Starting phenix.real_space_refine on Mon Jun 16 11:00:13 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8yf5_39211/06_2025/8yf5_39211.cif Found real_map, /net/cci-nas-00/data/ceres_data/8yf5_39211/06_2025/8yf5_39211.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.78 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8yf5_39211/06_2025/8yf5_39211.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8yf5_39211/06_2025/8yf5_39211.map" model { file = "/net/cci-nas-00/data/ceres_data/8yf5_39211/06_2025/8yf5_39211.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8yf5_39211/06_2025/8yf5_39211.cif" } resolution = 3.78 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= 0.000 sd= 0.004 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: 4 Type Number sf(0) Gaussians S 69 5.16 5 C 11848 2.51 5 N 3142 2.21 5 O 3417 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 14 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: 18476 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 5640 Number of conformers: 1 Conformer: "" Number of residues, atoms: 685, 5640 Classifications: {'peptide': 685} Link IDs: {'PTRANS': 45, 'TRANS': 639} Chain breaks: 4 Chain: "B" Number of atoms: 3122 Number of conformers: 1 Conformer: "" Number of residues, atoms: 381, 3122 Classifications: {'peptide': 381} Link IDs: {'PTRANS': 16, 'TRANS': 364} Chain: "C" Number of atoms: 5536 Number of conformers: 1 Conformer: "" Number of residues, atoms: 674, 5536 Classifications: {'peptide': 674} Link IDs: {'PTRANS': 43, 'TRANS': 630} Chain breaks: 5 Chain: "D" Number of atoms: 3114 Number of conformers: 1 Conformer: "" Number of residues, atoms: 380, 3114 Classifications: {'peptide': 380} Link IDs: {'PTRANS': 16, 'TRANS': 363} Chain: "E" Number of atoms: 1064 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 1064 Classifications: {'peptide': 130} Link IDs: {'PTRANS': 3, 'TRANS': 126} Time building chain proxies: 10.32, per 1000 atoms: 0.56 Number of scatterers: 18476 At special positions: 0 Unit cell: (152.388, 141.93, 125.496, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 69 16.00 O 3417 8.00 N 3142 7.00 C 11848 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 4.40 Conformation dependent library (CDL) restraints added in 2.3 seconds 4444 Ramachandran restraints generated. 2222 Oldfield, 0 Emsley, 2222 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4298 Finding SS restraints... Secondary structure from input PDB file: 99 helices and 14 sheets defined 50.2% alpha, 10.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.04 Creating SS restraints... Processing helix chain 'A' and resid 5 through 14 removed outlier: 3.698A pdb=" N TRP A 9 " --> pdb=" O ALA A 5 " (cutoff:3.500A) Processing helix chain 'A' and resid 28 through 32 removed outlier: 3.634A pdb=" N GLY A 31 " --> pdb=" O ASP A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 57 No H-bonds generated for 'chain 'A' and resid 55 through 57' Processing helix chain 'A' and resid 72 through 92 removed outlier: 3.661A pdb=" N MET A 76 " --> pdb=" O THR A 72 " (cutoff:3.500A) Processing helix chain 'A' and resid 106 through 129 removed outlier: 3.624A pdb=" N MET A 110 " --> pdb=" O PRO A 106 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N ASN A 111 " --> pdb=" O ARG A 107 " (cutoff:3.500A) removed outlier: 4.938A pdb=" N GLN A 112 " --> pdb=" O ALA A 108 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N GLN A 113 " --> pdb=" O LYS A 109 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N SER A 115 " --> pdb=" O ASN A 111 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N SER A 120 " --> pdb=" O ARG A 116 " (cutoff:3.500A) Processing helix chain 'A' and resid 156 through 160 Processing helix chain 'A' and resid 164 through 185 removed outlier: 3.670A pdb=" N HIS A 168 " --> pdb=" O THR A 164 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N ASP A 172 " --> pdb=" O HIS A 168 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ARG A 175 " --> pdb=" O ALA A 171 " (cutoff:3.500A) Processing helix chain 'A' and resid 186 through 189 removed outlier: 3.589A pdb=" N SER A 189 " --> pdb=" O PRO A 186 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 186 through 189' Processing helix chain 'A' and resid 203 through 217 removed outlier: 3.782A pdb=" N ILE A 208 " --> pdb=" O GLY A 204 " (cutoff:3.500A) Processing helix chain 'A' and resid 235 through 244 removed outlier: 3.801A pdb=" N THR A 243 " --> pdb=" O LEU A 239 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N HIS A 244 " --> pdb=" O GLY A 240 " (cutoff:3.500A) Processing helix chain 'A' and resid 254 through 259 removed outlier: 4.121A pdb=" N ASP A 259 " --> pdb=" O VAL A 255 " (cutoff:3.500A) Processing helix chain 'A' and resid 291 through 302 Processing helix chain 'A' and resid 312 through 327 removed outlier: 3.887A pdb=" N ASP A 318 " --> pdb=" O GLU A 314 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N PHE A 326 " --> pdb=" O PHE A 322 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N CYS A 327 " --> pdb=" O ILE A 323 " (cutoff:3.500A) Processing helix chain 'A' and resid 343 through 356 Processing helix chain 'A' and resid 370 through 407 removed outlier: 3.565A pdb=" N ARG A 376 " --> pdb=" O PRO A 372 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N LYS A 384 " --> pdb=" O GLU A 380 " (cutoff:3.500A) removed outlier: 4.863A pdb=" N ASP A 386 " --> pdb=" O ALA A 382 " (cutoff:3.500A) removed outlier: 4.813A pdb=" N TYR A 387 " --> pdb=" O LYS A 383 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N LYS A 391 " --> pdb=" O TYR A 387 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ARG A 392 " --> pdb=" O ILE A 388 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N TYR A 393 " --> pdb=" O PHE A 389 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N GLU A 396 " --> pdb=" O ARG A 392 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N GLN A 403 " --> pdb=" O SER A 399 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N LYS A 404 " --> pdb=" O LEU A 400 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N ARG A 405 " --> pdb=" O GLU A 401 " (cutoff:3.500A) Processing helix chain 'A' and resid 541 through 552 removed outlier: 4.273A pdb=" N TYR A 547 " --> pdb=" O ARG A 543 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N GLU A 548 " --> pdb=" O LYS A 544 " (cutoff:3.500A) Processing helix chain 'A' and resid 555 through 581 Processing helix chain 'A' and resid 599 through 603 Processing helix chain 'A' and resid 605 through 609 Processing helix chain 'A' and resid 620 through 629 Processing helix chain 'A' and resid 630 through 634 removed outlier: 3.536A pdb=" N SER A 633 " --> pdb=" O PRO A 630 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N SER A 634 " --> pdb=" O ALA A 631 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 630 through 634' Processing helix chain 'A' and resid 641 through 647 removed outlier: 3.500A pdb=" N MET A 645 " --> pdb=" O PHE A 641 " (cutoff:3.500A) Processing helix chain 'A' and resid 652 through 656 Processing helix chain 'A' and resid 669 through 673 Processing helix chain 'A' and resid 681 through 691 removed outlier: 3.613A pdb=" N LYS A 687 " --> pdb=" O ASN A 683 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N SER A 691 " --> pdb=" O LYS A 687 " (cutoff:3.500A) Processing helix chain 'A' and resid 692 through 696 Processing helix chain 'A' and resid 697 through 704 Processing helix chain 'A' and resid 719 through 728 removed outlier: 3.810A pdb=" N LEU A 723 " --> pdb=" O HIS A 719 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N VAL A 724 " --> pdb=" O TYR A 720 " (cutoff:3.500A) Processing helix chain 'A' and resid 812 through 819 Processing helix chain 'A' and resid 838 through 842 removed outlier: 3.540A pdb=" N TYR A 841 " --> pdb=" O PHE A 838 " (cutoff:3.500A) Processing helix chain 'A' and resid 856 through 864 Processing helix chain 'B' and resid 48 through 54 removed outlier: 3.839A pdb=" N ILE B 52 " --> pdb=" O PRO B 48 " (cutoff:3.500A) Processing helix chain 'B' and resid 61 through 65 Processing helix chain 'B' and resid 69 through 75 Processing helix chain 'B' and resid 76 through 91 Processing helix chain 'B' and resid 102 through 110 Processing helix chain 'B' and resid 135 through 148 Processing helix chain 'B' and resid 151 through 167 removed outlier: 3.547A pdb=" N ALA B 167 " --> pdb=" O PHE B 163 " (cutoff:3.500A) Processing helix chain 'B' and resid 172 through 176 Processing helix chain 'B' and resid 177 through 183 Processing helix chain 'B' and resid 184 through 187 Processing helix chain 'B' and resid 225 through 229 removed outlier: 4.259A pdb=" N ARG B 229 " --> pdb=" O ASP B 225 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 225 through 229' Processing helix chain 'B' and resid 241 through 261 Processing helix chain 'B' and resid 288 through 295 Processing helix chain 'B' and resid 306 through 326 removed outlier: 3.815A pdb=" N VAL B 326 " --> pdb=" O LEU B 322 " (cutoff:3.500A) Processing helix chain 'B' and resid 351 through 363 Processing helix chain 'B' and resid 364 through 380 Processing helix chain 'C' and resid 6 through 14 Processing helix chain 'C' and resid 54 through 59 Processing helix chain 'C' and resid 72 through 92 removed outlier: 3.625A pdb=" N MET C 76 " --> pdb=" O THR C 72 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N LEU C 78 " --> pdb=" O ASP C 74 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ASP C 79 " --> pdb=" O GLU C 75 " (cutoff:3.500A) Processing helix chain 'C' and resid 106 through 128 removed outlier: 3.852A pdb=" N ASN C 111 " --> pdb=" O ARG C 107 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N GLN C 112 " --> pdb=" O ALA C 108 " (cutoff:3.500A) Processing helix chain 'C' and resid 156 through 161 removed outlier: 4.024A pdb=" N ALA C 159 " --> pdb=" O ASP C 156 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N ILE C 160 " --> pdb=" O SER C 157 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N THR C 161 " --> pdb=" O ASN C 158 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 156 through 161' Processing helix chain 'C' and resid 164 through 184 removed outlier: 3.506A pdb=" N ASP C 172 " --> pdb=" O HIS C 168 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ARG C 175 " --> pdb=" O ALA C 171 " (cutoff:3.500A) Processing helix chain 'C' and resid 185 through 189 removed outlier: 3.708A pdb=" N SER C 189 " --> pdb=" O PRO C 186 " (cutoff:3.500A) Processing helix chain 'C' and resid 203 through 218 removed outlier: 3.533A pdb=" N ARG C 216 " --> pdb=" O VAL C 212 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N SER C 218 " --> pdb=" O SER C 214 " (cutoff:3.500A) Processing helix chain 'C' and resid 234 through 243 removed outlier: 4.483A pdb=" N PHE C 238 " --> pdb=" O ALA C 234 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N THR C 243 " --> pdb=" O LEU C 239 " (cutoff:3.500A) Processing helix chain 'C' and resid 291 through 302 Processing helix chain 'C' and resid 312 through 327 removed outlier: 3.781A pdb=" N PHE C 325 " --> pdb=" O VAL C 321 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N PHE C 326 " --> pdb=" O PHE C 322 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N CYS C 327 " --> pdb=" O ILE C 323 " (cutoff:3.500A) Processing helix chain 'C' and resid 339 through 342 Processing helix chain 'C' and resid 343 through 356 Processing helix chain 'C' and resid 357 through 359 No H-bonds generated for 'chain 'C' and resid 357 through 359' Processing helix chain 'C' and resid 370 through 378 Processing helix chain 'C' and resid 381 through 383 No H-bonds generated for 'chain 'C' and resid 381 through 383' Processing helix chain 'C' and resid 384 through 406 removed outlier: 3.642A pdb=" N LEU C 400 " --> pdb=" O GLU C 396 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N GLN C 403 " --> pdb=" O SER C 399 " (cutoff:3.500A) Processing helix chain 'C' and resid 541 through 552 removed outlier: 3.929A pdb=" N ARG C 545 " --> pdb=" O GLY C 541 " (cutoff:3.500A) Processing helix chain 'C' and resid 555 through 581 Processing helix chain 'C' and resid 599 through 603 removed outlier: 3.597A pdb=" N PHE C 603 " --> pdb=" O ALA C 600 " (cutoff:3.500A) Processing helix chain 'C' and resid 620 through 629 Processing helix chain 'C' and resid 638 through 647 removed outlier: 4.207A pdb=" N SER C 643 " --> pdb=" O ASP C 639 " (cutoff:3.500A) removed outlier: 4.631A pdb=" N LEU C 644 " --> pdb=" O VAL C 640 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N MET C 645 " --> pdb=" O PHE C 641 " (cutoff:3.500A) Processing helix chain 'C' and resid 652 through 656 Processing helix chain 'C' and resid 681 through 690 removed outlier: 3.524A pdb=" N ALA C 688 " --> pdb=" O ARG C 684 " (cutoff:3.500A) Processing helix chain 'C' and resid 697 through 703 Processing helix chain 'C' and resid 718 through 728 removed outlier: 4.448A pdb=" N THR C 722 " --> pdb=" O SER C 718 " (cutoff:3.500A) Processing helix chain 'C' and resid 810 through 819 removed outlier: 3.751A pdb=" N ILE C 817 " --> pdb=" O ASP C 813 " (cutoff:3.500A) Processing helix chain 'C' and resid 856 through 867 removed outlier: 3.629A pdb=" N ASP C 866 " --> pdb=" O GLN C 862 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N GLU C 867 " --> pdb=" O ILE C 863 " (cutoff:3.500A) Processing helix chain 'D' and resid 48 through 54 removed outlier: 3.955A pdb=" N ILE D 52 " --> pdb=" O PRO D 48 " (cutoff:3.500A) Processing helix chain 'D' and resid 61 through 65 Processing helix chain 'D' and resid 69 through 75 removed outlier: 3.587A pdb=" N LYS D 75 " --> pdb=" O VAL D 71 " (cutoff:3.500A) Processing helix chain 'D' and resid 76 through 91 Processing helix chain 'D' and resid 102 through 111 Processing helix chain 'D' and resid 135 through 149 Processing helix chain 'D' and resid 150 through 167 removed outlier: 4.040A pdb=" N LYS D 154 " --> pdb=" O THR D 150 " (cutoff:3.500A) Processing helix chain 'D' and resid 172 through 176 Processing helix chain 'D' and resid 177 through 183 Processing helix chain 'D' and resid 225 through 229 removed outlier: 4.143A pdb=" N ARG D 229 " --> pdb=" O ASP D 225 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 225 through 229' Processing helix chain 'D' and resid 241 through 263 Processing helix chain 'D' and resid 287 through 295 removed outlier: 4.523A pdb=" N LEU D 291 " --> pdb=" O ASN D 287 " (cutoff:3.500A) Processing helix chain 'D' and resid 306 through 326 removed outlier: 3.817A pdb=" N SER D 310 " --> pdb=" O ASN D 306 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N VAL D 326 " --> pdb=" O LEU D 322 " (cutoff:3.500A) Processing helix chain 'D' and resid 351 through 363 Processing helix chain 'D' and resid 364 through 380 removed outlier: 3.886A pdb=" N GLY D 379 " --> pdb=" O ARG D 375 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N ASN D 380 " --> pdb=" O ASN D 376 " (cutoff:3.500A) Processing helix chain 'E' and resid 4 through 14 removed outlier: 3.501A pdb=" N VAL E 8 " --> pdb=" O SER E 4 " (cutoff:3.500A) Processing helix chain 'E' and resid 18 through 32 removed outlier: 3.563A pdb=" N ILE E 22 " --> pdb=" O THR E 18 " (cutoff:3.500A) Processing helix chain 'E' and resid 35 through 50 Processing helix chain 'E' and resid 53 through 71 Processing helix chain 'E' and resid 73 through 82 removed outlier: 4.010A pdb=" N LEU E 77 " --> pdb=" O LYS E 73 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N ASP E 78 " --> pdb=" O THR E 74 " (cutoff:3.500A) Processing helix chain 'E' and resid 83 through 92 Processing helix chain 'E' and resid 93 through 95 No H-bonds generated for 'chain 'E' and resid 93 through 95' Processing helix chain 'E' and resid 96 through 113 Processing helix chain 'E' and resid 117 through 128 Processing sheet with id=AA1, first strand: chain 'A' and resid 18 through 20 removed outlier: 6.551A pdb=" N ILE A 229 " --> pdb=" O LEU A 251 " (cutoff:3.500A) removed outlier: 8.729A pdb=" N GLU A 253 " --> pdb=" O ILE A 229 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N TYR A 51 " --> pdb=" O TYR A 230 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N GLU A 709 " --> pdb=" O PHE A 786 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 364 through 365 Processing sheet with id=AA3, first strand: chain 'A' and resid 662 through 663 Processing sheet with id=AA4, first strand: chain 'A' and resid 759 through 760 Processing sheet with id=AA5, first strand: chain 'B' and resid 4 through 8 removed outlier: 3.844A pdb=" N VAL B 345 " --> pdb=" O SER B 335 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N SER B 335 " --> pdb=" O VAL B 345 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N PHE B 119 " --> pdb=" O TYR B 336 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N ILE B 99 " --> pdb=" O ILE B 132 " (cutoff:3.500A) removed outlier: 8.822A pdb=" N PHE B 134 " --> pdb=" O ILE B 99 " (cutoff:3.500A) removed outlier: 10.122A pdb=" N TRP B 101 " --> pdb=" O PHE B 134 " (cutoff:3.500A) removed outlier: 5.945A pdb=" N ILE B 98 " --> pdb=" O LEU B 209 " (cutoff:3.500A) removed outlier: 7.859A pdb=" N GLY B 211 " --> pdb=" O ILE B 98 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N THR B 100 " --> pdb=" O GLY B 211 " (cutoff:3.500A) removed outlier: 9.256A pdb=" N ALA B 213 " --> pdb=" O THR B 100 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N TYR B 195 " --> pdb=" O VAL B 214 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLN B 194 " --> pdb=" O ARG B 29 " (cutoff:3.500A) removed outlier: 5.957A pdb=" N ARG B 200 " --> pdb=" O GLN B 23 " (cutoff:3.500A) removed outlier: 5.486A pdb=" N GLN B 23 " --> pdb=" O ARG B 200 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 44 through 45 Processing sheet with id=AA7, first strand: chain 'B' and resid 216 through 217 removed outlier: 4.452A pdb=" N LYS B 266 " --> pdb=" O TYR B 230 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N GLU B 232 " --> pdb=" O LYS B 266 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N ILE B 267 " --> pdb=" O GLU B 283 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N GLU B 283 " --> pdb=" O ILE B 267 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N TYR B 269 " --> pdb=" O VAL B 281 " (cutoff:3.500A) removed outlier: 4.643A pdb=" N VAL B 281 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N PHE B 271 " --> pdb=" O ARG B 279 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 18 through 20 removed outlier: 6.513A pdb=" N HIS C 227 " --> pdb=" O LYS C 249 " (cutoff:3.500A) removed outlier: 7.798A pdb=" N LEU C 251 " --> pdb=" O HIS C 227 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N ILE C 229 " --> pdb=" O LEU C 251 " (cutoff:3.500A) removed outlier: 8.758A pdb=" N GLU C 253 " --> pdb=" O ILE C 229 " (cutoff:3.500A) removed outlier: 7.057A pdb=" N ASP C 48 " --> pdb=" O ARG C 94 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N VAL C 193 " --> pdb=" O VAL C 712 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 364 through 365 Processing sheet with id=AB1, first strand: chain 'C' and resid 662 through 663 Processing sheet with id=AB2, first strand: chain 'C' and resid 759 through 760 Processing sheet with id=AB3, first strand: chain 'D' and resid 5 through 8 removed outlier: 3.732A pdb=" N VAL D 123 " --> pdb=" O TRP D 332 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N PHE D 119 " --> pdb=" O TYR D 336 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N ILE D 99 " --> pdb=" O ILE D 132 " (cutoff:3.500A) removed outlier: 8.981A pdb=" N PHE D 134 " --> pdb=" O ILE D 99 " (cutoff:3.500A) removed outlier: 10.446A pdb=" N TRP D 101 " --> pdb=" O PHE D 134 " (cutoff:3.500A) removed outlier: 5.826A pdb=" N ILE D 98 " --> pdb=" O LEU D 209 " (cutoff:3.500A) removed outlier: 7.539A pdb=" N GLY D 211 " --> pdb=" O ILE D 98 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N THR D 100 " --> pdb=" O GLY D 211 " (cutoff:3.500A) removed outlier: 9.134A pdb=" N ALA D 213 " --> pdb=" O THR D 100 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N TYR D 195 " --> pdb=" O VAL D 214 " (cutoff:3.500A) removed outlier: 5.830A pdb=" N ARG D 200 " --> pdb=" O GLN D 23 " (cutoff:3.500A) removed outlier: 5.095A pdb=" N GLN D 23 " --> pdb=" O ARG D 200 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 44 through 45 Processing sheet with id=AB5, first strand: chain 'D' and resid 216 through 217 removed outlier: 3.586A pdb=" N CYS D 216 " --> pdb=" O ILE D 231 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N TYR D 230 " --> pdb=" O LYS D 266 " (cutoff:3.500A) removed outlier: 8.126A pdb=" N ILE D 268 " --> pdb=" O TYR D 230 " (cutoff:3.500A) removed outlier: 6.210A pdb=" N GLU D 232 " --> pdb=" O ILE D 268 " (cutoff:3.500A) removed outlier: 7.671A pdb=" N GLY D 270 " --> pdb=" O GLU D 232 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N LYS D 234 " --> pdb=" O GLY D 270 " (cutoff:3.500A) removed outlier: 7.611A pdb=" N ARG D 272 " --> pdb=" O LYS D 234 " (cutoff:3.500A) removed outlier: 5.786A pdb=" N THR D 236 " --> pdb=" O ARG D 272 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N ILE D 267 " --> pdb=" O GLU D 283 " (cutoff:3.500A) removed outlier: 4.895A pdb=" N GLU D 283 " --> pdb=" O ILE D 267 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N TYR D 269 " --> pdb=" O VAL D 281 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N VAL D 281 " --> pdb=" O TYR D 269 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N PHE D 271 " --> pdb=" O ARG D 279 " (cutoff:3.500A) 824 hydrogen bonds defined for protein. 2328 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.62 Time building geometry restraints manager: 5.21 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3786 1.33 - 1.45: 4473 1.45 - 1.57: 10559 1.57 - 1.69: 0 1.69 - 1.81: 115 Bond restraints: 18933 Sorted by residual: bond pdb=" CA CYS C 324 " pdb=" C CYS C 324 " ideal model delta sigma weight residual 1.523 1.497 0.026 1.80e-02 3.09e+03 2.08e+00 bond pdb=" CD GLN E 67 " pdb=" OE1 GLN E 67 " ideal model delta sigma weight residual 1.231 1.206 0.025 1.90e-02 2.77e+03 1.73e+00 bond pdb=" CA ILE C 22 " pdb=" CB ILE C 22 " ideal model delta sigma weight residual 1.540 1.524 0.016 1.36e-02 5.41e+03 1.33e+00 bond pdb=" C LEU E 84 " pdb=" N PRO E 85 " ideal model delta sigma weight residual 1.335 1.351 -0.015 1.36e-02 5.41e+03 1.29e+00 bond pdb=" C TYR A 14 " pdb=" N PRO A 15 " ideal model delta sigma weight residual 1.336 1.323 0.013 1.20e-02 6.94e+03 1.15e+00 ... (remaining 18928 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.50: 25061 1.50 - 3.01: 412 3.01 - 4.51: 87 4.51 - 6.01: 33 6.01 - 7.52: 6 Bond angle restraints: 25599 Sorted by residual: angle pdb=" N VAL A 628 " pdb=" CA VAL A 628 " pdb=" C VAL A 628 " ideal model delta sigma weight residual 113.53 109.46 4.07 9.80e-01 1.04e+00 1.72e+01 angle pdb=" CA ARG D 341 " pdb=" CB ARG D 341 " pdb=" CG ARG D 341 " ideal model delta sigma weight residual 114.10 121.62 -7.52 2.00e+00 2.50e-01 1.41e+01 angle pdb=" N GLN E 67 " pdb=" CA GLN E 67 " pdb=" CB GLN E 67 " ideal model delta sigma weight residual 110.40 116.28 -5.88 1.63e+00 3.76e-01 1.30e+01 angle pdb=" C GLN E 66 " pdb=" N GLN E 67 " pdb=" CA GLN E 67 " ideal model delta sigma weight residual 121.14 115.23 5.91 1.75e+00 3.27e-01 1.14e+01 angle pdb=" C TYR E 125 " pdb=" N GLN E 126 " pdb=" CA GLN E 126 " ideal model delta sigma weight residual 120.72 115.55 5.17 1.67e+00 3.59e-01 9.59e+00 ... (remaining 25594 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.41: 10275 17.41 - 34.81: 977 34.81 - 52.22: 191 52.22 - 69.63: 31 69.63 - 87.04: 12 Dihedral angle restraints: 11486 sinusoidal: 4837 harmonic: 6649 Sorted by residual: dihedral pdb=" CA VAL C 669 " pdb=" C VAL C 669 " pdb=" N ILE C 670 " pdb=" CA ILE C 670 " ideal model delta harmonic sigma weight residual -180.00 -162.12 -17.88 0 5.00e+00 4.00e-02 1.28e+01 dihedral pdb=" CA MET E 95 " pdb=" C MET E 95 " pdb=" N ILE E 96 " pdb=" CA ILE E 96 " ideal model delta harmonic sigma weight residual -180.00 -162.29 -17.71 0 5.00e+00 4.00e-02 1.25e+01 dihedral pdb=" CA ASP C 30 " pdb=" CB ASP C 30 " pdb=" CG ASP C 30 " pdb=" OD1 ASP C 30 " ideal model delta sinusoidal sigma weight residual -30.00 -89.28 59.28 1 2.00e+01 2.50e-03 1.17e+01 ... (remaining 11483 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 2005 0.042 - 0.084: 535 0.084 - 0.126: 175 0.126 - 0.168: 8 0.168 - 0.210: 2 Chirality restraints: 2725 Sorted by residual: chirality pdb=" CB ILE E 115 " pdb=" CA ILE E 115 " pdb=" CG1 ILE E 115 " pdb=" CG2 ILE E 115 " both_signs ideal model delta sigma weight residual False 2.64 2.43 0.21 2.00e-01 2.50e+01 1.11e+00 chirality pdb=" CA TYR E 125 " pdb=" N TYR E 125 " pdb=" C TYR E 125 " pdb=" CB TYR E 125 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.62e-01 chirality pdb=" CA ARG D 341 " pdb=" N ARG D 341 " pdb=" C ARG D 341 " pdb=" CB ARG D 341 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.64e-01 ... (remaining 2722 not shown) Planarity restraints: 3289 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP E 110 " 0.031 2.00e-02 2.50e+03 2.98e-02 2.21e+01 pdb=" CG TRP E 110 " -0.081 2.00e-02 2.50e+03 pdb=" CD1 TRP E 110 " 0.036 2.00e-02 2.50e+03 pdb=" CD2 TRP E 110 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP E 110 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP E 110 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP E 110 " 0.010 2.00e-02 2.50e+03 pdb=" CZ2 TRP E 110 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP E 110 " 0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP E 110 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU A 637 " -0.030 5.00e-02 4.00e+02 4.62e-02 3.41e+00 pdb=" N PRO A 638 " 0.080 5.00e-02 4.00e+02 pdb=" CA PRO A 638 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO A 638 " -0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS A 67 " 0.023 5.00e-02 4.00e+02 3.54e-02 2.01e+00 pdb=" N PRO A 68 " -0.061 5.00e-02 4.00e+02 pdb=" CA PRO A 68 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO A 68 " 0.020 5.00e-02 4.00e+02 ... (remaining 3286 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 335 2.66 - 3.22: 18288 3.22 - 3.78: 29637 3.78 - 4.34: 39142 4.34 - 4.90: 62432 Nonbonded interactions: 149834 Sorted by model distance: nonbonded pdb=" O MET C 626 " pdb=" OH TYR C 656 " model vdw 2.098 3.040 nonbonded pdb=" OH TYR A 850 " pdb=" OH TYR B 45 " model vdw 2.156 3.040 nonbonded pdb=" OH TYR C 850 " pdb=" OH TYR D 45 " model vdw 2.169 3.040 nonbonded pdb=" OH TYR C 596 " pdb=" OD2 ASP C 663 " model vdw 2.198 3.040 nonbonded pdb=" OH TYR A 596 " pdb=" OD2 ASP A 663 " model vdw 2.209 3.040 ... (remaining 149829 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 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 5 through 63 or resid 69 through 129 or resid 156 through \ 257 or resid 283 through 407 or resid 532 through 824 or resid 834 through 864)) \ selection = (chain 'C' and resid 5 through 864) } ncs_group { reference = (chain 'B' and resid 1 through 380) selection = chain 'D' } 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 group one per residue 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: 0.480 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: 0.010 Extract box with map and model: 0.670 Check model and map are aligned: 0.130 Set scattering table: 0.170 Process input model: 40.290 Find NCS groups from input model: 0.630 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:2.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.440 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8377 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 : 0.003 0.028 18933 Z= 0.147 Angle : 0.530 7.517 25599 Z= 0.269 Chirality : 0.041 0.210 2725 Planarity : 0.003 0.050 3289 Dihedral : 13.978 87.035 7188 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 11.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 0.00 % Allowed : 0.29 % Favored : 99.71 % 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: 1.15 (0.19), residues: 2222 helix: 1.49 (0.18), residues: 937 sheet: 0.08 (0.32), residues: 270 loop : 0.41 (0.21), residues: 1015 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.081 0.001 TRP E 110 HIS 0.003 0.001 HIS C 717 PHE 0.013 0.001 PHE B 152 TYR 0.018 0.001 TYR B 269 ARG 0.007 0.000 ARG E 69 Details of bonding type rmsd hydrogen bonds : bond 0.22628 ( 824) hydrogen bonds : angle 7.24057 ( 2328) covalent geometry : bond 0.00322 (18933) covalent geometry : angle 0.52981 (25599) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4444 Ramachandran restraints generated. 2222 Oldfield, 0 Emsley, 2222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4444 Ramachandran restraints generated. 2222 Oldfield, 0 Emsley, 2222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 2035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 143 time to evaluate : 2.315 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 566 MET cc_start: 0.8822 (tmm) cc_final: 0.8552 (tmm) REVERT: A 626 MET cc_start: 0.8757 (ptt) cc_final: 0.8008 (ppp) REVERT: A 838 PHE cc_start: 0.7323 (m-80) cc_final: 0.7049 (m-80) REVERT: B 189 CYS cc_start: 0.9363 (m) cc_final: 0.9106 (m) REVERT: C 76 MET cc_start: 0.9090 (ptt) cc_final: 0.8452 (ppp) REVERT: C 167 MET cc_start: 0.8213 (mmp) cc_final: 0.7651 (mmm) REVERT: C 360 LYS cc_start: 0.8573 (ptmt) cc_final: 0.8178 (tppt) REVERT: C 645 MET cc_start: 0.8399 (tmm) cc_final: 0.7239 (tmm) REVERT: C 783 MET cc_start: 0.7987 (mtp) cc_final: 0.7556 (mtm) REVERT: D 1 MET cc_start: 0.6673 (ppp) cc_final: 0.5640 (ppp) REVERT: D 17 MET cc_start: 0.7757 (tmm) cc_final: 0.7386 (tmm) REVERT: D 53 ASP cc_start: 0.8889 (m-30) cc_final: 0.8586 (m-30) REVERT: E 72 ARG cc_start: 0.7671 (mtp85) cc_final: 0.6627 (ptt-90) outliers start: 0 outliers final: 0 residues processed: 143 average time/residue: 0.2941 time to fit residues: 67.1303 Evaluate side-chains 119 residues out of total 2035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 119 time to evaluate : 2.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 189 optimal weight: 1.9990 chunk 169 optimal weight: 4.9990 chunk 94 optimal weight: 0.9980 chunk 57 optimal weight: 10.0000 chunk 114 optimal weight: 5.9990 chunk 90 optimal weight: 6.9990 chunk 175 optimal weight: 9.9990 chunk 67 optimal weight: 0.9990 chunk 106 optimal weight: 8.9990 chunk 130 optimal weight: 0.0050 chunk 203 optimal weight: 8.9990 overall best weight: 1.8000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 672 GLN C 402 ASN C 565 ASN D 191 ASN ** D 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.079345 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.2950 r_free = 0.2950 target = 0.054188 restraints weight = 72797.769| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.056094 restraints weight = 37991.641| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 61)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.057183 restraints weight = 26924.619| |-----------------------------------------------------------------------------| r_work (final): 0.3003 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8352 moved from start: 0.1096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 18933 Z= 0.149 Angle : 0.565 7.267 25599 Z= 0.291 Chirality : 0.043 0.208 2725 Planarity : 0.004 0.050 3289 Dihedral : 3.830 18.214 2479 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 0.49 % Allowed : 7.37 % Favored : 92.14 % 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: 1.05 (0.18), residues: 2222 helix: 1.46 (0.17), residues: 978 sheet: 0.05 (0.32), residues: 269 loop : 0.24 (0.21), residues: 975 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.001 TRP E 110 HIS 0.005 0.001 HIS E 122 PHE 0.020 0.001 PHE C 7 TYR 0.013 0.001 TYR B 269 ARG 0.006 0.000 ARG E 69 Details of bonding type rmsd hydrogen bonds : bond 0.05206 ( 824) hydrogen bonds : angle 5.31289 ( 2328) covalent geometry : bond 0.00320 (18933) covalent geometry : angle 0.56465 (25599) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4444 Ramachandran restraints generated. 2222 Oldfield, 0 Emsley, 2222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4444 Ramachandran restraints generated. 2222 Oldfield, 0 Emsley, 2222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 2035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 138 time to evaluate : 2.095 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 110 MET cc_start: 0.8814 (pmm) cc_final: 0.8270 (pmm) REVERT: A 566 MET cc_start: 0.8069 (tmm) cc_final: 0.7682 (tmm) REVERT: A 838 PHE cc_start: 0.7275 (m-80) cc_final: 0.6960 (m-80) REVERT: B 53 ASP cc_start: 0.8139 (m-30) cc_final: 0.7934 (m-30) REVERT: B 179 LYS cc_start: 0.9249 (mmmm) cc_final: 0.9047 (mmmm) REVERT: B 189 CYS cc_start: 0.9388 (m) cc_final: 0.9153 (m) REVERT: C 76 MET cc_start: 0.8923 (ptt) cc_final: 0.8332 (ppp) REVERT: C 167 MET cc_start: 0.8056 (mmp) cc_final: 0.7830 (mmm) REVERT: C 360 LYS cc_start: 0.8700 (ptmt) cc_final: 0.8238 (tppt) REVERT: C 645 MET cc_start: 0.7834 (tmm) cc_final: 0.6889 (tmm) REVERT: C 783 MET cc_start: 0.7817 (mtp) cc_final: 0.7463 (mtm) REVERT: D 17 MET cc_start: 0.7737 (tmm) cc_final: 0.7388 (tmm) REVERT: D 53 ASP cc_start: 0.8898 (m-30) cc_final: 0.8550 (m-30) REVERT: E 69 ARG cc_start: 0.8240 (ttm-80) cc_final: 0.7674 (mmm-85) REVERT: E 72 ARG cc_start: 0.7885 (mtp85) cc_final: 0.6674 (ptt-90) REVERT: E 80 PHE cc_start: 0.9078 (m-80) cc_final: 0.8736 (m-80) outliers start: 10 outliers final: 7 residues processed: 143 average time/residue: 0.2908 time to fit residues: 66.9664 Evaluate side-chains 128 residues out of total 2035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 121 time to evaluate : 2.191 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 672 GLN Chi-restraints excluded: chain A residue 686 LEU Chi-restraints excluded: chain B residue 64 HIS Chi-restraints excluded: chain C residue 236 LEU Chi-restraints excluded: chain C residue 239 LEU Chi-restraints excluded: chain E residue 20 ILE Chi-restraints excluded: chain E residue 67 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 155 optimal weight: 5.9990 chunk 198 optimal weight: 10.0000 chunk 81 optimal weight: 9.9990 chunk 175 optimal weight: 9.9990 chunk 146 optimal weight: 0.1980 chunk 27 optimal weight: 0.9990 chunk 159 optimal weight: 3.9990 chunk 183 optimal weight: 7.9990 chunk 148 optimal weight: 7.9990 chunk 36 optimal weight: 0.6980 chunk 191 optimal weight: 0.0670 overall best weight: 1.1922 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 636 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.080070 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.055039 restraints weight = 72467.392| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.056902 restraints weight = 39328.245| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 67)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.057957 restraints weight = 28255.609| |-----------------------------------------------------------------------------| r_work (final): 0.3022 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8335 moved from start: 0.1425 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 18933 Z= 0.116 Angle : 0.521 7.398 25599 Z= 0.265 Chirality : 0.042 0.209 2725 Planarity : 0.004 0.046 3289 Dihedral : 3.727 18.218 2479 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 0.69 % Allowed : 9.83 % Favored : 89.48 % 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: 1.17 (0.18), residues: 2222 helix: 1.60 (0.17), residues: 978 sheet: 0.08 (0.32), residues: 276 loop : 0.26 (0.21), residues: 968 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP E 110 HIS 0.003 0.001 HIS A 221 PHE 0.016 0.001 PHE C 7 TYR 0.014 0.001 TYR C 841 ARG 0.006 0.000 ARG E 69 Details of bonding type rmsd hydrogen bonds : bond 0.04294 ( 824) hydrogen bonds : angle 4.90737 ( 2328) covalent geometry : bond 0.00248 (18933) covalent geometry : angle 0.52081 (25599) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4444 Ramachandran restraints generated. 2222 Oldfield, 0 Emsley, 2222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4444 Ramachandran restraints generated. 2222 Oldfield, 0 Emsley, 2222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 2035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 136 time to evaluate : 2.292 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 110 MET cc_start: 0.8823 (pmm) cc_final: 0.8222 (pmm) REVERT: A 113 GLN cc_start: 0.9171 (OUTLIER) cc_final: 0.8796 (pm20) REVERT: A 380 GLU cc_start: 0.8554 (tp30) cc_final: 0.8283 (tp30) REVERT: A 566 MET cc_start: 0.7893 (tmm) cc_final: 0.7441 (tmm) REVERT: A 838 PHE cc_start: 0.7194 (m-80) cc_final: 0.6854 (m-80) REVERT: B 53 ASP cc_start: 0.8190 (m-30) cc_final: 0.7904 (m-30) REVERT: B 189 CYS cc_start: 0.9375 (m) cc_final: 0.9167 (m) REVERT: C 76 MET cc_start: 0.8922 (ptt) cc_final: 0.8352 (ppp) REVERT: C 167 MET cc_start: 0.7965 (mmp) cc_final: 0.7730 (mmm) REVERT: C 354 GLN cc_start: 0.8891 (tm-30) cc_final: 0.8668 (tm-30) REVERT: C 360 LYS cc_start: 0.8696 (ptmt) cc_final: 0.8186 (tppt) REVERT: C 645 MET cc_start: 0.7226 (tmm) cc_final: 0.6350 (tmm) REVERT: C 783 MET cc_start: 0.7785 (mtp) cc_final: 0.7451 (mtm) REVERT: C 797 MET cc_start: 0.8953 (ptp) cc_final: 0.8553 (ptp) REVERT: D 17 MET cc_start: 0.7842 (tmm) cc_final: 0.7503 (tmm) REVERT: D 53 ASP cc_start: 0.8864 (m-30) cc_final: 0.8568 (m-30) REVERT: E 69 ARG cc_start: 0.8015 (ttm-80) cc_final: 0.7762 (ttm-80) REVERT: E 72 ARG cc_start: 0.7765 (mtp85) cc_final: 0.6523 (ptt-90) REVERT: E 80 PHE cc_start: 0.9069 (m-80) cc_final: 0.8712 (m-80) outliers start: 14 outliers final: 9 residues processed: 145 average time/residue: 0.2874 time to fit residues: 67.2597 Evaluate side-chains 137 residues out of total 2035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 127 time to evaluate : 1.985 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 GLN Chi-restraints excluded: chain A residue 686 LEU Chi-restraints excluded: chain B residue 64 HIS Chi-restraints excluded: chain C residue 236 LEU Chi-restraints excluded: chain C residue 239 LEU Chi-restraints excluded: chain C residue 401 GLU Chi-restraints excluded: chain C residue 669 VAL Chi-restraints excluded: chain E residue 20 ILE Chi-restraints excluded: chain E residue 50 THR Chi-restraints excluded: chain E residue 100 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 11 optimal weight: 8.9990 chunk 1 optimal weight: 0.1980 chunk 220 optimal weight: 6.9990 chunk 171 optimal weight: 0.2980 chunk 207 optimal weight: 0.9980 chunk 161 optimal weight: 5.9990 chunk 100 optimal weight: 6.9990 chunk 31 optimal weight: 2.9990 chunk 20 optimal weight: 6.9990 chunk 59 optimal weight: 10.0000 chunk 212 optimal weight: 40.0000 overall best weight: 2.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 624 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 376 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.079186 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2952 r_free = 0.2952 target = 0.054162 restraints weight = 72834.608| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.055959 restraints weight = 39548.877| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.056967 restraints weight = 28545.254| |-----------------------------------------------------------------------------| r_work (final): 0.2997 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8362 moved from start: 0.1576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 18933 Z= 0.150 Angle : 0.531 7.823 25599 Z= 0.268 Chirality : 0.042 0.172 2725 Planarity : 0.004 0.045 3289 Dihedral : 3.753 17.761 2479 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 0.98 % Allowed : 11.11 % Favored : 87.91 % 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: 1.23 (0.18), residues: 2222 helix: 1.70 (0.17), residues: 975 sheet: -0.04 (0.31), residues: 284 loop : 0.29 (0.21), residues: 963 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP E 110 HIS 0.003 0.001 HIS E 99 PHE 0.012 0.001 PHE A 248 TYR 0.012 0.001 TYR A 547 ARG 0.005 0.000 ARG E 69 Details of bonding type rmsd hydrogen bonds : bond 0.03979 ( 824) hydrogen bonds : angle 4.69719 ( 2328) covalent geometry : bond 0.00330 (18933) covalent geometry : angle 0.53135 (25599) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4444 Ramachandran restraints generated. 2222 Oldfield, 0 Emsley, 2222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4444 Ramachandran restraints generated. 2222 Oldfield, 0 Emsley, 2222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 2035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 129 time to evaluate : 2.196 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 110 MET cc_start: 0.8905 (pmm) cc_final: 0.8476 (pmm) REVERT: A 113 GLN cc_start: 0.9244 (OUTLIER) cc_final: 0.8888 (pm20) REVERT: A 380 GLU cc_start: 0.8598 (tp30) cc_final: 0.8291 (tp30) REVERT: A 624 GLN cc_start: 0.8629 (tm-30) cc_final: 0.8401 (tm-30) REVERT: A 664 MET cc_start: 0.7596 (tpt) cc_final: 0.7253 (tpt) REVERT: A 838 PHE cc_start: 0.7195 (m-80) cc_final: 0.6827 (m-80) REVERT: B 53 ASP cc_start: 0.8269 (m-30) cc_final: 0.7932 (m-30) REVERT: C 76 MET cc_start: 0.8939 (ptt) cc_final: 0.8361 (ppp) REVERT: C 110 MET cc_start: 0.8287 (mmp) cc_final: 0.7924 (mmp) REVERT: C 167 MET cc_start: 0.8135 (mmp) cc_final: 0.7875 (mmm) REVERT: C 354 GLN cc_start: 0.8961 (tm-30) cc_final: 0.8717 (tm-30) REVERT: C 360 LYS cc_start: 0.8696 (ptmt) cc_final: 0.8196 (tppt) REVERT: C 655 PHE cc_start: 0.8807 (m-10) cc_final: 0.8601 (m-10) REVERT: C 783 MET cc_start: 0.7845 (mtp) cc_final: 0.7542 (mtm) REVERT: C 797 MET cc_start: 0.8882 (OUTLIER) cc_final: 0.8371 (ptp) REVERT: D 17 MET cc_start: 0.7930 (tmm) cc_final: 0.7617 (tmm) REVERT: D 53 ASP cc_start: 0.8822 (m-30) cc_final: 0.8505 (m-30) REVERT: E 69 ARG cc_start: 0.7898 (ttm-80) cc_final: 0.7660 (ttm-80) REVERT: E 72 ARG cc_start: 0.7733 (mtp85) cc_final: 0.6524 (ptt-90) REVERT: E 80 PHE cc_start: 0.9068 (m-80) cc_final: 0.8840 (m-80) REVERT: E 100 GLN cc_start: 0.7512 (OUTLIER) cc_final: 0.7196 (mm-40) outliers start: 20 outliers final: 11 residues processed: 144 average time/residue: 0.2752 time to fit residues: 63.8712 Evaluate side-chains 136 residues out of total 2035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 122 time to evaluate : 2.159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 GLN Chi-restraints excluded: chain A residue 326 PHE Chi-restraints excluded: chain A residue 652 ILE Chi-restraints excluded: chain A residue 686 LEU Chi-restraints excluded: chain B residue 64 HIS Chi-restraints excluded: chain C residue 236 LEU Chi-restraints excluded: chain C residue 239 LEU Chi-restraints excluded: chain C residue 401 GLU Chi-restraints excluded: chain C residue 669 VAL Chi-restraints excluded: chain C residue 797 MET Chi-restraints excluded: chain D residue 198 ILE Chi-restraints excluded: chain E residue 20 ILE Chi-restraints excluded: chain E residue 50 THR Chi-restraints excluded: chain E residue 100 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 85 optimal weight: 3.9990 chunk 10 optimal weight: 1.9990 chunk 197 optimal weight: 6.9990 chunk 210 optimal weight: 10.0000 chunk 116 optimal weight: 2.9990 chunk 61 optimal weight: 5.9990 chunk 81 optimal weight: 9.9990 chunk 17 optimal weight: 3.9990 chunk 119 optimal weight: 8.9990 chunk 58 optimal weight: 10.0000 chunk 84 optimal weight: 0.8980 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 624 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 301 GLN D 356 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.078429 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2928 r_free = 0.2928 target = 0.053406 restraints weight = 73559.137| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.2975 r_free = 0.2975 target = 0.055174 restraints weight = 40121.546| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.056200 restraints weight = 28982.478| |-----------------------------------------------------------------------------| r_work (final): 0.2974 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8380 moved from start: 0.1695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 18933 Z= 0.184 Angle : 0.552 7.990 25599 Z= 0.279 Chirality : 0.043 0.281 2725 Planarity : 0.004 0.045 3289 Dihedral : 3.848 18.694 2479 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 1.28 % Allowed : 11.79 % Favored : 86.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.18 (0.18), residues: 2222 helix: 1.68 (0.17), residues: 980 sheet: -0.17 (0.31), residues: 286 loop : 0.27 (0.21), residues: 956 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP E 110 HIS 0.004 0.001 HIS C 334 PHE 0.014 0.001 PHE A 248 TYR 0.018 0.001 TYR C 841 ARG 0.004 0.000 ARG E 69 Details of bonding type rmsd hydrogen bonds : bond 0.03955 ( 824) hydrogen bonds : angle 4.66976 ( 2328) covalent geometry : bond 0.00404 (18933) covalent geometry : angle 0.55209 (25599) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4444 Ramachandran restraints generated. 2222 Oldfield, 0 Emsley, 2222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4444 Ramachandran restraints generated. 2222 Oldfield, 0 Emsley, 2222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 2035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 130 time to evaluate : 2.332 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 110 MET cc_start: 0.8923 (pmm) cc_final: 0.8564 (pmm) REVERT: A 113 GLN cc_start: 0.9265 (OUTLIER) cc_final: 0.8927 (pm20) REVERT: A 380 GLU cc_start: 0.8685 (tp30) cc_final: 0.8405 (tp30) REVERT: A 566 MET cc_start: 0.7960 (tmm) cc_final: 0.7489 (tmm) REVERT: A 645 MET cc_start: 0.7755 (OUTLIER) cc_final: 0.6732 (tmm) REVERT: A 838 PHE cc_start: 0.7205 (m-80) cc_final: 0.6808 (m-80) REVERT: B 53 ASP cc_start: 0.8298 (m-30) cc_final: 0.7930 (m-30) REVERT: C 76 MET cc_start: 0.8947 (ptt) cc_final: 0.8384 (ppp) REVERT: C 167 MET cc_start: 0.8131 (mmp) cc_final: 0.7607 (mmp) REVERT: C 354 GLN cc_start: 0.8995 (tm-30) cc_final: 0.8747 (tm-30) REVERT: C 356 LEU cc_start: 0.9747 (OUTLIER) cc_final: 0.9479 (mt) REVERT: C 360 LYS cc_start: 0.8692 (ptmt) cc_final: 0.8179 (tppt) REVERT: C 783 MET cc_start: 0.7890 (mtp) cc_final: 0.7613 (mtm) REVERT: D 17 MET cc_start: 0.7956 (tmm) cc_final: 0.7755 (tmm) REVERT: D 53 ASP cc_start: 0.8832 (m-30) cc_final: 0.8552 (m-30) REVERT: D 164 GLU cc_start: 0.8887 (tm-30) cc_final: 0.8663 (pp20) REVERT: E 69 ARG cc_start: 0.7862 (ttm-80) cc_final: 0.7626 (ttm-80) REVERT: E 72 ARG cc_start: 0.7763 (mtp85) cc_final: 0.6527 (ptt-90) REVERT: E 80 PHE cc_start: 0.9083 (m-80) cc_final: 0.8850 (m-80) outliers start: 26 outliers final: 14 residues processed: 147 average time/residue: 0.2858 time to fit residues: 68.9015 Evaluate side-chains 139 residues out of total 2035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 122 time to evaluate : 2.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 HIS Chi-restraints excluded: chain A residue 113 GLN Chi-restraints excluded: chain A residue 326 PHE Chi-restraints excluded: chain A residue 577 VAL Chi-restraints excluded: chain A residue 645 MET Chi-restraints excluded: chain A residue 652 ILE Chi-restraints excluded: chain A residue 686 LEU Chi-restraints excluded: chain B residue 64 HIS Chi-restraints excluded: chain B residue 214 VAL Chi-restraints excluded: chain C residue 236 LEU Chi-restraints excluded: chain C residue 239 LEU Chi-restraints excluded: chain C residue 356 LEU Chi-restraints excluded: chain C residue 401 GLU Chi-restraints excluded: chain C residue 669 VAL Chi-restraints excluded: chain D residue 198 ILE Chi-restraints excluded: chain D residue 252 LEU Chi-restraints excluded: chain E residue 20 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 69 optimal weight: 7.9990 chunk 199 optimal weight: 0.7980 chunk 63 optimal weight: 0.0060 chunk 115 optimal weight: 5.9990 chunk 159 optimal weight: 2.9990 chunk 203 optimal weight: 10.0000 chunk 95 optimal weight: 8.9990 chunk 74 optimal weight: 6.9990 chunk 29 optimal weight: 1.9990 chunk 121 optimal weight: 0.9990 chunk 130 optimal weight: 6.9990 overall best weight: 1.3602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 55 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.079496 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2959 r_free = 0.2959 target = 0.054510 restraints weight = 73346.055| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.056345 restraints weight = 39560.578| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 63)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.057392 restraints weight = 28404.167| |-----------------------------------------------------------------------------| r_work (final): 0.3006 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8349 moved from start: 0.1831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 18933 Z= 0.114 Angle : 0.522 9.201 25599 Z= 0.260 Chirality : 0.042 0.274 2725 Planarity : 0.003 0.044 3289 Dihedral : 3.726 18.930 2479 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 1.38 % Allowed : 12.63 % Favored : 86.00 % 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: 1.26 (0.18), residues: 2222 helix: 1.74 (0.17), residues: 987 sheet: -0.07 (0.31), residues: 286 loop : 0.29 (0.21), residues: 949 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP E 110 HIS 0.003 0.001 HIS A 221 PHE 0.016 0.001 PHE C 655 TYR 0.018 0.001 TYR C 841 ARG 0.004 0.000 ARG E 69 Details of bonding type rmsd hydrogen bonds : bond 0.03653 ( 824) hydrogen bonds : angle 4.52783 ( 2328) covalent geometry : bond 0.00251 (18933) covalent geometry : angle 0.52156 (25599) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4444 Ramachandran restraints generated. 2222 Oldfield, 0 Emsley, 2222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4444 Ramachandran restraints generated. 2222 Oldfield, 0 Emsley, 2222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 2035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 131 time to evaluate : 2.274 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 110 MET cc_start: 0.8848 (pmm) cc_final: 0.8507 (pmm) REVERT: A 113 GLN cc_start: 0.9242 (OUTLIER) cc_final: 0.8927 (pm20) REVERT: A 380 GLU cc_start: 0.8648 (tp30) cc_final: 0.8315 (tp30) REVERT: A 645 MET cc_start: 0.8155 (tmm) cc_final: 0.7269 (tmm) REVERT: A 838 PHE cc_start: 0.7155 (m-80) cc_final: 0.6762 (m-80) REVERT: B 53 ASP cc_start: 0.8317 (m-30) cc_final: 0.7935 (m-30) REVERT: C 76 MET cc_start: 0.8908 (ptt) cc_final: 0.8374 (ppp) REVERT: C 110 MET cc_start: 0.8404 (mmp) cc_final: 0.8196 (mmp) REVERT: C 354 GLN cc_start: 0.8966 (tm-30) cc_final: 0.8697 (tm-30) REVERT: C 360 LYS cc_start: 0.8690 (ptmt) cc_final: 0.8179 (tppt) REVERT: C 783 MET cc_start: 0.7873 (mtp) cc_final: 0.7601 (mtm) REVERT: D 17 MET cc_start: 0.7932 (tmm) cc_final: 0.7642 (tmm) REVERT: D 53 ASP cc_start: 0.8789 (m-30) cc_final: 0.8521 (m-30) REVERT: E 69 ARG cc_start: 0.7838 (ttm-80) cc_final: 0.7614 (ttm-80) REVERT: E 72 ARG cc_start: 0.7778 (mtp85) cc_final: 0.6531 (ptt-90) REVERT: E 80 PHE cc_start: 0.9082 (m-80) cc_final: 0.8852 (m-80) REVERT: E 100 GLN cc_start: 0.7096 (OUTLIER) cc_final: 0.6896 (mm-40) outliers start: 28 outliers final: 19 residues processed: 156 average time/residue: 0.2762 time to fit residues: 70.1581 Evaluate side-chains 146 residues out of total 2035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 125 time to evaluate : 2.125 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 HIS Chi-restraints excluded: chain A residue 113 GLN Chi-restraints excluded: chain A residue 326 PHE Chi-restraints excluded: chain A residue 548 GLU Chi-restraints excluded: chain A residue 652 ILE Chi-restraints excluded: chain A residue 686 LEU Chi-restraints excluded: chain B residue 64 HIS Chi-restraints excluded: chain B residue 269 TYR Chi-restraints excluded: chain C residue 236 LEU Chi-restraints excluded: chain C residue 239 LEU Chi-restraints excluded: chain C residue 401 GLU Chi-restraints excluded: chain C residue 669 VAL Chi-restraints excluded: chain C residue 797 MET Chi-restraints excluded: chain D residue 60 VAL Chi-restraints excluded: chain D residue 123 VAL Chi-restraints excluded: chain D residue 198 ILE Chi-restraints excluded: chain D residue 252 LEU Chi-restraints excluded: chain D residue 262 LEU Chi-restraints excluded: chain D residue 269 TYR Chi-restraints excluded: chain E residue 20 ILE Chi-restraints excluded: chain E residue 100 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 198 optimal weight: 5.9990 chunk 203 optimal weight: 8.9990 chunk 10 optimal weight: 2.9990 chunk 81 optimal weight: 10.0000 chunk 13 optimal weight: 0.0370 chunk 201 optimal weight: 4.9990 chunk 9 optimal weight: 6.9990 chunk 56 optimal weight: 0.0970 chunk 221 optimal weight: 6.9990 chunk 25 optimal weight: 2.9990 chunk 42 optimal weight: 0.0030 overall best weight: 1.2270 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.079671 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2964 r_free = 0.2964 target = 0.054662 restraints weight = 72905.841| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.056532 restraints weight = 38748.519| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.057626 restraints weight = 27592.056| |-----------------------------------------------------------------------------| r_work (final): 0.3013 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8345 moved from start: 0.1966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 18933 Z= 0.113 Angle : 0.539 11.556 25599 Z= 0.266 Chirality : 0.042 0.283 2725 Planarity : 0.003 0.043 3289 Dihedral : 3.678 18.452 2479 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 1.18 % Allowed : 13.27 % Favored : 85.55 % 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: 1.29 (0.18), residues: 2222 helix: 1.77 (0.17), residues: 982 sheet: 0.01 (0.31), residues: 287 loop : 0.28 (0.21), residues: 953 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP E 110 HIS 0.005 0.001 HIS C 719 PHE 0.014 0.001 PHE C 655 TYR 0.019 0.001 TYR C 841 ARG 0.003 0.000 ARG E 69 Details of bonding type rmsd hydrogen bonds : bond 0.03560 ( 824) hydrogen bonds : angle 4.47253 ( 2328) covalent geometry : bond 0.00251 (18933) covalent geometry : angle 0.53921 (25599) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4444 Ramachandran restraints generated. 2222 Oldfield, 0 Emsley, 2222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4444 Ramachandran restraints generated. 2222 Oldfield, 0 Emsley, 2222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 2035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 132 time to evaluate : 2.242 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 110 MET cc_start: 0.8875 (pmm) cc_final: 0.8504 (pmm) REVERT: A 113 GLN cc_start: 0.9233 (OUTLIER) cc_final: 0.8921 (pm20) REVERT: A 318 ASP cc_start: 0.8616 (m-30) cc_final: 0.8334 (m-30) REVERT: A 380 GLU cc_start: 0.8640 (tp30) cc_final: 0.8297 (tp30) REVERT: A 566 MET cc_start: 0.7818 (tmm) cc_final: 0.7353 (tmm) REVERT: A 645 MET cc_start: 0.8168 (OUTLIER) cc_final: 0.7206 (tmm) REVERT: A 838 PHE cc_start: 0.7098 (m-80) cc_final: 0.6724 (m-80) REVERT: B 53 ASP cc_start: 0.8349 (m-30) cc_final: 0.7995 (m-30) REVERT: C 76 MET cc_start: 0.8919 (ptt) cc_final: 0.8367 (ppp) REVERT: C 167 MET cc_start: 0.8201 (mmp) cc_final: 0.7511 (mmm) REVERT: C 360 LYS cc_start: 0.8743 (ptmt) cc_final: 0.8233 (tppt) REVERT: C 783 MET cc_start: 0.7863 (mtp) cc_final: 0.7600 (mtm) REVERT: D 17 MET cc_start: 0.8040 (tmm) cc_final: 0.7742 (tmm) REVERT: D 53 ASP cc_start: 0.8768 (m-30) cc_final: 0.8507 (m-30) REVERT: D 164 GLU cc_start: 0.8840 (tm-30) cc_final: 0.8621 (pp20) REVERT: E 69 ARG cc_start: 0.7899 (ttm-80) cc_final: 0.7684 (ttm-80) REVERT: E 72 ARG cc_start: 0.7773 (mtp85) cc_final: 0.6533 (ptt-90) REVERT: E 80 PHE cc_start: 0.9077 (m-80) cc_final: 0.8839 (m-80) REVERT: E 110 TRP cc_start: 0.8922 (m-10) cc_final: 0.8574 (m-10) outliers start: 24 outliers final: 17 residues processed: 150 average time/residue: 0.2792 time to fit residues: 68.6029 Evaluate side-chains 147 residues out of total 2035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 128 time to evaluate : 2.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 HIS Chi-restraints excluded: chain A residue 113 GLN Chi-restraints excluded: chain A residue 326 PHE Chi-restraints excluded: chain A residue 548 GLU Chi-restraints excluded: chain A residue 645 MET Chi-restraints excluded: chain A residue 686 LEU Chi-restraints excluded: chain B residue 64 HIS Chi-restraints excluded: chain B residue 269 TYR Chi-restraints excluded: chain C residue 236 LEU Chi-restraints excluded: chain C residue 239 LEU Chi-restraints excluded: chain C residue 401 GLU Chi-restraints excluded: chain C residue 669 VAL Chi-restraints excluded: chain C residue 713 LEU Chi-restraints excluded: chain D residue 60 VAL Chi-restraints excluded: chain D residue 123 VAL Chi-restraints excluded: chain D residue 252 LEU Chi-restraints excluded: chain D residue 262 LEU Chi-restraints excluded: chain D residue 269 TYR Chi-restraints excluded: chain E residue 20 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 47 optimal weight: 5.9990 chunk 18 optimal weight: 0.6980 chunk 176 optimal weight: 8.9990 chunk 212 optimal weight: 8.9990 chunk 160 optimal weight: 3.9990 chunk 95 optimal weight: 0.7980 chunk 7 optimal weight: 9.9990 chunk 189 optimal weight: 8.9990 chunk 221 optimal weight: 20.0000 chunk 170 optimal weight: 5.9990 chunk 205 optimal weight: 1.9990 overall best weight: 2.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.078501 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2933 r_free = 0.2933 target = 0.053614 restraints weight = 73541.127| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.2977 r_free = 0.2977 target = 0.055340 restraints weight = 39944.554| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.056340 restraints weight = 28849.760| |-----------------------------------------------------------------------------| r_work (final): 0.2978 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8380 moved from start: 0.1966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 18933 Z= 0.182 Angle : 0.579 11.310 25599 Z= 0.287 Chirality : 0.043 0.275 2725 Planarity : 0.004 0.040 3289 Dihedral : 3.817 20.383 2479 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 1.47 % Allowed : 13.27 % Favored : 85.26 % 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: 1.22 (0.19), residues: 2222 helix: 1.75 (0.17), residues: 979 sheet: -0.12 (0.31), residues: 289 loop : 0.24 (0.21), residues: 954 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 332 HIS 0.005 0.001 HIS C 719 PHE 0.012 0.001 PHE C 655 TYR 0.020 0.001 TYR C 841 ARG 0.003 0.000 ARG E 69 Details of bonding type rmsd hydrogen bonds : bond 0.03760 ( 824) hydrogen bonds : angle 4.55915 ( 2328) covalent geometry : bond 0.00401 (18933) covalent geometry : angle 0.57871 (25599) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4444 Ramachandran restraints generated. 2222 Oldfield, 0 Emsley, 2222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4444 Ramachandran restraints generated. 2222 Oldfield, 0 Emsley, 2222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 2035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 126 time to evaluate : 2.069 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 110 MET cc_start: 0.8863 (pmm) cc_final: 0.8526 (pmm) REVERT: A 113 GLN cc_start: 0.9267 (OUTLIER) cc_final: 0.8917 (pm20) REVERT: A 380 GLU cc_start: 0.8695 (tp30) cc_final: 0.8295 (tp30) REVERT: A 566 MET cc_start: 0.7861 (tmm) cc_final: 0.7371 (tmm) REVERT: A 624 GLN cc_start: 0.8664 (tm-30) cc_final: 0.8419 (tm-30) REVERT: A 645 MET cc_start: 0.8131 (OUTLIER) cc_final: 0.7275 (tmm) REVERT: A 838 PHE cc_start: 0.7168 (m-80) cc_final: 0.6734 (m-80) REVERT: B 53 ASP cc_start: 0.8395 (m-30) cc_final: 0.8038 (m-30) REVERT: C 76 MET cc_start: 0.8977 (ptt) cc_final: 0.8413 (ppp) REVERT: C 110 MET cc_start: 0.8421 (mmp) cc_final: 0.8200 (mmp) REVERT: C 167 MET cc_start: 0.8137 (mmp) cc_final: 0.7362 (mmm) REVERT: C 360 LYS cc_start: 0.8720 (ptmt) cc_final: 0.8211 (tppt) REVERT: C 625 LEU cc_start: 0.8552 (mt) cc_final: 0.8262 (mt) REVERT: C 783 MET cc_start: 0.7822 (mtp) cc_final: 0.7520 (mtm) REVERT: C 797 MET cc_start: 0.8906 (OUTLIER) cc_final: 0.8688 (ptp) REVERT: D 1 MET cc_start: 0.6902 (ppp) cc_final: 0.6384 (ppp) REVERT: D 53 ASP cc_start: 0.8823 (m-30) cc_final: 0.8540 (m-30) REVERT: D 164 GLU cc_start: 0.8885 (tm-30) cc_final: 0.8648 (pp20) REVERT: E 69 ARG cc_start: 0.7899 (ttm-80) cc_final: 0.7688 (ttm-80) REVERT: E 72 ARG cc_start: 0.7785 (mtp85) cc_final: 0.6535 (ptt-90) REVERT: E 80 PHE cc_start: 0.9089 (m-80) cc_final: 0.8851 (m-80) outliers start: 30 outliers final: 21 residues processed: 150 average time/residue: 0.2728 time to fit residues: 67.2524 Evaluate side-chains 146 residues out of total 2035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 122 time to evaluate : 2.272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 HIS Chi-restraints excluded: chain A residue 113 GLN Chi-restraints excluded: chain A residue 326 PHE Chi-restraints excluded: chain A residue 548 GLU Chi-restraints excluded: chain A residue 577 VAL Chi-restraints excluded: chain A residue 645 MET Chi-restraints excluded: chain A residue 686 LEU Chi-restraints excluded: chain B residue 64 HIS Chi-restraints excluded: chain B residue 214 VAL Chi-restraints excluded: chain B residue 269 TYR Chi-restraints excluded: chain C residue 236 LEU Chi-restraints excluded: chain C residue 239 LEU Chi-restraints excluded: chain C residue 401 GLU Chi-restraints excluded: chain C residue 669 VAL Chi-restraints excluded: chain C residue 713 LEU Chi-restraints excluded: chain C residue 797 MET Chi-restraints excluded: chain D residue 60 VAL Chi-restraints excluded: chain D residue 123 VAL Chi-restraints excluded: chain D residue 198 ILE Chi-restraints excluded: chain D residue 252 LEU Chi-restraints excluded: chain D residue 262 LEU Chi-restraints excluded: chain D residue 269 TYR Chi-restraints excluded: chain E residue 20 ILE Chi-restraints excluded: chain E residue 95 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 33 optimal weight: 7.9990 chunk 95 optimal weight: 7.9990 chunk 92 optimal weight: 1.9990 chunk 164 optimal weight: 5.9990 chunk 137 optimal weight: 0.9990 chunk 105 optimal weight: 9.9990 chunk 90 optimal weight: 3.9990 chunk 118 optimal weight: 0.0270 chunk 76 optimal weight: 2.9990 chunk 79 optimal weight: 0.6980 chunk 47 optimal weight: 5.9990 overall best weight: 1.3444 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 62 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.079577 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.054518 restraints weight = 73189.143| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.056433 restraints weight = 37564.289| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 62)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.057556 restraints weight = 26399.519| |-----------------------------------------------------------------------------| r_work (final): 0.3011 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8337 moved from start: 0.2065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 18933 Z= 0.117 Angle : 0.563 11.272 25599 Z= 0.275 Chirality : 0.042 0.285 2725 Planarity : 0.003 0.041 3289 Dihedral : 3.708 19.458 2479 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 1.33 % Allowed : 13.71 % Favored : 84.96 % 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: 1.28 (0.19), residues: 2222 helix: 1.76 (0.17), residues: 986 sheet: 0.00 (0.31), residues: 287 loop : 0.26 (0.21), residues: 949 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 352 HIS 0.003 0.001 HIS A 247 PHE 0.012 0.001 PHE E 46 TYR 0.021 0.001 TYR C 841 ARG 0.003 0.000 ARG E 69 Details of bonding type rmsd hydrogen bonds : bond 0.03560 ( 824) hydrogen bonds : angle 4.45241 ( 2328) covalent geometry : bond 0.00259 (18933) covalent geometry : angle 0.56286 (25599) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4444 Ramachandran restraints generated. 2222 Oldfield, 0 Emsley, 2222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4444 Ramachandran restraints generated. 2222 Oldfield, 0 Emsley, 2222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 2035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 129 time to evaluate : 2.198 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 110 MET cc_start: 0.8870 (pmm) cc_final: 0.8601 (pmm) REVERT: A 113 GLN cc_start: 0.9229 (OUTLIER) cc_final: 0.8827 (pm20) REVERT: A 318 ASP cc_start: 0.8511 (m-30) cc_final: 0.8284 (m-30) REVERT: A 380 GLU cc_start: 0.8679 (tp30) cc_final: 0.8255 (tp30) REVERT: A 566 MET cc_start: 0.7773 (tmm) cc_final: 0.7266 (tmm) REVERT: A 624 GLN cc_start: 0.8548 (tm-30) cc_final: 0.8021 (tm-30) REVERT: A 645 MET cc_start: 0.8255 (OUTLIER) cc_final: 0.7377 (tmm) REVERT: A 838 PHE cc_start: 0.7144 (m-80) cc_final: 0.6709 (m-80) REVERT: B 53 ASP cc_start: 0.8373 (m-30) cc_final: 0.8014 (m-30) REVERT: C 76 MET cc_start: 0.8946 (ptt) cc_final: 0.8392 (ppp) REVERT: C 110 MET cc_start: 0.8406 (mmp) cc_final: 0.8161 (mmp) REVERT: C 167 MET cc_start: 0.8144 (mmp) cc_final: 0.7387 (mmm) REVERT: C 324 CYS cc_start: 0.8324 (m) cc_final: 0.7732 (m) REVERT: C 360 LYS cc_start: 0.8763 (ptmt) cc_final: 0.8216 (tppt) REVERT: C 783 MET cc_start: 0.8005 (mtp) cc_final: 0.7647 (mtm) REVERT: D 1 MET cc_start: 0.6832 (ppp) cc_final: 0.6479 (ppp) REVERT: D 53 ASP cc_start: 0.8800 (m-30) cc_final: 0.8539 (m-30) REVERT: D 164 GLU cc_start: 0.8875 (tm-30) cc_final: 0.8594 (pp20) REVERT: E 69 ARG cc_start: 0.7855 (ttm-80) cc_final: 0.7652 (ttm-80) REVERT: E 72 ARG cc_start: 0.7813 (mtp85) cc_final: 0.6537 (ptt-90) REVERT: E 80 PHE cc_start: 0.9091 (m-80) cc_final: 0.8842 (m-80) outliers start: 27 outliers final: 19 residues processed: 149 average time/residue: 0.2716 time to fit residues: 66.7240 Evaluate side-chains 148 residues out of total 2035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 127 time to evaluate : 2.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 HIS Chi-restraints excluded: chain A residue 113 GLN Chi-restraints excluded: chain A residue 326 PHE Chi-restraints excluded: chain A residue 548 GLU Chi-restraints excluded: chain A residue 645 MET Chi-restraints excluded: chain A residue 686 LEU Chi-restraints excluded: chain B residue 64 HIS Chi-restraints excluded: chain B residue 269 TYR Chi-restraints excluded: chain C residue 236 LEU Chi-restraints excluded: chain C residue 239 LEU Chi-restraints excluded: chain C residue 401 GLU Chi-restraints excluded: chain C residue 669 VAL Chi-restraints excluded: chain C residue 713 LEU Chi-restraints excluded: chain D residue 60 VAL Chi-restraints excluded: chain D residue 123 VAL Chi-restraints excluded: chain D residue 252 LEU Chi-restraints excluded: chain D residue 262 LEU Chi-restraints excluded: chain D residue 269 TYR Chi-restraints excluded: chain E residue 20 ILE Chi-restraints excluded: chain E residue 62 ASN Chi-restraints excluded: chain E residue 95 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 182 optimal weight: 3.9990 chunk 57 optimal weight: 10.0000 chunk 115 optimal weight: 4.9990 chunk 196 optimal weight: 0.8980 chunk 110 optimal weight: 2.9990 chunk 10 optimal weight: 6.9990 chunk 5 optimal weight: 0.7980 chunk 21 optimal weight: 2.9990 chunk 221 optimal weight: 20.0000 chunk 48 optimal weight: 0.7980 chunk 46 optimal weight: 8.9990 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 62 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.079361 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2959 r_free = 0.2959 target = 0.054526 restraints weight = 73762.835| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.056311 restraints weight = 39379.406| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.057342 restraints weight = 28266.607| |-----------------------------------------------------------------------------| r_work (final): 0.3005 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8353 moved from start: 0.2086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 18933 Z= 0.131 Angle : 0.573 11.329 25599 Z= 0.279 Chirality : 0.042 0.282 2725 Planarity : 0.003 0.041 3289 Dihedral : 3.709 19.248 2479 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 1.08 % Allowed : 14.00 % Favored : 84.91 % 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: 1.27 (0.19), residues: 2222 helix: 1.77 (0.17), residues: 987 sheet: -0.03 (0.31), residues: 289 loop : 0.26 (0.21), residues: 946 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 352 HIS 0.003 0.001 HIS C 719 PHE 0.011 0.001 PHE C 655 TYR 0.020 0.001 TYR C 841 ARG 0.002 0.000 ARG D 341 Details of bonding type rmsd hydrogen bonds : bond 0.03571 ( 824) hydrogen bonds : angle 4.44587 ( 2328) covalent geometry : bond 0.00293 (18933) covalent geometry : angle 0.57281 (25599) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4444 Ramachandran restraints generated. 2222 Oldfield, 0 Emsley, 2222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4444 Ramachandran restraints generated. 2222 Oldfield, 0 Emsley, 2222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 2035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 127 time to evaluate : 1.987 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 110 MET cc_start: 0.8874 (pmm) cc_final: 0.8601 (pmm) REVERT: A 113 GLN cc_start: 0.9225 (OUTLIER) cc_final: 0.8880 (pm20) REVERT: A 318 ASP cc_start: 0.8510 (m-30) cc_final: 0.8284 (m-30) REVERT: A 380 GLU cc_start: 0.8673 (tp30) cc_final: 0.8258 (tp30) REVERT: A 566 MET cc_start: 0.7651 (tmm) cc_final: 0.7114 (tmm) REVERT: A 624 GLN cc_start: 0.8586 (tm-30) cc_final: 0.8075 (tm-30) REVERT: A 645 MET cc_start: 0.8129 (OUTLIER) cc_final: 0.7238 (tmm) REVERT: A 838 PHE cc_start: 0.7126 (m-80) cc_final: 0.6703 (m-80) REVERT: B 53 ASP cc_start: 0.8360 (m-30) cc_final: 0.8009 (m-30) REVERT: C 76 MET cc_start: 0.8955 (ptt) cc_final: 0.8399 (ppp) REVERT: C 110 MET cc_start: 0.8403 (mmp) cc_final: 0.8170 (mmp) REVERT: C 167 MET cc_start: 0.8162 (mmp) cc_final: 0.7394 (mmm) REVERT: C 324 CYS cc_start: 0.8304 (m) cc_final: 0.7714 (m) REVERT: C 360 LYS cc_start: 0.8753 (ptmt) cc_final: 0.8270 (tppt) REVERT: C 625 LEU cc_start: 0.9022 (mt) cc_final: 0.8602 (mt) REVERT: C 783 MET cc_start: 0.8014 (mtp) cc_final: 0.7640 (mtm) REVERT: D 53 ASP cc_start: 0.8786 (m-30) cc_final: 0.8530 (m-30) REVERT: D 164 GLU cc_start: 0.8871 (tm-30) cc_final: 0.8590 (pp20) REVERT: E 69 ARG cc_start: 0.7862 (ttm-80) cc_final: 0.7655 (ttm-80) REVERT: E 72 ARG cc_start: 0.7785 (mtp85) cc_final: 0.6537 (ptt-90) REVERT: E 80 PHE cc_start: 0.9099 (m-80) cc_final: 0.8851 (m-80) outliers start: 22 outliers final: 19 residues processed: 144 average time/residue: 0.2575 time to fit residues: 60.8660 Evaluate side-chains 146 residues out of total 2035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 125 time to evaluate : 2.008 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 HIS Chi-restraints excluded: chain A residue 113 GLN Chi-restraints excluded: chain A residue 326 PHE Chi-restraints excluded: chain A residue 548 GLU Chi-restraints excluded: chain A residue 645 MET Chi-restraints excluded: chain A residue 686 LEU Chi-restraints excluded: chain B residue 64 HIS Chi-restraints excluded: chain B residue 269 TYR Chi-restraints excluded: chain C residue 236 LEU Chi-restraints excluded: chain C residue 239 LEU Chi-restraints excluded: chain C residue 401 GLU Chi-restraints excluded: chain C residue 669 VAL Chi-restraints excluded: chain C residue 713 LEU Chi-restraints excluded: chain D residue 60 VAL Chi-restraints excluded: chain D residue 123 VAL Chi-restraints excluded: chain D residue 252 LEU Chi-restraints excluded: chain D residue 262 LEU Chi-restraints excluded: chain D residue 269 TYR Chi-restraints excluded: chain E residue 20 ILE Chi-restraints excluded: chain E residue 62 ASN Chi-restraints excluded: chain E residue 95 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 219 optimal weight: 7.9990 chunk 142 optimal weight: 0.4980 chunk 84 optimal weight: 0.5980 chunk 64 optimal weight: 6.9990 chunk 126 optimal weight: 2.9990 chunk 192 optimal weight: 9.9990 chunk 27 optimal weight: 3.9990 chunk 99 optimal weight: 4.9990 chunk 159 optimal weight: 0.9980 chunk 212 optimal weight: 10.0000 chunk 73 optimal weight: 4.9990 overall best weight: 1.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 62 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.079284 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2956 r_free = 0.2956 target = 0.054421 restraints weight = 73204.592| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.056203 restraints weight = 38693.754| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.057244 restraints weight = 27520.440| |-----------------------------------------------------------------------------| r_work (final): 0.3003 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8357 moved from start: 0.2110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 18933 Z= 0.136 Angle : 0.581 12.873 25599 Z= 0.282 Chirality : 0.043 0.281 2725 Planarity : 0.003 0.040 3289 Dihedral : 3.732 20.975 2479 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 1.18 % Allowed : 13.91 % Favored : 84.91 % 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: 1.26 (0.19), residues: 2222 helix: 1.77 (0.17), residues: 987 sheet: -0.03 (0.31), residues: 289 loop : 0.24 (0.21), residues: 946 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 352 HIS 0.003 0.001 HIS C 719 PHE 0.010 0.001 PHE C 655 TYR 0.022 0.001 TYR C 841 ARG 0.002 0.000 ARG D 341 Details of bonding type rmsd hydrogen bonds : bond 0.03562 ( 824) hydrogen bonds : angle 4.43951 ( 2328) covalent geometry : bond 0.00304 (18933) covalent geometry : angle 0.58089 (25599) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5819.84 seconds wall clock time: 101 minutes 56.09 seconds (6116.09 seconds total)