Starting phenix.real_space_refine on Wed Jun 11 17:07:29 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7w7p_32346/06_2025/7w7p_32346.cif Found real_map, /net/cci-nas-00/data/ceres_data/7w7p_32346/06_2025/7w7p_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7w7p_32346/06_2025/7w7p_32346.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7w7p_32346/06_2025/7w7p_32346.map" model { file = "/net/cci-nas-00/data/ceres_data/7w7p_32346/06_2025/7w7p_32346.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7w7p_32346/06_2025/7w7p_32346.cif" } resolution = 3.67 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 8.14, per 1000 atoms: 0.62 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: 3.03 Conformation dependent library (CDL) restraints added in 1.8 seconds 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: 1.53 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: 3.74 Time building geometry restraints manager: 3.52 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: 0.020 Extract box with map and model: 0.540 Check model and map are aligned: 0.100 Set scattering table: 0.130 Process input model: 31.690 Find NCS groups from input model: 0.570 Set up NCS constraints: 0.060 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:3.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.270 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.030 0.002 TRP E 250 HIS 0.004 0.001 HIS C 39 PHE 0.025 0.001 PHE A 143 TYR 0.019 0.002 TYR A 18 ARG 0.009 0.001 ARG C 145 Details of bonding type rmsd hydrogen bonds : bond 0.20544 ( 459) hydrogen bonds : angle 7.50308 ( 1353) covalent geometry : bond 0.00322 (13428) covalent geometry : angle 0.67972 (18199) *********************** 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 : 1.468 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: 0.2710 time to fit residues: 201.4690 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 : 1.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 139 optimal weight: 0.8980 chunk 125 optimal weight: 5.9990 chunk 69 optimal weight: 10.0000 chunk 42 optimal weight: 1.9990 chunk 84 optimal weight: 0.8980 chunk 66 optimal weight: 0.0060 chunk 129 optimal weight: 4.9990 chunk 50 optimal weight: 0.0040 chunk 78 optimal weight: 0.2980 chunk 96 optimal weight: 3.9990 chunk 149 optimal weight: 2.9990 overall best weight: 0.4208 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 21 GLN A 115 HIS B 38 GLN B 147 GLN C 115 HIS ** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** E 39 HIS E 97 ASN F 46 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4568 r_free = 0.4568 target = 0.221074 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4121 r_free = 0.4121 target = 0.178673 restraints weight = 20820.389| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4177 r_free = 0.4177 target = 0.183807 restraints weight = 11901.061| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.4216 r_free = 0.4216 target = 0.187473 restraints weight = 8704.085| |-----------------------------------------------------------------------------| r_work (final): 0.4190 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6744 moved from start: 0.2666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 13428 Z= 0.138 Angle : 0.671 8.004 18199 Z= 0.345 Chirality : 0.046 0.194 2087 Planarity : 0.005 0.080 2354 Dihedral : 4.770 59.246 1820 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 13.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 2.55 % Allowed : 14.47 % Favored : 82.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.10 (0.21), residues: 1649 helix: 1.35 (0.24), residues: 474 sheet: -0.46 (0.27), residues: 345 loop : -0.37 (0.22), residues: 830 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP C 250 HIS 0.011 0.001 HIS A 22 PHE 0.017 0.002 PHE E 143 TYR 0.014 0.002 TYR C 166 ARG 0.008 0.001 ARG D 168 Details of bonding type rmsd hydrogen bonds : bond 0.04030 ( 459) hydrogen bonds : angle 5.54158 ( 1353) covalent geometry : bond 0.00309 (13428) covalent geometry : angle 0.67118 (18199) *********************** 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 463 residues out of total 1493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 425 time to evaluate : 1.558 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: A 31 LEU cc_start: 0.8626 (OUTLIER) cc_final: 0.8296 (mt) REVERT: A 61 ASN cc_start: 0.8043 (m-40) cc_final: 0.7625 (m110) REVERT: A 93 ARG cc_start: 0.8393 (mpp80) cc_final: 0.8192 (mpp80) REVERT: A 166 TYR cc_start: 0.5908 (m-10) cc_final: 0.5135 (m-10) REVERT: A 203 GLU cc_start: 0.6761 (tt0) cc_final: 0.6454 (tt0) REVERT: A 239 ASP cc_start: 0.7916 (p0) cc_final: 0.7455 (p0) REVERT: A 249 ARG cc_start: 0.8315 (mtp180) cc_final: 0.8105 (mtp180) REVERT: B 107 LYS cc_start: 0.8763 (pttm) cc_final: 0.8453 (pptt) REVERT: B 238 MET cc_start: 0.6111 (tpp) cc_final: 0.5567 (tpp) REVERT: B 303 SER cc_start: 0.8890 (t) cc_final: 0.8598 (p) REVERT: C 61 ASN cc_start: 0.8034 (m110) cc_final: 0.7399 (p0) REVERT: C 114 GLU cc_start: 0.7622 (pt0) cc_final: 0.7397 (pt0) REVERT: D 68 GLU cc_start: 0.8322 (mm-30) cc_final: 0.7864 (mp0) REVERT: D 95 GLN cc_start: 0.6975 (tm-30) cc_final: 0.6752 (tt0) REVERT: D 194 LEU cc_start: 0.8123 (OUTLIER) cc_final: 0.7903 (tp) REVERT: D 204 LYS cc_start: 0.8277 (ptmm) cc_final: 0.7962 (mtpt) REVERT: D 218 ASP cc_start: 0.7179 (t70) cc_final: 0.6658 (p0) REVERT: E 141 LEU cc_start: 0.8226 (tp) cc_final: 0.7953 (tp) REVERT: E 199 ARG cc_start: 0.8534 (pmt170) cc_final: 0.7689 (ptt-90) REVERT: E 228 ASP cc_start: 0.8303 (m-30) cc_final: 0.7909 (m-30) REVERT: F 253 GLU cc_start: 0.7799 (tt0) cc_final: 0.7503 (tp30) REVERT: F 255 GLU cc_start: 0.7760 (tt0) cc_final: 0.7534 (tt0) REVERT: F 303 SER cc_start: 0.8919 (t) cc_final: 0.8657 (t) outliers start: 38 outliers final: 26 residues processed: 443 average time/residue: 0.2706 time to fit residues: 168.3648 Evaluate side-chains 399 residues out of total 1493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 371 time to evaluate : 1.626 ------------------------------------------------------------------------------- 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 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 269 VAL Chi-restraints excluded: chain C residue 43 LEU Chi-restraints excluded: chain C residue 150 ASN 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 194 LEU 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 252 ILE Chi-restraints excluded: chain F residue 260 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 93 optimal weight: 8.9990 chunk 144 optimal weight: 0.9990 chunk 55 optimal weight: 10.0000 chunk 98 optimal weight: 1.9990 chunk 114 optimal weight: 2.9990 chunk 51 optimal weight: 1.9990 chunk 7 optimal weight: 3.9990 chunk 95 optimal weight: 5.9990 chunk 104 optimal weight: 0.4980 chunk 94 optimal weight: 0.9990 chunk 118 optimal weight: 10.0000 overall best weight: 1.2988 ------------------------------------------------------------------------------- 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 39 HIS A 115 HIS A 176 ASN ** B 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4518 r_free = 0.4518 target = 0.215736 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.4031 r_free = 0.4031 target = 0.169813 restraints weight = 21030.193| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.4081 r_free = 0.4081 target = 0.174813 restraints weight = 12573.291| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.4114 r_free = 0.4114 target = 0.178124 restraints weight = 9497.815| |-----------------------------------------------------------------------------| r_work (final): 0.4109 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6907 moved from start: 0.3367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 13428 Z= 0.162 Angle : 0.661 7.672 18199 Z= 0.338 Chirality : 0.045 0.242 2087 Planarity : 0.005 0.069 2354 Dihedral : 4.814 65.147 1820 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 14.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 4.09 % Allowed : 17.75 % Favored : 78.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.11 (0.21), residues: 1649 helix: 1.23 (0.24), residues: 479 sheet: -0.51 (0.27), residues: 354 loop : -0.26 (0.23), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP E 250 HIS 0.012 0.001 HIS E 39 PHE 0.029 0.002 PHE D 40 TYR 0.030 0.002 TYR E 59 ARG 0.006 0.001 ARG E 220 Details of bonding type rmsd hydrogen bonds : bond 0.03919 ( 459) hydrogen bonds : angle 5.33057 ( 1353) covalent geometry : bond 0.00368 (13428) covalent geometry : angle 0.66102 (18199) *********************** 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 455 residues out of total 1493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 394 time to evaluate : 1.570 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: A 31 LEU cc_start: 0.8625 (OUTLIER) cc_final: 0.8395 (mt) REVERT: A 166 TYR cc_start: 0.6146 (m-10) cc_final: 0.5284 (m-10) REVERT: A 203 GLU cc_start: 0.7146 (tt0) cc_final: 0.6850 (tt0) REVERT: A 239 ASP cc_start: 0.7789 (p0) cc_final: 0.7434 (p0) REVERT: B 68 GLU cc_start: 0.7920 (mp0) cc_final: 0.7578 (mp0) REVERT: B 99 LEU cc_start: 0.8174 (tt) cc_final: 0.7673 (mt) REVERT: B 181 PHE cc_start: 0.6931 (m-80) cc_final: 0.6584 (t80) REVERT: B 199 TYR cc_start: 0.7453 (p90) cc_final: 0.7227 (p90) REVERT: B 238 MET cc_start: 0.6051 (tpp) cc_final: 0.5484 (tpp) REVERT: C 114 GLU cc_start: 0.7803 (pt0) cc_final: 0.7586 (pt0) REVERT: D 194 LEU cc_start: 0.8239 (tp) cc_final: 0.7997 (tp) REVERT: D 204 LYS cc_start: 0.8292 (ptmm) cc_final: 0.8020 (mtpt) REVERT: E 52 THR cc_start: 0.8937 (p) cc_final: 0.8696 (t) REVERT: E 75 LEU cc_start: 0.7956 (mt) cc_final: 0.7451 (mt) REVERT: E 115 HIS cc_start: 0.7450 (t70) cc_final: 0.7219 (t70) REVERT: E 141 LEU cc_start: 0.8410 (tp) cc_final: 0.8112 (tp) REVERT: F 68 GLU cc_start: 0.7844 (mt-10) cc_final: 0.7398 (tt0) REVERT: F 253 GLU cc_start: 0.7914 (tt0) cc_final: 0.7526 (tp30) REVERT: F 277 LYS cc_start: 0.8260 (mptt) cc_final: 0.7872 (mptt) outliers start: 61 outliers final: 40 residues processed: 419 average time/residue: 0.2694 time to fit residues: 159.9825 Evaluate side-chains 405 residues out of total 1493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 364 time to evaluate : 1.419 ------------------------------------------------------------------------------- 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 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 175 LEU Chi-restraints excluded: chain B residue 218 ASP 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 102 ILE 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 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 101 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 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 106 optimal weight: 3.9990 chunk 82 optimal weight: 0.0970 chunk 157 optimal weight: 6.9990 chunk 119 optimal weight: 2.9990 chunk 25 optimal weight: 0.0000 chunk 130 optimal weight: 0.9990 chunk 123 optimal weight: 0.5980 chunk 19 optimal weight: 0.9990 chunk 1 optimal weight: 8.9990 chunk 91 optimal weight: 3.9990 chunk 100 optimal weight: 4.9990 overall best weight: 0.5386 ------------------------------------------------------------------------------- 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** C 21 GLN ** C 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 115 HIS ** 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 = 0.4547 r_free = 0.4547 target = 0.219018 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4078 r_free = 0.4078 target = 0.174383 restraints weight = 20879.043| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4131 r_free = 0.4131 target = 0.179668 restraints weight = 12341.676| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4165 r_free = 0.4165 target = 0.183034 restraints weight = 9183.462| |-----------------------------------------------------------------------------| r_work (final): 0.4161 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6844 moved from start: 0.3781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 13428 Z= 0.125 Angle : 0.621 8.456 18199 Z= 0.316 Chirality : 0.044 0.163 2087 Planarity : 0.004 0.068 2354 Dihedral : 4.541 64.033 1820 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 12.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 3.42 % Allowed : 20.76 % Favored : 75.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.11 (0.21), residues: 1649 helix: 1.24 (0.24), residues: 473 sheet: -0.45 (0.26), residues: 373 loop : -0.27 (0.23), residues: 803 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP E 250 HIS 0.007 0.001 HIS E 23 PHE 0.041 0.001 PHE D 40 TYR 0.019 0.001 TYR D 156 ARG 0.005 0.001 ARG E 76 Details of bonding type rmsd hydrogen bonds : bond 0.03512 ( 459) hydrogen bonds : angle 5.11735 ( 1353) covalent geometry : bond 0.00282 (13428) covalent geometry : angle 0.62085 (18199) *********************** 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 443 residues out of total 1493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 392 time to evaluate : 1.514 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: A 21 GLN cc_start: 0.8653 (OUTLIER) cc_final: 0.7214 (pp30) REVERT: A 166 TYR cc_start: 0.5914 (m-10) cc_final: 0.5147 (m-10) REVERT: B 40 PHE cc_start: 0.7262 (m-80) cc_final: 0.6697 (m-80) REVERT: B 68 GLU cc_start: 0.7968 (mp0) cc_final: 0.7654 (mp0) REVERT: B 99 LEU cc_start: 0.8203 (tt) cc_final: 0.7699 (mt) REVERT: B 238 MET cc_start: 0.6365 (tpp) cc_final: 0.5623 (tpp) REVERT: C 164 GLN cc_start: 0.8268 (mm-40) cc_final: 0.7840 (mm-40) REVERT: C 228 ASP cc_start: 0.8591 (m-30) cc_final: 0.8317 (m-30) REVERT: D 16 TYR cc_start: 0.7892 (t80) cc_final: 0.7422 (t80) REVERT: D 163 ARG cc_start: 0.7419 (tpt170) cc_final: 0.7157 (ttm-80) REVERT: E 52 THR cc_start: 0.9005 (p) cc_final: 0.8787 (t) REVERT: E 141 LEU cc_start: 0.8397 (tp) cc_final: 0.8068 (tp) REVERT: F 303 SER cc_start: 0.8876 (t) cc_final: 0.8541 (t) outliers start: 51 outliers final: 38 residues processed: 413 average time/residue: 0.3862 time to fit residues: 229.2069 Evaluate side-chains 390 residues out of total 1493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 351 time to evaluate : 2.681 ------------------------------------------------------------------------------- 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 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 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 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 139 LEU Chi-restraints excluded: chain D residue 165 THR Chi-restraints excluded: chain D residue 169 VAL Chi-restraints excluded: chain D residue 181 PHE Chi-restraints excluded: chain D residue 252 ILE Chi-restraints excluded: chain D residue 269 VAL 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 76 THR Chi-restraints excluded: chain F residue 109 LEU Chi-restraints excluded: chain F residue 141 ASN Chi-restraints excluded: chain F residue 148 LEU Chi-restraints excluded: chain F residue 165 THR Chi-restraints excluded: chain F residue 199 TYR Chi-restraints excluded: chain F residue 252 ILE Chi-restraints excluded: chain F residue 269 VAL Chi-restraints excluded: chain F residue 299 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 4 optimal weight: 6.9990 chunk 34 optimal weight: 6.9990 chunk 142 optimal weight: 5.9990 chunk 46 optimal weight: 0.7980 chunk 50 optimal weight: 2.9990 chunk 114 optimal weight: 0.0070 chunk 117 optimal weight: 0.9980 chunk 85 optimal weight: 6.9990 chunk 137 optimal weight: 0.7980 chunk 44 optimal weight: 20.0000 chunk 126 optimal weight: 7.9990 overall best weight: 1.1200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 21 GLN A 22 HIS A 39 HIS ** A 248 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 21 GLN ** E 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4520 r_free = 0.4520 target = 0.216961 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4057 r_free = 0.4057 target = 0.173477 restraints weight = 21177.125| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4110 r_free = 0.4110 target = 0.178478 restraints weight = 12356.218| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4147 r_free = 0.4147 target = 0.181929 restraints weight = 9123.944| |-----------------------------------------------------------------------------| r_work (final): 0.4106 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6902 moved from start: 0.4113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 13428 Z= 0.149 Angle : 0.640 8.954 18199 Z= 0.324 Chirality : 0.044 0.169 2087 Planarity : 0.005 0.065 2354 Dihedral : 4.594 63.581 1820 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 14.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 5.43 % Allowed : 21.17 % Favored : 73.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.07 (0.21), residues: 1649 helix: 1.21 (0.24), residues: 473 sheet: -0.51 (0.26), residues: 384 loop : -0.26 (0.23), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP F 19 HIS 0.011 0.001 HIS E 23 PHE 0.032 0.002 PHE D 40 TYR 0.021 0.001 TYR B 298 ARG 0.010 0.001 ARG B 219 Details of bonding type rmsd hydrogen bonds : bond 0.03461 ( 459) hydrogen bonds : angle 5.09493 ( 1353) covalent geometry : bond 0.00342 (13428) covalent geometry : angle 0.63980 (18199) *********************** 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: 81 poor density : 361 time to evaluate : 1.628 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: A 21 GLN cc_start: 0.8614 (OUTLIER) cc_final: 0.8333 (pp30) REVERT: A 31 LEU cc_start: 0.8530 (OUTLIER) cc_final: 0.8292 (mt) REVERT: A 40 TYR cc_start: 0.4125 (m-80) cc_final: 0.3900 (m-80) REVERT: A 93 ARG cc_start: 0.8533 (mpp80) cc_final: 0.8252 (mpp80) REVERT: A 166 TYR cc_start: 0.5936 (m-10) cc_final: 0.5129 (m-10) REVERT: A 239 ASP cc_start: 0.7990 (p0) cc_final: 0.7709 (p0) REVERT: B 40 PHE cc_start: 0.7330 (m-80) cc_final: 0.6804 (m-80) REVERT: B 99 LEU cc_start: 0.8255 (tt) cc_final: 0.7726 (mt) REVERT: B 149 LYS cc_start: 0.8164 (mmtt) cc_final: 0.7961 (mmmt) REVERT: B 218 ASP cc_start: 0.6745 (OUTLIER) cc_final: 0.6256 (p0) REVERT: B 238 MET cc_start: 0.6086 (tpp) cc_final: 0.5263 (tpp) REVERT: B 259 ASP cc_start: 0.7789 (t0) cc_final: 0.7535 (t0) REVERT: C 98 LEU cc_start: 0.6620 (mm) cc_final: 0.6355 (mm) REVERT: C 228 ASP cc_start: 0.8659 (m-30) cc_final: 0.8354 (m-30) REVERT: D 140 TYR cc_start: 0.6725 (p90) cc_final: 0.6153 (p90) REVERT: E 52 THR cc_start: 0.9005 (p) cc_final: 0.8773 (t) REVERT: E 61 ASN cc_start: 0.7565 (m110) cc_final: 0.7326 (p0) REVERT: E 141 LEU cc_start: 0.8376 (tp) cc_final: 0.8044 (tp) REVERT: E 228 ASP cc_start: 0.8254 (m-30) cc_final: 0.8046 (m-30) REVERT: F 181 PHE cc_start: 0.7283 (t80) cc_final: 0.7042 (t80) REVERT: F 277 LYS cc_start: 0.8286 (mptt) cc_final: 0.7858 (mptt) REVERT: F 303 SER cc_start: 0.8954 (t) cc_final: 0.8644 (t) outliers start: 81 outliers final: 63 residues processed: 398 average time/residue: 0.2639 time to fit residues: 149.9021 Evaluate side-chains 418 residues out of total 1493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 352 time to evaluate : 1.497 ------------------------------------------------------------------------------- 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 28 LEU Chi-restraints excluded: chain A residue 31 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 165 THR Chi-restraints excluded: chain B residue 169 VAL Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 218 ASP 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 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 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 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 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 201 TYR Chi-restraints excluded: chain E residue 250 TRP Chi-restraints excluded: chain E residue 261 LEU 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 134 LEU Chi-restraints excluded: chain F residue 141 ASN Chi-restraints excluded: chain F residue 148 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 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 297 LEU Chi-restraints excluded: chain F residue 298 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 131 optimal weight: 0.3980 chunk 113 optimal weight: 9.9990 chunk 1 optimal weight: 7.9990 chunk 9 optimal weight: 5.9990 chunk 105 optimal weight: 7.9990 chunk 157 optimal weight: 1.9990 chunk 141 optimal weight: 2.9990 chunk 108 optimal weight: 0.7980 chunk 100 optimal weight: 1.9990 chunk 90 optimal weight: 0.8980 chunk 139 optimal weight: 0.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- 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 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 21 GLN ** E 22 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 39 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4547 r_free = 0.4547 target = 0.218471 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4059 r_free = 0.4059 target = 0.171935 restraints weight = 21284.480| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.4113 r_free = 0.4113 target = 0.176891 restraints weight = 12674.273| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4145 r_free = 0.4145 target = 0.180137 restraints weight = 9531.061| |-----------------------------------------------------------------------------| r_work (final): 0.4139 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6962 moved from start: 0.4363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 13428 Z= 0.141 Angle : 0.639 8.897 18199 Z= 0.324 Chirality : 0.044 0.203 2087 Planarity : 0.005 0.060 2354 Dihedral : 4.581 62.212 1820 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 13.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 4.89 % Allowed : 21.97 % Favored : 73.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.05 (0.21), residues: 1649 helix: 1.15 (0.24), residues: 466 sheet: -0.45 (0.26), residues: 395 loop : -0.27 (0.23), residues: 788 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.003 TRP F 19 HIS 0.010 0.001 HIS E 23 PHE 0.027 0.002 PHE D 40 TYR 0.043 0.002 TYR E 59 ARG 0.008 0.001 ARG B 219 Details of bonding type rmsd hydrogen bonds : bond 0.03446 ( 459) hydrogen bonds : angle 5.06882 ( 1353) covalent geometry : bond 0.00323 (13428) covalent geometry : angle 0.63865 (18199) *********************** 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 440 residues out of total 1493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 367 time to evaluate : 1.436 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: A 31 LEU cc_start: 0.8513 (OUTLIER) cc_final: 0.8269 (mt) REVERT: B 40 PHE cc_start: 0.7358 (m-80) cc_final: 0.6811 (m-80) REVERT: B 68 GLU cc_start: 0.8164 (mm-30) cc_final: 0.7959 (mp0) REVERT: B 99 LEU cc_start: 0.8202 (tt) cc_final: 0.7705 (mt) REVERT: B 149 LYS cc_start: 0.8233 (mmtt) cc_final: 0.8029 (mmmt) REVERT: B 238 MET cc_start: 0.6152 (tpp) cc_final: 0.5203 (tpp) REVERT: C 21 GLN cc_start: 0.8654 (OUTLIER) cc_final: 0.7467 (pp30) REVERT: C 52 THR cc_start: 0.9055 (p) cc_final: 0.8853 (t) REVERT: D 140 TYR cc_start: 0.6644 (p90) cc_final: 0.6113 (p90) REVERT: D 201 LEU cc_start: 0.8265 (mm) cc_final: 0.8035 (mm) REVERT: D 235 GLN cc_start: 0.8419 (pp30) cc_final: 0.7621 (pp30) REVERT: D 236 GLU cc_start: 0.7058 (mp0) cc_final: 0.6815 (mp0) REVERT: D 238 MET cc_start: 0.4466 (tpt) cc_final: 0.4224 (tpt) REVERT: E 141 LEU cc_start: 0.8388 (tp) cc_final: 0.8020 (tp) REVERT: E 143 PHE cc_start: 0.6347 (m-10) cc_final: 0.6120 (m-80) REVERT: E 199 ARG cc_start: 0.8427 (pmt170) cc_final: 0.7873 (ptt-90) REVERT: F 62 ILE cc_start: 0.7935 (OUTLIER) cc_final: 0.7579 (pt) REVERT: F 181 PHE cc_start: 0.7375 (t80) cc_final: 0.7065 (t80) REVERT: F 237 LEU cc_start: 0.7875 (OUTLIER) cc_final: 0.7326 (mp) REVERT: F 277 LYS cc_start: 0.8195 (mptt) cc_final: 0.7920 (mptt) REVERT: F 303 SER cc_start: 0.8966 (t) cc_final: 0.8673 (t) outliers start: 73 outliers final: 62 residues processed: 404 average time/residue: 0.2544 time to fit residues: 146.6325 Evaluate side-chains 413 residues out of total 1493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 347 time to evaluate : 1.473 ------------------------------------------------------------------------------- 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 43 LEU Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 118 LYS 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 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 237 LEU 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 21 GLN 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 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 177 THR Chi-restraints excluded: chain D residue 181 PHE 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 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 247 MET Chi-restraints excluded: chain E residue 250 TRP 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 76 THR 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 160 ILE 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 237 LEU Chi-restraints excluded: chain F residue 252 ILE Chi-restraints excluded: chain F residue 269 VAL Chi-restraints excluded: chain F residue 298 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 132 optimal weight: 0.8980 chunk 116 optimal weight: 0.6980 chunk 80 optimal weight: 3.9990 chunk 102 optimal weight: 2.9990 chunk 12 optimal weight: 0.8980 chunk 122 optimal weight: 1.9990 chunk 2 optimal weight: 3.9990 chunk 156 optimal weight: 2.9990 chunk 123 optimal weight: 1.9990 chunk 93 optimal weight: 5.9990 chunk 1 optimal weight: 5.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- 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 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 248 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 21 GLN C 22 HIS E 21 GLN ** E 22 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 = 0.4503 r_free = 0.4503 target = 0.214957 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.169540 restraints weight = 21207.045| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.4066 r_free = 0.4066 target = 0.174421 restraints weight = 12654.870| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4092 r_free = 0.4092 target = 0.177070 restraints weight = 9543.879| |-----------------------------------------------------------------------------| r_work (final): 0.4085 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6983 moved from start: 0.4582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 13428 Z= 0.162 Angle : 0.670 9.513 18199 Z= 0.341 Chirality : 0.045 0.255 2087 Planarity : 0.005 0.059 2354 Dihedral : 4.659 61.425 1820 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 15.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer: Outliers : 5.16 % Allowed : 23.11 % Favored : 71.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.06 (0.21), residues: 1649 helix: 1.15 (0.24), residues: 466 sheet: -0.73 (0.26), residues: 389 loop : -0.28 (0.23), residues: 794 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.003 TRP F 19 HIS 0.010 0.001 HIS A 22 PHE 0.023 0.002 PHE D 40 TYR 0.030 0.002 TYR E 59 ARG 0.013 0.001 ARG A 220 Details of bonding type rmsd hydrogen bonds : bond 0.03562 ( 459) hydrogen bonds : angle 5.13586 ( 1353) covalent geometry : bond 0.00369 (13428) covalent geometry : angle 0.67020 (18199) *********************** 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 440 residues out of total 1493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 363 time to evaluate : 1.566 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 31 LEU cc_start: 0.8557 (OUTLIER) cc_final: 0.8200 (mt) REVERT: A 93 ARG cc_start: 0.8501 (mpp80) cc_final: 0.8233 (mpp80) REVERT: B 40 PHE cc_start: 0.7275 (m-80) cc_final: 0.6803 (m-80) REVERT: B 99 LEU cc_start: 0.8221 (tt) cc_final: 0.7645 (mt) REVERT: B 196 ASP cc_start: 0.7554 (m-30) cc_final: 0.7173 (t0) REVERT: B 238 MET cc_start: 0.5897 (tpp) cc_final: 0.4991 (tpp) REVERT: C 52 THR cc_start: 0.9071 (p) cc_final: 0.8858 (t) REVERT: C 98 LEU cc_start: 0.6280 (mm) cc_final: 0.5985 (mm) REVERT: D 140 TYR cc_start: 0.6651 (p90) cc_final: 0.5996 (p90) REVERT: D 201 LEU cc_start: 0.8395 (mm) cc_final: 0.8170 (mm) REVERT: E 61 ASN cc_start: 0.7500 (m110) cc_final: 0.7293 (p0) REVERT: E 141 LEU cc_start: 0.8501 (tp) cc_final: 0.8183 (tp) REVERT: F 62 ILE cc_start: 0.7904 (OUTLIER) cc_final: 0.7537 (pt) REVERT: F 181 PHE cc_start: 0.7330 (t80) cc_final: 0.6995 (t80) REVERT: F 237 LEU cc_start: 0.7960 (OUTLIER) cc_final: 0.7384 (mp) REVERT: F 303 SER cc_start: 0.8967 (t) cc_final: 0.8653 (t) outliers start: 77 outliers final: 66 residues processed: 400 average time/residue: 0.2727 time to fit residues: 157.2735 Evaluate side-chains 406 residues out of total 1493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 337 time to evaluate : 1.451 ------------------------------------------------------------------------------- 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 43 LEU Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 118 LYS 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 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 43 LEU Chi-restraints excluded: chain C residue 56 ILE 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 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 177 THR Chi-restraints excluded: chain D residue 181 PHE 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 265 VAL Chi-restraints excluded: chain D residue 269 VAL Chi-restraints excluded: chain D residue 299 ILE 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 250 TRP 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 139 LEU Chi-restraints excluded: chain F residue 160 ILE 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 229 TRP 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 298 TYR Chi-restraints excluded: chain F residue 299 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 138 optimal weight: 6.9990 chunk 141 optimal weight: 4.9990 chunk 31 optimal weight: 0.2980 chunk 89 optimal weight: 0.8980 chunk 54 optimal weight: 2.9990 chunk 148 optimal weight: 0.0170 chunk 59 optimal weight: 0.7980 chunk 115 optimal weight: 0.4980 chunk 152 optimal weight: 5.9990 chunk 73 optimal weight: 0.9990 chunk 92 optimal weight: 8.9990 overall best weight: 0.5018 ------------------------------------------------------------------------------- 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** ** C 22 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 115 HIS ** E 22 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 95 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4529 r_free = 0.4529 target = 0.218422 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4102 r_free = 0.4102 target = 0.177921 restraints weight = 20744.540| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4155 r_free = 0.4155 target = 0.182695 restraints weight = 12090.808| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4188 r_free = 0.4188 target = 0.185879 restraints weight = 8808.357| |-----------------------------------------------------------------------------| r_work (final): 0.4151 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6862 moved from start: 0.4787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 13428 Z= 0.132 Angle : 0.677 10.004 18199 Z= 0.341 Chirality : 0.044 0.194 2087 Planarity : 0.005 0.056 2354 Dihedral : 4.494 60.286 1820 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 13.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.97 % Favored : 95.03 % Rotamer: Outliers : 3.62 % Allowed : 24.65 % Favored : 71.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.05 (0.21), residues: 1649 helix: 1.00 (0.24), residues: 471 sheet: -0.53 (0.26), residues: 397 loop : -0.27 (0.23), residues: 781 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP F 19 HIS 0.015 0.001 HIS A 22 PHE 0.042 0.002 PHE B 43 TYR 0.023 0.001 TYR E 59 ARG 0.009 0.001 ARG C 199 Details of bonding type rmsd hydrogen bonds : bond 0.03405 ( 459) hydrogen bonds : angle 4.98731 ( 1353) covalent geometry : bond 0.00299 (13428) covalent geometry : angle 0.67677 (18199) *********************** 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 408 residues out of total 1493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 354 time to evaluate : 1.864 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 LEU cc_start: 0.8283 (OUTLIER) cc_final: 0.7926 (mt) REVERT: B 40 PHE cc_start: 0.7238 (m-80) cc_final: 0.6831 (m-80) REVERT: B 68 GLU cc_start: 0.7907 (mp0) cc_final: 0.7543 (mp0) REVERT: B 99 LEU cc_start: 0.8241 (tt) cc_final: 0.7699 (mt) REVERT: B 238 MET cc_start: 0.6023 (tpp) cc_final: 0.5125 (tpp) REVERT: B 303 SER cc_start: 0.8975 (t) cc_final: 0.8683 (p) REVERT: C 52 THR cc_start: 0.8931 (p) cc_final: 0.8727 (t) REVERT: C 72 ASP cc_start: 0.7304 (m-30) cc_final: 0.7009 (m-30) REVERT: D 140 TYR cc_start: 0.6642 (p90) cc_final: 0.5949 (p90) REVERT: D 201 LEU cc_start: 0.8383 (mm) cc_final: 0.8158 (mm) REVERT: D 235 GLN cc_start: 0.8350 (pp30) cc_final: 0.7591 (pp30) REVERT: E 141 LEU cc_start: 0.8375 (tp) cc_final: 0.8014 (tp) REVERT: E 199 ARG cc_start: 0.8355 (pmt170) cc_final: 0.7917 (ptt-90) REVERT: E 268 ASN cc_start: 0.8418 (t0) cc_final: 0.8151 (t0) REVERT: F 62 ILE cc_start: 0.7954 (OUTLIER) cc_final: 0.7542 (pt) REVERT: F 181 PHE cc_start: 0.6803 (t80) cc_final: 0.6602 (t80) REVERT: F 237 LEU cc_start: 0.7820 (OUTLIER) cc_final: 0.7290 (mp) REVERT: F 303 SER cc_start: 0.8955 (t) cc_final: 0.8620 (t) outliers start: 54 outliers final: 48 residues processed: 381 average time/residue: 0.3073 time to fit residues: 171.3765 Evaluate side-chains 393 residues out of total 1493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 342 time to evaluate : 1.688 ------------------------------------------------------------------------------- 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 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 76 THR Chi-restraints excluded: chain B residue 86 LEU 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 296 LEU Chi-restraints excluded: chain B residue 299 ILE 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 181 PHE Chi-restraints excluded: chain D residue 194 LEU Chi-restraints excluded: chain D residue 200 THR Chi-restraints excluded: chain D residue 237 LEU Chi-restraints excluded: chain D residue 269 VAL Chi-restraints excluded: chain D residue 299 ILE Chi-restraints excluded: chain E residue 56 ILE 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 62 ILE Chi-restraints excluded: chain F residue 76 THR 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 165 THR Chi-restraints excluded: chain F residue 194 LEU Chi-restraints excluded: chain F residue 196 ASP Chi-restraints excluded: chain F residue 199 TYR 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 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 0 optimal weight: 9.9990 chunk 128 optimal weight: 20.0000 chunk 81 optimal weight: 0.9990 chunk 80 optimal weight: 0.9990 chunk 73 optimal weight: 2.9990 chunk 58 optimal weight: 10.0000 chunk 21 optimal weight: 7.9990 chunk 123 optimal weight: 0.9980 chunk 143 optimal weight: 4.9990 chunk 15 optimal weight: 7.9990 chunk 94 optimal weight: 0.9990 overall best weight: 1.3988 ------------------------------------------------------------------------------- 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 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 273 ASN ** C 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 22 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 21 GLN ** E 22 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 115 HIS F 150 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4480 r_free = 0.4480 target = 0.213550 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4044 r_free = 0.4044 target = 0.172682 restraints weight = 20762.900| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4094 r_free = 0.4094 target = 0.177206 restraints weight = 12348.396| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4115 r_free = 0.4115 target = 0.179210 restraints weight = 9123.547| |-----------------------------------------------------------------------------| r_work (final): 0.4067 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6981 moved from start: 0.4990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 13428 Z= 0.171 Angle : 0.690 11.296 18199 Z= 0.351 Chirality : 0.045 0.181 2087 Planarity : 0.005 0.056 2354 Dihedral : 4.672 59.652 1820 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 14.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.70 % Favored : 94.30 % Rotamer: Outliers : 4.76 % Allowed : 24.18 % Favored : 71.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.10 (0.21), residues: 1649 helix: 1.06 (0.24), residues: 465 sheet: -0.67 (0.25), residues: 400 loop : -0.30 (0.23), residues: 784 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.003 TRP E 250 HIS 0.016 0.001 HIS A 22 PHE 0.039 0.002 PHE D 40 TYR 0.030 0.002 TYR A 40 ARG 0.014 0.001 ARG C 199 Details of bonding type rmsd hydrogen bonds : bond 0.03536 ( 459) hydrogen bonds : angle 5.17405 ( 1353) covalent geometry : bond 0.00393 (13428) covalent geometry : angle 0.69030 (18199) *********************** 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 423 residues out of total 1493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 352 time to evaluate : 1.666 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 LEU cc_start: 0.8442 (OUTLIER) cc_final: 0.8190 (mt) REVERT: A 93 ARG cc_start: 0.8017 (mpp80) cc_final: 0.7280 (ptp90) REVERT: B 40 PHE cc_start: 0.7315 (m-80) cc_final: 0.6964 (m-80) REVERT: B 68 GLU cc_start: 0.7903 (mp0) cc_final: 0.7499 (mp0) REVERT: B 99 LEU cc_start: 0.8262 (tt) cc_final: 0.7722 (mt) REVERT: B 196 ASP cc_start: 0.7554 (m-30) cc_final: 0.7173 (t0) REVERT: B 238 MET cc_start: 0.6115 (tpp) cc_final: 0.5191 (tpp) REVERT: C 52 THR cc_start: 0.8960 (p) cc_final: 0.8757 (t) REVERT: C 76 ARG cc_start: 0.7375 (mmp-170) cc_final: 0.7132 (mmp-170) REVERT: D 140 TYR cc_start: 0.6604 (p90) cc_final: 0.5939 (p90) REVERT: D 199 TYR cc_start: 0.7599 (p90) cc_final: 0.7360 (p90) REVERT: D 201 LEU cc_start: 0.8509 (mm) cc_final: 0.8286 (mm) REVERT: D 235 GLN cc_start: 0.8424 (pp30) cc_final: 0.7691 (pp30) REVERT: E 54 MET cc_start: 0.8095 (OUTLIER) cc_final: 0.7822 (mpp) REVERT: E 141 LEU cc_start: 0.8311 (tp) cc_final: 0.8068 (tp) REVERT: E 199 ARG cc_start: 0.8315 (pmt170) cc_final: 0.7875 (ptp90) REVERT: F 134 LEU cc_start: 0.7546 (OUTLIER) cc_final: 0.7321 (pp) REVERT: F 156 TYR cc_start: 0.8150 (t80) cc_final: 0.7865 (t80) REVERT: F 181 PHE cc_start: 0.7298 (t80) cc_final: 0.6929 (t80) REVERT: F 303 SER cc_start: 0.8977 (t) cc_final: 0.8679 (t) outliers start: 71 outliers final: 56 residues processed: 386 average time/residue: 0.2438 time to fit residues: 136.4587 Evaluate side-chains 397 residues out of total 1493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 338 time to evaluate : 1.411 ------------------------------------------------------------------------------- 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 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 165 THR Chi-restraints excluded: chain B residue 169 VAL Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 181 PHE Chi-restraints excluded: chain B residue 218 ASP 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 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 181 PHE Chi-restraints excluded: chain D residue 194 LEU Chi-restraints excluded: chain D residue 200 THR 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 E residue 54 MET Chi-restraints excluded: chain E residue 56 ILE Chi-restraints excluded: chain E residue 83 LEU Chi-restraints excluded: chain E residue 115 HIS Chi-restraints excluded: chain E residue 198 CYS Chi-restraints excluded: chain E residue 201 TYR Chi-restraints excluded: chain E residue 250 TRP Chi-restraints excluded: chain F residue 62 ILE Chi-restraints excluded: chain F residue 76 THR 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 160 ILE Chi-restraints excluded: chain F residue 165 THR Chi-restraints excluded: chain F residue 194 LEU Chi-restraints excluded: chain F residue 196 ASP Chi-restraints excluded: chain F residue 199 TYR Chi-restraints excluded: chain F residue 233 LYS Chi-restraints excluded: chain F residue 237 LEU Chi-restraints excluded: chain F residue 252 ILE 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 98 optimal weight: 0.6980 chunk 118 optimal weight: 0.0470 chunk 81 optimal weight: 0.6980 chunk 63 optimal weight: 7.9990 chunk 137 optimal weight: 2.9990 chunk 53 optimal weight: 5.9990 chunk 4 optimal weight: 0.9990 chunk 57 optimal weight: 3.9990 chunk 114 optimal weight: 0.5980 chunk 72 optimal weight: 9.9990 chunk 154 optimal weight: 0.7980 overall best weight: 0.5678 ------------------------------------------------------------------------------- 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 39 HIS A 273 ASN ** C 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 22 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 115 HIS ** E 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 22 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 115 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4527 r_free = 0.4527 target = 0.217980 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4077 r_free = 0.4077 target = 0.175139 restraints weight = 21117.708| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4129 r_free = 0.4129 target = 0.179906 restraints weight = 12157.684| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4155 r_free = 0.4155 target = 0.182696 restraints weight = 8926.536| |-----------------------------------------------------------------------------| r_work (final): 0.4115 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6911 moved from start: 0.5173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 13428 Z= 0.134 Angle : 0.684 11.922 18199 Z= 0.344 Chirality : 0.045 0.270 2087 Planarity : 0.005 0.055 2354 Dihedral : 4.501 58.826 1820 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 13.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.40 % Favored : 94.60 % Rotamer: Outliers : 3.75 % Allowed : 25.52 % Favored : 70.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.12 (0.21), residues: 1649 helix: 0.95 (0.24), residues: 464 sheet: -0.59 (0.25), residues: 399 loop : -0.30 (0.23), residues: 786 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP E 250 HIS 0.016 0.001 HIS A 22 PHE 0.044 0.002 PHE D 40 TYR 0.017 0.001 TYR D 156 ARG 0.010 0.001 ARG C 199 Details of bonding type rmsd hydrogen bonds : bond 0.03371 ( 459) hydrogen bonds : angle 5.07426 ( 1353) covalent geometry : bond 0.00310 (13428) covalent geometry : angle 0.68375 (18199) ********************** 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 408 residues out of total 1493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 352 time to evaluate : 1.832 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 93 ARG cc_start: 0.8085 (mpp80) cc_final: 0.7377 (ptp90) REVERT: A 249 ARG cc_start: 0.8273 (mtm180) cc_final: 0.7986 (mtp180) REVERT: B 40 PHE cc_start: 0.7340 (m-80) cc_final: 0.6911 (m-80) REVERT: B 68 GLU cc_start: 0.7979 (mp0) cc_final: 0.7624 (mp0) REVERT: B 99 LEU cc_start: 0.8187 (tt) cc_final: 0.7658 (mt) REVERT: B 196 ASP cc_start: 0.7504 (m-30) cc_final: 0.7089 (t0) REVERT: B 238 MET cc_start: 0.6053 (tpp) cc_final: 0.5049 (tpp) REVERT: B 303 SER cc_start: 0.9075 (t) cc_final: 0.8753 (p) REVERT: C 93 ARG cc_start: 0.7903 (ptp90) cc_final: 0.7662 (ptp90) REVERT: C 150 ASN cc_start: 0.6710 (OUTLIER) cc_final: 0.6346 (t0) REVERT: D 140 TYR cc_start: 0.6720 (p90) cc_final: 0.5989 (p90) REVERT: D 199 TYR cc_start: 0.7603 (p90) cc_final: 0.7319 (p90) REVERT: D 201 LEU cc_start: 0.8451 (mm) cc_final: 0.8218 (mm) REVERT: D 235 GLN cc_start: 0.8352 (pp30) cc_final: 0.7626 (pp30) REVERT: E 141 LEU cc_start: 0.8197 (tp) cc_final: 0.7934 (tp) REVERT: E 199 ARG cc_start: 0.8190 (pmt170) cc_final: 0.7986 (ptt-90) REVERT: F 62 ILE cc_start: 0.7972 (OUTLIER) cc_final: 0.7549 (pt) REVERT: F 68 GLU cc_start: 0.7943 (mt-10) cc_final: 0.7468 (tt0) REVERT: F 156 TYR cc_start: 0.8111 (t80) cc_final: 0.7793 (t80) REVERT: F 181 PHE cc_start: 0.7104 (t80) cc_final: 0.6791 (t80) REVERT: F 237 LEU cc_start: 0.7931 (OUTLIER) cc_final: 0.7452 (mp) REVERT: F 303 SER cc_start: 0.8934 (t) cc_final: 0.8608 (t) outliers start: 56 outliers final: 50 residues processed: 379 average time/residue: 0.2298 time to fit residues: 128.2283 Evaluate side-chains 393 residues out of total 1493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 340 time to evaluate : 1.569 ------------------------------------------------------------------------------- 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 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 C residue 19 LEU Chi-restraints excluded: chain C residue 150 ASN Chi-restraints excluded: chain C residue 157 VAL 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 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 181 PHE 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 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 E residue 56 ILE Chi-restraints excluded: chain E residue 83 LEU Chi-restraints excluded: chain E residue 115 HIS Chi-restraints excluded: chain E residue 198 CYS Chi-restraints excluded: chain E residue 201 TYR Chi-restraints excluded: chain E residue 250 TRP 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 196 ASP Chi-restraints excluded: chain F residue 199 TYR Chi-restraints excluded: chain F residue 237 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 121 optimal weight: 4.9990 chunk 22 optimal weight: 0.7980 chunk 138 optimal weight: 7.9990 chunk 49 optimal weight: 0.8980 chunk 86 optimal weight: 2.9990 chunk 59 optimal weight: 0.8980 chunk 1 optimal weight: 5.9990 chunk 143 optimal weight: 0.7980 chunk 14 optimal weight: 9.9990 chunk 113 optimal weight: 10.0000 chunk 8 optimal weight: 8.9990 overall best weight: 1.2782 ------------------------------------------------------------------------------- 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 39 HIS A 273 ASN ** B 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 103 GLN ** C 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 115 HIS F 150 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4471 r_free = 0.4471 target = 0.213325 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.169640 restraints weight = 21064.220| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4052 r_free = 0.4052 target = 0.174296 restraints weight = 12733.890| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4084 r_free = 0.4084 target = 0.177304 restraints weight = 9543.588| |-----------------------------------------------------------------------------| r_work (final): 0.4057 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6992 moved from start: 0.5282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 13428 Z= 0.163 Angle : 0.710 12.152 18199 Z= 0.359 Chirality : 0.045 0.174 2087 Planarity : 0.005 0.056 2354 Dihedral : 4.651 58.765 1820 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 15.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.00 % Favored : 94.00 % Rotamer: Outliers : 4.15 % Allowed : 25.59 % Favored : 70.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.22 (0.21), residues: 1649 helix: 0.87 (0.24), residues: 465 sheet: -0.74 (0.25), residues: 396 loop : -0.31 (0.23), residues: 788 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP E 250 HIS 0.015 0.001 HIS A 22 PHE 0.046 0.002 PHE D 40 TYR 0.037 0.002 TYR B 66 ARG 0.009 0.001 ARG B 219 Details of bonding type rmsd hydrogen bonds : bond 0.03603 ( 459) hydrogen bonds : angle 5.18729 ( 1353) covalent geometry : bond 0.00376 (13428) covalent geometry : angle 0.70974 (18199) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5598.03 seconds wall clock time: 100 minutes 0.16 seconds (6000.16 seconds total)