Starting phenix.real_space_refine on Thu Jun 26 01:37:48 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9hg8_52130/06_2025/9hg8_52130.cif Found real_map, /net/cci-nas-00/data/ceres_data/9hg8_52130/06_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_52130/06_2025/9hg8_52130.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9hg8_52130/06_2025/9hg8_52130.map" model { file = "/net/cci-nas-00/data/ceres_data/9hg8_52130/06_2025/9hg8_52130.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9hg8_52130/06_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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 30038 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 12175 Number of conformers: 1 Conformer: "" Number of residues, atoms: 788, 12175 Classifications: {'peptide': 788} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 29, 'TRANS': 758} Chain: "B" Number of atoms: 5534 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 5534 Classifications: {'peptide': 371} Link IDs: {'PTRANS': 11, 'TRANS': 359} Chain: "C" Number of atoms: 2845 Number of conformers: 1 Conformer: "" Number of residues, atoms: 189, 2845 Classifications: {'peptide': 189} Modifications used: {'NH1NOTPRO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 178} Chain: "D" Number of atoms: 3461 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 3461 Classifications: {'peptide': 218} Link IDs: {'PTRANS': 12, 'TRANS': 205} Chain: "E" Number of atoms: 1363 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 1363 Classifications: {'peptide': 88} Link IDs: {'PTRANS': 5, 'TRANS': 82} Chain: "F" Number of atoms: 4660 Number of conformers: 1 Conformer: "" Number of residues, atoms: 299, 4660 Classifications: {'peptide': 299} Link IDs: {'PTRANS': 8, 'TRANS': 290} Chain breaks: 1 Time building chain proxies: 15.06, per 1000 atoms: 0.50 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: 8.81 Conformation dependent library (CDL) restraints added in 2.7 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: 2.36 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: 12.82 Time building geometry restraints manager: 10.53 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 14801 1.03 - 1.23: 191 1.23 - 1.43: 6445 1.43 - 1.62: 8807 1.62 - 1.82: 93 Bond restraints: 30337 Sorted by residual: bond pdb=" C MET F 76 " pdb=" O MET F 76 " ideal model delta sigma weight residual 1.237 1.185 0.052 1.19e-02 7.06e+03 1.88e+01 bond pdb=" N CYS C 25 " pdb=" H1 CYS C 25 " ideal model delta sigma weight residual 0.960 0.890 0.070 2.00e-02 2.50e+03 1.22e+01 bond pdb=" N ARG A 162 " pdb=" H ARG A 162 " ideal model delta sigma weight residual 0.860 0.914 -0.054 2.00e-02 2.50e+03 7.21e+00 bond pdb=" N LYS B 280 " pdb=" CA LYS B 280 " ideal model delta sigma weight residual 1.455 1.486 -0.032 1.26e-02 6.30e+03 6.41e+00 bond pdb=" N GLY A 23 " pdb=" CA GLY A 23 " ideal model delta sigma weight residual 1.451 1.491 -0.040 1.60e-02 3.91e+03 6.29e+00 ... (remaining 30332 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.10: 54086 2.10 - 4.20: 468 4.20 - 6.31: 45 6.31 - 8.41: 4 8.41 - 10.51: 1 Bond angle restraints: 54604 Sorted by residual: angle pdb=" N ASP F 112 " pdb=" CA ASP F 112 " pdb=" C ASP F 112 " ideal model delta sigma weight residual 111.69 117.18 -5.49 1.23e+00 6.61e-01 1.99e+01 angle pdb=" N ARG A 162 " pdb=" CA ARG A 162 " pdb=" C ARG A 162 " ideal model delta sigma weight residual 109.69 103.41 6.28 1.44e+00 4.82e-01 1.90e+01 angle pdb=" N MET F 76 " pdb=" CA MET F 76 " pdb=" C MET F 76 " ideal model delta sigma weight residual 111.36 106.73 4.63 1.09e+00 8.42e-01 1.80e+01 angle pdb=" CA ARG A 162 " pdb=" C ARG A 162 " pdb=" O ARG A 162 " ideal model delta sigma weight residual 121.60 116.80 4.80 1.21e+00 6.83e-01 1.57e+01 angle pdb=" CA MET F 414 " pdb=" C MET F 414 " pdb=" O MET F 414 " ideal model delta sigma weight residual 120.42 116.23 4.19 1.06e+00 8.90e-01 1.56e+01 ... (remaining 54599 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.48: 12703 17.48 - 34.96: 1018 34.96 - 52.44: 442 52.44 - 69.92: 134 69.92 - 87.39: 36 Dihedral angle restraints: 14333 sinusoidal: 7806 harmonic: 6527 Sorted by residual: dihedral pdb=" CD ARG B 281 " pdb=" NE ARG B 281 " pdb=" CZ ARG B 281 " pdb=" NH1 ARG B 281 " ideal model delta sinusoidal sigma weight residual 0.00 -68.80 68.80 1 1.00e+01 1.00e-02 6.13e+01 dihedral pdb=" CD ARG A 162 " pdb=" NE ARG A 162 " pdb=" CZ ARG A 162 " pdb=" NH1 ARG A 162 " ideal model delta sinusoidal sigma weight residual 0.00 38.51 -38.51 1 1.00e+01 1.00e-02 2.09e+01 dihedral pdb=" CA TYR C 197 " pdb=" C TYR C 197 " pdb=" N SER C 198 " pdb=" CA SER C 198 " ideal model delta harmonic sigma weight residual 180.00 161.77 18.23 0 5.00e+00 4.00e-02 1.33e+01 ... (remaining 14330 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 1660 0.040 - 0.080: 439 0.080 - 0.120: 180 0.120 - 0.160: 31 0.160 - 0.201: 7 Chirality restraints: 2317 Sorted by residual: chirality pdb=" CA LYS B 280 " pdb=" N LYS B 280 " pdb=" C LYS B 280 " pdb=" CB LYS B 280 " both_signs ideal model delta sigma weight residual False 2.51 2.71 -0.20 2.00e-01 2.50e+01 1.01e+00 chirality pdb=" CA ARG B 281 " pdb=" N ARG B 281 " pdb=" C ARG B 281 " pdb=" CB ARG B 281 " both_signs ideal model delta sigma weight residual False 2.51 2.70 -0.18 2.00e-01 2.50e+01 8.53e-01 chirality pdb=" CA PRO A 159 " pdb=" N PRO A 159 " pdb=" C PRO A 159 " pdb=" CB PRO A 159 " both_signs ideal model delta sigma weight residual False 2.72 2.54 0.18 2.00e-01 2.50e+01 7.87e-01 ... (remaining 2314 not shown) Planarity restraints: 4662 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN F 186 " 0.247 2.00e-02 2.50e+03 3.80e-01 2.17e+03 pdb=" CG ASN F 186 " -0.017 2.00e-02 2.50e+03 pdb=" OD1 ASN F 186 " -0.239 2.00e-02 2.50e+03 pdb=" ND2 ASN F 186 " -0.000 2.00e-02 2.50e+03 pdb="HD21 ASN F 186 " -0.607 2.00e-02 2.50e+03 pdb="HD22 ASN F 186 " 0.617 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 281 " 0.681 9.50e-02 1.11e+02 3.11e-01 1.07e+03 pdb=" NE ARG B 281 " -0.304 2.00e-02 2.50e+03 pdb=" CZ ARG B 281 " -0.083 2.00e-02 2.50e+03 pdb=" NH1 ARG B 281 " 0.044 2.00e-02 2.50e+03 pdb=" NH2 ARG B 281 " 0.024 2.00e-02 2.50e+03 pdb="HH11 ARG B 281 " 0.229 2.00e-02 2.50e+03 pdb="HH12 ARG B 281 " -0.061 2.00e-02 2.50e+03 pdb="HH21 ARG B 281 " -0.286 2.00e-02 2.50e+03 pdb="HH22 ARG B 281 " 0.407 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 162 " -0.791 9.50e-02 1.11e+02 2.67e-01 1.11e+02 pdb=" NE ARG A 162 " -0.027 2.00e-02 2.50e+03 pdb=" CZ ARG A 162 " 0.001 2.00e-02 2.50e+03 pdb=" NH1 ARG A 162 " 0.009 2.00e-02 2.50e+03 pdb=" NH2 ARG A 162 " 0.005 2.00e-02 2.50e+03 pdb="HH11 ARG A 162 " 0.080 2.00e-02 2.50e+03 pdb="HH12 ARG A 162 " -0.050 2.00e-02 2.50e+03 pdb="HH21 ARG A 162 " 0.066 2.00e-02 2.50e+03 pdb="HH22 ARG A 162 " -0.050 2.00e-02 2.50e+03 ... (remaining 4659 not shown) Histogram of nonbonded interaction distances: 1.53 - 2.14: 925 2.14 - 2.76: 56086 2.76 - 3.37: 83279 3.37 - 3.99: 108876 3.99 - 4.60: 169113 Nonbonded interactions: 418279 Sorted by model distance: nonbonded pdb=" H GLY F 253 " pdb=" O VAL F 270 " model vdw 1.525 2.450 nonbonded pdb=" HZ1 LYS A 103 " pdb=" O GLU B 26 " model vdw 1.526 2.450 nonbonded pdb=" H ASN B 85 " pdb=" O LYS B 90 " model vdw 1.567 2.450 nonbonded pdb=" OD1 ASP B 300 " pdb=" H ARG B 304 " model vdw 1.586 2.450 nonbonded pdb=" O ARG C 112 " pdb=" HG1 THR C 115 " model vdw 1.605 2.450 ... (remaining 418274 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.730 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: 0.530 Extract box with map and model: 1.310 Check model and map are aligned: 0.230 Set scattering table: 0.300 Process input model: 67.130 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.090 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:13.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 87.270 ------------------------------------------------------------------------------- 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 : 2.329 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: 2.8420 time to fit residues: 661.0213 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 : 2.502 ------------------------------------------------------------------------------- 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 = 64)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.075153 restraints weight = 86411.543| |-----------------------------------------------------------------------------| r_work (start): 0.3171 rms_B_bonded: 3.23 r_work: 0.3022 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work: 0.2890 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.2890 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8068 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 : 2.451 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: 0.9512 (tptp) cc_final: 0.9246 (ttpp) REVERT: A 140 PHE cc_start: 0.9097 (t80) cc_final: 0.8894 (t80) REVERT: A 207 ASN cc_start: 0.8372 (t0) cc_final: 0.8037 (t0) REVERT: A 582 ASP cc_start: 0.9072 (t0) cc_final: 0.8828 (t0) REVERT: B 226 MET cc_start: 0.9143 (ttm) cc_final: 0.8347 (tmm) REVERT: B 278 MET cc_start: 0.8422 (mtt) cc_final: 0.7823 (mpm) REVERT: C 148 TRP cc_start: 0.8264 (m-90) cc_final: 0.7965 (m-90) REVERT: C 155 GLU cc_start: 0.7866 (tp30) cc_final: 0.7520 (tm-30) REVERT: C 157 TYR cc_start: 0.7389 (m-80) cc_final: 0.7186 (m-80) REVERT: C 194 MET cc_start: 0.8515 (mtp) cc_final: 0.8202 (mpp) REVERT: C 210 ASP cc_start: 0.7156 (OUTLIER) cc_final: 0.6909 (m-30) REVERT: D 49 ARG cc_start: 0.8179 (OUTLIER) cc_final: 0.7948 (ttp80) REVERT: D 56 GLU cc_start: 0.8787 (mt-10) cc_final: 0.8294 (mt-10) REVERT: F 71 MET cc_start: 0.8765 (tpp) cc_final: 0.8427 (tpt) REVERT: F 167 GLN cc_start: 0.7766 (mm110) cc_final: 0.7325 (tm-30) outliers start: 16 outliers final: 6 residues processed: 145 average time/residue: 2.3039 time to fit residues: 376.6150 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 : 2.229 ------------------------------------------------------------------------------- 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: 0.6980 chunk 120 optimal weight: 3.9990 chunk 176 optimal weight: 7.9990 chunk 136 optimal weight: 2.9990 chunk 151 optimal weight: 0.9980 chunk 3 optimal weight: 30.0000 chunk 21 optimal weight: 3.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 301 GLN ** D 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 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 = 0.4073 r_free = 0.4073 target = 0.131458 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.073674 restraints weight = 86570.062| |-----------------------------------------------------------------------------| r_work (start): 0.3108 rms_B_bonded: 3.27 r_work: 0.2953 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work: 0.2820 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.2820 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8079 moved from start: 0.2068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 15536 Z= 0.195 Angle : 0.524 5.985 21092 Z= 0.279 Chirality : 0.042 0.141 2317 Planarity : 0.004 0.064 2791 Dihedral : 4.688 59.972 2143 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 1.41 % Allowed : 14.44 % Favored : 84.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.97 (0.22), residues: 533 sheet: -0.49 (0.21), residues: 534 loop : -0.45 (0.21), residues: 872 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 0.014 0.001 PHE F 212 TYR 0.017 0.001 TYR D 184 ARG 0.007 0.000 ARG C 30 Details of bonding type rmsd hydrogen bonds : bond 0.04020 ( 722) hydrogen bonds : angle 4.79827 ( 2070) SS BOND : bond 0.00006 ( 1) SS BOND : angle 0.25800 ( 2) covalent geometry : bond 0.00436 (15535) covalent geometry : angle 0.52447 (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 143 residues out of total 1634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 120 time to evaluate : 2.368 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 111 LYS cc_start: 0.9500 (tptp) cc_final: 0.9268 (tmmm) REVERT: A 176 GLU cc_start: 0.8131 (pm20) cc_final: 0.7929 (pm20) REVERT: A 207 ASN cc_start: 0.8373 (t0) cc_final: 0.8046 (t0) REVERT: A 321 ARG cc_start: 0.8448 (mtm110) cc_final: 0.7799 (ttp-110) REVERT: A 582 ASP cc_start: 0.9057 (t0) cc_final: 0.8754 (t0) REVERT: B 278 MET cc_start: 0.8493 (mtt) cc_final: 0.7846 (mpm) REVERT: C 155 GLU cc_start: 0.7797 (tp30) cc_final: 0.7408 (tm-30) REVERT: C 160 ARG cc_start: 0.7492 (OUTLIER) cc_final: 0.7292 (mtp-110) REVERT: C 182 GLU cc_start: 0.7775 (mm-30) cc_final: 0.7337 (mm-30) REVERT: C 194 MET cc_start: 0.8511 (mtp) cc_final: 0.8216 (mpp) REVERT: C 210 ASP cc_start: 0.7176 (OUTLIER) cc_final: 0.6976 (m-30) REVERT: D 56 GLU cc_start: 0.8808 (mt-10) cc_final: 0.8319 (mt-10) REVERT: F 71 MET cc_start: 0.8812 (tpp) cc_final: 0.8468 (tpt) REVERT: F 167 GLN cc_start: 0.7788 (mm110) cc_final: 0.7334 (tm-30) REVERT: F 400 MET cc_start: 0.8125 (mtp) cc_final: 0.7830 (mmm) outliers start: 23 outliers final: 8 residues processed: 135 average time/residue: 2.7348 time to fit residues: 423.8776 Evaluate side-chains 119 residues out of total 1634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 109 time to evaluate : 4.299 ------------------------------------------------------------------------------- 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 160 ARG Chi-restraints excluded: chain C residue 177 LYS Chi-restraints excluded: chain C residue 210 ASP 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: 5.9990 chunk 1 optimal weight: 20.0000 chunk 139 optimal weight: 1.9990 chunk 11 optimal weight: 7.9990 chunk 61 optimal weight: 0.7980 chunk 162 optimal weight: 7.9990 chunk 168 optimal weight: 10.0000 chunk 115 optimal weight: 0.6980 chunk 112 optimal weight: 0.9980 chunk 111 optimal weight: 3.9990 overall best weight: 1.6984 ------------------------------------------------------------------------------- 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 = 0.4078 r_free = 0.4078 target = 0.131692 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.074105 restraints weight = 86659.218| |-----------------------------------------------------------------------------| r_work (start): 0.3111 rms_B_bonded: 3.25 r_work: 0.2956 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work: 0.2825 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.2825 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8080 moved from start: 0.2433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 15536 Z= 0.156 Angle : 0.502 7.527 21092 Z= 0.265 Chirality : 0.042 0.194 2317 Planarity : 0.004 0.054 2791 Dihedral : 4.382 57.915 2139 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 1.53 % Allowed : 14.69 % Favored : 83.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.35 (0.19), residues: 1939 helix: 2.09 (0.22), residues: 535 sheet: -0.38 (0.22), residues: 509 loop : -0.47 (0.21), residues: 895 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 317 HIS 0.002 0.001 HIS A 280 PHE 0.009 0.001 PHE F 212 TYR 0.017 0.001 TYR D 184 ARG 0.003 0.000 ARG D 94 Details of bonding type rmsd hydrogen bonds : bond 0.03704 ( 722) hydrogen bonds : angle 4.58728 ( 2070) SS BOND : bond 0.00008 ( 1) SS BOND : angle 0.23988 ( 2) covalent geometry : bond 0.00347 (15535) covalent geometry : angle 0.50166 (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 141 residues out of total 1634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 116 time to evaluate : 2.513 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: 0.9468 (tptp) cc_final: 0.9222 (ttpp) REVERT: A 176 GLU cc_start: 0.8215 (pm20) cc_final: 0.8014 (pm20) REVERT: A 207 ASN cc_start: 0.8383 (t0) cc_final: 0.8066 (t0) REVERT: A 321 ARG cc_start: 0.8466 (mtm110) cc_final: 0.7850 (ttp-110) REVERT: A 582 ASP cc_start: 0.9038 (t0) cc_final: 0.8718 (t0) REVERT: C 155 GLU cc_start: 0.7763 (tp30) cc_final: 0.7471 (tm-30) REVERT: C 194 MET cc_start: 0.8525 (mtp) cc_final: 0.8216 (mpp) REVERT: F 71 MET cc_start: 0.8826 (tpp) cc_final: 0.8518 (tpt) REVERT: F 114 MET cc_start: 0.4182 (tpp) cc_final: 0.3405 (tpp) REVERT: F 125 TYR cc_start: 0.6223 (t80) cc_final: 0.6008 (t80) REVERT: F 167 GLN cc_start: 0.7722 (mm110) cc_final: 0.7312 (tm-30) REVERT: F 400 MET cc_start: 0.8160 (mtp) cc_final: 0.7911 (mmm) outliers start: 25 outliers final: 10 residues processed: 133 average time/residue: 2.4048 time to fit residues: 361.7237 Evaluate side-chains 123 residues out of total 1634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 113 time to evaluate : 2.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 160 ARG Chi-restraints excluded: chain C residue 177 LYS Chi-restraints excluded: chain D residue 55 LEU Chi-restraints excluded: chain D residue 134 ASP Chi-restraints excluded: chain D residue 205 TYR Chi-restraints excluded: chain F residue 32 VAL Chi-restraints excluded: chain F residue 136 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 22 optimal weight: 1.9990 chunk 179 optimal weight: 7.9990 chunk 56 optimal weight: 1.9990 chunk 96 optimal weight: 3.9990 chunk 160 optimal weight: 2.9990 chunk 25 optimal weight: 0.3980 chunk 60 optimal weight: 2.9990 chunk 134 optimal weight: 5.9990 chunk 163 optimal weight: 20.0000 chunk 162 optimal weight: 10.0000 chunk 20 optimal weight: 3.9990 overall best weight: 2.0788 ------------------------------------------------------------------------------- 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 = 0.4075 r_free = 0.4075 target = 0.131378 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.073726 restraints weight = 86402.360| |-----------------------------------------------------------------------------| r_work (start): 0.3095 rms_B_bonded: 3.26 r_work: 0.2939 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work: 0.2814 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.2814 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8108 moved from start: 0.2591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 15536 Z= 0.188 Angle : 0.504 7.330 21092 Z= 0.267 Chirality : 0.042 0.141 2317 Planarity : 0.004 0.054 2791 Dihedral : 4.249 56.935 2137 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 1.53 % Allowed : 14.81 % 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: 0.34 (0.19), residues: 1939 helix: 2.15 (0.22), residues: 535 sheet: -0.46 (0.22), residues: 514 loop : -0.47 (0.21), residues: 890 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 0.015 0.001 PHE A 197 TYR 0.017 0.001 TYR D 184 ARG 0.006 0.000 ARG F 57 Details of bonding type rmsd hydrogen bonds : bond 0.03690 ( 722) hydrogen bonds : angle 4.54490 ( 2070) SS BOND : bond 0.00003 ( 1) SS BOND : angle 0.23428 ( 2) covalent geometry : bond 0.00422 (15535) covalent geometry : angle 0.50432 (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 : 4.024 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 132 ASP cc_start: 0.9298 (t0) cc_final: 0.9041 (m-30) REVERT: A 176 GLU cc_start: 0.8264 (pm20) cc_final: 0.8044 (pm20) REVERT: A 207 ASN cc_start: 0.8379 (t0) cc_final: 0.8075 (t0) REVERT: A 321 ARG cc_start: 0.8478 (mtm110) cc_final: 0.7795 (ttp-110) REVERT: A 582 ASP cc_start: 0.8999 (t0) cc_final: 0.8680 (t0) REVERT: A 607 GLU cc_start: 0.8957 (OUTLIER) cc_final: 0.8706 (mt-10) REVERT: C 155 GLU cc_start: 0.7775 (tp30) cc_final: 0.7421 (tm-30) REVERT: C 160 ARG cc_start: 0.7353 (OUTLIER) cc_final: 0.7054 (mtp-110) REVERT: C 194 MET cc_start: 0.8498 (mtp) cc_final: 0.8168 (mpp) REVERT: D 56 GLU cc_start: 0.8835 (mt-10) cc_final: 0.8338 (mt-10) REVERT: F 71 MET cc_start: 0.8848 (tpp) cc_final: 0.8042 (tmt) REVERT: F 114 MET cc_start: 0.4291 (tpp) cc_final: 0.3483 (tpp) REVERT: F 167 GLN cc_start: 0.7750 (mm110) cc_final: 0.7340 (tm-30) REVERT: F 400 MET cc_start: 0.8184 (mtp) cc_final: 0.7947 (mmm) outliers start: 25 outliers final: 11 residues processed: 128 average time/residue: 2.8477 time to fit residues: 413.0687 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 : 2.836 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 243 THR Chi-restraints excluded: chain A residue 465 TYR 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 C residue 160 ARG 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: 30.0000 chunk 67 optimal weight: 0.8980 chunk 47 optimal weight: 2.9990 chunk 0 optimal weight: 40.0000 chunk 64 optimal weight: 2.9990 chunk 163 optimal weight: 2.9990 chunk 76 optimal weight: 3.9990 chunk 65 optimal weight: 0.7980 chunk 23 optimal weight: 2.9990 chunk 189 optimal weight: 20.0000 chunk 96 optimal weight: 3.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 594 ASN B 266 ASN B 301 GLN F 223 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4072 r_free = 0.4072 target = 0.131394 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.073514 restraints weight = 86633.249| |-----------------------------------------------------------------------------| r_work (start): 0.3088 rms_B_bonded: 3.27 r_work: 0.2933 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work: 0.2798 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.2798 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8118 moved from start: 0.2853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 15536 Z= 0.187 Angle : 0.498 6.158 21092 Z= 0.264 Chirality : 0.042 0.143 2317 Planarity : 0.004 0.054 2791 Dihedral : 4.234 54.679 2137 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 3.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 1.65 % Allowed : 14.93 % 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: 0.35 (0.19), residues: 1939 helix: 2.19 (0.22), residues: 535 sheet: -0.48 (0.22), residues: 514 loop : -0.48 (0.21), residues: 890 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 745 HIS 0.003 0.001 HIS F 178 PHE 0.014 0.001 PHE F 212 TYR 0.017 0.001 TYR D 184 ARG 0.003 0.000 ARG D 173 Details of bonding type rmsd hydrogen bonds : bond 0.03662 ( 722) hydrogen bonds : angle 4.47881 ( 2070) SS BOND : bond 0.00038 ( 1) SS BOND : angle 0.22933 ( 2) covalent geometry : bond 0.00417 (15535) covalent geometry : angle 0.49784 (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 136 residues out of total 1634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 109 time to evaluate : 2.522 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 132 ASP cc_start: 0.9293 (t0) cc_final: 0.9039 (m-30) REVERT: A 176 GLU cc_start: 0.8298 (pm20) cc_final: 0.8059 (pm20) REVERT: A 207 ASN cc_start: 0.8370 (t0) cc_final: 0.8071 (t0) REVERT: A 321 ARG cc_start: 0.8504 (mtm110) cc_final: 0.7918 (ttp-110) REVERT: A 582 ASP cc_start: 0.8997 (t0) cc_final: 0.8674 (t0) REVERT: A 607 GLU cc_start: 0.8969 (OUTLIER) cc_final: 0.8722 (mt-10) REVERT: C 155 GLU cc_start: 0.7734 (tp30) cc_final: 0.7388 (tm-30) REVERT: C 194 MET cc_start: 0.8492 (mtp) cc_final: 0.8166 (mpp) REVERT: D 232 GLU cc_start: 0.8818 (mm-30) cc_final: 0.8450 (mp0) REVERT: F 71 MET cc_start: 0.8860 (tpp) cc_final: 0.8042 (tmt) REVERT: F 167 GLN cc_start: 0.7767 (mm110) cc_final: 0.7349 (tm-30) REVERT: F 400 MET cc_start: 0.8226 (mtp) cc_final: 0.8005 (mmm) outliers start: 27 outliers final: 16 residues processed: 128 average time/residue: 2.6075 time to fit residues: 384.8464 Evaluate side-chains 124 residues out of total 1634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 107 time to evaluate : 2.935 ------------------------------------------------------------------------------- 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 465 TYR 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 160 ARG 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 178 HIS 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: 30.0000 chunk 13 optimal weight: 6.9990 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: 0.9980 chunk 1 optimal weight: 10.0000 chunk 20 optimal weight: 2.9990 chunk 114 optimal weight: 4.9990 chunk 164 optimal weight: 30.0000 overall best weight: 2.9988 ------------------------------------------------------------------------------- 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 = 0.4060 r_free = 0.4060 target = 0.130514 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.072293 restraints weight = 87076.902| |-----------------------------------------------------------------------------| r_work (start): 0.3064 rms_B_bonded: 3.28 r_work: 0.2908 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work: 0.2776 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.2776 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8148 moved from start: 0.3012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 15536 Z= 0.250 Angle : 0.521 6.582 21092 Z= 0.278 Chirality : 0.043 0.182 2317 Planarity : 0.004 0.054 2791 Dihedral : 4.315 53.016 2137 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 1.29 % Allowed : 15.54 % Favored : 83.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.27 (0.19), residues: 1939 helix: 2.15 (0.22), residues: 535 sheet: -0.53 (0.22), residues: 520 loop : -0.55 (0.21), residues: 884 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 745 HIS 0.003 0.001 HIS B 165 PHE 0.085 0.002 PHE B 204 TYR 0.017 0.001 TYR F 422 ARG 0.003 0.000 ARG D 173 Details of bonding type rmsd hydrogen bonds : bond 0.03816 ( 722) hydrogen bonds : angle 4.54942 ( 2070) SS BOND : bond 0.00071 ( 1) SS BOND : angle 0.28623 ( 2) covalent geometry : bond 0.00561 (15535) covalent geometry : angle 0.52130 (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 129 residues out of total 1634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 108 time to evaluate : 2.501 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 132 ASP cc_start: 0.9298 (t0) cc_final: 0.9026 (m-30) REVERT: A 176 GLU cc_start: 0.8302 (pm20) cc_final: 0.8067 (pm20) REVERT: A 207 ASN cc_start: 0.8364 (t0) cc_final: 0.8060 (t0) REVERT: A 321 ARG cc_start: 0.8497 (mtm110) cc_final: 0.7854 (ttp-110) REVERT: A 582 ASP cc_start: 0.8985 (t0) cc_final: 0.8660 (t0) REVERT: A 607 GLU cc_start: 0.8991 (OUTLIER) cc_final: 0.8745 (mt-10) REVERT: C 155 GLU cc_start: 0.7677 (tp30) cc_final: 0.7288 (tm-30) REVERT: C 160 ARG cc_start: 0.7349 (OUTLIER) cc_final: 0.7070 (mtp-110) REVERT: C 194 MET cc_start: 0.8487 (mtp) cc_final: 0.8202 (mtp) REVERT: F 71 MET cc_start: 0.8863 (tpp) cc_final: 0.8048 (tmt) REVERT: F 114 MET cc_start: 0.3414 (tpp) cc_final: 0.3029 (tpp) REVERT: F 167 GLN cc_start: 0.7820 (mm110) cc_final: 0.7405 (tm-30) REVERT: F 400 MET cc_start: 0.8236 (mtp) cc_final: 0.8035 (mmm) outliers start: 21 outliers final: 15 residues processed: 122 average time/residue: 2.6933 time to fit residues: 370.1044 Evaluate side-chains 124 residues out of total 1634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 107 time to evaluate : 2.659 ------------------------------------------------------------------------------- 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 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 331 VAL Chi-restraints excluded: chain C residue 160 ARG 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 178 HIS 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: 0.9990 chunk 97 optimal weight: 3.9990 chunk 35 optimal weight: 1.9990 chunk 107 optimal weight: 10.0000 chunk 88 optimal weight: 2.9990 chunk 17 optimal weight: 3.9990 chunk 102 optimal weight: 4.9990 chunk 174 optimal weight: 6.9990 chunk 129 optimal weight: 5.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- 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 = 0.4063 r_free = 0.4063 target = 0.130608 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.073008 restraints weight = 86453.223| |-----------------------------------------------------------------------------| r_work (start): 0.3079 rms_B_bonded: 3.24 r_work: 0.2920 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work: 0.2785 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.2785 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8132 moved from start: 0.3142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 15536 Z= 0.187 Angle : 0.505 6.766 21092 Z= 0.267 Chirality : 0.042 0.143 2317 Planarity : 0.004 0.053 2791 Dihedral : 4.239 50.552 2137 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 1.29 % Allowed : 15.85 % 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: 0.33 (0.19), residues: 1939 helix: 2.20 (0.22), residues: 535 sheet: -0.49 (0.22), residues: 520 loop : -0.52 (0.21), residues: 884 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 0.020 0.001 PHE F 212 TYR 0.018 0.001 TYR F 422 ARG 0.003 0.000 ARG D 112 Details of bonding type rmsd hydrogen bonds : bond 0.03636 ( 722) hydrogen bonds : angle 4.44523 ( 2070) SS BOND : bond 0.00053 ( 1) SS BOND : angle 0.18893 ( 2) covalent geometry : bond 0.00421 (15535) covalent geometry : angle 0.50521 (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 129 residues out of total 1634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 108 time to evaluate : 2.477 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 132 ASP cc_start: 0.9292 (t0) cc_final: 0.9026 (m-30) REVERT: A 176 GLU cc_start: 0.8295 (pm20) cc_final: 0.8053 (pm20) REVERT: A 207 ASN cc_start: 0.8356 (t0) cc_final: 0.8060 (t0) REVERT: A 321 ARG cc_start: 0.8482 (mtm110) cc_final: 0.7844 (ttp-110) REVERT: A 582 ASP cc_start: 0.8997 (t0) cc_final: 0.8662 (t0) REVERT: A 607 GLU cc_start: 0.8996 (OUTLIER) cc_final: 0.8749 (mt-10) REVERT: C 155 GLU cc_start: 0.7651 (tp30) cc_final: 0.7331 (tm-30) REVERT: C 160 ARG cc_start: 0.7397 (OUTLIER) cc_final: 0.7121 (mtp-110) REVERT: C 194 MET cc_start: 0.8469 (mtp) cc_final: 0.8197 (mtp) REVERT: D 56 GLU cc_start: 0.8854 (mt-10) cc_final: 0.8612 (mt-10) REVERT: F 71 MET cc_start: 0.8866 (tpp) cc_final: 0.8573 (tpt) REVERT: F 125 TYR cc_start: 0.6844 (OUTLIER) cc_final: 0.6575 (t80) REVERT: F 167 GLN cc_start: 0.7834 (mm110) cc_final: 0.7427 (tm-30) REVERT: F 400 MET cc_start: 0.8242 (mtp) cc_final: 0.8040 (mmm) outliers start: 21 outliers final: 12 residues processed: 122 average time/residue: 2.5004 time to fit residues: 344.5180 Evaluate side-chains 121 residues out of total 1634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 106 time to evaluate : 2.569 ------------------------------------------------------------------------------- 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 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 331 VAL Chi-restraints excluded: chain C residue 160 ARG 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 125 TYR 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: 1.9990 chunk 149 optimal weight: 1.9990 chunk 12 optimal weight: 5.9990 chunk 179 optimal weight: 30.0000 chunk 7 optimal weight: 2.9990 chunk 20 optimal weight: 3.9990 chunk 143 optimal weight: 0.6980 chunk 158 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 chunk 169 optimal weight: 30.0000 chunk 146 optimal weight: 2.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- 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 = 0.4066 r_free = 0.4066 target = 0.131342 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.073437 restraints weight = 85740.031| |-----------------------------------------------------------------------------| r_work (start): 0.3081 rms_B_bonded: 3.28 r_work: 0.2923 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work: 0.2786 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.2786 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8125 moved from start: 0.3233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 15536 Z= 0.176 Angle : 0.505 8.305 21092 Z= 0.266 Chirality : 0.042 0.195 2317 Planarity : 0.003 0.052 2791 Dihedral : 4.211 48.171 2137 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 1.10 % Allowed : 16.34 % Favored : 82.56 % 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: 0.36 (0.19), residues: 1939 helix: 2.26 (0.22), residues: 535 sheet: -0.50 (0.22), residues: 520 loop : -0.50 (0.21), residues: 884 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 0.025 0.001 PHE F 212 TYR 0.018 0.001 TYR D 184 ARG 0.002 0.000 ARG D 173 Details of bonding type rmsd hydrogen bonds : bond 0.03579 ( 722) hydrogen bonds : angle 4.42221 ( 2070) SS BOND : bond 0.00050 ( 1) SS BOND : angle 0.18241 ( 2) covalent geometry : bond 0.00396 (15535) covalent geometry : angle 0.50494 (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 124 residues out of total 1634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 106 time to evaluate : 2.357 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 132 ASP cc_start: 0.9285 (t0) cc_final: 0.9013 (m-30) REVERT: A 176 GLU cc_start: 0.8302 (pm20) cc_final: 0.8061 (pm20) REVERT: A 207 ASN cc_start: 0.8353 (t0) cc_final: 0.8081 (t160) REVERT: A 321 ARG cc_start: 0.8500 (mtm110) cc_final: 0.7865 (ttp-110) REVERT: A 582 ASP cc_start: 0.8978 (t0) cc_final: 0.8641 (t0) REVERT: A 607 GLU cc_start: 0.8981 (OUTLIER) cc_final: 0.8737 (mt-10) REVERT: B 278 MET cc_start: 0.8607 (mtt) cc_final: 0.8000 (mpm) REVERT: C 155 GLU cc_start: 0.7628 (tp30) cc_final: 0.7323 (tm-30) REVERT: C 160 ARG cc_start: 0.7407 (OUTLIER) cc_final: 0.7118 (mtp-110) REVERT: C 194 MET cc_start: 0.8472 (mtp) cc_final: 0.8197 (mtp) REVERT: F 71 MET cc_start: 0.8852 (tpp) cc_final: 0.8547 (tpt) REVERT: F 125 TYR cc_start: 0.6760 (OUTLIER) cc_final: 0.6467 (t80) REVERT: F 167 GLN cc_start: 0.7823 (mm110) cc_final: 0.7415 (tm-30) outliers start: 18 outliers final: 11 residues processed: 117 average time/residue: 2.6447 time to fit residues: 353.9649 Evaluate side-chains 119 residues out of total 1634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 105 time to evaluate : 2.515 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 243 THR 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 331 VAL Chi-restraints excluded: chain C residue 160 ARG 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 125 TYR 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 108 optimal weight: 0.9980 chunk 12 optimal weight: 5.9990 chunk 153 optimal weight: 2.9990 chunk 20 optimal weight: 2.9990 chunk 151 optimal weight: 0.8980 chunk 190 optimal weight: 20.0000 chunk 5 optimal weight: 20.0000 chunk 35 optimal weight: 2.9990 chunk 73 optimal weight: 0.5980 chunk 175 optimal weight: 5.9990 chunk 39 optimal weight: 0.7980 overall best weight: 1.2582 ------------------------------------------------------------------------------- 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 = 0.4077 r_free = 0.4077 target = 0.131836 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.073936 restraints weight = 86313.691| |-----------------------------------------------------------------------------| r_work (start): 0.3096 rms_B_bonded: 3.28 r_work: 0.2938 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work: 0.2807 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.2807 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8114 moved from start: 0.3303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 15536 Z= 0.128 Angle : 0.491 8.164 21092 Z= 0.257 Chirality : 0.042 0.163 2317 Planarity : 0.003 0.051 2791 Dihedral : 4.106 45.518 2137 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 3.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 0.73 % Allowed : 16.89 % 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: 0.48 (0.19), residues: 1939 helix: 2.32 (0.22), residues: 535 sheet: -0.42 (0.22), residues: 507 loop : -0.42 (0.21), residues: 897 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 745 HIS 0.002 0.000 HIS D 102 PHE 0.025 0.001 PHE F 212 TYR 0.018 0.001 TYR D 184 ARG 0.003 0.000 ARG D 112 Details of bonding type rmsd hydrogen bonds : bond 0.03395 ( 722) hydrogen bonds : angle 4.31012 ( 2070) SS BOND : bond 0.00010 ( 1) SS BOND : angle 0.23367 ( 2) covalent geometry : bond 0.00286 (15535) covalent geometry : angle 0.49073 (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: 12 poor density : 110 time to evaluate : 2.288 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 132 ASP cc_start: 0.9275 (t0) cc_final: 0.9008 (m-30) REVERT: A 176 GLU cc_start: 0.8310 (pm20) cc_final: 0.8056 (pm20) REVERT: A 207 ASN cc_start: 0.8345 (t0) cc_final: 0.8068 (t160) REVERT: A 321 ARG cc_start: 0.8492 (mtm110) cc_final: 0.7856 (ttp-110) REVERT: A 582 ASP cc_start: 0.8971 (t0) cc_final: 0.8639 (t0) REVERT: A 607 GLU cc_start: 0.8969 (OUTLIER) cc_final: 0.8706 (mt-10) REVERT: B 278 MET cc_start: 0.8611 (mtt) cc_final: 0.7991 (mpm) REVERT: C 91 LEU cc_start: 0.7764 (OUTLIER) cc_final: 0.7535 (mm) REVERT: C 155 GLU cc_start: 0.7661 (tp30) cc_final: 0.7326 (tm-30) REVERT: C 160 ARG cc_start: 0.7423 (OUTLIER) cc_final: 0.7136 (mtp-110) REVERT: C 194 MET cc_start: 0.8440 (mtp) cc_final: 0.8159 (mtp) REVERT: D 232 GLU cc_start: 0.8814 (mm-30) cc_final: 0.8443 (mp0) REVERT: F 71 MET cc_start: 0.8853 (tpp) cc_final: 0.8552 (tpt) REVERT: F 167 GLN cc_start: 0.7829 (mm110) cc_final: 0.7413 (tm-30) outliers start: 12 outliers final: 9 residues processed: 117 average time/residue: 2.5272 time to fit residues: 331.1873 Evaluate side-chains 117 residues out of total 1634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 105 time to evaluate : 2.243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 91 LEU Chi-restraints excluded: chain C residue 160 ARG 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 94 optimal weight: 0.9980 chunk 182 optimal weight: 0.3980 chunk 159 optimal weight: 0.9980 chunk 61 optimal weight: 0.9990 chunk 85 optimal weight: 1.9990 chunk 143 optimal weight: 0.3980 chunk 29 optimal weight: 1.9990 chunk 82 optimal weight: 3.9990 chunk 10 optimal weight: 1.9990 chunk 169 optimal weight: 30.0000 chunk 142 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 = 0.4086 r_free = 0.4086 target = 0.132427 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.075037 restraints weight = 85459.496| |-----------------------------------------------------------------------------| r_work (start): 0.3119 rms_B_bonded: 3.25 r_work: 0.2960 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work: 0.2831 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.2831 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8095 moved from start: 0.3352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.054 15536 Z= 0.101 Angle : 0.485 9.637 21092 Z= 0.253 Chirality : 0.041 0.148 2317 Planarity : 0.003 0.050 2791 Dihedral : 3.996 41.979 2137 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 3.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 0.80 % Allowed : 17.07 % Favored : 82.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.56 (0.19), residues: 1939 helix: 2.39 (0.22), residues: 535 sheet: -0.35 (0.22), residues: 502 loop : -0.38 (0.21), residues: 902 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 348 HIS 0.002 0.000 HIS F 266 PHE 0.026 0.001 PHE F 212 TYR 0.022 0.001 TYR F 422 ARG 0.004 0.000 ARG F 147 Details of bonding type rmsd hydrogen bonds : bond 0.03219 ( 722) hydrogen bonds : angle 4.20504 ( 2070) SS BOND : bond 0.00029 ( 1) SS BOND : angle 0.32672 ( 2) covalent geometry : bond 0.00228 (15535) covalent geometry : angle 0.48541 (21090) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 28501.03 seconds wall clock time: 497 minutes 55.22 seconds (29875.22 seconds total)