Starting phenix.real_space_refine on Thu Nov 20 03:23:18 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9hg7_52129/11_2025/9hg7_52129.cif Found real_map, /net/cci-nas-00/data/ceres_data/9hg7_52129/11_2025/9hg7_52129.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.83 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9hg7_52129/11_2025/9hg7_52129.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9hg7_52129/11_2025/9hg7_52129.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9hg7_52129/11_2025/9hg7_52129.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9hg7_52129/11_2025/9hg7_52129.map" } resolution = 2.83 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= 0.009 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 48 5.16 5 C 9545 2.51 5 N 2643 2.21 5 O 3000 1.98 5 H 14802 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 30038 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 12175 Number of conformers: 1 Conformer: "" Number of residues, atoms: 788, 12175 Classifications: {'peptide': 788} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 29, 'TRANS': 758} Chain: "B" Number of atoms: 5534 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 5534 Classifications: {'peptide': 371} Link IDs: {'PTRANS': 11, 'TRANS': 359} Chain: "C" Number of atoms: 2845 Number of conformers: 1 Conformer: "" Number of residues, atoms: 189, 2845 Classifications: {'peptide': 189} Modifications used: {'NH1NOTPRO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 178} Chain: "D" Number of atoms: 3461 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 3461 Classifications: {'peptide': 218} Link IDs: {'PTRANS': 12, 'TRANS': 205} Chain: "E" Number of atoms: 1363 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 1363 Classifications: {'peptide': 88} Link IDs: {'PTRANS': 5, 'TRANS': 82} Chain: "F" Number of atoms: 4660 Number of conformers: 1 Conformer: "" Number of residues, atoms: 299, 4660 Classifications: {'peptide': 299} Link IDs: {'PTRANS': 8, 'TRANS': 290} Chain breaks: 1 Time building chain proxies: 4.91, per 1000 atoms: 0.16 Number of scatterers: 30038 At special positions: 0 Unit cell: (110.96, 124.1, 167.9, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 48 16.00 O 3000 8.00 N 2643 7.00 C 9545 6.00 H 14802 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 690 " - pdb=" SG CYS A 700 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.40 Conformation dependent library (CDL) restraints added in 777.1 milliseconds 3878 Ramachandran restraints generated. 1939 Oldfield, 0 Emsley, 1939 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3588 Finding SS restraints... Secondary structure from input PDB file: 50 helices and 20 sheets defined 31.6% alpha, 28.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.99 Creating SS restraints... Processing helix chain 'A' and resid 38 through 45 Processing helix chain 'A' and resid 55 through 69 Processing helix chain 'A' and resid 106 through 117 Processing helix chain 'A' and resid 126 through 128 No H-bonds generated for 'chain 'A' and resid 126 through 128' Processing helix chain 'A' and resid 129 through 145 Processing helix chain 'A' and resid 189 through 196 removed outlier: 4.081A pdb=" N HIS A 196 " --> pdb=" O GLU A 192 " (cutoff:3.500A) Processing helix chain 'A' and resid 215 through 233 Processing helix chain 'A' and resid 280 through 288 Processing helix chain 'A' and resid 297 through 315 removed outlier: 3.870A pdb=" N TYR A 315 " --> pdb=" O LEU A 311 " (cutoff:3.500A) Processing helix chain 'A' and resid 361 through 367 removed outlier: 3.607A pdb=" N LEU A 365 " --> pdb=" O LYS A 361 " (cutoff:3.500A) Processing helix chain 'A' and resid 379 through 393 removed outlier: 3.844A pdb=" N GLY A 393 " --> pdb=" O LEU A 389 " (cutoff:3.500A) Processing helix chain 'A' and resid 448 through 452 Processing helix chain 'A' and resid 496 through 500 removed outlier: 4.070A pdb=" N ASP A 500 " --> pdb=" O ASP A 497 " (cutoff:3.500A) Processing helix chain 'A' and resid 542 through 552 Processing helix chain 'A' and resid 647 through 651 removed outlier: 3.667A pdb=" N ASN A 651 " --> pdb=" O PHE A 648 " (cutoff:3.500A) Processing helix chain 'A' and resid 726 through 731 removed outlier: 5.398A pdb=" N ASN A 731 " --> pdb=" O LYS A 728 " (cutoff:3.500A) Processing helix chain 'B' and resid 239 through 244 removed outlier: 4.074A pdb=" N LEU B 244 " --> pdb=" O ILE B 241 " (cutoff:3.500A) Processing helix chain 'C' and resid 28 through 32 removed outlier: 3.996A pdb=" N LYS C 32 " --> pdb=" O SER C 29 " (cutoff:3.500A) Processing helix chain 'C' and resid 39 through 44 removed outlier: 3.673A pdb=" N LEU C 42 " --> pdb=" O GLU C 39 " (cutoff:3.500A) Processing helix chain 'C' and resid 76 through 80 Processing helix chain 'C' and resid 112 through 114 No H-bonds generated for 'chain 'C' and resid 112 through 114' Processing helix chain 'C' and resid 115 through 127 Processing helix chain 'C' and resid 190 through 213 Processing helix chain 'D' and resid 31 through 46 Processing helix chain 'D' and resid 47 through 62 removed outlier: 3.666A pdb=" N ALA D 51 " --> pdb=" O ASN D 47 " (cutoff:3.500A) Processing helix chain 'D' and resid 69 through 82 Processing helix chain 'D' and resid 84 through 99 Processing helix chain 'D' and resid 104 through 119 removed outlier: 3.606A pdb=" N VAL D 108 " --> pdb=" O ASN D 104 " (cutoff:3.500A) Processing helix chain 'D' and resid 122 through 128 removed outlier: 3.588A pdb=" N GLY D 126 " --> pdb=" O SER D 122 " (cutoff:3.500A) Processing helix chain 'D' and resid 131 through 135 removed outlier: 4.256A pdb=" N ASP D 134 " --> pdb=" O ASP D 131 " (cutoff:3.500A) Processing helix chain 'D' and resid 137 through 154 Processing helix chain 'D' and resid 159 through 189 Processing helix chain 'D' and resid 190 through 205 Processing helix chain 'D' and resid 208 through 225 removed outlier: 3.635A pdb=" N ARG D 212 " --> pdb=" O THR D 208 " (cutoff:3.500A) Proline residue: D 216 - end of helix Processing helix chain 'D' and resid 227 through 243 removed outlier: 4.117A pdb=" N SER D 243 " --> pdb=" O ALA D 239 " (cutoff:3.500A) Processing helix chain 'E' and resid 39 through 46 removed outlier: 3.842A pdb=" N ILE E 46 " --> pdb=" O ASP E 42 " (cutoff:3.500A) Processing helix chain 'E' and resid 51 through 60 Processing helix chain 'F' and resid 39 through 57 removed outlier: 3.727A pdb=" N GLY F 44 " --> pdb=" O SER F 40 " (cutoff:3.500A) Processing helix chain 'F' and resid 62 through 88 removed outlier: 3.564A pdb=" N GLN F 69 " --> pdb=" O THR F 65 " (cutoff:3.500A) Processing helix chain 'F' and resid 92 through 103 removed outlier: 3.571A pdb=" N LEU F 96 " --> pdb=" O SER F 92 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N ALA F 101 " --> pdb=" O ASP F 97 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N ASN F 102 " --> pdb=" O GLN F 98 " (cutoff:3.500A) Processing helix chain 'F' and resid 113 through 117 removed outlier: 3.756A pdb=" N SER F 116 " --> pdb=" O GLN F 113 " (cutoff:3.500A) Processing helix chain 'F' and resid 120 through 123 removed outlier: 4.199A pdb=" N LEU F 123 " --> pdb=" O TYR F 120 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 120 through 123' Processing helix chain 'F' and resid 124 through 150 removed outlier: 4.408A pdb=" N TYR F 128 " --> pdb=" O ASN F 124 " (cutoff:3.500A) Processing helix chain 'F' and resid 153 through 164 Processing helix chain 'F' and resid 188 through 209 Processing helix chain 'F' and resid 211 through 219 Processing helix chain 'F' and resid 222 through 228 removed outlier: 3.903A pdb=" N LEU F 226 " --> pdb=" O GLN F 223 " (cutoff:3.500A) Processing helix chain 'F' and resid 237 through 239 No H-bonds generated for 'chain 'F' and resid 237 through 239' Processing helix chain 'F' and resid 243 through 248 Processing helix chain 'F' and resid 392 through 421 removed outlier: 3.734A pdb=" N ARG F 396 " --> pdb=" O ALA F 392 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 32 removed outlier: 13.152A pdb=" N GLU A 73 " --> pdb=" O ALA F 29 " (cutoff:3.500A) removed outlier: 8.841A pdb=" N ALA F 29 " --> pdb=" O GLU A 73 " (cutoff:3.500A) removed outlier: 7.668A pdb=" N VAL A 75 " --> pdb=" O LYS F 27 " (cutoff:3.500A) removed outlier: 5.323A pdb=" N LYS F 27 " --> pdb=" O VAL A 75 " (cutoff:3.500A) removed outlier: 7.490A pdb=" N VAL A 77 " --> pdb=" O VAL F 25 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N VAL F 25 " --> pdb=" O VAL A 77 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N VAL F 37 " --> pdb=" O ALA F 29 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 28 through 32 removed outlier: 13.152A pdb=" N GLU A 73 " --> pdb=" O ALA F 29 " (cutoff:3.500A) removed outlier: 8.841A pdb=" N ALA F 29 " --> pdb=" O GLU A 73 " (cutoff:3.500A) removed outlier: 7.668A pdb=" N VAL A 75 " --> pdb=" O LYS F 27 " (cutoff:3.500A) removed outlier: 5.323A pdb=" N LYS F 27 " --> pdb=" O VAL A 75 " (cutoff:3.500A) removed outlier: 7.490A pdb=" N VAL A 77 " --> pdb=" O VAL F 25 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N VAL F 25 " --> pdb=" O VAL A 77 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 93 through 100 removed outlier: 7.321A pdb=" N LEU A 165 " --> pdb=" O ALA A 95 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N ILE A 97 " --> pdb=" O LEU A 165 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N LEU A 167 " --> pdb=" O ILE A 97 " (cutoff:3.500A) removed outlier: 4.675A pdb=" N PHE A 99 " --> pdb=" O LEU A 167 " (cutoff:3.500A) removed outlier: 7.110A pdb=" N PHE A 169 " --> pdb=" O PHE A 99 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N THR A 156 " --> pdb=" O ASP A 164 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 176 through 183 removed outlier: 7.523A pdb=" N VAL A 256 " --> pdb=" O GLN A 178 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N ILE A 180 " --> pdb=" O VAL A 256 " (cutoff:3.500A) removed outlier: 7.198A pdb=" N VAL A 258 " --> pdb=" O ILE A 180 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N ILE A 182 " --> pdb=" O VAL A 258 " (cutoff:3.500A) removed outlier: 7.057A pdb=" N ILE A 260 " --> pdb=" O ILE A 182 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N THR A 261 " --> pdb=" O ILE A 240 " (cutoff:3.500A) removed outlier: 5.568A pdb=" N ILE A 240 " --> pdb=" O THR A 261 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N SER B 193 " --> pdb=" O VAL A 245 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 267 through 276 removed outlier: 6.040A pdb=" N LYS A 267 " --> pdb=" O VAL A 335 " (cutoff:3.500A) removed outlier: 7.682A pdb=" N LEU A 337 " --> pdb=" O LYS A 267 " (cutoff:3.500A) removed outlier: 8.009A pdb=" N SER A 269 " --> pdb=" O LEU A 337 " (cutoff:3.500A) removed outlier: 12.134A pdb=" N VAL A 339 " --> pdb=" O SER A 269 " (cutoff:3.500A) removed outlier: 9.337A pdb=" N VAL A 271 " --> pdb=" O VAL A 339 " (cutoff:3.500A) removed outlier: 11.466A pdb=" N VAL A 341 " --> pdb=" O VAL A 271 " (cutoff:3.500A) removed outlier: 9.122A pdb=" N VAL A 273 " --> pdb=" O VAL A 341 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 348 through 355 removed outlier: 7.553A pdb=" N VAL A 414 " --> pdb=" O ARG A 350 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N ILE A 352 " --> pdb=" O VAL A 414 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N TYR A 416 " --> pdb=" O ILE A 352 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N PHE A 354 " --> pdb=" O TYR A 416 " (cutoff:3.500A) removed outlier: 7.162A pdb=" N VAL A 418 " --> pdb=" O PHE A 354 " (cutoff:3.500A) removed outlier: 7.753A pdb=" N GLN A 411 " --> pdb=" O ARG A 404 " (cutoff:3.500A) removed outlier: 5.051A pdb=" N ARG A 404 " --> pdb=" O GLN A 411 " (cutoff:3.500A) removed outlier: 6.128A pdb=" N ASP A 413 " --> pdb=" O THR A 402 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N THR A 402 " --> pdb=" O ASP A 413 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N VAL A 415 " --> pdb=" O THR A 400 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N THR A 400 " --> pdb=" O VAL A 415 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N LYS A 417 " --> pdb=" O VAL A 398 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N VAL A 398 " --> pdb=" O LYS A 417 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N LYS A 419 " --> pdb=" O GLU A 396 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 425 through 429 removed outlier: 3.606A pdb=" N GLY A 590 " --> pdb=" O TYR A 618 " (cutoff:3.500A) removed outlier: 5.839A pdb=" N TYR A 608 " --> pdb=" O THR A 600 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N THR A 735 " --> pdb=" O THR A 720 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N MET A 768 " --> pdb=" O PHE A 791 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N PHE A 791 " --> pdb=" O MET A 768 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 671 through 674 removed outlier: 5.556A pdb=" N ASP A 704 " --> pdb=" O ALA A 672 " (cutoff:3.500A) removed outlier: 8.125A pdb=" N TYR A 674 " --> pdb=" O SER A 702 " (cutoff:3.500A) removed outlier: 7.818A pdb=" N SER A 702 " --> pdb=" O TYR A 674 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 45 through 51 removed outlier: 5.059A pdb=" N THR B 46 " --> pdb=" O THR B 391 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N THR B 391 " --> pdb=" O THR B 46 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N TRP B 48 " --> pdb=" O SER B 389 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N LEU B 378 " --> pdb=" O ILE B 390 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 66 through 67 removed outlier: 4.065A pdb=" N TRP B 93 " --> pdb=" O ALA B 83 " (cutoff:3.500A) removed outlier: 6.005A pdb=" N ASN B 85 " --> pdb=" O GLU B 91 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N GLU B 91 " --> pdb=" O ASN B 85 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 116 through 118 removed outlier: 4.392A pdb=" N TRP B 143 " --> pdb=" O ALA B 133 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N ASN B 135 " --> pdb=" O VAL B 141 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N VAL B 141 " --> pdb=" O ASN B 135 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 156 through 158 removed outlier: 3.995A pdb=" N GLN B 170 " --> pdb=" O THR B 166 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N LEU B 171 " --> pdb=" O THR B 184 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N THR B 184 " --> pdb=" O LEU B 171 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N ALA B 173 " --> pdb=" O LYS B 182 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 206 through 209 removed outlier: 6.659A pdb=" N VAL B 216 " --> pdb=" O GLN B 229 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N GLN B 229 " --> pdb=" O VAL B 216 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N ALA B 218 " --> pdb=" O ILE B 227 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 252 through 254 removed outlier: 6.740A pdb=" N ALA B 269 " --> pdb=" O MET B 278 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 290 through 292 Processing sheet with id=AB7, first strand: chain 'B' and resid 331 through 333 removed outlier: 3.724A pdb=" N ALA B 358 " --> pdb=" O TRP B 348 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 94 through 99 removed outlier: 5.693A pdb=" N ARG C 96 " --> pdb=" O LEU C 107 " (cutoff:3.500A) removed outlier: 4.851A pdb=" N LEU C 107 " --> pdb=" O ARG C 96 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N VAL C 108 " --> pdb=" O GLN C 172 " (cutoff:3.500A) removed outlier: 5.951A pdb=" N GLN C 172 " --> pdb=" O VAL C 108 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N ARG C 160 " --> pdb=" O LEU C 179 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N LEU C 181 " --> pdb=" O ARG C 158 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N ARG C 158 " --> pdb=" O LEU C 181 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 131 through 135 removed outlier: 6.431A pdb=" N THR C 142 " --> pdb=" O THR C 132 " (cutoff:3.500A) removed outlier: 4.647A pdb=" N ARG C 134 " --> pdb=" O THR C 140 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N THR C 140 " --> pdb=" O ARG C 134 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N TYR C 161 " --> pdb=" O THR C 143 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N ARG C 158 " --> pdb=" O LEU C 181 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N LEU C 181 " --> pdb=" O ARG C 158 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N ARG C 160 " --> pdb=" O LEU C 179 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N LEU C 181 " --> pdb=" O VAL C 188 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 34 through 35 Processing sheet with id=AC2, first strand: chain 'F' and resid 230 through 235 removed outlier: 6.210A pdb=" N LEU F 176 " --> pdb=" O MET F 231 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N TRP F 233 " --> pdb=" O LEU F 174 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N LEU F 174 " --> pdb=" O TRP F 233 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N GLU F 173 " --> pdb=" O LEU F 273 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N LEU F 273 " --> pdb=" O GLU F 173 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N ASN F 175 " --> pdb=" O ASN F 271 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N GLY F 264 " --> pdb=" O ARG F 260 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N ARG F 260 " --> pdb=" O GLY F 264 " (cutoff:3.500A) removed outlier: 5.890A pdb=" N HIS F 266 " --> pdb=" O PRO F 258 " (cutoff:3.500A) 746 hydrogen bonds defined for protein. 2070 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: 8.31 Time building geometry restraints manager: 3.49 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 14801 1.03 - 1.23: 214 1.23 - 1.43: 6423 1.43 - 1.62: 8806 1.62 - 1.82: 93 Bond restraints: 30337 Sorted by residual: bond pdb=" C MET F 76 " pdb=" O MET F 76 " ideal model delta sigma weight residual 1.237 1.184 0.053 1.19e-02 7.06e+03 1.96e+01 bond pdb=" N CYS C 25 " pdb=" H1 CYS C 25 " ideal model delta sigma weight residual 0.960 0.890 0.070 2.00e-02 2.50e+03 1.21e+01 bond pdb=" N ARG A 162 " pdb=" H ARG A 162 " ideal model delta sigma weight residual 0.860 0.913 -0.053 2.00e-02 2.50e+03 7.14e+00 bond pdb=" N LYS B 280 " pdb=" CA LYS B 280 " ideal model delta sigma weight residual 1.455 1.487 -0.032 1.26e-02 6.30e+03 6.58e+00 bond pdb=" N GLY A 23 " pdb=" CA GLY A 23 " ideal model delta sigma weight residual 1.451 1.492 -0.041 1.60e-02 3.91e+03 6.42e+00 ... (remaining 30332 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.11: 54091 2.11 - 4.22: 462 4.22 - 6.33: 46 6.33 - 8.44: 4 8.44 - 10.55: 1 Bond angle restraints: 54604 Sorted by residual: angle pdb=" N ASP F 112 " pdb=" CA ASP F 112 " pdb=" C ASP F 112 " ideal model delta sigma weight residual 111.69 117.22 -5.53 1.23e+00 6.61e-01 2.02e+01 angle pdb=" N ARG A 162 " pdb=" CA ARG A 162 " pdb=" C ARG A 162 " ideal model delta sigma weight residual 109.69 103.38 6.31 1.44e+00 4.82e-01 1.92e+01 angle pdb=" N MET F 76 " pdb=" CA MET F 76 " pdb=" C MET F 76 " ideal model delta sigma weight residual 111.36 106.72 4.64 1.09e+00 8.42e-01 1.81e+01 angle pdb=" CA MET F 414 " pdb=" C MET F 414 " pdb=" O MET F 414 " ideal model delta sigma weight residual 120.42 116.18 4.24 1.06e+00 8.90e-01 1.60e+01 angle pdb=" CA ARG A 162 " pdb=" C ARG A 162 " pdb=" O ARG A 162 " ideal model delta sigma weight residual 121.60 116.81 4.79 1.21e+00 6.83e-01 1.57e+01 ... (remaining 54599 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.47: 12702 17.47 - 34.94: 1019 34.94 - 52.41: 441 52.41 - 69.88: 135 69.88 - 87.35: 36 Dihedral angle restraints: 14333 sinusoidal: 7806 harmonic: 6527 Sorted by residual: dihedral pdb=" CD ARG B 281 " pdb=" NE ARG B 281 " pdb=" CZ ARG B 281 " pdb=" NH1 ARG B 281 " ideal model delta sinusoidal sigma weight residual 0.00 -68.82 68.82 1 1.00e+01 1.00e-02 6.13e+01 dihedral pdb=" CD ARG A 162 " pdb=" NE ARG A 162 " pdb=" CZ ARG A 162 " pdb=" NH1 ARG A 162 " ideal model delta sinusoidal sigma weight residual 0.00 38.54 -38.54 1 1.00e+01 1.00e-02 2.09e+01 dihedral pdb=" CA TYR C 197 " pdb=" C TYR C 197 " pdb=" N SER C 198 " pdb=" CA SER C 198 " ideal model delta harmonic sigma weight residual 180.00 161.74 18.26 0 5.00e+00 4.00e-02 1.33e+01 ... (remaining 14330 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 1676 0.041 - 0.081: 425 0.081 - 0.122: 182 0.122 - 0.162: 29 0.162 - 0.203: 5 Chirality restraints: 2317 Sorted by residual: chirality pdb=" CA LYS B 280 " pdb=" N LYS B 280 " pdb=" C LYS B 280 " pdb=" CB LYS B 280 " both_signs ideal model delta sigma weight residual False 2.51 2.71 -0.20 2.00e-01 2.50e+01 1.03e+00 chirality pdb=" CA ARG B 281 " pdb=" N ARG B 281 " pdb=" C ARG B 281 " pdb=" CB ARG B 281 " both_signs ideal model delta sigma weight residual False 2.51 2.70 -0.19 2.00e-01 2.50e+01 8.82e-01 chirality pdb=" CA PRO A 159 " pdb=" N PRO A 159 " pdb=" C PRO A 159 " pdb=" CB PRO A 159 " both_signs ideal model delta sigma weight residual False 2.72 2.54 0.18 2.00e-01 2.50e+01 7.93e-01 ... (remaining 2314 not shown) Planarity restraints: 4662 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN F 186 " 0.246 2.00e-02 2.50e+03 3.80e-01 2.17e+03 pdb=" CG ASN F 186 " -0.017 2.00e-02 2.50e+03 pdb=" OD1 ASN F 186 " -0.239 2.00e-02 2.50e+03 pdb=" ND2 ASN F 186 " 0.000 2.00e-02 2.50e+03 pdb="HD21 ASN F 186 " -0.607 2.00e-02 2.50e+03 pdb="HD22 ASN F 186 " 0.617 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 281 " 0.683 9.50e-02 1.11e+02 3.11e-01 1.07e+03 pdb=" NE ARG B 281 " -0.304 2.00e-02 2.50e+03 pdb=" CZ ARG B 281 " -0.083 2.00e-02 2.50e+03 pdb=" NH1 ARG B 281 " 0.044 2.00e-02 2.50e+03 pdb=" NH2 ARG B 281 " 0.024 2.00e-02 2.50e+03 pdb="HH11 ARG B 281 " 0.229 2.00e-02 2.50e+03 pdb="HH12 ARG B 281 " -0.061 2.00e-02 2.50e+03 pdb="HH21 ARG B 281 " -0.286 2.00e-02 2.50e+03 pdb="HH22 ARG B 281 " 0.407 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 162 " -0.790 9.50e-02 1.11e+02 2.67e-01 1.11e+02 pdb=" NE ARG A 162 " -0.027 2.00e-02 2.50e+03 pdb=" CZ ARG A 162 " 0.000 2.00e-02 2.50e+03 pdb=" NH1 ARG A 162 " 0.009 2.00e-02 2.50e+03 pdb=" NH2 ARG A 162 " 0.006 2.00e-02 2.50e+03 pdb="HH11 ARG A 162 " 0.080 2.00e-02 2.50e+03 pdb="HH12 ARG A 162 " -0.050 2.00e-02 2.50e+03 pdb="HH21 ARG A 162 " 0.066 2.00e-02 2.50e+03 pdb="HH22 ARG A 162 " -0.050 2.00e-02 2.50e+03 ... (remaining 4659 not shown) Histogram of nonbonded interaction distances: 1.53 - 2.14: 923 2.14 - 2.76: 56068 2.76 - 3.37: 83277 3.37 - 3.99: 108887 3.99 - 4.60: 169121 Nonbonded interactions: 418276 Sorted by model distance: nonbonded pdb=" H GLY F 253 " pdb=" O VAL F 270 " model vdw 1.525 2.450 nonbonded pdb=" HZ1 LYS A 103 " pdb=" O GLU B 26 " model vdw 1.526 2.450 nonbonded pdb=" H ASN B 85 " pdb=" O LYS B 90 " model vdw 1.567 2.450 nonbonded pdb=" OD1 ASP B 300 " pdb=" H ARG B 304 " model vdw 1.587 2.450 nonbonded pdb=" O ARG C 112 " pdb=" HG1 THR C 115 " model vdw 1.604 2.450 ... (remaining 418271 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.040 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: 0.170 Extract box with map and model: 0.400 Check model and map are aligned: 0.090 Set scattering table: 0.080 Process input model: 29.070 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.040 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:8.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.610 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7691 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 : 0.004 0.053 15536 Z= 0.198 Angle : 0.649 7.831 21092 Z= 0.374 Chirality : 0.045 0.203 2317 Planarity : 0.011 0.467 2791 Dihedral : 14.775 87.186 5687 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.21 % Allowed : 3.09 % Favored : 96.70 % Rotamer: Outliers : 1.16 % Allowed : 11.02 % Favored : 87.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.16 (0.19), residues: 1939 helix: 1.50 (0.23), residues: 533 sheet: -0.40 (0.21), residues: 553 loop : -0.32 (0.22), residues: 853 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG F 399 TYR 0.022 0.001 TYR C 31 PHE 0.009 0.001 PHE A 791 TRP 0.016 0.001 TRP C 145 HIS 0.002 0.001 HIS D 139 Details of bonding type rmsd covalent geometry : bond 0.00408 (15535) covalent geometry : angle 0.64901 (21090) SS BOND : bond 0.00162 ( 1) SS BOND : angle 2.17493 ( 2) hydrogen bonds : bond 0.13543 ( 722) hydrogen bonds : angle 6.03404 ( 2070) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3878 Ramachandran restraints generated. 1939 Oldfield, 0 Emsley, 1939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3878 Ramachandran restraints generated. 1939 Oldfield, 0 Emsley, 1939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 162 time to evaluate : 0.848 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: A 224 GLU cc_start: 0.8993 (tp30) cc_final: 0.8758 (mm-30) REVERT: A 465 TYR cc_start: 0.7363 (m-80) cc_final: 0.7013 (m-80) REVERT: A 582 ASP cc_start: 0.8585 (t0) cc_final: 0.8129 (t0) REVERT: A 787 TYR cc_start: 0.8434 (t80) cc_final: 0.8231 (t80) REVERT: B 76 ASP cc_start: 0.7430 (t0) cc_final: 0.7136 (t70) REVERT: B 226 MET cc_start: 0.9195 (ttm) cc_final: 0.8142 (tmm) REVERT: B 240 GLU cc_start: 0.8918 (mt-10) cc_final: 0.8621 (mm-30) REVERT: D 34 GLU cc_start: 0.8849 (mt-10) cc_final: 0.8648 (mt-10) REVERT: D 232 GLU cc_start: 0.8478 (mm-30) cc_final: 0.8182 (mm-30) REVERT: F 31 VAL cc_start: 0.8700 (t) cc_final: 0.8495 (t) REVERT: F 63 ASP cc_start: 0.8350 (m-30) cc_final: 0.8099 (t0) REVERT: F 71 MET cc_start: 0.8583 (tpp) cc_final: 0.8147 (tmm) REVERT: F 83 MET cc_start: 0.9470 (ptm) cc_final: 0.8889 (tmm) outliers start: 19 outliers final: 7 residues processed: 179 average time/residue: 1.4443 time to fit residues: 283.6851 Evaluate side-chains 125 residues out of total 1634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 118 time to evaluate : 0.650 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 751 SER Chi-restraints excluded: chain B residue 85 ASN Chi-restraints excluded: chain B residue 153 SER Chi-restraints excluded: chain D residue 164 THR Chi-restraints excluded: chain F residue 32 VAL Chi-restraints excluded: chain F residue 81 LEU Chi-restraints excluded: chain F residue 259 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 98 optimal weight: 0.2980 chunk 107 optimal weight: 5.9990 chunk 10 optimal weight: 0.9980 chunk 66 optimal weight: 6.9990 chunk 130 optimal weight: 20.0000 chunk 124 optimal weight: 8.9990 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 4.9990 chunk 122 optimal weight: 30.0000 chunk 91 optimal weight: 2.9990 chunk 149 optimal weight: 1.9990 overall best weight: 1.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 445 GLN B 266 ASN B 301 GLN ** D 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 106 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4130 r_free = 0.4130 target = 0.139698 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.082167 restraints weight = 87884.015| |-----------------------------------------------------------------------------| r_work (start): 0.3121 rms_B_bonded: 3.25 r_work: 0.2962 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work: 0.2828 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.2828 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8072 moved from start: 0.1248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 15536 Z= 0.185 Angle : 0.543 5.881 21092 Z= 0.293 Chirality : 0.043 0.160 2317 Planarity : 0.005 0.122 2791 Dihedral : 4.761 58.995 2146 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 1.41 % Allowed : 13.59 % Favored : 85.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.19 (0.19), residues: 1939 helix: 1.72 (0.22), residues: 537 sheet: -0.45 (0.21), residues: 538 loop : -0.40 (0.22), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 79 TYR 0.017 0.001 TYR D 184 PHE 0.020 0.001 PHE A 494 TRP 0.013 0.001 TRP B 317 HIS 0.004 0.001 HIS F 266 Details of bonding type rmsd covalent geometry : bond 0.00403 (15535) covalent geometry : angle 0.54327 (21090) SS BOND : bond 0.00115 ( 1) SS BOND : angle 0.73402 ( 2) hydrogen bonds : bond 0.04345 ( 722) hydrogen bonds : angle 5.08247 ( 2070) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3878 Ramachandran restraints generated. 1939 Oldfield, 0 Emsley, 1939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3878 Ramachandran restraints generated. 1939 Oldfield, 0 Emsley, 1939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 117 time to evaluate : 0.820 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 410 ASP cc_start: 0.8162 (OUTLIER) cc_final: 0.7883 (t0) REVERT: A 582 ASP cc_start: 0.8938 (t0) cc_final: 0.8535 (t0) REVERT: B 85 ASN cc_start: 0.8923 (OUTLIER) cc_final: 0.8257 (t0) REVERT: B 240 GLU cc_start: 0.8915 (mt-10) cc_final: 0.8591 (mm-30) REVERT: D 232 GLU cc_start: 0.8698 (mm-30) cc_final: 0.8430 (mm-30) REVERT: F 63 ASP cc_start: 0.8696 (m-30) cc_final: 0.8407 (t0) REVERT: F 71 MET cc_start: 0.8713 (tpp) cc_final: 0.8247 (tmm) REVERT: F 83 MET cc_start: 0.9319 (ptm) cc_final: 0.8904 (tmm) REVERT: F 266 HIS cc_start: 0.5799 (OUTLIER) cc_final: 0.5487 (m90) outliers start: 23 outliers final: 12 residues processed: 130 average time/residue: 1.3031 time to fit residues: 187.8310 Evaluate side-chains 124 residues out of total 1634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 109 time to evaluate : 0.829 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 243 THR Chi-restraints excluded: chain A residue 410 ASP Chi-restraints excluded: chain A residue 511 THR Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 85 ASN Chi-restraints excluded: chain B residue 153 SER Chi-restraints excluded: chain C residue 31 TYR Chi-restraints excluded: chain C residue 38 ASP Chi-restraints excluded: chain D residue 44 GLN Chi-restraints excluded: chain D residue 164 THR Chi-restraints excluded: chain F residue 32 VAL Chi-restraints excluded: chain F residue 46 MET Chi-restraints excluded: chain F residue 136 MET Chi-restraints excluded: chain F residue 160 LEU Chi-restraints excluded: chain F residue 266 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 51 optimal weight: 3.9990 chunk 166 optimal weight: 5.9990 chunk 89 optimal weight: 4.9990 chunk 98 optimal weight: 0.5980 chunk 68 optimal weight: 3.9990 chunk 128 optimal weight: 30.0000 chunk 84 optimal weight: 5.9990 chunk 174 optimal weight: 10.0000 chunk 96 optimal weight: 3.9990 chunk 57 optimal weight: 1.9990 chunk 101 optimal weight: 0.9980 overall best weight: 2.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 301 GLN ** D 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 59 GLN F 175 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4114 r_free = 0.4114 target = 0.137996 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.079935 restraints weight = 87883.228| |-----------------------------------------------------------------------------| r_work (start): 0.3101 rms_B_bonded: 3.27 r_work: 0.2939 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work: 0.2803 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.2803 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8111 moved from start: 0.1601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 15536 Z= 0.207 Angle : 0.525 6.349 21092 Z= 0.282 Chirality : 0.043 0.145 2317 Planarity : 0.004 0.059 2791 Dihedral : 4.545 58.591 2141 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 1.35 % Allowed : 13.65 % Favored : 85.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.20 (0.19), residues: 1939 helix: 1.83 (0.22), residues: 536 sheet: -0.48 (0.22), residues: 530 loop : -0.46 (0.21), residues: 873 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 79 TYR 0.017 0.001 TYR D 184 PHE 0.015 0.001 PHE A 494 TRP 0.011 0.001 TRP B 317 HIS 0.005 0.001 HIS F 266 Details of bonding type rmsd covalent geometry : bond 0.00461 (15535) covalent geometry : angle 0.52478 (21090) SS BOND : bond 0.00050 ( 1) SS BOND : angle 0.43326 ( 2) hydrogen bonds : bond 0.04100 ( 722) hydrogen bonds : angle 4.87759 ( 2070) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3878 Ramachandran restraints generated. 1939 Oldfield, 0 Emsley, 1939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3878 Ramachandran restraints generated. 1939 Oldfield, 0 Emsley, 1939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 1634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 109 time to evaluate : 0.707 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 410 ASP cc_start: 0.8240 (OUTLIER) cc_final: 0.7986 (t0) REVERT: A 582 ASP cc_start: 0.8959 (t0) cc_final: 0.8558 (t0) REVERT: B 32 MET cc_start: 0.8753 (ttt) cc_final: 0.8401 (tpt) REVERT: B 85 ASN cc_start: 0.9030 (OUTLIER) cc_final: 0.8358 (t0) REVERT: B 240 GLU cc_start: 0.8939 (mt-10) cc_final: 0.8606 (mm-30) REVERT: B 280 LYS cc_start: 0.9001 (OUTLIER) cc_final: 0.8772 (mttp) REVERT: D 232 GLU cc_start: 0.8729 (mm-30) cc_final: 0.8445 (mm-30) REVERT: F 63 ASP cc_start: 0.8663 (m-30) cc_final: 0.8373 (t0) REVERT: F 71 MET cc_start: 0.8743 (tpp) cc_final: 0.8304 (tmm) REVERT: F 83 MET cc_start: 0.9294 (ptm) cc_final: 0.8942 (tmm) outliers start: 22 outliers final: 10 residues processed: 126 average time/residue: 1.3107 time to fit residues: 183.3399 Evaluate side-chains 118 residues out of total 1634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 105 time to evaluate : 0.876 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 243 THR Chi-restraints excluded: chain A residue 410 ASP Chi-restraints excluded: chain A residue 511 THR Chi-restraints excluded: chain A residue 573 ASN Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 85 ASN Chi-restraints excluded: chain B residue 153 SER Chi-restraints excluded: chain B residue 280 LYS Chi-restraints excluded: chain C residue 31 TYR Chi-restraints excluded: chain D residue 44 GLN Chi-restraints excluded: chain D residue 134 ASP Chi-restraints excluded: chain D residue 164 THR Chi-restraints excluded: chain F residue 32 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 156 optimal weight: 0.4980 chunk 53 optimal weight: 0.9990 chunk 174 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 132 optimal weight: 30.0000 chunk 94 optimal weight: 3.9990 chunk 66 optimal weight: 9.9990 chunk 149 optimal weight: 1.9990 chunk 29 optimal weight: 0.7980 chunk 118 optimal weight: 2.9990 chunk 46 optimal weight: 0.5980 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 301 GLN ** C 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4127 r_free = 0.4127 target = 0.138979 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.081196 restraints weight = 87010.752| |-----------------------------------------------------------------------------| r_work (start): 0.3126 rms_B_bonded: 3.28 r_work: 0.2965 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work: 0.2829 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.2829 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8088 moved from start: 0.1775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 15536 Z= 0.117 Angle : 0.487 6.299 21092 Z= 0.259 Chirality : 0.042 0.148 2317 Planarity : 0.003 0.048 2791 Dihedral : 4.415 59.310 2141 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 1.16 % Allowed : 13.77 % Favored : 85.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.33 (0.19), residues: 1939 helix: 1.94 (0.22), residues: 537 sheet: -0.35 (0.22), residues: 520 loop : -0.41 (0.22), residues: 882 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 79 TYR 0.018 0.001 TYR F 422 PHE 0.016 0.001 PHE F 212 TRP 0.010 0.001 TRP B 317 HIS 0.004 0.001 HIS F 266 Details of bonding type rmsd covalent geometry : bond 0.00258 (15535) covalent geometry : angle 0.48715 (21090) SS BOND : bond 0.00072 ( 1) SS BOND : angle 0.39566 ( 2) hydrogen bonds : bond 0.03706 ( 722) hydrogen bonds : angle 4.66175 ( 2070) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3878 Ramachandran restraints generated. 1939 Oldfield, 0 Emsley, 1939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3878 Ramachandran restraints generated. 1939 Oldfield, 0 Emsley, 1939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 1634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 114 time to evaluate : 0.863 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 410 ASP cc_start: 0.8199 (OUTLIER) cc_final: 0.7967 (t0) REVERT: A 582 ASP cc_start: 0.8933 (t0) cc_final: 0.8539 (t0) REVERT: B 32 MET cc_start: 0.8724 (ttt) cc_final: 0.8424 (tpt) REVERT: B 85 ASN cc_start: 0.9103 (OUTLIER) cc_final: 0.8385 (t0) REVERT: B 240 GLU cc_start: 0.8960 (mt-10) cc_final: 0.8623 (mm-30) REVERT: B 280 LYS cc_start: 0.8999 (OUTLIER) cc_final: 0.8773 (mttp) REVERT: D 232 GLU cc_start: 0.8694 (mm-30) cc_final: 0.8414 (mm-30) REVERT: F 71 MET cc_start: 0.8757 (tpp) cc_final: 0.8249 (tmm) REVERT: F 83 MET cc_start: 0.9285 (ptm) cc_final: 0.8968 (tmm) outliers start: 19 outliers final: 8 residues processed: 127 average time/residue: 1.2754 time to fit residues: 180.6842 Evaluate side-chains 114 residues out of total 1634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 103 time to evaluate : 0.822 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 410 ASP Chi-restraints excluded: chain A residue 511 THR Chi-restraints excluded: chain A residue 551 SER Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 85 ASN Chi-restraints excluded: chain B residue 136 THR Chi-restraints excluded: chain B residue 280 LYS Chi-restraints excluded: chain D residue 44 GLN Chi-restraints excluded: chain D residue 134 ASP Chi-restraints excluded: chain F residue 32 VAL Chi-restraints excluded: chain F residue 46 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 4 optimal weight: 9.9990 chunk 150 optimal weight: 1.9990 chunk 128 optimal weight: 40.0000 chunk 14 optimal weight: 6.9990 chunk 115 optimal weight: 5.9990 chunk 170 optimal weight: 20.0000 chunk 94 optimal weight: 4.9990 chunk 30 optimal weight: 4.9990 chunk 38 optimal weight: 0.2980 chunk 62 optimal weight: 2.9990 chunk 139 optimal weight: 2.9990 overall best weight: 2.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 301 GLN ** C 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 41 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4102 r_free = 0.4102 target = 0.136737 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.078406 restraints weight = 88071.936| |-----------------------------------------------------------------------------| r_work (start): 0.3080 rms_B_bonded: 3.27 r_work: 0.2921 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work: 0.2784 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.2784 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8136 moved from start: 0.2021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 15536 Z= 0.234 Angle : 0.518 6.622 21092 Z= 0.277 Chirality : 0.042 0.141 2317 Planarity : 0.004 0.051 2791 Dihedral : 4.433 59.157 2139 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 1.41 % Allowed : 13.95 % Favored : 84.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.17 (0.19), residues: 1939 helix: 1.99 (0.22), residues: 533 sheet: -0.62 (0.22), residues: 523 loop : -0.52 (0.21), residues: 883 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 79 TYR 0.017 0.001 TYR D 184 PHE 0.022 0.001 PHE A 67 TRP 0.009 0.001 TRP B 317 HIS 0.005 0.001 HIS F 178 Details of bonding type rmsd covalent geometry : bond 0.00521 (15535) covalent geometry : angle 0.51794 (21090) SS BOND : bond 0.00004 ( 1) SS BOND : angle 0.29499 ( 2) hydrogen bonds : bond 0.03916 ( 722) hydrogen bonds : angle 4.67345 ( 2070) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3878 Ramachandran restraints generated. 1939 Oldfield, 0 Emsley, 1939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3878 Ramachandran restraints generated. 1939 Oldfield, 0 Emsley, 1939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 1634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 109 time to evaluate : 0.817 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: A 410 ASP cc_start: 0.8375 (OUTLIER) cc_final: 0.8090 (t0) REVERT: A 582 ASP cc_start: 0.8972 (t0) cc_final: 0.8580 (t0) REVERT: A 787 TYR cc_start: 0.8533 (t80) cc_final: 0.8303 (t80) REVERT: B 85 ASN cc_start: 0.9165 (OUTLIER) cc_final: 0.8453 (t0) REVERT: D 232 GLU cc_start: 0.8726 (mm-30) cc_final: 0.8411 (mm-30) REVERT: E 50 MET cc_start: 0.9217 (mtp) cc_final: 0.8657 (mtp) REVERT: F 71 MET cc_start: 0.8795 (tpp) cc_final: 0.8326 (tmm) REVERT: F 83 MET cc_start: 0.9342 (ptm) cc_final: 0.8959 (tmm) outliers start: 23 outliers final: 9 residues processed: 129 average time/residue: 1.3373 time to fit residues: 191.3895 Evaluate side-chains 112 residues out of total 1634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 101 time to evaluate : 0.862 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 243 THR Chi-restraints excluded: chain A residue 410 ASP Chi-restraints excluded: chain A residue 511 THR Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 85 ASN Chi-restraints excluded: chain D residue 44 GLN Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain D residue 134 ASP Chi-restraints excluded: chain D residue 164 THR Chi-restraints excluded: chain F residue 32 VAL Chi-restraints excluded: chain F residue 46 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 70 optimal weight: 0.7980 chunk 188 optimal weight: 9.9990 chunk 65 optimal weight: 5.9990 chunk 61 optimal weight: 3.9990 chunk 60 optimal weight: 0.6980 chunk 41 optimal weight: 10.0000 chunk 110 optimal weight: 6.9990 chunk 113 optimal weight: 0.8980 chunk 15 optimal weight: 2.9990 chunk 54 optimal weight: 4.9990 chunk 73 optimal weight: 0.4980 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 594 ASN B 301 GLN ** C 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 241 ASN ** 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 = 0.4116 r_free = 0.4116 target = 0.137983 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.080554 restraints weight = 87253.940| |-----------------------------------------------------------------------------| r_work (start): 0.3114 rms_B_bonded: 3.24 r_work: 0.2952 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work: 0.2816 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.2816 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8099 moved from start: 0.2165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 15536 Z= 0.124 Angle : 0.491 6.371 21092 Z= 0.261 Chirality : 0.042 0.147 2317 Planarity : 0.003 0.047 2791 Dihedral : 4.300 59.763 2139 Min Nonbonded Distance : 2.281 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 1.16 % Allowed : 14.08 % Favored : 84.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.34 (0.19), residues: 1939 helix: 2.11 (0.22), residues: 535 sheet: -0.50 (0.22), residues: 521 loop : -0.42 (0.22), residues: 883 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 79 TYR 0.018 0.001 TYR D 184 PHE 0.017 0.001 PHE A 67 TRP 0.008 0.001 TRP B 317 HIS 0.004 0.001 HIS F 178 Details of bonding type rmsd covalent geometry : bond 0.00278 (15535) covalent geometry : angle 0.49113 (21090) SS BOND : bond 0.00040 ( 1) SS BOND : angle 0.24617 ( 2) hydrogen bonds : bond 0.03584 ( 722) hydrogen bonds : angle 4.49032 ( 2070) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3878 Ramachandran restraints generated. 1939 Oldfield, 0 Emsley, 1939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3878 Ramachandran restraints generated. 1939 Oldfield, 0 Emsley, 1939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 1634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 106 time to evaluate : 0.839 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 410 ASP cc_start: 0.8290 (OUTLIER) cc_final: 0.7939 (t0) REVERT: A 582 ASP cc_start: 0.8948 (t0) cc_final: 0.8559 (t0) REVERT: A 787 TYR cc_start: 0.8533 (t80) cc_final: 0.8303 (t80) REVERT: B 85 ASN cc_start: 0.9171 (OUTLIER) cc_final: 0.8458 (t0) REVERT: D 232 GLU cc_start: 0.8719 (mm-30) cc_final: 0.8405 (mm-30) REVERT: E 50 MET cc_start: 0.9172 (mtp) cc_final: 0.8668 (mtp) REVERT: F 71 MET cc_start: 0.8790 (tpp) cc_final: 0.8322 (tmm) REVERT: F 83 MET cc_start: 0.9344 (ptm) cc_final: 0.8989 (tmm) REVERT: F 219 HIS cc_start: 0.6956 (OUTLIER) cc_final: 0.6594 (m90) outliers start: 19 outliers final: 7 residues processed: 121 average time/residue: 1.3551 time to fit residues: 182.2532 Evaluate side-chains 112 residues out of total 1634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 102 time to evaluate : 0.755 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 410 ASP Chi-restraints excluded: chain A residue 511 THR Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 85 ASN Chi-restraints excluded: chain B residue 136 THR Chi-restraints excluded: chain D residue 44 GLN Chi-restraints excluded: chain D residue 134 ASP Chi-restraints excluded: chain D residue 164 THR Chi-restraints excluded: chain F residue 32 VAL Chi-restraints excluded: chain F residue 219 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 7 optimal weight: 8.9990 chunk 138 optimal weight: 2.9990 chunk 46 optimal weight: 2.9990 chunk 82 optimal weight: 4.9990 chunk 184 optimal weight: 4.9990 chunk 79 optimal weight: 7.9990 chunk 4 optimal weight: 10.0000 chunk 120 optimal weight: 1.9990 chunk 96 optimal weight: 1.9990 chunk 135 optimal weight: 0.9980 chunk 126 optimal weight: 40.0000 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 301 GLN C 119 GLN ** D 241 ASN ** 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 = 0.4105 r_free = 0.4105 target = 0.137186 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.079187 restraints weight = 87827.894| |-----------------------------------------------------------------------------| r_work (start): 0.3164 rms_B_bonded: 3.28 r_work: 0.2993 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work: 0.2858 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.2858 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8228 moved from start: 0.2304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 15536 Z= 0.198 Angle : 0.502 6.783 21092 Z= 0.267 Chirality : 0.042 0.141 2317 Planarity : 0.004 0.049 2791 Dihedral : 4.329 59.109 2139 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 1.16 % Allowed : 14.32 % Favored : 84.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.28 (0.19), residues: 1939 helix: 2.14 (0.22), residues: 534 sheet: -0.64 (0.22), residues: 521 loop : -0.44 (0.21), residues: 884 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 321 TYR 0.018 0.001 TYR D 184 PHE 0.011 0.001 PHE A 67 TRP 0.008 0.001 TRP B 143 HIS 0.004 0.001 HIS F 178 Details of bonding type rmsd covalent geometry : bond 0.00444 (15535) covalent geometry : angle 0.50159 (21090) SS BOND : bond 0.00014 ( 1) SS BOND : angle 0.30748 ( 2) hydrogen bonds : bond 0.03692 ( 722) hydrogen bonds : angle 4.51846 ( 2070) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3878 Ramachandran restraints generated. 1939 Oldfield, 0 Emsley, 1939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3878 Ramachandran restraints generated. 1939 Oldfield, 0 Emsley, 1939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 1634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 106 time to evaluate : 0.809 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 410 ASP cc_start: 0.8401 (OUTLIER) cc_final: 0.8162 (t0) REVERT: A 582 ASP cc_start: 0.8980 (t0) cc_final: 0.8618 (t0) REVERT: A 787 TYR cc_start: 0.8593 (t80) cc_final: 0.8366 (t80) REVERT: B 85 ASN cc_start: 0.9249 (OUTLIER) cc_final: 0.8535 (t0) REVERT: D 232 GLU cc_start: 0.8739 (mm-30) cc_final: 0.8450 (mm-30) REVERT: E 50 MET cc_start: 0.9252 (mtp) cc_final: 0.8813 (mtp) REVERT: F 71 MET cc_start: 0.8807 (tpp) cc_final: 0.8340 (tmm) REVERT: F 83 MET cc_start: 0.9324 (ptm) cc_final: 0.8994 (tmm) REVERT: F 219 HIS cc_start: 0.7008 (OUTLIER) cc_final: 0.6667 (m90) outliers start: 19 outliers final: 10 residues processed: 122 average time/residue: 1.2749 time to fit residues: 172.7607 Evaluate side-chains 112 residues out of total 1634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 99 time to evaluate : 0.762 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 243 THR Chi-restraints excluded: chain A residue 410 ASP Chi-restraints excluded: chain A residue 511 THR Chi-restraints excluded: chain A residue 573 ASN Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 85 ASN Chi-restraints excluded: chain B residue 153 SER Chi-restraints excluded: chain C residue 32 LYS Chi-restraints excluded: chain D residue 44 GLN Chi-restraints excluded: chain D residue 134 ASP Chi-restraints excluded: chain D residue 164 THR Chi-restraints excluded: chain F residue 32 VAL Chi-restraints excluded: chain F residue 219 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 166 optimal weight: 1.9990 chunk 137 optimal weight: 3.9990 chunk 81 optimal weight: 0.8980 chunk 146 optimal weight: 2.9990 chunk 168 optimal weight: 7.9990 chunk 2 optimal weight: 30.0000 chunk 84 optimal weight: 2.9990 chunk 72 optimal weight: 2.9990 chunk 177 optimal weight: 40.0000 chunk 102 optimal weight: 4.9990 chunk 62 optimal weight: 0.0040 overall best weight: 1.7798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 301 GLN ** D 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4109 r_free = 0.4109 target = 0.137347 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.079296 restraints weight = 88195.309| |-----------------------------------------------------------------------------| r_work (start): 0.3090 rms_B_bonded: 3.28 r_work: 0.2930 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work: 0.2795 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.2795 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8126 moved from start: 0.2410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 15536 Z= 0.162 Angle : 0.492 6.880 21092 Z= 0.262 Chirality : 0.042 0.161 2317 Planarity : 0.004 0.052 2791 Dihedral : 4.267 57.982 2139 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 1.04 % Allowed : 14.50 % Favored : 84.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.30 (0.19), residues: 1939 helix: 2.16 (0.22), residues: 534 sheet: -0.63 (0.22), residues: 525 loop : -0.42 (0.21), residues: 880 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 79 TYR 0.018 0.001 TYR D 184 PHE 0.017 0.001 PHE A 67 TRP 0.008 0.001 TRP A 745 HIS 0.004 0.001 HIS F 178 Details of bonding type rmsd covalent geometry : bond 0.00365 (15535) covalent geometry : angle 0.49210 (21090) SS BOND : bond 0.00045 ( 1) SS BOND : angle 0.33341 ( 2) hydrogen bonds : bond 0.03586 ( 722) hydrogen bonds : angle 4.45683 ( 2070) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3878 Ramachandran restraints generated. 1939 Oldfield, 0 Emsley, 1939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3878 Ramachandran restraints generated. 1939 Oldfield, 0 Emsley, 1939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 1634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 103 time to evaluate : 0.701 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 410 ASP cc_start: 0.8362 (OUTLIER) cc_final: 0.8127 (t0) REVERT: A 582 ASP cc_start: 0.8967 (t0) cc_final: 0.8581 (t0) REVERT: A 787 TYR cc_start: 0.8547 (t80) cc_final: 0.8311 (t80) REVERT: B 85 ASN cc_start: 0.9210 (OUTLIER) cc_final: 0.8491 (t0) REVERT: D 232 GLU cc_start: 0.8718 (mm-30) cc_final: 0.8410 (mm-30) REVERT: E 50 MET cc_start: 0.9200 (mtp) cc_final: 0.8734 (mtp) REVERT: F 71 MET cc_start: 0.8823 (tpp) cc_final: 0.8359 (tmm) REVERT: F 83 MET cc_start: 0.9310 (ptm) cc_final: 0.8981 (tmm) REVERT: F 190 ASP cc_start: 0.9241 (m-30) cc_final: 0.9022 (p0) REVERT: F 219 HIS cc_start: 0.7023 (OUTLIER) cc_final: 0.6704 (m90) outliers start: 17 outliers final: 10 residues processed: 116 average time/residue: 1.3223 time to fit residues: 170.5800 Evaluate side-chains 114 residues out of total 1634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 101 time to evaluate : 0.762 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 243 THR Chi-restraints excluded: chain A residue 410 ASP Chi-restraints excluded: chain A residue 511 THR Chi-restraints excluded: chain A residue 741 MET Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 85 ASN Chi-restraints excluded: chain B residue 153 SER Chi-restraints excluded: chain C residue 32 LYS Chi-restraints excluded: chain D residue 44 GLN Chi-restraints excluded: chain D residue 134 ASP Chi-restraints excluded: chain D residue 164 THR Chi-restraints excluded: chain F residue 32 VAL Chi-restraints excluded: chain F residue 219 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 126 optimal weight: 40.0000 chunk 169 optimal weight: 9.9990 chunk 52 optimal weight: 2.9990 chunk 154 optimal weight: 0.5980 chunk 69 optimal weight: 2.9990 chunk 121 optimal weight: 0.5980 chunk 131 optimal weight: 0.6980 chunk 102 optimal weight: 4.9990 chunk 47 optimal weight: 9.9990 chunk 79 optimal weight: 8.9990 chunk 91 optimal weight: 2.9990 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 301 GLN ** D 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4110 r_free = 0.4110 target = 0.137184 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.079414 restraints weight = 87516.028| |-----------------------------------------------------------------------------| r_work (start): 0.3096 rms_B_bonded: 3.25 r_work: 0.2936 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work: 0.2798 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.2798 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8126 moved from start: 0.2488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 15536 Z= 0.149 Angle : 0.489 9.036 21092 Z= 0.259 Chirality : 0.042 0.144 2317 Planarity : 0.004 0.054 2791 Dihedral : 4.226 56.423 2139 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 1.04 % Allowed : 14.57 % Favored : 84.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.33 (0.19), residues: 1939 helix: 2.19 (0.22), residues: 534 sheet: -0.64 (0.22), residues: 516 loop : -0.39 (0.21), residues: 889 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 321 TYR 0.018 0.001 TYR D 184 PHE 0.022 0.001 PHE A 67 TRP 0.008 0.001 TRP F 413 HIS 0.005 0.001 HIS F 178 Details of bonding type rmsd covalent geometry : bond 0.00334 (15535) covalent geometry : angle 0.48934 (21090) SS BOND : bond 0.00032 ( 1) SS BOND : angle 0.33617 ( 2) hydrogen bonds : bond 0.03488 ( 722) hydrogen bonds : angle 4.40071 ( 2070) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3878 Ramachandran restraints generated. 1939 Oldfield, 0 Emsley, 1939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3878 Ramachandran restraints generated. 1939 Oldfield, 0 Emsley, 1939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 1634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 108 time to evaluate : 0.759 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 410 ASP cc_start: 0.8325 (OUTLIER) cc_final: 0.8093 (t0) REVERT: A 582 ASP cc_start: 0.8970 (t0) cc_final: 0.8575 (t0) REVERT: A 787 TYR cc_start: 0.8535 (t80) cc_final: 0.8305 (t80) REVERT: B 85 ASN cc_start: 0.9236 (OUTLIER) cc_final: 0.8510 (t0) REVERT: D 232 GLU cc_start: 0.8698 (mm-30) cc_final: 0.8389 (mm-30) REVERT: E 50 MET cc_start: 0.9194 (mtp) cc_final: 0.8718 (mtp) REVERT: F 71 MET cc_start: 0.8823 (tpp) cc_final: 0.8369 (tmm) REVERT: F 83 MET cc_start: 0.9313 (ptm) cc_final: 0.9006 (tmm) REVERT: F 190 ASP cc_start: 0.9244 (m-30) cc_final: 0.9031 (p0) REVERT: F 219 HIS cc_start: 0.7002 (OUTLIER) cc_final: 0.6736 (m90) outliers start: 17 outliers final: 9 residues processed: 121 average time/residue: 1.3155 time to fit residues: 177.0870 Evaluate side-chains 115 residues out of total 1634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 103 time to evaluate : 0.841 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 243 THR Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 410 ASP Chi-restraints excluded: chain A residue 511 THR Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain B residue 85 ASN Chi-restraints excluded: chain B residue 153 SER Chi-restraints excluded: chain C residue 32 LYS Chi-restraints excluded: chain D residue 44 GLN Chi-restraints excluded: chain D residue 134 ASP Chi-restraints excluded: chain F residue 32 VAL Chi-restraints excluded: chain F residue 219 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 190 optimal weight: 9.9990 chunk 63 optimal weight: 2.9990 chunk 73 optimal weight: 0.7980 chunk 43 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 59 optimal weight: 0.5980 chunk 172 optimal weight: 20.0000 chunk 122 optimal weight: 40.0000 chunk 177 optimal weight: 40.0000 chunk 96 optimal weight: 3.9990 chunk 28 optimal weight: 1.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 301 GLN ** D 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4112 r_free = 0.4112 target = 0.137596 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.079802 restraints weight = 87180.397| |-----------------------------------------------------------------------------| r_work (start): 0.3099 rms_B_bonded: 3.26 r_work: 0.2938 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work: 0.2803 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.2803 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8121 moved from start: 0.2577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 15536 Z= 0.142 Angle : 0.488 8.086 21092 Z= 0.259 Chirality : 0.042 0.144 2317 Planarity : 0.004 0.055 2791 Dihedral : 4.189 54.905 2139 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 0.67 % Allowed : 15.12 % Favored : 84.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.36 (0.19), residues: 1939 helix: 2.24 (0.22), residues: 534 sheet: -0.62 (0.22), residues: 517 loop : -0.39 (0.21), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 33 TYR 0.028 0.001 TYR C 197 PHE 0.012 0.001 PHE A 67 TRP 0.008 0.001 TRP F 413 HIS 0.005 0.001 HIS F 178 Details of bonding type rmsd covalent geometry : bond 0.00318 (15535) covalent geometry : angle 0.48829 (21090) SS BOND : bond 0.00016 ( 1) SS BOND : angle 0.28651 ( 2) hydrogen bonds : bond 0.03454 ( 722) hydrogen bonds : angle 4.37236 ( 2070) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3878 Ramachandran restraints generated. 1939 Oldfield, 0 Emsley, 1939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3878 Ramachandran restraints generated. 1939 Oldfield, 0 Emsley, 1939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 1634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 108 time to evaluate : 0.933 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 410 ASP cc_start: 0.8310 (OUTLIER) cc_final: 0.8081 (t0) REVERT: A 582 ASP cc_start: 0.8968 (t0) cc_final: 0.8574 (t0) REVERT: A 607 GLU cc_start: 0.9001 (OUTLIER) cc_final: 0.8749 (mt-10) REVERT: B 85 ASN cc_start: 0.9249 (OUTLIER) cc_final: 0.8512 (t0) REVERT: D 232 GLU cc_start: 0.8697 (mm-30) cc_final: 0.8390 (mm-30) REVERT: E 50 MET cc_start: 0.9189 (mtp) cc_final: 0.8748 (mtp) REVERT: F 71 MET cc_start: 0.8833 (tpp) cc_final: 0.8380 (tmm) REVERT: F 83 MET cc_start: 0.9275 (ptm) cc_final: 0.8963 (tmm) REVERT: F 190 ASP cc_start: 0.9262 (m-30) cc_final: 0.9043 (p0) REVERT: F 219 HIS cc_start: 0.7077 (OUTLIER) cc_final: 0.6834 (m90) outliers start: 11 outliers final: 8 residues processed: 118 average time/residue: 1.4140 time to fit residues: 184.6334 Evaluate side-chains 117 residues out of total 1634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 105 time to evaluate : 0.718 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 243 THR Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 410 ASP Chi-restraints excluded: chain A residue 511 THR Chi-restraints excluded: chain A residue 607 GLU Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain B residue 85 ASN Chi-restraints excluded: chain B residue 153 SER Chi-restraints excluded: chain D residue 44 GLN Chi-restraints excluded: chain D residue 134 ASP Chi-restraints excluded: chain F residue 32 VAL Chi-restraints excluded: chain F residue 219 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 129 optimal weight: 30.0000 chunk 43 optimal weight: 0.0980 chunk 156 optimal weight: 2.9990 chunk 6 optimal weight: 9.9990 chunk 87 optimal weight: 2.9990 chunk 176 optimal weight: 9.9990 chunk 70 optimal weight: 2.9990 chunk 103 optimal weight: 5.9990 chunk 99 optimal weight: 6.9990 chunk 121 optimal weight: 0.6980 chunk 72 optimal weight: 3.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 301 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4106 r_free = 0.4106 target = 0.137119 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.079108 restraints weight = 87811.822| |-----------------------------------------------------------------------------| r_work (start): 0.3088 rms_B_bonded: 3.26 r_work: 0.2929 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work: 0.2793 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.2793 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8133 moved from start: 0.2627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 15536 Z= 0.176 Angle : 0.504 10.331 21092 Z= 0.266 Chirality : 0.042 0.142 2317 Planarity : 0.004 0.061 2791 Dihedral : 4.223 53.728 2139 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 0.73 % Allowed : 15.30 % Favored : 83.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.34 (0.19), residues: 1939 helix: 2.22 (0.22), residues: 534 sheet: -0.68 (0.22), residues: 525 loop : -0.37 (0.21), residues: 880 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 321 TYR 0.025 0.001 TYR F 422 PHE 0.020 0.001 PHE A 67 TRP 0.008 0.001 TRP F 413 HIS 0.005 0.001 HIS F 178 Details of bonding type rmsd covalent geometry : bond 0.00394 (15535) covalent geometry : angle 0.50447 (21090) SS BOND : bond 0.00008 ( 1) SS BOND : angle 0.29399 ( 2) hydrogen bonds : bond 0.03508 ( 722) hydrogen bonds : angle 4.40035 ( 2070) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14292.31 seconds wall clock time: 241 minutes 26.51 seconds (14486.51 seconds total)