500A) Processing helix chain 'F' and resid 222 through 230 Processing helix chain 'F' and resid 245 through 261 Proline residue: F 251 - end of helix removed outlier: 3.994A pdb=" N LEU F 257 " --> pdb=" O VAL F 253 " (cutoff:3.500A) Processing helix chain 'E' and resid 14 through 24 removed outlier: 3.876A pdb=" N VAL E 22 " --> pdb=" O ILE E 18 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N ASN E 24 " --> pdb=" O SER E 20 " (cutoff:3.500A) Processing helix chain 'E' and resid 95 through 98 Processing helix chain 'E' and resid 99 through 104 removed outlier: 3.508A pdb=" N ALA E 103 " --> pdb=" O LEU E 99 " (cutoff:3.500A) Processing helix chain 'E' and resid 111 through 132 removed outlier: 3.651A pdb=" N LEU E 115 " --> pdb=" O GLU E 111 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N VAL E 116 " --> pdb=" O CYS E 112 " (cutoff:3.500A) Processing helix chain 'E' and resid 138 through 145 Processing helix chain 'E' and resid 146 through 147 No H-bonds generated for 'chain 'E' and resid 146 through 147' Processing helix chain 'E' and resid 148 through 153 removed outlier: 3.797A pdb=" N GLU E 153 " --> pdb=" O GLN E 150 " (cutoff:3.500A) Processing helix chain 'E' and resid 222 through 229 removed outlier: 3.791A pdb=" N GLU E 226 " --> pdb=" O SER E 222 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N LEU E 229 " --> pdb=" O ILE E 225 " (cutoff:3.500A) Processing helix chain 'E' and resid 248 through 266 removed outlier: 3.553A pdb=" N GLN E 252 " --> pdb=" O ASP E 248 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N HIS E 255 " --> pdb=" O PRO E 251 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N LEU E 256 " --> pdb=" O GLN E 252 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N TYR E 263 " --> pdb=" O ASN E 259 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N VAL E 264 " --> pdb=" O LYS E 260 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'G' and resid 12 through 16 removed outlier: 8.867A pdb=" N LEU G 67 " --> pdb=" O GLN G 2 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N PHE G 4 " --> pdb=" O LEU G 67 " (cutoff:3.500A) removed outlier: 7.559A pdb=" N LEU G 69 " --> pdb=" O PHE G 4 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N LYS G 6 " --> pdb=" O LEU G 69 " (cutoff:3.500A) removed outlier: 7.981A pdb=" N LEU G 71 " --> pdb=" O LYS G 6 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N VAL G 70 " --> pdb=" O ARG G 42 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ARG G 42 " --> pdb=" O VAL G 70 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'H' and resid 12 through 16 Processing sheet with id=AA3, first strand: chain 'H' and resid 73 through 75 removed outlier: 4.817A pdb=" N LEU H 73 " --> pdb=" O ILE A 92 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ILE A 92 " --> pdb=" O LEU H 73 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ASP A 84 " --> pdb=" O GLU A 91 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 166 through 169 removed outlier: 4.110A pdb=" N SER C 11 " --> pdb=" O ILE C 61 " (cutoff:3.500A) removed outlier: 8.757A pdb=" N LYS C 63 " --> pdb=" O SER C 11 " (cutoff:3.500A) removed outlier: 5.512A pdb=" N ILE C 59 " --> pdb=" O LYS C 38 " (cutoff:3.500A) removed outlier: 7.151A pdb=" N LYS C 38 " --> pdb=" O ILE C 59 " (cutoff:3.500A) removed outlier: 5.431A pdb=" N ILE C 61 " --> pdb=" O GLU C 36 " (cutoff:3.500A) removed outlier: 7.449A pdb=" N GLU C 36 " --> pdb=" O ILE C 61 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LYS C 63 " --> pdb=" O LEU C 34 " (cutoff:3.500A) removed outlier: 4.647A pdb=" N GLU C 30 " --> pdb=" O CYS C 67 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N THR C 29 " --> pdb=" O PHE C 102 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLY C 31 " --> pdb=" O TYR C 100 " (cutoff:3.500A) removed outlier: 6.100A pdb=" N GLY C 35 " --> pdb=" O VAL C 96 " (cutoff:3.500A) removed outlier: 4.811A pdb=" N VAL C 96 " --> pdb=" O GLY C 35 " (cutoff:3.500A) removed outlier: 9.966A pdb=" N VAL C 131 " --> pdb=" O ASN C 95 " (cutoff:3.500A) removed outlier: 7.072A pdb=" N VAL C 97 " --> pdb=" O VAL C 131 " (cutoff:3.500A) removed outlier: 8.129A pdb=" N LEU C 133 " --> pdb=" O VAL C 97 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N TRP C 99 " --> pdb=" O LEU C 133 " (cutoff:3.500A) removed outlier: 8.298A pdb=" N LEU C 135 " --> pdb=" O TRP C 99 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N LYS C 101 " --> pdb=" O LEU C 135 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N LEU C 134 " --> pdb=" O SER C 152 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N GLU C 150 " --> pdb=" O THR C 136 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N HIS C 151 " --> pdb=" O GLY B 166 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LEU B 169 " --> pdb=" O SER B 155 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ILE B 153 " --> pdb=" O THR B 171 " (cutoff:3.500A) removed outlier: 8.310A pdb=" N LEU B 152 " --> pdb=" O VAL B 118 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N TRP B 120 " --> pdb=" O LEU B 152 " (cutoff:3.500A) removed outlier: 8.478A pdb=" N PHE B 154 " --> pdb=" O TRP B 120 " (cutoff:3.500A) removed outlier: 7.190A pdb=" N HIS B 122 " --> pdb=" O PHE B 154 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N CYS B 38 " --> pdb=" O VAL B 118 " (cutoff:3.500A) removed outlier: 5.395A pdb=" N TRP B 120 " --> pdb=" O GLY B 36 " (cutoff:3.500A) removed outlier: 7.267A pdb=" N GLY B 36 " --> pdb=" O TRP B 120 " (cutoff:3.500A) removed outlier: 4.645A pdb=" N MET B 35 " --> pdb=" O LEU B 80 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LEU B 80 " --> pdb=" O MET B 35 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N GLU B 41 " --> pdb=" O ILE B 74 " (cutoff:3.500A) removed outlier: 5.001A pdb=" N ILE B 74 " --> pdb=" O GLU B 41 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N HIS B 13 " --> pdb=" O ILE B 74 " (cutoff:3.500A) removed outlier: 8.033A pdb=" N SER B 76 " --> pdb=" O HIS B 13 " (cutoff:3.500A) removed outlier: 8.554A pdb=" N GLU B 15 " --> pdb=" O SER B 76 " (cutoff:3.500A) removed outlier: 11.518A pdb=" N ILE B 78 " --> pdb=" O GLU B 15 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N VAL B 12 " --> pdb=" O HIS B 217 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N VAL B 219 " --> pdb=" O VAL B 12 " (cutoff:3.500A) removed outlier: 5.895A pdb=" N LEU B 14 " --> pdb=" O VAL B 219 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 166 through 169 removed outlier: 4.279A pdb=" N SER D 11 " --> pdb=" O ILE D 61 " (cutoff:3.500A) removed outlier: 8.595A pdb=" N LYS D 63 " --> pdb=" O SER D 11 " (cutoff:3.500A) removed outlier: 5.683A pdb=" N ILE D 61 " --> pdb=" O GLU D 36 " (cutoff:3.500A) removed outlier: 7.584A pdb=" N GLU D 36 " --> pdb=" O ILE D 61 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N GLU D 30 " --> pdb=" O CYS D 67 " (cutoff:3.500A) removed outlier: 5.974A pdb=" N GLY D 35 " --> pdb=" O VAL D 96 " (cutoff:3.500A) removed outlier: 5.001A pdb=" N VAL D 96 " --> pdb=" O GLY D 35 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N TYR A 170 " --> pdb=" O HIS D 147 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 166 through 169 removed outlier: 4.279A pdb=" N SER D 11 " --> pdb=" O ILE D 61 " (cutoff:3.500A) removed outlier: 8.595A pdb=" N LYS D 63 " --> pdb=" O SER D 11 " (cutoff:3.500A) removed outlier: 5.683A pdb=" N ILE D 61 " --> pdb=" O GLU D 36 " (cutoff:3.500A) removed outlier: 7.584A pdb=" N GLU D 36 " --> pdb=" O ILE D 61 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N GLU D 30 " --> pdb=" O CYS D 67 " (cutoff:3.500A) removed outlier: 5.974A pdb=" N GLY D 35 " --> pdb=" O VAL D 96 " (cutoff:3.500A) removed outlier: 5.001A pdb=" N VAL D 96 " --> pdb=" O GLY D 35 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N TYR A 170 " --> pdb=" O HIS D 147 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N ILE A 153 " --> pdb=" O THR A 171 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N GLY A 151 " --> pdb=" O PHE A 173 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N CYS A 156 " --> pdb=" O HIS A 124 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N CYS A 38 " --> pdb=" O VAL A 118 " (cutoff:3.500A) removed outlier: 4.995A pdb=" N TRP A 120 " --> pdb=" O GLY A 36 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N GLY A 36 " --> pdb=" O TRP A 120 " (cutoff:3.500A) removed outlier: 7.353A pdb=" N GLU A 41 " --> pdb=" O ILE A 74 " (cutoff:3.500A) removed outlier: 5.451A pdb=" N ILE A 74 " --> pdb=" O GLU A 41 " (cutoff:3.500A) removed outlier: 7.387A pdb=" N SER A 76 " --> pdb=" O GLU A 15 " (cutoff:3.500A) removed outlier: 6.148A pdb=" N VAL A 12 " --> pdb=" O HIS A 217 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N VAL A 219 " --> pdb=" O VAL A 12 " (cutoff:3.500A) removed outlier: 6.081A pdb=" N LEU A 14 " --> pdb=" O VAL A 219 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'F' and resid 36 through 41 removed outlier: 6.343A pdb=" N ILE F 37 " --> pdb=" O HIS F 59 " (cutoff:3.500A) removed outlier: 7.477A pdb=" N HIS F 59 " --> pdb=" O ILE F 37 " (cutoff:3.500A) removed outlier: 5.096A pdb=" N ASP F 39 " --> pdb=" O LYS F 57 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N LYS F 57 " --> pdb=" O ASP F 39 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ARG F 55 " --> pdb=" O LYS F 41 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'F' and resid 161 through 162 removed outlier: 3.680A pdb=" N GLU F 168 " --> pdb=" O LYS F 161 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'F' and resid 171 through 172 Processing sheet with id=AB1, first strand: chain 'E' and resid 37 through 41 removed outlier: 6.398A pdb=" N ILE E 37 " --> pdb=" O HIS E 59 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N HIS E 59 " --> pdb=" O ILE E 37 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N ASP E 39 " --> pdb=" O LYS E 57 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N LYS E 57 " --> pdb=" O ASP E 39 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 156 through 158 559 hydrogen bonds defined for protein. 1581 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.94 Time building geometry restraints manager: 1.36 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4139 1.34 - 1.46: 2326 1.46 - 1.58: 6237 1.58 - 1.69: 0 1.69 - 1.81: 92 Bond restraints: 12794 Sorted by residual: bond pdb=" N ASP A 289 " pdb=" CA ASP A 289 " ideal model delta sigma weight residual 1.456 1.501 -0.045 1.32e-02 5.74e+03 1.19e+01 bond pdb=" N ILE A 176 " pdb=" CA ILE A 176 " ideal model delta sigma weight residual 1.459 1.497 -0.038 1.25e-02 6.40e+03 9.09e+00 bond pdb=" CA PHE C 125 " pdb=" C PHE C 125 " ideal model delta sigma weight residual 1.522 1.484 0.038 1.25e-02 6.40e+03 9.00e+00 bond pdb=" CA PHE A 149 " pdb=" C PHE A 149 " ideal model delta sigma weight residual 1.521 1.485 0.036 1.24e-02 6.50e+03 8.44e+00 bond pdb=" N ILE E 247 " pdb=" CA ILE E 247 " ideal model delta sigma weight residual 1.457 1.494 -0.037 1.29e-02 6.01e+03 8.21e+00 ... (remaining 12789 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.50: 17235 3.50 - 7.00: 53 7.00 - 10.50: 6 10.50 - 14.00: 0 14.00 - 17.50: 2 Bond angle restraints: 17296 Sorted by residual: angle pdb=" C ARG A 211 " pdb=" CA ARG A 211 " pdb=" CB ARG A 211 " ideal model delta sigma weight residual 109.61 92.11 17.50 1.58e+00 4.01e-01 1.23e+02 angle pdb=" N ARG A 211 " pdb=" CA ARG A 211 " pdb=" CB ARG A 211 " ideal model delta sigma weight residual 109.56 94.38 15.18 1.65e+00 3.67e-01 8.46e+01 angle pdb=" CA PHE C 125 " pdb=" CB PHE C 125 " pdb=" CG PHE C 125 " ideal model delta sigma weight residual 113.80 118.77 -4.97 1.00e+00 1.00e+00 2.47e+01 angle pdb=" N ARG A 290 " pdb=" CA ARG A 290 " pdb=" C ARG A 290 " ideal model delta sigma weight residual 111.36 106.17 5.19 1.09e+00 8.42e-01 2.27e+01 angle pdb=" N ILE E 247 " pdb=" CA ILE E 247 " pdb=" C ILE E 247 " ideal model delta sigma weight residual 112.17 107.66 4.51 9.50e-01 1.11e+00 2.25e+01 ... (remaining 17291 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 6773 17.97 - 35.93: 746 35.93 - 53.90: 194 53.90 - 71.87: 30 71.87 - 89.83: 20 Dihedral angle restraints: 7763 sinusoidal: 3185 harmonic: 4578 Sorted by residual: dihedral pdb=" C ARG A 211 " pdb=" N ARG A 211 " pdb=" CA ARG A 211 " pdb=" CB ARG A 211 " ideal model delta harmonic sigma weight residual -122.60 -94.24 -28.36 0 2.50e+00 1.60e-01 1.29e+02 dihedral pdb=" N ARG A 211 " pdb=" C ARG A 211 " pdb=" CA ARG A 211 " pdb=" CB ARG A 211 " ideal model delta harmonic sigma weight residual 122.80 95.72 27.08 0 2.50e+00 1.60e-01 1.17e+02 dihedral pdb=" CD ARG A 211 " pdb=" NE ARG A 211 " pdb=" CZ ARG A 211 " pdb=" NH1 ARG A 211 " ideal model delta sinusoidal sigma weight residual 0.00 -87.48 87.48 1 1.00e+01 1.00e-02 9.18e+01 ... (remaining 7760 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.111: 1903 0.111 - 0.221: 49 0.221 - 0.332: 2 0.332 - 0.442: 0 0.442 - 0.553: 1 Chirality restraints: 1955 Sorted by residual: chirality pdb=" CA ARG A 211 " pdb=" N ARG A 211 " pdb=" C ARG A 211 " pdb=" CB ARG A 211 " both_signs ideal model delta sigma weight residual False 2.51 3.06 -0.55 2.00e-01 2.50e+01 7.63e+00 chirality pdb=" CA ILE A 212 " pdb=" N ILE A 212 " pdb=" C ILE A 212 " pdb=" CB ILE A 212 " both_signs ideal model delta sigma weight residual False 2.43 2.70 -0.27 2.00e-01 2.50e+01 1.83e+00 chirality pdb=" CA PHE C 125 " pdb=" N PHE C 125 " pdb=" C PHE C 125 " pdb=" CB PHE C 125 " both_signs ideal model delta sigma weight residual False 2.51 2.75 -0.24 2.00e-01 2.50e+01 1.46e+00 ... (remaining 1952 not shown) Planarity restraints: 2222 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 211 " -1.108 9.50e-02 1.11e+02 4.97e-01 1.49e+02 pdb=" NE ARG A 211 " 0.067 2.00e-02 2.50e+03 pdb=" CZ ARG A 211 " 0.013 2.00e-02 2.50e+03 pdb=" NH1 ARG A 211 " -0.014 2.00e-02 2.50e+03 pdb=" NH2 ARG A 211 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 86 " -0.559 9.50e-02 1.11e+02 2.51e-01 3.84e+01 pdb=" NE ARG A 86 " 0.033 2.00e-02 2.50e+03 pdb=" CZ ARG A 86 " 0.007 2.00e-02 2.50e+03 pdb=" NH1 ARG A 86 " 0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG A 86 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY A 148 " -0.015 2.00e-02 2.50e+03 3.02e-02 9.10e+00 pdb=" C GLY A 148 " 0.052 2.00e-02 2.50e+03 pdb=" O GLY A 148 " -0.019 2.00e-02 2.50e+03 pdb=" N PHE A 149 " -0.018 2.00e-02 2.50e+03 ... (remaining 2219 not shown) Histogram of nonbonded interaction distances: 1.36 - 2.07: 16 2.07 - 2.78: 2633 2.78 - 3.49: 16310 3.49 - 4.19: 27768 4.19 - 4.90: 48453 Nonbonded interactions: 95180 Sorted by model distance: nonbonded pdb=" O TYR E 151 " pdb=" CE MET E 155 " model vdw 1.365 3.460 nonbonded pdb=" OD1 ASP D 26 " pdb=" OG1 THR E 45 " model vdw 1.398 3.040 nonbonded pdb=" OE1 GLU G 51 " pdb=" NH1 ARG G 54 " model vdw 1.613 3.120 nonbonded pdb=" OE1 GLU G 51 " pdb=" CZ ARG G 54 " model vdw 1.731 3.270 nonbonded pdb=" CD GLU G 51 " pdb=" NH1 ARG G 54 " model vdw 1.753 3.350 ... (remaining 95175 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 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 9 through 42 or resid 71 through 72 or resid 74 through 17 \ 4 or resid 210 through 401)) selection = (chain 'B' and (resid 9 through 72 or resid 74 through 401)) } ncs_group { reference = (chain 'C' and (resid 6 through 39 or resid 57 through 250)) selection = (chain 'D' and resid 6 through 250) } ncs_group { reference = (chain 'E' and (resid 6 through 177 or resid 202 through 262)) selection = (chain 'F' and (resid 6 through 177 or resid 202 through 262)) } ncs_group { reference = (chain 'G' and (resid 1 through 75 or (resid 76 and (name N or name CA or name C \ or name O )))) selection = chain 'H' } 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=0.00 max=1.00 mean=0.92 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: 5.130 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.000 Extract box with map and model: 0.330 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 14.000 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.030 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:1.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.230 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7170 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 0.185 12799 Z= 0.241 Angle : 0.576 17.505 17296 Z= 0.331 Chirality : 0.044 0.553 1955 Planarity : 0.012 0.497 2222 Dihedral : 16.352 89.832 4789 Min Nonbonded Distance : 1.365 Molprobity Statistics. All-atom Clashscore : 17.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 0.07 % Allowed : 23.41 % Favored : 76.52 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.25 (0.22), residues: 1541 helix: 0.59 (0.23), residues: 533 sheet: 0.18 (0.30), residues: 306 loop : -0.86 (0.24), residues: 702 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 115 TYR 0.021 0.001 TYR E 142 PHE 0.012 0.001 PHE E 127 TRP 0.012 0.001 TRP A 130 HIS 0.003 0.001 HIS A 122 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.18 (12794) covalent geometry : angle 0.57638 / 0.33 (17296) hydrogen bonds : bond 0.28417 / 19.28 ( 531) hydrogen bonds : angle 8.45277 / 5.69 ( 1581) metal coordination : bond 0.00447 / 0.22 ( 4) Misc. bond : bond 0.18464 / 9.72 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3082 Ramachandran restraints generated. 1541 Oldfield, 0 Emsley, 1541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3082 Ramachandran restraints generated. 1541 Oldfield, 0 Emsley, 1541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 1412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 291 time to evaluate : 0.506 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 42 ARG cc_start: 0.7019 (mmt180) cc_final: 0.6757 (mmt180) REVERT: C 187 MET cc_start: 0.7181 (mtm) cc_final: 0.6973 (mtm) REVERT: C 225 GLU cc_start: 0.6958 (mm-30) cc_final: 0.6451 (mm-30) REVERT: C 231 LYS cc_start: 0.8148 (tttt) cc_final: 0.7938 (tttt) REVERT: D 23 LEU cc_start: 0.8335 (mt) cc_final: 0.8105 (mp) REVERT: D 38 LYS cc_start: 0.7585 (tttt) cc_final: 0.7239 (tttt) REVERT: D 187 MET cc_start: 0.5342 (ttm) cc_final: 0.5096 (ttm) REVERT: D 214 LYS cc_start: 0.8144 (mtpp) cc_final: 0.7681 (mtpp) REVERT: D 225 GLU cc_start: 0.7896 (mm-30) cc_final: 0.7630 (mm-30) REVERT: D 234 GLU cc_start: 0.7136 (tt0) cc_final: 0.6826 (tt0) REVERT: A 141 MET cc_start: 0.7268 (mtm) cc_final: 0.6853 (mtm) REVERT: B 143 GLN cc_start: 0.8245 (tt0) cc_final: 0.7470 (tt0) REVERT: B 152 LEU cc_start: 0.7251 (mp) cc_final: 0.6990 (mp) REVERT: E 22 VAL cc_start: 0.8126 (m) cc_final: 0.7816 (p) REVERT: E 100 GLN cc_start: 0.8085 (tt0) cc_final: 0.7826 (tt0) outliers start: 0 outliers final: 0 residues processed: 291 average time/residue: 0.1221 time to fit residues: 50.6979 Evaluate side-chains 286 residues out of total 1412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 286 time to evaluate : 0.450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 98 optimal weight: 0.0970 chunk 107 optimal weight: 0.7980 chunk 10 optimal weight: 0.1980 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 0.5980 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 0.9980 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 0.8980 chunk 149 optimal weight: 0.8980 overall best weight: 0.5178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** H 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 118 HIS ** C 124 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 24 ASN ** B 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 126 HIS F 123 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4238 r_free = 0.4238 target = 0.174765 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.146268 restraints weight = 32264.943| |-----------------------------------------------------------------------------| r_work (start): 0.3850 rms_B_bonded: 4.01 r_work: 0.3651 rms_B_bonded: 4.41 restraints_weight: 0.5000 r_work (final): 0.3651 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3651 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3651 r_free = 0.3651 target_work(ls_wunit_k1) = 0.133 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 998 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3651 r_free = 0.3651 target_work(ls_wunit_k1) = 0.133 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 998 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (7 function evaluations) r_final: 0.3651 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7219 moved from start: 0.1310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 12799 Z= 0.151 Angle : 0.579 7.615 17296 Z= 0.305 Chirality : 0.042 0.165 1955 Planarity : 0.004 0.047 2222 Dihedral : 4.046 24.873 1675 Min Nonbonded Distance : 1.897 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 2.76 % Allowed : 22.42 % Favored : 74.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.14 (0.22), residues: 1541 helix: 1.23 (0.21), residues: 571 sheet: 0.35 (0.29), residues: 311 loop : -1.02 (0.25), residues: 659 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 113 TYR 0.034 0.001 TYR E 142 PHE 0.016 0.001 PHE E 127 TRP 0.013 0.001 TRP A 130 HIS 0.008 0.001 HIS C 124 Details of bonding type rmsd/Z covalent geometry : bond 0.00309 / 0.15 (12794) covalent geometry : angle 0.57901 / 0.30 (17296) hydrogen bonds : bond 0.06733 / 4.56 ( 531) hydrogen bonds : angle 5.25615 / 3.53 ( 1581) metal coordination : bond 0.00746 / 0.37 ( 4) Misc. bond : bond 0.00010 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3082 Ramachandran restraints generated. 1541 Oldfield, 0 Emsley, 1541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3082 Ramachandran restraints generated. 1541 Oldfield, 0 Emsley, 1541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 334 residues out of total 1412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 296 time to evaluate : 0.483 Fit side-chains revert: symmetry clash REVERT: C 63 LYS cc_start: 0.8372 (mtpt) cc_final: 0.7954 (mtpt) REVERT: C 187 MET cc_start: 0.7208 (mtm) cc_final: 0.6977 (mtm) REVERT: C 225 GLU cc_start: 0.7033 (mm-30) cc_final: 0.6595 (mm-30) REVERT: C 227 LYS cc_start: 0.8395 (ttpt) cc_final: 0.8158 (ttpt) REVERT: C 231 LYS cc_start: 0.8397 (tttt) cc_final: 0.8150 (tttt) REVERT: D 21 GLN cc_start: 0.8582 (OUTLIER) cc_final: 0.8076 (tt0) REVERT: D 23 LEU cc_start: 0.8483 (mt) cc_final: 0.8214 (mp) REVERT: D 38 LYS cc_start: 0.7609 (tttt) cc_final: 0.7218 (tttt) REVERT: D 82 GLU cc_start: 0.7076 (mt-10) cc_final: 0.6822 (mt-10) REVERT: D 187 MET cc_start: 0.5438 (ttm) cc_final: 0.5169 (ttm) REVERT: D 225 GLU cc_start: 0.7676 (mm-30) cc_final: 0.7375 (mm-30) REVERT: D 234 GLU cc_start: 0.7459 (tt0) cc_final: 0.7129 (tt0) REVERT: B 77 VAL cc_start: 0.8121 (m) cc_final: 0.7882 (t) REVERT: B 152 LEU cc_start: 0.7544 (mp) cc_final: 0.7259 (mp) REVERT: B 221 HIS cc_start: 0.6118 (OUTLIER) cc_final: 0.5460 (t-90) REVERT: B 295 GLN cc_start: 0.7134 (mt0) cc_final: 0.6752 (mt0) REVERT: E 22 VAL cc_start: 0.8161 (m) cc_final: 0.7849 (p) REVERT: E 58 LEU cc_start: 0.7847 (OUTLIER) cc_final: 0.7589 (tp) REVERT: E 119 GLU cc_start: 0.7441 (tt0) cc_final: 0.7212 (tt0) REVERT: E 126 GLN cc_start: 0.8157 (tt0) cc_final: 0.7938 (tt0) outliers start: 38 outliers final: 15 residues processed: 313 average time/residue: 0.1203 time to fit residues: 53.8265 Evaluate side-chains 307 residues out of total 1412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 289 time to evaluate : 0.488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 43 LEU Chi-restraints excluded: chain C residue 24 ASN Chi-restraints excluded: chain C residue 130 LEU Chi-restraints excluded: chain C residue 182 VAL Chi-restraints excluded: chain D residue 21 GLN Chi-restraints excluded: chain D residue 26 ASP Chi-restraints excluded: chain A residue 30 GLU Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain B residue 35 MET Chi-restraints excluded: chain B residue 141 MET Chi-restraints excluded: chain B residue 221 HIS Chi-restraints excluded: chain B residue 222 VAL Chi-restraints excluded: chain B residue 250 ILE Chi-restraints excluded: chain F residue 22 VAL Chi-restraints excluded: chain E residue 18 ILE Chi-restraints excluded: chain E residue 58 LEU Chi-restraints excluded: chain E residue 91 GLU Chi-restraints excluded: chain E residue 179 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 78 optimal weight: 0.9990 chunk 9 optimal weight: 5.9990 chunk 99 optimal weight: 0.5980 chunk 7 optimal weight: 6.9990 chunk 147 optimal weight: 0.0070 chunk 130 optimal weight: 0.5980 chunk 101 optimal weight: 1.9990 chunk 105 optimal weight: 2.9990 chunk 25 optimal weight: 0.5980 chunk 88 optimal weight: 5.9990 chunk 54 optimal weight: 0.6980 overall best weight: 0.4998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 41 GLN ** C 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 96 GLN E 123 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4240 r_free = 0.4240 target = 0.175052 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.146667 restraints weight = 25520.881| |-----------------------------------------------------------------------------| r_work (start): 0.3851 rms_B_bonded: 3.47 r_work: 0.3680 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.3680 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3680 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3680 r_free = 0.3680 target_work(ls_wunit_k1) = 0.135 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 998 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3680 r_free = 0.3680 target_work(ls_wunit_k1) = 0.135 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 998 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (7 function evaluations) r_final: 0.3680 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7180 moved from start: 0.1661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 12799 Z= 0.130 Angle : 0.534 8.561 17296 Z= 0.276 Chirality : 0.041 0.159 1955 Planarity : 0.003 0.042 2222 Dihedral : 3.932 18.743 1675 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 2.76 % Allowed : 23.62 % Favored : 73.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.28 (0.22), residues: 1541 helix: 1.47 (0.22), residues: 579 sheet: 0.32 (0.29), residues: 311 loop : -1.05 (0.25), residues: 651 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 248 TYR 0.033 0.001 TYR E 142 PHE 0.014 0.001 PHE F 84 TRP 0.015 0.001 TRP A 130 HIS 0.005 0.001 HIS A 263 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.13 (12794) covalent geometry : angle 0.53393 / 0.28 (17296) hydrogen bonds : bond 0.05717 / 3.86 ( 531) hydrogen bonds : angle 4.82589 / 3.23 ( 1581) metal coordination : bond 0.00629 / 0.31 ( 4) Misc. bond : bond 0.00064 / 0.03 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3082 Ramachandran restraints generated. 1541 Oldfield, 0 Emsley, 1541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3082 Ramachandran restraints generated. 1541 Oldfield, 0 Emsley, 1541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 327 residues out of total 1412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 289 time to evaluate : 0.463 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 63 LYS cc_start: 0.8278 (mtpt) cc_final: 0.7908 (mtpt) REVERT: C 187 MET cc_start: 0.7124 (mtm) cc_final: 0.6914 (mtm) REVERT: C 225 GLU cc_start: 0.6934 (mm-30) cc_final: 0.6537 (mm-30) REVERT: C 227 LYS cc_start: 0.8368 (ttpt) cc_final: 0.8117 (ttpt) REVERT: C 231 LYS cc_start: 0.8412 (tttt) cc_final: 0.8158 (tttt) REVERT: D 21 GLN cc_start: 0.8513 (OUTLIER) cc_final: 0.8021 (tt0) REVERT: D 23 LEU cc_start: 0.8484 (mt) cc_final: 0.8231 (mp) REVERT: D 82 GLU cc_start: 0.7030 (mt-10) cc_final: 0.6797 (mt-10) REVERT: D 187 MET cc_start: 0.5390 (ttm) cc_final: 0.5121 (ttm) REVERT: D 225 GLU cc_start: 0.7561 (mm-30) cc_final: 0.7248 (mm-30) REVERT: D 234 GLU cc_start: 0.7400 (tt0) cc_final: 0.7185 (tt0) REVERT: A 82 ARG cc_start: 0.8204 (mtm180) cc_final: 0.7972 (mtm180) REVERT: A 255 HIS cc_start: 0.8114 (p90) cc_final: 0.7877 (p90) REVERT: B 139 GLN cc_start: 0.7530 (tp40) cc_final: 0.6882 (tm-30) REVERT: B 152 LEU cc_start: 0.7413 (mp) cc_final: 0.7123 (mp) REVERT: B 221 HIS cc_start: 0.6105 (OUTLIER) cc_final: 0.5454 (t-90) REVERT: B 295 GLN cc_start: 0.7107 (mt0) cc_final: 0.6741 (mt0) REVERT: E 22 VAL cc_start: 0.8133 (m) cc_final: 0.7833 (p) REVERT: E 58 LEU cc_start: 0.7777 (OUTLIER) cc_final: 0.7533 (tp) REVERT: E 119 GLU cc_start: 0.7350 (tt0) cc_final: 0.7116 (tt0) outliers start: 38 outliers final: 17 residues processed: 315 average time/residue: 0.1180 time to fit residues: 53.1165 Evaluate side-chains 304 residues out of total 1412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 284 time to evaluate : 0.499 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 43 LEU Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 130 LEU Chi-restraints excluded: chain C residue 182 VAL Chi-restraints excluded: chain D residue 21 GLN Chi-restraints excluded: chain D residue 26 ASP Chi-restraints excluded: chain D residue 238 GLN Chi-restraints excluded: chain D residue 243 LEU Chi-restraints excluded: chain A residue 30 GLU Chi-restraints excluded: chain A residue 156 CYS Chi-restraints excluded: chain B residue 221 HIS Chi-restraints excluded: chain B residue 250 ILE Chi-restraints excluded: chain B residue 298 LEU Chi-restraints excluded: chain F residue 22 VAL Chi-restraints excluded: chain E residue 13 MET Chi-restraints excluded: chain E residue 18 ILE Chi-restraints excluded: chain E residue 58 LEU Chi-restraints excluded: chain E residue 91 GLU Chi-restraints excluded: chain E residue 139 MET Chi-restraints excluded: chain E residue 237 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 71 optimal weight: 0.1980 chunk 104 optimal weight: 1.9990 chunk 143 optimal weight: 4.9990 chunk 96 optimal weight: 3.9990 chunk 147 optimal weight: 2.9990 chunk 150 optimal weight: 2.9990 chunk 117 optimal weight: 0.8980 chunk 0 optimal weight: 10.0000 chunk 144 optimal weight: 6.9990 chunk 48 optimal weight: 1.9990 chunk 63 optimal weight: 2.9990 overall best weight: 1.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 124 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 275 GLN ** B 124 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 126 HIS B 139 GLN F 123 GLN F 125 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4198 r_free = 0.4198 target = 0.171588 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.140872 restraints weight = 37532.297| |-----------------------------------------------------------------------------| r_work (start): 0.3770 rms_B_bonded: 4.07 r_work: 0.3592 rms_B_bonded: 4.35 restraints_weight: 0.5000 r_work (final): 0.3592 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3581 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3581 r_free = 0.3581 target_work(ls_wunit_k1) = 0.126 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 998 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3580 r_free = 0.3580 target_work(ls_wunit_k1) = 0.126 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 998 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 6 (11 function evaluations) r_final: 0.3580 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7286 moved from start: 0.1923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.064 12799 Z= 0.291 Angle : 0.662 9.152 17296 Z= 0.346 Chirality : 0.047 0.199 1955 Planarity : 0.005 0.057 2222 Dihedral : 4.600 19.118 1675 Min Nonbonded Distance : 1.801 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.97 % Favored : 94.03 % Rotamer: Outliers : 4.17 % Allowed : 23.62 % Favored : 72.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.17 (0.21), residues: 1541 helix: 1.21 (0.21), residues: 564 sheet: 0.11 (0.29), residues: 310 loop : -1.40 (0.24), residues: 667 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 104 TYR 0.029 0.002 TYR E 142 PHE 0.021 0.002 PHE F 56 TRP 0.023 0.003 TRP A 130 HIS 0.009 0.002 HIS C 124 Details of bonding type rmsd/Z covalent geometry : bond 0.00656 / 0.29 (12794) covalent geometry : angle 0.66198 / 0.35 (17296) hydrogen bonds : bond 0.06659 / 4.56 ( 531) hydrogen bonds : angle 5.11095 / 3.44 ( 1581) metal coordination : bond 0.01712 / 0.83 ( 4) Misc. bond : bond 0.00063 / 0.03 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3082 Ramachandran restraints generated. 1541 Oldfield, 0 Emsley, 1541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3082 Ramachandran restraints generated. 1541 Oldfield, 0 Emsley, 1541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 359 residues out of total 1412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 301 time to evaluate : 0.465 Fit side-chains revert: symmetry clash REVERT: G 51 GLU cc_start: 0.6643 (mt-10) cc_final: 0.6421 (mt-10) REVERT: C 63 LYS cc_start: 0.8348 (mtpt) cc_final: 0.7936 (mtpt) REVERT: C 130 LEU cc_start: 0.8185 (OUTLIER) cc_final: 0.7891 (mt) REVERT: C 187 MET cc_start: 0.7312 (mtm) cc_final: 0.7054 (mtm) REVERT: C 225 GLU cc_start: 0.7045 (mm-30) cc_final: 0.6550 (mm-30) REVERT: C 227 LYS cc_start: 0.8444 (ttpt) cc_final: 0.8204 (ttpt) REVERT: C 231 LYS cc_start: 0.8484 (tttt) cc_final: 0.8211 (tttt) REVERT: D 21 GLN cc_start: 0.8582 (OUTLIER) cc_final: 0.8098 (tt0) REVERT: D 23 LEU cc_start: 0.8552 (mt) cc_final: 0.8315 (mp) REVERT: D 38 LYS cc_start: 0.7567 (tttt) cc_final: 0.7171 (tttt) REVERT: D 82 GLU cc_start: 0.7066 (mt-10) cc_final: 0.6847 (mt-10) REVERT: D 149 LEU cc_start: 0.8738 (OUTLIER) cc_final: 0.8332 (tt) REVERT: D 187 MET cc_start: 0.5555 (ttm) cc_final: 0.5315 (ttm) REVERT: D 225 GLU cc_start: 0.7748 (mm-30) cc_final: 0.7452 (mm-30) REVERT: D 234 GLU cc_start: 0.7490 (tt0) cc_final: 0.7147 (tt0) REVERT: B 139 GLN cc_start: 0.7583 (tp-100) cc_final: 0.6537 (tm-30) REVERT: B 152 LEU cc_start: 0.7792 (mp) cc_final: 0.7393 (mp) REVERT: B 213 GLU cc_start: 0.6599 (OUTLIER) cc_final: 0.5496 (mm-30) REVERT: B 221 HIS cc_start: 0.6221 (OUTLIER) cc_final: 0.5576 (t-90) REVERT: B 295 GLN cc_start: 0.7145 (mt0) cc_final: 0.6785 (mt0) REVERT: F 45 THR cc_start: 0.8415 (t) cc_final: 0.7910 (p) REVERT: E 22 VAL cc_start: 0.8294 (m) cc_final: 0.8067 (p) REVERT: E 119 GLU cc_start: 0.7466 (tt0) cc_final: 0.7195 (tt0) outliers start: 58 outliers final: 35 residues processed: 332 average time/residue: 0.1214 time to fit residues: 57.5203 Evaluate side-chains 333 residues out of total 1412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 293 time to evaluate : 0.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 33 LYS Chi-restraints excluded: chain G residue 43 LEU Chi-restraints excluded: chain G residue 62 GLN Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 79 GLU Chi-restraints excluded: chain C residue 130 LEU Chi-restraints excluded: chain C residue 138 SER Chi-restraints excluded: chain C residue 182 VAL Chi-restraints excluded: chain D residue 21 GLN Chi-restraints excluded: chain D residue 26 ASP Chi-restraints excluded: chain D residue 149 LEU Chi-restraints excluded: chain A residue 30 GLU Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain B residue 73 HIS Chi-restraints excluded: chain B residue 141 MET Chi-restraints excluded: chain B residue 172 CYS Chi-restraints excluded: chain B residue 213 GLU Chi-restraints excluded: chain B residue 221 HIS Chi-restraints excluded: chain B residue 250 ILE Chi-restraints excluded: chain B residue 298 LEU Chi-restraints excluded: chain F residue 21 VAL Chi-restraints excluded: chain F residue 22 VAL Chi-restraints excluded: chain F residue 35 LEU Chi-restraints excluded: chain F residue 99 LEU Chi-restraints excluded: chain F residue 101 ASN Chi-restraints excluded: chain F residue 117 VAL Chi-restraints excluded: chain F residue 125 HIS Chi-restraints excluded: chain E residue 11 SER Chi-restraints excluded: chain E residue 13 MET Chi-restraints excluded: chain E residue 17 PHE Chi-restraints excluded: chain E residue 18 ILE Chi-restraints excluded: chain E residue 91 GLU Chi-restraints excluded: chain E residue 133 ARG Chi-restraints excluded: chain E residue 139 MET Chi-restraints excluded: chain E residue 155 MET Chi-restraints excluded: chain E residue 207 PHE Chi-restraints excluded: chain E residue 237 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 133 optimal weight: 0.2980 chunk 89 optimal weight: 3.9990 chunk 63 optimal weight: 0.5980 chunk 135 optimal weight: 0.5980 chunk 130 optimal weight: 1.9990 chunk 90 optimal weight: 0.9990 chunk 139 optimal weight: 1.9990 chunk 138 optimal weight: 0.0570 chunk 49 optimal weight: 0.9990 chunk 56 optimal weight: 0.5980 chunk 66 optimal weight: 3.9990 overall best weight: 0.4298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 21 GLN C 157 GLN ** B 124 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 139 GLN B 285 GLN E 123 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4224 r_free = 0.4224 target = 0.176396 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.148561 restraints weight = 19716.124| |-----------------------------------------------------------------------------| r_work (start): 0.3841 rms_B_bonded: 2.81 r_work: 0.3708 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3708 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3711 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3711 r_free = 0.3711 target_work(ls_wunit_k1) = 0.135 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 998 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3711 r_free = 0.3711 target_work(ls_wunit_k1) = 0.135 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 998 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (5 function evaluations) r_final: 0.3711 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7129 moved from start: 0.2025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 12799 Z= 0.123 Angle : 0.552 9.108 17296 Z= 0.282 Chirality : 0.042 0.184 1955 Planarity : 0.004 0.048 2222 Dihedral : 4.214 18.197 1675 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 2.76 % Allowed : 25.25 % Favored : 71.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.22 (0.22), residues: 1541 helix: 1.61 (0.22), residues: 568 sheet: 0.19 (0.29), residues: 312 loop : -1.18 (0.25), residues: 661 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 115 TYR 0.029 0.002 TYR E 142 PHE 0.013 0.001 PHE C 112 TRP 0.018 0.001 TRP A 130 HIS 0.005 0.001 HIS F 125 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.12 (12794) covalent geometry : angle 0.55164 / 0.28 (17296) hydrogen bonds : bond 0.05220 / 3.55 ( 531) hydrogen bonds : angle 4.68210 / 3.14 ( 1581) metal coordination : bond 0.00629 / 0.30 ( 4) Misc. bond : bond 0.00065 / 0.03 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3082 Ramachandran restraints generated. 1541 Oldfield, 0 Emsley, 1541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3082 Ramachandran restraints generated. 1541 Oldfield, 0 Emsley, 1541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 335 residues out of total 1412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 297 time to evaluate : 0.475 Fit side-chains revert: symmetry clash REVERT: G 51 GLU cc_start: 0.6294 (mt-10) cc_final: 0.6053 (mt-10) REVERT: C 63 LYS cc_start: 0.8273 (mtpt) cc_final: 0.7851 (mtpt) REVERT: C 130 LEU cc_start: 0.8118 (OUTLIER) cc_final: 0.7816 (mt) REVERT: C 187 MET cc_start: 0.7124 (mtm) cc_final: 0.6898 (mtm) REVERT: C 223 GLN cc_start: 0.7718 (tp40) cc_final: 0.7246 (tp40) REVERT: C 225 GLU cc_start: 0.6925 (mm-30) cc_final: 0.6493 (mm-30) REVERT: C 227 LYS cc_start: 0.8277 (ttpt) cc_final: 0.8014 (ttpt) REVERT: C 231 LYS cc_start: 0.8325 (tttt) cc_final: 0.8057 (tttt) REVERT: D 21 GLN cc_start: 0.8495 (OUTLIER) cc_final: 0.7975 (tt0) REVERT: D 23 LEU cc_start: 0.8469 (mt) cc_final: 0.8205 (mp) REVERT: D 38 LYS cc_start: 0.7487 (tttt) cc_final: 0.7127 (tttt) REVERT: D 82 GLU cc_start: 0.6925 (mt-10) cc_final: 0.6704 (mt-10) REVERT: D 187 MET cc_start: 0.5284 (ttm) cc_final: 0.5049 (ttm) REVERT: D 225 GLU cc_start: 0.7490 (mm-30) cc_final: 0.7175 (mm-30) REVERT: B 139 GLN cc_start: 0.7415 (tp40) cc_final: 0.6742 (tm-30) REVERT: B 152 LEU cc_start: 0.7458 (OUTLIER) cc_final: 0.7180 (mp) REVERT: B 154 PHE cc_start: 0.8269 (m-80) cc_final: 0.7944 (m-80) REVERT: B 213 GLU cc_start: 0.6537 (OUTLIER) cc_final: 0.5436 (mm-30) REVERT: B 221 HIS cc_start: 0.6114 (OUTLIER) cc_final: 0.5458 (t-90) REVERT: B 295 GLN cc_start: 0.6886 (mt0) cc_final: 0.6557 (mt0) REVERT: F 45 THR cc_start: 0.8378 (t) cc_final: 0.7905 (p) REVERT: F 257 LEU cc_start: 0.5027 (tp) cc_final: 0.4615 (tp) REVERT: E 22 VAL cc_start: 0.8123 (m) cc_final: 0.7867 (p) REVERT: E 100 GLN cc_start: 0.7819 (tm-30) cc_final: 0.7566 (tm-30) REVERT: E 119 GLU cc_start: 0.7312 (tt0) cc_final: 0.7058 (tt0) outliers start: 38 outliers final: 26 residues processed: 320 average time/residue: 0.1191 time to fit residues: 54.3378 Evaluate side-chains 323 residues out of total 1412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 292 time to evaluate : 0.465 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 43 LEU Chi-restraints excluded: chain G residue 62 GLN Chi-restraints excluded: chain C residue 24 ASN Chi-restraints excluded: chain C residue 26 ASP Chi-restraints excluded: chain C residue 130 LEU Chi-restraints excluded: chain C residue 138 SER Chi-restraints excluded: chain C residue 182 VAL Chi-restraints excluded: chain D residue 21 GLN Chi-restraints excluded: chain D residue 26 ASP Chi-restraints excluded: chain D residue 34 LEU Chi-restraints excluded: chain D residue 238 GLN Chi-restraints excluded: chain D residue 243 LEU Chi-restraints excluded: chain A residue 30 GLU Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 224 ILE Chi-restraints excluded: chain B residue 76 SER Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 213 GLU Chi-restraints excluded: chain B residue 221 HIS Chi-restraints excluded: chain B residue 250 ILE Chi-restraints excluded: chain B residue 298 LEU Chi-restraints excluded: chain F residue 35 LEU Chi-restraints excluded: chain F residue 99 LEU Chi-restraints excluded: chain F residue 101 ASN Chi-restraints excluded: chain F residue 117 VAL Chi-restraints excluded: chain E residue 13 MET Chi-restraints excluded: chain E residue 18 ILE Chi-restraints excluded: chain E residue 67 LEU Chi-restraints excluded: chain E residue 139 MET Chi-restraints excluded: chain E residue 155 MET Chi-restraints excluded: chain E residue 237 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 99 optimal weight: 0.3980 chunk 54 optimal weight: 1.9990 chunk 85 optimal weight: 5.9990 chunk 32 optimal weight: 0.8980 chunk 152 optimal weight: 3.9990 chunk 61 optimal weight: 0.8980 chunk 120 optimal weight: 7.9990 chunk 42 optimal weight: 2.9990 chunk 121 optimal weight: 0.0980 chunk 5 optimal weight: 4.9990 chunk 56 optimal weight: 0.9980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 124 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 285 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4213 r_free = 0.4213 target = 0.173016 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.144200 restraints weight = 25131.382| |-----------------------------------------------------------------------------| r_work (start): 0.3817 rms_B_bonded: 3.27 r_work: 0.3668 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.3668 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3672 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3672 r_free = 0.3672 target_work(ls_wunit_k1) = 0.133 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 998 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3672 r_free = 0.3672 target_work(ls_wunit_k1) = 0.133 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 998 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (5 function evaluations) r_final: 0.3672 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7166 moved from start: 0.2149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 12799 Z= 0.144 Angle : 0.546 8.263 17296 Z= 0.279 Chirality : 0.042 0.182 1955 Planarity : 0.004 0.047 2222 Dihedral : 4.136 17.788 1675 Min Nonbonded Distance : 1.903 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % Rotamer: Outliers : 3.25 % Allowed : 24.40 % Favored : 72.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.30 (0.22), residues: 1541 helix: 1.66 (0.22), residues: 572 sheet: 0.22 (0.29), residues: 312 loop : -1.14 (0.25), residues: 657 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 248 TYR 0.029 0.001 TYR E 142 PHE 0.014 0.001 PHE D 112 TRP 0.017 0.001 TRP A 130 HIS 0.005 0.001 HIS A 263 Details of bonding type rmsd/Z covalent geometry : bond 0.00322 / 0.14 (12794) covalent geometry : angle 0.54639 / 0.28 (17296) hydrogen bonds : bond 0.05104 / 3.47 ( 531) hydrogen bonds : angle 4.58035 / 3.08 ( 1581) metal coordination : bond 0.00837 / 0.41 ( 4) Misc. bond : bond 0.00060 / 0.03 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3082 Ramachandran restraints generated. 1541 Oldfield, 0 Emsley, 1541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3082 Ramachandran restraints generated. 1541 Oldfield, 0 Emsley, 1541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 341 residues out of total 1412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 296 time to evaluate : 0.489 Fit side-chains revert: symmetry clash REVERT: G 51 GLU cc_start: 0.6441 (mt-10) cc_final: 0.6191 (mt-10) REVERT: C 63 LYS cc_start: 0.8330 (mtpt) cc_final: 0.7902 (mtpt) REVERT: C 130 LEU cc_start: 0.8127 (OUTLIER) cc_final: 0.7844 (mt) REVERT: C 187 MET cc_start: 0.7185 (mtm) cc_final: 0.6922 (mtm) REVERT: C 225 GLU cc_start: 0.6952 (mm-30) cc_final: 0.6522 (mm-30) REVERT: C 227 LYS cc_start: 0.8366 (ttpt) cc_final: 0.8107 (ttpt) REVERT: C 231 LYS cc_start: 0.8360 (tttt) cc_final: 0.8100 (tttt) REVERT: D 21 GLN cc_start: 0.8512 (OUTLIER) cc_final: 0.8009 (tt0) REVERT: D 23 LEU cc_start: 0.8477 (mt) cc_final: 0.8216 (mp) REVERT: D 38 LYS cc_start: 0.7540 (tttt) cc_final: 0.7147 (tttt) REVERT: D 82 GLU cc_start: 0.7012 (mt-10) cc_final: 0.6800 (mt-10) REVERT: D 187 MET cc_start: 0.5375 (ttm) cc_final: 0.5131 (ttm) REVERT: D 225 GLU cc_start: 0.7555 (mm-30) cc_final: 0.7235 (mm-30) REVERT: A 37 LEU cc_start: 0.8214 (mp) cc_final: 0.7975 (mt) REVERT: A 82 ARG cc_start: 0.8219 (mtp180) cc_final: 0.7902 (mtm180) REVERT: A 248 ARG cc_start: 0.7685 (ttp80) cc_final: 0.7353 (mtm110) REVERT: B 139 GLN cc_start: 0.7563 (tp40) cc_final: 0.6809 (tm-30) REVERT: B 152 LEU cc_start: 0.7473 (mp) cc_final: 0.7185 (mp) REVERT: B 221 HIS cc_start: 0.6174 (OUTLIER) cc_final: 0.5531 (t-90) REVERT: B 295 GLN cc_start: 0.6988 (mt0) cc_final: 0.6659 (mt0) REVERT: F 45 THR cc_start: 0.8363 (t) cc_final: 0.7915 (p) REVERT: E 22 VAL cc_start: 0.8169 (m) cc_final: 0.7921 (p) REVERT: E 36 ARG cc_start: 0.7639 (mtp85) cc_final: 0.7381 (mtp85) REVERT: E 58 LEU cc_start: 0.7810 (OUTLIER) cc_final: 0.7604 (tp) REVERT: E 100 GLN cc_start: 0.7873 (tm-30) cc_final: 0.7616 (tm-30) REVERT: E 119 GLU cc_start: 0.7419 (tt0) cc_final: 0.7161 (tt0) outliers start: 45 outliers final: 35 residues processed: 322 average time/residue: 0.1201 time to fit residues: 55.0057 Evaluate side-chains 332 residues out of total 1412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 293 time to evaluate : 0.474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 43 LEU Chi-restraints excluded: chain G residue 62 GLN Chi-restraints excluded: chain C residue 24 ASN Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 79 GLU Chi-restraints excluded: chain C residue 92 VAL Chi-restraints excluded: chain C residue 130 LEU Chi-restraints excluded: chain C residue 138 SER Chi-restraints excluded: chain C residue 182 VAL Chi-restraints excluded: chain D residue 21 GLN Chi-restraints excluded: chain D residue 26 ASP Chi-restraints excluded: chain D residue 34 LEU Chi-restraints excluded: chain D residue 70 LEU Chi-restraints excluded: chain D residue 238 GLN Chi-restraints excluded: chain D residue 243 LEU Chi-restraints excluded: chain A residue 30 GLU Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 224 ILE Chi-restraints excluded: chain B residue 73 HIS Chi-restraints excluded: chain B residue 76 SER Chi-restraints excluded: chain B residue 116 ARG Chi-restraints excluded: chain B residue 221 HIS Chi-restraints excluded: chain B residue 250 ILE Chi-restraints excluded: chain B residue 298 LEU Chi-restraints excluded: chain F residue 35 LEU Chi-restraints excluded: chain F residue 99 LEU Chi-restraints excluded: chain F residue 101 ASN Chi-restraints excluded: chain F residue 115 LEU Chi-restraints excluded: chain F residue 117 VAL Chi-restraints excluded: chain F residue 125 HIS Chi-restraints excluded: chain E residue 13 MET Chi-restraints excluded: chain E residue 18 ILE Chi-restraints excluded: chain E residue 58 LEU Chi-restraints excluded: chain E residue 67 LEU Chi-restraints excluded: chain E residue 139 MET Chi-restraints excluded: chain E residue 155 MET Chi-restraints excluded: chain E residue 179 VAL Chi-restraints excluded: chain E residue 232 SER Chi-restraints excluded: chain E residue 237 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 113 optimal weight: 1.9990 chunk 34 optimal weight: 0.8980 chunk 11 optimal weight: 1.9990 chunk 32 optimal weight: 0.5980 chunk 117 optimal weight: 1.9990 chunk 33 optimal weight: 0.6980 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 3.9990 chunk 120 optimal weight: 0.0270 chunk 78 optimal weight: 3.9990 chunk 97 optimal weight: 0.9980 overall best weight: 0.6438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 124 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 285 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4219 r_free = 0.4219 target = 0.175527 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.146726 restraints weight = 31479.341| |-----------------------------------------------------------------------------| r_work (start): 0.3814 rms_B_bonded: 3.81 r_work: 0.3615 rms_B_bonded: 4.42 restraints_weight: 0.5000 r_work (final): 0.3615 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3621 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3621 r_free = 0.3621 target_work(ls_wunit_k1) = 0.129 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 998 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3621 r_free = 0.3621 target_work(ls_wunit_k1) = 0.129 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 998 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3621 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7227 moved from start: 0.2253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 12799 Z= 0.139 Angle : 0.547 8.175 17296 Z= 0.277 Chirality : 0.042 0.169 1955 Planarity : 0.004 0.047 2222 Dihedral : 4.110 17.675 1675 Min Nonbonded Distance : 1.909 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 3.11 % Allowed : 24.89 % Favored : 71.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.38 (0.22), residues: 1541 helix: 1.78 (0.22), residues: 569 sheet: 0.26 (0.29), residues: 318 loop : -1.16 (0.25), residues: 654 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 115 TYR 0.029 0.001 TYR E 142 PHE 0.014 0.001 PHE D 112 TRP 0.017 0.001 TRP A 130 HIS 0.008 0.001 HIS C 124 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.14 (12794) covalent geometry : angle 0.54743 / 0.28 (17296) hydrogen bonds : bond 0.04923 / 3.35 ( 531) hydrogen bonds : angle 4.48612 / 3.01 ( 1581) metal coordination : bond 0.00801 / 0.39 ( 4) Misc. bond : bond 0.00058 / 0.03 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3082 Ramachandran restraints generated. 1541 Oldfield, 0 Emsley, 1541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3082 Ramachandran restraints generated. 1541 Oldfield, 0 Emsley, 1541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 339 residues out of total 1412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 296 time to evaluate : 0.484 Fit side-chains revert: symmetry clash REVERT: G 51 GLU cc_start: 0.6580 (mt-10) cc_final: 0.6340 (mt-10) REVERT: C 63 LYS cc_start: 0.8398 (mtpt) cc_final: 0.7978 (mtpt) REVERT: C 130 LEU cc_start: 0.8150 (OUTLIER) cc_final: 0.7881 (mt) REVERT: C 187 MET cc_start: 0.7335 (mtm) cc_final: 0.7034 (mtm) REVERT: C 223 GLN cc_start: 0.7861 (tp40) cc_final: 0.7426 (tp40) REVERT: C 225 GLU cc_start: 0.7037 (mm-30) cc_final: 0.6617 (mm-30) REVERT: C 227 LYS cc_start: 0.8418 (ttpt) cc_final: 0.8179 (ttpt) REVERT: C 231 LYS cc_start: 0.8452 (tttt) cc_final: 0.8199 (tttt) REVERT: D 21 GLN cc_start: 0.8536 (OUTLIER) cc_final: 0.8041 (tt0) REVERT: D 23 LEU cc_start: 0.8505 (mt) cc_final: 0.8245 (mp) REVERT: D 38 LYS cc_start: 0.7566 (tttt) cc_final: 0.7156 (tttt) REVERT: D 82 GLU cc_start: 0.7071 (mt-10) cc_final: 0.6852 (mt-10) REVERT: D 115 ARG cc_start: 0.8333 (mtm110) cc_final: 0.7525 (ttp-110) REVERT: D 187 MET cc_start: 0.5500 (ttm) cc_final: 0.5234 (ttm) REVERT: A 37 LEU cc_start: 0.8270 (mp) cc_final: 0.8022 (mt) REVERT: A 248 ARG cc_start: 0.7768 (ttp80) cc_final: 0.7429 (mtm110) REVERT: B 139 GLN cc_start: 0.7578 (tp40) cc_final: 0.6798 (tm-30) REVERT: B 152 LEU cc_start: 0.7531 (mp) cc_final: 0.7249 (mp) REVERT: B 213 GLU cc_start: 0.6600 (OUTLIER) cc_final: 0.5479 (mm-30) REVERT: B 221 HIS cc_start: 0.6186 (OUTLIER) cc_final: 0.5564 (t-90) REVERT: B 295 GLN cc_start: 0.7059 (mt0) cc_final: 0.6745 (mt0) REVERT: F 45 THR cc_start: 0.8412 (t) cc_final: 0.7960 (p) REVERT: E 22 VAL cc_start: 0.8205 (m) cc_final: 0.7960 (p) REVERT: E 58 LEU cc_start: 0.7863 (OUTLIER) cc_final: 0.7649 (tp) REVERT: E 100 GLN cc_start: 0.7931 (tm-30) cc_final: 0.7670 (tm-30) REVERT: E 119 GLU cc_start: 0.7503 (tt0) cc_final: 0.7252 (tt0) outliers start: 43 outliers final: 32 residues processed: 321 average time/residue: 0.1203 time to fit residues: 54.8877 Evaluate side-chains 332 residues out of total 1412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 295 time to evaluate : 0.488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 43 LEU Chi-restraints excluded: chain G residue 62 GLN Chi-restraints excluded: chain C residue 24 ASN Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 92 VAL Chi-restraints excluded: chain C residue 130 LEU Chi-restraints excluded: chain C residue 138 SER Chi-restraints excluded: chain C residue 182 VAL Chi-restraints excluded: chain D residue 21 GLN Chi-restraints excluded: chain D residue 26 ASP Chi-restraints excluded: chain D residue 34 LEU Chi-restraints excluded: chain D residue 243 LEU Chi-restraints excluded: chain A residue 30 GLU Chi-restraints excluded: chain A residue 224 ILE Chi-restraints excluded: chain B residue 73 HIS Chi-restraints excluded: chain B residue 76 SER Chi-restraints excluded: chain B residue 116 ARG Chi-restraints excluded: chain B residue 213 GLU Chi-restraints excluded: chain B residue 221 HIS Chi-restraints excluded: chain B residue 250 ILE Chi-restraints excluded: chain B residue 276 MET Chi-restraints excluded: chain B residue 298 LEU Chi-restraints excluded: chain F residue 99 LEU Chi-restraints excluded: chain F residue 101 ASN Chi-restraints excluded: chain F residue 115 LEU Chi-restraints excluded: chain F residue 117 VAL Chi-restraints excluded: chain F residue 125 HIS Chi-restraints excluded: chain E residue 13 MET Chi-restraints excluded: chain E residue 17 PHE Chi-restraints excluded: chain E residue 18 ILE Chi-restraints excluded: chain E residue 58 LEU Chi-restraints excluded: chain E residue 67 LEU Chi-restraints excluded: chain E residue 139 MET Chi-restraints excluded: chain E residue 155 MET Chi-restraints excluded: chain E residue 179 VAL Chi-restraints excluded: chain E residue 232 SER Chi-restraints excluded: chain E residue 237 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 24 optimal weight: 0.6980 chunk 63 optimal weight: 0.5980 chunk 57 optimal weight: 0.7980 chunk 82 optimal weight: 0.5980 chunk 47 optimal weight: 0.9980 chunk 139 optimal weight: 0.8980 chunk 107 optimal weight: 0.9980 chunk 14 optimal weight: 1.9990 chunk 55 optimal weight: 1.9990 chunk 96 optimal weight: 0.7980 chunk 78 optimal weight: 0.5980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 124 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 285 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4220 r_free = 0.4220 target = 0.175384 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.147126 restraints weight = 22797.825| |-----------------------------------------------------------------------------| r_work (start): 0.3825 rms_B_bonded: 3.01 r_work: 0.3685 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3685 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3693 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3693 r_free = 0.3693 target_work(ls_wunit_k1) = 0.134 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 998 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3693 r_free = 0.3693 target_work(ls_wunit_k1) = 0.134 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 998 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3693 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7155 moved from start: 0.2313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 12799 Z= 0.141 Angle : 0.546 7.950 17296 Z= 0.277 Chirality : 0.042 0.169 1955 Planarity : 0.004 0.047 2222 Dihedral : 4.078 17.544 1675 Min Nonbonded Distance : 1.909 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 3.39 % Allowed : 24.96 % Favored : 71.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.37 (0.22), residues: 1541 helix: 1.84 (0.22), residues: 572 sheet: 0.23 (0.29), residues: 318 loop : -1.23 (0.25), residues: 651 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 82 TYR 0.030 0.001 TYR E 142 PHE 0.015 0.001 PHE F 84 TRP 0.018 0.001 TRP A 130 HIS 0.005 0.001 HIS C 124 Details of bonding type rmsd/Z covalent geometry : bond 0.00316 / 0.14 (12794) covalent geometry : angle 0.54605 / 0.28 (17296) hydrogen bonds : bond 0.04865 / 3.31 ( 531) hydrogen bonds : angle 4.45798 / 2.99 ( 1581) metal coordination : bond 0.00816 / 0.40 ( 4) Misc. bond : bond 0.00052 / 0.03 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3082 Ramachandran restraints generated. 1541 Oldfield, 0 Emsley, 1541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3082 Ramachandran restraints generated. 1541 Oldfield, 0 Emsley, 1541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 344 residues out of total 1412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 297 time to evaluate : 0.443 Fit side-chains revert: symmetry clash REVERT: G 51 GLU cc_start: 0.6437 (mt-10) cc_final: 0.6208 (mt-10) REVERT: C 63 LYS cc_start: 0.8322 (mtpt) cc_final: 0.7912 (mtpt) REVERT: C 187 MET cc_start: 0.7189 (mtm) cc_final: 0.6931 (mtm) REVERT: C 223 GLN cc_start: 0.7753 (tp40) cc_final: 0.7296 (tp40) REVERT: C 225 GLU cc_start: 0.6947 (mm-30) cc_final: 0.6531 (mm-30) REVERT: C 227 LYS cc_start: 0.8358 (ttpt) cc_final: 0.8111 (ttpt) REVERT: C 231 LYS cc_start: 0.8373 (tttt) cc_final: 0.8127 (tttt) REVERT: D 21 GLN cc_start: 0.8507 (OUTLIER) cc_final: 0.8005 (tt0) REVERT: D 23 LEU cc_start: 0.8474 (mt) cc_final: 0.8217 (mp) REVERT: D 38 LYS cc_start: 0.7518 (tttt) cc_final: 0.7160 (tttt) REVERT: D 187 MET cc_start: 0.5313 (ttm) cc_final: 0.5071 (ttm) REVERT: D 225 GLU cc_start: 0.7485 (mm-30) cc_final: 0.7197 (mm-30) REVERT: A 37 LEU cc_start: 0.8220 (mp) cc_final: 0.7991 (mt) REVERT: A 292 GLU cc_start: 0.7921 (tt0) cc_final: 0.7696 (mt-10) REVERT: B 139 GLN cc_start: 0.7477 (tp40) cc_final: 0.6720 (tm-30) REVERT: B 152 LEU cc_start: 0.7458 (mp) cc_final: 0.7169 (mp) REVERT: B 213 GLU cc_start: 0.6571 (OUTLIER) cc_final: 0.5450 (mm-30) REVERT: B 221 HIS cc_start: 0.6131 (OUTLIER) cc_final: 0.5496 (t-90) REVERT: B 295 GLN cc_start: 0.6951 (mt0) cc_final: 0.6654 (mt0) REVERT: F 45 THR cc_start: 0.8367 (t) cc_final: 0.7960 (p) REVERT: E 22 VAL cc_start: 0.8143 (m) cc_final: 0.7904 (p) REVERT: E 58 LEU cc_start: 0.7776 (OUTLIER) cc_final: 0.7561 (tp) REVERT: E 100 GLN cc_start: 0.7792 (tm-30) cc_final: 0.7545 (tm-30) REVERT: E 119 GLU cc_start: 0.7341 (tt0) cc_final: 0.7087 (tt0) outliers start: 47 outliers final: 38 residues processed: 322 average time/residue: 0.1164 time to fit residues: 53.8157 Evaluate side-chains 335 residues out of total 1412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 293 time to evaluate : 0.477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 33 LYS Chi-restraints excluded: chain G residue 43 LEU Chi-restraints excluded: chain G residue 62 GLN Chi-restraints excluded: chain C residue 24 ASN Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 79 GLU Chi-restraints excluded: chain C residue 92 VAL Chi-restraints excluded: chain C residue 110 MET Chi-restraints excluded: chain C residue 130 LEU Chi-restraints excluded: chain C residue 138 SER Chi-restraints excluded: chain C residue 182 VAL Chi-restraints excluded: chain D residue 21 GLN Chi-restraints excluded: chain D residue 26 ASP Chi-restraints excluded: chain D residue 34 LEU Chi-restraints excluded: chain D residue 243 LEU Chi-restraints excluded: chain A residue 30 GLU Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 224 ILE Chi-restraints excluded: chain B residue 73 HIS Chi-restraints excluded: chain B residue 116 ARG Chi-restraints excluded: chain B residue 213 GLU Chi-restraints excluded: chain B residue 221 HIS Chi-restraints excluded: chain B residue 250 ILE Chi-restraints excluded: chain B residue 298 LEU Chi-restraints excluded: chain F residue 35 LEU Chi-restraints excluded: chain F residue 99 LEU Chi-restraints excluded: chain F residue 101 ASN Chi-restraints excluded: chain F residue 115 LEU Chi-restraints excluded: chain F residue 117 VAL Chi-restraints excluded: chain F residue 125 HIS Chi-restraints excluded: chain E residue 13 MET Chi-restraints excluded: chain E residue 17 PHE Chi-restraints excluded: chain E residue 18 ILE Chi-restraints excluded: chain E residue 58 LEU Chi-restraints excluded: chain E residue 67 LEU Chi-restraints excluded: chain E residue 91 GLU Chi-restraints excluded: chain E residue 126 GLN Chi-restraints excluded: chain E residue 139 MET Chi-restraints excluded: chain E residue 155 MET Chi-restraints excluded: chain E residue 179 VAL Chi-restraints excluded: chain E residue 232 SER Chi-restraints excluded: chain E residue 237 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 120 optimal weight: 8.9990 chunk 122 optimal weight: 1.9990 chunk 105 optimal weight: 2.9990 chunk 150 optimal weight: 6.9990 chunk 136 optimal weight: 0.2980 chunk 52 optimal weight: 3.9990 chunk 32 optimal weight: 0.3980 chunk 83 optimal weight: 1.9990 chunk 6 optimal weight: 0.0270 chunk 69 optimal weight: 0.9990 chunk 36 optimal weight: 10.0000 overall best weight: 0.7442 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 170 ASN ** B 124 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 285 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4212 r_free = 0.4212 target = 0.174988 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.147553 restraints weight = 19686.722| |-----------------------------------------------------------------------------| r_work (start): 0.3843 rms_B_bonded: 2.75 r_work: 0.3712 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3712 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3704 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3704 r_free = 0.3704 target_work(ls_wunit_k1) = 0.134 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 998 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3704 r_free = 0.3704 target_work(ls_wunit_k1) = 0.134 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 998 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (11 function evaluations) r_final: 0.3704 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7133 moved from start: 0.2386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 12799 Z= 0.153 Angle : 0.560 7.707 17296 Z= 0.284 Chirality : 0.042 0.183 1955 Planarity : 0.004 0.047 2222 Dihedral : 4.134 17.392 1675 Min Nonbonded Distance : 1.893 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.81 % Favored : 95.19 % Rotamer: Outliers : 3.18 % Allowed : 25.74 % Favored : 71.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.38 (0.22), residues: 1541 helix: 1.86 (0.22), residues: 572 sheet: 0.22 (0.30), residues: 317 loop : -1.21 (0.25), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 86 TYR 0.032 0.002 TYR E 142 PHE 0.019 0.001 PHE C 71 TRP 0.018 0.001 TRP A 130 HIS 0.005 0.001 HIS A 263 Details of bonding type rmsd/Z covalent geometry : bond 0.00345 / 0.15 (12794) covalent geometry : angle 0.55992 / 0.28 (17296) hydrogen bonds : bond 0.04923 / 3.36 ( 531) hydrogen bonds : angle 4.46144 / 2.99 ( 1581) metal coordination : bond 0.00927 / 0.45 ( 4) Misc. bond : bond 0.00047 / 0.02 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3082 Ramachandran restraints generated. 1541 Oldfield, 0 Emsley, 1541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3082 Ramachandran restraints generated. 1541 Oldfield, 0 Emsley, 1541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 346 residues out of total 1412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 302 time to evaluate : 0.407 Fit side-chains revert: symmetry clash REVERT: G 51 GLU cc_start: 0.6367 (mt-10) cc_final: 0.6131 (mt-10) REVERT: C 63 LYS cc_start: 0.8290 (mtpt) cc_final: 0.7872 (mtpt) REVERT: C 130 LEU cc_start: 0.8115 (OUTLIER) cc_final: 0.7865 (mt) REVERT: C 187 MET cc_start: 0.7154 (mtm) cc_final: 0.6900 (mtm) REVERT: C 223 GLN cc_start: 0.7727 (tp40) cc_final: 0.7249 (tp40) REVERT: C 225 GLU cc_start: 0.6945 (mm-30) cc_final: 0.6516 (mm-30) REVERT: C 227 LYS cc_start: 0.8349 (ttpt) cc_final: 0.8095 (ttpt) REVERT: C 231 LYS cc_start: 0.8363 (tttt) cc_final: 0.8113 (tttt) REVERT: D 21 GLN cc_start: 0.8493 (OUTLIER) cc_final: 0.7982 (tt0) REVERT: D 23 LEU cc_start: 0.8487 (mt) cc_final: 0.8232 (mp) REVERT: D 38 LYS cc_start: 0.7495 (tttt) cc_final: 0.7132 (tttt) REVERT: D 115 ARG cc_start: 0.8278 (mtm110) cc_final: 0.7371 (ttp-110) REVERT: D 187 MET cc_start: 0.5295 (ttm) cc_final: 0.5043 (ttm) REVERT: A 37 LEU cc_start: 0.8199 (mp) cc_final: 0.7969 (mt) REVERT: A 292 GLU cc_start: 0.7875 (tt0) cc_final: 0.7647 (mt-10) REVERT: B 152 LEU cc_start: 0.7460 (mp) cc_final: 0.7175 (mp) REVERT: B 213 GLU cc_start: 0.6559 (OUTLIER) cc_final: 0.5422 (mm-30) REVERT: B 221 HIS cc_start: 0.6125 (OUTLIER) cc_final: 0.5442 (t-90) REVERT: B 295 GLN cc_start: 0.6920 (mt0) cc_final: 0.6620 (mt0) REVERT: F 45 THR cc_start: 0.8359 (t) cc_final: 0.7947 (p) REVERT: E 22 VAL cc_start: 0.8154 (m) cc_final: 0.7916 (p) REVERT: E 58 LEU cc_start: 0.7758 (OUTLIER) cc_final: 0.7554 (tp) REVERT: E 100 GLN cc_start: 0.7789 (tm-30) cc_final: 0.7530 (tm-30) REVERT: E 119 GLU cc_start: 0.7348 (tt0) cc_final: 0.7086 (tt0) outliers start: 44 outliers final: 35 residues processed: 324 average time/residue: 0.1218 time to fit residues: 56.1899 Evaluate side-chains 339 residues out of total 1412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 299 time to evaluate : 0.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 33 LYS Chi-restraints excluded: chain G residue 62 GLN Chi-restraints excluded: chain C residue 24 ASN Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 79 GLU Chi-restraints excluded: chain C residue 92 VAL Chi-restraints excluded: chain C residue 110 MET Chi-restraints excluded: chain C residue 130 LEU Chi-restraints excluded: chain C residue 138 SER Chi-restraints excluded: chain C residue 182 VAL Chi-restraints excluded: chain D residue 21 GLN Chi-restraints excluded: chain D residue 26 ASP Chi-restraints excluded: chain D residue 34 LEU Chi-restraints excluded: chain D residue 243 LEU Chi-restraints excluded: chain A residue 30 GLU Chi-restraints excluded: chain A residue 41 GLU Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 224 ILE Chi-restraints excluded: chain B residue 73 HIS Chi-restraints excluded: chain B residue 213 GLU Chi-restraints excluded: chain B residue 221 HIS Chi-restraints excluded: chain B residue 250 ILE Chi-restraints excluded: chain B residue 276 MET Chi-restraints excluded: chain B residue 298 LEU Chi-restraints excluded: chain F residue 35 LEU Chi-restraints excluded: chain F residue 101 ASN Chi-restraints excluded: chain F residue 115 LEU Chi-restraints excluded: chain F residue 117 VAL Chi-restraints excluded: chain F residue 125 HIS Chi-restraints excluded: chain E residue 13 MET Chi-restraints excluded: chain E residue 17 PHE Chi-restraints excluded: chain E residue 18 ILE Chi-restraints excluded: chain E residue 58 LEU Chi-restraints excluded: chain E residue 67 LEU Chi-restraints excluded: chain E residue 126 GLN Chi-restraints excluded: chain E residue 139 MET Chi-restraints excluded: chain E residue 155 MET Chi-restraints excluded: chain E residue 179 VAL Chi-restraints excluded: chain E residue 232 SER Chi-restraints excluded: chain E residue 237 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 128 optimal weight: 3.9990 chunk 15 optimal weight: 0.5980 chunk 61 optimal weight: 0.0040 chunk 37 optimal weight: 0.9980 chunk 119 optimal weight: 0.8980 chunk 9 optimal weight: 5.9990 chunk 92 optimal weight: 0.6980 chunk 112 optimal weight: 0.0570 chunk 12 optimal weight: 10.0000 chunk 51 optimal weight: 2.9990 chunk 1 optimal weight: 0.7980 overall best weight: 0.4310 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 124 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 285 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4233 r_free = 0.4233 target = 0.176881 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.147780 restraints weight = 24678.905| |-----------------------------------------------------------------------------| r_work (start): 0.3835 rms_B_bonded: 3.25 r_work: 0.3690 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.3690 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3693 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3693 r_free = 0.3693 target_work(ls_wunit_k1) = 0.134 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 998 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3693 r_free = 0.3693 target_work(ls_wunit_k1) = 0.134 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 998 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (10 function evaluations) r_final: 0.3693 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7147 moved from start: 0.2468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 12799 Z= 0.115 Angle : 0.541 8.196 17296 Z= 0.271 Chirality : 0.041 0.206 1955 Planarity : 0.004 0.052 2222 Dihedral : 3.976 16.758 1675 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 2.83 % Allowed : 26.45 % Favored : 70.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.53 (0.22), residues: 1541 helix: 1.99 (0.22), residues: 579 sheet: 0.26 (0.29), residues: 320 loop : -1.15 (0.25), residues: 642 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 86 TYR 0.032 0.001 TYR E 142 PHE 0.016 0.001 PHE C 71 TRP 0.018 0.001 TRP A 130 HIS 0.005 0.001 HIS A 263 Details of bonding type rmsd/Z covalent geometry : bond 0.00255 / 0.12 (12794) covalent geometry : angle 0.54093 / 0.27 (17296) hydrogen bonds : bond 0.04451 / 3.03 ( 531) hydrogen bonds : angle 4.33364 / 2.91 ( 1581) metal coordination : bond 0.00539 / 0.26 ( 4) Misc. bond : bond 0.00051 / 0.03 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3082 Ramachandran restraints generated. 1541 Oldfield, 0 Emsley, 1541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3082 Ramachandran restraints generated. 1541 Oldfield, 0 Emsley, 1541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 341 residues out of total 1412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 302 time to evaluate : 0.476 Fit side-chains revert: symmetry clash REVERT: G 33 LYS cc_start: 0.8094 (OUTLIER) cc_final: 0.7767 (tptt) REVERT: G 51 GLU cc_start: 0.6432 (mt-10) cc_final: 0.6212 (mt-10) REVERT: C 63 LYS cc_start: 0.8332 (mtpt) cc_final: 0.7888 (mtpt) REVERT: C 187 MET cc_start: 0.7212 (mtm) cc_final: 0.6934 (mtm) REVERT: C 223 GLN cc_start: 0.7777 (tp40) cc_final: 0.7301 (tp40) REVERT: C 225 GLU cc_start: 0.6956 (mm-30) cc_final: 0.6559 (mm-30) REVERT: C 227 LYS cc_start: 0.8379 (ttpt) cc_final: 0.8125 (ttpt) REVERT: C 231 LYS cc_start: 0.8355 (tttt) cc_final: 0.8114 (tttt) REVERT: D 21 GLN cc_start: 0.8486 (OUTLIER) cc_final: 0.7982 (tt0) REVERT: D 23 LEU cc_start: 0.8476 (mt) cc_final: 0.8210 (mp) REVERT: D 187 MET cc_start: 0.5338 (ttm) cc_final: 0.5069 (ttm) REVERT: D 225 GLU cc_start: 0.7496 (mm-30) cc_final: 0.7202 (mm-30) REVERT: D 242 LYS cc_start: 0.7748 (mmmm) cc_final: 0.7441 (ttmm) REVERT: A 86 ARG cc_start: 0.7387 (ptp90) cc_final: 0.6840 (ptp-170) REVERT: A 107 LEU cc_start: 0.7941 (OUTLIER) cc_final: 0.7703 (tp) REVERT: A 248 ARG cc_start: 0.7656 (ttp80) cc_final: 0.7301 (mtm110) REVERT: A 292 GLU cc_start: 0.7939 (tt0) cc_final: 0.7722 (mt-10) REVERT: B 152 LEU cc_start: 0.7363 (mp) cc_final: 0.7070 (mp) REVERT: B 154 PHE cc_start: 0.8160 (m-80) cc_final: 0.7872 (m-80) REVERT: B 213 GLU cc_start: 0.6579 (OUTLIER) cc_final: 0.5483 (mm-30) REVERT: B 221 HIS cc_start: 0.6109 (OUTLIER) cc_final: 0.5489 (t-90) REVERT: B 295 GLN cc_start: 0.6945 (mt0) cc_final: 0.6634 (mt0) REVERT: F 45 THR cc_start: 0.8350 (t) cc_final: 0.7986 (p) REVERT: E 22 VAL cc_start: 0.8129 (m) cc_final: 0.7882 (p) REVERT: E 58 LEU cc_start: 0.7805 (OUTLIER) cc_final: 0.7603 (tp) REVERT: E 100 GLN cc_start: 0.7809 (tm-30) cc_final: 0.7527 (tm-30) REVERT: E 119 GLU cc_start: 0.7409 (tt0) cc_final: 0.7162 (tt0) outliers start: 39 outliers final: 30 residues processed: 322 average time/residue: 0.1234 time to fit residues: 56.4316 Evaluate side-chains 336 residues out of total 1412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 300 time to evaluate : 0.516 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 33 LYS Chi-restraints excluded: chain G residue 62 GLN Chi-restraints excluded: chain C residue 24 ASN Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 79 GLU Chi-restraints excluded: chain C residue 92 VAL Chi-restraints excluded: chain C residue 110 MET Chi-restraints excluded: chain C residue 130 LEU Chi-restraints excluded: chain C residue 182 VAL Chi-restraints excluded: chain D residue 21 GLN Chi-restraints excluded: chain D residue 26 ASP Chi-restraints excluded: chain D residue 34 LEU Chi-restraints excluded: chain D residue 243 LEU Chi-restraints excluded: chain A residue 30 GLU Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 224 ILE Chi-restraints excluded: chain B residue 73 HIS Chi-restraints excluded: chain B residue 213 GLU Chi-restraints excluded: chain B residue 221 HIS Chi-restraints excluded: chain B residue 250 ILE Chi-restraints excluded: chain B residue 298 LEU Chi-restraints excluded: chain F residue 35 LEU Chi-restraints excluded: chain F residue 101 ASN Chi-restraints excluded: chain F residue 115 LEU Chi-restraints excluded: chain F residue 117 VAL Chi-restraints excluded: chain F residue 125 HIS Chi-restraints excluded: chain E residue 13 MET Chi-restraints excluded: chain E residue 18 ILE Chi-restraints excluded: chain E residue 58 LEU Chi-restraints excluded: chain E residue 67 LEU Chi-restraints excluded: chain E residue 91 GLU Chi-restraints excluded: chain E residue 139 MET Chi-restraints excluded: chain E residue 155 MET Chi-restraints excluded: chain E residue 179 VAL Chi-restraints excluded: chain E residue 232 SER Chi-restraints excluded: chain E residue 237 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 6 optimal weight: 0.7980 chunk 87 optimal weight: 0.6980 chunk 124 optimal weight: 0.2980 chunk 45 optimal weight: 0.8980 chunk 63 optimal weight: 0.9980 chunk 75 optimal weight: 1.9990 chunk 141 optimal weight: 0.5980 chunk 96 optimal weight: 0.9980 chunk 51 optimal weight: 0.9980 chunk 55 optimal weight: 1.9990 chunk 5 optimal weight: 3.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 174 GLN ** B 124 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 285 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4221 r_free = 0.4221 target = 0.175538 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.147410 restraints weight = 37108.391| |-----------------------------------------------------------------------------| r_work (start): 0.3822 rms_B_bonded: 4.51 r_work: 0.3609 rms_B_bonded: 4.60 restraints_weight: 0.5000 r_work (final): 0.3609 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3613 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3613 r_free = 0.3613 target_work(ls_wunit_k1) = 0.129 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 998 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3613 r_free = 0.3613 target_work(ls_wunit_k1) = 0.129 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 998 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (7 function evaluations) r_final: 0.3613 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7242 moved from start: 0.2497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 12799 Z= 0.142 Angle : 0.564 8.058 17296 Z= 0.283 Chirality : 0.043 0.228 1955 Planarity : 0.004 0.047 2222 Dihedral : 4.032 16.870 1675 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 2.55 % Allowed : 26.73 % Favored : 70.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.50 (0.22), residues: 1541 helix: 1.91 (0.22), residues: 584 sheet: 0.23 (0.29), residues: 319 loop : -1.13 (0.26), residues: 638 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 115 TYR 0.032 0.001 TYR E 142 PHE 0.017 0.001 PHE C 71 TRP 0.018 0.001 TRP A 130 HIS 0.005 0.001 HIS A 263 Details of bonding type rmsd/Z covalent geometry : bond 0.00322 / 0.14 (12794) covalent geometry : angle 0.56428 / 0.28 (17296) hydrogen bonds : bond 0.04685 / 3.20 ( 531) hydrogen bonds : angle 4.35549 / 2.93 ( 1581) metal coordination : bond 0.00803 / 0.39 ( 4) Misc. bond : bond 0.00048 / 0.03 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3705.76 seconds wall clock time: 64 minutes 11.17 seconds (3851.17 seconds total)