Starting phenix.real_space_refine on Fri Sep 19 13:06:45 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/5g06_3366/09_2025/5g06_3366.cif Found real_map, /net/cci-nas-00/data/ceres_data/5g06_3366/09_2025/5g06_3366.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/5g06_3366/09_2025/5g06_3366.cif" } default_model = "/net/cci-nas-00/data/ceres_data/5g06_3366/09_2025/5g06_3366.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/5g06_3366/09_2025/5g06_3366.map" default_real_map = "/net/cci-nas-00/data/ceres_data/5g06_3366/09_2025/5g06_3366.map" } resolution = 4.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 130 5.16 5 C 16865 2.51 5 N 4641 2.21 5 O 5158 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 26794 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 2350 Number of conformers: 1 Conformer: "" Number of residues, atoms: 302, 2350 Classifications: {'peptide': 302} Link IDs: {'PTRANS': 10, 'TRANS': 291} Chain: "B" Number of atoms: 1890 Number of conformers: 1 Conformer: "" Number of residues, atoms: 240, 1890 Classifications: {'peptide': 240} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 232} Chain: "C" Number of atoms: 2622 Number of conformers: 1 Conformer: "" Number of residues, atoms: 335, 2622 Classifications: {'peptide': 335} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 14, 'TRANS': 319} Chain breaks: 3 Chain: "D" Number of atoms: 1707 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1707 Classifications: {'peptide': 223} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 213} Chain: "E" Number of atoms: 2048 Number of conformers: 1 Conformer: "" Number of residues, atoms: 265, 2048 Classifications: {'peptide': 265} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 250} Chain: "F" Number of atoms: 1627 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1627 Classifications: {'peptide': 211} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 205} Chain breaks: 2 Chain: "G" Number of atoms: 1831 Number of conformers: 1 Conformer: "" Number of residues, atoms: 236, 1831 Classifications: {'peptide': 236} Link IDs: {'PTRANS': 11, 'TRANS': 224} Chain: "H" Number of atoms: 2277 Number of conformers: 1 Conformer: "" Number of residues, atoms: 293, 2277 Classifications: {'peptide': 293} Link IDs: {'PTRANS': 8, 'TRANS': 284} Chain breaks: 2 Chain: "I" Number of atoms: 1750 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1750 Classifications: {'peptide': 227} Link IDs: {'PTRANS': 10, 'TRANS': 216} Chain breaks: 3 Chain: "J" Number of atoms: 7942 Number of conformers: 1 Conformer: "" Number of residues, atoms: 993, 7942 Classifications: {'peptide': 993} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 50, 'TRANS': 941} Chain: "P" Number of atoms: 750 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 750 Classifications: {'peptide': 95} Link IDs: {'CIS': 1, 'PTRANS': 6, 'TRANS': 87} Time building chain proxies: 5.79, per 1000 atoms: 0.22 Number of scatterers: 26794 At special positions: 0 Unit cell: (155.478, 142.413, 138.493, 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 130 16.00 O 5158 8.00 N 4641 7.00 C 16865 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS I 3 " - pdb=" SG CYS I 66 " distance=2.04 Simple disulfide: pdb=" SG CYS J 52 " - pdb=" SG CYS J 55 " distance=2.02 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.94 Conformation dependent library (CDL) restraints added in 1.2 seconds Enol-peptide restraints added in 715.3 nanoseconds 6756 Ramachandran restraints generated. 3378 Oldfield, 0 Emsley, 3378 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6472 Finding SS restraints... Secondary structure from input PDB file: 88 helices and 44 sheets defined 31.5% alpha, 27.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.74 Creating SS restraints... Processing helix chain 'A' and resid 8 through 21 removed outlier: 3.590A pdb=" N LEU A 16 " --> pdb=" O SER A 12 " (cutoff:3.500A) Processing helix chain 'A' and resid 98 through 113 Processing helix chain 'A' and resid 120 through 122 No H-bonds generated for 'chain 'A' and resid 120 through 122' Processing helix chain 'A' and resid 146 through 162 Processing helix chain 'A' and resid 205 through 211 removed outlier: 4.182A pdb=" N LYS A 211 " --> pdb=" O GLU A 207 " (cutoff:3.500A) Processing helix chain 'A' and resid 224 through 231 Processing helix chain 'A' and resid 257 through 291 removed outlier: 3.553A pdb=" N GLU A 273 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LYS A 274 " --> pdb=" O SER A 270 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N LYS A 289 " --> pdb=" O GLU A 285 " (cutoff:3.500A) Processing helix chain 'B' and resid 61 through 65 removed outlier: 3.583A pdb=" N GLN B 64 " --> pdb=" O LEU B 61 " (cutoff:3.500A) Processing helix chain 'B' and resid 94 through 112 removed outlier: 3.506A pdb=" N ARG B 106 " --> pdb=" O THR B 102 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LYS B 110 " --> pdb=" O ARG B 106 " (cutoff:3.500A) Processing helix chain 'B' and resid 134 through 151 removed outlier: 4.189A pdb=" N ILE B 140 " --> pdb=" O MET B 136 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ASN B 141 " --> pdb=" O GLY B 137 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ILE B 143 " --> pdb=" O LEU B 139 " (cutoff:3.500A) Processing helix chain 'B' and resid 175 through 180 Processing helix chain 'B' and resid 209 through 239 removed outlier: 3.605A pdb=" N VAL B 213 " --> pdb=" O ARG B 209 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ILE B 216 " --> pdb=" O ASN B 212 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N HIS B 222 " --> pdb=" O ILE B 218 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ARG B 223 " --> pdb=" O ALA B 219 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N VAL B 224 " --> pdb=" O GLY B 220 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N LEU B 227 " --> pdb=" O ARG B 223 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N MET B 228 " --> pdb=" O VAL B 224 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LYS B 238 " --> pdb=" O LYS B 234 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ARG B 239 " --> pdb=" O HIS B 235 " (cutoff:3.500A) Processing helix chain 'C' and resid 18 through 26 Processing helix chain 'C' and resid 26 through 37 removed outlier: 4.245A pdb=" N LEU C 37 " --> pdb=" O ARG C 33 " (cutoff:3.500A) Processing helix chain 'C' and resid 60 through 64 removed outlier: 4.347A pdb=" N ASP C 64 " --> pdb=" O ARG C 61 " (cutoff:3.500A) Processing helix chain 'C' and resid 123 through 126 Processing helix chain 'C' and resid 145 through 163 removed outlier: 3.511A pdb=" N ILE C 151 " --> pdb=" O GLU C 147 " (cutoff:3.500A) Processing helix chain 'C' and resid 167 through 170 Processing helix chain 'C' and resid 226 through 239 removed outlier: 3.831A pdb=" N TYR C 236 " --> pdb=" O ASN C 232 " (cutoff:3.500A) Processing helix chain 'C' and resid 251 through 254 removed outlier: 3.530A pdb=" N ASP C 254 " --> pdb=" O ARG C 251 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 251 through 254' Processing helix chain 'C' and resid 336 through 343 removed outlier: 3.522A pdb=" N SER C 342 " --> pdb=" O ALA C 338 " (cutoff:3.500A) Processing helix chain 'C' and resid 370 through 392 removed outlier: 4.150A pdb=" N ILE C 374 " --> pdb=" O THR C 370 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N LEU C 379 " --> pdb=" O LYS C 375 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ARG C 382 " --> pdb=" O LEU C 378 " (cutoff:3.500A) Processing helix chain 'D' and resid 37 through 41 removed outlier: 3.583A pdb=" N GLU D 41 " --> pdb=" O ALA D 38 " (cutoff:3.500A) Processing helix chain 'D' and resid 61 through 78 removed outlier: 3.503A pdb=" N VAL D 65 " --> pdb=" O THR D 61 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N VAL D 73 " --> pdb=" O LYS D 69 " (cutoff:3.500A) Proline residue: D 76 - end of helix Processing helix chain 'D' and resid 79 through 83 removed outlier: 3.822A pdb=" N TYR D 83 " --> pdb=" O ARG D 80 " (cutoff:3.500A) Processing helix chain 'D' and resid 105 through 124 Processing helix chain 'D' and resid 150 through 156 removed outlier: 3.578A pdb=" N ILE D 156 " --> pdb=" O GLU D 152 " (cutoff:3.500A) Processing helix chain 'D' and resid 187 through 218 removed outlier: 3.555A pdb=" N SER D 193 " --> pdb=" O ASP D 189 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N GLN D 200 " --> pdb=" O GLU D 196 " (cutoff:3.500A) Processing helix chain 'E' and resid 4 through 17 removed outlier: 3.527A pdb=" N SER E 17 " --> pdb=" O ASP E 13 " (cutoff:3.500A) Processing helix chain 'E' and resid 89 through 103 removed outlier: 3.507A pdb=" N GLU E 93 " --> pdb=" O ALA E 89 " (cutoff:3.500A) Processing helix chain 'E' and resid 137 through 150 Processing helix chain 'E' and resid 202 through 207 Processing helix chain 'E' and resid 240 through 264 removed outlier: 3.530A pdb=" N LEU E 244 " --> pdb=" O LYS E 240 " (cutoff:3.500A) Proline residue: E 256 - end of helix removed outlier: 3.814A pdb=" N ASN E 264 " --> pdb=" O ARG E 260 " (cutoff:3.500A) Processing helix chain 'F' and resid 106 through 125 removed outlier: 3.746A pdb=" N SER F 123 " --> pdb=" O GLY F 119 " (cutoff:3.500A) Processing helix chain 'F' and resid 165 through 167 No H-bonds generated for 'chain 'F' and resid 165 through 167' Processing helix chain 'F' and resid 168 through 184 Processing helix chain 'F' and resid 222 through 245 removed outlier: 3.684A pdb=" N GLU F 232 " --> pdb=" O ASP F 228 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N ASP F 239 " --> pdb=" O ASN F 235 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N LEU F 240 " --> pdb=" O ARG F 236 " (cutoff:3.500A) Processing helix chain 'G' and resid 159 through 169 Processing helix chain 'G' and resid 173 through 182 removed outlier: 3.869A pdb=" N ALA G 180 " --> pdb=" O LYS G 176 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N HIS G 181 " --> pdb=" O VAL G 177 " (cutoff:3.500A) Processing helix chain 'G' and resid 200 through 218 removed outlier: 3.503A pdb=" N LYS G 217 " --> pdb=" O GLU G 213 " (cutoff:3.500A) Processing helix chain 'G' and resid 221 through 234 removed outlier: 4.057A pdb=" N ASP G 225 " --> pdb=" O ALA G 221 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LYS G 228 " --> pdb=" O LYS G 224 " (cutoff:3.500A) Processing helix chain 'H' and resid 139 through 141 No H-bonds generated for 'chain 'H' and resid 139 through 141' Processing helix chain 'H' and resid 155 through 163 removed outlier: 3.850A pdb=" N PHE H 162 " --> pdb=" O GLN H 158 " (cutoff:3.500A) Processing helix chain 'H' and resid 237 through 241 Processing helix chain 'H' and resid 290 through 310 Processing helix chain 'H' and resid 315 through 326 removed outlier: 3.586A pdb=" N ILE H 319 " --> pdb=" O THR H 315 " (cutoff:3.500A) Processing helix chain 'H' and resid 327 through 329 No H-bonds generated for 'chain 'H' and resid 327 through 329' Processing helix chain 'H' and resid 331 through 335 Processing helix chain 'H' and resid 337 through 356 Processing helix chain 'I' and resid 208 through 210 No H-bonds generated for 'chain 'I' and resid 208 through 210' Processing helix chain 'I' and resid 219 through 223 Processing helix chain 'I' and resid 259 through 263 Processing helix chain 'J' and resid 54 through 59 removed outlier: 3.658A pdb=" N ILE J 58 " --> pdb=" O LYS J 54 " (cutoff:3.500A) Processing helix chain 'J' and resid 91 through 98 removed outlier: 3.536A pdb=" N VAL J 95 " --> pdb=" O ASP J 91 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N LEU J 96 " --> pdb=" O THR J 92 " (cutoff:3.500A) Processing helix chain 'J' and resid 98 through 104 Processing helix chain 'J' and resid 115 through 125 removed outlier: 3.646A pdb=" N GLU J 120 " --> pdb=" O ILE J 116 " (cutoff:3.500A) Processing helix chain 'J' and resid 125 through 138 removed outlier: 3.515A pdb=" N TYR J 129 " --> pdb=" O SER J 125 " (cutoff:3.500A) Processing helix chain 'J' and resid 165 through 185 removed outlier: 3.858A pdb=" N ARG J 169 " --> pdb=" O THR J 165 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N ILE J 174 " --> pdb=" O ASN J 170 " (cutoff:3.500A) Processing helix chain 'J' and resid 186 through 189 Processing helix chain 'J' and resid 198 through 208 Processing helix chain 'J' and resid 218 through 225 removed outlier: 3.614A pdb=" N LEU J 224 " --> pdb=" O GLN J 220 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LEU J 225 " --> pdb=" O TYR J 221 " (cutoff:3.500A) Processing helix chain 'J' and resid 260 through 270 Processing helix chain 'J' and resid 303 through 308 removed outlier: 3.936A pdb=" N ASN J 308 " --> pdb=" O GLN J 304 " (cutoff:3.500A) Processing helix chain 'J' and resid 366 through 381 Processing helix chain 'J' and resid 440 through 446 removed outlier: 4.409A pdb=" N ASP J 446 " --> pdb=" O ALA J 442 " (cutoff:3.500A) Processing helix chain 'J' and resid 476 through 488 Processing helix chain 'J' and resid 496 through 502 removed outlier: 3.840A pdb=" N GLU J 501 " --> pdb=" O LYS J 497 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N CYS J 502 " --> pdb=" O LYS J 498 " (cutoff:3.500A) Processing helix chain 'J' and resid 520 through 525 Processing helix chain 'J' and resid 526 through 531 removed outlier: 4.411A pdb=" N THR J 529 " --> pdb=" O PRO J 526 " (cutoff:3.500A) Processing helix chain 'J' and resid 581 through 591 Processing helix chain 'J' and resid 605 through 611 Processing helix chain 'J' and resid 654 through 663 Processing helix chain 'J' and resid 668 through 693 removed outlier: 3.899A pdb=" N VAL J 682 " --> pdb=" O LEU J 678 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N LYS J 683 " --> pdb=" O LYS J 679 " (cutoff:3.500A) Processing helix chain 'J' and resid 698 through 703 Processing helix chain 'J' and resid 721 through 746 removed outlier: 3.523A pdb=" N VAL J 727 " --> pdb=" O THR J 723 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N GLU J 728 " --> pdb=" O ASN J 724 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N GLU J 729 " --> pdb=" O SER J 725 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N PHE J 730 " --> pdb=" O LEU J 726 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N MET J 731 " --> pdb=" O VAL J 727 " (cutoff:3.500A) Processing helix chain 'J' and resid 759 through 775 Processing helix chain 'J' and resid 782 through 792 Processing helix chain 'J' and resid 800 through 813 Processing helix chain 'J' and resid 825 through 829 removed outlier: 3.503A pdb=" N PHE J 829 " --> pdb=" O TYR J 826 " (cutoff:3.500A) Processing helix chain 'J' and resid 848 through 862 removed outlier: 3.624A pdb=" N VAL J 852 " --> pdb=" O ARG J 848 " (cutoff:3.500A) Processing helix chain 'J' and resid 868 through 872 Processing helix chain 'J' and resid 873 through 911 removed outlier: 3.632A pdb=" N MET J 877 " --> pdb=" O ASP J 873 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N ILE J 880 " --> pdb=" O LYS J 876 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ILE J 899 " --> pdb=" O GLY J 895 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N TYR J 902 " --> pdb=" O SER J 898 " (cutoff:3.500A) Processing helix chain 'J' and resid 940 through 944 Processing helix chain 'P' and resid 2 through 20 removed outlier: 3.766A pdb=" N SER P 19 " --> pdb=" O LYS P 15 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N THR P 20 " --> pdb=" O ASN P 16 " (cutoff:3.500A) Processing helix chain 'P' and resid 31 through 37 removed outlier: 3.784A pdb=" N LYS P 35 " --> pdb=" O PHE P 31 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N HIS P 37 " --> pdb=" O SER P 33 " (cutoff:3.500A) Processing helix chain 'P' and resid 53 through 64 removed outlier: 3.821A pdb=" N VAL P 57 " --> pdb=" O THR P 53 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N ALA P 58 " --> pdb=" O THR P 54 " (cutoff:3.500A) Processing helix chain 'P' and resid 64 through 72 removed outlier: 4.589A pdb=" N ASP P 68 " --> pdb=" O ARG P 64 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ILE P 71 " --> pdb=" O PRO P 67 " (cutoff:3.500A) Processing helix chain 'P' and resid 76 through 95 removed outlier: 3.515A pdb=" N ASN P 85 " --> pdb=" O GLU P 81 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N LYS P 89 " --> pdb=" O ASN P 85 " (cutoff:3.500A) Proline residue: P 92 - end of helix Processing sheet with id=AA, first strand: chain 'A' and resid 36 through 40 removed outlier: 6.231A pdb=" N LYS A 55 " --> pdb=" O LEU A 141 " (cutoff:3.500A) removed outlier: 8.295A pdb=" N TRP A 132 " --> pdb=" O ILE A 125 " (cutoff:3.500A) Processing sheet with id=AB, first strand: chain 'A' and resid 36 through 40 removed outlier: 6.231A pdb=" N LYS A 55 " --> pdb=" O LEU A 141 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LEU A 76 " --> pdb=" O TRP A 132 " (cutoff:3.500A) Processing sheet with id=AC, first strand: chain 'A' and resid 124 through 126 removed outlier: 7.460A pdb=" N LYS A 130 " --> pdb=" O CYS A 124 " (cutoff:3.500A) removed outlier: 7.545A pdb=" N TRP A 132 " --> pdb=" O VAL A 126 " (cutoff:3.500A) Processing sheet with id=AD, first strand: chain 'A' and resid 163 through 164 Processing sheet with id=AE, first strand: chain 'A' and resid 167 through 170 Processing sheet with id=AF, first strand: chain 'A' and resid 218 through 221 removed outlier: 3.520A pdb=" N LEU A 239 " --> pdb=" O ILE A 194 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N THR A 236 " --> pdb=" O VAL A 248 " (cutoff:3.500A) removed outlier: 4.634A pdb=" N VAL A 248 " --> pdb=" O THR A 236 " (cutoff:3.500A) removed outlier: 7.059A pdb=" N THR A 238 " --> pdb=" O VAL A 246 " (cutoff:3.500A) Processing sheet with id=AG, first strand: chain 'A' and resid 301 through 302 Processing sheet with id=BA, first strand: chain 'B' and resid 25 through 29 removed outlier: 7.365A pdb=" N ILE B 49 " --> pdb=" O LEU B 129 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N LEU B 129 " --> pdb=" O ILE B 49 " (cutoff:3.500A) removed outlier: 5.194A pdb=" N THR B 51 " --> pdb=" O HIS B 127 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N HIS B 127 " --> pdb=" O THR B 51 " (cutoff:3.500A) removed outlier: 5.231A pdb=" N VAL B 53 " --> pdb=" O GLU B 125 " (cutoff:3.500A) removed outlier: 7.194A pdb=" N GLU B 125 " --> pdb=" O VAL B 53 " (cutoff:3.500A) removed outlier: 5.167A pdb=" N GLY B 55 " --> pdb=" O ASP B 123 " (cutoff:3.500A) removed outlier: 6.220A pdb=" N ASP B 123 " --> pdb=" O GLY B 55 " (cutoff:3.500A) Processing sheet with id=BB, first strand: chain 'B' and resid 169 through 172 removed outlier: 8.374A pdb=" N THR B 184 " --> pdb=" O VAL B 201 " (cutoff:3.500A) removed outlier: 5.641A pdb=" N VAL B 201 " --> pdb=" O THR B 184 " (cutoff:3.500A) removed outlier: 7.244A pdb=" N THR B 186 " --> pdb=" O LEU B 199 " (cutoff:3.500A) removed outlier: 4.776A pdb=" N LEU B 199 " --> pdb=" O THR B 186 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N GLY B 188 " --> pdb=" O SER B 197 " (cutoff:3.500A) Processing sheet with id=CA, first strand: chain 'C' and resid 53 through 56 removed outlier: 3.663A pdb=" N GLY C 76 " --> pdb=" O ILE C 91 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ILE C 86 " --> pdb=" O LEU C 220 " (cutoff:3.500A) Processing sheet with id=CB, first strand: chain 'C' and resid 96 through 97 Processing sheet with id=CC, first strand: chain 'C' and resid 185 through 188 removed outlier: 3.575A pdb=" N GLY C 175 " --> pdb=" O ALA C 246 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ILE C 248 " --> pdb=" O GLY C 175 " (cutoff:3.500A) removed outlier: 11.012A pdb=" N LEU C 243 " --> pdb=" O THR C 279 " (cutoff:3.500A) removed outlier: 8.318A pdb=" N THR C 279 " --> pdb=" O LEU C 243 " (cutoff:3.500A) Processing sheet with id=CD, first strand: chain 'C' and resid 255 through 257 removed outlier: 3.901A pdb=" N LEU C 255 " --> pdb=" O THR C 271 " (cutoff:3.500A) Processing sheet with id=CE, first strand: chain 'C' and resid 329 through 332 removed outlier: 3.812A pdb=" N ILE C 349 " --> pdb=" O SER C 295 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N ILE C 347 " --> pdb=" O TYR C 297 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N SER C 345 " --> pdb=" O ILE C 299 " (cutoff:3.500A) removed outlier: 7.023A pdb=" N THR C 346 " --> pdb=" O LEU C 362 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N LEU C 362 " --> pdb=" O THR C 346 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N SER C 348 " --> pdb=" O LEU C 360 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N LEU C 360 " --> pdb=" O SER C 348 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N LEU C 350 " --> pdb=" O LYS C 358 " (cutoff:3.500A) removed outlier: 4.704A pdb=" N LYS C 358 " --> pdb=" O GLY D 184 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N GLY D 184 " --> pdb=" O LYS C 358 " (cutoff:3.500A) removed outlier: 4.898A pdb=" N LEU D 178 " --> pdb=" O GLY C 364 " (cutoff:3.500A) removed outlier: 6.180A pdb=" N LYS D 175 " --> pdb=" O VAL D 168 " (cutoff:3.500A) removed outlier: 7.964A pdb=" N VAL D 168 " --> pdb=" O LYS D 175 " (cutoff:3.500A) removed outlier: 6.192A pdb=" N VAL D 177 " --> pdb=" O GLU D 166 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N GLU D 166 " --> pdb=" O VAL D 177 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N ASP D 185 " --> pdb=" O LEU D 158 " (cutoff:3.500A) removed outlier: 7.316A pdb=" N LEU D 158 " --> pdb=" O ASP D 185 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N SER D 159 " --> pdb=" O ILE D 138 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N LEU D 163 " --> pdb=" O ILE D 134 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ILE D 134 " --> pdb=" O LEU D 163 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N LEU D 165 " --> pdb=" O ALA D 132 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N ALA D 132 " --> pdb=" O LEU D 165 " (cutoff:3.500A) Processing sheet with id=DA, first strand: chain 'D' and resid 3 through 7 removed outlier: 7.051A pdb=" N VAL D 26 " --> pdb=" O LEU D 95 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N LEU D 95 " --> pdb=" O VAL D 26 " (cutoff:3.500A) removed outlier: 5.036A pdb=" N CYS D 28 " --> pdb=" O GLN D 93 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N GLN D 93 " --> pdb=" O CYS D 28 " (cutoff:3.500A) removed outlier: 5.445A pdb=" N VAL D 30 " --> pdb=" O THR D 91 " (cutoff:3.500A) removed outlier: 7.324A pdb=" N THR D 91 " --> pdb=" O VAL D 30 " (cutoff:3.500A) removed outlier: 5.357A pdb=" N GLY D 32 " --> pdb=" O GLN D 89 " (cutoff:3.500A) removed outlier: 7.154A pdb=" N GLN D 89 " --> pdb=" O GLY D 32 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLU D 49 " --> pdb=" O CYS D 88 " (cutoff:3.500A) Processing sheet with id=EA, first strand: chain 'E' and resid 76 through 82 Processing sheet with id=EB, first strand: chain 'E' and resid 115 through 117 removed outlier: 9.337A pdb=" N PHE E 122 " --> pdb=" O LEU E 116 " (cutoff:3.500A) Processing sheet with id=HA, first strand: chain 'H' and resid 7 through 9 removed outlier: 3.665A pdb=" N ILE E 36 " --> pdb=" O THR H 8 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N GLU E 57 " --> pdb=" O ILE E 131 " (cutoff:3.500A) removed outlier: 9.337A pdb=" N PHE E 122 " --> pdb=" O LEU E 116 " (cutoff:3.500A) Processing sheet with id=HB, first strand: chain 'H' and resid 7 through 9 removed outlier: 3.665A pdb=" N ILE E 36 " --> pdb=" O THR H 8 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N GLU E 57 " --> pdb=" O ILE E 131 " (cutoff:3.500A) Processing sheet with id=EC, first strand: chain 'E' and resid 153 through 157 removed outlier: 8.698A pdb=" N LEU E 154 " --> pdb=" O TYR E 175 " (cutoff:3.500A) removed outlier: 9.024A pdb=" N TYR E 175 " --> pdb=" O LEU E 154 " (cutoff:3.500A) removed outlier: 5.300A pdb=" N LYS E 156 " --> pdb=" O HIS E 173 " (cutoff:3.500A) Processing sheet with id=ED, first strand: chain 'E' and resid 196 through 199 removed outlier: 3.707A pdb=" N ASN E 211 " --> pdb=" O VAL E 192 " (cutoff:3.500A) removed outlier: 7.117A pdb=" N GLY E 212 " --> pdb=" O ARG E 227 " (cutoff:3.500A) removed outlier: 7.332A pdb=" N ARG E 227 " --> pdb=" O GLY E 212 " (cutoff:3.500A) removed outlier: 7.180A pdb=" N ILE E 214 " --> pdb=" O PRO E 225 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N SER E 216 " --> pdb=" O THR E 223 " (cutoff:3.500A) removed outlier: 5.775A pdb=" N PHE F 213 " --> pdb=" O SER E 228 " (cutoff:3.500A) removed outlier: 5.152A pdb=" N ILE F 210 " --> pdb=" O ILE F 204 " (cutoff:3.500A) removed outlier: 6.111A pdb=" N ILE F 204 " --> pdb=" O ILE F 210 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLY F 212 " --> pdb=" O SER F 202 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N GLY F 192 " --> pdb=" O PHE F 203 " (cutoff:3.500A) Processing sheet with id=FA, first strand: chain 'F' and resid 45 through 50 removed outlier: 3.798A pdb=" N GLY F 58 " --> pdb=" O VAL F 77 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N HIS F 69 " --> pdb=" O ASP F 146 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N ASP F 146 " --> pdb=" O HIS F 69 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N THR F 71 " --> pdb=" O ASP F 144 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N ASP F 144 " --> pdb=" O THR F 71 " (cutoff:3.500A) removed outlier: 7.596A pdb=" N LEU F 73 " --> pdb=" O THR F 142 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N THR F 142 " --> pdb=" O LEU F 73 " (cutoff:3.500A) removed outlier: 5.333A pdb=" N SER F 75 " --> pdb=" O TYR F 140 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N TYR F 140 " --> pdb=" O SER F 75 " (cutoff:3.500A) removed outlier: 5.275A pdb=" N VAL F 77 " --> pdb=" O PHE F 138 " (cutoff:3.500A) removed outlier: 7.065A pdb=" N PHE F 138 " --> pdb=" O VAL F 77 " (cutoff:3.500A) removed outlier: 5.169A pdb=" N GLY F 79 " --> pdb=" O ASP F 136 " (cutoff:3.500A) removed outlier: 5.609A pdb=" N ASP F 136 " --> pdb=" O GLY F 79 " (cutoff:3.500A) Processing sheet with id=GA, first strand: chain 'G' and resid 2 through 5 Processing sheet with id=GB, first strand: chain 'G' and resid 25 through 27 Processing sheet with id=GC, first strand: chain 'G' and resid 71 through 79 removed outlier: 6.773A pdb=" N GLU G 133 " --> pdb=" O CYS G 124 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N SER G 98 " --> pdb=" O ILE G 134 " (cutoff:3.500A) Processing sheet with id=GD, first strand: chain 'G' and resid 154 through 157 removed outlier: 3.540A pdb=" N VAL G 196 " --> pdb=" O MET G 154 " (cutoff:3.500A) Processing sheet with id=HC, first strand: chain 'H' and resid 75 through 76 Processing sheet with id=HD, first strand: chain 'H' and resid 86 through 91 Processing sheet with id=HE, first strand: chain 'H' and resid 111 through 119 removed outlier: 7.586A pdb=" N SER H 183 " --> pdb=" O VAL H 173 " (cutoff:3.500A) removed outlier: 7.860A pdb=" N HIS H 185 " --> pdb=" O SER H 175 " (cutoff:3.500A) removed outlier: 12.618A pdb=" N ALA H 182 " --> pdb=" O MET H 137 " (cutoff:3.500A) removed outlier: 7.956A pdb=" N MET H 137 " --> pdb=" O ALA H 182 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N VAL H 135 " --> pdb=" O LEU H 184 " (cutoff:3.500A) Processing sheet with id=HF, first strand: chain 'H' and resid 197 through 201 removed outlier: 3.700A pdb=" N ILE H 221 " --> pdb=" O LEU H 217 " (cutoff:3.500A) Processing sheet with id=IA, first strand: chain 'I' and resid 10 through 11 removed outlier: 3.555A pdb=" N THR I 63 " --> pdb=" O LEU I 111 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LEU I 111 " --> pdb=" O THR I 63 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N SER I 109 " --> pdb=" O ARG I 65 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N GLU I 67 " --> pdb=" O LEU I 107 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N LYS I 104 " --> pdb=" O ILE I 32 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ASN I 34 " --> pdb=" O LYS I 104 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ILE I 106 " --> pdb=" O ASN I 34 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N VAL I 36 " --> pdb=" O ILE I 106 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N GLU I 24 " --> pdb=" O ILE I 31 " (cutoff:3.500A) Processing sheet with id=IB, first strand: chain 'I' and resid 16 through 19 removed outlier: 7.035A pdb=" N ILE I 56 " --> pdb=" O ILE I 17 " (cutoff:3.500A) removed outlier: 8.653A pdb=" N GLU I 54 " --> pdb=" O PRO I 19 " (cutoff:3.500A) Processing sheet with id=IC, first strand: chain 'I' and resid 138 through 146 removed outlier: 6.879A pdb=" N TYR I 244 " --> pdb=" O GLN I 233 " (cutoff:3.500A) removed outlier: 7.502A pdb=" N THR I 246 " --> pdb=" O LEU I 235 " (cutoff:3.500A) removed outlier: 7.051A pdb=" N ILE I 204 " --> pdb=" O LEU I 245 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 150 through 158 current: chain 'I' and resid 138 through 146 Processing sheet with id=ID, first strand: chain 'I' and resid 269 through 271 removed outlier: 6.422A pdb=" N MET I 274 " --> pdb=" O THR I 270 " (cutoff:3.500A) Processing sheet with id=JA, first strand: chain 'J' and resid 11 through 14 removed outlier: 7.071A pdb=" N LEU J 17 " --> pdb=" O LEU J 13 " (cutoff:3.500A) Processing sheet with id=JB, first strand: chain 'J' and resid 78 through 79 removed outlier: 6.696A pdb=" N HIS J 86 " --> pdb=" O LEU J 79 " (cutoff:3.500A) Processing sheet with id=JC, first strand: chain 'J' and resid 144 through 148 removed outlier: 5.767A pdb=" N ASP J 110 " --> pdb=" O HIS J 86 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N ILE J 214 " --> pdb=" O VAL J 192 " (cutoff:3.500A) Processing sheet with id=JD, first strand: chain 'J' and resid 144 through 148 removed outlier: 5.767A pdb=" N ASP J 110 " --> pdb=" O HIS J 86 " (cutoff:3.500A) Processing sheet with id=JE, first strand: chain 'J' and resid 274 through 280 removed outlier: 7.211A pdb=" N GLN J 315 " --> pdb=" O ILE J 395 " (cutoff:3.500A) removed outlier: 5.165A pdb=" N ILE J 395 " --> pdb=" O GLN J 315 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N ILE J 317 " --> pdb=" O VAL J 393 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N VAL J 302 " --> pdb=" O ALA J 390 " (cutoff:3.500A) removed outlier: 8.103A pdb=" N VAL J 392 " --> pdb=" O VAL J 302 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N SER J 291 " --> pdb=" O ASN J 277 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N ASN J 277 " --> pdb=" O SER J 291 " (cutoff:3.500A) Processing sheet with id=JF, first strand: chain 'J' and resid 403 through 407 removed outlier: 4.849A pdb=" N LEU J 407 " --> pdb=" O LYS J 447 " (cutoff:3.500A) removed outlier: 7.447A pdb=" N LYS J 447 " --> pdb=" O LEU J 407 " (cutoff:3.500A) removed outlier: 7.379A pdb=" N ARG J 448 " --> pdb=" O ASP J 470 " (cutoff:3.500A) removed outlier: 5.186A pdb=" N ASP J 470 " --> pdb=" O ARG J 448 " (cutoff:3.500A) removed outlier: 7.020A pdb=" N VAL J 450 " --> pdb=" O VAL J 468 " (cutoff:3.500A) removed outlier: 7.213A pdb=" N LEU J 464 " --> pdb=" O ASP J 454 " (cutoff:3.500A) removed outlier: 5.667A pdb=" N ARG J 437 " --> pdb=" O GLY J 465 " (cutoff:3.500A) removed outlier: 6.286A pdb=" N PHE J 467 " --> pdb=" O ARG J 437 " (cutoff:3.500A) Processing sheet with id=JG, first strand: chain 'J' and resid 532 through 533 removed outlier: 3.968A pdb=" N ASN J 638 " --> pdb=" O GLU J 629 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N SER J 648 " --> pdb=" O VAL J 619 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N VAL J 619 " --> pdb=" O SER J 648 " (cutoff:3.500A) removed outlier: 6.104A pdb=" N ASP J 552 " --> pdb=" O ILE J 542 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N ILE J 542 " --> pdb=" O ASP J 552 " (cutoff:3.500A) Processing sheet with id=JH, first strand: chain 'J' and resid 751 through 754 Processing sheet with id=JI, first strand: chain 'J' and resid 936 through 939 removed outlier: 6.766A pdb=" N VAL J 927 " --> pdb=" O ILE J 919 " (cutoff:3.500A) Processing sheet with id=JJ, first strand: chain 'J' and resid 952 through 954 1154 hydrogen bonds defined for protein. 3216 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: 4.73 Time building geometry restraints manager: 2.65 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.31: 4834 1.31 - 1.46: 9304 1.46 - 1.61: 12755 1.61 - 1.77: 164 1.77 - 1.92: 176 Bond restraints: 27233 Sorted by residual: bond pdb=" CA GLY I 265 " pdb=" C GLY I 265 " ideal model delta sigma weight residual 1.516 1.418 0.099 8.90e-03 1.26e+04 1.23e+02 bond pdb=" N VAL J 113 " pdb=" CA VAL J 113 " ideal model delta sigma weight residual 1.460 1.378 0.082 7.60e-03 1.73e+04 1.18e+02 bond pdb=" CA LYS A 130 " pdb=" C LYS A 130 " ideal model delta sigma weight residual 1.520 1.391 0.129 1.22e-02 6.72e+03 1.12e+02 bond pdb=" CA GLY B 188 " pdb=" C GLY B 188 " ideal model delta sigma weight residual 1.513 1.404 0.108 1.03e-02 9.43e+03 1.11e+02 bond pdb=" CA GLY C 298 " pdb=" C GLY C 298 " ideal model delta sigma weight residual 1.510 1.394 0.116 1.11e-02 8.12e+03 1.10e+02 ... (remaining 27228 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.48: 25427 3.48 - 6.96: 9541 6.96 - 10.45: 1698 10.45 - 13.93: 168 13.93 - 17.41: 12 Bond angle restraints: 36846 Sorted by residual: angle pdb=" CA PHE J 641 " pdb=" CB PHE J 641 " pdb=" CG PHE J 641 " ideal model delta sigma weight residual 113.80 99.54 14.26 1.00e+00 1.00e+00 2.03e+02 angle pdb=" CA LEU J 225 " pdb=" C LEU J 225 " pdb=" O LEU J 225 " ideal model delta sigma weight residual 119.75 108.32 11.43 9.40e-01 1.13e+00 1.48e+02 angle pdb=" N ASP B 132 " pdb=" CA ASP B 132 " pdb=" C ASP B 132 " ideal model delta sigma weight residual 112.03 96.52 15.51 1.31e+00 5.83e-01 1.40e+02 angle pdb=" CA LEU A 254 " pdb=" C LEU A 254 " pdb=" N PRO A 255 " ideal model delta sigma weight residual 118.85 129.76 -10.91 9.50e-01 1.11e+00 1.32e+02 angle pdb=" CA LEU J 225 " pdb=" C LEU J 225 " pdb=" N PRO J 226 " ideal model delta sigma weight residual 118.87 129.20 -10.33 9.00e-01 1.23e+00 1.32e+02 ... (remaining 36841 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 19.29: 15231 19.29 - 38.58: 1102 38.58 - 57.87: 241 57.87 - 77.16: 114 77.16 - 96.45: 69 Dihedral angle restraints: 16757 sinusoidal: 6794 harmonic: 9963 Sorted by residual: dihedral pdb=" C ILE C 12 " pdb=" N ILE C 12 " pdb=" CA ILE C 12 " pdb=" CB ILE C 12 " ideal model delta harmonic sigma weight residual -122.00 -151.11 29.11 0 2.50e+00 1.60e-01 1.36e+02 dihedral pdb=" N ILE C 12 " pdb=" C ILE C 12 " pdb=" CA ILE C 12 " pdb=" CB ILE C 12 " ideal model delta harmonic sigma weight residual 123.40 147.06 -23.66 0 2.50e+00 1.60e-01 8.96e+01 dihedral pdb=" N ALA J 634 " pdb=" C ALA J 634 " pdb=" CA ALA J 634 " pdb=" CB ALA J 634 " ideal model delta harmonic sigma weight residual 122.90 145.13 -22.23 0 2.50e+00 1.60e-01 7.91e+01 ... (remaining 16754 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.213: 3004 0.213 - 0.426: 1107 0.426 - 0.638: 143 0.638 - 0.851: 16 0.851 - 1.064: 1 Chirality restraints: 4271 Sorted by residual: chirality pdb=" CA ILE C 12 " pdb=" N ILE C 12 " pdb=" C ILE C 12 " pdb=" CB ILE C 12 " both_signs ideal model delta sigma weight residual False 2.43 1.37 1.06 2.00e-01 2.50e+01 2.83e+01 chirality pdb=" CA ALA J 634 " pdb=" N ALA J 634 " pdb=" C ALA J 634 " pdb=" CB ALA J 634 " both_signs ideal model delta sigma weight residual False 2.48 1.64 0.84 2.00e-01 2.50e+01 1.77e+01 chirality pdb=" CA LEU J 48 " pdb=" N LEU J 48 " pdb=" C LEU J 48 " pdb=" CB LEU J 48 " both_signs ideal model delta sigma weight residual False 2.51 1.71 0.80 2.00e-01 2.50e+01 1.62e+01 ... (remaining 4268 not shown) Planarity restraints: 4773 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR I 21 " 0.168 2.00e-02 2.50e+03 1.30e-01 3.35e+02 pdb=" CG TYR I 21 " 0.036 2.00e-02 2.50e+03 pdb=" CD1 TYR I 21 " -0.062 2.00e-02 2.50e+03 pdb=" CD2 TYR I 21 " -0.099 2.00e-02 2.50e+03 pdb=" CE1 TYR I 21 " -0.140 2.00e-02 2.50e+03 pdb=" CE2 TYR I 21 " -0.083 2.00e-02 2.50e+03 pdb=" CZ TYR I 21 " -0.065 2.00e-02 2.50e+03 pdb=" OH TYR I 21 " 0.245 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP J 180 " -0.232 2.00e-02 2.50e+03 1.15e-01 3.33e+02 pdb=" CG TRP J 180 " 0.077 2.00e-02 2.50e+03 pdb=" CD1 TRP J 180 " 0.083 2.00e-02 2.50e+03 pdb=" CD2 TRP J 180 " 0.080 2.00e-02 2.50e+03 pdb=" NE1 TRP J 180 " -0.006 2.00e-02 2.50e+03 pdb=" CE2 TRP J 180 " 0.051 2.00e-02 2.50e+03 pdb=" CE3 TRP J 180 " 0.134 2.00e-02 2.50e+03 pdb=" CZ2 TRP J 180 " -0.095 2.00e-02 2.50e+03 pdb=" CZ3 TRP J 180 " 0.068 2.00e-02 2.50e+03 pdb=" CH2 TRP J 180 " -0.161 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR J 221 " 0.141 2.00e-02 2.50e+03 1.08e-01 2.34e+02 pdb=" CG TYR J 221 " 0.006 2.00e-02 2.50e+03 pdb=" CD1 TYR J 221 " -0.044 2.00e-02 2.50e+03 pdb=" CD2 TYR J 221 " -0.041 2.00e-02 2.50e+03 pdb=" CE1 TYR J 221 " -0.090 2.00e-02 2.50e+03 pdb=" CE2 TYR J 221 " -0.129 2.00e-02 2.50e+03 pdb=" CZ TYR J 221 " -0.050 2.00e-02 2.50e+03 pdb=" OH TYR J 221 " 0.207 2.00e-02 2.50e+03 ... (remaining 4770 not shown) Histogram of nonbonded interaction distances: 1.19 - 1.93: 8 1.93 - 2.67: 1396 2.67 - 3.42: 32699 3.42 - 4.16: 64893 4.16 - 4.90: 113998 Nonbonded interactions: 212994 Sorted by model distance: nonbonded pdb=" OE2 GLU C 48 " pdb=" CB ASN P 49 " model vdw 1.189 3.440 nonbonded pdb=" CD GLU C 48 " pdb=" CB ASN P 49 " model vdw 1.410 3.670 nonbonded pdb=" CD LYS C 81 " pdb=" CD LYS P 35 " model vdw 1.485 3.840 nonbonded pdb=" N LEU I 16 " pdb=" NZ LYS P 15 " model vdw 1.542 3.200 nonbonded pdb=" CG GLU C 48 " pdb=" CB ASN P 49 " model vdw 1.620 3.840 ... (remaining 212989 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 0.340 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.370 Check model and map are aligned: 0.080 Set scattering table: 0.070 Process input model: 22.870 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.280 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4815 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 : 0.036 0.151 27236 Z= 2.318 Angle : 3.534 17.412 36850 Z= 2.392 Chirality : 0.208 1.064 4271 Planarity : 0.029 0.366 4773 Dihedral : 17.027 96.449 10279 Min Nonbonded Distance : 1.189 Molprobity Statistics. All-atom Clashscore : 3.05 Ramachandran Plot: Outliers : 1.87 % Allowed : 5.86 % Favored : 92.27 % Rotamer: Outliers : 3.01 % Allowed : 8.31 % Favored : 88.68 % Cbeta Deviations : 7.60 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.06 % Twisted Proline : 0.69 % Twisted General : 0.12 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.39 (0.12), residues: 3378 helix: -0.80 (0.15), residues: 927 sheet: -0.35 (0.19), residues: 656 loop : -2.59 (0.12), residues: 1795 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.077 0.012 ARG J 531 TYR 0.245 0.045 TYR I 21 PHE 0.165 0.038 PHE E 40 TRP 0.232 0.050 TRP J 180 HIS 0.056 0.018 HIS C 161 Details of bonding type rmsd covalent geometry : bond 0.03566 (27233) covalent geometry : angle 3.53438 (36846) SS BOND : bond 0.01236 ( 2) SS BOND : angle 2.89999 ( 4) hydrogen bonds : bond 0.24649 ( 1097) hydrogen bonds : angle 8.75015 ( 3216) Misc. bond : bond 0.11183 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6756 Ramachandran restraints generated. 3378 Oldfield, 0 Emsley, 3378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6756 Ramachandran restraints generated. 3378 Oldfield, 0 Emsley, 3378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1074 residues out of total 3020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 983 time to evaluate : 0.987 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: 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 136 MET cc_start: 0.6028 (tpt) cc_final: 0.5786 (tpp) REVERT: B 165 LEU cc_start: 0.6725 (tp) cc_final: 0.6454 (tp) REVERT: B 201 VAL cc_start: 0.7133 (t) cc_final: 0.6736 (t) REVERT: B 228 MET cc_start: 0.4334 (mtp) cc_final: 0.4033 (mtm) REVERT: C 153 GLN cc_start: 0.6389 (tm-30) cc_final: 0.6081 (tm-30) REVERT: D 1 MET cc_start: 0.3335 (ppp) cc_final: 0.2525 (ppp) REVERT: D 9 ILE cc_start: 0.6568 (OUTLIER) cc_final: 0.6180 (mt) REVERT: D 52 VAL cc_start: 0.7493 (t) cc_final: 0.7027 (t) REVERT: E 182 ILE cc_start: 0.6597 (tt) cc_final: 0.6194 (tt) REVERT: F 53 ILE cc_start: 0.5186 (pt) cc_final: 0.4718 (pt) REVERT: F 245 LEU cc_start: 0.7627 (mt) cc_final: 0.7221 (mt) REVERT: G 96 SER cc_start: 0.4557 (OUTLIER) cc_final: 0.3459 (t) REVERT: H 329 TYR cc_start: 0.5148 (m-80) cc_final: 0.4855 (m-10) REVERT: I 161 LYS cc_start: 0.1978 (OUTLIER) cc_final: 0.1247 (pptt) REVERT: J 231 ILE cc_start: 0.3336 (mt) cc_final: 0.2949 (mp) REVERT: J 326 TRP cc_start: 0.3527 (m-10) cc_final: 0.3262 (m-10) REVERT: J 341 VAL cc_start: 0.6063 (m) cc_final: 0.5568 (p) REVERT: J 411 SER cc_start: 0.5963 (m) cc_final: 0.5382 (t) REVERT: J 870 THR cc_start: 0.6236 (OUTLIER) cc_final: 0.5896 (p) outliers start: 91 outliers final: 14 residues processed: 1056 average time/residue: 0.1905 time to fit residues: 303.4186 Evaluate side-chains 467 residues out of total 3020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 449 time to evaluate : 0.840 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 338 random chunks: chunk 197 optimal weight: 5.9990 chunk 215 optimal weight: 8.9990 chunk 20 optimal weight: 0.9990 chunk 132 optimal weight: 8.9990 chunk 261 optimal weight: 20.0000 chunk 248 optimal weight: 5.9990 chunk 207 optimal weight: 10.0000 chunk 155 optimal weight: 6.9990 chunk 244 optimal weight: 6.9990 chunk 183 optimal weight: 5.9990 chunk 298 optimal weight: 8.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 215 ASN ** A 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 291 ASN ** B 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 131 GLN B 175 ASN ** D 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 114 ASN D 208 ASN E 85 GLN E 150 ASN E 173 HIS E 195 ASN E 196 ASN E 204 ASN E 210 ASN F 99 ASN F 235 ASN G 53 GLN H 53 GLN H 92 ASN ** H 170 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 285 ASN H 302 ASN ** H 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 6 GLN ** I 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 126 ASN I 192 GLN J 277 ASN J 284 ASN J 406 GLN J 420 GLN J 460 HIS J 555 HIS J 569 HIS J 667 ASN ** J 755 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 771 ASN J 923 ASN ** P 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 16 ASN P 49 ASN Total number of N/Q/H flips: 35 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.083085 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.064219 restraints weight = 137454.585| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.066483 restraints weight = 87410.127| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.068106 restraints weight = 62767.502| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.069281 restraints weight = 48840.436| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 52)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.070172 restraints weight = 40272.734| |-----------------------------------------------------------------------------| r_work (final): 0.3588 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7760 moved from start: 0.4915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.074 27236 Z= 0.251 Angle : 0.813 10.206 36850 Z= 0.439 Chirality : 0.048 0.191 4271 Planarity : 0.007 0.078 4773 Dihedral : 6.285 54.712 3690 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 13.25 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.32 % Favored : 96.51 % Rotamer: Outliers : 0.20 % Allowed : 4.40 % Favored : 95.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.94 (0.13), residues: 3378 helix: 0.88 (0.16), residues: 975 sheet: 0.00 (0.18), residues: 707 loop : -1.88 (0.13), residues: 1696 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.001 ARG J 28 TYR 0.032 0.002 TYR C 272 PHE 0.031 0.003 PHE G 91 TRP 0.047 0.004 TRP I 272 HIS 0.008 0.002 HIS J 149 Details of bonding type rmsd covalent geometry : bond 0.00510 (27233) covalent geometry : angle 0.81311 (36846) SS BOND : bond 0.00270 ( 2) SS BOND : angle 1.28209 ( 4) hydrogen bonds : bond 0.05312 ( 1097) hydrogen bonds : angle 5.73049 ( 3216) Misc. bond : bond 0.01052 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6756 Ramachandran restraints generated. 3378 Oldfield, 0 Emsley, 3378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6756 Ramachandran restraints generated. 3378 Oldfield, 0 Emsley, 3378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 535 residues out of total 3020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 529 time to evaluate : 0.876 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: 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: symmetry clash REVERT: A 21 GLN cc_start: 0.9600 (mm110) cc_final: 0.9171 (mm110) REVERT: A 101 GLU cc_start: 0.8795 (tm-30) cc_final: 0.8410 (tm-30) REVERT: A 177 HIS cc_start: 0.7437 (m-70) cc_final: 0.7179 (m-70) REVERT: A 256 MET cc_start: 0.8550 (tpp) cc_final: 0.7960 (tpt) REVERT: B 99 GLU cc_start: 0.8810 (pp20) cc_final: 0.7839 (pt0) REVERT: B 136 MET cc_start: 0.8906 (tpt) cc_final: 0.8353 (tpp) REVERT: B 157 TYR cc_start: 0.8296 (m-10) cc_final: 0.8070 (m-10) REVERT: B 202 GLU cc_start: 0.7638 (mm-30) cc_final: 0.7341 (tm-30) REVERT: B 235 HIS cc_start: 0.8059 (m170) cc_final: 0.7717 (m170) REVERT: C 151 ILE cc_start: 0.9441 (mm) cc_final: 0.9224 (mm) REVERT: C 153 GLN cc_start: 0.9191 (tm-30) cc_final: 0.8838 (tp40) REVERT: C 296 ASN cc_start: 0.9137 (t0) cc_final: 0.8840 (t0) REVERT: D 82 CYS cc_start: 0.7812 (t) cc_final: 0.7111 (t) REVERT: D 83 TYR cc_start: 0.7610 (m-80) cc_final: 0.7353 (m-80) REVERT: D 125 ILE cc_start: 0.9529 (mm) cc_final: 0.9272 (mp) REVERT: D 153 GLN cc_start: 0.9526 (mt0) cc_final: 0.9229 (mt0) REVERT: E 73 ASN cc_start: 0.9083 (p0) cc_final: 0.8388 (t0) REVERT: E 143 PHE cc_start: 0.9118 (m-10) cc_final: 0.8893 (m-10) REVERT: F 84 ARG cc_start: 0.6528 (ppt170) cc_final: 0.6246 (ppt170) REVERT: F 94 SER cc_start: 0.9173 (t) cc_final: 0.8819 (p) REVERT: F 108 ASN cc_start: 0.9240 (m-40) cc_final: 0.8988 (m-40) REVERT: F 132 LYS cc_start: 0.8599 (mtmt) cc_final: 0.8326 (mtmt) REVERT: F 233 GLN cc_start: 0.9304 (mt0) cc_final: 0.8870 (mt0) REVERT: F 241 MET cc_start: 0.9492 (mtt) cc_final: 0.8981 (tmm) REVERT: F 246 MET cc_start: 0.8860 (ppp) cc_final: 0.8639 (ppp) REVERT: G 11 PHE cc_start: 0.7771 (t80) cc_final: 0.7478 (t80) REVERT: G 53 GLN cc_start: 0.7541 (pt0) cc_final: 0.7229 (mt0) REVERT: G 165 GLN cc_start: 0.9130 (tp-100) cc_final: 0.8664 (tp40) REVERT: G 213 GLU cc_start: 0.8661 (tt0) cc_final: 0.8406 (tt0) REVERT: H 54 ILE cc_start: 0.7693 (tp) cc_final: 0.7477 (tp) REVERT: H 79 MET cc_start: 0.9484 (mpp) cc_final: 0.9102 (mpp) REVERT: H 191 TYR cc_start: 0.7145 (m-10) cc_final: 0.6591 (m-80) REVERT: H 281 TYR cc_start: 0.7708 (m-10) cc_final: 0.7212 (m-10) REVERT: H 341 MET cc_start: 0.8980 (ttm) cc_final: 0.8631 (ttm) REVERT: I 146 LEU cc_start: 0.9344 (tp) cc_final: 0.8571 (mt) REVERT: I 156 LEU cc_start: 0.8619 (pp) cc_final: 0.8269 (tp) REVERT: I 267 MET cc_start: 0.6553 (ptm) cc_final: 0.6047 (ptt) REVERT: I 275 MET cc_start: 0.8242 (mtt) cc_final: 0.8026 (mtt) REVERT: J 312 ASN cc_start: 0.7332 (t0) cc_final: 0.6889 (t0) REVERT: J 411 SER cc_start: 0.8936 (m) cc_final: 0.7829 (t) REVERT: J 451 ILE cc_start: 0.9574 (pt) cc_final: 0.9374 (mm) REVERT: J 485 LEU cc_start: 0.9298 (mt) cc_final: 0.8852 (tt) REVERT: J 603 MET cc_start: 0.8599 (tmm) cc_final: 0.6640 (ptm) REVERT: J 628 TRP cc_start: 0.8676 (p-90) cc_final: 0.8283 (p-90) REVERT: J 674 MET cc_start: 0.5171 (mtt) cc_final: 0.4246 (ptp) REVERT: J 853 VAL cc_start: 0.9015 (t) cc_final: 0.8557 (t) REVERT: J 879 MET cc_start: 0.8080 (ptt) cc_final: 0.7768 (pmm) REVERT: J 907 MET cc_start: 0.8965 (tpt) cc_final: 0.8585 (tpt) REVERT: J 926 ILE cc_start: 0.9073 (pt) cc_final: 0.8519 (mm) outliers start: 6 outliers final: 0 residues processed: 533 average time/residue: 0.1909 time to fit residues: 154.8887 Evaluate side-chains 348 residues out of total 3020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 348 time to evaluate : 1.066 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 338 random chunks: chunk 287 optimal weight: 8.9990 chunk 333 optimal weight: 50.0000 chunk 82 optimal weight: 8.9990 chunk 297 optimal weight: 5.9990 chunk 269 optimal weight: 8.9990 chunk 91 optimal weight: 0.9990 chunk 294 optimal weight: 10.0000 chunk 64 optimal weight: 9.9990 chunk 125 optimal weight: 20.0000 chunk 221 optimal weight: 10.0000 chunk 134 optimal weight: 7.9990 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 GLN ** A 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 20 ASN ** B 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 131 GLN ** D 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 86 GLN D 208 ASN D 216 ASN ** E 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 69 HIS ** F 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 53 GLN ** G 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 213 HIS H 295 GLN I 45 GLN J 97 GLN ** J 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 338 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 466 HIS J 638 ASN ** J 755 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 841 HIS P 8 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.077028 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.058159 restraints weight = 143501.756| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.060413 restraints weight = 88343.893| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.062046 restraints weight = 62392.106| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.063208 restraints weight = 48060.030| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.064047 restraints weight = 39470.598| |-----------------------------------------------------------------------------| r_work (final): 0.3390 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7875 moved from start: 0.6128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.086 27236 Z= 0.265 Angle : 0.764 11.705 36850 Z= 0.411 Chirality : 0.047 0.248 4271 Planarity : 0.006 0.080 4773 Dihedral : 5.846 51.122 3690 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 17.06 Ramachandran Plot: Outliers : 0.15 % Allowed : 3.79 % Favored : 96.06 % Rotamer: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.77 (0.13), residues: 3378 helix: 0.86 (0.16), residues: 975 sheet: 0.06 (0.19), residues: 701 loop : -1.63 (0.13), residues: 1702 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG J 896 TYR 0.025 0.002 TYR G 84 PHE 0.025 0.003 PHE C 247 TRP 0.025 0.003 TRP J 400 HIS 0.007 0.002 HIS J 755 Details of bonding type rmsd covalent geometry : bond 0.00543 (27233) covalent geometry : angle 0.76389 (36846) SS BOND : bond 0.00255 ( 2) SS BOND : angle 1.91958 ( 4) hydrogen bonds : bond 0.04837 ( 1097) hydrogen bonds : angle 5.57568 ( 3216) Misc. bond : bond 0.00155 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6756 Ramachandran restraints generated. 3378 Oldfield, 0 Emsley, 3378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6756 Ramachandran restraints generated. 3378 Oldfield, 0 Emsley, 3378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 435 residues out of total 3020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 435 time to evaluate : 1.094 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: 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 101 GLU cc_start: 0.8848 (tm-30) cc_final: 0.8476 (tm-30) REVERT: A 114 ARG cc_start: 0.8513 (mtt-85) cc_final: 0.8091 (mtp85) REVERT: A 121 GLU cc_start: 0.8157 (mm-30) cc_final: 0.7674 (mt-10) REVERT: A 256 MET cc_start: 0.8958 (tpp) cc_final: 0.8623 (tpp) REVERT: B 77 ASN cc_start: 0.9075 (m-40) cc_final: 0.8794 (m-40) REVERT: B 136 MET cc_start: 0.9246 (tpt) cc_final: 0.8882 (tpp) REVERT: B 154 MET cc_start: 0.8835 (pmm) cc_final: 0.8632 (pmm) REVERT: B 157 TYR cc_start: 0.8106 (m-10) cc_final: 0.7765 (m-10) REVERT: B 228 MET cc_start: 0.9134 (mtm) cc_final: 0.8879 (mtm) REVERT: B 235 HIS cc_start: 0.8088 (m170) cc_final: 0.7742 (m170) REVERT: C 146 ASP cc_start: 0.8369 (p0) cc_final: 0.7801 (p0) REVERT: C 149 MET cc_start: 0.8877 (ptp) cc_final: 0.8271 (ptp) REVERT: C 153 GLN cc_start: 0.9139 (tm-30) cc_final: 0.8909 (tm-30) REVERT: C 362 LEU cc_start: 0.9580 (tp) cc_final: 0.8954 (tp) REVERT: C 363 MET cc_start: 0.9061 (mtp) cc_final: 0.8331 (mpp) REVERT: D 82 CYS cc_start: 0.8289 (t) cc_final: 0.7547 (t) REVERT: D 83 TYR cc_start: 0.8237 (m-80) cc_final: 0.7763 (m-80) REVERT: D 141 ASP cc_start: 0.8495 (m-30) cc_final: 0.8122 (m-30) REVERT: D 153 GLN cc_start: 0.9536 (mt0) cc_final: 0.9260 (mt0) REVERT: E 1 MET cc_start: 0.6823 (mtt) cc_final: 0.5330 (ptp) REVERT: E 31 PHE cc_start: 0.8813 (m-80) cc_final: 0.8520 (m-10) REVERT: E 93 GLU cc_start: 0.9382 (tt0) cc_final: 0.8638 (tt0) REVERT: E 143 PHE cc_start: 0.9300 (m-10) cc_final: 0.8986 (m-80) REVERT: E 188 PHE cc_start: 0.9142 (m-80) cc_final: 0.8825 (m-80) REVERT: E 210 ASN cc_start: 0.9080 (m110) cc_final: 0.7572 (m-40) REVERT: E 216 SER cc_start: 0.9553 (m) cc_final: 0.9300 (p) REVERT: E 237 LYS cc_start: 0.9062 (mttp) cc_final: 0.8798 (mmtm) REVERT: F 84 ARG cc_start: 0.6763 (ppt170) cc_final: 0.6191 (ppt170) REVERT: F 94 SER cc_start: 0.8998 (t) cc_final: 0.8621 (p) REVERT: F 108 ASN cc_start: 0.9284 (m-40) cc_final: 0.8790 (m-40) REVERT: F 112 GLU cc_start: 0.9140 (mm-30) cc_final: 0.8824 (mm-30) REVERT: F 132 LYS cc_start: 0.8977 (mtmt) cc_final: 0.8619 (mtmt) REVERT: G 1 MET cc_start: 0.7549 (ppp) cc_final: 0.7343 (ppp) REVERT: G 165 GLN cc_start: 0.9259 (tp-100) cc_final: 0.8981 (tp40) REVERT: G 213 GLU cc_start: 0.8839 (tt0) cc_final: 0.8435 (tt0) REVERT: H 79 MET cc_start: 0.9363 (mpp) cc_final: 0.9102 (mpp) REVERT: H 191 TYR cc_start: 0.8128 (m-10) cc_final: 0.7909 (m-10) REVERT: H 341 MET cc_start: 0.9049 (ttm) cc_final: 0.8536 (ttm) REVERT: I 146 LEU cc_start: 0.9260 (tp) cc_final: 0.8775 (mt) REVERT: I 156 LEU cc_start: 0.8483 (pp) cc_final: 0.8034 (tp) REVERT: I 202 ARG cc_start: 0.7984 (mtm180) cc_final: 0.7600 (mtm-85) REVERT: I 233 GLN cc_start: 0.8678 (tt0) cc_final: 0.8217 (tp40) REVERT: J 415 GLN cc_start: 0.8659 (mm-40) cc_final: 0.8291 (tp-100) REVERT: J 586 GLU cc_start: 0.8487 (tp30) cc_final: 0.8206 (tp30) REVERT: J 603 MET cc_start: 0.7728 (tmm) cc_final: 0.5841 (ptm) REVERT: J 606 MET cc_start: 0.9289 (tmm) cc_final: 0.8980 (tmm) REVERT: J 620 ASP cc_start: 0.5377 (m-30) cc_final: 0.4786 (t70) REVERT: J 674 MET cc_start: 0.5233 (mtt) cc_final: 0.4282 (ptp) REVERT: J 751 MET cc_start: 0.8311 (ttt) cc_final: 0.7625 (ttt) REVERT: J 907 MET cc_start: 0.8957 (tpt) cc_final: 0.8537 (tpt) REVERT: J 922 PHE cc_start: 0.8929 (m-80) cc_final: 0.8698 (m-80) REVERT: J 940 ARG cc_start: 0.8344 (tpp-160) cc_final: 0.7900 (mmm160) REVERT: J 942 ASP cc_start: 0.9030 (t0) cc_final: 0.8080 (m-30) REVERT: J 976 PHE cc_start: 0.9282 (m-80) cc_final: 0.8895 (m-80) REVERT: P 7 THR cc_start: 0.8145 (p) cc_final: 0.7528 (p) outliers start: 0 outliers final: 0 residues processed: 435 average time/residue: 0.1879 time to fit residues: 127.4082 Evaluate side-chains 326 residues out of total 3020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 326 time to evaluate : 0.991 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 338 random chunks: chunk 284 optimal weight: 20.0000 chunk 246 optimal weight: 9.9990 chunk 224 optimal weight: 4.9990 chunk 45 optimal weight: 10.0000 chunk 48 optimal weight: 40.0000 chunk 114 optimal weight: 8.9990 chunk 33 optimal weight: 7.9990 chunk 38 optimal weight: 20.0000 chunk 39 optimal weight: 5.9990 chunk 293 optimal weight: 20.0000 chunk 118 optimal weight: 7.9990 overall best weight: 7.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 177 HIS ** A 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 72 ASN C 359 GLN ** D 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 171 HIS G 30 ASN ** G 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 133 HIS H 185 HIS H 213 HIS ** I 48 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 130 ASN ** I 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 21 GLN ** J 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 284 ASN ** J 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 478 GLN J 713 ASN ** J 755 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 85 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.074358 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.056197 restraints weight = 146902.781| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.058337 restraints weight = 91052.750| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.059889 restraints weight = 64385.627| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.060985 restraints weight = 49616.640| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.061750 restraints weight = 40882.634| |-----------------------------------------------------------------------------| r_work (final): 0.3336 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7961 moved from start: 0.6958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.123 27236 Z= 0.272 Angle : 0.748 11.280 36850 Z= 0.401 Chirality : 0.046 0.216 4271 Planarity : 0.006 0.053 4773 Dihedral : 5.804 51.439 3690 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 19.16 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.26 % Favored : 95.59 % Rotamer: Outliers : 0.07 % Allowed : 4.50 % Favored : 95.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.89 (0.14), residues: 3378 helix: 0.57 (0.16), residues: 974 sheet: -0.12 (0.19), residues: 680 loop : -1.50 (0.14), residues: 1724 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG J 28 TYR 0.018 0.002 TYR C 297 PHE 0.032 0.003 PHE I 256 TRP 0.020 0.003 TRP J 326 HIS 0.007 0.002 HIS J 555 Details of bonding type rmsd covalent geometry : bond 0.00562 (27233) covalent geometry : angle 0.74822 (36846) SS BOND : bond 0.00323 ( 2) SS BOND : angle 1.44329 ( 4) hydrogen bonds : bond 0.04684 ( 1097) hydrogen bonds : angle 5.62840 ( 3216) Misc. bond : bond 0.00034 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6756 Ramachandran restraints generated. 3378 Oldfield, 0 Emsley, 3378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6756 Ramachandran restraints generated. 3378 Oldfield, 0 Emsley, 3378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 419 residues out of total 3020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 417 time to evaluate : 1.132 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: 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 51 MET cc_start: 0.6912 (ppp) cc_final: 0.6394 (ppp) REVERT: A 81 THR cc_start: 0.7879 (t) cc_final: 0.7480 (t) REVERT: A 101 GLU cc_start: 0.8876 (tm-30) cc_final: 0.8343 (tm-30) REVERT: A 278 GLN cc_start: 0.8752 (tp-100) cc_final: 0.8435 (tp-100) REVERT: B 77 ASN cc_start: 0.9082 (m-40) cc_final: 0.8855 (m-40) REVERT: B 136 MET cc_start: 0.9104 (tpt) cc_final: 0.8700 (tpp) REVERT: B 149 ASP cc_start: 0.7926 (p0) cc_final: 0.7662 (p0) REVERT: B 154 MET cc_start: 0.8845 (pmm) cc_final: 0.8642 (pmm) REVERT: C 146 ASP cc_start: 0.8749 (p0) cc_final: 0.8360 (p0) REVERT: C 149 MET cc_start: 0.8878 (ptp) cc_final: 0.8594 (ptp) REVERT: C 153 GLN cc_start: 0.9115 (tm-30) cc_final: 0.8900 (tm-30) REVERT: C 276 CYS cc_start: 0.8025 (m) cc_final: 0.7789 (m) REVERT: C 372 GLU cc_start: 0.9189 (pm20) cc_final: 0.8852 (pm20) REVERT: D 83 TYR cc_start: 0.8393 (m-80) cc_final: 0.7989 (m-80) REVERT: D 202 CYS cc_start: 0.9177 (m) cc_final: 0.8975 (m) REVERT: E 1 MET cc_start: 0.6669 (mtt) cc_final: 0.4770 (ptt) REVERT: E 10 TYR cc_start: 0.9303 (t80) cc_final: 0.9065 (t80) REVERT: E 31 PHE cc_start: 0.8815 (m-80) cc_final: 0.8372 (m-80) REVERT: E 93 GLU cc_start: 0.9355 (tt0) cc_final: 0.8707 (tt0) REVERT: E 143 PHE cc_start: 0.9285 (m-10) cc_final: 0.8993 (m-80) REVERT: E 188 PHE cc_start: 0.9077 (m-80) cc_final: 0.8814 (m-80) REVERT: E 210 ASN cc_start: 0.8998 (m110) cc_final: 0.7558 (m-40) REVERT: E 216 SER cc_start: 0.9371 (m) cc_final: 0.9039 (p) REVERT: F 84 ARG cc_start: 0.6980 (ppt170) cc_final: 0.6534 (ppt170) REVERT: F 94 SER cc_start: 0.9011 (t) cc_final: 0.8629 (p) REVERT: F 96 GLN cc_start: 0.9021 (tp40) cc_final: 0.7922 (tm-30) REVERT: F 110 LEU cc_start: 0.9302 (mt) cc_final: 0.9062 (mt) REVERT: F 112 GLU cc_start: 0.9165 (mm-30) cc_final: 0.8787 (mm-30) REVERT: F 129 ARG cc_start: 0.8422 (ttp80) cc_final: 0.7846 (ttt-90) REVERT: F 132 LYS cc_start: 0.9048 (mtmt) cc_final: 0.8665 (mtmt) REVERT: F 246 MET cc_start: 0.8975 (ppp) cc_final: 0.8763 (ppp) REVERT: G 88 LEU cc_start: 0.9011 (mt) cc_final: 0.8654 (mm) REVERT: G 100 MET cc_start: 0.8983 (ppp) cc_final: 0.8453 (ppp) REVERT: G 165 GLN cc_start: 0.9349 (tp-100) cc_final: 0.8918 (tp40) REVERT: G 213 GLU cc_start: 0.8836 (tt0) cc_final: 0.8409 (tt0) REVERT: H 79 MET cc_start: 0.9361 (mpp) cc_final: 0.9056 (mpp) REVERT: H 311 GLU cc_start: 0.8508 (mt-10) cc_final: 0.8290 (tm-30) REVERT: H 341 MET cc_start: 0.9075 (ttm) cc_final: 0.8554 (ttm) REVERT: I 146 LEU cc_start: 0.9178 (tp) cc_final: 0.8650 (mp) REVERT: I 233 GLN cc_start: 0.8848 (tt0) cc_final: 0.8309 (tp-100) REVERT: I 243 TYR cc_start: 0.9311 (m-80) cc_final: 0.8682 (m-80) REVERT: I 275 MET cc_start: 0.8571 (ttm) cc_final: 0.7923 (ttt) REVERT: J 326 TRP cc_start: 0.7992 (m-10) cc_final: 0.7788 (m-10) REVERT: J 385 LYS cc_start: 0.8156 (mttm) cc_final: 0.7683 (tptp) REVERT: J 415 GLN cc_start: 0.8765 (mm-40) cc_final: 0.8430 (mm-40) REVERT: J 586 GLU cc_start: 0.8595 (tp30) cc_final: 0.8192 (tp30) REVERT: J 603 MET cc_start: 0.7314 (tmm) cc_final: 0.5498 (ptm) REVERT: J 606 MET cc_start: 0.9371 (tmm) cc_final: 0.9125 (tmm) REVERT: J 620 ASP cc_start: 0.5136 (m-30) cc_final: 0.4739 (t0) REVERT: J 674 MET cc_start: 0.5844 (mtt) cc_final: 0.4835 (ptp) REVERT: J 694 LEU cc_start: 0.6782 (pt) cc_final: 0.6563 (pt) REVERT: J 713 ASN cc_start: 0.8289 (OUTLIER) cc_final: 0.7634 (t0) REVERT: J 813 MET cc_start: 0.8111 (tpp) cc_final: 0.7785 (tpp) REVERT: J 907 MET cc_start: 0.8970 (tpt) cc_final: 0.8676 (tpt) REVERT: J 922 PHE cc_start: 0.8955 (m-80) cc_final: 0.8620 (m-80) REVERT: J 940 ARG cc_start: 0.8430 (tpp-160) cc_final: 0.7667 (tpp-160) REVERT: P 12 LYS cc_start: 0.5722 (mmmt) cc_final: 0.4702 (mmtm) outliers start: 2 outliers final: 0 residues processed: 418 average time/residue: 0.1999 time to fit residues: 131.5917 Evaluate side-chains 320 residues out of total 3020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 319 time to evaluate : 1.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 338 random chunks: chunk 92 optimal weight: 6.9990 chunk 307 optimal weight: 20.0000 chunk 100 optimal weight: 5.9990 chunk 167 optimal weight: 4.9990 chunk 65 optimal weight: 20.0000 chunk 277 optimal weight: 10.0000 chunk 234 optimal weight: 4.9990 chunk 319 optimal weight: 9.9990 chunk 46 optimal weight: 8.9990 chunk 131 optimal weight: 5.9990 chunk 174 optimal weight: 8.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 53 GLN ** G 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 230 GLN ** H 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 213 HIS ** H 285 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 48 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 250 ASN ** J 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 312 ASN J 551 ASN ** J 755 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 841 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 888 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.074428 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.056220 restraints weight = 146213.700| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.058369 restraints weight = 89758.579| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.059900 restraints weight = 63391.931| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.060987 restraints weight = 49047.053| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.061793 restraints weight = 40498.002| |-----------------------------------------------------------------------------| r_work (final): 0.3337 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7963 moved from start: 0.7364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.090 27236 Z= 0.223 Angle : 0.676 8.667 36850 Z= 0.363 Chirality : 0.045 0.204 4271 Planarity : 0.005 0.049 4773 Dihedral : 5.574 50.297 3690 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 17.70 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.38 % Favored : 95.47 % Rotamer: Outliers : 0.07 % Allowed : 3.15 % Favored : 96.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.82 (0.14), residues: 3378 helix: 0.70 (0.16), residues: 980 sheet: -0.23 (0.19), residues: 687 loop : -1.44 (0.14), residues: 1711 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG J 773 TYR 0.019 0.002 TYR J 958 PHE 0.020 0.002 PHE F 121 TRP 0.047 0.003 TRP I 272 HIS 0.008 0.001 HIS J 149 Details of bonding type rmsd covalent geometry : bond 0.00467 (27233) covalent geometry : angle 0.67600 (36846) SS BOND : bond 0.01384 ( 2) SS BOND : angle 1.21603 ( 4) hydrogen bonds : bond 0.04266 ( 1097) hydrogen bonds : angle 5.48947 ( 3216) Misc. bond : bond 0.00131 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6756 Ramachandran restraints generated. 3378 Oldfield, 0 Emsley, 3378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6756 Ramachandran restraints generated. 3378 Oldfield, 0 Emsley, 3378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 404 residues out of total 3020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 402 time to evaluate : 1.125 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 MET cc_start: 0.7153 (ppp) cc_final: 0.6645 (ppp) REVERT: A 81 THR cc_start: 0.7887 (t) cc_final: 0.7271 (t) REVERT: A 101 GLU cc_start: 0.8861 (tm-30) cc_final: 0.8263 (tm-30) REVERT: A 114 ARG cc_start: 0.9054 (tpm170) cc_final: 0.8148 (tpm170) REVERT: A 278 GLN cc_start: 0.8662 (tp-100) cc_final: 0.8432 (tp-100) REVERT: A 300 GLU cc_start: 0.8759 (mt-10) cc_final: 0.8298 (tp30) REVERT: B 136 MET cc_start: 0.9172 (tpt) cc_final: 0.8884 (tpp) REVERT: B 140 ILE cc_start: 0.8991 (mt) cc_final: 0.8782 (tp) REVERT: B 154 MET cc_start: 0.8657 (pmm) cc_final: 0.8438 (pmm) REVERT: C 146 ASP cc_start: 0.8796 (p0) cc_final: 0.8409 (p0) REVERT: C 149 MET cc_start: 0.8827 (ptp) cc_final: 0.8572 (ptp) REVERT: C 214 TYR cc_start: 0.8727 (m-80) cc_final: 0.8290 (m-80) REVERT: C 276 CYS cc_start: 0.7849 (m) cc_final: 0.7632 (m) REVERT: C 372 GLU cc_start: 0.9255 (pm20) cc_final: 0.8991 (pm20) REVERT: D 82 CYS cc_start: 0.8660 (t) cc_final: 0.8129 (t) REVERT: D 83 TYR cc_start: 0.8451 (m-80) cc_final: 0.7829 (m-80) REVERT: D 163 LEU cc_start: 0.9118 (pp) cc_final: 0.8781 (pp) REVERT: D 202 CYS cc_start: 0.9294 (m) cc_final: 0.9086 (m) REVERT: E 1 MET cc_start: 0.7150 (mtt) cc_final: 0.5235 (ptt) REVERT: E 31 PHE cc_start: 0.8790 (m-80) cc_final: 0.8369 (m-80) REVERT: E 73 ASN cc_start: 0.9127 (p0) cc_final: 0.8638 (t0) REVERT: E 79 ASP cc_start: 0.8657 (t0) cc_final: 0.8198 (p0) REVERT: E 93 GLU cc_start: 0.9369 (tt0) cc_final: 0.9023 (tt0) REVERT: E 143 PHE cc_start: 0.9184 (m-10) cc_final: 0.8873 (m-80) REVERT: E 188 PHE cc_start: 0.9124 (m-80) cc_final: 0.8831 (m-80) REVERT: E 216 SER cc_start: 0.9303 (m) cc_final: 0.8969 (p) REVERT: E 250 MET cc_start: 0.9351 (ptt) cc_final: 0.8930 (ptt) REVERT: F 96 GLN cc_start: 0.9018 (tp40) cc_final: 0.7890 (tm-30) REVERT: F 108 ASN cc_start: 0.9214 (m-40) cc_final: 0.8922 (m-40) REVERT: F 111 LYS cc_start: 0.9502 (mmtt) cc_final: 0.9128 (mmtp) REVERT: F 112 GLU cc_start: 0.9231 (mm-30) cc_final: 0.8908 (mm-30) REVERT: F 132 LYS cc_start: 0.8854 (mtmt) cc_final: 0.8557 (mtmt) REVERT: F 246 MET cc_start: 0.8939 (ppp) cc_final: 0.8698 (ppp) REVERT: G 88 LEU cc_start: 0.9095 (mt) cc_final: 0.8820 (mt) REVERT: G 100 MET cc_start: 0.9065 (ppp) cc_final: 0.8294 (ppp) REVERT: G 164 ARG cc_start: 0.8813 (mtm110) cc_final: 0.8527 (mtm180) REVERT: G 165 GLN cc_start: 0.9357 (tp-100) cc_final: 0.8884 (tp40) REVERT: G 213 GLU cc_start: 0.8728 (tt0) cc_final: 0.8319 (tt0) REVERT: G 225 ASP cc_start: 0.9576 (m-30) cc_final: 0.9360 (p0) REVERT: H 54 ILE cc_start: 0.8097 (tp) cc_final: 0.7846 (tp) REVERT: H 79 MET cc_start: 0.9251 (mpp) cc_final: 0.8997 (mpp) REVERT: H 311 GLU cc_start: 0.8546 (mt-10) cc_final: 0.8319 (tm-30) REVERT: H 341 MET cc_start: 0.9097 (ttm) cc_final: 0.8476 (ttm) REVERT: I 146 LEU cc_start: 0.9205 (tp) cc_final: 0.8800 (mp) REVERT: I 233 GLN cc_start: 0.8800 (tt0) cc_final: 0.8344 (tp-100) REVERT: I 243 TYR cc_start: 0.9297 (m-80) cc_final: 0.8687 (m-80) REVERT: J 238 MET cc_start: 0.1372 (mmm) cc_final: 0.0920 (tpp) REVERT: J 312 ASN cc_start: 0.8641 (OUTLIER) cc_final: 0.8243 (t0) REVERT: J 415 GLN cc_start: 0.8759 (mm-40) cc_final: 0.8423 (mm-40) REVERT: J 456 TRP cc_start: 0.8305 (t60) cc_final: 0.8095 (t60) REVERT: J 586 GLU cc_start: 0.8613 (tp30) cc_final: 0.8169 (tp30) REVERT: J 603 MET cc_start: 0.7153 (tmm) cc_final: 0.5358 (ptm) REVERT: J 606 MET cc_start: 0.9330 (tmm) cc_final: 0.9023 (tmm) REVERT: J 694 LEU cc_start: 0.6873 (pt) cc_final: 0.6582 (pt) REVERT: J 751 MET cc_start: 0.8240 (ttp) cc_final: 0.7506 (ptm) REVERT: J 813 MET cc_start: 0.8338 (tpp) cc_final: 0.8096 (tpp) REVERT: J 907 MET cc_start: 0.8970 (tpt) cc_final: 0.8580 (tpt) REVERT: J 922 PHE cc_start: 0.8949 (m-80) cc_final: 0.8586 (m-80) REVERT: J 940 ARG cc_start: 0.8165 (tpp-160) cc_final: 0.7600 (mmm160) REVERT: J 942 ASP cc_start: 0.8617 (m-30) cc_final: 0.7497 (m-30) REVERT: P 7 THR cc_start: 0.8152 (p) cc_final: 0.7584 (p) outliers start: 2 outliers final: 0 residues processed: 404 average time/residue: 0.1903 time to fit residues: 122.1154 Evaluate side-chains 307 residues out of total 3020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 306 time to evaluate : 1.136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 338 random chunks: chunk 331 optimal weight: 30.0000 chunk 118 optimal weight: 5.9990 chunk 301 optimal weight: 0.9980 chunk 164 optimal weight: 8.9990 chunk 34 optimal weight: 5.9990 chunk 165 optimal weight: 5.9990 chunk 211 optimal weight: 6.9990 chunk 107 optimal weight: 0.9990 chunk 294 optimal weight: 10.0000 chunk 302 optimal weight: 5.9990 chunk 308 optimal weight: 0.0370 overall best weight: 2.8064 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 22 ASN ** A 57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 20 ASN ** B 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 44 GLN B 111 ASN ** B 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 29 HIS E 134 HIS E 210 ASN ** F 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 213 HIS ** H 285 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 149 GLN ** J 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 755 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 871 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.076228 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.058360 restraints weight = 141369.267| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.060543 restraints weight = 87286.474| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.062104 restraints weight = 61749.931| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.063206 restraints weight = 47631.048| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.064021 restraints weight = 39182.897| |-----------------------------------------------------------------------------| r_work (final): 0.3399 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7931 moved from start: 0.7491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 27236 Z= 0.145 Angle : 0.612 9.236 36850 Z= 0.327 Chirality : 0.044 0.226 4271 Planarity : 0.004 0.063 4773 Dihedral : 5.180 48.048 3690 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 14.39 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.55 % Favored : 96.27 % Rotamer: Outliers : 0.07 % Allowed : 1.79 % Favored : 98.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.56 (0.14), residues: 3378 helix: 1.05 (0.16), residues: 961 sheet: -0.18 (0.19), residues: 688 loop : -1.29 (0.14), residues: 1729 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.022 0.001 ARG J 872 TYR 0.024 0.001 TYR J 188 PHE 0.034 0.002 PHE P 9 TRP 0.024 0.002 TRP I 272 HIS 0.005 0.001 HIS B 235 Details of bonding type rmsd covalent geometry : bond 0.00316 (27233) covalent geometry : angle 0.61236 (36846) SS BOND : bond 0.00152 ( 2) SS BOND : angle 0.98433 ( 4) hydrogen bonds : bond 0.03934 ( 1097) hydrogen bonds : angle 5.20284 ( 3216) Misc. bond : bond 0.00244 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6756 Ramachandran restraints generated. 3378 Oldfield, 0 Emsley, 3378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6756 Ramachandran restraints generated. 3378 Oldfield, 0 Emsley, 3378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 425 residues out of total 3020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 423 time to evaluate : 1.149 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 MET cc_start: 0.7031 (ppp) cc_final: 0.6554 (ppp) REVERT: A 81 THR cc_start: 0.8138 (t) cc_final: 0.7565 (t) REVERT: A 101 GLU cc_start: 0.8812 (tm-30) cc_final: 0.8120 (tm-30) REVERT: A 114 ARG cc_start: 0.8965 (tpm170) cc_final: 0.7918 (tpm170) REVERT: A 228 GLU cc_start: 0.8801 (tp30) cc_final: 0.8004 (mm-30) REVERT: A 300 GLU cc_start: 0.8734 (mt-10) cc_final: 0.8317 (tp30) REVERT: B 136 MET cc_start: 0.9048 (tpt) cc_final: 0.8741 (tpp) REVERT: B 154 MET cc_start: 0.8684 (pmm) cc_final: 0.8189 (pmm) REVERT: C 146 ASP cc_start: 0.8649 (p0) cc_final: 0.8297 (p0) REVERT: C 149 MET cc_start: 0.8714 (ptp) cc_final: 0.8396 (ptp) REVERT: C 153 GLN cc_start: 0.9115 (tm-30) cc_final: 0.8836 (tm-30) REVERT: C 214 TYR cc_start: 0.8706 (m-80) cc_final: 0.8292 (m-80) REVERT: C 372 GLU cc_start: 0.9194 (pm20) cc_final: 0.8883 (pm20) REVERT: D 82 CYS cc_start: 0.8566 (t) cc_final: 0.8035 (t) REVERT: D 83 TYR cc_start: 0.8262 (m-80) cc_final: 0.7618 (m-80) REVERT: D 103 GLU cc_start: 0.8895 (pm20) cc_final: 0.8498 (pm20) REVERT: D 163 LEU cc_start: 0.9120 (pp) cc_final: 0.8707 (pp) REVERT: D 202 CYS cc_start: 0.9340 (m) cc_final: 0.9101 (m) REVERT: E 1 MET cc_start: 0.6081 (mtt) cc_final: 0.4088 (ptt) REVERT: E 7 GLU cc_start: 0.8612 (mt-10) cc_final: 0.8170 (mt-10) REVERT: E 73 ASN cc_start: 0.9060 (p0) cc_final: 0.8569 (t0) REVERT: E 77 GLN cc_start: 0.8782 (tm-30) cc_final: 0.8337 (tm-30) REVERT: E 79 ASP cc_start: 0.8583 (t0) cc_final: 0.8180 (p0) REVERT: E 93 GLU cc_start: 0.9305 (tt0) cc_final: 0.8943 (tt0) REVERT: E 127 ASP cc_start: 0.8997 (t0) cc_final: 0.7478 (t0) REVERT: E 143 PHE cc_start: 0.9145 (m-10) cc_final: 0.8904 (m-10) REVERT: E 188 PHE cc_start: 0.9105 (m-80) cc_final: 0.8844 (m-80) REVERT: E 250 MET cc_start: 0.9223 (ptt) cc_final: 0.8784 (ptt) REVERT: F 96 GLN cc_start: 0.9053 (tp40) cc_final: 0.7960 (tm-30) REVERT: F 108 ASN cc_start: 0.9192 (m-40) cc_final: 0.8877 (m-40) REVERT: F 111 LYS cc_start: 0.9459 (mmtt) cc_final: 0.9035 (mmtp) REVERT: F 112 GLU cc_start: 0.9098 (mm-30) cc_final: 0.8798 (mm-30) REVERT: F 132 LYS cc_start: 0.8779 (mtmt) cc_final: 0.8453 (mtmt) REVERT: F 201 VAL cc_start: 0.8892 (p) cc_final: 0.8596 (p) REVERT: F 203 PHE cc_start: 0.8953 (m-10) cc_final: 0.8669 (m-10) REVERT: F 246 MET cc_start: 0.8854 (ppp) cc_final: 0.8639 (ppp) REVERT: G 100 MET cc_start: 0.9087 (ppp) cc_final: 0.8272 (ppp) REVERT: G 104 ASN cc_start: 0.7354 (m110) cc_final: 0.7042 (t0) REVERT: G 165 GLN cc_start: 0.9309 (tp-100) cc_final: 0.8860 (tp40) REVERT: G 213 GLU cc_start: 0.8710 (tt0) cc_final: 0.8296 (tt0) REVERT: G 225 ASP cc_start: 0.9533 (m-30) cc_final: 0.9305 (p0) REVERT: H 79 MET cc_start: 0.9342 (mpp) cc_final: 0.9091 (mpp) REVERT: H 189 LEU cc_start: 0.8578 (mt) cc_final: 0.8373 (tt) REVERT: H 281 TYR cc_start: 0.8017 (m-10) cc_final: 0.7675 (m-10) REVERT: H 309 PHE cc_start: 0.9171 (t80) cc_final: 0.8907 (t80) REVERT: H 341 MET cc_start: 0.9106 (ttm) cc_final: 0.8425 (ttm) REVERT: I 146 LEU cc_start: 0.9221 (tp) cc_final: 0.8850 (mp) REVERT: I 233 GLN cc_start: 0.8812 (tt0) cc_final: 0.8350 (tp-100) REVERT: I 243 TYR cc_start: 0.9275 (m-80) cc_final: 0.8673 (m-80) REVERT: J 138 ASP cc_start: 0.9010 (m-30) cc_final: 0.8610 (p0) REVERT: J 238 MET cc_start: 0.1257 (mmm) cc_final: 0.0822 (tpp) REVERT: J 312 ASN cc_start: 0.8643 (t0) cc_final: 0.8259 (m-40) REVERT: J 385 LYS cc_start: 0.8148 (mttm) cc_final: 0.7701 (tptp) REVERT: J 415 GLN cc_start: 0.8731 (mm-40) cc_final: 0.8393 (mm-40) REVERT: J 586 GLU cc_start: 0.8631 (tp30) cc_final: 0.8188 (tp30) REVERT: J 603 MET cc_start: 0.7239 (tmm) cc_final: 0.5523 (ptm) REVERT: J 606 MET cc_start: 0.9309 (tmm) cc_final: 0.9057 (tmm) REVERT: J 672 MET cc_start: 0.8131 (mmp) cc_final: 0.7749 (mmm) REVERT: J 674 MET cc_start: 0.5865 (mtt) cc_final: 0.4855 (ptp) REVERT: J 751 MET cc_start: 0.8087 (ttp) cc_final: 0.7593 (ptm) REVERT: J 813 MET cc_start: 0.8255 (tpp) cc_final: 0.8001 (tpp) REVERT: J 907 MET cc_start: 0.8994 (tpt) cc_final: 0.8700 (tpt) REVERT: J 922 PHE cc_start: 0.8951 (m-80) cc_final: 0.8624 (m-80) REVERT: J 940 ARG cc_start: 0.8132 (tpp-160) cc_final: 0.7608 (mmm160) REVERT: J 942 ASP cc_start: 0.8635 (m-30) cc_final: 0.7436 (m-30) REVERT: P 7 THR cc_start: 0.8053 (p) cc_final: 0.7580 (p) outliers start: 2 outliers final: 0 residues processed: 425 average time/residue: 0.1913 time to fit residues: 128.2464 Evaluate side-chains 309 residues out of total 3020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 309 time to evaluate : 1.159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 338 random chunks: chunk 192 optimal weight: 0.9990 chunk 282 optimal weight: 10.0000 chunk 320 optimal weight: 9.9990 chunk 213 optimal weight: 0.0970 chunk 304 optimal weight: 8.9990 chunk 239 optimal weight: 5.9990 chunk 78 optimal weight: 0.9980 chunk 211 optimal weight: 7.9990 chunk 176 optimal weight: 7.9990 chunk 156 optimal weight: 9.9990 chunk 183 optimal weight: 7.9990 overall best weight: 3.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 131 GLN B 235 HIS ** D 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 210 ASN ** F 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 181 HIS H 111 HIS ** H 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 215 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 285 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 755 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.076027 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.058212 restraints weight = 140835.657| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.060398 restraints weight = 86626.881| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.061946 restraints weight = 61196.050| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.063050 restraints weight = 47269.509| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.063846 restraints weight = 38890.088| |-----------------------------------------------------------------------------| r_work (final): 0.3394 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7939 moved from start: 0.7703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 27236 Z= 0.151 Angle : 0.623 9.529 36850 Z= 0.331 Chirality : 0.044 0.207 4271 Planarity : 0.005 0.059 4773 Dihedral : 5.071 44.659 3690 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 14.48 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.14 % Favored : 95.71 % Rotamer: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.52 (0.14), residues: 3378 helix: 1.14 (0.17), residues: 969 sheet: -0.29 (0.19), residues: 714 loop : -1.26 (0.15), residues: 1695 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG C 222 TYR 0.018 0.001 TYR J 188 PHE 0.032 0.002 PHE J 730 TRP 0.047 0.002 TRP J 456 HIS 0.013 0.001 HIS B 235 Details of bonding type rmsd covalent geometry : bond 0.00324 (27233) covalent geometry : angle 0.62312 (36846) SS BOND : bond 0.00166 ( 2) SS BOND : angle 0.90311 ( 4) hydrogen bonds : bond 0.03879 ( 1097) hydrogen bonds : angle 5.18575 ( 3216) Misc. bond : bond 0.00168 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6756 Ramachandran restraints generated. 3378 Oldfield, 0 Emsley, 3378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6756 Ramachandran restraints generated. 3378 Oldfield, 0 Emsley, 3378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 400 residues out of total 3020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 400 time to evaluate : 1.015 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: symmetry clash revert: symmetry clash REVERT: A 51 MET cc_start: 0.6973 (ppp) cc_final: 0.6494 (ppp) REVERT: A 81 THR cc_start: 0.7993 (t) cc_final: 0.7496 (t) REVERT: A 101 GLU cc_start: 0.8914 (tm-30) cc_final: 0.8197 (tm-30) REVERT: A 114 ARG cc_start: 0.8976 (tpm170) cc_final: 0.8723 (mtp-110) REVERT: A 228 GLU cc_start: 0.8762 (tp30) cc_final: 0.8477 (tp30) REVERT: A 229 LEU cc_start: 0.9461 (tt) cc_final: 0.9229 (pp) REVERT: A 300 GLU cc_start: 0.8704 (mt-10) cc_final: 0.8317 (tp30) REVERT: B 113 MET cc_start: 0.9257 (ttp) cc_final: 0.8972 (ttp) REVERT: B 136 MET cc_start: 0.9032 (tpt) cc_final: 0.8727 (tpp) REVERT: B 154 MET cc_start: 0.8635 (pmm) cc_final: 0.8121 (pmm) REVERT: C 146 ASP cc_start: 0.8490 (p0) cc_final: 0.8233 (p0) REVERT: C 149 MET cc_start: 0.8718 (ptp) cc_final: 0.8416 (ptp) REVERT: C 153 GLN cc_start: 0.9127 (tm-30) cc_final: 0.8881 (tm-30) REVERT: C 214 TYR cc_start: 0.8782 (m-80) cc_final: 0.8315 (m-80) REVERT: C 227 PHE cc_start: 0.8945 (t80) cc_final: 0.8358 (t80) REVERT: C 276 CYS cc_start: 0.7902 (m) cc_final: 0.7256 (t) REVERT: C 372 GLU cc_start: 0.9191 (pm20) cc_final: 0.8877 (pm20) REVERT: D 82 CYS cc_start: 0.8565 (t) cc_final: 0.7959 (t) REVERT: D 83 TYR cc_start: 0.8247 (m-80) cc_final: 0.7358 (m-80) REVERT: D 103 GLU cc_start: 0.8875 (pm20) cc_final: 0.8527 (pm20) REVERT: D 163 LEU cc_start: 0.9120 (pp) cc_final: 0.8780 (pp) REVERT: D 202 CYS cc_start: 0.9371 (m) cc_final: 0.9160 (m) REVERT: E 1 MET cc_start: 0.6205 (mtt) cc_final: 0.4050 (ptt) REVERT: E 58 CYS cc_start: 0.9102 (t) cc_final: 0.8804 (t) REVERT: E 73 ASN cc_start: 0.9078 (p0) cc_final: 0.8637 (t0) REVERT: E 77 GLN cc_start: 0.8923 (tm-30) cc_final: 0.8496 (tm-30) REVERT: E 79 ASP cc_start: 0.8531 (t0) cc_final: 0.8170 (p0) REVERT: E 93 GLU cc_start: 0.9298 (tt0) cc_final: 0.8811 (tt0) REVERT: E 127 ASP cc_start: 0.9045 (t0) cc_final: 0.7718 (t0) REVERT: E 143 PHE cc_start: 0.9159 (m-10) cc_final: 0.8911 (m-10) REVERT: E 153 TYR cc_start: 0.8975 (m-80) cc_final: 0.8646 (m-10) REVERT: E 188 PHE cc_start: 0.9116 (m-80) cc_final: 0.8856 (m-80) REVERT: E 210 ASN cc_start: 0.9077 (m110) cc_final: 0.8861 (m-40) REVERT: E 213 LEU cc_start: 0.9362 (tp) cc_final: 0.9135 (tp) REVERT: E 250 MET cc_start: 0.9206 (ptt) cc_final: 0.8818 (ptt) REVERT: F 61 LEU cc_start: 0.9435 (tp) cc_final: 0.9090 (tp) REVERT: F 96 GLN cc_start: 0.9019 (tp40) cc_final: 0.7980 (tm-30) REVERT: F 108 ASN cc_start: 0.9158 (m-40) cc_final: 0.8667 (m-40) REVERT: F 112 GLU cc_start: 0.9096 (mm-30) cc_final: 0.8731 (mm-30) REVERT: F 129 ARG cc_start: 0.8683 (mtm110) cc_final: 0.8433 (mtm110) REVERT: F 132 LYS cc_start: 0.8796 (mtmt) cc_final: 0.8504 (mtmt) REVERT: F 203 PHE cc_start: 0.8818 (m-10) cc_final: 0.8543 (m-10) REVERT: G 100 MET cc_start: 0.9116 (ppp) cc_final: 0.8284 (ppp) REVERT: G 104 ASN cc_start: 0.7344 (m110) cc_final: 0.7057 (t0) REVERT: G 117 ASP cc_start: 0.9119 (m-30) cc_final: 0.8917 (m-30) REVERT: G 165 GLN cc_start: 0.9290 (tp-100) cc_final: 0.8819 (tp40) REVERT: G 190 LEU cc_start: 0.8610 (mt) cc_final: 0.8360 (mt) REVERT: G 225 ASP cc_start: 0.9517 (m-30) cc_final: 0.9279 (p0) REVERT: H 79 MET cc_start: 0.9331 (mpp) cc_final: 0.9095 (mpp) REVERT: H 169 LEU cc_start: 0.8349 (pt) cc_final: 0.8033 (mp) REVERT: H 189 LEU cc_start: 0.8788 (mt) cc_final: 0.8571 (tt) REVERT: I 1 MET cc_start: 0.8237 (mpp) cc_final: 0.8020 (mpp) REVERT: I 146 LEU cc_start: 0.9270 (tp) cc_final: 0.8933 (mp) REVERT: I 233 GLN cc_start: 0.8779 (tt0) cc_final: 0.8327 (tp-100) REVERT: I 243 TYR cc_start: 0.9306 (m-80) cc_final: 0.8734 (m-80) REVERT: J 138 ASP cc_start: 0.9012 (m-30) cc_final: 0.8592 (p0) REVERT: J 238 MET cc_start: 0.1311 (mmm) cc_final: 0.0860 (tpp) REVERT: J 312 ASN cc_start: 0.8588 (t0) cc_final: 0.8229 (m-40) REVERT: J 385 LYS cc_start: 0.8281 (mttm) cc_final: 0.7800 (tptp) REVERT: J 415 GLN cc_start: 0.8767 (mm-40) cc_final: 0.8413 (mm-40) REVERT: J 586 GLU cc_start: 0.8686 (tp30) cc_final: 0.8224 (tp30) REVERT: J 603 MET cc_start: 0.7269 (tmm) cc_final: 0.5531 (ptm) REVERT: J 606 MET cc_start: 0.9309 (tmm) cc_final: 0.9053 (tmm) REVERT: J 751 MET cc_start: 0.8198 (ttp) cc_final: 0.7942 (ptm) REVERT: J 813 MET cc_start: 0.8118 (tpp) cc_final: 0.7776 (tpp) REVERT: J 907 MET cc_start: 0.9012 (tpt) cc_final: 0.8719 (tpt) REVERT: J 922 PHE cc_start: 0.8935 (m-80) cc_final: 0.8627 (m-80) REVERT: J 940 ARG cc_start: 0.8110 (tpp-160) cc_final: 0.7509 (mmm160) REVERT: J 942 ASP cc_start: 0.8300 (m-30) cc_final: 0.7048 (m-30) REVERT: P 7 THR cc_start: 0.8041 (p) cc_final: 0.7417 (p) REVERT: P 32 LEU cc_start: 0.8584 (mm) cc_final: 0.8336 (pt) outliers start: 0 outliers final: 0 residues processed: 400 average time/residue: 0.1824 time to fit residues: 117.3417 Evaluate side-chains 312 residues out of total 3020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 312 time to evaluate : 1.147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 338 random chunks: chunk 113 optimal weight: 6.9990 chunk 138 optimal weight: 8.9990 chunk 98 optimal weight: 5.9990 chunk 207 optimal weight: 10.0000 chunk 297 optimal weight: 20.0000 chunk 265 optimal weight: 50.0000 chunk 223 optimal weight: 9.9990 chunk 101 optimal weight: 0.9990 chunk 94 optimal weight: 5.9990 chunk 154 optimal weight: 10.0000 chunk 119 optimal weight: 0.0010 overall best weight: 3.9994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 131 GLN ** D 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 45 ASN ** F 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 53 GLN ** G 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 285 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 755 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.075323 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.057599 restraints weight = 142955.566| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.059751 restraints weight = 88215.836| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.061297 restraints weight = 62411.921| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.062383 restraints weight = 48149.581| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.063174 restraints weight = 39643.426| |-----------------------------------------------------------------------------| r_work (final): 0.3380 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7961 moved from start: 0.7919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.079 27236 Z= 0.168 Angle : 0.629 9.784 36850 Z= 0.333 Chirality : 0.044 0.245 4271 Planarity : 0.005 0.060 4773 Dihedral : 5.067 42.309 3690 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 15.80 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.32 % Favored : 95.56 % Rotamer: Outliers : 0.00 % Allowed : 0.86 % Favored : 99.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.55 (0.14), residues: 3378 helix: 1.08 (0.17), residues: 969 sheet: -0.26 (0.19), residues: 705 loop : -1.27 (0.14), residues: 1704 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG J 773 TYR 0.019 0.001 TYR J 188 PHE 0.025 0.002 PHE J 730 TRP 0.031 0.002 TRP J 456 HIS 0.005 0.001 HIS B 32 Details of bonding type rmsd covalent geometry : bond 0.00361 (27233) covalent geometry : angle 0.62911 (36846) SS BOND : bond 0.00202 ( 2) SS BOND : angle 0.89895 ( 4) hydrogen bonds : bond 0.03857 ( 1097) hydrogen bonds : angle 5.22239 ( 3216) Misc. bond : bond 0.00097 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6756 Ramachandran restraints generated. 3378 Oldfield, 0 Emsley, 3378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6756 Ramachandran restraints generated. 3378 Oldfield, 0 Emsley, 3378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 398 residues out of total 3020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 398 time to evaluate : 1.038 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: A 51 MET cc_start: 0.6857 (ppp) cc_final: 0.6276 (ppp) REVERT: A 101 GLU cc_start: 0.8978 (tm-30) cc_final: 0.8289 (tm-30) REVERT: A 114 ARG cc_start: 0.8894 (tpm170) cc_final: 0.8647 (mtp-110) REVERT: A 144 ASP cc_start: 0.8532 (t0) cc_final: 0.7962 (t0) REVERT: A 168 THR cc_start: 0.6910 (m) cc_final: 0.6593 (p) REVERT: A 229 LEU cc_start: 0.9474 (tt) cc_final: 0.9250 (pp) REVERT: A 300 GLU cc_start: 0.8725 (mt-10) cc_final: 0.8359 (tp30) REVERT: B 136 MET cc_start: 0.9051 (tpt) cc_final: 0.8782 (tpp) REVERT: B 154 MET cc_start: 0.8627 (pmm) cc_final: 0.8220 (pmm) REVERT: C 81 LYS cc_start: 0.9243 (tmmt) cc_final: 0.8653 (ttpp) REVERT: C 146 ASP cc_start: 0.8467 (p0) cc_final: 0.8204 (p0) REVERT: C 149 MET cc_start: 0.8734 (ptp) cc_final: 0.8379 (ptp) REVERT: C 153 GLN cc_start: 0.9151 (tm-30) cc_final: 0.8911 (tm-30) REVERT: C 214 TYR cc_start: 0.8739 (m-80) cc_final: 0.8123 (m-80) REVERT: C 276 CYS cc_start: 0.7755 (m) cc_final: 0.7075 (t) REVERT: C 363 MET cc_start: 0.8831 (mtp) cc_final: 0.8345 (mpp) REVERT: C 372 GLU cc_start: 0.9259 (pm20) cc_final: 0.9046 (pm20) REVERT: D 82 CYS cc_start: 0.8485 (t) cc_final: 0.7807 (t) REVERT: D 83 TYR cc_start: 0.8317 (m-80) cc_final: 0.7514 (m-80) REVERT: D 103 GLU cc_start: 0.8889 (pm20) cc_final: 0.8590 (pm20) REVERT: D 163 LEU cc_start: 0.9068 (pp) cc_final: 0.8678 (pp) REVERT: D 202 CYS cc_start: 0.9381 (m) cc_final: 0.9165 (m) REVERT: E 1 MET cc_start: 0.6366 (mtt) cc_final: 0.4136 (ptt) REVERT: E 31 PHE cc_start: 0.8556 (m-80) cc_final: 0.8038 (m-80) REVERT: E 73 ASN cc_start: 0.9085 (p0) cc_final: 0.8691 (t0) REVERT: E 77 GLN cc_start: 0.8834 (tm-30) cc_final: 0.8410 (tm-30) REVERT: E 79 ASP cc_start: 0.8607 (t0) cc_final: 0.8139 (p0) REVERT: E 93 GLU cc_start: 0.9312 (tt0) cc_final: 0.8934 (tt0) REVERT: E 127 ASP cc_start: 0.9072 (t0) cc_final: 0.7643 (t0) REVERT: E 143 PHE cc_start: 0.9252 (m-10) cc_final: 0.8859 (m-80) REVERT: E 172 PHE cc_start: 0.8674 (m-80) cc_final: 0.7565 (m-80) REVERT: E 188 PHE cc_start: 0.9143 (m-80) cc_final: 0.8911 (m-80) REVERT: E 250 MET cc_start: 0.9249 (ptt) cc_final: 0.8817 (ptt) REVERT: F 55 ASN cc_start: 0.8742 (t0) cc_final: 0.8533 (p0) REVERT: F 96 GLN cc_start: 0.8905 (tp40) cc_final: 0.7925 (tm-30) REVERT: F 108 ASN cc_start: 0.9192 (m-40) cc_final: 0.8968 (m-40) REVERT: F 124 VAL cc_start: 0.8762 (t) cc_final: 0.8559 (t) REVERT: F 129 ARG cc_start: 0.8754 (mtm110) cc_final: 0.8527 (mtm110) REVERT: F 201 VAL cc_start: 0.8973 (p) cc_final: 0.8772 (p) REVERT: F 203 PHE cc_start: 0.8931 (m-10) cc_final: 0.8716 (m-10) REVERT: F 246 MET cc_start: 0.8888 (ppp) cc_final: 0.8681 (ppp) REVERT: G 100 MET cc_start: 0.9132 (ppp) cc_final: 0.8303 (ppp) REVERT: G 104 ASN cc_start: 0.7033 (m110) cc_final: 0.6740 (t0) REVERT: G 120 TYR cc_start: 0.7636 (t80) cc_final: 0.7417 (t80) REVERT: G 165 GLN cc_start: 0.9313 (tp-100) cc_final: 0.8857 (tp40) REVERT: G 190 LEU cc_start: 0.8672 (mt) cc_final: 0.8400 (mt) REVERT: G 225 ASP cc_start: 0.9530 (m-30) cc_final: 0.9295 (p0) REVERT: H 54 ILE cc_start: 0.8223 (tp) cc_final: 0.8004 (tp) REVERT: H 169 LEU cc_start: 0.8454 (pt) cc_final: 0.8084 (mp) REVERT: H 341 MET cc_start: 0.8964 (ttm) cc_final: 0.8450 (ptm) REVERT: I 146 LEU cc_start: 0.9277 (tp) cc_final: 0.8965 (mp) REVERT: I 233 GLN cc_start: 0.8830 (tt0) cc_final: 0.8390 (tp-100) REVERT: I 243 TYR cc_start: 0.9334 (m-80) cc_final: 0.8865 (m-80) REVERT: J 138 ASP cc_start: 0.9056 (m-30) cc_final: 0.8619 (p0) REVERT: J 238 MET cc_start: 0.1496 (mmm) cc_final: 0.1021 (tpp) REVERT: J 312 ASN cc_start: 0.8589 (t0) cc_final: 0.8204 (m-40) REVERT: J 385 LYS cc_start: 0.8308 (mttm) cc_final: 0.7825 (tptp) REVERT: J 586 GLU cc_start: 0.8714 (tp30) cc_final: 0.8237 (tp30) REVERT: J 603 MET cc_start: 0.7217 (tmm) cc_final: 0.5541 (ptm) REVERT: J 606 MET cc_start: 0.9314 (tmm) cc_final: 0.9055 (tmm) REVERT: J 674 MET cc_start: 0.5959 (mtt) cc_final: 0.4983 (ptp) REVERT: J 751 MET cc_start: 0.8370 (ttp) cc_final: 0.8064 (ptm) REVERT: J 813 MET cc_start: 0.8015 (tpp) cc_final: 0.7694 (tpp) REVERT: J 907 MET cc_start: 0.9012 (tpt) cc_final: 0.8712 (tpt) REVERT: J 922 PHE cc_start: 0.8882 (m-80) cc_final: 0.8486 (m-80) REVERT: J 940 ARG cc_start: 0.8136 (tpp-160) cc_final: 0.7596 (mmm160) REVERT: J 942 ASP cc_start: 0.8309 (m-30) cc_final: 0.7047 (m-30) REVERT: P 7 THR cc_start: 0.8106 (p) cc_final: 0.7467 (p) outliers start: 0 outliers final: 0 residues processed: 398 average time/residue: 0.1677 time to fit residues: 107.7479 Evaluate side-chains 306 residues out of total 3020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 306 time to evaluate : 1.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 338 random chunks: chunk 223 optimal weight: 9.9990 chunk 313 optimal weight: 2.9990 chunk 164 optimal weight: 6.9990 chunk 240 optimal weight: 0.7980 chunk 108 optimal weight: 0.3980 chunk 250 optimal weight: 20.0000 chunk 255 optimal weight: 10.0000 chunk 180 optimal weight: 4.9990 chunk 110 optimal weight: 2.9990 chunk 295 optimal weight: 9.9990 chunk 238 optimal weight: 5.9990 overall best weight: 2.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 131 GLN ** F 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 285 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 227 ASN ** J 755 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.077069 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.059380 restraints weight = 144417.943| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.061549 restraints weight = 89378.456| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.063085 restraints weight = 63375.292| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.064189 restraints weight = 49024.559| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.064980 restraints weight = 40354.094| |-----------------------------------------------------------------------------| r_work (final): 0.3458 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7969 moved from start: 0.8006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 27236 Z= 0.136 Angle : 0.607 9.525 36850 Z= 0.321 Chirality : 0.044 0.183 4271 Planarity : 0.004 0.058 4773 Dihedral : 4.894 39.657 3690 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 14.02 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.00 % Favored : 95.89 % Rotamer: Outliers : 0.00 % Allowed : 0.46 % Favored : 99.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.49 (0.14), residues: 3378 helix: 1.13 (0.17), residues: 964 sheet: -0.25 (0.19), residues: 698 loop : -1.21 (0.14), residues: 1716 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG J 773 TYR 0.016 0.001 TYR J 188 PHE 0.031 0.002 PHE P 9 TRP 0.067 0.002 TRP J 456 HIS 0.008 0.001 HIS B 235 Details of bonding type rmsd covalent geometry : bond 0.00299 (27233) covalent geometry : angle 0.60646 (36846) SS BOND : bond 0.00180 ( 2) SS BOND : angle 3.28573 ( 4) hydrogen bonds : bond 0.03721 ( 1097) hydrogen bonds : angle 5.13341 ( 3216) Misc. bond : bond 0.00146 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6756 Ramachandran restraints generated. 3378 Oldfield, 0 Emsley, 3378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6756 Ramachandran restraints generated. 3378 Oldfield, 0 Emsley, 3378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 391 residues out of total 3020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 391 time to evaluate : 1.077 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 MET cc_start: 0.6642 (ppp) cc_final: 0.6053 (ppp) REVERT: A 101 GLU cc_start: 0.8898 (tm-30) cc_final: 0.8158 (tm-30) REVERT: A 144 ASP cc_start: 0.8382 (t0) cc_final: 0.7828 (t0) REVERT: A 168 THR cc_start: 0.7139 (m) cc_final: 0.6864 (p) REVERT: A 300 GLU cc_start: 0.8728 (mt-10) cc_final: 0.8383 (tp30) REVERT: B 136 MET cc_start: 0.8881 (tpt) cc_final: 0.8619 (tpp) REVERT: B 154 MET cc_start: 0.8582 (pmm) cc_final: 0.8140 (pmm) REVERT: C 81 LYS cc_start: 0.9229 (tmmt) cc_final: 0.8829 (ttpp) REVERT: C 146 ASP cc_start: 0.8272 (p0) cc_final: 0.8039 (p0) REVERT: C 149 MET cc_start: 0.8703 (ptp) cc_final: 0.8358 (ptp) REVERT: C 153 GLN cc_start: 0.9148 (tm-30) cc_final: 0.8877 (tm-30) REVERT: C 214 TYR cc_start: 0.8658 (m-80) cc_final: 0.8112 (m-80) REVERT: C 276 CYS cc_start: 0.7906 (m) cc_final: 0.7378 (t) REVERT: C 362 LEU cc_start: 0.9479 (tp) cc_final: 0.9214 (tp) REVERT: C 363 MET cc_start: 0.8708 (mtp) cc_final: 0.8209 (mpp) REVERT: C 372 GLU cc_start: 0.9240 (pm20) cc_final: 0.9019 (pm20) REVERT: D 82 CYS cc_start: 0.8461 (t) cc_final: 0.7778 (t) REVERT: D 83 TYR cc_start: 0.8140 (m-80) cc_final: 0.7304 (m-80) REVERT: D 163 LEU cc_start: 0.9021 (pp) cc_final: 0.8735 (pp) REVERT: D 175 LYS cc_start: 0.9031 (tptp) cc_final: 0.8806 (tptt) REVERT: E 1 MET cc_start: 0.6515 (mtt) cc_final: 0.4239 (ptt) REVERT: E 31 PHE cc_start: 0.8615 (m-80) cc_final: 0.8158 (m-80) REVERT: E 73 ASN cc_start: 0.9011 (p0) cc_final: 0.8641 (t0) REVERT: E 77 GLN cc_start: 0.8821 (tm-30) cc_final: 0.8358 (tm-30) REVERT: E 79 ASP cc_start: 0.8623 (t0) cc_final: 0.8297 (p0) REVERT: E 93 GLU cc_start: 0.9244 (tt0) cc_final: 0.8784 (tt0) REVERT: E 143 PHE cc_start: 0.9227 (m-10) cc_final: 0.8802 (m-80) REVERT: E 172 PHE cc_start: 0.8667 (m-80) cc_final: 0.7643 (m-80) REVERT: E 188 PHE cc_start: 0.9077 (m-80) cc_final: 0.8875 (m-80) REVERT: E 198 LEU cc_start: 0.9227 (mt) cc_final: 0.8864 (mp) REVERT: E 210 ASN cc_start: 0.9008 (m110) cc_final: 0.8592 (m110) REVERT: E 250 MET cc_start: 0.9144 (ptt) cc_final: 0.8747 (ptt) REVERT: F 61 LEU cc_start: 0.9386 (tp) cc_final: 0.8968 (tp) REVERT: F 96 GLN cc_start: 0.8856 (tp40) cc_final: 0.7648 (tm-30) REVERT: F 108 ASN cc_start: 0.9155 (m-40) cc_final: 0.8856 (m-40) REVERT: F 112 GLU cc_start: 0.9123 (mm-30) cc_final: 0.8837 (mm-30) REVERT: F 201 VAL cc_start: 0.8908 (p) cc_final: 0.8680 (p) REVERT: F 203 PHE cc_start: 0.8811 (m-10) cc_final: 0.8605 (m-10) REVERT: F 246 MET cc_start: 0.8825 (ppp) cc_final: 0.8613 (ppp) REVERT: G 100 MET cc_start: 0.9129 (ppp) cc_final: 0.8346 (ppp) REVERT: G 104 ASN cc_start: 0.6935 (m110) cc_final: 0.6686 (t0) REVERT: G 136 CYS cc_start: 0.8571 (m) cc_final: 0.8287 (t) REVERT: G 164 ARG cc_start: 0.8884 (mtm110) cc_final: 0.8530 (mtm180) REVERT: G 165 GLN cc_start: 0.9253 (tp-100) cc_final: 0.8808 (tp40) REVERT: G 190 LEU cc_start: 0.8524 (mt) cc_final: 0.8301 (mt) REVERT: G 225 ASP cc_start: 0.9493 (m-30) cc_final: 0.9265 (p0) REVERT: H 54 ILE cc_start: 0.8180 (tp) cc_final: 0.7966 (tp) REVERT: H 79 MET cc_start: 0.9332 (mpp) cc_final: 0.9079 (mpp) REVERT: H 169 LEU cc_start: 0.8439 (pt) cc_final: 0.8097 (mp) REVERT: H 311 GLU cc_start: 0.8872 (tm-30) cc_final: 0.8252 (tm-30) REVERT: H 341 MET cc_start: 0.9006 (ttm) cc_final: 0.8466 (ptm) REVERT: I 146 LEU cc_start: 0.9321 (tp) cc_final: 0.8966 (mp) REVERT: I 233 GLN cc_start: 0.8846 (tt0) cc_final: 0.8383 (tp-100) REVERT: I 243 TYR cc_start: 0.9332 (m-80) cc_final: 0.8894 (m-80) REVERT: I 267 MET cc_start: 0.7488 (ttt) cc_final: 0.7165 (ttt) REVERT: J 138 ASP cc_start: 0.9023 (m-30) cc_final: 0.8587 (p0) REVERT: J 238 MET cc_start: 0.1469 (mmm) cc_final: 0.1024 (tpp) REVERT: J 385 LYS cc_start: 0.8306 (mttm) cc_final: 0.7816 (tptp) REVERT: J 586 GLU cc_start: 0.8742 (tp30) cc_final: 0.8250 (tp30) REVERT: J 603 MET cc_start: 0.7433 (tmm) cc_final: 0.5690 (ptm) REVERT: J 606 MET cc_start: 0.9311 (tmm) cc_final: 0.9018 (tmm) REVERT: J 674 MET cc_start: 0.5975 (mtt) cc_final: 0.4986 (ptp) REVERT: J 705 MET cc_start: 0.6437 (ptt) cc_final: 0.5784 (ppp) REVERT: J 751 MET cc_start: 0.8324 (ttp) cc_final: 0.8110 (ptm) REVERT: J 813 MET cc_start: 0.7925 (tpp) cc_final: 0.7580 (tpp) REVERT: J 907 MET cc_start: 0.9030 (tpt) cc_final: 0.8648 (tpt) REVERT: J 922 PHE cc_start: 0.8892 (m-80) cc_final: 0.8463 (m-80) REVERT: J 940 ARG cc_start: 0.8198 (tpp-160) cc_final: 0.7614 (mmm160) REVERT: J 942 ASP cc_start: 0.8209 (m-30) cc_final: 0.6904 (m-30) REVERT: P 6 PHE cc_start: 0.9389 (t80) cc_final: 0.9112 (t80) REVERT: P 7 THR cc_start: 0.8105 (p) cc_final: 0.7524 (p) REVERT: P 32 LEU cc_start: 0.8664 (mm) cc_final: 0.8419 (pt) outliers start: 0 outliers final: 0 residues processed: 391 average time/residue: 0.1620 time to fit residues: 102.7793 Evaluate side-chains 303 residues out of total 3020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 303 time to evaluate : 1.046 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 338 random chunks: chunk 275 optimal weight: 9.9990 chunk 335 optimal weight: 0.4980 chunk 35 optimal weight: 5.9990 chunk 108 optimal weight: 6.9990 chunk 133 optimal weight: 10.0000 chunk 139 optimal weight: 9.9990 chunk 222 optimal weight: 20.0000 chunk 313 optimal weight: 4.9990 chunk 242 optimal weight: 2.9990 chunk 73 optimal weight: 8.9990 chunk 76 optimal weight: 10.0000 overall best weight: 4.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 285 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 755 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.075811 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.058308 restraints weight = 147842.215| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.060445 restraints weight = 91776.860| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.061954 restraints weight = 65120.162| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.063041 restraints weight = 50388.661| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.063827 restraints weight = 41551.611| |-----------------------------------------------------------------------------| r_work (final): 0.3425 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8009 moved from start: 0.8218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.080 27236 Z= 0.178 Angle : 0.636 9.745 36850 Z= 0.338 Chirality : 0.044 0.191 4271 Planarity : 0.005 0.060 4773 Dihedral : 5.031 37.533 3690 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 16.34 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.44 % Favored : 95.44 % Rotamer: Outliers : 0.00 % Allowed : 0.23 % Favored : 99.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.59 (0.14), residues: 3378 helix: 1.00 (0.17), residues: 980 sheet: -0.28 (0.19), residues: 684 loop : -1.27 (0.14), residues: 1714 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG J 896 TYR 0.020 0.002 TYR J 188 PHE 0.034 0.002 PHE P 9 TRP 0.054 0.002 TRP J 456 HIS 0.008 0.001 HIS B 235 Details of bonding type rmsd covalent geometry : bond 0.00383 (27233) covalent geometry : angle 0.63602 (36846) SS BOND : bond 0.00222 ( 2) SS BOND : angle 2.41563 ( 4) hydrogen bonds : bond 0.03850 ( 1097) hydrogen bonds : angle 5.25482 ( 3216) Misc. bond : bond 0.00085 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6756 Ramachandran restraints generated. 3378 Oldfield, 0 Emsley, 3378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6756 Ramachandran restraints generated. 3378 Oldfield, 0 Emsley, 3378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 376 residues out of total 3020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 376 time to evaluate : 1.000 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: A 51 MET cc_start: 0.6600 (ppp) cc_final: 0.6024 (ppp) REVERT: A 101 GLU cc_start: 0.8988 (tm-30) cc_final: 0.8257 (tm-30) REVERT: A 121 GLU cc_start: 0.8191 (mt-10) cc_final: 0.7883 (pm20) REVERT: A 144 ASP cc_start: 0.8433 (t0) cc_final: 0.7889 (t0) REVERT: A 168 THR cc_start: 0.6770 (m) cc_final: 0.6463 (p) REVERT: A 300 GLU cc_start: 0.8737 (mt-10) cc_final: 0.8417 (tp30) REVERT: B 136 MET cc_start: 0.8869 (tpt) cc_final: 0.8596 (tpp) REVERT: B 154 MET cc_start: 0.8574 (pmm) cc_final: 0.8162 (pmm) REVERT: C 35 LEU cc_start: 0.9534 (mm) cc_final: 0.9324 (mm) REVERT: C 81 LYS cc_start: 0.9143 (tmmt) cc_final: 0.8753 (ttpp) REVERT: C 146 ASP cc_start: 0.8296 (p0) cc_final: 0.8079 (p0) REVERT: C 149 MET cc_start: 0.8750 (ptp) cc_final: 0.8376 (ptp) REVERT: C 214 TYR cc_start: 0.8664 (m-80) cc_final: 0.8075 (m-80) REVERT: C 372 GLU cc_start: 0.9190 (pm20) cc_final: 0.8982 (pm20) REVERT: D 82 CYS cc_start: 0.8425 (t) cc_final: 0.7722 (t) REVERT: D 83 TYR cc_start: 0.8182 (m-80) cc_final: 0.7307 (m-80) REVERT: D 89 GLN cc_start: 0.8484 (mm110) cc_final: 0.8076 (mm110) REVERT: E 1 MET cc_start: 0.6605 (mtt) cc_final: 0.4290 (ptt) REVERT: E 31 PHE cc_start: 0.8621 (m-80) cc_final: 0.8174 (m-80) REVERT: E 73 ASN cc_start: 0.8989 (p0) cc_final: 0.8671 (t0) REVERT: E 77 GLN cc_start: 0.8869 (tm-30) cc_final: 0.8424 (tm-30) REVERT: E 79 ASP cc_start: 0.8687 (t0) cc_final: 0.8298 (p0) REVERT: E 93 GLU cc_start: 0.9251 (tt0) cc_final: 0.8844 (tt0) REVERT: E 127 ASP cc_start: 0.8906 (t0) cc_final: 0.7589 (t0) REVERT: E 143 PHE cc_start: 0.9224 (m-10) cc_final: 0.8797 (m-80) REVERT: E 172 PHE cc_start: 0.8653 (m-80) cc_final: 0.7580 (m-80) REVERT: E 198 LEU cc_start: 0.9202 (mt) cc_final: 0.8760 (mp) REVERT: E 250 MET cc_start: 0.9166 (ptt) cc_final: 0.8732 (ptt) REVERT: F 96 GLN cc_start: 0.8896 (tp40) cc_final: 0.7886 (tm-30) REVERT: F 108 ASN cc_start: 0.9218 (m-40) cc_final: 0.8960 (m-40) REVERT: F 112 GLU cc_start: 0.9141 (mm-30) cc_final: 0.8900 (mm-30) REVERT: F 118 MET cc_start: 0.9362 (mmm) cc_final: 0.8930 (mmm) REVERT: F 203 PHE cc_start: 0.8776 (m-10) cc_final: 0.8517 (m-10) REVERT: F 246 MET cc_start: 0.8825 (ppp) cc_final: 0.8618 (ppp) REVERT: G 100 MET cc_start: 0.9222 (ppp) cc_final: 0.8505 (ppp) REVERT: G 104 ASN cc_start: 0.6882 (m110) cc_final: 0.6574 (t0) REVERT: G 136 CYS cc_start: 0.8360 (m) cc_final: 0.8013 (t) REVERT: G 165 GLN cc_start: 0.9274 (tp-100) cc_final: 0.8811 (tp40) REVERT: G 190 LEU cc_start: 0.8606 (mt) cc_final: 0.8340 (mt) REVERT: G 225 ASP cc_start: 0.9487 (m-30) cc_final: 0.9275 (p0) REVERT: H 54 ILE cc_start: 0.8213 (tp) cc_final: 0.7989 (tp) REVERT: H 79 MET cc_start: 0.9227 (mpp) cc_final: 0.8627 (mpp) REVERT: H 169 LEU cc_start: 0.8592 (pt) cc_final: 0.8228 (mp) REVERT: H 311 GLU cc_start: 0.8940 (tm-30) cc_final: 0.8297 (tm-30) REVERT: H 341 MET cc_start: 0.9011 (ttm) cc_final: 0.8495 (ptm) REVERT: I 146 LEU cc_start: 0.9253 (tp) cc_final: 0.8903 (mp) REVERT: I 233 GLN cc_start: 0.8885 (tt0) cc_final: 0.8403 (tp-100) REVERT: I 243 TYR cc_start: 0.9343 (m-80) cc_final: 0.8925 (m-80) REVERT: J 238 MET cc_start: 0.1226 (mmm) cc_final: 0.0781 (tpp) REVERT: J 385 LYS cc_start: 0.8342 (mttm) cc_final: 0.8063 (tptp) REVERT: J 387 GLN cc_start: 0.9033 (pt0) cc_final: 0.8367 (tt0) REVERT: J 415 GLN cc_start: 0.8878 (mm-40) cc_final: 0.8369 (mm-40) REVERT: J 586 GLU cc_start: 0.8776 (tp30) cc_final: 0.8277 (tp30) REVERT: J 603 MET cc_start: 0.7401 (tmm) cc_final: 0.5721 (ptm) REVERT: J 606 MET cc_start: 0.9325 (tmm) cc_final: 0.9036 (tmm) REVERT: J 674 MET cc_start: 0.6000 (mtt) cc_final: 0.5025 (ptp) REVERT: J 705 MET cc_start: 0.6642 (ptt) cc_final: 0.5970 (ppp) REVERT: J 813 MET cc_start: 0.7895 (tpp) cc_final: 0.7575 (tpp) REVERT: J 907 MET cc_start: 0.9027 (tpt) cc_final: 0.8632 (tpt) REVERT: J 940 ARG cc_start: 0.8305 (tpp-160) cc_final: 0.7705 (mmm160) REVERT: J 942 ASP cc_start: 0.8184 (m-30) cc_final: 0.6960 (m-30) REVERT: P 6 PHE cc_start: 0.9434 (t80) cc_final: 0.9172 (t80) REVERT: P 7 THR cc_start: 0.8198 (p) cc_final: 0.7619 (p) outliers start: 0 outliers final: 0 residues processed: 376 average time/residue: 0.1568 time to fit residues: 96.1312 Evaluate side-chains 294 residues out of total 3020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 294 time to evaluate : 1.003 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 338 random chunks: chunk 307 optimal weight: 8.9990 chunk 6 optimal weight: 8.9990 chunk 22 optimal weight: 5.9990 chunk 204 optimal weight: 0.0770 chunk 186 optimal weight: 9.9990 chunk 19 optimal weight: 3.9990 chunk 311 optimal weight: 8.9990 chunk 281 optimal weight: 0.0060 chunk 96 optimal weight: 6.9990 chunk 208 optimal weight: 50.0000 chunk 108 optimal weight: 3.9990 overall best weight: 2.8160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 131 GLN C 13 HIS C 32 GLN D 45 GLN D 208 ASN ** F 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 285 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 48 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 227 ASN ** J 755 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.076854 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.059183 restraints weight = 145998.835| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.061330 restraints weight = 90673.751| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.062865 restraints weight = 64462.366| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.063961 restraints weight = 49921.304| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.064747 restraints weight = 41142.391| |-----------------------------------------------------------------------------| r_work (final): 0.3450 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7960 moved from start: 0.8292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 27236 Z= 0.139 Angle : 0.608 9.867 36850 Z= 0.321 Chirality : 0.044 0.185 4271 Planarity : 0.004 0.059 4773 Dihedral : 4.923 35.241 3690 Min Nonbonded Distance : 2.333 Molprobity Statistics. All-atom Clashscore : 14.63 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.00 % Favored : 95.91 % Rotamer: Outliers : 0.00 % Allowed : 0.20 % Favored : 99.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.48 (0.14), residues: 3378 helix: 1.10 (0.17), residues: 975 sheet: -0.19 (0.19), residues: 672 loop : -1.22 (0.14), residues: 1731 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 114 TYR 0.040 0.001 TYR H 329 PHE 0.033 0.002 PHE P 9 TRP 0.049 0.002 TRP J 456 HIS 0.007 0.001 HIS B 235 Details of bonding type rmsd covalent geometry : bond 0.00307 (27233) covalent geometry : angle 0.60784 (36846) SS BOND : bond 0.00123 ( 2) SS BOND : angle 1.83092 ( 4) hydrogen bonds : bond 0.03687 ( 1097) hydrogen bonds : angle 5.14877 ( 3216) Misc. bond : bond 0.00142 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4947.60 seconds wall clock time: 86 minutes 33.25 seconds (5193.25 seconds total)