Starting phenix.real_space_refine on Mon Dec 30 11:47:45 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7w7p_32346/12_2024/7w7p_32346.cif Found real_map, /net/cci-nas-00/data/ceres_data/7w7p_32346/12_2024/7w7p_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_32346/12_2024/7w7p_32346.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7w7p_32346/12_2024/7w7p_32346.map" model { file = "/net/cci-nas-00/data/ceres_data/7w7p_32346/12_2024/7w7p_32346.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7w7p_32346/12_2024/7w7p_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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/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: 8.03, per 1000 atoms: 0.61 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: 3.21 Conformation dependent library (CDL) restraints added in 1.7 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: 1.57 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: 3.80 Time building geometry restraints manager: 3.70 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: 0.820 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.530 Check model and map are aligned: 0.100 Set scattering table: 0.120 Process input model: 30.820 Find NCS groups from input model: 0.590 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: 0.010 Load rotamer database and sin/cos tables:2.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.960 ------------------------------------------------------------------------------- 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= 0.213 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 *********************** 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 : 1.589 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: 0.2885 time to fit residues: 214.7167 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 : 1.582 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6505 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= 0.206 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 *********************** 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 : 1.491 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: 0.6846 (OUTLIER) cc_final: 0.6459 (mt) REVERT: A 166 TYR cc_start: 0.5414 (m-10) cc_final: 0.4813 (m-10) REVERT: A 239 ASP cc_start: 0.7358 (p0) cc_final: 0.7090 (p0) REVERT: B 107 LYS cc_start: 0.8017 (pttm) cc_final: 0.7664 (pptt) REVERT: B 238 MET cc_start: 0.6348 (tpp) cc_final: 0.5884 (tpp) REVERT: C 61 ASN cc_start: 0.7631 (m110) cc_final: 0.7379 (p0) REVERT: D 154 ASN cc_start: 0.7335 (p0) cc_final: 0.7091 (p0) REVERT: E 228 ASP cc_start: 0.7272 (m-30) cc_final: 0.7012 (m-30) outliers start: 38 outliers final: 26 residues processed: 443 average time/residue: 0.2759 time to fit residues: 171.2350 Evaluate side-chains 389 residues out of total 1493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 362 time to evaluate : 1.577 ------------------------------------------------------------------------------- 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 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 83 optimal weight: 3.9990 chunk 46 optimal weight: 7.9990 chunk 124 optimal weight: 3.9990 chunk 102 optimal weight: 0.7980 chunk 41 optimal weight: 0.9990 chunk 150 optimal weight: 3.9990 chunk 162 optimal weight: 4.9990 chunk 133 optimal weight: 0.0970 chunk 148 optimal weight: 2.9990 chunk 51 optimal weight: 2.9990 chunk 120 optimal weight: 3.9990 overall best weight: 1.5784 ------------------------------------------------------------------------------- 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** D 95 GLN 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: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6694 moved from start: 0.3487 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= 0.273 Angle : 0.681 8.737 18199 Z= 0.349 Chirality : 0.046 0.227 2087 Planarity : 0.005 0.071 2354 Dihedral : 4.933 65.404 1820 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 15.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 4.49 % Allowed : 17.95 % Favored : 77.56 % 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: 1.28 (0.24), residues: 473 sheet: -0.58 (0.26), residues: 375 loop : -0.24 (0.23), residues: 801 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.003 TRP E 250 HIS 0.010 0.001 HIS E 39 PHE 0.029 0.002 PHE D 40 TYR 0.030 0.002 TYR E 59 ARG 0.007 0.001 ARG E 220 *********************** 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: 67 poor density : 388 time to evaluate : 1.439 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 31 LEU cc_start: 0.6915 (OUTLIER) cc_final: 0.6501 (mt) REVERT: A 166 TYR cc_start: 0.5437 (m-10) cc_final: 0.4828 (m-10) REVERT: A 239 ASP cc_start: 0.7262 (p0) cc_final: 0.7009 (p0) REVERT: B 238 MET cc_start: 0.6509 (tpp) cc_final: 0.5838 (tpp) REVERT: C 228 ASP cc_start: 0.7525 (m-30) cc_final: 0.7256 (m-30) REVERT: E 52 THR cc_start: 0.8093 (p) cc_final: 0.7836 (t) REVERT: E 75 LEU cc_start: 0.6902 (mt) cc_final: 0.6675 (mt) REVERT: F 238 MET cc_start: 0.6915 (tpp) cc_final: 0.6473 (tpt) outliers start: 67 outliers final: 40 residues processed: 420 average time/residue: 0.2651 time to fit residues: 158.4919 Evaluate side-chains 390 residues out of total 1493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 349 time to evaluate : 1.613 ------------------------------------------------------------------------------- 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 165 THR Chi-restraints excluded: chain B residue 169 VAL 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 56 ILE Chi-restraints excluded: chain C residue 140 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 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 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 206 ILE 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 196 ASP Chi-restraints excluded: chain F residue 199 TYR Chi-restraints excluded: chain F residue 234 VAL Chi-restraints excluded: chain F residue 252 ILE Chi-restraints excluded: chain F residue 260 LEU Chi-restraints excluded: chain F residue 269 VAL Chi-restraints excluded: chain F residue 303 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 148 optimal weight: 7.9990 chunk 112 optimal weight: 0.0050 chunk 77 optimal weight: 0.9990 chunk 16 optimal weight: 2.9990 chunk 71 optimal weight: 6.9990 chunk 100 optimal weight: 3.9990 chunk 150 optimal weight: 0.1980 chunk 159 optimal weight: 4.9990 chunk 78 optimal weight: 3.9990 chunk 142 optimal weight: 4.9990 chunk 42 optimal weight: 7.9990 overall best weight: 1.6400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 21 GLN A 39 HIS ** A 248 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 21 GLN C 115 HIS ** 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: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6739 moved from start: 0.4001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 13428 Z= 0.277 Angle : 0.670 8.351 18199 Z= 0.345 Chirality : 0.045 0.185 2087 Planarity : 0.005 0.072 2354 Dihedral : 4.921 63.912 1820 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 15.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer: Outliers : 5.09 % Allowed : 19.96 % Favored : 74.95 % 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: 0.01 (0.21), residues: 1649 helix: 1.29 (0.24), residues: 461 sheet: -0.76 (0.26), residues: 386 loop : -0.24 (0.23), residues: 802 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.003 TRP E 250 HIS 0.009 0.001 HIS E 23 PHE 0.043 0.002 PHE D 40 TYR 0.022 0.002 TYR B 298 ARG 0.011 0.001 ARG B 219 *********************** 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 449 residues out of total 1493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 373 time to evaluate : 1.911 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 21 GLN cc_start: 0.8143 (OUTLIER) cc_final: 0.6274 (pp30) REVERT: A 31 LEU cc_start: 0.6789 (OUTLIER) cc_final: 0.6347 (mt) REVERT: B 40 PHE cc_start: 0.6028 (m-80) cc_final: 0.5734 (m-80) REVERT: B 238 MET cc_start: 0.6545 (tpp) cc_final: 0.5921 (tpp) REVERT: E 52 THR cc_start: 0.8147 (p) cc_final: 0.7897 (t) REVERT: E 61 ASN cc_start: 0.7548 (m110) cc_final: 0.7255 (p0) REVERT: F 277 LYS cc_start: 0.6967 (mptt) cc_final: 0.5865 (mptt) outliers start: 76 outliers final: 56 residues processed: 410 average time/residue: 0.2973 time to fit residues: 176.0542 Evaluate side-chains 398 residues out of total 1493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 340 time to evaluate : 1.519 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 VAL Chi-restraints excluded: chain A residue 21 GLN Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 56 ILE 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 76 THR 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 303 SER Chi-restraints excluded: chain C residue 19 LEU Chi-restraints excluded: chain C residue 21 GLN 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 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 181 PHE Chi-restraints excluded: chain D residue 252 ILE Chi-restraints excluded: chain D residue 256 LEU 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 159 LYS Chi-restraints excluded: chain E residue 201 TYR Chi-restraints excluded: chain E residue 206 ILE Chi-restraints excluded: chain E residue 250 TRP Chi-restraints excluded: chain F residue 56 ILE Chi-restraints excluded: chain F residue 76 THR Chi-restraints excluded: chain F residue 101 ILE Chi-restraints excluded: chain F residue 109 LEU Chi-restraints excluded: chain F residue 139 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 177 THR Chi-restraints excluded: chain F residue 199 TYR Chi-restraints excluded: chain F residue 229 TRP Chi-restraints excluded: chain F residue 233 LYS Chi-restraints excluded: chain F residue 252 ILE Chi-restraints excluded: chain F residue 260 LEU Chi-restraints excluded: chain F residue 269 VAL Chi-restraints excluded: chain F residue 275 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 132 optimal weight: 0.8980 chunk 90 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 118 optimal weight: 10.0000 chunk 65 optimal weight: 0.9990 chunk 136 optimal weight: 0.7980 chunk 110 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 81 optimal weight: 0.0020 chunk 143 optimal weight: 9.9990 chunk 40 optimal weight: 3.9990 overall best weight: 0.9392 ------------------------------------------------------------------------------- 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 C 115 HIS E 21 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6702 moved from start: 0.4253 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= 0.218 Angle : 0.651 7.792 18199 Z= 0.333 Chirality : 0.045 0.175 2087 Planarity : 0.005 0.065 2354 Dihedral : 4.793 62.995 1820 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 13.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.97 % Favored : 95.03 % Rotamer: Outliers : 5.09 % Allowed : 22.37 % Favored : 72.54 % 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: -0.01 (0.21), residues: 1649 helix: 1.15 (0.24), residues: 461 sheet: -0.65 (0.26), residues: 386 loop : -0.25 (0.23), residues: 802 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP F 19 HIS 0.010 0.001 HIS E 23 PHE 0.033 0.002 PHE D 40 TYR 0.039 0.002 TYR E 59 ARG 0.008 0.001 ARG B 219 *********************** 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 446 residues out of total 1493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 370 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: A 21 GLN cc_start: 0.7783 (OUTLIER) cc_final: 0.7579 (pp30) REVERT: A 31 LEU cc_start: 0.6658 (OUTLIER) cc_final: 0.6428 (mt) REVERT: B 40 PHE cc_start: 0.5936 (m-80) cc_final: 0.5678 (m-80) REVERT: B 238 MET cc_start: 0.6438 (tpp) cc_final: 0.5616 (tpp) REVERT: C 21 GLN cc_start: 0.7360 (OUTLIER) cc_final: 0.6943 (pp30) REVERT: D 99 LEU cc_start: 0.8287 (tt) cc_final: 0.8002 (tt) REVERT: E 52 THR cc_start: 0.8170 (p) cc_final: 0.7898 (t) REVERT: F 69 LEU cc_start: 0.7345 (OUTLIER) cc_final: 0.7056 (mm) REVERT: F 277 LYS cc_start: 0.6723 (mptt) cc_final: 0.6313 (mptt) outliers start: 76 outliers final: 60 residues processed: 412 average time/residue: 0.2750 time to fit residues: 160.0477 Evaluate side-chains 407 residues out of total 1493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 343 time to evaluate : 1.739 ------------------------------------------------------------------------------- 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 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 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 218 ASP 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 56 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 108 ASP Chi-restraints excluded: chain D residue 112 HIS Chi-restraints excluded: chain D residue 139 LEU Chi-restraints excluded: chain D residue 165 THR Chi-restraints excluded: chain D residue 169 VAL Chi-restraints excluded: chain D residue 181 PHE 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 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 159 LYS 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 62 ILE Chi-restraints excluded: chain F residue 69 LEU 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 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 196 ASP Chi-restraints excluded: chain F residue 199 TYR Chi-restraints excluded: chain F residue 229 TRP Chi-restraints excluded: chain F residue 252 ILE Chi-restraints excluded: chain F residue 260 LEU Chi-restraints excluded: chain F residue 269 VAL Chi-restraints excluded: chain F residue 275 VAL Chi-restraints excluded: chain F residue 303 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 53 optimal weight: 6.9990 chunk 143 optimal weight: 0.6980 chunk 31 optimal weight: 0.0670 chunk 93 optimal weight: 0.0370 chunk 39 optimal weight: 3.9990 chunk 159 optimal weight: 0.2980 chunk 132 optimal weight: 0.8980 chunk 73 optimal weight: 9.9990 chunk 13 optimal weight: 4.9990 chunk 52 optimal weight: 7.9990 chunk 83 optimal weight: 20.0000 overall best weight: 0.3996 ------------------------------------------------------------------------------- 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 248 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 13 GLN ** E 22 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6629 moved from start: 0.4508 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= 0.185 Angle : 0.646 9.233 18199 Z= 0.329 Chirality : 0.044 0.166 2087 Planarity : 0.005 0.061 2354 Dihedral : 4.645 62.285 1820 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 12.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.28 % Favored : 94.72 % Rotamer: Outliers : 4.09 % Allowed : 23.31 % Favored : 72.61 % 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: -0.02 (0.21), residues: 1649 helix: 1.14 (0.24), residues: 461 sheet: -0.51 (0.26), residues: 380 loop : -0.34 (0.22), residues: 808 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP F 19 HIS 0.010 0.001 HIS A 115 PHE 0.030 0.001 PHE D 40 TYR 0.031 0.001 TYR E 59 ARG 0.006 0.000 ARG B 219 *********************** 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 430 residues out of total 1493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 369 time to evaluate : 1.563 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 40 PHE cc_start: 0.6137 (m-80) cc_final: 0.5823 (m-80) REVERT: B 238 MET cc_start: 0.6473 (tpp) cc_final: 0.5775 (tpp) REVERT: C 52 THR cc_start: 0.8034 (p) cc_final: 0.7832 (t) REVERT: C 229 ASP cc_start: 0.6794 (p0) cc_final: 0.6233 (t70) REVERT: D 94 LEU cc_start: 0.8063 (mt) cc_final: 0.7757 (mt) REVERT: D 99 LEU cc_start: 0.8280 (tt) cc_final: 0.7938 (tt) REVERT: D 238 MET cc_start: 0.4772 (tpt) cc_final: 0.4364 (tpt) REVERT: E 61 ASN cc_start: 0.7421 (m110) cc_final: 0.7189 (p0) REVERT: F 62 ILE cc_start: 0.8132 (OUTLIER) cc_final: 0.7880 (pt) REVERT: F 69 LEU cc_start: 0.7373 (OUTLIER) cc_final: 0.7101 (mm) REVERT: F 237 LEU cc_start: 0.7264 (OUTLIER) cc_final: 0.7008 (mp) outliers start: 61 outliers final: 50 residues processed: 403 average time/residue: 0.2604 time to fit residues: 149.5840 Evaluate side-chains 384 residues out of total 1493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 331 time to evaluate : 1.606 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 VAL Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 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 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 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 43 LEU Chi-restraints excluded: chain C residue 56 ILE 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 108 ASP Chi-restraints excluded: chain D residue 112 HIS Chi-restraints excluded: chain D residue 139 LEU Chi-restraints excluded: chain D residue 165 THR Chi-restraints excluded: chain D residue 169 VAL Chi-restraints excluded: chain D residue 181 PHE 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 201 TYR Chi-restraints excluded: chain E residue 250 TRP Chi-restraints excluded: chain F residue 62 ILE Chi-restraints excluded: chain F residue 69 LEU 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 165 THR Chi-restraints excluded: chain F residue 196 ASP 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 275 VAL Chi-restraints excluded: chain F residue 298 TYR Chi-restraints excluded: chain F residue 303 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 153 optimal weight: 0.8980 chunk 17 optimal weight: 0.0570 chunk 90 optimal weight: 0.8980 chunk 116 optimal weight: 0.9980 chunk 134 optimal weight: 0.9980 chunk 89 optimal weight: 0.8980 chunk 159 optimal weight: 0.7980 chunk 99 optimal weight: 0.9990 chunk 96 optimal weight: 4.9990 chunk 73 optimal weight: 10.0000 chunk 98 optimal weight: 0.0570 overall best weight: 0.5416 ------------------------------------------------------------------------------- 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 248 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 61 ASN ** E 22 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 115 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6631 moved from start: 0.4724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 13428 Z= 0.191 Angle : 0.657 9.756 18199 Z= 0.333 Chirality : 0.044 0.167 2087 Planarity : 0.005 0.060 2354 Dihedral : 4.573 61.604 1820 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 13.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 4.29 % Allowed : 23.58 % Favored : 72.14 % 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: 0.04 (0.21), residues: 1649 helix: 1.29 (0.24), residues: 452 sheet: -0.43 (0.25), residues: 406 loop : -0.37 (0.23), residues: 791 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP F 19 HIS 0.010 0.001 HIS A 115 PHE 0.026 0.001 PHE D 40 TYR 0.026 0.002 TYR E 59 ARG 0.007 0.000 ARG C 199 *********************** 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 417 residues out of total 1493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 353 time to evaluate : 1.650 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 40 PHE cc_start: 0.5913 (m-80) cc_final: 0.5649 (m-80) REVERT: B 238 MET cc_start: 0.6500 (tpp) cc_final: 0.5563 (tpp) REVERT: C 229 ASP cc_start: 0.6869 (p0) cc_final: 0.6345 (t70) REVERT: D 94 LEU cc_start: 0.8022 (mt) cc_final: 0.7705 (mt) REVERT: D 238 MET cc_start: 0.5041 (tpt) cc_final: 0.4749 (tpt) REVERT: E 52 THR cc_start: 0.8087 (p) cc_final: 0.7876 (t) REVERT: E 61 ASN cc_start: 0.7419 (m110) cc_final: 0.7117 (p0) REVERT: F 62 ILE cc_start: 0.8125 (OUTLIER) cc_final: 0.7890 (pt) REVERT: F 69 LEU cc_start: 0.7400 (OUTLIER) cc_final: 0.7156 (mm) REVERT: F 237 LEU cc_start: 0.7227 (OUTLIER) cc_final: 0.7013 (mp) outliers start: 64 outliers final: 53 residues processed: 391 average time/residue: 0.2824 time to fit residues: 159.2897 Evaluate side-chains 390 residues out of total 1493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 334 time to evaluate : 1.724 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 VAL Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 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 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 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 224 VAL Chi-restraints excluded: chain C residue 250 TRP Chi-restraints excluded: chain D residue 82 ILE Chi-restraints excluded: chain D residue 86 LEU Chi-restraints excluded: chain D residue 108 ASP Chi-restraints excluded: chain D residue 112 HIS Chi-restraints excluded: chain D residue 139 LEU Chi-restraints excluded: chain D residue 165 THR Chi-restraints excluded: chain D residue 169 VAL Chi-restraints excluded: chain D residue 196 ASP Chi-restraints excluded: chain D residue 237 LEU 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 201 TYR Chi-restraints excluded: chain E residue 250 TRP Chi-restraints excluded: chain F residue 62 ILE Chi-restraints excluded: chain F residue 69 LEU 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 229 TRP Chi-restraints excluded: chain F residue 232 VAL 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 275 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 63 optimal weight: 3.9990 chunk 94 optimal weight: 2.9990 chunk 47 optimal weight: 10.0000 chunk 31 optimal weight: 0.1980 chunk 30 optimal weight: 2.9990 chunk 101 optimal weight: 3.9990 chunk 108 optimal weight: 5.9990 chunk 78 optimal weight: 5.9990 chunk 14 optimal weight: 20.0000 chunk 125 optimal weight: 10.0000 chunk 144 optimal weight: 3.9990 overall best weight: 2.8388 ------------------------------------------------------------------------------- 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** B 103 GLN C 115 HIS 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: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6900 moved from start: 0.5128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 13428 Z= 0.409 Angle : 0.795 11.890 18199 Z= 0.411 Chirality : 0.049 0.210 2087 Planarity : 0.006 0.061 2354 Dihedral : 5.434 61.117 1820 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 19.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.49 % Favored : 93.51 % Rotamer: Outliers : 5.69 % Allowed : 23.44 % Favored : 70.86 % Cbeta Deviations : 0.06 % 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: -0.26 (0.21), residues: 1649 helix: 1.12 (0.24), residues: 455 sheet: -0.83 (0.26), residues: 369 loop : -0.50 (0.23), residues: 825 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.004 TRP E 250 HIS 0.012 0.002 HIS A 22 PHE 0.029 0.002 PHE E 143 TYR 0.031 0.003 TYR E 59 ARG 0.014 0.001 ARG C 199 *********************** 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 434 residues out of total 1493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 349 time to evaluate : 1.553 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 LEU cc_start: 0.6768 (OUTLIER) cc_final: 0.6499 (mt) REVERT: A 121 ASP cc_start: 0.7934 (m-30) cc_final: 0.7724 (m-30) REVERT: B 40 PHE cc_start: 0.6243 (m-80) cc_final: 0.6001 (m-80) REVERT: B 231 SER cc_start: 0.7420 (t) cc_final: 0.7025 (t) REVERT: B 238 MET cc_start: 0.6551 (tpp) cc_final: 0.6062 (tpp) REVERT: E 52 THR cc_start: 0.8186 (p) cc_final: 0.7971 (t) REVERT: E 61 ASN cc_start: 0.7601 (m110) cc_final: 0.7163 (p0) REVERT: F 69 LEU cc_start: 0.7628 (OUTLIER) cc_final: 0.7302 (mm) REVERT: F 134 LEU cc_start: 0.7368 (OUTLIER) cc_final: 0.7125 (pp) outliers start: 85 outliers final: 57 residues processed: 398 average time/residue: 0.2458 time to fit residues: 141.2495 Evaluate side-chains 374 residues out of total 1493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 314 time to evaluate : 1.690 ------------------------------------------------------------------------------- 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 75 LEU Chi-restraints excluded: chain A residue 206 ILE Chi-restraints excluded: chain A residue 250 TRP Chi-restraints excluded: chain B residue 62 ILE Chi-restraints excluded: chain B residue 76 THR Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 160 ILE Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 169 VAL Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 181 PHE Chi-restraints excluded: chain B residue 269 VAL Chi-restraints excluded: chain B residue 297 LEU 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 135 THR Chi-restraints excluded: chain C residue 150 ASN Chi-restraints excluded: chain C residue 157 VAL Chi-restraints excluded: chain C residue 224 VAL Chi-restraints excluded: chain C residue 250 TRP Chi-restraints excluded: chain D residue 86 LEU Chi-restraints excluded: chain D residue 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 196 ASP Chi-restraints excluded: chain D residue 200 THR Chi-restraints excluded: chain D residue 234 VAL Chi-restraints excluded: chain D residue 237 LEU Chi-restraints excluded: chain D residue 252 ILE Chi-restraints excluded: chain D residue 269 VAL Chi-restraints excluded: chain D residue 273 THR Chi-restraints excluded: chain E residue 56 ILE Chi-restraints excluded: chain E residue 198 CYS Chi-restraints excluded: chain E residue 250 TRP Chi-restraints excluded: chain F residue 69 LEU Chi-restraints excluded: chain F residue 76 THR 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 139 LEU Chi-restraints excluded: chain F residue 148 LEU Chi-restraints excluded: chain F residue 165 THR Chi-restraints excluded: chain F residue 175 LEU Chi-restraints excluded: chain F residue 194 LEU Chi-restraints excluded: chain F residue 199 TYR Chi-restraints excluded: chain F residue 229 TRP Chi-restraints excluded: chain F residue 232 VAL 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 275 VAL Chi-restraints excluded: chain F residue 303 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 152 optimal weight: 3.9990 chunk 139 optimal weight: 1.9990 chunk 148 optimal weight: 0.7980 chunk 89 optimal weight: 0.6980 chunk 64 optimal weight: 1.9990 chunk 116 optimal weight: 0.5980 chunk 45 optimal weight: 0.8980 chunk 133 optimal weight: 4.9990 chunk 140 optimal weight: 1.9990 chunk 147 optimal weight: 8.9990 chunk 97 optimal weight: 2.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- 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** E 21 GLN ** E 22 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 255 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 147 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6768 moved from start: 0.5263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 13428 Z= 0.243 Angle : 0.726 11.007 18199 Z= 0.370 Chirality : 0.046 0.192 2087 Planarity : 0.005 0.058 2354 Dihedral : 4.976 59.203 1820 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 16.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.76 % Favored : 94.24 % Rotamer: Outliers : 3.55 % Allowed : 27.13 % Favored : 69.32 % 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: -0.17 (0.21), residues: 1649 helix: 1.10 (0.24), residues: 448 sheet: -0.74 (0.27), residues: 370 loop : -0.39 (0.23), residues: 831 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP E 250 HIS 0.017 0.002 HIS A 22 PHE 0.027 0.002 PHE A 143 TYR 0.026 0.002 TYR E 59 ARG 0.009 0.001 ARG C 199 *********************** 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 404 residues out of total 1493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 351 time to evaluate : 1.465 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 40 PHE cc_start: 0.6077 (m-80) cc_final: 0.5836 (m-80) REVERT: B 238 MET cc_start: 0.6667 (tpp) cc_final: 0.5752 (tpp) REVERT: D 238 MET cc_start: 0.4657 (tpt) cc_final: 0.4406 (tpt) REVERT: F 69 LEU cc_start: 0.7474 (OUTLIER) cc_final: 0.7204 (mm) REVERT: F 134 LEU cc_start: 0.7227 (OUTLIER) cc_final: 0.6964 (pp) REVERT: F 237 LEU cc_start: 0.7348 (OUTLIER) cc_final: 0.7124 (mp) outliers start: 53 outliers final: 43 residues processed: 382 average time/residue: 0.2559 time to fit residues: 140.9985 Evaluate side-chains 371 residues out of total 1493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 325 time to evaluate : 2.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 VAL Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 206 ILE Chi-restraints excluded: chain A residue 250 TRP Chi-restraints excluded: chain B residue 62 ILE Chi-restraints excluded: chain B residue 76 THR Chi-restraints excluded: chain B residue 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 140 VAL Chi-restraints excluded: chain C residue 150 ASN Chi-restraints excluded: chain C residue 157 VAL Chi-restraints excluded: chain C residue 224 VAL Chi-restraints excluded: chain C residue 250 TRP Chi-restraints excluded: chain D residue 86 LEU Chi-restraints excluded: chain D residue 108 ASP Chi-restraints excluded: chain D residue 112 HIS Chi-restraints excluded: chain D residue 169 VAL Chi-restraints excluded: chain D residue 181 PHE Chi-restraints excluded: chain D residue 196 ASP Chi-restraints excluded: chain D residue 200 THR Chi-restraints excluded: chain D residue 204 LYS Chi-restraints excluded: chain D residue 252 ILE Chi-restraints excluded: chain D residue 269 VAL Chi-restraints excluded: chain D residue 299 ILE Chi-restraints excluded: chain E residue 56 ILE Chi-restraints excluded: chain E residue 250 TRP Chi-restraints excluded: chain F residue 69 LEU 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 148 LEU Chi-restraints excluded: chain F residue 165 THR Chi-restraints excluded: chain F residue 194 LEU Chi-restraints excluded: chain F residue 199 TYR Chi-restraints excluded: chain F residue 229 TRP Chi-restraints excluded: chain F residue 232 VAL 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 275 VAL Chi-restraints excluded: chain F residue 299 ILE Chi-restraints excluded: chain F residue 303 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 156 optimal weight: 9.9990 chunk 95 optimal weight: 1.9990 chunk 74 optimal weight: 7.9990 chunk 108 optimal weight: 2.9990 chunk 164 optimal weight: 0.6980 chunk 151 optimal weight: 1.9990 chunk 130 optimal weight: 0.6980 chunk 13 optimal weight: 0.4980 chunk 101 optimal weight: 6.9990 chunk 80 optimal weight: 3.9990 chunk 103 optimal weight: 2.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- 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** ** E 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 22 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 255 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6777 moved from start: 0.5434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 13428 Z= 0.250 Angle : 0.727 11.239 18199 Z= 0.372 Chirality : 0.046 0.199 2087 Planarity : 0.005 0.059 2354 Dihedral : 4.966 59.135 1820 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 17.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.06 % Favored : 93.94 % Rotamer: Outliers : 3.22 % Allowed : 27.86 % Favored : 68.92 % 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: -0.18 (0.21), residues: 1649 helix: 1.04 (0.24), residues: 447 sheet: -0.64 (0.26), residues: 379 loop : -0.41 (0.23), residues: 823 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP E 250 HIS 0.017 0.002 HIS C 22 PHE 0.022 0.002 PHE D 40 TYR 0.025 0.002 TYR E 59 ARG 0.009 0.001 ARG F 168 ********************** 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 386 residues out of total 1493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 338 time to evaluate : 1.581 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 40 PHE cc_start: 0.6141 (m-80) cc_final: 0.5882 (m-80) REVERT: B 238 MET cc_start: 0.6510 (tpp) cc_final: 0.5835 (tpp) REVERT: D 238 MET cc_start: 0.4501 (tpt) cc_final: 0.4281 (tpt) REVERT: E 250 TRP cc_start: 0.6730 (OUTLIER) cc_final: 0.6399 (p-90) REVERT: F 69 LEU cc_start: 0.7466 (OUTLIER) cc_final: 0.7175 (mm) REVERT: F 134 LEU cc_start: 0.7240 (OUTLIER) cc_final: 0.6958 (pp) REVERT: F 237 LEU cc_start: 0.7393 (OUTLIER) cc_final: 0.7106 (mp) REVERT: F 238 MET cc_start: 0.6762 (tpt) cc_final: 0.5641 (tpp) REVERT: F 258 GLN cc_start: 0.6348 (tm-30) cc_final: 0.5917 (tm-30) outliers start: 48 outliers final: 40 residues processed: 365 average time/residue: 0.2528 time to fit residues: 133.0573 Evaluate side-chains 370 residues out of total 1493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 326 time to evaluate : 1.579 ------------------------------------------------------------------------------- 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 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 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 157 VAL Chi-restraints excluded: chain C residue 224 VAL Chi-restraints excluded: chain C residue 250 TRP Chi-restraints excluded: chain D residue 86 LEU Chi-restraints excluded: chain D residue 108 ASP Chi-restraints excluded: chain D residue 112 HIS Chi-restraints excluded: chain D residue 169 VAL Chi-restraints excluded: chain D residue 181 PHE Chi-restraints excluded: chain D residue 196 ASP Chi-restraints excluded: chain D residue 200 THR Chi-restraints excluded: chain D residue 234 VAL Chi-restraints excluded: chain D residue 252 ILE Chi-restraints excluded: chain D residue 269 VAL Chi-restraints excluded: chain D residue 299 ILE Chi-restraints excluded: chain E residue 56 ILE Chi-restraints excluded: chain E residue 250 TRP Chi-restraints excluded: chain F residue 69 LEU 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 148 LEU Chi-restraints excluded: chain F residue 165 THR Chi-restraints excluded: chain F residue 194 LEU Chi-restraints excluded: chain F residue 199 TYR Chi-restraints excluded: chain F residue 229 TRP Chi-restraints excluded: chain F residue 232 VAL 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 275 VAL Chi-restraints excluded: chain F residue 299 ILE Chi-restraints excluded: chain F residue 303 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 139 optimal weight: 1.9990 chunk 40 optimal weight: 0.5980 chunk 120 optimal weight: 0.9980 chunk 19 optimal weight: 2.9990 chunk 36 optimal weight: 4.9990 chunk 131 optimal weight: 8.9990 chunk 54 optimal weight: 2.9990 chunk 134 optimal weight: 0.7980 chunk 16 optimal weight: 1.9990 chunk 24 optimal weight: 0.9980 chunk 115 optimal weight: 3.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 22 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 255 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4481 r_free = 0.4481 target = 0.214410 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.170752 restraints weight = 21326.711| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.4059 r_free = 0.4059 target = 0.175447 restraints weight = 12859.206| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4090 r_free = 0.4090 target = 0.178309 restraints weight = 9615.406| |-----------------------------------------------------------------------------| r_work (final): 0.4050 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7021 moved from start: 0.5578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 13428 Z= 0.244 Angle : 0.741 11.456 18199 Z= 0.379 Chirality : 0.046 0.249 2087 Planarity : 0.005 0.058 2354 Dihedral : 4.991 58.963 1820 Min Nonbonded Distance : 2.311 Molprobity Statistics. All-atom Clashscore : 16.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.82 % Favored : 94.18 % Rotamer: Outliers : 3.48 % Allowed : 27.93 % Favored : 68.59 % 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: -0.19 (0.21), residues: 1649 helix: 1.02 (0.24), residues: 447 sheet: -0.64 (0.26), residues: 379 loop : -0.43 (0.23), residues: 823 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP E 250 HIS 0.019 0.002 HIS C 22 PHE 0.025 0.002 PHE E 143 TYR 0.024 0.002 TYR E 59 ARG 0.024 0.001 ARG A 77 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3565.78 seconds wall clock time: 65 minutes 46.35 seconds (3946.35 seconds total)