Starting phenix.real_space_refine on Mon Aug 25 19:00:47 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9hg8_52130/08_2025/9hg8_52130.cif Found real_map, /net/cci-nas-00/data/ceres_data/9hg8_52130/08_2025/9hg8_52130.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9hg8_52130/08_2025/9hg8_52130.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9hg8_52130/08_2025/9hg8_52130.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9hg8_52130/08_2025/9hg8_52130.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9hg8_52130/08_2025/9hg8_52130.map" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.009 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 48 5.16 5 C 9545 2.51 5 N 2643 2.21 5 O 3000 1.98 5 H 14802 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 30038 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 12175 Number of conformers: 1 Conformer: "" Number of residues, atoms: 788, 12175 Classifications: {'peptide': 788} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 29, 'TRANS': 758} Chain: "B" Number of atoms: 5534 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 5534 Classifications: {'peptide': 371} Link IDs: {'PTRANS': 11, 'TRANS': 359} Chain: "C" Number of atoms: 2845 Number of conformers: 1 Conformer: "" Number of residues, atoms: 189, 2845 Classifications: {'peptide': 189} Modifications used: {'NH1NOTPRO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 178} Chain: "D" Number of atoms: 3461 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 3461 Classifications: {'peptide': 218} Link IDs: {'PTRANS': 12, 'TRANS': 205} Chain: "E" Number of atoms: 1363 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 1363 Classifications: {'peptide': 88} Link IDs: {'PTRANS': 5, 'TRANS': 82} Chain: "F" Number of atoms: 4660 Number of conformers: 1 Conformer: "" Number of residues, atoms: 299, 4660 Classifications: {'peptide': 299} Link IDs: {'PTRANS': 8, 'TRANS': 290} Chain breaks: 1 Time building chain proxies: 4.29, per 1000 atoms: 0.14 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: 1.70 Conformation dependent library (CDL) restraints added in 952.0 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 3878 Ramachandran restraints generated. 1939 Oldfield, 0 Emsley, 1939 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3588 Finding SS restraints... Secondary structure from input PDB file: 50 helices and 20 sheets defined 31.6% alpha, 28.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.79 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: 4.080A 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: 3.608A 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: 5.399A 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: 3.997A 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: 3.634A 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: 4.116A 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: 3.726A pdb=" N GLY F 44 " --> pdb=" O SER F 40 " (cutoff:3.500A) Processing helix chain 'F' and resid 62 through 88 removed outlier: 3.565A 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: 4.139A 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: 7.669A 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: 3.612A 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: 7.669A 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: 3.612A 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: 7.109A pdb=" N PHE A 169 " --> pdb=" O PHE A 99 " (cutoff:3.500A) removed outlier: 3.553A 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: 7.058A 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: 6.039A pdb=" N LYS A 267 " --> pdb=" O VAL A 335 " (cutoff:3.500A) removed outlier: 7.683A 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: 7.552A 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: 4.415A 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: 7.752A 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: 4.393A 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: 4.417A 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: 3.657A 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: 8.124A 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: 6.365A 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: 4.064A pdb=" N TRP B 93 " --> pdb=" O ALA B 83 " (cutoff:3.500A) removed outlier: 6.004A pdb=" N ASN B 85 " --> pdb=" O GLU B 91 " (cutoff:3.500A) removed outlier: 6.405A 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: 4.393A 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: 6.876A 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: 6.658A 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: 6.709A 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: 6.630A pdb=" N ARG C 160 " --> pdb=" O LEU C 179 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N LEU C 181 " --> pdb=" O ARG C 158 " (cutoff:3.500A) removed outlier: 6.720A 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: 4.646A 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: 6.720A pdb=" N ARG C 158 " --> pdb=" O LEU C 181 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N LEU C 181 " --> pdb=" O ARG C 158 " (cutoff:3.500A) removed outlier: 6.630A 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: 6.736A 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: 5.889A 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: 5.99 Time building geometry restraints manager: 2.54 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: 191 1.23 - 1.43: 6445 1.43 - 1.62: 8807 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 1.185 0.052 1.19e-02 7.06e+03 1.88e+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 1.22e+01 bond pdb=" N ARG A 162 " pdb=" H ARG A 162 " ideal model delta sigma weight residual 0.860 0.914 -0.054 2.00e-02 2.50e+03 7.21e+00 bond pdb=" N LYS B 280 " pdb=" CA LYS B 280 " ideal model delta sigma weight residual 1.455 1.486 -0.032 1.26e-02 6.30e+03 6.41e+00 bond pdb=" N GLY A 23 " pdb=" CA GLY A 23 " ideal model delta sigma weight residual 1.451 1.491 -0.040 1.60e-02 3.91e+03 6.29e+00 ... (remaining 30332 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.10: 54086 2.10 - 4.20: 468 4.20 - 6.31: 45 6.31 - 8.41: 4 8.41 - 10.51: 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 111.69 117.18 -5.49 1.23e+00 6.61e-01 1.99e+01 angle pdb=" N ARG A 162 " pdb=" CA ARG A 162 " pdb=" C ARG A 162 " ideal model delta sigma weight residual 109.69 103.41 6.28 1.44e+00 4.82e-01 1.90e+01 angle pdb=" N MET F 76 " pdb=" CA MET F 76 " pdb=" C MET F 76 " ideal model delta sigma weight residual 111.36 106.73 4.63 1.09e+00 8.42e-01 1.80e+01 angle pdb=" CA ARG A 162 " pdb=" C ARG A 162 " pdb=" O ARG A 162 " ideal model delta sigma weight residual 121.60 116.80 4.80 1.21e+00 6.83e-01 1.57e+01 angle pdb=" CA MET F 414 " pdb=" C MET F 414 " pdb=" O MET F 414 " ideal model delta sigma weight residual 120.42 116.23 4.19 1.06e+00 8.90e-01 1.56e+01 ... (remaining 54599 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.48: 12703 17.48 - 34.96: 1018 34.96 - 52.44: 442 52.44 - 69.92: 134 69.92 - 87.39: 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 -68.80 68.80 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 38.51 -38.51 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 180.00 161.77 18.23 0 5.00e+00 4.00e-02 1.33e+01 ... (remaining 14330 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 1660 0.040 - 0.080: 439 0.080 - 0.120: 180 0.120 - 0.160: 31 0.160 - 0.201: 7 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 1.01e+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 -0.18 2.00e-01 2.50e+01 8.53e-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 7.87e-01 ... (remaining 2314 not shown) Planarity restraints: 4662 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN F 186 " 0.247 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 " 0.681 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 " -0.791 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 " 0.001 2.00e-02 2.50e+03 pdb=" NH1 ARG A 162 " 0.009 2.00e-02 2.50e+03 pdb=" NH2 ARG A 162 " 0.005 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: 925 2.14 - 2.76: 56086 2.76 - 3.37: 83279 3.37 - 3.99: 108876 3.99 - 4.60: 169113 Nonbonded interactions: 418279 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 1.586 2.450 nonbonded pdb=" O ARG C 112 " pdb=" HG1 THR C 115 " model vdw 1.605 2.450 ... (remaining 418274 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: 3.560 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: 0.180 Extract box with map and model: 0.510 Check model and map are aligned: 0.090 Set scattering table: 0.080 Process input model: 23.500 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.030 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:6.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.050 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7672 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 0.052 15536 Z= 0.200 Angle : 0.650 7.838 21092 Z= 0.375 Chirality : 0.045 0.201 2317 Planarity : 0.011 0.467 2791 Dihedral : 14.776 87.141 5687 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.21 % Allowed : 3.09 % Favored : 96.70 % Rotamer: Outliers : 1.16 % Allowed : 11.02 % Favored : 87.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.16 (0.19), residues: 1939 helix: 1.50 (0.23), residues: 533 sheet: -0.40 (0.21), residues: 553 loop : -0.32 (0.22), residues: 853 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG F 399 TYR 0.023 0.001 TYR C 31 PHE 0.009 0.001 PHE A 791 TRP 0.016 0.001 TRP C 145 HIS 0.002 0.001 HIS D 139 Details of bonding type rmsd covalent geometry : bond 0.00410 (15535) covalent geometry : angle 0.64949 (21090) SS BOND : bond 0.00137 ( 1) SS BOND : angle 2.18064 ( 2) hydrogen bonds : bond 0.13541 ( 722) hydrogen bonds : angle 6.03387 ( 2070) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3878 Ramachandran restraints generated. 1939 Oldfield, 0 Emsley, 1939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3878 Ramachandran restraints generated. 1939 Oldfield, 0 Emsley, 1939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 1634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 194 time to evaluate : 0.833 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 140 PHE cc_start: 0.9064 (t80) cc_final: 0.8838 (t80) REVERT: A 169 PHE cc_start: 0.7845 (m-80) cc_final: 0.7640 (m-80) REVERT: A 207 ASN cc_start: 0.8384 (t0) cc_final: 0.8028 (t0) REVERT: A 224 GLU cc_start: 0.9138 (tp30) cc_final: 0.8883 (mm-30) REVERT: A 292 PRO cc_start: 0.9320 (Cg_exo) cc_final: 0.9045 (Cg_endo) REVERT: A 465 TYR cc_start: 0.7807 (m-80) cc_final: 0.7563 (m-10) REVERT: A 582 ASP cc_start: 0.8774 (t0) cc_final: 0.8465 (t0) REVERT: B 76 ASP cc_start: 0.7653 (t0) cc_final: 0.7406 (t70) REVERT: B 226 MET cc_start: 0.9048 (ttm) cc_final: 0.8198 (tmm) REVERT: B 278 MET cc_start: 0.8145 (mtt) cc_final: 0.7623 (mpm) REVERT: C 144 ASP cc_start: 0.8909 (t0) cc_final: 0.8693 (t70) REVERT: C 155 GLU cc_start: 0.7919 (tp30) cc_final: 0.7685 (tm-30) REVERT: C 157 TYR cc_start: 0.7595 (m-80) cc_final: 0.7384 (m-80) REVERT: C 160 ARG cc_start: 0.7809 (ttm110) cc_final: 0.7380 (mtp-110) REVERT: C 194 MET cc_start: 0.8548 (mtp) cc_final: 0.8188 (mpp) REVERT: C 210 ASP cc_start: 0.7170 (OUTLIER) cc_final: 0.6939 (m-30) REVERT: D 56 GLU cc_start: 0.8807 (mt-10) cc_final: 0.8334 (mt-10) REVERT: F 71 MET cc_start: 0.8649 (tpp) cc_final: 0.8348 (tpt) REVERT: F 167 GLN cc_start: 0.7674 (mm110) cc_final: 0.7226 (tm-30) outliers start: 19 outliers final: 7 residues processed: 210 average time/residue: 1.1730 time to fit residues: 270.6414 Evaluate side-chains 139 residues out of total 1634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 131 time to evaluate : 0.687 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 751 SER Chi-restraints excluded: chain B residue 153 SER Chi-restraints excluded: chain C residue 210 ASP Chi-restraints excluded: chain D residue 164 THR Chi-restraints excluded: chain F residue 32 VAL Chi-restraints excluded: chain F residue 81 LEU Chi-restraints excluded: chain F residue 259 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 98 optimal weight: 6.9990 chunk 107 optimal weight: 6.9990 chunk 10 optimal weight: 9.9990 chunk 66 optimal weight: 5.9990 chunk 130 optimal weight: 4.9990 chunk 124 optimal weight: 9.9990 chunk 103 optimal weight: 3.9990 chunk 77 optimal weight: 4.9990 chunk 122 optimal weight: 10.0000 chunk 91 optimal weight: 2.9990 chunk 149 optimal weight: 0.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 445 GLN B 85 ASN B 301 GLN ** D 102 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 241 ASN ** 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 = 0.4062 r_free = 0.4062 target = 0.130586 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.072465 restraints weight = 87022.300| |-----------------------------------------------------------------------------| r_work (start): 0.3081 rms_B_bonded: 3.26 r_work: 0.2927 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work: 0.2792 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.2792 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8108 moved from start: 0.1846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.063 15536 Z= 0.308 Angle : 0.604 5.525 21092 Z= 0.327 Chirality : 0.045 0.171 2317 Planarity : 0.005 0.060 2791 Dihedral : 5.031 59.190 2148 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 1.41 % Allowed : 14.44 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.08 (0.19), residues: 1939 helix: 1.66 (0.23), residues: 533 sheet: -0.35 (0.21), residues: 513 loop : -0.62 (0.21), residues: 893 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG F 57 TYR 0.017 0.002 TYR D 184 PHE 0.019 0.002 PHE F 212 TRP 0.014 0.002 TRP A 745 HIS 0.004 0.001 HIS A 280 Details of bonding type rmsd covalent geometry : bond 0.00685 (15535) covalent geometry : angle 0.60419 (21090) SS BOND : bond 0.00156 ( 1) SS BOND : angle 0.38671 ( 2) hydrogen bonds : bond 0.04495 ( 722) hydrogen bonds : angle 5.16091 ( 2070) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3878 Ramachandran restraints generated. 1939 Oldfield, 0 Emsley, 1939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3878 Ramachandran restraints generated. 1939 Oldfield, 0 Emsley, 1939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 133 time to evaluate : 0.736 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 SER cc_start: 0.9448 (t) cc_final: 0.9238 (p) REVERT: A 111 LYS cc_start: 0.9511 (tptp) cc_final: 0.9249 (ttpp) REVERT: A 140 PHE cc_start: 0.9147 (t80) cc_final: 0.8929 (t80) REVERT: A 207 ASN cc_start: 0.8392 (t0) cc_final: 0.8065 (t0) REVERT: A 252 LYS cc_start: 0.9074 (ptpt) cc_final: 0.8548 (ptmt) REVERT: A 582 ASP cc_start: 0.9087 (t0) cc_final: 0.8781 (t0) REVERT: B 226 MET cc_start: 0.9191 (ttm) cc_final: 0.8408 (tmm) REVERT: B 278 MET cc_start: 0.8477 (mtt) cc_final: 0.7833 (mpm) REVERT: C 155 GLU cc_start: 0.7805 (tp30) cc_final: 0.7505 (tm-30) REVERT: C 157 TYR cc_start: 0.7377 (m-80) cc_final: 0.7129 (m-80) REVERT: C 160 ARG cc_start: 0.7679 (ttm110) cc_final: 0.7433 (mtp-110) REVERT: C 194 MET cc_start: 0.8521 (mtp) cc_final: 0.8209 (mpp) REVERT: C 210 ASP cc_start: 0.7159 (OUTLIER) cc_final: 0.6926 (m-30) REVERT: D 56 GLU cc_start: 0.8817 (mt-10) cc_final: 0.8545 (mt-10) REVERT: D 232 GLU cc_start: 0.8841 (mm-30) cc_final: 0.8367 (mp0) REVERT: F 71 MET cc_start: 0.8795 (tpp) cc_final: 0.8448 (tpt) REVERT: F 83 MET cc_start: 0.9356 (tmm) cc_final: 0.9036 (tmm) REVERT: F 114 MET cc_start: 0.4048 (tpp) cc_final: 0.3781 (tpp) REVERT: F 167 GLN cc_start: 0.7769 (mm110) cc_final: 0.7317 (tm-30) outliers start: 23 outliers final: 9 residues processed: 150 average time/residue: 0.9793 time to fit residues: 166.3778 Evaluate side-chains 126 residues out of total 1634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 116 time to evaluate : 0.723 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 243 THR Chi-restraints excluded: chain A residue 573 ASN Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 136 THR Chi-restraints excluded: chain B residue 153 SER Chi-restraints excluded: chain C residue 210 ASP Chi-restraints excluded: chain D residue 134 ASP Chi-restraints excluded: chain D residue 164 THR Chi-restraints excluded: chain F residue 32 VAL Chi-restraints excluded: chain F residue 160 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 51 optimal weight: 0.0970 chunk 166 optimal weight: 8.9990 chunk 89 optimal weight: 3.9990 chunk 98 optimal weight: 6.9990 chunk 68 optimal weight: 1.9990 chunk 128 optimal weight: 20.0000 chunk 84 optimal weight: 8.9990 chunk 174 optimal weight: 20.0000 chunk 96 optimal weight: 0.3980 chunk 57 optimal weight: 0.9990 chunk 101 optimal weight: 0.9980 overall best weight: 0.8982 ------------------------------------------------------------------------------- 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 = 0.4084 r_free = 0.4084 target = 0.131947 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.074426 restraints weight = 86659.882| |-----------------------------------------------------------------------------| r_work (start): 0.3125 rms_B_bonded: 3.28 r_work: 0.2973 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work: 0.2847 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.2847 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8058 moved from start: 0.2106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 15536 Z= 0.118 Angle : 0.506 6.559 21092 Z= 0.268 Chirality : 0.042 0.151 2317 Planarity : 0.004 0.056 2791 Dihedral : 4.550 59.910 2141 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 4.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 1.41 % Allowed : 13.89 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.22 (0.19), residues: 1939 helix: 1.89 (0.22), residues: 534 sheet: -0.44 (0.21), residues: 527 loop : -0.49 (0.21), residues: 878 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 321 TYR 0.017 0.001 TYR D 184 PHE 0.012 0.001 PHE A 140 TRP 0.011 0.001 TRP B 317 HIS 0.002 0.001 HIS A 280 Details of bonding type rmsd covalent geometry : bond 0.00257 (15535) covalent geometry : angle 0.50599 (21090) SS BOND : bond 0.00056 ( 1) SS BOND : angle 0.44827 ( 2) hydrogen bonds : bond 0.03854 ( 722) hydrogen bonds : angle 4.79432 ( 2070) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3878 Ramachandran restraints generated. 1939 Oldfield, 0 Emsley, 1939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3878 Ramachandran restraints generated. 1939 Oldfield, 0 Emsley, 1939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 1634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 122 time to evaluate : 0.589 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 111 LYS cc_start: 0.9486 (tptp) cc_final: 0.9231 (ttpp) REVERT: A 140 PHE cc_start: 0.9161 (t80) cc_final: 0.8942 (t80) REVERT: A 207 ASN cc_start: 0.8384 (t0) cc_final: 0.8057 (t0) REVERT: A 321 ARG cc_start: 0.8429 (mtm110) cc_final: 0.7762 (ttp-110) REVERT: A 410 ASP cc_start: 0.8262 (OUTLIER) cc_final: 0.7947 (t0) REVERT: A 582 ASP cc_start: 0.9043 (t0) cc_final: 0.8738 (t0) REVERT: B 278 MET cc_start: 0.8459 (mtt) cc_final: 0.7839 (mpm) REVERT: C 155 GLU cc_start: 0.7782 (tp30) cc_final: 0.7439 (tm-30) REVERT: C 182 GLU cc_start: 0.8084 (mm-30) cc_final: 0.7753 (mm-30) REVERT: C 194 MET cc_start: 0.8525 (mtp) cc_final: 0.8209 (mpp) REVERT: D 56 GLU cc_start: 0.8775 (mt-10) cc_final: 0.8290 (mt-10) REVERT: F 71 MET cc_start: 0.8802 (tpp) cc_final: 0.8487 (tpt) REVERT: F 114 MET cc_start: 0.3825 (tpp) cc_final: 0.3604 (tpp) REVERT: F 167 GLN cc_start: 0.7742 (mm110) cc_final: 0.7318 (tm-30) outliers start: 23 outliers final: 8 residues processed: 137 average time/residue: 0.9648 time to fit residues: 148.4511 Evaluate side-chains 123 residues out of total 1634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 114 time to evaluate : 0.544 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 410 ASP Chi-restraints excluded: chain A residue 465 TYR Chi-restraints excluded: chain B residue 136 THR Chi-restraints excluded: chain C residue 177 LYS Chi-restraints excluded: chain C residue 205 ILE Chi-restraints excluded: chain D residue 134 ASP Chi-restraints excluded: chain F residue 32 VAL Chi-restraints excluded: chain F residue 160 LEU Chi-restraints excluded: chain F residue 268 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 156 optimal weight: 3.9990 chunk 53 optimal weight: 3.9990 chunk 174 optimal weight: 20.0000 chunk 28 optimal weight: 2.9990 chunk 132 optimal weight: 10.0000 chunk 94 optimal weight: 0.6980 chunk 66 optimal weight: 8.9990 chunk 149 optimal weight: 1.9990 chunk 29 optimal weight: 0.9980 chunk 118 optimal weight: 3.9990 chunk 46 optimal weight: 3.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 301 GLN ** D 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 85 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4073 r_free = 0.4073 target = 0.131033 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.073361 restraints weight = 86105.635| |-----------------------------------------------------------------------------| r_work (start): 0.3089 rms_B_bonded: 3.25 r_work: 0.2932 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work: 0.2807 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.2807 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8112 moved from start: 0.2478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 15536 Z= 0.201 Angle : 0.522 7.480 21092 Z= 0.277 Chirality : 0.042 0.164 2317 Planarity : 0.004 0.055 2791 Dihedral : 4.310 57.988 2137 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 1.29 % Allowed : 15.06 % Favored : 83.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.19 (0.19), residues: 1939 helix: 1.95 (0.22), residues: 533 sheet: -0.53 (0.21), residues: 515 loop : -0.51 (0.21), residues: 891 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 160 TYR 0.018 0.001 TYR D 184 PHE 0.020 0.001 PHE F 212 TRP 0.011 0.001 TRP B 317 HIS 0.002 0.001 HIS A 280 Details of bonding type rmsd covalent geometry : bond 0.00450 (15535) covalent geometry : angle 0.52209 (21090) SS BOND : bond 0.00028 ( 1) SS BOND : angle 0.21648 ( 2) hydrogen bonds : bond 0.03854 ( 722) hydrogen bonds : angle 4.70340 ( 2070) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3878 Ramachandran restraints generated. 1939 Oldfield, 0 Emsley, 1939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3878 Ramachandran restraints generated. 1939 Oldfield, 0 Emsley, 1939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 1634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 115 time to evaluate : 0.777 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 104 SER cc_start: 0.9414 (t) cc_final: 0.9185 (p) REVERT: A 111 LYS cc_start: 0.9478 (tptp) cc_final: 0.9244 (tmmm) REVERT: A 132 ASP cc_start: 0.9291 (t0) cc_final: 0.9083 (m-30) REVERT: A 140 PHE cc_start: 0.9189 (t80) cc_final: 0.8987 (t80) REVERT: A 207 ASN cc_start: 0.8383 (t0) cc_final: 0.8075 (t0) REVERT: A 321 ARG cc_start: 0.8478 (mtm110) cc_final: 0.7900 (ttp-110) REVERT: A 410 ASP cc_start: 0.8410 (OUTLIER) cc_final: 0.8022 (t0) REVERT: A 582 ASP cc_start: 0.9041 (t0) cc_final: 0.8713 (t0) REVERT: A 607 GLU cc_start: 0.8967 (OUTLIER) cc_final: 0.8719 (mt-10) REVERT: B 278 MET cc_start: 0.8464 (mtt) cc_final: 0.7840 (mpm) REVERT: C 155 GLU cc_start: 0.7763 (tp30) cc_final: 0.7358 (tm-30) REVERT: C 182 GLU cc_start: 0.7933 (mm-30) cc_final: 0.7528 (mm-30) REVERT: C 194 MET cc_start: 0.8519 (mtp) cc_final: 0.8201 (mpp) REVERT: D 56 GLU cc_start: 0.8769 (mt-10) cc_final: 0.8266 (mt-10) REVERT: F 71 MET cc_start: 0.8868 (tpp) cc_final: 0.8572 (tpt) REVERT: F 87 MET cc_start: 0.8435 (ptt) cc_final: 0.7805 (ppp) REVERT: F 114 MET cc_start: 0.3875 (tpp) cc_final: 0.3310 (tpp) REVERT: F 125 TYR cc_start: 0.6424 (t80) cc_final: 0.6088 (t80) REVERT: F 167 GLN cc_start: 0.7784 (mm110) cc_final: 0.7349 (tm-30) outliers start: 21 outliers final: 10 residues processed: 131 average time/residue: 1.1001 time to fit residues: 160.7837 Evaluate side-chains 124 residues out of total 1634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 112 time to evaluate : 0.740 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 243 THR Chi-restraints excluded: chain A residue 362 ASP Chi-restraints excluded: chain A residue 410 ASP Chi-restraints excluded: chain A residue 465 TYR Chi-restraints excluded: chain A residue 607 GLU Chi-restraints excluded: chain B residue 331 VAL Chi-restraints excluded: chain C residue 177 LYS Chi-restraints excluded: chain C residue 205 ILE Chi-restraints excluded: chain D residue 134 ASP Chi-restraints excluded: chain F residue 32 VAL Chi-restraints excluded: chain F residue 160 LEU Chi-restraints excluded: chain F residue 268 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 4 optimal weight: 20.0000 chunk 150 optimal weight: 0.9980 chunk 128 optimal weight: 20.0000 chunk 14 optimal weight: 7.9990 chunk 115 optimal weight: 0.2980 chunk 170 optimal weight: 40.0000 chunk 94 optimal weight: 0.7980 chunk 30 optimal weight: 0.6980 chunk 38 optimal weight: 0.1980 chunk 62 optimal weight: 0.6980 chunk 139 optimal weight: 0.6980 overall best weight: 0.5180 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4091 r_free = 0.4091 target = 0.132331 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.075126 restraints weight = 86467.078| |-----------------------------------------------------------------------------| r_work (start): 0.3133 rms_B_bonded: 3.25 r_work: 0.2977 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work: 0.2840 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.2840 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8042 moved from start: 0.2615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.053 15536 Z= 0.094 Angle : 0.477 6.521 21092 Z= 0.252 Chirality : 0.042 0.151 2317 Planarity : 0.003 0.051 2791 Dihedral : 4.150 57.437 2137 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 3.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 1.22 % Allowed : 14.93 % Favored : 83.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.40 (0.19), residues: 1939 helix: 2.13 (0.22), residues: 536 sheet: -0.41 (0.22), residues: 511 loop : -0.41 (0.21), residues: 892 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 57 TYR 0.018 0.001 TYR F 422 PHE 0.011 0.001 PHE F 212 TRP 0.009 0.001 TRP B 317 HIS 0.002 0.000 HIS B 324 Details of bonding type rmsd covalent geometry : bond 0.00207 (15535) covalent geometry : angle 0.47658 (21090) SS BOND : bond 0.00054 ( 1) SS BOND : angle 0.34401 ( 2) hydrogen bonds : bond 0.03449 ( 722) hydrogen bonds : angle 4.46628 ( 2070) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3878 Ramachandran restraints generated. 1939 Oldfield, 0 Emsley, 1939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3878 Ramachandran restraints generated. 1939 Oldfield, 0 Emsley, 1939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 1634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 113 time to evaluate : 0.518 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 111 LYS cc_start: 0.9451 (tptp) cc_final: 0.9221 (ttpp) REVERT: A 132 ASP cc_start: 0.9291 (t0) cc_final: 0.9037 (m-30) REVERT: A 207 ASN cc_start: 0.8351 (t0) cc_final: 0.8071 (t0) REVERT: A 321 ARG cc_start: 0.8472 (mtm110) cc_final: 0.7799 (ttp-110) REVERT: A 410 ASP cc_start: 0.8260 (OUTLIER) cc_final: 0.7775 (t0) REVERT: A 582 ASP cc_start: 0.9011 (t0) cc_final: 0.8682 (t0) REVERT: C 155 GLU cc_start: 0.7723 (tp30) cc_final: 0.7446 (tm-30) REVERT: C 194 MET cc_start: 0.8502 (mtp) cc_final: 0.8198 (mpp) REVERT: D 232 GLU cc_start: 0.8783 (mm-30) cc_final: 0.8428 (mp0) REVERT: F 71 MET cc_start: 0.8881 (tpp) cc_final: 0.8598 (tpt) REVERT: F 87 MET cc_start: 0.8360 (ptt) cc_final: 0.7781 (ppp) REVERT: F 114 MET cc_start: 0.3884 (tpp) cc_final: 0.3284 (tpp) REVERT: F 125 TYR cc_start: 0.6396 (t80) cc_final: 0.6077 (t80) REVERT: F 167 GLN cc_start: 0.7771 (mm110) cc_final: 0.7354 (tm-30) outliers start: 20 outliers final: 10 residues processed: 124 average time/residue: 1.0554 time to fit residues: 145.8997 Evaluate side-chains 119 residues out of total 1634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 108 time to evaluate : 0.577 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 410 ASP Chi-restraints excluded: chain A residue 465 TYR Chi-restraints excluded: chain B residue 136 THR Chi-restraints excluded: chain B residue 153 SER Chi-restraints excluded: chain C residue 205 ILE Chi-restraints excluded: chain D residue 134 ASP Chi-restraints excluded: chain D residue 205 TYR Chi-restraints excluded: chain F residue 32 VAL Chi-restraints excluded: chain F residue 136 MET Chi-restraints excluded: chain F residue 160 LEU Chi-restraints excluded: chain F residue 268 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 70 optimal weight: 3.9990 chunk 188 optimal weight: 8.9990 chunk 65 optimal weight: 0.6980 chunk 61 optimal weight: 3.9990 chunk 60 optimal weight: 0.9980 chunk 41 optimal weight: 5.9990 chunk 110 optimal weight: 5.9990 chunk 113 optimal weight: 0.9980 chunk 15 optimal weight: 3.9990 chunk 54 optimal weight: 2.9990 chunk 73 optimal weight: 2.9990 overall best weight: 1.7384 ------------------------------------------------------------------------------- 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 = 0.4080 r_free = 0.4080 target = 0.131491 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.074083 restraints weight = 86602.477| |-----------------------------------------------------------------------------| r_work (start): 0.3100 rms_B_bonded: 3.24 r_work: 0.2944 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work: 0.2818 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.2818 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8111 moved from start: 0.2769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 15536 Z= 0.164 Angle : 0.488 6.338 21092 Z= 0.258 Chirality : 0.041 0.194 2317 Planarity : 0.003 0.053 2791 Dihedral : 4.157 56.450 2137 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 1.10 % Allowed : 15.36 % Favored : 83.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.38 (0.19), residues: 1939 helix: 2.20 (0.22), residues: 535 sheet: -0.47 (0.22), residues: 511 loop : -0.45 (0.21), residues: 893 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 30 TYR 0.018 0.001 TYR D 184 PHE 0.011 0.001 PHE F 212 TRP 0.009 0.001 TRP A 745 HIS 0.002 0.001 HIS A 280 Details of bonding type rmsd covalent geometry : bond 0.00366 (15535) covalent geometry : angle 0.48821 (21090) SS BOND : bond 0.00002 ( 1) SS BOND : angle 0.24460 ( 2) hydrogen bonds : bond 0.03546 ( 722) hydrogen bonds : angle 4.47044 ( 2070) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3878 Ramachandran restraints generated. 1939 Oldfield, 0 Emsley, 1939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3878 Ramachandran restraints generated. 1939 Oldfield, 0 Emsley, 1939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 1634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 112 time to evaluate : 0.918 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 SER cc_start: 0.9404 (t) cc_final: 0.9185 (p) REVERT: A 132 ASP cc_start: 0.9287 (t0) cc_final: 0.9036 (m-30) REVERT: A 207 ASN cc_start: 0.8368 (t0) cc_final: 0.8087 (t0) REVERT: A 321 ARG cc_start: 0.8472 (mtm110) cc_final: 0.7887 (ttp-110) REVERT: A 410 ASP cc_start: 0.8392 (OUTLIER) cc_final: 0.8012 (t0) REVERT: A 582 ASP cc_start: 0.8970 (t0) cc_final: 0.8662 (t0) REVERT: B 278 MET cc_start: 0.8515 (mtt) cc_final: 0.7894 (mpm) REVERT: C 155 GLU cc_start: 0.7786 (tp30) cc_final: 0.7475 (tm-30) REVERT: C 194 MET cc_start: 0.8500 (mtp) cc_final: 0.8163 (mpp) REVERT: D 56 GLU cc_start: 0.8803 (mt-10) cc_final: 0.8325 (mt-10) REVERT: D 232 GLU cc_start: 0.8833 (mm-30) cc_final: 0.8485 (mp0) REVERT: F 71 MET cc_start: 0.8887 (tpp) cc_final: 0.8082 (tmt) REVERT: F 114 MET cc_start: 0.3642 (tpp) cc_final: 0.3007 (tpp) REVERT: F 125 TYR cc_start: 0.6391 (t80) cc_final: 0.6115 (t80) REVERT: F 167 GLN cc_start: 0.7757 (mm110) cc_final: 0.7347 (tm-30) outliers start: 18 outliers final: 9 residues processed: 124 average time/residue: 1.2539 time to fit residues: 175.1086 Evaluate side-chains 120 residues out of total 1634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 110 time to evaluate : 0.895 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 362 ASP Chi-restraints excluded: chain A residue 410 ASP Chi-restraints excluded: chain A residue 465 TYR Chi-restraints excluded: chain B residue 153 SER Chi-restraints excluded: chain B residue 204 PHE Chi-restraints excluded: chain D residue 134 ASP Chi-restraints excluded: chain F residue 32 VAL Chi-restraints excluded: chain F residue 136 MET Chi-restraints excluded: chain F residue 160 LEU Chi-restraints excluded: chain F residue 268 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 7 optimal weight: 6.9990 chunk 138 optimal weight: 2.9990 chunk 46 optimal weight: 2.9990 chunk 82 optimal weight: 4.9990 chunk 184 optimal weight: 8.9990 chunk 79 optimal weight: 0.5980 chunk 4 optimal weight: 20.0000 chunk 120 optimal weight: 0.7980 chunk 96 optimal weight: 4.9990 chunk 135 optimal weight: 0.7980 chunk 126 optimal weight: 9.9990 overall best weight: 1.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 301 GLN ** D 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 223 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4081 r_free = 0.4081 target = 0.131785 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.074211 restraints weight = 86197.775| |-----------------------------------------------------------------------------| r_work (start): 0.3102 rms_B_bonded: 3.26 r_work: 0.2945 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work: 0.2818 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.2818 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8110 moved from start: 0.2912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 15536 Z= 0.152 Angle : 0.494 8.221 21092 Z= 0.261 Chirality : 0.042 0.190 2317 Planarity : 0.004 0.054 2791 Dihedral : 4.174 55.092 2137 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 1.04 % Allowed : 15.67 % Favored : 83.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.43 (0.19), residues: 1939 helix: 2.29 (0.22), residues: 535 sheet: -0.43 (0.22), residues: 511 loop : -0.45 (0.21), residues: 893 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 160 TYR 0.019 0.001 TYR F 422 PHE 0.053 0.001 PHE B 204 TRP 0.009 0.001 TRP A 745 HIS 0.002 0.001 HIS F 178 Details of bonding type rmsd covalent geometry : bond 0.00340 (15535) covalent geometry : angle 0.49409 (21090) SS BOND : bond 0.00005 ( 1) SS BOND : angle 0.22757 ( 2) hydrogen bonds : bond 0.03466 ( 722) hydrogen bonds : angle 4.39437 ( 2070) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3878 Ramachandran restraints generated. 1939 Oldfield, 0 Emsley, 1939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3878 Ramachandran restraints generated. 1939 Oldfield, 0 Emsley, 1939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 1634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 109 time to evaluate : 0.871 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 111 LYS cc_start: 0.9406 (tptp) cc_final: 0.9196 (ttpp) REVERT: A 132 ASP cc_start: 0.9293 (t0) cc_final: 0.9028 (m-30) REVERT: A 207 ASN cc_start: 0.8350 (t0) cc_final: 0.8067 (t0) REVERT: A 321 ARG cc_start: 0.8484 (mtm110) cc_final: 0.7841 (ttp-110) REVERT: A 410 ASP cc_start: 0.8438 (OUTLIER) cc_final: 0.7987 (t0) REVERT: A 582 ASP cc_start: 0.8976 (t0) cc_final: 0.8662 (t0) REVERT: A 607 GLU cc_start: 0.8962 (OUTLIER) cc_final: 0.8703 (mt-10) REVERT: C 155 GLU cc_start: 0.7739 (tp30) cc_final: 0.7356 (tm-30) REVERT: C 194 MET cc_start: 0.8482 (mtp) cc_final: 0.8154 (mpp) REVERT: D 56 GLU cc_start: 0.8825 (mt-10) cc_final: 0.8360 (mt-10) REVERT: F 71 MET cc_start: 0.8892 (tpp) cc_final: 0.8091 (tmt) REVERT: F 114 MET cc_start: 0.3595 (tpp) cc_final: 0.2954 (tpp) REVERT: F 125 TYR cc_start: 0.6442 (t80) cc_final: 0.6163 (t80) REVERT: F 167 GLN cc_start: 0.7780 (mm110) cc_final: 0.7368 (tm-30) outliers start: 17 outliers final: 12 residues processed: 123 average time/residue: 1.2659 time to fit residues: 174.2664 Evaluate side-chains 122 residues out of total 1634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 108 time to evaluate : 0.859 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 243 THR Chi-restraints excluded: chain A residue 362 ASP Chi-restraints excluded: chain A residue 410 ASP Chi-restraints excluded: chain A residue 607 GLU Chi-restraints excluded: chain B residue 136 THR Chi-restraints excluded: chain B residue 153 SER Chi-restraints excluded: chain C residue 204 VAL Chi-restraints excluded: chain C residue 205 ILE Chi-restraints excluded: chain D residue 134 ASP Chi-restraints excluded: chain F residue 32 VAL Chi-restraints excluded: chain F residue 136 MET Chi-restraints excluded: chain F residue 160 LEU Chi-restraints excluded: chain F residue 178 HIS Chi-restraints excluded: chain F residue 268 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 166 optimal weight: 40.0000 chunk 137 optimal weight: 2.9990 chunk 81 optimal weight: 4.9990 chunk 146 optimal weight: 2.9990 chunk 168 optimal weight: 20.0000 chunk 2 optimal weight: 0.0030 chunk 84 optimal weight: 2.9990 chunk 72 optimal weight: 1.9990 chunk 177 optimal weight: 40.0000 chunk 102 optimal weight: 5.9990 chunk 62 optimal weight: 2.9990 overall best weight: 2.1998 ------------------------------------------------------------------------------- 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 = 0.4068 r_free = 0.4068 target = 0.130563 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.073049 restraints weight = 87030.664| |-----------------------------------------------------------------------------| r_work (start): 0.3084 rms_B_bonded: 3.23 r_work: 0.2927 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work: 0.2795 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.2795 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8127 moved from start: 0.3054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 15536 Z= 0.195 Angle : 0.511 8.209 21092 Z= 0.270 Chirality : 0.042 0.184 2317 Planarity : 0.004 0.054 2791 Dihedral : 4.185 53.674 2137 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 0.98 % Allowed : 15.79 % Favored : 83.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.37 (0.19), residues: 1939 helix: 2.25 (0.22), residues: 535 sheet: -0.49 (0.22), residues: 512 loop : -0.48 (0.21), residues: 892 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG C 160 TYR 0.020 0.001 TYR C 197 PHE 0.024 0.001 PHE B 204 TRP 0.009 0.001 TRP A 745 HIS 0.002 0.001 HIS B 165 Details of bonding type rmsd covalent geometry : bond 0.00440 (15535) covalent geometry : angle 0.51142 (21090) SS BOND : bond 0.00036 ( 1) SS BOND : angle 0.22473 ( 2) hydrogen bonds : bond 0.03589 ( 722) hydrogen bonds : angle 4.42343 ( 2070) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3878 Ramachandran restraints generated. 1939 Oldfield, 0 Emsley, 1939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3878 Ramachandran restraints generated. 1939 Oldfield, 0 Emsley, 1939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 1634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 109 time to evaluate : 0.770 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 132 ASP cc_start: 0.9297 (t0) cc_final: 0.9025 (m-30) REVERT: A 207 ASN cc_start: 0.8333 (t0) cc_final: 0.8051 (t0) REVERT: A 321 ARG cc_start: 0.8473 (mtm110) cc_final: 0.7828 (ttp-110) REVERT: A 410 ASP cc_start: 0.8516 (OUTLIER) cc_final: 0.8261 (t0) REVERT: A 582 ASP cc_start: 0.8982 (t0) cc_final: 0.8661 (t0) REVERT: A 607 GLU cc_start: 0.8974 (OUTLIER) cc_final: 0.8725 (mt-10) REVERT: C 155 GLU cc_start: 0.7694 (tp30) cc_final: 0.7278 (tm-30) REVERT: C 194 MET cc_start: 0.8479 (mtp) cc_final: 0.8195 (mtp) REVERT: D 56 GLU cc_start: 0.8833 (mt-10) cc_final: 0.8356 (mt-10) REVERT: F 71 MET cc_start: 0.8909 (tpp) cc_final: 0.8110 (tmm) REVERT: F 114 MET cc_start: 0.3613 (tpp) cc_final: 0.3008 (tpp) REVERT: F 125 TYR cc_start: 0.6441 (t80) cc_final: 0.6214 (t80) REVERT: F 167 GLN cc_start: 0.7834 (mm110) cc_final: 0.7424 (tm-30) outliers start: 16 outliers final: 11 residues processed: 121 average time/residue: 1.1645 time to fit residues: 158.3036 Evaluate side-chains 119 residues out of total 1634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 106 time to evaluate : 0.850 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 243 THR Chi-restraints excluded: chain A residue 362 ASP Chi-restraints excluded: chain A residue 410 ASP Chi-restraints excluded: chain A residue 607 GLU Chi-restraints excluded: chain B residue 153 SER Chi-restraints excluded: chain B residue 331 VAL Chi-restraints excluded: chain C residue 204 VAL Chi-restraints excluded: chain C residue 205 ILE Chi-restraints excluded: chain D residue 134 ASP Chi-restraints excluded: chain F residue 32 VAL Chi-restraints excluded: chain F residue 136 MET Chi-restraints excluded: chain F residue 160 LEU Chi-restraints excluded: chain F residue 268 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 126 optimal weight: 9.9990 chunk 169 optimal weight: 30.0000 chunk 52 optimal weight: 2.9990 chunk 154 optimal weight: 0.8980 chunk 69 optimal weight: 4.9990 chunk 121 optimal weight: 0.3980 chunk 131 optimal weight: 9.9990 chunk 102 optimal weight: 5.9990 chunk 47 optimal weight: 0.8980 chunk 79 optimal weight: 6.9990 chunk 91 optimal weight: 2.9990 overall best weight: 1.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4076 r_free = 0.4076 target = 0.131165 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.073703 restraints weight = 86306.818| |-----------------------------------------------------------------------------| r_work (start): 0.3097 rms_B_bonded: 3.24 r_work: 0.2938 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work: 0.2807 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.2807 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8119 moved from start: 0.3152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 15536 Z= 0.153 Angle : 0.500 8.352 21092 Z= 0.263 Chirality : 0.042 0.166 2317 Planarity : 0.003 0.052 2791 Dihedral : 4.126 51.855 2137 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 0.92 % Allowed : 16.03 % Favored : 83.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.44 (0.19), residues: 1939 helix: 2.32 (0.22), residues: 535 sheet: -0.45 (0.22), residues: 512 loop : -0.44 (0.21), residues: 892 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG C 160 TYR 0.022 0.001 TYR C 197 PHE 0.023 0.001 PHE F 212 TRP 0.009 0.001 TRP A 745 HIS 0.002 0.001 HIS A 280 Details of bonding type rmsd covalent geometry : bond 0.00343 (15535) covalent geometry : angle 0.49965 (21090) SS BOND : bond 0.00005 ( 1) SS BOND : angle 0.19878 ( 2) hydrogen bonds : bond 0.03436 ( 722) hydrogen bonds : angle 4.34375 ( 2070) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3878 Ramachandran restraints generated. 1939 Oldfield, 0 Emsley, 1939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3878 Ramachandran restraints generated. 1939 Oldfield, 0 Emsley, 1939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 1634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 111 time to evaluate : 0.615 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 132 ASP cc_start: 0.9283 (t0) cc_final: 0.9017 (m-30) REVERT: A 176 GLU cc_start: 0.8265 (pm20) cc_final: 0.8055 (pm20) REVERT: A 207 ASN cc_start: 0.8351 (t0) cc_final: 0.8068 (t160) REVERT: A 321 ARG cc_start: 0.8489 (mtm110) cc_final: 0.7861 (ttp-110) REVERT: A 410 ASP cc_start: 0.8461 (OUTLIER) cc_final: 0.7941 (t0) REVERT: A 582 ASP cc_start: 0.8962 (t0) cc_final: 0.8639 (t0) REVERT: A 607 GLU cc_start: 0.8974 (OUTLIER) cc_final: 0.8715 (mt-10) REVERT: C 155 GLU cc_start: 0.7692 (tp30) cc_final: 0.7379 (tm-30) REVERT: C 194 MET cc_start: 0.8455 (mtp) cc_final: 0.8172 (mtp) REVERT: D 56 GLU cc_start: 0.8821 (mt-10) cc_final: 0.8347 (mt-10) REVERT: D 232 GLU cc_start: 0.8819 (mm-30) cc_final: 0.8469 (mp0) REVERT: F 71 MET cc_start: 0.8915 (tpp) cc_final: 0.8131 (tmt) REVERT: F 114 MET cc_start: 0.3484 (tpp) cc_final: 0.2897 (tpp) REVERT: F 125 TYR cc_start: 0.6553 (t80) cc_final: 0.6271 (t80) REVERT: F 167 GLN cc_start: 0.7841 (mm110) cc_final: 0.7433 (tm-30) outliers start: 15 outliers final: 11 residues processed: 122 average time/residue: 1.0741 time to fit residues: 147.6668 Evaluate side-chains 119 residues out of total 1634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 106 time to evaluate : 0.654 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 243 THR Chi-restraints excluded: chain A residue 362 ASP Chi-restraints excluded: chain A residue 410 ASP Chi-restraints excluded: chain A residue 607 GLU Chi-restraints excluded: chain B residue 136 THR Chi-restraints excluded: chain B residue 153 SER Chi-restraints excluded: chain C residue 204 VAL Chi-restraints excluded: chain C residue 205 ILE Chi-restraints excluded: chain D residue 134 ASP Chi-restraints excluded: chain F residue 32 VAL Chi-restraints excluded: chain F residue 136 MET Chi-restraints excluded: chain F residue 160 LEU Chi-restraints excluded: chain F residue 268 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 190 optimal weight: 20.0000 chunk 63 optimal weight: 1.9990 chunk 73 optimal weight: 4.9990 chunk 43 optimal weight: 1.9990 chunk 27 optimal weight: 4.9990 chunk 59 optimal weight: 1.9990 chunk 172 optimal weight: 9.9990 chunk 122 optimal weight: 9.9990 chunk 177 optimal weight: 40.0000 chunk 96 optimal weight: 3.9990 chunk 28 optimal weight: 0.8980 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 301 GLN ** C 87 GLN ** 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 = 0.4053 r_free = 0.4053 target = 0.129748 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.072481 restraints weight = 86060.955| |-----------------------------------------------------------------------------| r_work (start): 0.3083 rms_B_bonded: 3.22 r_work: 0.2923 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work: 0.2793 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.2793 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8127 moved from start: 0.3232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 15536 Z= 0.193 Angle : 0.514 7.812 21092 Z= 0.272 Chirality : 0.042 0.144 2317 Planarity : 0.004 0.053 2791 Dihedral : 4.159 50.538 2137 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 0.86 % Allowed : 15.97 % Favored : 83.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.38 (0.19), residues: 1939 helix: 2.26 (0.22), residues: 535 sheet: -0.49 (0.22), residues: 512 loop : -0.48 (0.21), residues: 892 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG C 160 TYR 0.023 0.001 TYR C 197 PHE 0.023 0.001 PHE F 212 TRP 0.013 0.001 TRP C 148 HIS 0.004 0.001 HIS D 102 Details of bonding type rmsd covalent geometry : bond 0.00435 (15535) covalent geometry : angle 0.51436 (21090) SS BOND : bond 0.00033 ( 1) SS BOND : angle 0.22733 ( 2) hydrogen bonds : bond 0.03531 ( 722) hydrogen bonds : angle 4.39241 ( 2070) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3878 Ramachandran restraints generated. 1939 Oldfield, 0 Emsley, 1939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3878 Ramachandran restraints generated. 1939 Oldfield, 0 Emsley, 1939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 1634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 107 time to evaluate : 0.644 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 132 ASP cc_start: 0.9284 (t0) cc_final: 0.9018 (m-30) REVERT: A 176 GLU cc_start: 0.8268 (pm20) cc_final: 0.8057 (pm20) REVERT: A 207 ASN cc_start: 0.8341 (t0) cc_final: 0.8084 (t160) REVERT: A 321 ARG cc_start: 0.8487 (mtm110) cc_final: 0.7846 (ttp-110) REVERT: A 410 ASP cc_start: 0.8488 (OUTLIER) cc_final: 0.8233 (t0) REVERT: A 582 ASP cc_start: 0.8959 (t0) cc_final: 0.8632 (t0) REVERT: A 607 GLU cc_start: 0.8975 (OUTLIER) cc_final: 0.8697 (mt-10) REVERT: C 155 GLU cc_start: 0.7706 (tp30) cc_final: 0.7365 (tm-30) REVERT: C 194 MET cc_start: 0.8452 (mtp) cc_final: 0.8166 (mtp) REVERT: D 232 GLU cc_start: 0.8834 (mm-30) cc_final: 0.8482 (mp0) REVERT: F 71 MET cc_start: 0.8917 (tpp) cc_final: 0.8136 (tmt) REVERT: F 114 MET cc_start: 0.3529 (tpp) cc_final: 0.2938 (tpp) REVERT: F 125 TYR cc_start: 0.6534 (t80) cc_final: 0.6261 (t80) REVERT: F 167 GLN cc_start: 0.7864 (mm110) cc_final: 0.7446 (tm-30) outliers start: 14 outliers final: 10 residues processed: 118 average time/residue: 1.0530 time to fit residues: 139.5270 Evaluate side-chains 118 residues out of total 1634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 106 time to evaluate : 0.824 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 243 THR Chi-restraints excluded: chain A residue 362 ASP Chi-restraints excluded: chain A residue 410 ASP Chi-restraints excluded: chain A residue 607 GLU Chi-restraints excluded: chain B residue 153 SER Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain C residue 204 VAL Chi-restraints excluded: chain D residue 134 ASP Chi-restraints excluded: chain F residue 32 VAL Chi-restraints excluded: chain F residue 136 MET Chi-restraints excluded: chain F residue 160 LEU Chi-restraints excluded: chain F residue 268 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 129 optimal weight: 9.9990 chunk 43 optimal weight: 1.9990 chunk 156 optimal weight: 2.9990 chunk 6 optimal weight: 10.0000 chunk 87 optimal weight: 0.3980 chunk 176 optimal weight: 10.0000 chunk 70 optimal weight: 0.0570 chunk 103 optimal weight: 0.9990 chunk 99 optimal weight: 4.9990 chunk 121 optimal weight: 0.0980 chunk 72 optimal weight: 2.9990 overall best weight: 0.7102 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 301 GLN ** C 87 GLN ** 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 = 0.4075 r_free = 0.4075 target = 0.131374 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.074021 restraints weight = 86467.166| |-----------------------------------------------------------------------------| r_work (start): 0.3113 rms_B_bonded: 3.25 r_work: 0.2956 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work: 0.2821 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.2821 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8094 moved from start: 0.3292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.055 15536 Z= 0.101 Angle : 0.492 8.942 21092 Z= 0.258 Chirality : 0.042 0.147 2317 Planarity : 0.003 0.050 2791 Dihedral : 4.052 48.538 2137 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 4.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 0.67 % Allowed : 16.40 % Favored : 82.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.52 (0.19), residues: 1939 helix: 2.37 (0.23), residues: 535 sheet: -0.39 (0.22), residues: 501 loop : -0.40 (0.21), residues: 903 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG C 160 TYR 0.024 0.001 TYR C 197 PHE 0.023 0.001 PHE F 212 TRP 0.016 0.001 TRP C 148 HIS 0.002 0.000 HIS D 102 Details of bonding type rmsd covalent geometry : bond 0.00226 (15535) covalent geometry : angle 0.49166 (21090) SS BOND : bond 0.00032 ( 1) SS BOND : angle 0.25872 ( 2) hydrogen bonds : bond 0.03264 ( 722) hydrogen bonds : angle 4.25534 ( 2070) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12653.63 seconds wall clock time: 214 minutes 0.15 seconds (12840.15 seconds total)