Starting phenix.real_space_refine on Thu Jun 26 01:28:49 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9hg7_52129/06_2025/9hg7_52129.cif Found real_map, /net/cci-nas-00/data/ceres_data/9hg7_52129/06_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9hg7_52129/06_2025/9hg7_52129.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9hg7_52129/06_2025/9hg7_52129.map" model { file = "/net/cci-nas-00/data/ceres_data/9hg7_52129/06_2025/9hg7_52129.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9hg7_52129/06_2025/9hg7_52129.cif" } resolution = 2.83 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 13.95, per 1000 atoms: 0.46 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: 7.51 Conformation dependent library (CDL) restraints added in 2.3 seconds 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: 2.56 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: 12.01 Time building geometry restraints manager: 9.16 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: 3.750 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: 0.550 Extract box with map and model: 1.280 Check model and map are aligned: 0.220 Set scattering table: 0.290 Process input model: 62.050 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.080 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:11.530 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 79.960 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.16 (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 TRP 0.016 0.001 TRP C 145 HIS 0.002 0.001 HIS D 139 PHE 0.009 0.001 PHE A 791 TYR 0.022 0.001 TYR C 31 ARG 0.010 0.001 ARG F 399 Details of bonding type rmsd hydrogen bonds : bond 0.13543 ( 722) hydrogen bonds : angle 6.03404 ( 2070) SS BOND : bond 0.00162 ( 1) SS BOND : angle 2.17493 ( 2) covalent geometry : bond 0.00408 (15535) covalent geometry : angle 0.64901 (21090) *********************** 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 : 2.385 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 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: 0.8264 (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: 0.8867 (tmm) outliers start: 19 outliers final: 6 residues processed: 179 average time/residue: 2.8720 time to fit residues: 569.4100 Evaluate side-chains 123 residues out of total 1634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 117 time to evaluate : 2.582 ------------------------------------------------------------------------------- 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 259 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 161 optimal weight: 0.2980 chunk 144 optimal weight: 3.9990 chunk 80 optimal weight: 9.9990 chunk 49 optimal weight: 0.8980 chunk 97 optimal weight: 5.9990 chunk 77 optimal weight: 4.9990 chunk 149 optimal weight: 1.9990 chunk 57 optimal weight: 1.9990 chunk 91 optimal weight: 2.9990 chunk 111 optimal weight: 1.9990 chunk 173 optimal weight: 30.0000 overall best weight: 1.4386 ------------------------------------------------------------------------------- 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 ** F 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 106 GLN F 175 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4185 r_free = 0.4185 target = 0.148742 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.090661 restraints weight = 87117.587| |-----------------------------------------------------------------------------| r_work (start): 0.3133 rms_B_bonded: 3.30 r_work: 0.2965 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work: 0.2830 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.2830 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8065 moved from start: 0.1268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 15536 Z= 0.153 Angle : 0.536 5.982 21092 Z= 0.288 Chirality : 0.043 0.161 2317 Planarity : 0.005 0.118 2791 Dihedral : 4.671 59.070 2144 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 1.29 % Allowed : 13.59 % Favored : 85.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.22 (0.19), residues: 1939 helix: 1.73 (0.22), residues: 537 sheet: -0.43 (0.21), residues: 537 loop : -0.39 (0.22), residues: 865 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 317 HIS 0.004 0.001 HIS F 266 PHE 0.020 0.001 PHE A 494 TYR 0.018 0.001 TYR D 184 ARG 0.009 0.001 ARG A 79 Details of bonding type rmsd hydrogen bonds : bond 0.04200 ( 722) hydrogen bonds : angle 5.02675 ( 2070) SS BOND : bond 0.00065 ( 1) SS BOND : angle 0.73466 ( 2) covalent geometry : bond 0.00338 (15535) covalent geometry : angle 0.53604 (21090) *********************** 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 138 residues out of total 1634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 117 time to evaluate : 2.227 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: 0.8128 (OUTLIER) cc_final: 0.7828 (t0) REVERT: A 582 ASP cc_start: 0.8932 (t0) cc_final: 0.8529 (t0) REVERT: B 32 MET cc_start: 0.8738 (ttt) cc_final: 0.8368 (tpt) REVERT: B 240 GLU cc_start: 0.8931 (mt-10) cc_final: 0.8603 (mm-30) REVERT: D 232 GLU cc_start: 0.8695 (mm-30) cc_final: 0.8430 (mm-30) REVERT: F 63 ASP cc_start: 0.8689 (m-30) cc_final: 0.8397 (t0) REVERT: F 71 MET cc_start: 0.8696 (tpp) cc_final: 0.8230 (tmm) REVERT: F 83 MET cc_start: 0.9324 (ptm) cc_final: 0.8954 (tmm) REVERT: F 266 HIS cc_start: 0.5777 (OUTLIER) cc_final: 0.5455 (m90) outliers start: 21 outliers final: 11 residues processed: 129 average time/residue: 2.7891 time to fit residues: 404.0709 Evaluate side-chains 123 residues out of total 1634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 110 time to evaluate : 4.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 252 LYS 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 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 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 12 optimal weight: 6.9990 chunk 156 optimal weight: 0.0870 chunk 42 optimal weight: 2.9990 chunk 16 optimal weight: 2.9990 chunk 112 optimal weight: 0.9980 chunk 120 optimal weight: 0.2980 chunk 176 optimal weight: 8.9990 chunk 136 optimal weight: 3.9990 chunk 151 optimal weight: 0.8980 chunk 3 optimal weight: 40.0000 chunk 21 optimal weight: 3.9990 overall best weight: 1.0560 ------------------------------------------------------------------------------- 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 ** D 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 59 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4134 r_free = 0.4134 target = 0.139780 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.082792 restraints weight = 87463.095| |-----------------------------------------------------------------------------| r_work (start): 0.3143 rms_B_bonded: 3.23 r_work: 0.2981 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work: 0.2845 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.2845 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8064 moved from start: 0.1576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 15536 Z= 0.124 Angle : 0.495 6.272 21092 Z= 0.265 Chirality : 0.042 0.149 2317 Planarity : 0.004 0.052 2791 Dihedral : 4.367 58.837 2140 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 1.22 % Allowed : 13.77 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.34 (0.19), residues: 1939 helix: 1.92 (0.22), residues: 537 sheet: -0.38 (0.21), residues: 529 loop : -0.37 (0.22), residues: 873 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 317 HIS 0.005 0.001 HIS F 266 PHE 0.014 0.001 PHE A 494 TYR 0.017 0.001 TYR D 184 ARG 0.006 0.000 ARG A 79 Details of bonding type rmsd hydrogen bonds : bond 0.03852 ( 722) hydrogen bonds : angle 4.74537 ( 2070) SS BOND : bond 0.00097 ( 1) SS BOND : angle 0.51598 ( 2) covalent geometry : bond 0.00270 (15535) covalent geometry : angle 0.49502 (21090) *********************** 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 136 residues out of total 1634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 116 time to evaluate : 2.416 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: 0.8101 (OUTLIER) cc_final: 0.7829 (t0) REVERT: A 582 ASP cc_start: 0.8928 (t0) cc_final: 0.8531 (t0) REVERT: B 32 MET cc_start: 0.8739 (ttt) cc_final: 0.8424 (tpt) REVERT: B 85 ASN cc_start: 0.8991 (OUTLIER) cc_final: 0.8299 (t0) REVERT: B 240 GLU cc_start: 0.8944 (mt-10) cc_final: 0.8596 (mm-30) REVERT: D 232 GLU cc_start: 0.8687 (mm-30) cc_final: 0.8441 (mm-30) REVERT: F 63 ASP cc_start: 0.8670 (m-30) cc_final: 0.8384 (t0) REVERT: F 71 MET cc_start: 0.8731 (tpp) cc_final: 0.8245 (tmm) REVERT: F 83 MET cc_start: 0.9300 (ptm) cc_final: 0.8959 (tmm) REVERT: F 426 LEU cc_start: 0.7021 (mm) cc_final: 0.6780 (mt) outliers start: 20 outliers final: 8 residues processed: 130 average time/residue: 2.5298 time to fit residues: 372.5125 Evaluate side-chains 116 residues out of total 1634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 106 time to evaluate : 2.236 ------------------------------------------------------------------------------- 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 B residue 153 SER 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 177 optimal weight: 30.0000 chunk 47 optimal weight: 9.9990 chunk 1 optimal weight: 9.9990 chunk 139 optimal weight: 0.5980 chunk 11 optimal weight: 6.9990 chunk 61 optimal weight: 1.9990 chunk 162 optimal weight: 0.9980 chunk 168 optimal weight: 6.9990 chunk 115 optimal weight: 7.9990 chunk 112 optimal weight: 0.0370 chunk 111 optimal weight: 7.9990 overall best weight: 2.1262 ------------------------------------------------------------------------------- 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** E 41 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4116 r_free = 0.4116 target = 0.138140 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.079984 restraints weight = 88058.134| |-----------------------------------------------------------------------------| r_work (start): 0.3102 rms_B_bonded: 3.30 r_work: 0.2941 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work: 0.2811 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.2811 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8107 moved from start: 0.1849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 15536 Z= 0.193 Angle : 0.506 5.913 21092 Z= 0.270 Chirality : 0.042 0.143 2317 Planarity : 0.004 0.050 2791 Dihedral : 4.393 59.014 2140 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 1.53 % Allowed : 13.46 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.30 (0.19), residues: 1939 helix: 1.98 (0.22), residues: 536 sheet: -0.44 (0.22), residues: 522 loop : -0.45 (0.21), residues: 881 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 317 HIS 0.004 0.001 HIS F 178 PHE 0.014 0.001 PHE F 212 TYR 0.019 0.001 TYR F 422 ARG 0.005 0.000 ARG A 79 Details of bonding type rmsd hydrogen bonds : bond 0.03821 ( 722) hydrogen bonds : angle 4.66483 ( 2070) SS BOND : bond 0.00034 ( 1) SS BOND : angle 0.33245 ( 2) covalent geometry : bond 0.00430 (15535) covalent geometry : angle 0.50646 (21090) *********************** 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: 25 poor density : 108 time to evaluate : 2.245 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: A 410 ASP cc_start: 0.8286 (OUTLIER) cc_final: 0.8012 (t0) REVERT: A 582 ASP cc_start: 0.8968 (t0) cc_final: 0.8567 (t0) REVERT: B 85 ASN cc_start: 0.9138 (OUTLIER) cc_final: 0.8420 (t0) REVERT: B 240 GLU cc_start: 0.8947 (mt-10) cc_final: 0.8632 (mm-30) REVERT: D 232 GLU cc_start: 0.8710 (mm-30) cc_final: 0.8470 (mm-30) REVERT: F 71 MET cc_start: 0.8770 (tpp) cc_final: 0.8307 (tmm) REVERT: F 83 MET cc_start: 0.9365 (ptm) cc_final: 0.9004 (tmm) REVERT: F 426 LEU cc_start: 0.6982 (mm) cc_final: 0.6732 (mt) outliers start: 25 outliers final: 12 residues processed: 128 average time/residue: 2.9501 time to fit residues: 423.4281 Evaluate side-chains 119 residues out of total 1634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 105 time to evaluate : 2.336 ------------------------------------------------------------------------------- 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 551 SER 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 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 Chi-restraints excluded: chain F residue 85 GLN Chi-restraints excluded: chain F residue 160 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 22 optimal weight: 2.9990 chunk 179 optimal weight: 10.0000 chunk 56 optimal weight: 0.5980 chunk 96 optimal weight: 2.9990 chunk 160 optimal weight: 0.5980 chunk 25 optimal weight: 0.8980 chunk 60 optimal weight: 1.9990 chunk 134 optimal weight: 6.9990 chunk 163 optimal weight: 10.0000 chunk 162 optimal weight: 0.0670 chunk 20 optimal weight: 3.9990 overall best weight: 0.8320 ------------------------------------------------------------------------------- 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 = 0.4131 r_free = 0.4131 target = 0.138940 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.081285 restraints weight = 87391.799| |-----------------------------------------------------------------------------| r_work (start): 0.3132 rms_B_bonded: 3.27 r_work: 0.2972 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work: 0.2837 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.2837 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8081 moved from start: 0.1997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 15536 Z= 0.105 Angle : 0.477 6.534 21092 Z= 0.252 Chirality : 0.042 0.148 2317 Planarity : 0.004 0.067 2791 Dihedral : 4.282 59.440 2139 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 3.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 1.29 % Allowed : 13.83 % Favored : 84.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.45 (0.19), residues: 1939 helix: 2.10 (0.22), residues: 535 sheet: -0.34 (0.22), residues: 519 loop : -0.35 (0.22), residues: 885 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 317 HIS 0.004 0.001 HIS F 178 PHE 0.018 0.001 PHE A 67 TYR 0.017 0.001 TYR D 184 ARG 0.013 0.000 ARG C 30 Details of bonding type rmsd hydrogen bonds : bond 0.03503 ( 722) hydrogen bonds : angle 4.49384 ( 2070) SS BOND : bond 0.00056 ( 1) SS BOND : angle 0.29884 ( 2) covalent geometry : bond 0.00231 (15535) covalent geometry : angle 0.47708 (21090) *********************** 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 129 residues out of total 1634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 108 time to evaluate : 2.376 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: 0.8208 (OUTLIER) cc_final: 0.7992 (t0) REVERT: A 582 ASP cc_start: 0.8943 (t0) cc_final: 0.8539 (t0) REVERT: A 787 TYR cc_start: 0.8523 (t80) cc_final: 0.8304 (t80) REVERT: B 85 ASN cc_start: 0.9136 (OUTLIER) cc_final: 0.8406 (t0) REVERT: B 240 GLU cc_start: 0.8959 (mt-10) cc_final: 0.8621 (mm-30) REVERT: D 232 GLU cc_start: 0.8702 (mm-30) cc_final: 0.8425 (mm-30) REVERT: E 50 MET cc_start: 0.9062 (mtp) cc_final: 0.8442 (mtp) REVERT: F 71 MET cc_start: 0.8762 (tpp) cc_final: 0.8296 (tmm) REVERT: F 76 MET cc_start: 0.9384 (tmm) cc_final: 0.9171 (tmm) REVERT: F 83 MET cc_start: 0.9378 (ptm) cc_final: 0.9037 (tmm) REVERT: F 136 MET cc_start: 0.8675 (mpm) cc_final: 0.7721 (ptp) REVERT: F 219 HIS cc_start: 0.6856 (OUTLIER) cc_final: 0.6429 (m90) REVERT: F 426 LEU cc_start: 0.7090 (mm) cc_final: 0.6842 (mt) outliers start: 21 outliers final: 10 residues processed: 123 average time/residue: 2.5439 time to fit residues: 351.0377 Evaluate side-chains 113 residues out of total 1634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 100 time to evaluate : 2.583 ------------------------------------------------------------------------------- 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 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 Chi-restraints excluded: chain F residue 85 GLN Chi-restraints excluded: chain F residue 160 LEU Chi-restraints excluded: chain F residue 219 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 123 optimal weight: 50.0000 chunk 67 optimal weight: 0.1980 chunk 47 optimal weight: 8.9990 chunk 0 optimal weight: 20.0000 chunk 64 optimal weight: 2.9990 chunk 163 optimal weight: 8.9990 chunk 76 optimal weight: 0.7980 chunk 65 optimal weight: 0.9990 chunk 23 optimal weight: 1.9990 chunk 189 optimal weight: 20.0000 chunk 96 optimal weight: 3.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- 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 = 0.4124 r_free = 0.4124 target = 0.138570 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.080650 restraints weight = 87978.606| |-----------------------------------------------------------------------------| r_work (start): 0.3187 rms_B_bonded: 3.29 r_work: 0.3021 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work: 0.2884 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.2884 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8196 moved from start: 0.2133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 15536 Z= 0.141 Angle : 0.481 7.382 21092 Z= 0.255 Chirality : 0.041 0.144 2317 Planarity : 0.003 0.048 2791 Dihedral : 4.230 59.927 2139 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 3.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 1.22 % Allowed : 13.65 % Favored : 85.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.45 (0.19), residues: 1939 helix: 2.19 (0.22), residues: 535 sheet: -0.43 (0.22), residues: 525 loop : -0.34 (0.22), residues: 879 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 143 HIS 0.004 0.001 HIS F 178 PHE 0.013 0.001 PHE A 67 TYR 0.018 0.001 TYR D 184 ARG 0.004 0.000 ARG A 79 Details of bonding type rmsd hydrogen bonds : bond 0.03524 ( 722) hydrogen bonds : angle 4.42918 ( 2070) SS BOND : bond 0.00033 ( 1) SS BOND : angle 0.28132 ( 2) covalent geometry : bond 0.00316 (15535) covalent geometry : angle 0.48145 (21090) *********************** 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: 20 poor density : 105 time to evaluate : 3.208 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: 0.8279 (OUTLIER) cc_final: 0.8070 (t0) REVERT: A 582 ASP cc_start: 0.8946 (t0) cc_final: 0.8582 (t0) REVERT: A 787 TYR cc_start: 0.8582 (t80) cc_final: 0.8365 (t80) REVERT: B 85 ASN cc_start: 0.9210 (OUTLIER) cc_final: 0.8491 (t0) REVERT: B 240 GLU cc_start: 0.8940 (mt-10) cc_final: 0.8623 (mm-30) REVERT: D 232 GLU cc_start: 0.8719 (mm-30) cc_final: 0.8446 (mm-30) REVERT: E 50 MET cc_start: 0.9142 (mtp) cc_final: 0.8508 (mtp) REVERT: F 71 MET cc_start: 0.8768 (tpp) cc_final: 0.8298 (tmm) REVERT: F 83 MET cc_start: 0.9324 (ptm) cc_final: 0.8979 (tmm) REVERT: F 136 MET cc_start: 0.8662 (mpm) cc_final: 0.7748 (ptp) REVERT: F 219 HIS cc_start: 0.6882 (OUTLIER) cc_final: 0.6508 (m90) REVERT: F 426 LEU cc_start: 0.7160 (mm) cc_final: 0.6920 (mt) outliers start: 20 outliers final: 8 residues processed: 120 average time/residue: 3.5484 time to fit residues: 487.1753 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 : 2.981 ------------------------------------------------------------------------------- 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 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 85 GLN 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 186 optimal weight: 30.0000 chunk 13 optimal weight: 8.9990 chunk 162 optimal weight: 0.2980 chunk 169 optimal weight: 30.0000 chunk 34 optimal weight: 1.9990 chunk 93 optimal weight: 4.9990 chunk 33 optimal weight: 0.6980 chunk 1 optimal weight: 20.0000 chunk 20 optimal weight: 2.9990 chunk 114 optimal weight: 4.9990 chunk 164 optimal weight: 20.0000 overall best weight: 2.1986 ------------------------------------------------------------------------------- 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 = 0.4116 r_free = 0.4116 target = 0.139939 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.081847 restraints weight = 88173.401| |-----------------------------------------------------------------------------| r_work (start): 0.3095 rms_B_bonded: 3.27 r_work: 0.2934 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work: 0.2801 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.2801 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8127 moved from start: 0.2263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 15536 Z= 0.192 Angle : 0.496 7.520 21092 Z= 0.263 Chirality : 0.042 0.198 2317 Planarity : 0.004 0.048 2791 Dihedral : 4.277 59.310 2139 Min Nonbonded Distance : 2.292 Molprobity Statistics. All-atom Clashscore : 4.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 1.04 % Allowed : 14.26 % Favored : 84.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.39 (0.19), residues: 1939 helix: 2.20 (0.22), residues: 534 sheet: -0.53 (0.22), residues: 511 loop : -0.38 (0.21), residues: 894 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 143 HIS 0.004 0.001 HIS F 178 PHE 0.019 0.001 PHE A 67 TYR 0.017 0.001 TYR D 184 ARG 0.004 0.000 ARG A 321 Details of bonding type rmsd hydrogen bonds : bond 0.03609 ( 722) hydrogen bonds : angle 4.47010 ( 2070) SS BOND : bond 0.00006 ( 1) SS BOND : angle 0.27769 ( 2) covalent geometry : bond 0.00431 (15535) covalent geometry : angle 0.49580 (21090) *********************** 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 120 residues out of total 1634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 103 time to evaluate : 2.211 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: 0.8320 (OUTLIER) cc_final: 0.7918 (t0) REVERT: A 582 ASP cc_start: 0.8988 (t0) cc_final: 0.8594 (t0) REVERT: A 787 TYR cc_start: 0.8536 (t80) cc_final: 0.8312 (t80) REVERT: B 85 ASN cc_start: 0.9187 (OUTLIER) cc_final: 0.8471 (t0) REVERT: B 240 GLU cc_start: 0.8964 (mt-10) cc_final: 0.8624 (mm-30) REVERT: D 232 GLU cc_start: 0.8711 (mm-30) cc_final: 0.8457 (mm-30) REVERT: E 50 MET cc_start: 0.9163 (mtp) cc_final: 0.8588 (mtp) REVERT: F 71 MET cc_start: 0.8798 (tpp) cc_final: 0.8338 (tmm) REVERT: F 83 MET cc_start: 0.9371 (ptm) cc_final: 0.9048 (tmm) REVERT: F 190 ASP cc_start: 0.9309 (m-30) cc_final: 0.9080 (p0) REVERT: F 219 HIS cc_start: 0.6974 (OUTLIER) cc_final: 0.6660 (m90) outliers start: 17 outliers final: 8 residues processed: 118 average time/residue: 2.7087 time to fit residues: 355.3771 Evaluate side-chains 111 residues out of total 1634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 100 time to evaluate : 2.185 ------------------------------------------------------------------------------- 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 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 85 GLN 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 147 optimal weight: 1.9990 chunk 53 optimal weight: 7.9990 chunk 58 optimal weight: 1.9990 chunk 97 optimal weight: 4.9990 chunk 35 optimal weight: 0.6980 chunk 107 optimal weight: 8.9990 chunk 88 optimal weight: 3.9990 chunk 17 optimal weight: 3.9990 chunk 102 optimal weight: 4.9990 chunk 174 optimal weight: 9.9990 chunk 129 optimal weight: 40.0000 overall best weight: 2.5388 ------------------------------------------------------------------------------- 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 = 0.4102 r_free = 0.4102 target = 0.137177 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.078914 restraints weight = 87964.805| |-----------------------------------------------------------------------------| r_work (start): 0.3076 rms_B_bonded: 3.27 r_work: 0.2917 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work: 0.2779 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.2779 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8149 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 : 0.005 0.069 15536 Z= 0.219 Angle : 0.517 7.476 21092 Z= 0.274 Chirality : 0.042 0.141 2317 Planarity : 0.004 0.049 2791 Dihedral : 4.311 58.103 2139 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 1.04 % Allowed : 14.44 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.25 (0.19), residues: 1939 helix: 2.10 (0.22), residues: 540 sheet: -0.69 (0.22), residues: 518 loop : -0.44 (0.21), residues: 881 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 745 HIS 0.005 0.001 HIS F 178 PHE 0.023 0.001 PHE A 67 TYR 0.018 0.001 TYR F 398 ARG 0.004 0.000 ARG A 321 Details of bonding type rmsd hydrogen bonds : bond 0.03743 ( 722) hydrogen bonds : angle 4.50942 ( 2070) SS BOND : bond 0.00003 ( 1) SS BOND : angle 0.29930 ( 2) covalent geometry : bond 0.00492 (15535) covalent geometry : angle 0.51671 (21090) *********************** 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 122 residues out of total 1634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 105 time to evaluate : 2.672 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: 0.8396 (OUTLIER) cc_final: 0.8114 (t0) REVERT: A 582 ASP cc_start: 0.8988 (t0) cc_final: 0.8593 (t0) REVERT: A 787 TYR cc_start: 0.8540 (t80) cc_final: 0.8309 (t80) REVERT: B 85 ASN cc_start: 0.9201 (OUTLIER) cc_final: 0.8492 (t0) REVERT: B 240 GLU cc_start: 0.8975 (mt-10) cc_final: 0.8647 (mm-30) REVERT: D 232 GLU cc_start: 0.8718 (mm-30) cc_final: 0.8470 (mm-30) REVERT: E 50 MET cc_start: 0.9224 (mtp) cc_final: 0.8685 (mtp) REVERT: F 71 MET cc_start: 0.8855 (tpp) cc_final: 0.8398 (tmm) REVERT: F 83 MET cc_start: 0.9314 (ptm) cc_final: 0.9002 (tmm) REVERT: F 190 ASP cc_start: 0.9279 (m-30) cc_final: 0.9050 (p0) REVERT: F 219 HIS cc_start: 0.7018 (OUTLIER) cc_final: 0.6738 (m90) REVERT: F 426 LEU cc_start: 0.7281 (mm) cc_final: 0.7025 (mt) outliers start: 17 outliers final: 7 residues processed: 119 average time/residue: 2.7200 time to fit residues: 359.3925 Evaluate side-chains 113 residues out of total 1634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 103 time to evaluate : 2.299 ------------------------------------------------------------------------------- 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 D residue 44 GLN Chi-restraints excluded: chain F residue 32 VAL Chi-restraints excluded: chain F residue 85 GLN 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 93 optimal weight: 2.9990 chunk 149 optimal weight: 0.9980 chunk 12 optimal weight: 6.9990 chunk 179 optimal weight: 10.0000 chunk 7 optimal weight: 5.9990 chunk 20 optimal weight: 2.9990 chunk 143 optimal weight: 0.2980 chunk 158 optimal weight: 0.9980 chunk 31 optimal weight: 2.9990 chunk 169 optimal weight: 20.0000 chunk 146 optimal weight: 0.6980 overall best weight: 1.1982 ------------------------------------------------------------------------------- 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 = 0.4118 r_free = 0.4118 target = 0.138045 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.080084 restraints weight = 87439.889| |-----------------------------------------------------------------------------| r_work (start): 0.3104 rms_B_bonded: 3.27 r_work: 0.2944 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work: 0.2807 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.2807 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8121 moved from start: 0.2484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 15536 Z= 0.120 Angle : 0.491 9.176 21092 Z= 0.257 Chirality : 0.042 0.147 2317 Planarity : 0.003 0.049 2791 Dihedral : 4.223 56.758 2139 Min Nonbonded Distance : 2.291 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 0.67 % Allowed : 14.93 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.37 (0.19), residues: 1939 helix: 2.19 (0.22), residues: 540 sheet: -0.57 (0.22), residues: 513 loop : -0.40 (0.21), residues: 886 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP F 413 HIS 0.005 0.001 HIS F 178 PHE 0.019 0.001 PHE A 67 TYR 0.018 0.001 TYR D 184 ARG 0.005 0.000 ARG A 321 Details of bonding type rmsd hydrogen bonds : bond 0.03425 ( 722) hydrogen bonds : angle 4.36551 ( 2070) SS BOND : bond 0.00051 ( 1) SS BOND : angle 0.26317 ( 2) covalent geometry : bond 0.00269 (15535) covalent geometry : angle 0.49125 (21090) *********************** 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 119 residues out of total 1634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 108 time to evaluate : 2.458 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: 0.8335 (OUTLIER) cc_final: 0.8081 (t0) REVERT: A 582 ASP cc_start: 0.8970 (t0) cc_final: 0.8589 (t0) REVERT: B 85 ASN cc_start: 0.9216 (OUTLIER) cc_final: 0.8499 (t0) REVERT: B 240 GLU cc_start: 0.8961 (mt-10) cc_final: 0.8614 (mm-30) REVERT: D 232 GLU cc_start: 0.8713 (mm-30) cc_final: 0.8444 (mm-30) REVERT: E 50 MET cc_start: 0.9155 (mtp) cc_final: 0.8673 (mtp) REVERT: F 71 MET cc_start: 0.8830 (tpp) cc_final: 0.8385 (tmm) REVERT: F 83 MET cc_start: 0.9328 (ptm) cc_final: 0.9015 (tmm) REVERT: F 136 MET cc_start: 0.8581 (mpm) cc_final: 0.7685 (ptp) REVERT: F 190 ASP cc_start: 0.9274 (m-30) cc_final: 0.9045 (p0) REVERT: F 219 HIS cc_start: 0.7005 (OUTLIER) cc_final: 0.6742 (m90) outliers start: 11 outliers final: 5 residues processed: 117 average time/residue: 2.6474 time to fit residues: 350.3947 Evaluate side-chains 111 residues out of total 1634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 103 time to evaluate : 2.454 ------------------------------------------------------------------------------- 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 153 SER Chi-restraints excluded: chain D residue 44 GLN 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 108 optimal weight: 4.9990 chunk 12 optimal weight: 7.9990 chunk 153 optimal weight: 2.9990 chunk 20 optimal weight: 2.9990 chunk 151 optimal weight: 0.9990 chunk 190 optimal weight: 10.0000 chunk 5 optimal weight: 20.0000 chunk 35 optimal weight: 0.9990 chunk 73 optimal weight: 3.9990 chunk 175 optimal weight: 8.9990 chunk 39 optimal weight: 0.7980 overall best weight: 1.7588 ------------------------------------------------------------------------------- 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 = 0.4111 r_free = 0.4111 target = 0.137509 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.079509 restraints weight = 87639.857| |-----------------------------------------------------------------------------| r_work (start): 0.3095 rms_B_bonded: 3.25 r_work: 0.2936 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work: 0.2801 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.2801 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8129 moved from start: 0.2562 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= 0.163 Angle : 0.504 9.354 21092 Z= 0.263 Chirality : 0.042 0.142 2317 Planarity : 0.004 0.056 2791 Dihedral : 4.215 55.644 2139 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 0.61 % Allowed : 15.30 % Favored : 84.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.35 (0.19), residues: 1939 helix: 2.21 (0.22), residues: 540 sheet: -0.61 (0.22), residues: 517 loop : -0.42 (0.21), residues: 882 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP F 413 HIS 0.005 0.001 HIS F 178 PHE 0.015 0.001 PHE A 67 TYR 0.024 0.001 TYR C 197 ARG 0.009 0.000 ARG C 33 Details of bonding type rmsd hydrogen bonds : bond 0.03473 ( 722) hydrogen bonds : angle 4.37914 ( 2070) SS BOND : bond 0.00020 ( 1) SS BOND : angle 0.28817 ( 2) covalent geometry : bond 0.00366 (15535) covalent geometry : angle 0.50397 (21090) ********************** 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 113 residues out of total 1634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 103 time to evaluate : 2.316 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: 0.8373 (OUTLIER) cc_final: 0.8128 (t0) REVERT: A 582 ASP cc_start: 0.8977 (t0) cc_final: 0.8598 (t0) REVERT: A 607 GLU cc_start: 0.8990 (OUTLIER) cc_final: 0.8738 (mt-10) REVERT: B 85 ASN cc_start: 0.9236 (OUTLIER) cc_final: 0.8519 (t0) REVERT: B 240 GLU cc_start: 0.8964 (mt-10) cc_final: 0.8622 (mm-30) REVERT: D 232 GLU cc_start: 0.8689 (mm-30) cc_final: 0.8422 (mm-30) REVERT: E 50 MET cc_start: 0.9168 (mtp) cc_final: 0.8668 (mtp) REVERT: F 71 MET cc_start: 0.8847 (tpp) cc_final: 0.8455 (tmm) REVERT: F 83 MET cc_start: 0.9318 (ptm) cc_final: 0.9005 (tmm) REVERT: F 136 MET cc_start: 0.8580 (mpm) cc_final: 0.7698 (ptp) REVERT: F 190 ASP cc_start: 0.9273 (m-30) cc_final: 0.9044 (p0) REVERT: F 219 HIS cc_start: 0.7018 (OUTLIER) cc_final: 0.6779 (m90) outliers start: 10 outliers final: 6 residues processed: 113 average time/residue: 2.5828 time to fit residues: 326.0261 Evaluate side-chains 111 residues out of total 1634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 101 time to evaluate : 2.408 ------------------------------------------------------------------------------- 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 607 GLU 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 D residue 44 GLN 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 94 optimal weight: 0.9980 chunk 182 optimal weight: 30.0000 chunk 159 optimal weight: 0.1980 chunk 61 optimal weight: 2.9990 chunk 85 optimal weight: 7.9990 chunk 143 optimal weight: 0.8980 chunk 29 optimal weight: 0.9980 chunk 82 optimal weight: 0.9990 chunk 10 optimal weight: 9.9990 chunk 169 optimal weight: 20.0000 chunk 142 optimal weight: 2.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- 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 = 0.4123 r_free = 0.4123 target = 0.138395 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.080578 restraints weight = 87105.374| |-----------------------------------------------------------------------------| r_work (start): 0.3114 rms_B_bonded: 3.27 r_work: 0.2957 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work: 0.2820 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.2820 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8106 moved from start: 0.2602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 15536 Z= 0.104 Angle : 0.491 9.752 21092 Z= 0.255 Chirality : 0.041 0.146 2317 Planarity : 0.004 0.052 2791 Dihedral : 4.137 54.059 2139 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 0.55 % Allowed : 15.30 % Favored : 84.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.46 (0.19), residues: 1939 helix: 2.32 (0.22), residues: 535 sheet: -0.57 (0.22), residues: 522 loop : -0.33 (0.21), residues: 882 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP F 413 HIS 0.005 0.001 HIS F 178 PHE 0.019 0.001 PHE A 67 TYR 0.026 0.001 TYR C 197 ARG 0.006 0.000 ARG C 30 Details of bonding type rmsd hydrogen bonds : bond 0.03299 ( 722) hydrogen bonds : angle 4.28334 ( 2070) SS BOND : bond 0.00022 ( 1) SS BOND : angle 0.27087 ( 2) covalent geometry : bond 0.00233 (15535) covalent geometry : angle 0.49117 (21090) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 29128.47 seconds wall clock time: 507 minutes 43.72 seconds (30463.72 seconds total)