Starting phenix.real_space_refine on Wed May 28 00:19:43 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9hg8_52130/05_2025/9hg8_52130.cif Found real_map, /net/cci-nas-00/data/ceres_data/9hg8_52130/05_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9hg8_52130/05_2025/9hg8_52130.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9hg8_52130/05_2025/9hg8_52130.map" model { file = "/net/cci-nas-00/data/ceres_data/9hg8_52130/05_2025/9hg8_52130.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9hg8_52130/05_2025/9hg8_52130.cif" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.009 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 48 5.16 5 C 9545 2.51 5 N 2643 2.21 5 O 3000 1.98 5 H 14802 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 30038 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 12175 Number of conformers: 1 Conformer: "" Number of residues, atoms: 788, 12175 Classifications: {'peptide': 788} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 29, 'TRANS': 758} Chain: "B" Number of atoms: 5534 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 5534 Classifications: {'peptide': 371} Link IDs: {'PTRANS': 11, 'TRANS': 359} Chain: "C" Number of atoms: 2845 Number of conformers: 1 Conformer: "" Number of residues, atoms: 189, 2845 Classifications: {'peptide': 189} Modifications used: {'NH1NOTPRO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 178} Chain: "D" Number of atoms: 3461 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 3461 Classifications: {'peptide': 218} Link IDs: {'PTRANS': 12, 'TRANS': 205} Chain: "E" Number of atoms: 1363 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 1363 Classifications: {'peptide': 88} Link IDs: {'PTRANS': 5, 'TRANS': 82} Chain: "F" Number of atoms: 4660 Number of conformers: 1 Conformer: "" Number of residues, atoms: 299, 4660 Classifications: {'peptide': 299} Link IDs: {'PTRANS': 8, 'TRANS': 290} Chain breaks: 1 Time building chain proxies: 14.04, per 1000 atoms: 0.47 Number of scatterers: 30038 At special positions: 0 Unit cell: (110.96, 124.1, 167.9, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 48 16.00 O 3000 8.00 N 2643 7.00 C 9545 6.00 H 14802 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 690 " - pdb=" SG CYS A 700 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 7.13 Conformation dependent library (CDL) restraints added in 2.4 seconds 3878 Ramachandran restraints generated. 1939 Oldfield, 0 Emsley, 1939 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3588 Finding SS restraints... Secondary structure from input PDB file: 50 helices and 20 sheets defined 31.6% alpha, 28.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.74 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: 11.25 Time building geometry restraints manager: 8.63 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: 6.860 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: 0.500 Extract box with map and model: 1.160 Check model and map are aligned: 0.210 Set scattering table: 0.240 Process input model: 61.680 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:10.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 81.790 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.16 (0.19), residues: 1939 helix: 1.50 (0.23), residues: 533 sheet: -0.40 (0.21), residues: 553 loop : -0.32 (0.22), residues: 853 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 145 HIS 0.002 0.001 HIS D 139 PHE 0.009 0.001 PHE A 791 TYR 0.023 0.001 TYR C 31 ARG 0.010 0.001 ARG F 399 Details of bonding type rmsd hydrogen bonds : bond 0.13541 ( 722) hydrogen bonds : angle 6.03387 ( 2070) SS BOND : bond 0.00137 ( 1) SS BOND : angle 2.18064 ( 2) covalent geometry : bond 0.00410 (15535) covalent geometry : angle 0.64949 (21090) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3878 Ramachandran restraints generated. 1939 Oldfield, 0 Emsley, 1939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3878 Ramachandran restraints generated. 1939 Oldfield, 0 Emsley, 1939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 1634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 194 time to evaluate : 2.545 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 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: 0.7624 (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 83 MET cc_start: 0.9463 (ptm) cc_final: 0.9229 (tmm) REVERT: F 167 GLN cc_start: 0.7674 (mm110) cc_final: 0.7226 (tm-30) REVERT: F 400 MET cc_start: 0.8094 (mtp) cc_final: 0.7850 (mtm) outliers start: 19 outliers final: 7 residues processed: 210 average time/residue: 2.7471 time to fit residues: 638.2629 Evaluate side-chains 140 residues out of total 1634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 132 time to evaluate : 2.422 ------------------------------------------------------------------------------- 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 259 ILE Chi-restraints excluded: chain F residue 402 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 161 optimal weight: 0.7980 chunk 144 optimal weight: 1.9990 chunk 80 optimal weight: 8.9990 chunk 49 optimal weight: 0.6980 chunk 97 optimal weight: 4.9990 chunk 77 optimal weight: 4.9990 chunk 149 optimal weight: 0.9990 chunk 57 optimal weight: 1.9990 chunk 91 optimal weight: 2.9990 chunk 111 optimal weight: 3.9990 chunk 173 optimal weight: 5.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- 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 266 ASN B 301 GLN F 106 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4101 r_free = 0.4101 target = 0.133355 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.075174 restraints weight = 86411.624| |-----------------------------------------------------------------------------| r_work (start): 0.3172 rms_B_bonded: 3.22 r_work: 0.3021 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work: 0.2897 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.2897 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8071 moved from start: 0.1531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 15536 Z= 0.149 Angle : 0.537 5.112 21092 Z= 0.289 Chirality : 0.043 0.155 2317 Planarity : 0.005 0.111 2791 Dihedral : 4.861 59.049 2149 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 0.98 % Allowed : 14.87 % Favored : 84.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.26 (0.19), residues: 1939 helix: 1.81 (0.22), residues: 535 sheet: -0.37 (0.21), residues: 535 loop : -0.42 (0.22), residues: 869 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 317 HIS 0.002 0.001 HIS A 280 PHE 0.017 0.001 PHE F 212 TYR 0.018 0.001 TYR D 184 ARG 0.006 0.000 ARG F 57 Details of bonding type rmsd hydrogen bonds : bond 0.04466 ( 722) hydrogen bonds : angle 5.06373 ( 2070) SS BOND : bond 0.00104 ( 1) SS BOND : angle 0.79580 ( 2) covalent geometry : bond 0.00322 (15535) covalent geometry : angle 0.53746 (21090) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3878 Ramachandran restraints generated. 1939 Oldfield, 0 Emsley, 1939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3878 Ramachandran restraints generated. 1939 Oldfield, 0 Emsley, 1939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 134 time to evaluate : 2.429 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: 0.9511 (tptp) cc_final: 0.9246 (ttpp) REVERT: A 140 PHE cc_start: 0.9097 (t80) cc_final: 0.8891 (t80) REVERT: A 207 ASN cc_start: 0.8386 (t0) cc_final: 0.8045 (t0) REVERT: A 582 ASP cc_start: 0.9062 (t0) cc_final: 0.8819 (t0) REVERT: B 226 MET cc_start: 0.9144 (ttm) cc_final: 0.8364 (tmm) REVERT: B 278 MET cc_start: 0.8413 (mtt) cc_final: 0.7816 (mpm) REVERT: C 148 TRP cc_start: 0.8258 (m-90) cc_final: 0.7961 (m-90) REVERT: C 155 GLU cc_start: 0.7893 (tp30) cc_final: 0.7554 (tm-30) REVERT: C 157 TYR cc_start: 0.7393 (m-80) cc_final: 0.7187 (m-80) REVERT: C 194 MET cc_start: 0.8513 (mtp) cc_final: 0.8196 (mpp) REVERT: C 210 ASP cc_start: 0.7159 (OUTLIER) cc_final: 0.6912 (m-30) REVERT: D 49 ARG cc_start: 0.8174 (OUTLIER) cc_final: 0.7941 (ttp80) REVERT: D 56 GLU cc_start: 0.8784 (mt-10) cc_final: 0.8287 (mt-10) REVERT: F 71 MET cc_start: 0.8769 (tpp) cc_final: 0.8436 (tpt) REVERT: F 167 GLN cc_start: 0.7773 (mm110) cc_final: 0.7326 (tm-30) outliers start: 16 outliers final: 6 residues processed: 145 average time/residue: 2.2736 time to fit residues: 372.9249 Evaluate side-chains 125 residues out of total 1634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 117 time to evaluate : 2.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 153 SER Chi-restraints excluded: chain C residue 210 ASP Chi-restraints excluded: chain D residue 49 ARG 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 259 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 12 optimal weight: 6.9990 chunk 156 optimal weight: 3.9990 chunk 42 optimal weight: 2.9990 chunk 16 optimal weight: 2.9990 chunk 112 optimal weight: 0.4980 chunk 120 optimal weight: 2.9990 chunk 176 optimal weight: 8.9990 chunk 136 optimal weight: 1.9990 chunk 151 optimal weight: 0.9990 chunk 3 optimal weight: 30.0000 chunk 21 optimal weight: 4.9990 overall best weight: 1.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 301 GLN ** D 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 175 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4076 r_free = 0.4076 target = 0.131622 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.074001 restraints weight = 86642.930| |-----------------------------------------------------------------------------| r_work (start): 0.3121 rms_B_bonded: 3.25 r_work: 0.2967 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work: 0.2833 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.2833 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8068 moved from start: 0.2012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 15536 Z= 0.180 Angle : 0.519 6.778 21092 Z= 0.276 Chirality : 0.042 0.151 2317 Planarity : 0.004 0.061 2791 Dihedral : 4.659 59.866 2143 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 1.29 % Allowed : 14.44 % Favored : 84.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.30 (0.19), residues: 1939 helix: 1.98 (0.22), residues: 534 sheet: -0.45 (0.21), residues: 538 loop : -0.42 (0.21), residues: 867 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 317 HIS 0.004 0.001 HIS D 102 PHE 0.019 0.001 PHE F 212 TYR 0.017 0.001 TYR F 422 ARG 0.005 0.000 ARG C 33 Details of bonding type rmsd hydrogen bonds : bond 0.03975 ( 722) hydrogen bonds : angle 4.79173 ( 2070) SS BOND : bond 0.00016 ( 1) SS BOND : angle 0.32596 ( 2) covalent geometry : bond 0.00403 (15535) covalent geometry : angle 0.51921 (21090) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3878 Ramachandran restraints generated. 1939 Oldfield, 0 Emsley, 1939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3878 Ramachandran restraints generated. 1939 Oldfield, 0 Emsley, 1939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 1634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 123 time to evaluate : 2.554 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 111 LYS cc_start: 0.9496 (tptp) cc_final: 0.9261 (tmmm) REVERT: A 176 GLU cc_start: 0.8110 (pm20) cc_final: 0.7906 (pm20) REVERT: A 207 ASN cc_start: 0.8382 (t0) cc_final: 0.8048 (t0) REVERT: A 321 ARG cc_start: 0.8432 (mtm110) cc_final: 0.7786 (ttp-110) REVERT: A 582 ASP cc_start: 0.9060 (t0) cc_final: 0.8758 (t0) REVERT: B 278 MET cc_start: 0.8472 (mtt) cc_final: 0.7832 (mpm) REVERT: C 155 GLU cc_start: 0.7801 (tp30) cc_final: 0.7447 (tm-30) REVERT: C 182 GLU cc_start: 0.7825 (mm-30) cc_final: 0.7416 (mm-30) REVERT: C 194 MET cc_start: 0.8518 (mtp) cc_final: 0.8216 (mpp) REVERT: D 56 GLU cc_start: 0.8803 (mt-10) cc_final: 0.8314 (mt-10) REVERT: F 71 MET cc_start: 0.8789 (tpp) cc_final: 0.8441 (tpt) REVERT: F 167 GLN cc_start: 0.7783 (mm110) cc_final: 0.7331 (tm-30) outliers start: 21 outliers final: 9 residues processed: 136 average time/residue: 2.2345 time to fit residues: 346.3616 Evaluate side-chains 118 residues out of total 1634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 109 time to evaluate : 2.489 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 136 THR Chi-restraints excluded: chain C residue 144 ASP 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 268 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 177 optimal weight: 40.0000 chunk 47 optimal weight: 6.9990 chunk 1 optimal weight: 20.0000 chunk 139 optimal weight: 1.9990 chunk 11 optimal weight: 7.9990 chunk 61 optimal weight: 0.8980 chunk 162 optimal weight: 40.0000 chunk 168 optimal weight: 0.9990 chunk 115 optimal weight: 1.9990 chunk 112 optimal weight: 4.9990 chunk 111 optimal weight: 6.9990 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 ** D 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 59 GLN F 85 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4079 r_free = 0.4079 target = 0.131535 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.073884 restraints weight = 86700.434| |-----------------------------------------------------------------------------| r_work (start): 0.3100 rms_B_bonded: 3.25 r_work: 0.2944 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work: 0.2809 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.2809 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8095 moved from start: 0.2397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 15536 Z= 0.192 Angle : 0.513 7.191 21092 Z= 0.273 Chirality : 0.042 0.173 2317 Planarity : 0.004 0.057 2791 Dihedral : 4.280 58.180 2137 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 1.65 % Allowed : 14.50 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.30 (0.19), residues: 1939 helix: 2.05 (0.22), residues: 535 sheet: -0.39 (0.22), residues: 510 loop : -0.51 (0.21), residues: 894 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 745 HIS 0.003 0.001 HIS D 102 PHE 0.011 0.001 PHE F 212 TYR 0.017 0.001 TYR F 422 ARG 0.003 0.000 ARG D 173 Details of bonding type rmsd hydrogen bonds : bond 0.03822 ( 722) hydrogen bonds : angle 4.66212 ( 2070) SS BOND : bond 0.00004 ( 1) SS BOND : angle 0.19581 ( 2) covalent geometry : bond 0.00428 (15535) covalent geometry : angle 0.51259 (21090) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3878 Ramachandran restraints generated. 1939 Oldfield, 0 Emsley, 1939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3878 Ramachandran restraints generated. 1939 Oldfield, 0 Emsley, 1939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 113 time to evaluate : 2.594 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: 0.9473 (tptp) cc_final: 0.9233 (ttpp) REVERT: A 132 ASP cc_start: 0.9293 (t0) cc_final: 0.9090 (m-30) REVERT: A 176 GLU cc_start: 0.8203 (pm20) cc_final: 0.7994 (pm20) REVERT: A 207 ASN cc_start: 0.8386 (t0) cc_final: 0.8066 (t0) REVERT: A 321 ARG cc_start: 0.8474 (mtm110) cc_final: 0.7903 (ttp-110) REVERT: A 582 ASP cc_start: 0.9049 (t0) cc_final: 0.8726 (t0) REVERT: B 278 MET cc_start: 0.8506 (mtt) cc_final: 0.7894 (mpm) REVERT: C 155 GLU cc_start: 0.7779 (tp30) cc_final: 0.7369 (tm-30) REVERT: C 194 MET cc_start: 0.8517 (mtp) cc_final: 0.8216 (mpp) REVERT: D 56 GLU cc_start: 0.8812 (mt-10) cc_final: 0.8317 (mt-10) REVERT: F 71 MET cc_start: 0.8831 (tpp) cc_final: 0.8527 (tpt) REVERT: F 114 MET cc_start: 0.4301 (tpp) cc_final: 0.3705 (tpp) REVERT: F 125 TYR cc_start: 0.6267 (t80) cc_final: 0.5981 (t80) REVERT: F 167 GLN cc_start: 0.7749 (mm110) cc_final: 0.7325 (tm-30) REVERT: F 400 MET cc_start: 0.8173 (mtp) cc_final: 0.7912 (mmm) outliers start: 27 outliers final: 10 residues processed: 131 average time/residue: 2.3020 time to fit residues: 340.6006 Evaluate side-chains 122 residues out of total 1634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 112 time to evaluate : 2.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 465 TYR Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain B residue 136 THR Chi-restraints excluded: chain B residue 153 SER Chi-restraints excluded: chain C residue 144 ASP Chi-restraints excluded: chain C residue 177 LYS 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 268 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 22 optimal weight: 0.8980 chunk 179 optimal weight: 5.9990 chunk 56 optimal weight: 1.9990 chunk 96 optimal weight: 3.9990 chunk 160 optimal weight: 2.9990 chunk 25 optimal weight: 2.9990 chunk 60 optimal weight: 2.9990 chunk 134 optimal weight: 5.9990 chunk 163 optimal weight: 20.0000 chunk 162 optimal weight: 20.0000 chunk 20 optimal weight: 2.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- 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 = 0.4071 r_free = 0.4071 target = 0.131011 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.073330 restraints weight = 86367.903| |-----------------------------------------------------------------------------| r_work (start): 0.3087 rms_B_bonded: 3.25 r_work: 0.2931 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work: 0.2794 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.2794 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8113 moved from start: 0.2569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 15536 Z= 0.207 Angle : 0.512 6.937 21092 Z= 0.272 Chirality : 0.042 0.144 2317 Planarity : 0.004 0.054 2791 Dihedral : 4.295 57.208 2137 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 1.53 % Allowed : 15.06 % Favored : 83.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.28 (0.19), residues: 1939 helix: 2.09 (0.22), residues: 535 sheet: -0.49 (0.22), residues: 513 loop : -0.52 (0.21), residues: 891 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 745 HIS 0.002 0.001 HIS A 280 PHE 0.013 0.001 PHE A 197 TYR 0.018 0.001 TYR F 422 ARG 0.007 0.000 ARG F 57 Details of bonding type rmsd hydrogen bonds : bond 0.03781 ( 722) hydrogen bonds : angle 4.59866 ( 2070) SS BOND : bond 0.00024 ( 1) SS BOND : angle 0.23387 ( 2) covalent geometry : bond 0.00464 (15535) covalent geometry : angle 0.51191 (21090) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3878 Ramachandran restraints generated. 1939 Oldfield, 0 Emsley, 1939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3878 Ramachandran restraints generated. 1939 Oldfield, 0 Emsley, 1939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 1634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 113 time to evaluate : 2.388 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: 0.9458 (tptp) cc_final: 0.9239 (ttpp) REVERT: A 176 GLU cc_start: 0.8264 (pm20) cc_final: 0.8038 (pm20) REVERT: A 207 ASN cc_start: 0.8382 (t0) cc_final: 0.8083 (t0) REVERT: A 321 ARG cc_start: 0.8505 (mtm110) cc_final: 0.7810 (ttp-110) REVERT: A 410 ASP cc_start: 0.8331 (OUTLIER) cc_final: 0.7996 (t0) REVERT: A 582 ASP cc_start: 0.9044 (t0) cc_final: 0.8711 (t0) REVERT: A 607 GLU cc_start: 0.8965 (OUTLIER) cc_final: 0.8706 (mt-10) REVERT: C 155 GLU cc_start: 0.7777 (tp30) cc_final: 0.7409 (tm-30) REVERT: C 160 ARG cc_start: 0.7976 (ttm110) cc_final: 0.7614 (mtp-110) REVERT: C 194 MET cc_start: 0.8504 (mtp) cc_final: 0.8174 (mpp) REVERT: D 56 GLU cc_start: 0.8846 (mt-10) cc_final: 0.8348 (mt-10) REVERT: F 71 MET cc_start: 0.8847 (tpp) cc_final: 0.8042 (tmt) REVERT: F 114 MET cc_start: 0.4231 (tpp) cc_final: 0.3432 (tpp) REVERT: F 125 TYR cc_start: 0.6275 (t80) cc_final: 0.6072 (t80) REVERT: F 167 GLN cc_start: 0.7764 (mm110) cc_final: 0.7348 (tm-30) REVERT: F 400 MET cc_start: 0.8182 (mtp) cc_final: 0.7950 (mmm) outliers start: 25 outliers final: 15 residues processed: 129 average time/residue: 2.3062 time to fit residues: 335.8221 Evaluate side-chains 125 residues out of total 1634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 108 time to evaluate : 2.394 ------------------------------------------------------------------------------- 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 573 ASN Chi-restraints excluded: chain A residue 607 GLU Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain B residue 136 THR Chi-restraints excluded: chain B residue 153 SER Chi-restraints excluded: chain B residue 204 PHE Chi-restraints excluded: chain B residue 331 VAL Chi-restraints excluded: chain C residue 144 ASP Chi-restraints excluded: chain C residue 177 LYS 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 268 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 123 optimal weight: 40.0000 chunk 67 optimal weight: 4.9990 chunk 47 optimal weight: 4.9990 chunk 0 optimal weight: 40.0000 chunk 64 optimal weight: 1.9990 chunk 163 optimal weight: 0.9980 chunk 76 optimal weight: 0.9990 chunk 65 optimal weight: 0.4980 chunk 23 optimal weight: 2.9990 chunk 189 optimal weight: 10.0000 chunk 96 optimal weight: 2.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- 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 = 0.4083 r_free = 0.4083 target = 0.132178 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.074372 restraints weight = 86258.146| |-----------------------------------------------------------------------------| r_work (start): 0.3103 rms_B_bonded: 3.27 r_work: 0.2946 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work: 0.2812 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.2812 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8108 moved from start: 0.2749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 15536 Z= 0.140 Angle : 0.489 6.721 21092 Z= 0.258 Chirality : 0.041 0.186 2317 Planarity : 0.003 0.053 2791 Dihedral : 4.192 55.235 2137 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 3.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.38 (0.19), residues: 1939 helix: 2.21 (0.22), residues: 535 sheet: -0.46 (0.22), residues: 511 loop : -0.46 (0.21), residues: 893 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 745 HIS 0.002 0.001 HIS A 280 PHE 0.009 0.001 PHE F 212 TYR 0.018 0.001 TYR D 184 ARG 0.003 0.000 ARG D 94 Details of bonding type rmsd hydrogen bonds : bond 0.03557 ( 722) hydrogen bonds : angle 4.44369 ( 2070) SS BOND : bond 0.00004 ( 1) SS BOND : angle 0.21755 ( 2) covalent geometry : bond 0.00313 (15535) covalent geometry : angle 0.48944 (21090) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3878 Ramachandran restraints generated. 1939 Oldfield, 0 Emsley, 1939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3878 Ramachandran restraints generated. 1939 Oldfield, 0 Emsley, 1939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 1634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 113 time to evaluate : 2.427 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: 0.9447 (tptp) cc_final: 0.9220 (ttpp) REVERT: A 176 GLU cc_start: 0.8273 (pm20) cc_final: 0.8034 (pm20) REVERT: A 207 ASN cc_start: 0.8360 (t0) cc_final: 0.8057 (t0) REVERT: A 321 ARG cc_start: 0.8482 (mtm110) cc_final: 0.7905 (ttp-110) REVERT: A 410 ASP cc_start: 0.8332 (OUTLIER) cc_final: 0.8074 (t0) REVERT: A 582 ASP cc_start: 0.9008 (t0) cc_final: 0.8681 (t0) REVERT: C 155 GLU cc_start: 0.7728 (tp30) cc_final: 0.7376 (tm-30) REVERT: C 194 MET cc_start: 0.8489 (mtp) cc_final: 0.8161 (mpp) REVERT: D 56 GLU cc_start: 0.8806 (mt-10) cc_final: 0.8325 (mt-10) REVERT: D 232 GLU cc_start: 0.8809 (mm-30) cc_final: 0.8457 (mp0) REVERT: F 71 MET cc_start: 0.8857 (tpp) cc_final: 0.8559 (tpt) REVERT: F 114 MET cc_start: 0.4282 (tpp) cc_final: 0.3461 (tpp) REVERT: F 125 TYR cc_start: 0.6330 (t80) cc_final: 0.6107 (t80) REVERT: F 167 GLN cc_start: 0.7789 (mm110) cc_final: 0.7366 (tm-30) REVERT: F 400 MET cc_start: 0.8229 (mtp) cc_final: 0.7997 (mmm) outliers start: 21 outliers final: 9 residues processed: 128 average time/residue: 2.3628 time to fit residues: 344.6923 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 : 2.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 410 ASP Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain B residue 136 THR Chi-restraints excluded: chain B residue 204 PHE Chi-restraints excluded: chain C residue 144 ASP Chi-restraints excluded: chain C residue 177 LYS 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 268 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 186 optimal weight: 20.0000 chunk 13 optimal weight: 5.9990 chunk 162 optimal weight: 50.0000 chunk 169 optimal weight: 30.0000 chunk 34 optimal weight: 1.9990 chunk 93 optimal weight: 3.9990 chunk 33 optimal weight: 0.6980 chunk 1 optimal weight: 10.0000 chunk 20 optimal weight: 3.9990 chunk 114 optimal weight: 4.9990 chunk 164 optimal weight: 30.0000 overall best weight: 3.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 301 GLN F 223 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4058 r_free = 0.4058 target = 0.130125 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.072255 restraints weight = 86807.582| |-----------------------------------------------------------------------------| r_work (start): 0.3065 rms_B_bonded: 3.25 r_work: 0.2905 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work: 0.2767 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.2767 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8152 moved from start: 0.2967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.059 15536 Z= 0.263 Angle : 0.536 7.733 21092 Z= 0.285 Chirality : 0.043 0.199 2317 Planarity : 0.004 0.055 2791 Dihedral : 4.344 53.305 2137 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 1.35 % Allowed : 15.79 % Favored : 82.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.26 (0.19), residues: 1939 helix: 2.18 (0.22), residues: 535 sheet: -0.50 (0.22), residues: 521 loop : -0.60 (0.21), residues: 883 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 745 HIS 0.004 0.001 HIS B 165 PHE 0.053 0.002 PHE B 204 TYR 0.019 0.001 TYR C 197 ARG 0.007 0.000 ARG C 160 Details of bonding type rmsd hydrogen bonds : bond 0.03853 ( 722) hydrogen bonds : angle 4.58624 ( 2070) SS BOND : bond 0.00082 ( 1) SS BOND : angle 0.27808 ( 2) covalent geometry : bond 0.00586 (15535) covalent geometry : angle 0.53603 (21090) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3878 Ramachandran restraints generated. 1939 Oldfield, 0 Emsley, 1939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3878 Ramachandran restraints generated. 1939 Oldfield, 0 Emsley, 1939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 1634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 111 time to evaluate : 2.393 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 111 LYS cc_start: 0.9441 (tptp) cc_final: 0.9204 (ttpp) REVERT: A 176 GLU cc_start: 0.8316 (pm20) cc_final: 0.8074 (pm20) REVERT: A 207 ASN cc_start: 0.8349 (t0) cc_final: 0.8052 (t0) REVERT: A 321 ARG cc_start: 0.8496 (mtm110) cc_final: 0.7856 (ttp-110) REVERT: A 410 ASP cc_start: 0.8501 (OUTLIER) cc_final: 0.8179 (t0) REVERT: A 582 ASP cc_start: 0.8994 (t0) cc_final: 0.8666 (t0) REVERT: A 607 GLU cc_start: 0.8990 (OUTLIER) cc_final: 0.8725 (mt-10) REVERT: C 155 GLU cc_start: 0.7703 (tp30) cc_final: 0.7366 (tm-30) REVERT: C 194 MET cc_start: 0.8477 (mtp) cc_final: 0.8198 (mtp) REVERT: D 56 GLU cc_start: 0.8862 (mt-10) cc_final: 0.8392 (mt-10) REVERT: D 232 GLU cc_start: 0.8842 (mm-30) cc_final: 0.8459 (mp0) REVERT: F 71 MET cc_start: 0.8872 (tpp) cc_final: 0.8071 (tmt) REVERT: F 114 MET cc_start: 0.4349 (tpp) cc_final: 0.3688 (tpp) REVERT: F 125 TYR cc_start: 0.6357 (t80) cc_final: 0.6148 (t80) REVERT: F 167 GLN cc_start: 0.7799 (mm110) cc_final: 0.7366 (tm-30) REVERT: F 400 MET cc_start: 0.8244 (mtp) cc_final: 0.8034 (mmm) outliers start: 22 outliers final: 15 residues processed: 128 average time/residue: 2.3295 time to fit residues: 337.0953 Evaluate side-chains 123 residues out of total 1634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 106 time to evaluate : 2.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 243 THR Chi-restraints excluded: chain A residue 410 ASP Chi-restraints excluded: chain A residue 573 ASN Chi-restraints excluded: chain A residue 607 GLU Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain B residue 136 THR Chi-restraints excluded: chain B residue 153 SER Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 331 VAL Chi-restraints excluded: chain C residue 144 ASP Chi-restraints excluded: chain C residue 177 LYS 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 268 LEU Chi-restraints excluded: chain F residue 402 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 147 optimal weight: 0.9990 chunk 53 optimal weight: 5.9990 chunk 58 optimal weight: 0.9980 chunk 97 optimal weight: 2.9990 chunk 35 optimal weight: 0.6980 chunk 107 optimal weight: 9.9990 chunk 88 optimal weight: 2.9990 chunk 17 optimal weight: 3.9990 chunk 102 optimal weight: 4.9990 chunk 174 optimal weight: 9.9990 chunk 129 optimal weight: 0.1980 overall best weight: 1.1784 ------------------------------------------------------------------------------- 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 = 0.4084 r_free = 0.4084 target = 0.132635 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.074584 restraints weight = 85899.515| |-----------------------------------------------------------------------------| r_work (start): 0.3100 rms_B_bonded: 3.31 r_work: 0.2942 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work: 0.2808 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.2808 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8106 moved from start: 0.3037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 15536 Z= 0.125 Angle : 0.497 8.656 21092 Z= 0.260 Chirality : 0.042 0.167 2317 Planarity : 0.003 0.054 2791 Dihedral : 4.196 51.396 2137 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 1.10 % Allowed : 16.03 % Favored : 82.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.44 (0.19), residues: 1939 helix: 2.28 (0.22), residues: 535 sheet: -0.42 (0.22), residues: 510 loop : -0.45 (0.21), residues: 894 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 745 HIS 0.002 0.000 HIS A 280 PHE 0.025 0.001 PHE B 204 TYR 0.019 0.001 TYR C 197 ARG 0.010 0.000 ARG C 160 Details of bonding type rmsd hydrogen bonds : bond 0.03498 ( 722) hydrogen bonds : angle 4.40359 ( 2070) SS BOND : bond 0.00009 ( 1) SS BOND : angle 0.18796 ( 2) covalent geometry : bond 0.00281 (15535) covalent geometry : angle 0.49684 (21090) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3878 Ramachandran restraints generated. 1939 Oldfield, 0 Emsley, 1939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3878 Ramachandran restraints generated. 1939 Oldfield, 0 Emsley, 1939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 1634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 108 time to evaluate : 2.493 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 176 GLU cc_start: 0.8294 (pm20) cc_final: 0.8043 (pm20) REVERT: A 207 ASN cc_start: 0.8345 (t0) cc_final: 0.8069 (t0) REVERT: A 321 ARG cc_start: 0.8469 (mtm110) cc_final: 0.7845 (ttp-110) REVERT: A 410 ASP cc_start: 0.8426 (OUTLIER) cc_final: 0.7923 (t0) REVERT: A 582 ASP cc_start: 0.8995 (t0) cc_final: 0.8672 (t0) REVERT: A 607 GLU cc_start: 0.8970 (OUTLIER) cc_final: 0.8709 (mt-10) REVERT: B 278 MET cc_start: 0.8592 (mtt) cc_final: 0.7967 (mpm) REVERT: C 155 GLU cc_start: 0.7717 (tp30) cc_final: 0.7357 (tm-30) REVERT: C 160 ARG cc_start: 0.7827 (ttm110) cc_final: 0.7607 (ttm110) REVERT: C 182 GLU cc_start: 0.7161 (mm-30) cc_final: 0.6675 (mm-30) REVERT: C 194 MET cc_start: 0.8471 (mtp) cc_final: 0.8201 (mtp) REVERT: D 56 GLU cc_start: 0.8824 (mt-10) cc_final: 0.8341 (mt-10) REVERT: F 71 MET cc_start: 0.8842 (tpp) cc_final: 0.8540 (tpt) REVERT: F 114 MET cc_start: 0.4444 (tpp) cc_final: 0.3703 (tpp) REVERT: F 167 GLN cc_start: 0.7816 (mm110) cc_final: 0.7419 (tm-30) outliers start: 18 outliers final: 11 residues processed: 120 average time/residue: 2.4257 time to fit residues: 327.5986 Evaluate side-chains 121 residues out of total 1634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 108 time to evaluate : 2.180 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 410 ASP Chi-restraints excluded: chain A residue 607 GLU Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain B residue 136 THR Chi-restraints excluded: chain B residue 153 SER Chi-restraints excluded: chain C residue 144 ASP Chi-restraints excluded: chain C residue 177 LYS 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 268 LEU Chi-restraints excluded: chain F residue 402 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 93 optimal weight: 3.9990 chunk 149 optimal weight: 1.9990 chunk 12 optimal weight: 5.9990 chunk 179 optimal weight: 30.0000 chunk 7 optimal weight: 6.9990 chunk 20 optimal weight: 2.9990 chunk 143 optimal weight: 1.9990 chunk 158 optimal weight: 1.9990 chunk 31 optimal weight: 3.9990 chunk 169 optimal weight: 30.0000 chunk 146 optimal weight: 2.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 266 ASN B 301 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4062 r_free = 0.4062 target = 0.130667 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.072976 restraints weight = 85989.581| |-----------------------------------------------------------------------------| r_work (start): 0.3074 rms_B_bonded: 3.25 r_work: 0.2914 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work: 0.2776 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.2776 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8129 moved from start: 0.3168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 15536 Z= 0.212 Angle : 0.521 9.048 21092 Z= 0.275 Chirality : 0.042 0.171 2317 Planarity : 0.004 0.054 2791 Dihedral : 4.237 49.075 2137 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 1.10 % Allowed : 16.46 % Favored : 82.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.34 (0.19), residues: 1939 helix: 2.24 (0.22), residues: 535 sheet: -0.48 (0.22), residues: 522 loop : -0.54 (0.21), residues: 882 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 148 HIS 0.003 0.001 HIS B 165 PHE 0.025 0.001 PHE F 212 TYR 0.022 0.001 TYR C 197 ARG 0.011 0.000 ARG C 160 Details of bonding type rmsd hydrogen bonds : bond 0.03675 ( 722) hydrogen bonds : angle 4.46821 ( 2070) SS BOND : bond 0.00074 ( 1) SS BOND : angle 0.24849 ( 2) covalent geometry : bond 0.00474 (15535) covalent geometry : angle 0.52108 (21090) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3878 Ramachandran restraints generated. 1939 Oldfield, 0 Emsley, 1939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3878 Ramachandran restraints generated. 1939 Oldfield, 0 Emsley, 1939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 1634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 108 time to evaluate : 2.516 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 176 GLU cc_start: 0.8311 (pm20) cc_final: 0.8072 (pm20) REVERT: A 207 ASN cc_start: 0.8346 (t0) cc_final: 0.8074 (t0) REVERT: A 321 ARG cc_start: 0.8494 (mtm110) cc_final: 0.7858 (ttp-110) REVERT: A 410 ASP cc_start: 0.8499 (OUTLIER) cc_final: 0.7945 (t0) REVERT: A 582 ASP cc_start: 0.9009 (t0) cc_final: 0.8663 (t0) REVERT: A 607 GLU cc_start: 0.8994 (OUTLIER) cc_final: 0.8728 (mt-10) REVERT: C 155 GLU cc_start: 0.7739 (tp30) cc_final: 0.7394 (tm-30) REVERT: C 194 MET cc_start: 0.8487 (mtp) cc_final: 0.8211 (mtp) REVERT: D 56 GLU cc_start: 0.8852 (mt-10) cc_final: 0.8377 (mt-10) REVERT: F 71 MET cc_start: 0.8877 (tpp) cc_final: 0.8060 (tmt) REVERT: F 167 GLN cc_start: 0.7788 (mm110) cc_final: 0.7403 (tm-30) outliers start: 18 outliers final: 13 residues processed: 120 average time/residue: 2.3141 time to fit residues: 316.2560 Evaluate side-chains 119 residues out of total 1634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 104 time to evaluate : 2.435 ------------------------------------------------------------------------------- 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 76 ASP Chi-restraints excluded: chain B residue 136 THR Chi-restraints excluded: chain B residue 153 SER Chi-restraints excluded: chain C residue 144 ASP Chi-restraints excluded: chain C residue 177 LYS 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 268 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 108 optimal weight: 1.9990 chunk 12 optimal weight: 3.9990 chunk 153 optimal weight: 2.9990 chunk 20 optimal weight: 2.9990 chunk 151 optimal weight: 0.9980 chunk 190 optimal weight: 9.9990 chunk 5 optimal weight: 20.0000 chunk 35 optimal weight: 1.9990 chunk 73 optimal weight: 0.7980 chunk 175 optimal weight: 3.9990 chunk 39 optimal weight: 0.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- 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 = 0.4081 r_free = 0.4081 target = 0.133674 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.075616 restraints weight = 84970.585| |-----------------------------------------------------------------------------| r_work (start): 0.3102 rms_B_bonded: 3.31 r_work: 0.2936 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work: 0.2805 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.2805 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8127 moved from start: 0.3235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 15536 Z= 0.136 Angle : 0.498 9.237 21092 Z= 0.261 Chirality : 0.041 0.145 2317 Planarity : 0.004 0.081 2791 Dihedral : 4.152 47.087 2137 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 0.98 % Allowed : 16.65 % Favored : 82.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.45 (0.19), residues: 1939 helix: 2.32 (0.22), residues: 536 sheet: -0.42 (0.22), residues: 517 loop : -0.47 (0.21), residues: 886 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 148 HIS 0.002 0.001 HIS D 102 PHE 0.024 0.001 PHE F 212 TYR 0.023 0.001 TYR C 197 ARG 0.017 0.000 ARG C 160 Details of bonding type rmsd hydrogen bonds : bond 0.03445 ( 722) hydrogen bonds : angle 4.34304 ( 2070) SS BOND : bond 0.00022 ( 1) SS BOND : angle 0.19176 ( 2) covalent geometry : bond 0.00304 (15535) covalent geometry : angle 0.49812 (21090) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3878 Ramachandran restraints generated. 1939 Oldfield, 0 Emsley, 1939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3878 Ramachandran restraints generated. 1939 Oldfield, 0 Emsley, 1939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 1634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 106 time to evaluate : 2.634 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 176 GLU cc_start: 0.8294 (pm20) cc_final: 0.8048 (pm20) REVERT: A 207 ASN cc_start: 0.8334 (t0) cc_final: 0.8057 (t160) REVERT: A 321 ARG cc_start: 0.8476 (mtm110) cc_final: 0.7839 (ttp-110) REVERT: A 410 ASP cc_start: 0.8445 (OUTLIER) cc_final: 0.7937 (t0) REVERT: A 582 ASP cc_start: 0.8981 (t0) cc_final: 0.8650 (t0) REVERT: A 607 GLU cc_start: 0.8983 (OUTLIER) cc_final: 0.8703 (mt-10) REVERT: B 278 MET cc_start: 0.8629 (mtt) cc_final: 0.8010 (mpm) REVERT: C 155 GLU cc_start: 0.7716 (tp30) cc_final: 0.7357 (tm-30) REVERT: C 163 ILE cc_start: 0.9452 (mp) cc_final: 0.9243 (tp) REVERT: C 194 MET cc_start: 0.8450 (mtp) cc_final: 0.8174 (mtp) REVERT: D 232 GLU cc_start: 0.8831 (mm-30) cc_final: 0.8462 (mp0) REVERT: F 71 MET cc_start: 0.8887 (tpp) cc_final: 0.8083 (tmt) REVERT: F 114 MET cc_start: 0.3537 (tpp) cc_final: 0.3141 (tpp) REVERT: F 167 GLN cc_start: 0.7856 (mm110) cc_final: 0.7427 (tm-30) REVERT: F 400 MET cc_start: 0.8377 (mmm) cc_final: 0.8109 (mmm) outliers start: 16 outliers final: 10 residues processed: 115 average time/residue: 2.4202 time to fit residues: 313.3146 Evaluate side-chains 115 residues out of total 1634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 103 time to evaluate : 2.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 144 ASP 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 268 LEU Chi-restraints excluded: chain F residue 402 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 94 optimal weight: 0.9990 chunk 182 optimal weight: 5.9990 chunk 159 optimal weight: 1.9990 chunk 61 optimal weight: 3.9990 chunk 85 optimal weight: 1.9990 chunk 143 optimal weight: 0.0470 chunk 29 optimal weight: 1.9990 chunk 82 optimal weight: 3.9990 chunk 10 optimal weight: 0.5980 chunk 169 optimal weight: 30.0000 chunk 142 optimal weight: 0.9980 overall best weight: 0.9282 ------------------------------------------------------------------------------- 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 = 0.4091 r_free = 0.4091 target = 0.133689 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.075648 restraints weight = 85205.238| |-----------------------------------------------------------------------------| r_work (start): 0.3115 rms_B_bonded: 3.32 r_work: 0.2952 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work: 0.2821 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.2821 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8110 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= 0.110 Angle : 0.485 9.112 21092 Z= 0.253 Chirality : 0.041 0.147 2317 Planarity : 0.004 0.087 2791 Dihedral : 4.034 43.929 2137 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 3.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 0.92 % Allowed : 16.83 % Favored : 82.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.60 (0.19), residues: 1939 helix: 2.48 (0.22), residues: 536 sheet: -0.36 (0.22), residues: 507 loop : -0.37 (0.21), residues: 896 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP C 148 HIS 0.002 0.000 HIS D 102 PHE 0.026 0.001 PHE F 212 TYR 0.024 0.001 TYR C 197 ARG 0.022 0.000 ARG C 160 Details of bonding type rmsd hydrogen bonds : bond 0.03254 ( 722) hydrogen bonds : angle 4.22516 ( 2070) SS BOND : bond 0.00028 ( 1) SS BOND : angle 0.32773 ( 2) covalent geometry : bond 0.00248 (15535) covalent geometry : angle 0.48550 (21090) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 25926.67 seconds wall clock time: 442 minutes 30.54 seconds (26550.54 seconds total)