Starting phenix.real_space_refine on Wed Feb 4 20:37:14 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7w7p_32346/02_2026/7w7p_32346.cif Found real_map, /net/cci-nas-00/data/ceres_data/7w7p_32346/02_2026/7w7p_32346.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.67 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7w7p_32346/02_2026/7w7p_32346.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7w7p_32346/02_2026/7w7p_32346.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7w7p_32346/02_2026/7w7p_32346.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7w7p_32346/02_2026/7w7p_32346.map" } resolution = 3.67 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.018 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: 4 Type Number sf(0) Gaussians S 89 5.16 5 C 8337 2.51 5 N 2255 2.21 5 O 2495 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 36 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 13176 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 2146 Number of conformers: 1 Conformer: "" Number of residues, atoms: 272, 2146 Classifications: {'peptide': 272} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 13, 'TRANS': 258} Chain: "B" Number of atoms: 2242 Number of conformers: 1 Conformer: "" Number of residues, atoms: 283, 2242 Classifications: {'peptide': 283} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 16, 'TRANS': 266} Chain breaks: 1 Chain: "C" Number of atoms: 2146 Number of conformers: 1 Conformer: "" Number of residues, atoms: 272, 2146 Classifications: {'peptide': 272} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 13, 'TRANS': 258} Chain: "D" Number of atoms: 2248 Number of conformers: 1 Conformer: "" Number of residues, atoms: 284, 2248 Classifications: {'peptide': 284} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 16, 'TRANS': 267} Chain breaks: 1 Chain: "E" Number of atoms: 2146 Number of conformers: 1 Conformer: "" Number of residues, atoms: 272, 2146 Classifications: {'peptide': 272} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 13, 'TRANS': 258} Chain: "F" Number of atoms: 2248 Number of conformers: 1 Conformer: "" Number of residues, atoms: 284, 2248 Classifications: {'peptide': 284} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 16, 'TRANS': 267} Chain breaks: 1 Time building chain proxies: 2.96, per 1000 atoms: 0.22 Number of scatterers: 13176 At special positions: 0 Unit cell: (147, 140, 85, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 89 16.00 O 2495 8.00 N 2255 7.00 C 8337 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.08 Conformation dependent library (CDL) restraints added in 645.8 milliseconds 3298 Ramachandran restraints generated. 1649 Oldfield, 0 Emsley, 1649 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3172 Finding SS restraints... Secondary structure from input PDB file: 51 helices and 21 sheets defined 33.0% alpha, 26.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.46 Creating SS restraints... Processing helix chain 'A' and resid 4 through 23 removed outlier: 3.587A pdb=" N VAL A 8 " --> pdb=" O ARG A 4 " (cutoff:3.500A) Processing helix chain 'A' and resid 23 through 33 Processing helix chain 'A' and resid 46 through 53 Processing helix chain 'A' and resid 53 through 63 removed outlier: 3.591A pdb=" N GLY A 57 " --> pdb=" O ASN A 53 " (cutoff:3.500A) Processing helix chain 'A' and resid 63 through 86 Proline residue: A 69 - end of helix Processing helix chain 'A' and resid 118 through 122 removed outlier: 3.726A pdb=" N VAL A 122 " --> pdb=" O THR A 119 " (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 192 Processing helix chain 'A' and resid 229 through 231 No H-bonds generated for 'chain 'A' and resid 229 through 231' Processing helix chain 'B' and resid 31 through 48 removed outlier: 3.669A pdb=" N GLN B 35 " --> pdb=" O SER B 31 " (cutoff:3.500A) Processing helix chain 'B' and resid 52 through 60 Processing helix chain 'B' and resid 66 through 70 Processing helix chain 'B' and resid 73 through 79 removed outlier: 4.026A pdb=" N ILE B 79 " --> pdb=" O LEU B 75 " (cutoff:3.500A) Processing helix chain 'B' and resid 81 through 89 Processing helix chain 'B' and resid 89 through 121 Processing helix chain 'B' and resid 152 through 156 Processing helix chain 'B' and resid 259 through 261 No H-bonds generated for 'chain 'B' and resid 259 through 261' Processing helix chain 'C' and resid 4 through 23 Processing helix chain 'C' and resid 23 through 33 removed outlier: 3.634A pdb=" N GLN C 33 " --> pdb=" O GLY C 29 " (cutoff:3.500A) Processing helix chain 'C' and resid 46 through 53 Processing helix chain 'C' and resid 53 through 63 removed outlier: 3.597A pdb=" N GLY C 57 " --> pdb=" O ASN C 53 " (cutoff:3.500A) Processing helix chain 'C' and resid 63 through 86 Proline residue: C 69 - end of helix Processing helix chain 'C' and resid 118 through 122 removed outlier: 3.580A pdb=" N VAL C 122 " --> pdb=" O THR C 119 " (cutoff:3.500A) Processing helix chain 'C' and resid 161 through 165 Processing helix chain 'C' and resid 179 through 184 removed outlier: 3.615A pdb=" N THR C 183 " --> pdb=" O GLY C 179 " (cutoff:3.500A) Processing helix chain 'C' and resid 187 through 192 removed outlier: 3.518A pdb=" N SER C 192 " --> pdb=" O LEU C 188 " (cutoff:3.500A) Processing helix chain 'C' and resid 227 through 231 Processing helix chain 'D' and resid 31 through 48 removed outlier: 4.167A pdb=" N GLN D 35 " --> pdb=" O SER D 31 " (cutoff:3.500A) Processing helix chain 'D' and resid 52 through 60 Processing helix chain 'D' and resid 66 through 70 Processing helix chain 'D' and resid 73 through 79 removed outlier: 4.155A pdb=" N ILE D 79 " --> pdb=" O LEU D 75 " (cutoff:3.500A) Processing helix chain 'D' and resid 81 through 89 Processing helix chain 'D' and resid 89 through 121 Processing helix chain 'D' and resid 259 through 261 No H-bonds generated for 'chain 'D' and resid 259 through 261' Processing helix chain 'E' and resid 4 through 23 Processing helix chain 'E' and resid 23 through 33 removed outlier: 4.026A pdb=" N GLN E 33 " --> pdb=" O GLY E 29 " (cutoff:3.500A) Processing helix chain 'E' and resid 46 through 53 Processing helix chain 'E' and resid 53 through 63 removed outlier: 3.524A pdb=" N GLY E 57 " --> pdb=" O ASN E 53 " (cutoff:3.500A) Processing helix chain 'E' and resid 63 through 86 Proline residue: E 69 - end of helix Processing helix chain 'E' and resid 118 through 122 removed outlier: 3.609A pdb=" N VAL E 122 " --> pdb=" O THR E 119 " (cutoff:3.500A) Processing helix chain 'E' and resid 179 through 184 removed outlier: 3.854A pdb=" N THR E 183 " --> pdb=" O GLY E 179 " (cutoff:3.500A) Processing helix chain 'E' and resid 187 through 192 Processing helix chain 'E' and resid 229 through 231 No H-bonds generated for 'chain 'E' and resid 229 through 231' Processing helix chain 'F' and resid 18 through 23 removed outlier: 3.532A pdb=" N TYR F 22 " --> pdb=" O GLY F 18 " (cutoff:3.500A) Processing helix chain 'F' and resid 32 through 48 removed outlier: 3.619A pdb=" N LYS F 36 " --> pdb=" O PRO F 32 " (cutoff:3.500A) Processing helix chain 'F' and resid 52 through 60 Processing helix chain 'F' and resid 66 through 70 Processing helix chain 'F' and resid 73 through 79 Processing helix chain 'F' and resid 81 through 89 Processing helix chain 'F' and resid 89 through 121 Processing helix chain 'F' and resid 152 through 156 Processing helix chain 'F' and resid 259 through 261 No H-bonds generated for 'chain 'F' and resid 259 through 261' Processing sheet with id=AA1, first strand: chain 'A' and resid 40 through 41 removed outlier: 6.315A pdb=" N TYR A 40 " --> pdb=" O HIS A 99 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 44 through 45 removed outlier: 6.457A pdb=" N VAL A 44 " --> pdb=" O SER A 103 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 125 through 135 removed outlier: 6.847A pdb=" N LYS A 205 " --> pdb=" O ILE A 133 " (cutoff:3.500A) removed outlier: 4.994A pdb=" N THR A 135 " --> pdb=" O GLU A 203 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N GLU A 203 " --> pdb=" O THR A 135 " (cutoff:3.500A) removed outlier: 12.529A pdb=" N CYS A 221 " --> pdb=" O LEU A 261 " (cutoff:3.500A) removed outlier: 7.289A pdb=" N LEU A 263 " --> pdb=" O CYS A 221 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N VAL A 223 " --> pdb=" O LEU A 263 " (cutoff:3.500A) removed outlier: 5.521A pdb=" N GLU A 227 " --> pdb=" O ALA A 267 " (cutoff:3.500A) removed outlier: 7.982A pdb=" N TYR A 269 " --> pdb=" O GLU A 227 " (cutoff:3.500A) removed outlier: 7.089A pdb=" N TYR A 243 " --> pdb=" O ASN A 268 " (cutoff:3.500A) removed outlier: 4.740A pdb=" N VAL A 270 " --> pdb=" O THR A 241 " (cutoff:3.500A) removed outlier: 5.736A pdb=" N THR A 241 " --> pdb=" O VAL A 270 " (cutoff:3.500A) removed outlier: 5.245A pdb=" N VAL A 272 " --> pdb=" O ASP A 239 " (cutoff:3.500A) removed outlier: 7.758A pdb=" N ASP A 239 " --> pdb=" O VAL A 272 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 61 through 65 removed outlier: 3.513A pdb=" N ILE B 62 " --> pdb=" O HIS B 136 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 189 through 193 removed outlier: 3.621A pdb=" N LEU B 179 " --> pdb=" O VAL B 192 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N ALA B 225 " --> pdb=" O THR B 177 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 189 through 193 removed outlier: 3.621A pdb=" N LEU B 179 " --> pdb=" O VAL B 192 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 173 through 182 current: chain 'B' and resid 296 through 305 removed outlier: 4.186A pdb=" N LEU B 296 " --> pdb=" O SER B 279 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ASN B 302 " --> pdb=" O THR B 273 " (cutoff:3.500A) removed outlier: 7.098A pdb=" N THR B 273 " --> pdb=" O ASN B 302 " (cutoff:3.500A) removed outlier: 4.975A pdb=" N VAL B 304 " --> pdb=" O THR B 271 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N THR B 271 " --> pdb=" O VAL B 304 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LEU B 162 " --> pdb=" O ILE B 272 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N LYS B 233 " --> pdb=" O VAL B 167 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N VAL B 169 " --> pdb=" O SER B 231 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N SER B 231 " --> pdb=" O VAL B 169 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 40 through 41 removed outlier: 5.908A pdb=" N TYR C 40 " --> pdb=" O HIS C 99 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'C' and resid 44 through 45 removed outlier: 6.354A pdb=" N VAL C 44 " --> pdb=" O SER C 103 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'C' and resid 125 through 135 removed outlier: 6.932A pdb=" N LYS C 205 " --> pdb=" O ILE C 133 " (cutoff:3.500A) removed outlier: 5.006A pdb=" N THR C 135 " --> pdb=" O GLU C 203 " (cutoff:3.500A) removed outlier: 7.162A pdb=" N GLU C 203 " --> pdb=" O THR C 135 " (cutoff:3.500A) removed outlier: 12.495A pdb=" N CYS C 221 " --> pdb=" O LEU C 261 " (cutoff:3.500A) removed outlier: 7.548A pdb=" N LEU C 263 " --> pdb=" O CYS C 221 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N VAL C 223 " --> pdb=" O LEU C 263 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N GLU C 262 " --> pdb=" O ARG C 249 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ARG C 249 " --> pdb=" O GLU C 262 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N TYR C 243 " --> pdb=" O ASN C 268 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N VAL C 270 " --> pdb=" O THR C 241 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N THR C 241 " --> pdb=" O VAL C 270 " (cutoff:3.500A) removed outlier: 5.079A pdb=" N VAL C 272 " --> pdb=" O ASP C 239 " (cutoff:3.500A) removed outlier: 7.623A pdb=" N ASP C 239 " --> pdb=" O VAL C 272 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ILE C 240 " --> pdb=" O GLY C 130 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 144 through 147 removed outlier: 3.739A pdb=" N ALA C 158 " --> pdb=" O ARG C 145 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 61 through 65 removed outlier: 5.510A pdb=" N ILE D 62 " --> pdb=" O ARG D 138 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N TYR D 140 " --> pdb=" O ILE D 62 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N VAL D 64 " --> pdb=" O TYR D 140 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'D' and resid 189 through 193 removed outlier: 3.605A pdb=" N LEU D 179 " --> pdb=" O VAL D 192 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N ALA D 225 " --> pdb=" O THR D 177 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 189 through 193 removed outlier: 3.605A pdb=" N LEU D 179 " --> pdb=" O VAL D 192 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 173 through 182 current: chain 'D' and resid 297 through 305 removed outlier: 3.583A pdb=" N VAL D 275 " --> pdb=" O GLU D 300 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ASN D 302 " --> pdb=" O THR D 273 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N THR D 273 " --> pdb=" O ASN D 302 " (cutoff:3.500A) removed outlier: 4.699A pdb=" N VAL D 304 " --> pdb=" O THR D 271 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N THR D 271 " --> pdb=" O VAL D 304 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N VAL D 270 " --> pdb=" O GLY D 164 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N GLY D 164 " --> pdb=" O VAL D 270 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N LYS D 233 " --> pdb=" O VAL D 167 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N VAL D 169 " --> pdb=" O SER D 231 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N SER D 231 " --> pdb=" O VAL D 169 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 40 through 41 removed outlier: 5.921A pdb=" N TYR E 40 " --> pdb=" O HIS E 99 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'E' and resid 44 through 45 removed outlier: 6.342A pdb=" N VAL E 44 " --> pdb=" O SER E 103 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'E' and resid 125 through 135 removed outlier: 6.804A pdb=" N LYS E 205 " --> pdb=" O ILE E 133 " (cutoff:3.500A) removed outlier: 4.951A pdb=" N THR E 135 " --> pdb=" O GLU E 203 " (cutoff:3.500A) removed outlier: 7.349A pdb=" N GLU E 203 " --> pdb=" O THR E 135 " (cutoff:3.500A) removed outlier: 9.106A pdb=" N CYS E 221 " --> pdb=" O LEU E 263 " (cutoff:3.500A) removed outlier: 9.205A pdb=" N LEU E 265 " --> pdb=" O CYS E 221 " (cutoff:3.500A) removed outlier: 7.272A pdb=" N VAL E 223 " --> pdb=" O LEU E 265 " (cutoff:3.500A) removed outlier: 7.441A pdb=" N ALA E 267 " --> pdb=" O VAL E 223 " (cutoff:3.500A) removed outlier: 7.231A pdb=" N VAL E 225 " --> pdb=" O ALA E 267 " (cutoff:3.500A) removed outlier: 7.949A pdb=" N TYR E 269 " --> pdb=" O VAL E 225 " (cutoff:3.500A) removed outlier: 9.388A pdb=" N GLU E 227 " --> pdb=" O TYR E 269 " (cutoff:3.500A) removed outlier: 11.140A pdb=" N LYS E 271 " --> pdb=" O GLU E 227 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N TYR E 243 " --> pdb=" O ASN E 268 " (cutoff:3.500A) removed outlier: 4.598A pdb=" N VAL E 270 " --> pdb=" O THR E 241 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N THR E 241 " --> pdb=" O VAL E 270 " (cutoff:3.500A) removed outlier: 5.104A pdb=" N VAL E 272 " --> pdb=" O ASP E 239 " (cutoff:3.500A) removed outlier: 7.525A pdb=" N ASP E 239 " --> pdb=" O VAL E 272 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N GLY E 244 " --> pdb=" O LEU E 126 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LEU E 126 " --> pdb=" O GLY E 244 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 141 through 144 removed outlier: 3.689A pdb=" N LEU E 141 " --> pdb=" O ARG E 199 " (cutoff:3.500A) removed outlier: 7.795A pdb=" N SER E 197 " --> pdb=" O PHE E 143 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 160 through 161 removed outlier: 3.781A pdb=" N ASP E 161 " --> pdb=" O ALA E 167 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ALA E 167 " --> pdb=" O ASP E 161 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'F' and resid 61 through 65 removed outlier: 5.510A pdb=" N ILE F 62 " --> pdb=" O ARG F 138 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N TYR F 140 " --> pdb=" O ILE F 62 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N VAL F 64 " --> pdb=" O TYR F 140 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC1 Processing sheet with id=AC2, first strand: chain 'F' and resid 189 through 193 removed outlier: 3.971A pdb=" N VAL F 192 " --> pdb=" O LEU F 179 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N LEU F 179 " --> pdb=" O VAL F 192 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N ALA F 225 " --> pdb=" O THR F 177 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 189 through 193 removed outlier: 3.971A pdb=" N VAL F 192 " --> pdb=" O LEU F 179 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N LEU F 179 " --> pdb=" O VAL F 192 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 173 through 182 current: chain 'F' and resid 297 through 306 removed outlier: 5.350A pdb=" N ILE F 299 " --> pdb=" O LYS F 277 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N LYS F 277 " --> pdb=" O ILE F 299 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N ALA F 301 " --> pdb=" O VAL F 275 " (cutoff:3.500A) removed outlier: 5.989A pdb=" N VAL F 275 " --> pdb=" O ALA F 301 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N SER F 305 " --> pdb=" O THR F 271 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ILE F 160 " --> pdb=" O GLY F 274 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N LYS F 233 " --> pdb=" O VAL F 167 " (cutoff:3.500A) removed outlier: 4.653A pdb=" N VAL F 169 " --> pdb=" O SER F 231 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N SER F 231 " --> pdb=" O VAL F 169 " (cutoff:3.500A) 467 hydrogen bonds defined for protein. 1353 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: 1.44 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 4370 1.34 - 1.46: 2643 1.46 - 1.58: 6299 1.58 - 1.69: 0 1.69 - 1.81: 116 Bond restraints: 13428 Sorted by residual: bond pdb=" C THR E 87 " pdb=" N PRO E 88 " ideal model delta sigma weight residual 1.335 1.353 -0.018 8.70e-03 1.32e+04 4.37e+00 bond pdb=" C THR C 87 " pdb=" N PRO C 88 " ideal model delta sigma weight residual 1.333 1.352 -0.018 1.01e-02 9.80e+03 3.25e+00 bond pdb=" C MET A 94 " pdb=" N LYS A 95 " ideal model delta sigma weight residual 1.327 1.347 -0.020 1.32e-02 5.74e+03 2.23e+00 bond pdb=" CB PRO A 96 " pdb=" CG PRO A 96 " ideal model delta sigma weight residual 1.492 1.565 -0.073 5.00e-02 4.00e+02 2.13e+00 bond pdb=" N LEU D 194 " pdb=" CA LEU D 194 " ideal model delta sigma weight residual 1.462 1.448 0.014 1.05e-02 9.07e+03 1.83e+00 ... (remaining 13423 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.73: 17667 1.73 - 3.47: 432 3.47 - 5.20: 80 5.20 - 6.94: 16 6.94 - 8.67: 4 Bond angle restraints: 18199 Sorted by residual: angle pdb=" C HIS A 39 " pdb=" N TYR A 40 " pdb=" CA TYR A 40 " ideal model delta sigma weight residual 122.28 113.61 8.67 1.77e+00 3.19e-01 2.40e+01 angle pdb=" C CYS E 152 " pdb=" N LYS E 153 " pdb=" CA LYS E 153 " ideal model delta sigma weight residual 121.54 129.83 -8.29 1.91e+00 2.74e-01 1.88e+01 angle pdb=" N VAL A 270 " pdb=" CA VAL A 270 " pdb=" C VAL A 270 " ideal model delta sigma weight residual 106.21 110.54 -4.33 1.07e+00 8.73e-01 1.64e+01 angle pdb=" CA PRO A 96 " pdb=" N PRO A 96 " pdb=" CD PRO A 96 " ideal model delta sigma weight residual 112.00 106.69 5.31 1.40e+00 5.10e-01 1.44e+01 angle pdb=" N CYS C 149 " pdb=" CA CYS C 149 " pdb=" C CYS C 149 " ideal model delta sigma weight residual 108.07 112.37 -4.30 1.38e+00 5.25e-01 9.70e+00 ... (remaining 18194 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.96: 7459 17.96 - 35.92: 618 35.92 - 53.89: 137 53.89 - 71.85: 31 71.85 - 89.81: 13 Dihedral angle restraints: 8258 sinusoidal: 3368 harmonic: 4890 Sorted by residual: dihedral pdb=" CA ARG E 199 " pdb=" C ARG E 199 " pdb=" N ASP E 200 " pdb=" CA ASP E 200 " ideal model delta harmonic sigma weight residual -180.00 -154.64 -25.36 0 5.00e+00 4.00e-02 2.57e+01 dihedral pdb=" CA ARG F 73 " pdb=" C ARG F 73 " pdb=" N GLU F 74 " pdb=" CA GLU F 74 " ideal model delta harmonic sigma weight residual -180.00 -162.30 -17.70 0 5.00e+00 4.00e-02 1.25e+01 dihedral pdb=" CA PRO E 252 " pdb=" C PRO E 252 " pdb=" N PHE E 253 " pdb=" CA PHE E 253 " ideal model delta harmonic sigma weight residual -180.00 -162.45 -17.55 0 5.00e+00 4.00e-02 1.23e+01 ... (remaining 8255 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 1680 0.053 - 0.105: 356 0.105 - 0.158: 43 0.158 - 0.210: 5 0.210 - 0.263: 3 Chirality restraints: 2087 Sorted by residual: chirality pdb=" CB ILE E 107 " pdb=" CA ILE E 107 " pdb=" CG1 ILE E 107 " pdb=" CG2 ILE E 107 " both_signs ideal model delta sigma weight residual False 2.64 2.38 0.26 2.00e-01 2.50e+01 1.72e+00 chirality pdb=" CB ILE B 299 " pdb=" CA ILE B 299 " pdb=" CG1 ILE B 299 " pdb=" CG2 ILE B 299 " both_signs ideal model delta sigma weight residual False 2.64 2.38 0.26 2.00e-01 2.50e+01 1.69e+00 chirality pdb=" CG LEU F 297 " pdb=" CB LEU F 297 " pdb=" CD1 LEU F 297 " pdb=" CD2 LEU F 297 " both_signs ideal model delta sigma weight residual False -2.59 -2.38 -0.21 2.00e-01 2.50e+01 1.11e+00 ... (remaining 2084 not shown) Planarity restraints: 2354 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS A 95 " -0.088 5.00e-02 4.00e+02 1.32e-01 2.77e+01 pdb=" N PRO A 96 " 0.227 5.00e-02 4.00e+02 pdb=" CA PRO A 96 " -0.070 5.00e-02 4.00e+02 pdb=" CD PRO A 96 " -0.069 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS B 173 " -0.067 5.00e-02 4.00e+02 1.01e-01 1.64e+01 pdb=" N PRO B 174 " 0.175 5.00e-02 4.00e+02 pdb=" CA PRO B 174 " -0.054 5.00e-02 4.00e+02 pdb=" CD PRO B 174 " -0.054 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS F 173 " 0.058 5.00e-02 4.00e+02 8.82e-02 1.24e+01 pdb=" N PRO F 174 " -0.152 5.00e-02 4.00e+02 pdb=" CA PRO F 174 " 0.046 5.00e-02 4.00e+02 pdb=" CD PRO F 174 " 0.048 5.00e-02 4.00e+02 ... (remaining 2351 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.73: 604 2.73 - 3.27: 14133 3.27 - 3.81: 21996 3.81 - 4.36: 25681 4.36 - 4.90: 43502 Nonbonded interactions: 105916 Sorted by model distance: nonbonded pdb=" OH TYR A 18 " pdb=" OG1 THR A 48 " model vdw 2.183 3.040 nonbonded pdb=" O VAL D 182 " pdb=" OG1 THR D 216 " model vdw 2.187 3.040 nonbonded pdb=" OG1 THR B 281 " pdb=" OE1 GLU B 282 " model vdw 2.207 3.040 nonbonded pdb=" O VAL B 182 " pdb=" OG1 THR B 216 " model vdw 2.207 3.040 nonbonded pdb=" O PRO E 90 " pdb=" NH1 ARG E 93 " model vdw 2.207 3.120 ... (remaining 105911 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' selection = chain 'C' selection = chain 'E' } ncs_group { reference = chain 'B' selection = (chain 'D' and (resid 15 through 282 or resid 294 through 308)) selection = (chain 'F' and (resid 15 through 282 or resid 294 through 308)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.090 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.210 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 12.790 Find NCS groups from input model: 0.200 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: 0.000 Load rotamer database and sin/cos tables:1.580 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.980 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6449 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 0.073 13428 Z= 0.158 Angle : 0.680 8.673 18199 Z= 0.365 Chirality : 0.044 0.263 2087 Planarity : 0.006 0.132 2354 Dihedral : 14.560 89.810 5086 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 13.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 0.00 % Allowed : 0.20 % Favored : 99.80 % 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: 0.05 (0.20), residues: 1649 helix: 1.29 (0.23), residues: 467 sheet: -0.61 (0.29), residues: 297 loop : -0.36 (0.21), residues: 885 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 145 TYR 0.019 0.002 TYR A 18 PHE 0.025 0.001 PHE A 143 TRP 0.030 0.002 TRP E 250 HIS 0.004 0.001 HIS C 39 Details of bonding type rmsd covalent geometry : bond 0.00322 (13428) covalent geometry : angle 0.67972 (18199) hydrogen bonds : bond 0.20544 ( 459) hydrogen bonds : angle 7.50308 ( 1353) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3298 Ramachandran restraints generated. 1649 Oldfield, 0 Emsley, 1649 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3298 Ramachandran restraints generated. 1649 Oldfield, 0 Emsley, 1649 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 536 residues out of total 1493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 536 time to evaluate : 0.609 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 166 TYR cc_start: 0.5396 (m-10) cc_final: 0.4840 (m-10) REVERT: B 255 GLU cc_start: 0.7342 (tt0) cc_final: 0.7106 (tt0) REVERT: B 277 LYS cc_start: 0.6543 (mttt) cc_final: 0.5845 (mttt) REVERT: D 235 GLN cc_start: 0.7670 (pp30) cc_final: 0.7330 (pp30) REVERT: E 56 ILE cc_start: 0.7785 (pt) cc_final: 0.7452 (pt) REVERT: E 141 LEU cc_start: 0.6345 (tp) cc_final: 0.6102 (tp) REVERT: E 228 ASP cc_start: 0.6550 (m-30) cc_final: 0.6327 (m-30) outliers start: 0 outliers final: 0 residues processed: 536 average time/residue: 0.1233 time to fit residues: 92.5361 Evaluate side-chains 380 residues out of total 1493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 380 time to evaluate : 0.496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 98 optimal weight: 0.7980 chunk 107 optimal weight: 4.9990 chunk 10 optimal weight: 0.6980 chunk 66 optimal weight: 0.4980 chunk 130 optimal weight: 4.9990 chunk 124 optimal weight: 9.9990 chunk 103 optimal weight: 3.9990 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 0.0170 chunk 91 optimal weight: 4.9990 chunk 149 optimal weight: 2.9990 overall best weight: 1.0020 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 21 GLN A 39 HIS A 115 HIS A 176 ASN B 38 GLN B 147 GLN B 150 ASN C 164 GLN ** C 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 255 GLN D 35 GLN D 46 GLN D 81 ASN D 147 GLN E 21 GLN E 39 HIS E 97 ASN F 46 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4534 r_free = 0.4534 target = 0.217629 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4086 r_free = 0.4086 target = 0.175577 restraints weight = 21051.656| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4145 r_free = 0.4145 target = 0.181008 restraints weight = 12021.192| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4182 r_free = 0.4182 target = 0.184522 restraints weight = 8707.861| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4207 r_free = 0.4207 target = 0.186879 restraints weight = 7144.396| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4218 r_free = 0.4218 target = 0.188038 restraints weight = 6295.050| |-----------------------------------------------------------------------------| r_work (final): 0.4192 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6756 moved from start: 0.2597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 13428 Z= 0.163 Angle : 0.683 7.895 18199 Z= 0.352 Chirality : 0.046 0.188 2087 Planarity : 0.006 0.084 2354 Dihedral : 4.839 59.627 1820 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 15.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 3.08 % Allowed : 14.53 % Favored : 82.38 % 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: 0.07 (0.21), residues: 1649 helix: 1.33 (0.24), residues: 480 sheet: -0.62 (0.27), residues: 351 loop : -0.33 (0.22), residues: 818 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 168 TYR 0.013 0.002 TYR C 166 PHE 0.018 0.002 PHE E 143 TRP 0.019 0.002 TRP C 250 HIS 0.011 0.001 HIS A 22 Details of bonding type rmsd covalent geometry : bond 0.00363 (13428) covalent geometry : angle 0.68339 (18199) hydrogen bonds : bond 0.04182 ( 459) hydrogen bonds : angle 5.61580 ( 1353) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3298 Ramachandran restraints generated. 1649 Oldfield, 0 Emsley, 1649 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3298 Ramachandran restraints generated. 1649 Oldfield, 0 Emsley, 1649 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 454 residues out of total 1493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 408 time to evaluate : 0.509 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 GLN cc_start: 0.8510 (OUTLIER) cc_final: 0.7876 (pp30) REVERT: A 31 LEU cc_start: 0.8549 (OUTLIER) cc_final: 0.8166 (mt) REVERT: A 61 ASN cc_start: 0.7964 (m-40) cc_final: 0.7460 (p0) REVERT: A 166 TYR cc_start: 0.6151 (m-10) cc_final: 0.5388 (m-10) REVERT: A 203 GLU cc_start: 0.6902 (tt0) cc_final: 0.6670 (tt0) REVERT: A 239 ASP cc_start: 0.7926 (p0) cc_final: 0.7341 (p0) REVERT: B 107 LYS cc_start: 0.8728 (pttm) cc_final: 0.8434 (pptt) REVERT: B 238 MET cc_start: 0.6382 (tpp) cc_final: 0.5793 (tpp) REVERT: C 61 ASN cc_start: 0.8012 (m110) cc_final: 0.7466 (p0) REVERT: C 114 GLU cc_start: 0.7595 (pt0) cc_final: 0.7370 (pt0) REVERT: D 68 GLU cc_start: 0.8260 (mm-30) cc_final: 0.7855 (mp0) REVERT: D 95 GLN cc_start: 0.7111 (tm-30) cc_final: 0.6839 (tt0) REVERT: D 194 LEU cc_start: 0.8107 (tp) cc_final: 0.7877 (tp) REVERT: D 204 LYS cc_start: 0.8322 (ptmm) cc_final: 0.8053 (mtpt) REVERT: E 141 LEU cc_start: 0.8322 (tp) cc_final: 0.8021 (tp) REVERT: E 199 ARG cc_start: 0.8534 (pmt170) cc_final: 0.7719 (ptt-90) REVERT: E 228 ASP cc_start: 0.8443 (m-30) cc_final: 0.8092 (m-30) REVERT: F 47 ARG cc_start: 0.7974 (OUTLIER) cc_final: 0.7328 (mtp-110) REVERT: F 297 LEU cc_start: 0.6826 (mm) cc_final: 0.6599 (mm) outliers start: 46 outliers final: 30 residues processed: 428 average time/residue: 0.1078 time to fit residues: 65.3611 Evaluate side-chains 398 residues out of total 1493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 365 time to evaluate : 0.519 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 VAL Chi-restraints excluded: chain A residue 21 GLN Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 250 TRP Chi-restraints excluded: chain B residue 76 THR Chi-restraints excluded: chain B residue 162 LEU Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 169 VAL Chi-restraints excluded: chain B residue 269 VAL Chi-restraints excluded: chain B residue 303 SER Chi-restraints excluded: chain C residue 43 LEU Chi-restraints excluded: chain C residue 150 ASN Chi-restraints excluded: chain C residue 224 VAL Chi-restraints excluded: chain C residue 250 TRP Chi-restraints excluded: chain D residue 82 ILE Chi-restraints excluded: chain D residue 112 HIS Chi-restraints excluded: chain D residue 165 THR Chi-restraints excluded: chain D residue 182 VAL Chi-restraints excluded: chain D residue 252 ILE Chi-restraints excluded: chain D residue 269 VAL Chi-restraints excluded: chain D residue 299 ILE Chi-restraints excluded: chain D residue 303 SER Chi-restraints excluded: chain E residue 83 LEU Chi-restraints excluded: chain E residue 250 TRP Chi-restraints excluded: chain F residue 47 ARG Chi-restraints excluded: chain F residue 101 ILE Chi-restraints excluded: chain F residue 108 ASP Chi-restraints excluded: chain F residue 216 THR Chi-restraints excluded: chain F residue 234 VAL Chi-restraints excluded: chain F residue 252 ILE Chi-restraints excluded: chain F residue 260 LEU Chi-restraints excluded: chain F residue 269 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 146 optimal weight: 1.9990 chunk 122 optimal weight: 0.0970 chunk 80 optimal weight: 0.7980 chunk 36 optimal weight: 0.7980 chunk 95 optimal weight: 0.9990 chunk 26 optimal weight: 1.9990 chunk 157 optimal weight: 0.9980 chunk 131 optimal weight: 9.9990 chunk 54 optimal weight: 1.9990 chunk 53 optimal weight: 0.7980 chunk 141 optimal weight: 0.4980 overall best weight: 0.5978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 115 HIS ** C 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 81 ASN E 21 GLN ** E 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 61 ASN E 154 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4540 r_free = 0.4540 target = 0.218046 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4101 r_free = 0.4101 target = 0.175523 restraints weight = 20788.221| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.4149 r_free = 0.4149 target = 0.180446 restraints weight = 12346.747| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.4180 r_free = 0.4180 target = 0.183712 restraints weight = 9165.557| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.4201 r_free = 0.4201 target = 0.185748 restraints weight = 7630.512| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.4214 r_free = 0.4214 target = 0.187089 restraints weight = 6819.806| |-----------------------------------------------------------------------------| r_work (final): 0.4179 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6782 moved from start: 0.3288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 13428 Z= 0.134 Angle : 0.648 7.905 18199 Z= 0.330 Chirality : 0.045 0.256 2087 Planarity : 0.005 0.073 2354 Dihedral : 4.727 64.916 1820 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 14.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 3.62 % Allowed : 17.75 % Favored : 78.63 % 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: 0.10 (0.21), residues: 1649 helix: 1.25 (0.24), residues: 473 sheet: -0.44 (0.27), residues: 350 loop : -0.30 (0.22), residues: 826 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 76 TYR 0.017 0.002 TYR A 40 PHE 0.031 0.002 PHE D 40 TRP 0.015 0.002 TRP A 250 HIS 0.011 0.001 HIS E 39 Details of bonding type rmsd covalent geometry : bond 0.00303 (13428) covalent geometry : angle 0.64846 (18199) hydrogen bonds : bond 0.03711 ( 459) hydrogen bonds : angle 5.31954 ( 1353) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3298 Ramachandran restraints generated. 1649 Oldfield, 0 Emsley, 1649 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3298 Ramachandran restraints generated. 1649 Oldfield, 0 Emsley, 1649 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 451 residues out of total 1493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 397 time to evaluate : 0.545 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 GLN cc_start: 0.8966 (pp30) cc_final: 0.7765 (pp30) REVERT: A 31 LEU cc_start: 0.8397 (OUTLIER) cc_final: 0.8146 (mt) REVERT: A 166 TYR cc_start: 0.6108 (m-10) cc_final: 0.5330 (m-10) REVERT: A 203 GLU cc_start: 0.7056 (tt0) cc_final: 0.6689 (tt0) REVERT: A 239 ASP cc_start: 0.7891 (p0) cc_final: 0.7558 (p0) REVERT: A 249 ARG cc_start: 0.8396 (mtp180) cc_final: 0.8069 (mtp180) REVERT: B 68 GLU cc_start: 0.7739 (mp0) cc_final: 0.7476 (mp0) REVERT: B 178 LYS cc_start: 0.8348 (mmmm) cc_final: 0.7818 (tptm) REVERT: B 238 MET cc_start: 0.6208 (tpp) cc_final: 0.5788 (tpp) REVERT: D 178 LYS cc_start: 0.8500 (mmmt) cc_final: 0.7926 (tptm) REVERT: D 204 LYS cc_start: 0.8310 (ptmm) cc_final: 0.8028 (mtpt) REVERT: D 218 ASP cc_start: 0.7116 (t70) cc_final: 0.6602 (p0) REVERT: E 52 THR cc_start: 0.8885 (p) cc_final: 0.8627 (t) REVERT: E 75 LEU cc_start: 0.7914 (mt) cc_final: 0.7466 (mt) REVERT: E 141 LEU cc_start: 0.8342 (tp) cc_final: 0.8033 (tp) REVERT: F 47 ARG cc_start: 0.7672 (OUTLIER) cc_final: 0.6775 (mtp-110) REVERT: F 68 GLU cc_start: 0.7611 (mt-10) cc_final: 0.6540 (mt-10) REVERT: F 303 SER cc_start: 0.8853 (t) cc_final: 0.8495 (t) outliers start: 54 outliers final: 36 residues processed: 419 average time/residue: 0.1025 time to fit residues: 61.8005 Evaluate side-chains 404 residues out of total 1493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 366 time to evaluate : 0.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 VAL Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 56 ILE Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 250 TRP Chi-restraints excluded: chain B residue 76 THR Chi-restraints excluded: chain B residue 162 LEU Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 169 VAL Chi-restraints excluded: chain B residue 181 PHE Chi-restraints excluded: chain B residue 269 VAL Chi-restraints excluded: chain B residue 303 SER Chi-restraints excluded: chain C residue 43 LEU Chi-restraints excluded: chain C residue 150 ASN Chi-restraints excluded: chain C residue 224 VAL Chi-restraints excluded: chain C residue 250 TRP Chi-restraints excluded: chain D residue 82 ILE Chi-restraints excluded: chain D residue 101 ILE Chi-restraints excluded: chain D residue 108 ASP Chi-restraints excluded: chain D residue 112 HIS Chi-restraints excluded: chain D residue 165 THR Chi-restraints excluded: chain D residue 182 VAL Chi-restraints excluded: chain D residue 252 ILE Chi-restraints excluded: chain D residue 269 VAL Chi-restraints excluded: chain D residue 299 ILE Chi-restraints excluded: chain D residue 303 SER Chi-restraints excluded: chain E residue 83 LEU Chi-restraints excluded: chain E residue 201 TYR Chi-restraints excluded: chain E residue 250 TRP Chi-restraints excluded: chain F residue 47 ARG Chi-restraints excluded: chain F residue 101 ILE Chi-restraints excluded: chain F residue 109 LEU Chi-restraints excluded: chain F residue 148 LEU Chi-restraints excluded: chain F residue 196 ASP Chi-restraints excluded: chain F residue 252 ILE Chi-restraints excluded: chain F residue 269 VAL Chi-restraints excluded: chain F residue 275 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 135 optimal weight: 2.9990 chunk 69 optimal weight: 7.9990 chunk 99 optimal weight: 0.0470 chunk 121 optimal weight: 0.7980 chunk 4 optimal weight: 2.9990 chunk 98 optimal weight: 0.9980 chunk 113 optimal weight: 9.9990 chunk 129 optimal weight: 1.9990 chunk 134 optimal weight: 3.9990 chunk 54 optimal weight: 0.8980 chunk 5 optimal weight: 2.9990 overall best weight: 0.9480 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 21 GLN ** A 248 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 21 GLN ** E 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 38 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4552 r_free = 0.4552 target = 0.219215 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4066 r_free = 0.4066 target = 0.173148 restraints weight = 21085.433| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.4122 r_free = 0.4122 target = 0.178431 restraints weight = 12483.601| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4159 r_free = 0.4159 target = 0.182020 restraints weight = 9277.285| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.4182 r_free = 0.4182 target = 0.184340 restraints weight = 7747.088| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4191 r_free = 0.4191 target = 0.185320 restraints weight = 6937.036| |-----------------------------------------------------------------------------| r_work (final): 0.4188 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6855 moved from start: 0.3696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 13428 Z= 0.139 Angle : 0.625 6.515 18199 Z= 0.319 Chirality : 0.044 0.162 2087 Planarity : 0.005 0.069 2354 Dihedral : 4.661 64.829 1820 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 13.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 4.15 % Allowed : 20.09 % Favored : 75.75 % 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: 0.07 (0.21), residues: 1649 helix: 1.21 (0.24), residues: 472 sheet: -0.55 (0.25), residues: 393 loop : -0.22 (0.23), residues: 784 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG D 168 TYR 0.041 0.002 TYR E 59 PHE 0.039 0.002 PHE C 50 TRP 0.019 0.002 TRP E 250 HIS 0.013 0.001 HIS A 22 Details of bonding type rmsd covalent geometry : bond 0.00317 (13428) covalent geometry : angle 0.62521 (18199) hydrogen bonds : bond 0.03670 ( 459) hydrogen bonds : angle 5.17324 ( 1353) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3298 Ramachandran restraints generated. 1649 Oldfield, 0 Emsley, 1649 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3298 Ramachandran restraints generated. 1649 Oldfield, 0 Emsley, 1649 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 447 residues out of total 1493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 385 time to evaluate : 0.516 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 GLN cc_start: 0.9014 (OUTLIER) cc_final: 0.8545 (pp30) REVERT: A 166 TYR cc_start: 0.5977 (m-10) cc_final: 0.5153 (m-10) REVERT: A 203 GLU cc_start: 0.7067 (tt0) cc_final: 0.6782 (tt0) REVERT: B 40 PHE cc_start: 0.7413 (m-80) cc_final: 0.6832 (m-80) REVERT: B 68 GLU cc_start: 0.7953 (mp0) cc_final: 0.7639 (mp0) REVERT: B 99 LEU cc_start: 0.8262 (tt) cc_final: 0.7735 (mt) REVERT: B 238 MET cc_start: 0.6264 (tpp) cc_final: 0.5544 (tpp) REVERT: D 178 LYS cc_start: 0.8362 (mmmt) cc_final: 0.7773 (tptm) REVERT: D 194 LEU cc_start: 0.8265 (tp) cc_final: 0.8056 (tp) REVERT: E 52 THR cc_start: 0.8939 (p) cc_final: 0.8716 (t) REVERT: E 141 LEU cc_start: 0.8424 (tp) cc_final: 0.8077 (tp) REVERT: F 47 ARG cc_start: 0.7860 (mmm160) cc_final: 0.7217 (mtp-110) REVERT: F 68 GLU cc_start: 0.7703 (mt-10) cc_final: 0.6900 (mt-10) REVERT: F 277 LYS cc_start: 0.8027 (mptt) cc_final: 0.6642 (mptt) REVERT: F 300 GLU cc_start: 0.6015 (mt-10) cc_final: 0.5053 (mt-10) REVERT: F 303 SER cc_start: 0.8876 (t) cc_final: 0.8559 (t) outliers start: 62 outliers final: 45 residues processed: 413 average time/residue: 0.1160 time to fit residues: 68.0662 Evaluate side-chains 395 residues out of total 1493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 349 time to evaluate : 0.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 VAL Chi-restraints excluded: chain A residue 21 GLN Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 56 ILE Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 250 TRP Chi-restraints excluded: chain B residue 76 THR Chi-restraints excluded: chain B residue 160 ILE Chi-restraints excluded: chain B residue 162 LEU Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 169 VAL Chi-restraints excluded: chain B residue 175 LEU Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 237 LEU Chi-restraints excluded: chain B residue 269 VAL Chi-restraints excluded: chain B residue 296 LEU Chi-restraints excluded: chain B residue 303 SER Chi-restraints excluded: chain C residue 19 LEU Chi-restraints excluded: chain C residue 56 ILE Chi-restraints excluded: chain C residue 61 ASN Chi-restraints excluded: chain C residue 207 GLN Chi-restraints excluded: chain C residue 224 VAL Chi-restraints excluded: chain C residue 250 TRP Chi-restraints excluded: chain D residue 82 ILE Chi-restraints excluded: chain D residue 101 ILE Chi-restraints excluded: chain D residue 108 ASP Chi-restraints excluded: chain D residue 112 HIS Chi-restraints excluded: chain D residue 165 THR Chi-restraints excluded: chain D residue 169 VAL Chi-restraints excluded: chain D residue 182 VAL Chi-restraints excluded: chain D residue 252 ILE Chi-restraints excluded: chain D residue 269 VAL Chi-restraints excluded: chain D residue 297 LEU Chi-restraints excluded: chain D residue 303 SER Chi-restraints excluded: chain E residue 83 LEU Chi-restraints excluded: chain E residue 201 TYR Chi-restraints excluded: chain E residue 250 TRP Chi-restraints excluded: chain F residue 56 ILE Chi-restraints excluded: chain F residue 109 LEU Chi-restraints excluded: chain F residue 134 LEU Chi-restraints excluded: chain F residue 148 LEU Chi-restraints excluded: chain F residue 194 LEU Chi-restraints excluded: chain F residue 234 VAL Chi-restraints excluded: chain F residue 252 ILE Chi-restraints excluded: chain F residue 260 LEU Chi-restraints excluded: chain F residue 269 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 77 optimal weight: 0.6980 chunk 29 optimal weight: 0.9980 chunk 156 optimal weight: 7.9990 chunk 163 optimal weight: 2.9990 chunk 30 optimal weight: 8.9990 chunk 86 optimal weight: 0.8980 chunk 108 optimal weight: 5.9990 chunk 135 optimal weight: 0.7980 chunk 70 optimal weight: 30.0000 chunk 119 optimal weight: 2.9990 chunk 57 optimal weight: 1.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 22 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 248 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 21 GLN ** E 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4545 r_free = 0.4545 target = 0.218754 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.4055 r_free = 0.4055 target = 0.171778 restraints weight = 21434.743| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.4109 r_free = 0.4109 target = 0.177166 restraints weight = 12663.662| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.4145 r_free = 0.4145 target = 0.180651 restraints weight = 9440.607| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.4167 r_free = 0.4167 target = 0.182837 restraints weight = 7964.373| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.4181 r_free = 0.4181 target = 0.184207 restraints weight = 7161.929| |-----------------------------------------------------------------------------| r_work (final): 0.4150 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6897 moved from start: 0.4045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 13428 Z= 0.148 Angle : 0.640 8.053 18199 Z= 0.327 Chirality : 0.044 0.180 2087 Planarity : 0.005 0.065 2354 Dihedral : 4.659 64.211 1820 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 14.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 4.89 % Allowed : 21.90 % Favored : 73.21 % 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: 0.11 (0.21), residues: 1649 helix: 1.19 (0.24), residues: 472 sheet: -0.48 (0.26), residues: 374 loop : -0.21 (0.23), residues: 803 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 199 TYR 0.033 0.002 TYR E 59 PHE 0.042 0.002 PHE D 40 TRP 0.025 0.002 TRP F 19 HIS 0.010 0.001 HIS E 23 Details of bonding type rmsd covalent geometry : bond 0.00339 (13428) covalent geometry : angle 0.64045 (18199) hydrogen bonds : bond 0.03509 ( 459) hydrogen bonds : angle 5.14750 ( 1353) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3298 Ramachandran restraints generated. 1649 Oldfield, 0 Emsley, 1649 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3298 Ramachandran restraints generated. 1649 Oldfield, 0 Emsley, 1649 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 442 residues out of total 1493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 369 time to evaluate : 0.475 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 TYR cc_start: 0.4170 (m-80) cc_final: 0.3859 (m-80) REVERT: A 166 TYR cc_start: 0.5858 (m-10) cc_final: 0.5090 (m-10) REVERT: A 203 GLU cc_start: 0.7103 (tt0) cc_final: 0.6868 (tt0) REVERT: B 40 PHE cc_start: 0.7380 (m-80) cc_final: 0.6865 (m-80) REVERT: B 68 GLU cc_start: 0.7923 (mp0) cc_final: 0.7674 (mp0) REVERT: B 99 LEU cc_start: 0.8270 (tt) cc_final: 0.7741 (mt) REVERT: B 178 LYS cc_start: 0.8405 (mmmm) cc_final: 0.7875 (tptp) REVERT: B 238 MET cc_start: 0.6212 (tpp) cc_final: 0.5340 (tpp) REVERT: B 259 ASP cc_start: 0.7743 (t0) cc_final: 0.7476 (t0) REVERT: C 59 TYR cc_start: 0.7636 (m-80) cc_final: 0.7436 (m-80) REVERT: D 259 ASP cc_start: 0.8167 (t0) cc_final: 0.7905 (t0) REVERT: E 52 THR cc_start: 0.8949 (p) cc_final: 0.8717 (t) REVERT: E 61 ASN cc_start: 0.7577 (m110) cc_final: 0.7298 (p0) REVERT: E 141 LEU cc_start: 0.8418 (tp) cc_final: 0.8103 (tp) REVERT: F 62 ILE cc_start: 0.7932 (OUTLIER) cc_final: 0.7528 (pt) REVERT: F 181 PHE cc_start: 0.7089 (t80) cc_final: 0.6861 (t80) REVERT: F 238 MET cc_start: 0.6158 (tpp) cc_final: 0.5862 (tpt) REVERT: F 277 LYS cc_start: 0.8241 (mptt) cc_final: 0.8004 (mptt) outliers start: 73 outliers final: 55 residues processed: 408 average time/residue: 0.1032 time to fit residues: 60.5313 Evaluate side-chains 396 residues out of total 1493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 340 time to evaluate : 0.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 VAL Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 206 ILE Chi-restraints excluded: chain A residue 250 TRP Chi-restraints excluded: chain B residue 62 ILE Chi-restraints excluded: chain B residue 76 THR Chi-restraints excluded: chain B residue 79 ILE Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 160 ILE Chi-restraints excluded: chain B residue 162 LEU Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 169 VAL Chi-restraints excluded: chain B residue 181 PHE Chi-restraints excluded: chain B residue 260 LEU Chi-restraints excluded: chain B residue 269 VAL Chi-restraints excluded: chain B residue 296 LEU Chi-restraints excluded: chain B residue 299 ILE Chi-restraints excluded: chain B residue 303 SER Chi-restraints excluded: chain C residue 19 LEU Chi-restraints excluded: chain C residue 43 LEU Chi-restraints excluded: chain C residue 56 ILE Chi-restraints excluded: chain C residue 61 ASN Chi-restraints excluded: chain C residue 140 VAL Chi-restraints excluded: chain C residue 150 ASN Chi-restraints excluded: chain C residue 207 GLN Chi-restraints excluded: chain C residue 224 VAL Chi-restraints excluded: chain C residue 250 TRP Chi-restraints excluded: chain D residue 82 ILE Chi-restraints excluded: chain D residue 93 ILE Chi-restraints excluded: chain D residue 108 ASP Chi-restraints excluded: chain D residue 112 HIS Chi-restraints excluded: chain D residue 165 THR Chi-restraints excluded: chain D residue 169 VAL Chi-restraints excluded: chain D residue 200 THR Chi-restraints excluded: chain D residue 234 VAL Chi-restraints excluded: chain D residue 252 ILE Chi-restraints excluded: chain D residue 265 VAL Chi-restraints excluded: chain D residue 269 VAL Chi-restraints excluded: chain D residue 299 ILE Chi-restraints excluded: chain D residue 303 SER Chi-restraints excluded: chain E residue 56 ILE Chi-restraints excluded: chain E residue 83 LEU Chi-restraints excluded: chain E residue 140 VAL Chi-restraints excluded: chain E residue 201 TYR Chi-restraints excluded: chain E residue 206 ILE Chi-restraints excluded: chain E residue 250 TRP Chi-restraints excluded: chain E residue 261 LEU Chi-restraints excluded: chain F residue 62 ILE Chi-restraints excluded: chain F residue 109 LEU Chi-restraints excluded: chain F residue 148 LEU Chi-restraints excluded: chain F residue 199 TYR Chi-restraints excluded: chain F residue 252 ILE Chi-restraints excluded: chain F residue 260 LEU Chi-restraints excluded: chain F residue 269 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 103 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 chunk 138 optimal weight: 3.9990 chunk 46 optimal weight: 0.0170 chunk 8 optimal weight: 8.9990 chunk 148 optimal weight: 0.7980 chunk 116 optimal weight: 0.8980 chunk 80 optimal weight: 0.8980 chunk 30 optimal weight: 0.7980 chunk 66 optimal weight: 0.9980 chunk 4 optimal weight: 4.9990 overall best weight: 0.6818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 248 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 22 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 115 HIS F 38 GLN F 95 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4533 r_free = 0.4533 target = 0.217980 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4057 r_free = 0.4057 target = 0.173083 restraints weight = 21232.548| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.4112 r_free = 0.4112 target = 0.178030 restraints weight = 12553.118| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4147 r_free = 0.4147 target = 0.181429 restraints weight = 9360.667| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.4171 r_free = 0.4171 target = 0.183725 restraints weight = 7837.520| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.4185 r_free = 0.4185 target = 0.185139 restraints weight = 6982.115| |-----------------------------------------------------------------------------| r_work (final): 0.4155 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6843 moved from start: 0.4293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 13428 Z= 0.130 Angle : 0.642 9.119 18199 Z= 0.326 Chirality : 0.044 0.170 2087 Planarity : 0.005 0.067 2354 Dihedral : 4.538 63.193 1820 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 13.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 4.29 % Allowed : 22.37 % Favored : 73.34 % 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: 0.09 (0.21), residues: 1649 helix: 1.12 (0.24), residues: 478 sheet: -0.45 (0.26), residues: 381 loop : -0.22 (0.23), residues: 790 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG B 219 TYR 0.028 0.001 TYR E 59 PHE 0.039 0.002 PHE D 40 TRP 0.046 0.003 TRP F 19 HIS 0.013 0.001 HIS A 22 Details of bonding type rmsd covalent geometry : bond 0.00295 (13428) covalent geometry : angle 0.64171 (18199) hydrogen bonds : bond 0.03377 ( 459) hydrogen bonds : angle 4.99716 ( 1353) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3298 Ramachandran restraints generated. 1649 Oldfield, 0 Emsley, 1649 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3298 Ramachandran restraints generated. 1649 Oldfield, 0 Emsley, 1649 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 434 residues out of total 1493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 370 time to evaluate : 0.490 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 166 TYR cc_start: 0.5842 (m-10) cc_final: 0.5047 (m-10) REVERT: A 203 GLU cc_start: 0.7169 (tt0) cc_final: 0.6888 (tt0) REVERT: A 239 ASP cc_start: 0.8005 (p0) cc_final: 0.7768 (p0) REVERT: B 40 PHE cc_start: 0.7251 (m-80) cc_final: 0.6784 (m-80) REVERT: B 99 LEU cc_start: 0.8253 (tt) cc_final: 0.7706 (mt) REVERT: B 178 LYS cc_start: 0.8299 (mmmm) cc_final: 0.7984 (ttmt) REVERT: B 196 ASP cc_start: 0.7677 (m-30) cc_final: 0.7326 (t70) REVERT: B 238 MET cc_start: 0.6192 (tpp) cc_final: 0.5263 (tpp) REVERT: D 86 LEU cc_start: 0.7690 (OUTLIER) cc_final: 0.7267 (tp) REVERT: D 140 TYR cc_start: 0.6663 (p90) cc_final: 0.6115 (p90) REVERT: D 238 MET cc_start: 0.4539 (tpt) cc_final: 0.4239 (tpt) REVERT: E 61 ASN cc_start: 0.7535 (m110) cc_final: 0.7282 (p0) REVERT: E 141 LEU cc_start: 0.8378 (tp) cc_final: 0.8039 (tp) REVERT: E 199 ARG cc_start: 0.8316 (pmt170) cc_final: 0.7815 (ptt-90) REVERT: E 268 ASN cc_start: 0.8510 (t0) cc_final: 0.8183 (t0) REVERT: F 62 ILE cc_start: 0.7905 (OUTLIER) cc_final: 0.7479 (pt) REVERT: F 181 PHE cc_start: 0.7026 (t80) cc_final: 0.6793 (t80) REVERT: F 238 MET cc_start: 0.5911 (tpp) cc_final: 0.5619 (tpt) outliers start: 64 outliers final: 54 residues processed: 401 average time/residue: 0.1087 time to fit residues: 62.6118 Evaluate side-chains 392 residues out of total 1493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 336 time to evaluate : 0.492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 VAL Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 250 TRP Chi-restraints excluded: chain B residue 62 ILE Chi-restraints excluded: chain B residue 76 THR Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 160 ILE Chi-restraints excluded: chain B residue 162 LEU Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 169 VAL Chi-restraints excluded: chain B residue 181 PHE Chi-restraints excluded: chain B residue 260 LEU Chi-restraints excluded: chain B residue 269 VAL Chi-restraints excluded: chain B residue 296 LEU Chi-restraints excluded: chain B residue 299 ILE Chi-restraints excluded: chain B residue 303 SER Chi-restraints excluded: chain C residue 19 LEU Chi-restraints excluded: chain C residue 43 LEU Chi-restraints excluded: chain C residue 56 ILE Chi-restraints excluded: chain C residue 140 VAL Chi-restraints excluded: chain C residue 150 ASN Chi-restraints excluded: chain C residue 207 GLN Chi-restraints excluded: chain C residue 224 VAL Chi-restraints excluded: chain C residue 250 TRP Chi-restraints excluded: chain D residue 82 ILE Chi-restraints excluded: chain D residue 86 LEU Chi-restraints excluded: chain D residue 108 ASP Chi-restraints excluded: chain D residue 112 HIS Chi-restraints excluded: chain D residue 139 LEU Chi-restraints excluded: chain D residue 165 THR Chi-restraints excluded: chain D residue 169 VAL Chi-restraints excluded: chain D residue 196 ASP Chi-restraints excluded: chain D residue 200 THR Chi-restraints excluded: chain D residue 234 VAL Chi-restraints excluded: chain D residue 252 ILE Chi-restraints excluded: chain D residue 269 VAL Chi-restraints excluded: chain D residue 299 ILE Chi-restraints excluded: chain E residue 83 LEU Chi-restraints excluded: chain E residue 115 HIS Chi-restraints excluded: chain E residue 201 TYR Chi-restraints excluded: chain E residue 206 ILE Chi-restraints excluded: chain E residue 261 LEU Chi-restraints excluded: chain F residue 56 ILE Chi-restraints excluded: chain F residue 62 ILE Chi-restraints excluded: chain F residue 109 LEU Chi-restraints excluded: chain F residue 134 LEU Chi-restraints excluded: chain F residue 148 LEU Chi-restraints excluded: chain F residue 194 LEU Chi-restraints excluded: chain F residue 199 TYR Chi-restraints excluded: chain F residue 234 VAL Chi-restraints excluded: chain F residue 252 ILE Chi-restraints excluded: chain F residue 260 LEU Chi-restraints excluded: chain F residue 269 VAL Chi-restraints excluded: chain F residue 299 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 59 optimal weight: 2.9990 chunk 46 optimal weight: 7.9990 chunk 68 optimal weight: 0.9990 chunk 83 optimal weight: 0.5980 chunk 55 optimal weight: 10.0000 chunk 108 optimal weight: 0.9980 chunk 71 optimal weight: 6.9990 chunk 17 optimal weight: 20.0000 chunk 39 optimal weight: 3.9990 chunk 119 optimal weight: 0.9980 chunk 18 optimal weight: 3.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 248 GLN C 66 GLN C 115 HIS ** D 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 22 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 39 HIS E 164 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4501 r_free = 0.4501 target = 0.215336 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.170209 restraints weight = 21324.217| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4070 r_free = 0.4070 target = 0.175098 restraints weight = 12690.772| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4105 r_free = 0.4105 target = 0.178400 restraints weight = 9460.114| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4122 r_free = 0.4122 target = 0.180126 restraints weight = 7924.078| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.4139 r_free = 0.4139 target = 0.181563 restraints weight = 7204.656| |-----------------------------------------------------------------------------| r_work (final): 0.4135 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6917 moved from start: 0.4530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 13428 Z= 0.160 Angle : 0.674 9.528 18199 Z= 0.342 Chirality : 0.045 0.168 2087 Planarity : 0.005 0.059 2354 Dihedral : 4.649 62.241 1820 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 14.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 5.16 % Allowed : 22.91 % Favored : 71.94 % 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: 0.02 (0.21), residues: 1649 helix: 1.21 (0.24), residues: 472 sheet: -0.65 (0.26), residues: 379 loop : -0.27 (0.23), residues: 798 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 219 TYR 0.027 0.002 TYR E 59 PHE 0.035 0.002 PHE D 40 TRP 0.035 0.003 TRP F 19 HIS 0.011 0.001 HIS A 22 Details of bonding type rmsd covalent geometry : bond 0.00366 (13428) covalent geometry : angle 0.67441 (18199) hydrogen bonds : bond 0.03541 ( 459) hydrogen bonds : angle 5.11161 ( 1353) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3298 Ramachandran restraints generated. 1649 Oldfield, 0 Emsley, 1649 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3298 Ramachandran restraints generated. 1649 Oldfield, 0 Emsley, 1649 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 431 residues out of total 1493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 354 time to evaluate : 0.516 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 40 PHE cc_start: 0.7347 (m-80) cc_final: 0.6853 (m-80) REVERT: B 68 GLU cc_start: 0.7947 (mp0) cc_final: 0.7602 (mp0) REVERT: B 99 LEU cc_start: 0.8241 (tt) cc_final: 0.7647 (mt) REVERT: B 178 LYS cc_start: 0.8291 (mmmm) cc_final: 0.7985 (ttmt) REVERT: B 196 ASP cc_start: 0.7791 (m-30) cc_final: 0.7480 (t0) REVERT: B 238 MET cc_start: 0.6098 (tpp) cc_final: 0.5109 (tpp) REVERT: D 140 TYR cc_start: 0.6715 (p90) cc_final: 0.6151 (p90) REVERT: D 235 GLN cc_start: 0.8444 (pp30) cc_final: 0.7653 (pp30) REVERT: D 238 MET cc_start: 0.4594 (tpt) cc_final: 0.4388 (tpt) REVERT: E 50 PHE cc_start: 0.7993 (m-80) cc_final: 0.7721 (m-80) REVERT: E 52 THR cc_start: 0.8975 (p) cc_final: 0.8773 (t) REVERT: E 61 ASN cc_start: 0.7515 (m110) cc_final: 0.7182 (p0) REVERT: E 141 LEU cc_start: 0.8301 (tp) cc_final: 0.8022 (tp) REVERT: E 261 LEU cc_start: 0.7636 (OUTLIER) cc_final: 0.7269 (mt) REVERT: F 62 ILE cc_start: 0.7998 (OUTLIER) cc_final: 0.7568 (pt) REVERT: F 181 PHE cc_start: 0.7165 (t80) cc_final: 0.6862 (t80) REVERT: F 238 MET cc_start: 0.5941 (tpp) cc_final: 0.5681 (tpt) outliers start: 77 outliers final: 64 residues processed: 393 average time/residue: 0.1056 time to fit residues: 60.7735 Evaluate side-chains 397 residues out of total 1493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 331 time to evaluate : 0.491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 VAL Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 206 ILE Chi-restraints excluded: chain A residue 250 TRP Chi-restraints excluded: chain B residue 62 ILE Chi-restraints excluded: chain B residue 76 THR Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 160 ILE Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 169 VAL Chi-restraints excluded: chain B residue 181 PHE Chi-restraints excluded: chain B residue 260 LEU Chi-restraints excluded: chain B residue 269 VAL Chi-restraints excluded: chain B residue 299 ILE Chi-restraints excluded: chain B residue 303 SER Chi-restraints excluded: chain C residue 19 LEU Chi-restraints excluded: chain C residue 102 ILE Chi-restraints excluded: chain C residue 140 VAL Chi-restraints excluded: chain C residue 150 ASN Chi-restraints excluded: chain C residue 207 GLN Chi-restraints excluded: chain C residue 224 VAL Chi-restraints excluded: chain C residue 250 TRP Chi-restraints excluded: chain D residue 82 ILE Chi-restraints excluded: chain D residue 86 LEU Chi-restraints excluded: chain D residue 108 ASP Chi-restraints excluded: chain D residue 112 HIS Chi-restraints excluded: chain D residue 165 THR Chi-restraints excluded: chain D residue 169 VAL Chi-restraints excluded: chain D residue 194 LEU Chi-restraints excluded: chain D residue 196 ASP Chi-restraints excluded: chain D residue 200 THR Chi-restraints excluded: chain D residue 234 VAL Chi-restraints excluded: chain D residue 237 LEU Chi-restraints excluded: chain D residue 252 ILE Chi-restraints excluded: chain D residue 260 LEU Chi-restraints excluded: chain D residue 265 VAL Chi-restraints excluded: chain D residue 269 VAL Chi-restraints excluded: chain D residue 299 ILE Chi-restraints excluded: chain D residue 303 SER Chi-restraints excluded: chain E residue 56 ILE Chi-restraints excluded: chain E residue 83 LEU Chi-restraints excluded: chain E residue 132 VAL Chi-restraints excluded: chain E residue 140 VAL Chi-restraints excluded: chain E residue 201 TYR Chi-restraints excluded: chain E residue 206 ILE Chi-restraints excluded: chain E residue 223 VAL Chi-restraints excluded: chain E residue 261 LEU Chi-restraints excluded: chain F residue 56 ILE Chi-restraints excluded: chain F residue 62 ILE Chi-restraints excluded: chain F residue 79 ILE Chi-restraints excluded: chain F residue 109 LEU Chi-restraints excluded: chain F residue 134 LEU Chi-restraints excluded: chain F residue 148 LEU Chi-restraints excluded: chain F residue 165 THR Chi-restraints excluded: chain F residue 175 LEU Chi-restraints excluded: chain F residue 194 LEU Chi-restraints excluded: chain F residue 199 TYR Chi-restraints excluded: chain F residue 219 ARG Chi-restraints excluded: chain F residue 229 TRP Chi-restraints excluded: chain F residue 234 VAL Chi-restraints excluded: chain F residue 252 ILE Chi-restraints excluded: chain F residue 260 LEU Chi-restraints excluded: chain F residue 269 VAL Chi-restraints excluded: chain F residue 275 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 125 optimal weight: 0.9980 chunk 60 optimal weight: 1.9990 chunk 20 optimal weight: 2.9990 chunk 56 optimal weight: 0.8980 chunk 143 optimal weight: 0.9990 chunk 132 optimal weight: 4.9990 chunk 142 optimal weight: 2.9990 chunk 21 optimal weight: 0.0980 chunk 16 optimal weight: 8.9990 chunk 52 optimal weight: 2.9990 chunk 81 optimal weight: 0.9990 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 248 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 21 GLN C 115 HIS ** D 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 21 GLN ** E 22 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4517 r_free = 0.4517 target = 0.216939 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4057 r_free = 0.4057 target = 0.173614 restraints weight = 21026.474| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4111 r_free = 0.4111 target = 0.178359 restraints weight = 12301.359| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4146 r_free = 0.4146 target = 0.181592 restraints weight = 9107.211| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.4168 r_free = 0.4168 target = 0.183795 restraints weight = 7608.913| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.4182 r_free = 0.4182 target = 0.185151 restraints weight = 6795.507| |-----------------------------------------------------------------------------| r_work (final): 0.4174 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6860 moved from start: 0.4719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 13428 Z= 0.135 Angle : 0.663 10.627 18199 Z= 0.333 Chirality : 0.044 0.170 2087 Planarity : 0.005 0.060 2354 Dihedral : 4.548 61.343 1820 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 13.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 4.69 % Allowed : 23.84 % Favored : 71.47 % 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: 0.01 (0.21), residues: 1649 helix: 1.07 (0.24), residues: 477 sheet: -0.61 (0.27), residues: 363 loop : -0.23 (0.23), residues: 809 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 219 TYR 0.025 0.002 TYR E 59 PHE 0.031 0.002 PHE D 40 TRP 0.026 0.002 TRP E 250 HIS 0.009 0.001 HIS A 22 Details of bonding type rmsd covalent geometry : bond 0.00309 (13428) covalent geometry : angle 0.66278 (18199) hydrogen bonds : bond 0.03390 ( 459) hydrogen bonds : angle 5.03740 ( 1353) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3298 Ramachandran restraints generated. 1649 Oldfield, 0 Emsley, 1649 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3298 Ramachandran restraints generated. 1649 Oldfield, 0 Emsley, 1649 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 425 residues out of total 1493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 355 time to evaluate : 0.505 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 273 ASN cc_start: 0.5849 (m-40) cc_final: 0.5556 (m110) REVERT: B 40 PHE cc_start: 0.7328 (m-80) cc_final: 0.6855 (m-80) REVERT: B 99 LEU cc_start: 0.8241 (tt) cc_final: 0.7655 (mt) REVERT: B 178 LYS cc_start: 0.8216 (mmmm) cc_final: 0.7979 (ttmt) REVERT: B 196 ASP cc_start: 0.7730 (m-30) cc_final: 0.7421 (t0) REVERT: B 238 MET cc_start: 0.6016 (tpp) cc_final: 0.5079 (tpp) REVERT: C 21 GLN cc_start: 0.8583 (OUTLIER) cc_final: 0.7569 (pp30) REVERT: C 80 MET cc_start: 0.8343 (mmm) cc_final: 0.8075 (mmt) REVERT: D 140 TYR cc_start: 0.6715 (p90) cc_final: 0.6091 (p90) REVERT: D 235 GLN cc_start: 0.8423 (pp30) cc_final: 0.7589 (pp30) REVERT: E 141 LEU cc_start: 0.8230 (tp) cc_final: 0.7935 (tp) REVERT: E 199 ARG cc_start: 0.7976 (pmt170) cc_final: 0.7275 (ptp-170) REVERT: E 268 ASN cc_start: 0.8515 (t0) cc_final: 0.8079 (t0) REVERT: F 62 ILE cc_start: 0.7982 (OUTLIER) cc_final: 0.7539 (pt) REVERT: F 237 LEU cc_start: 0.7817 (pp) cc_final: 0.7370 (mp) REVERT: F 238 MET cc_start: 0.6056 (tpp) cc_final: 0.5720 (tpt) REVERT: F 253 GLU cc_start: 0.7777 (tt0) cc_final: 0.7474 (tp30) outliers start: 70 outliers final: 61 residues processed: 394 average time/residue: 0.1038 time to fit residues: 60.6752 Evaluate side-chains 402 residues out of total 1493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 339 time to evaluate : 0.503 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 VAL Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 206 ILE Chi-restraints excluded: chain A residue 250 TRP Chi-restraints excluded: chain B residue 62 ILE Chi-restraints excluded: chain B residue 76 THR Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 135 ILE Chi-restraints excluded: chain B residue 160 ILE Chi-restraints excluded: chain B residue 162 LEU Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 169 VAL Chi-restraints excluded: chain B residue 181 PHE Chi-restraints excluded: chain B residue 260 LEU Chi-restraints excluded: chain B residue 269 VAL Chi-restraints excluded: chain B residue 299 ILE Chi-restraints excluded: chain B residue 303 SER Chi-restraints excluded: chain C residue 19 LEU Chi-restraints excluded: chain C residue 21 GLN Chi-restraints excluded: chain C residue 43 LEU Chi-restraints excluded: chain C residue 140 VAL Chi-restraints excluded: chain C residue 150 ASN Chi-restraints excluded: chain C residue 207 GLN Chi-restraints excluded: chain C residue 224 VAL Chi-restraints excluded: chain C residue 250 TRP Chi-restraints excluded: chain D residue 82 ILE Chi-restraints excluded: chain D residue 86 LEU Chi-restraints excluded: chain D residue 108 ASP Chi-restraints excluded: chain D residue 112 HIS Chi-restraints excluded: chain D residue 165 THR Chi-restraints excluded: chain D residue 169 VAL Chi-restraints excluded: chain D residue 194 LEU Chi-restraints excluded: chain D residue 200 THR Chi-restraints excluded: chain D residue 234 VAL Chi-restraints excluded: chain D residue 252 ILE Chi-restraints excluded: chain D residue 260 LEU Chi-restraints excluded: chain D residue 264 CYS Chi-restraints excluded: chain D residue 265 VAL Chi-restraints excluded: chain D residue 269 VAL Chi-restraints excluded: chain D residue 299 ILE Chi-restraints excluded: chain D residue 303 SER Chi-restraints excluded: chain E residue 56 ILE Chi-restraints excluded: chain E residue 83 LEU Chi-restraints excluded: chain E residue 132 VAL Chi-restraints excluded: chain E residue 201 TYR Chi-restraints excluded: chain E residue 206 ILE Chi-restraints excluded: chain F residue 62 ILE Chi-restraints excluded: chain F residue 79 ILE Chi-restraints excluded: chain F residue 109 LEU Chi-restraints excluded: chain F residue 134 LEU Chi-restraints excluded: chain F residue 148 LEU Chi-restraints excluded: chain F residue 165 THR Chi-restraints excluded: chain F residue 194 LEU Chi-restraints excluded: chain F residue 199 TYR Chi-restraints excluded: chain F residue 234 VAL Chi-restraints excluded: chain F residue 252 ILE Chi-restraints excluded: chain F residue 260 LEU Chi-restraints excluded: chain F residue 269 VAL Chi-restraints excluded: chain F residue 298 TYR Chi-restraints excluded: chain F residue 299 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 134 optimal weight: 2.9990 chunk 33 optimal weight: 0.7980 chunk 19 optimal weight: 6.9990 chunk 122 optimal weight: 5.9990 chunk 105 optimal weight: 7.9990 chunk 1 optimal weight: 8.9990 chunk 118 optimal weight: 30.0000 chunk 73 optimal weight: 3.9990 chunk 74 optimal weight: 5.9990 chunk 145 optimal weight: 0.9990 chunk 164 optimal weight: 0.8980 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 103 GLN C 21 GLN C 22 HIS C 61 ASN ** D 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 21 GLN ** E 22 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 150 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4422 r_free = 0.4422 target = 0.198551 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3940 r_free = 0.3940 target = 0.154512 restraints weight = 21160.185| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.160946 restraints weight = 12075.098| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4024 r_free = 0.4024 target = 0.162049 restraints weight = 8268.497| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4032 r_free = 0.4032 target = 0.162584 restraints weight = 7434.971| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4034 r_free = 0.4034 target = 0.162871 restraints weight = 7203.916| |-----------------------------------------------------------------------------| r_work (final): 0.4019 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6999 moved from start: 0.4960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 13428 Z= 0.199 Angle : 0.722 10.298 18199 Z= 0.366 Chirality : 0.046 0.266 2087 Planarity : 0.005 0.060 2354 Dihedral : 4.905 60.885 1820 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 16.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.19 % Favored : 93.81 % Rotamer: Outliers : 5.29 % Allowed : 23.71 % Favored : 71.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.12 (0.21), residues: 1649 helix: 1.04 (0.24), residues: 464 sheet: -0.69 (0.26), residues: 369 loop : -0.34 (0.23), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 219 TYR 0.028 0.002 TYR A 40 PHE 0.026 0.002 PHE D 40 TRP 0.040 0.003 TRP E 250 HIS 0.008 0.001 HIS A 22 Details of bonding type rmsd covalent geometry : bond 0.00452 (13428) covalent geometry : angle 0.72212 (18199) hydrogen bonds : bond 0.03820 ( 459) hydrogen bonds : angle 5.33954 ( 1353) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3298 Ramachandran restraints generated. 1649 Oldfield, 0 Emsley, 1649 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3298 Ramachandran restraints generated. 1649 Oldfield, 0 Emsley, 1649 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 427 residues out of total 1493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 348 time to evaluate : 0.427 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 TYR cc_start: 0.5140 (m-80) cc_final: 0.4901 (m-10) REVERT: A 142 GLU cc_start: 0.7940 (mt-10) cc_final: 0.7647 (mp0) REVERT: A 273 ASN cc_start: 0.5849 (m-40) cc_final: 0.5621 (m110) REVERT: B 40 PHE cc_start: 0.7478 (m-80) cc_final: 0.7088 (m-80) REVERT: B 99 LEU cc_start: 0.8249 (tt) cc_final: 0.7674 (mt) REVERT: B 196 ASP cc_start: 0.7735 (m-30) cc_final: 0.7300 (t0) REVERT: B 238 MET cc_start: 0.6082 (tpp) cc_final: 0.5102 (tpp) REVERT: C 76 ARG cc_start: 0.7947 (mmp80) cc_final: 0.7729 (mmp80) REVERT: D 140 TYR cc_start: 0.6674 (p90) cc_final: 0.5959 (p90) REVERT: D 235 GLN cc_start: 0.8526 (pp30) cc_final: 0.7565 (pp30) REVERT: E 141 LEU cc_start: 0.8259 (tp) cc_final: 0.8005 (tp) REVERT: E 247 MET cc_start: 0.7470 (mtt) cc_final: 0.6957 (mtm) REVERT: F 68 GLU cc_start: 0.8083 (tt0) cc_final: 0.7356 (tt0) REVERT: F 88 ASP cc_start: 0.7967 (m-30) cc_final: 0.7766 (m-30) REVERT: F 156 TYR cc_start: 0.8201 (t80) cc_final: 0.7838 (t80) REVERT: F 237 LEU cc_start: 0.7800 (pp) cc_final: 0.7395 (mp) REVERT: F 238 MET cc_start: 0.5920 (tpp) cc_final: 0.5615 (tpt) REVERT: F 253 GLU cc_start: 0.7795 (tt0) cc_final: 0.7478 (tp30) REVERT: F 303 SER cc_start: 0.8895 (t) cc_final: 0.8526 (t) outliers start: 79 outliers final: 64 residues processed: 392 average time/residue: 0.0969 time to fit residues: 56.8265 Evaluate side-chains 397 residues out of total 1493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 333 time to evaluate : 0.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 VAL Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 206 ILE Chi-restraints excluded: chain A residue 250 TRP Chi-restraints excluded: chain B residue 62 ILE Chi-restraints excluded: chain B residue 76 THR Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 135 ILE Chi-restraints excluded: chain B residue 160 ILE Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 169 VAL Chi-restraints excluded: chain B residue 181 PHE Chi-restraints excluded: chain B residue 260 LEU Chi-restraints excluded: chain B residue 269 VAL Chi-restraints excluded: chain B residue 299 ILE Chi-restraints excluded: chain B residue 303 SER Chi-restraints excluded: chain C residue 19 LEU Chi-restraints excluded: chain C residue 21 GLN Chi-restraints excluded: chain C residue 43 LEU Chi-restraints excluded: chain C residue 135 THR Chi-restraints excluded: chain C residue 140 VAL Chi-restraints excluded: chain C residue 150 ASN Chi-restraints excluded: chain C residue 157 VAL Chi-restraints excluded: chain C residue 224 VAL Chi-restraints excluded: chain C residue 250 TRP Chi-restraints excluded: chain D residue 82 ILE Chi-restraints excluded: chain D residue 86 LEU Chi-restraints excluded: chain D residue 108 ASP Chi-restraints excluded: chain D residue 112 HIS Chi-restraints excluded: chain D residue 165 THR Chi-restraints excluded: chain D residue 169 VAL Chi-restraints excluded: chain D residue 182 VAL Chi-restraints excluded: chain D residue 194 LEU Chi-restraints excluded: chain D residue 196 ASP Chi-restraints excluded: chain D residue 200 THR Chi-restraints excluded: chain D residue 234 VAL Chi-restraints excluded: chain D residue 252 ILE Chi-restraints excluded: chain D residue 260 LEU Chi-restraints excluded: chain D residue 264 CYS Chi-restraints excluded: chain D residue 265 VAL Chi-restraints excluded: chain D residue 269 VAL Chi-restraints excluded: chain D residue 297 LEU Chi-restraints excluded: chain D residue 299 ILE Chi-restraints excluded: chain D residue 303 SER Chi-restraints excluded: chain E residue 56 ILE Chi-restraints excluded: chain E residue 83 LEU Chi-restraints excluded: chain E residue 132 VAL Chi-restraints excluded: chain E residue 140 VAL Chi-restraints excluded: chain E residue 206 ILE Chi-restraints excluded: chain F residue 56 ILE Chi-restraints excluded: chain F residue 79 ILE Chi-restraints excluded: chain F residue 101 ILE Chi-restraints excluded: chain F residue 109 LEU Chi-restraints excluded: chain F residue 160 ILE Chi-restraints excluded: chain F residue 165 THR Chi-restraints excluded: chain F residue 199 TYR Chi-restraints excluded: chain F residue 229 TRP Chi-restraints excluded: chain F residue 232 VAL Chi-restraints excluded: chain F residue 234 VAL Chi-restraints excluded: chain F residue 252 ILE Chi-restraints excluded: chain F residue 260 LEU Chi-restraints excluded: chain F residue 269 VAL Chi-restraints excluded: chain F residue 299 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 50 optimal weight: 0.0980 chunk 30 optimal weight: 0.7980 chunk 78 optimal weight: 2.9990 chunk 154 optimal weight: 1.9990 chunk 150 optimal weight: 3.9990 chunk 16 optimal weight: 6.9990 chunk 75 optimal weight: 0.9990 chunk 57 optimal weight: 3.9990 chunk 112 optimal weight: 1.9990 chunk 144 optimal weight: 2.9990 chunk 157 optimal weight: 2.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 61 ASN C 21 GLN C 115 HIS ** D 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 22 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4456 r_free = 0.4456 target = 0.204445 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.159178 restraints weight = 21162.320| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.4021 r_free = 0.4021 target = 0.163752 restraints weight = 12712.197| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.4052 r_free = 0.4052 target = 0.166686 restraints weight = 9598.083| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.4070 r_free = 0.4070 target = 0.168390 restraints weight = 8130.944| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4078 r_free = 0.4078 target = 0.169156 restraints weight = 7374.736| |-----------------------------------------------------------------------------| r_work (final): 0.4055 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6986 moved from start: 0.5094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 13428 Z= 0.157 Angle : 0.701 10.932 18199 Z= 0.356 Chirality : 0.045 0.191 2087 Planarity : 0.005 0.057 2354 Dihedral : 4.806 60.048 1820 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 15.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.88 % Favored : 94.12 % Rotamer: Outliers : 4.09 % Allowed : 25.45 % Favored : 70.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.17 (0.21), residues: 1649 helix: 0.94 (0.24), residues: 465 sheet: -0.73 (0.27), residues: 360 loop : -0.33 (0.23), residues: 824 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG F 219 TYR 0.024 0.002 TYR E 59 PHE 0.029 0.002 PHE D 40 TRP 0.035 0.002 TRP E 250 HIS 0.009 0.001 HIS C 22 Details of bonding type rmsd covalent geometry : bond 0.00360 (13428) covalent geometry : angle 0.70064 (18199) hydrogen bonds : bond 0.03595 ( 459) hydrogen bonds : angle 5.26875 ( 1353) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3298 Ramachandran restraints generated. 1649 Oldfield, 0 Emsley, 1649 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3298 Ramachandran restraints generated. 1649 Oldfield, 0 Emsley, 1649 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 403 residues out of total 1493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 342 time to evaluate : 0.415 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 40 PHE cc_start: 0.7400 (m-80) cc_final: 0.7030 (m-80) REVERT: B 99 LEU cc_start: 0.8275 (tt) cc_final: 0.7717 (mt) REVERT: B 196 ASP cc_start: 0.7675 (m-30) cc_final: 0.7343 (t0) REVERT: B 199 TYR cc_start: 0.7454 (p90) cc_final: 0.7247 (p90) REVERT: B 238 MET cc_start: 0.6100 (tpp) cc_final: 0.5097 (tpp) REVERT: B 303 SER cc_start: 0.9055 (OUTLIER) cc_final: 0.8790 (p) REVERT: D 140 TYR cc_start: 0.6570 (p90) cc_final: 0.5922 (p90) REVERT: D 235 GLN cc_start: 0.8568 (pp30) cc_final: 0.7728 (pp30) REVERT: E 141 LEU cc_start: 0.8127 (tp) cc_final: 0.7872 (tp) REVERT: E 199 ARG cc_start: 0.7938 (pmt170) cc_final: 0.7709 (ptp-170) REVERT: E 247 MET cc_start: 0.7309 (mtt) cc_final: 0.6827 (mtm) REVERT: F 156 TYR cc_start: 0.8200 (t80) cc_final: 0.7853 (t80) REVERT: F 237 LEU cc_start: 0.7832 (OUTLIER) cc_final: 0.7470 (mp) REVERT: F 238 MET cc_start: 0.6300 (tpp) cc_final: 0.6061 (tpt) REVERT: F 253 GLU cc_start: 0.7663 (tt0) cc_final: 0.7393 (tp30) REVERT: F 303 SER cc_start: 0.8873 (t) cc_final: 0.8488 (t) outliers start: 61 outliers final: 52 residues processed: 375 average time/residue: 0.0954 time to fit residues: 52.6392 Evaluate side-chains 396 residues out of total 1493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 342 time to evaluate : 0.480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 VAL Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 206 ILE Chi-restraints excluded: chain A residue 250 TRP Chi-restraints excluded: chain B residue 62 ILE Chi-restraints excluded: chain B residue 76 THR Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 160 ILE Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 169 VAL Chi-restraints excluded: chain B residue 181 PHE Chi-restraints excluded: chain B residue 260 LEU Chi-restraints excluded: chain B residue 269 VAL Chi-restraints excluded: chain B residue 303 SER Chi-restraints excluded: chain C residue 150 ASN Chi-restraints excluded: chain C residue 157 VAL Chi-restraints excluded: chain C residue 224 VAL Chi-restraints excluded: chain C residue 250 TRP Chi-restraints excluded: chain D residue 86 LEU Chi-restraints excluded: chain D residue 108 ASP Chi-restraints excluded: chain D residue 112 HIS Chi-restraints excluded: chain D residue 165 THR Chi-restraints excluded: chain D residue 169 VAL Chi-restraints excluded: chain D residue 182 VAL Chi-restraints excluded: chain D residue 194 LEU Chi-restraints excluded: chain D residue 196 ASP Chi-restraints excluded: chain D residue 200 THR Chi-restraints excluded: chain D residue 234 VAL Chi-restraints excluded: chain D residue 252 ILE Chi-restraints excluded: chain D residue 260 LEU Chi-restraints excluded: chain D residue 264 CYS Chi-restraints excluded: chain D residue 269 VAL Chi-restraints excluded: chain D residue 299 ILE Chi-restraints excluded: chain D residue 303 SER Chi-restraints excluded: chain E residue 56 ILE Chi-restraints excluded: chain E residue 83 LEU Chi-restraints excluded: chain E residue 132 VAL Chi-restraints excluded: chain E residue 206 ILE Chi-restraints excluded: chain F residue 56 ILE Chi-restraints excluded: chain F residue 79 ILE Chi-restraints excluded: chain F residue 101 ILE Chi-restraints excluded: chain F residue 109 LEU Chi-restraints excluded: chain F residue 165 THR Chi-restraints excluded: chain F residue 194 LEU Chi-restraints excluded: chain F residue 199 TYR Chi-restraints excluded: chain F residue 234 VAL Chi-restraints excluded: chain F residue 237 LEU Chi-restraints excluded: chain F residue 252 ILE Chi-restraints excluded: chain F residue 260 LEU Chi-restraints excluded: chain F residue 269 VAL Chi-restraints excluded: chain F residue 299 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 13 optimal weight: 2.9990 chunk 39 optimal weight: 5.9990 chunk 144 optimal weight: 0.0030 chunk 48 optimal weight: 0.8980 chunk 57 optimal weight: 3.9990 chunk 115 optimal weight: 0.8980 chunk 154 optimal weight: 1.9990 chunk 122 optimal weight: 0.3980 chunk 86 optimal weight: 3.9990 chunk 150 optimal weight: 0.8980 chunk 142 optimal weight: 0.0770 overall best weight: 0.4548 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 273 ASN ** C 22 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 22 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4513 r_free = 0.4513 target = 0.217208 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4084 r_free = 0.4084 target = 0.176227 restraints weight = 20902.398| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4134 r_free = 0.4134 target = 0.180722 restraints weight = 12360.505| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.4168 r_free = 0.4168 target = 0.184059 restraints weight = 9108.576| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.4182 r_free = 0.4182 target = 0.185479 restraints weight = 7519.541| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4192 r_free = 0.4192 target = 0.186587 restraints weight = 6847.365| |-----------------------------------------------------------------------------| r_work (final): 0.4154 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6871 moved from start: 0.5286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 13428 Z= 0.134 Angle : 0.701 10.968 18199 Z= 0.354 Chirality : 0.045 0.201 2087 Planarity : 0.005 0.057 2354 Dihedral : 4.542 59.773 1820 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 14.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.46 % Favored : 94.54 % Rotamer: Outliers : 3.55 % Allowed : 26.52 % Favored : 69.93 % 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: -0.19 (0.21), residues: 1649 helix: 0.93 (0.24), residues: 459 sheet: -0.72 (0.26), residues: 386 loop : -0.32 (0.23), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 219 TYR 0.022 0.002 TYR E 59 PHE 0.046 0.002 PHE D 40 TRP 0.015 0.002 TRP E 250 HIS 0.009 0.001 HIS A 22 Details of bonding type rmsd covalent geometry : bond 0.00303 (13428) covalent geometry : angle 0.70127 (18199) hydrogen bonds : bond 0.03419 ( 459) hydrogen bonds : angle 5.13872 ( 1353) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2553.21 seconds wall clock time: 44 minutes 53.25 seconds (2693.25 seconds total)