Starting phenix.real_space_refine on Thu Sep 18 17:03:23 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8yf5_39211/09_2025/8yf5_39211.cif Found real_map, /net/cci-nas-00/data/ceres_data/8yf5_39211/09_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 { model { file = "/net/cci-nas-00/data/ceres_data/8yf5_39211/09_2025/8yf5_39211.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8yf5_39211/09_2025/8yf5_39211.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8yf5_39211/09_2025/8yf5_39211.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8yf5_39211/09_2025/8yf5_39211.map" } resolution = 3.78 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: 4.34, per 1000 atoms: 0.23 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: 1.55 Conformation dependent library (CDL) restraints added in 689.5 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 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: 0.71 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: 2.51 Time building geometry restraints manager: 2.01 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: 0.430 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: 0.180 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 16.360 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.560 ------------------------------------------------------------------------------- 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 : 10.98 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 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 ARG 0.007 0.000 ARG E 69 TYR 0.018 0.001 TYR B 269 PHE 0.013 0.001 PHE B 152 TRP 0.081 0.001 TRP E 110 HIS 0.003 0.001 HIS C 717 Details of bonding type rmsd covalent geometry : bond 0.00322 (18933) covalent geometry : angle 0.52981 (25599) hydrogen bonds : bond 0.22628 ( 824) hydrogen bonds : angle 7.24057 ( 2328) *********************** 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 : 0.776 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: 0.7238 (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: 0.1261 time to fit residues: 29.0733 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 : 0.752 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 216 optimal weight: 30.0000 chunk 98 optimal weight: 6.9990 chunk 194 optimal weight: 4.9990 chunk 107 optimal weight: 0.7980 chunk 10 optimal weight: 0.8980 chunk 66 optimal weight: 7.9990 chunk 130 optimal weight: 0.4980 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 10.0000 chunk 200 optimal weight: 10.0000 chunk 212 optimal weight: 4.9990 overall best weight: 2.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 55 ASN A 672 GLN C 402 ASN D 191 ASN D 194 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.079159 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2952 r_free = 0.2952 target = 0.054192 restraints weight = 72792.117| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.056026 restraints weight = 39526.998| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.057049 restraints weight = 28428.073| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.057636 restraints weight = 23890.416| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 50)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.057984 restraints weight = 21830.006| |-----------------------------------------------------------------------------| r_work (final): 0.3025 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8328 moved from start: 0.1081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 18933 Z= 0.160 Angle : 0.570 8.056 25599 Z= 0.295 Chirality : 0.043 0.223 2725 Planarity : 0.004 0.052 3289 Dihedral : 3.854 18.233 2479 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 0.49 % Allowed : 7.42 % Favored : 92.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.04 (0.18), residues: 2222 helix: 1.47 (0.17), residues: 977 sheet: 0.03 (0.32), residues: 276 loop : 0.21 (0.21), residues: 969 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 69 TYR 0.014 0.001 TYR B 269 PHE 0.020 0.001 PHE C 7 TRP 0.046 0.002 TRP E 110 HIS 0.005 0.001 HIS C 717 Details of bonding type rmsd covalent geometry : bond 0.00346 (18933) covalent geometry : angle 0.57011 (25599) hydrogen bonds : bond 0.05213 ( 824) hydrogen bonds : angle 5.33028 ( 2328) *********************** 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 147 residues out of total 2035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 137 time to evaluate : 0.694 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 110 MET cc_start: 0.8816 (pmm) cc_final: 0.8267 (pmm) REVERT: A 566 MET cc_start: 0.8070 (tmm) cc_final: 0.7680 (tmm) REVERT: A 838 PHE cc_start: 0.7236 (m-80) cc_final: 0.6936 (m-80) REVERT: B 53 ASP cc_start: 0.8120 (m-30) cc_final: 0.7913 (m-30) REVERT: B 179 LYS cc_start: 0.9247 (mmmm) cc_final: 0.9043 (mmmm) REVERT: B 189 CYS cc_start: 0.9389 (m) cc_final: 0.9173 (m) REVERT: C 76 MET cc_start: 0.8917 (ptt) cc_final: 0.8329 (ppp) REVERT: C 110 MET cc_start: 0.8310 (mmp) cc_final: 0.8032 (mmp) REVERT: C 167 MET cc_start: 0.8045 (mmp) cc_final: 0.7815 (mmm) REVERT: C 360 LYS cc_start: 0.8682 (ptmt) cc_final: 0.8228 (tppt) REVERT: C 645 MET cc_start: 0.7844 (tmm) cc_final: 0.6878 (tmm) REVERT: C 783 MET cc_start: 0.7804 (mtp) cc_final: 0.7477 (mtm) REVERT: D 17 MET cc_start: 0.7714 (tmm) cc_final: 0.7382 (tmm) REVERT: D 53 ASP cc_start: 0.8888 (m-30) cc_final: 0.8538 (m-30) REVERT: E 69 ARG cc_start: 0.8255 (ttm-80) cc_final: 0.7896 (ttm-80) REVERT: E 72 ARG cc_start: 0.7896 (mtp85) cc_final: 0.6678 (ptt-90) REVERT: E 80 PHE cc_start: 0.9080 (m-80) cc_final: 0.8739 (m-80) REVERT: E 125 TYR cc_start: 0.9022 (p90) cc_final: 0.8819 (p90) outliers start: 10 outliers final: 6 residues processed: 142 average time/residue: 0.1279 time to fit residues: 29.1953 Evaluate side-chains 128 residues out of total 2035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 122 time to evaluate : 0.741 ------------------------------------------------------------------------------- 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 Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 177 optimal weight: 6.9990 chunk 123 optimal weight: 4.9990 chunk 219 optimal weight: 5.9990 chunk 7 optimal weight: 6.9990 chunk 4 optimal weight: 5.9990 chunk 213 optimal weight: 30.0000 chunk 187 optimal weight: 3.9990 chunk 145 optimal weight: 3.9990 chunk 8 optimal weight: 1.9990 chunk 60 optimal weight: 9.9990 chunk 94 optimal weight: 6.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS ** C 624 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 636 ASN D 301 GLN D 356 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.077542 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.2903 r_free = 0.2903 target = 0.052509 restraints weight = 74815.699| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2949 r_free = 0.2949 target = 0.054239 restraints weight = 40724.074| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 64)----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.055213 restraints weight = 29672.545| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.055785 restraints weight = 25063.830| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.056108 restraints weight = 22946.862| |-----------------------------------------------------------------------------| r_work (final): 0.2974 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8388 moved from start: 0.1401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 18933 Z= 0.267 Angle : 0.614 7.582 25599 Z= 0.315 Chirality : 0.044 0.209 2725 Planarity : 0.004 0.049 3289 Dihedral : 4.086 18.582 2479 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 9.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer: Outliers : 1.13 % Allowed : 10.47 % Favored : 88.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.95 (0.18), residues: 2222 helix: 1.50 (0.17), residues: 970 sheet: -0.22 (0.32), residues: 277 loop : 0.12 (0.21), residues: 975 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 69 TYR 0.015 0.001 TYR C 841 PHE 0.018 0.001 PHE A 248 TRP 0.028 0.002 TRP E 110 HIS 0.006 0.001 HIS C 334 Details of bonding type rmsd covalent geometry : bond 0.00582 (18933) covalent geometry : angle 0.61377 (25599) hydrogen bonds : bond 0.04851 ( 824) hydrogen bonds : angle 5.18553 ( 2328) *********************** 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 148 residues out of total 2035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 125 time to evaluate : 0.780 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 110 MET cc_start: 0.8891 (pmm) cc_final: 0.8430 (pmm) REVERT: A 113 GLN cc_start: 0.9270 (OUTLIER) cc_final: 0.8838 (pm20) REVERT: A 838 PHE cc_start: 0.7284 (m-80) cc_final: 0.6914 (m-80) REVERT: B 53 ASP cc_start: 0.8279 (m-30) cc_final: 0.8039 (m-30) REVERT: C 167 MET cc_start: 0.7935 (mmp) cc_final: 0.7684 (mmm) REVERT: C 360 LYS cc_start: 0.8616 (ptmt) cc_final: 0.8121 (tppt) REVERT: C 645 MET cc_start: 0.7532 (tmm) cc_final: 0.7097 (tmm) REVERT: C 783 MET cc_start: 0.7856 (mtp) cc_final: 0.7588 (mtm) REVERT: C 797 MET cc_start: 0.8996 (OUTLIER) cc_final: 0.8613 (ptp) REVERT: D 53 ASP cc_start: 0.8856 (m-30) cc_final: 0.8492 (m-30) REVERT: E 69 ARG cc_start: 0.8157 (ttm-80) cc_final: 0.7900 (ttm-80) REVERT: E 72 ARG cc_start: 0.7874 (mtp85) cc_final: 0.6676 (ptt-90) REVERT: E 80 PHE cc_start: 0.9125 (m-80) cc_final: 0.8790 (m-80) REVERT: E 100 GLN cc_start: 0.7318 (OUTLIER) cc_final: 0.7032 (mp10) outliers start: 23 outliers final: 12 residues processed: 139 average time/residue: 0.1169 time to fit residues: 26.3655 Evaluate side-chains 133 residues out of total 2035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 118 time to evaluate : 0.753 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 GLN Chi-restraints excluded: chain A residue 577 VAL 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 669 VAL Chi-restraints excluded: chain C residue 797 MET Chi-restraints excluded: chain D residue 100 THR Chi-restraints excluded: chain D residue 198 ILE Chi-restraints excluded: chain D residue 309 MET Chi-restraints excluded: chain E residue 20 ILE 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 167 optimal weight: 5.9990 chunk 48 optimal weight: 9.9990 chunk 190 optimal weight: 0.9980 chunk 60 optimal weight: 9.9990 chunk 185 optimal weight: 9.9990 chunk 22 optimal weight: 1.9990 chunk 10 optimal weight: 0.9980 chunk 137 optimal weight: 0.8980 chunk 146 optimal weight: 0.9990 chunk 109 optimal weight: 3.9990 chunk 194 optimal weight: 4.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 565 ASN ** C 624 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.079566 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.2961 r_free = 0.2961 target = 0.054662 restraints weight = 73416.651| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.056477 restraints weight = 39141.761| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.057542 restraints weight = 28124.765| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.058135 restraints weight = 23630.852| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.058475 restraints weight = 21633.664| |-----------------------------------------------------------------------------| r_work (final): 0.3035 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8317 moved from start: 0.1613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 18933 Z= 0.113 Angle : 0.521 8.429 25599 Z= 0.264 Chirality : 0.042 0.172 2725 Planarity : 0.004 0.047 3289 Dihedral : 3.817 17.296 2479 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 0.84 % Allowed : 11.89 % Favored : 87.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.14 (0.18), residues: 2222 helix: 1.65 (0.17), residues: 975 sheet: -0.14 (0.31), residues: 278 loop : 0.24 (0.21), residues: 969 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 69 TYR 0.025 0.001 TYR E 125 PHE 0.012 0.001 PHE D 158 TRP 0.021 0.001 TRP E 110 HIS 0.004 0.001 HIS A 221 Details of bonding type rmsd covalent geometry : bond 0.00246 (18933) covalent geometry : angle 0.52126 (25599) hydrogen bonds : bond 0.03962 ( 824) hydrogen bonds : angle 4.76051 ( 2328) *********************** 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 160 residues out of total 2035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 143 time to evaluate : 0.773 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 110 MET cc_start: 0.8915 (pmm) cc_final: 0.8555 (pmm) REVERT: A 113 GLN cc_start: 0.9226 (OUTLIER) cc_final: 0.8897 (pm20) REVERT: A 380 GLU cc_start: 0.8514 (tp30) cc_final: 0.8251 (tp30) REVERT: A 566 MET cc_start: 0.7998 (tmm) cc_final: 0.7526 (tmm) REVERT: A 624 GLN cc_start: 0.8701 (tm-30) cc_final: 0.8446 (tm-30) REVERT: A 838 PHE cc_start: 0.7138 (m-80) cc_final: 0.6770 (m-80) REVERT: B 53 ASP cc_start: 0.8215 (m-30) cc_final: 0.7887 (m-30) REVERT: B 232 GLU cc_start: 0.8499 (pm20) cc_final: 0.8254 (pm20) REVERT: C 76 MET cc_start: 0.8930 (ptt) cc_final: 0.8299 (ppp) REVERT: C 167 MET cc_start: 0.8081 (mmp) cc_final: 0.7857 (mmm) REVERT: C 360 LYS cc_start: 0.8666 (ptmt) cc_final: 0.8174 (tppt) REVERT: C 655 PHE cc_start: 0.8782 (m-10) cc_final: 0.8581 (m-10) REVERT: C 783 MET cc_start: 0.7825 (mtp) cc_final: 0.7546 (mtm) REVERT: D 53 ASP cc_start: 0.8773 (m-30) cc_final: 0.8471 (m-30) REVERT: E 69 ARG cc_start: 0.8057 (ttm-80) cc_final: 0.7805 (ttm-80) REVERT: E 72 ARG cc_start: 0.7806 (mtp85) cc_final: 0.6539 (ptt-90) REVERT: E 80 PHE cc_start: 0.9076 (m-80) cc_final: 0.8806 (m-80) outliers start: 17 outliers final: 10 residues processed: 157 average time/residue: 0.1214 time to fit residues: 30.9093 Evaluate side-chains 140 residues out of total 2035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 129 time to evaluate : 0.586 ------------------------------------------------------------------------------- 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 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 669 VAL Chi-restraints excluded: chain D residue 262 LEU Chi-restraints excluded: chain E residue 20 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 49 optimal weight: 20.0000 chunk 180 optimal weight: 9.9990 chunk 123 optimal weight: 4.9990 chunk 41 optimal weight: 4.9990 chunk 11 optimal weight: 8.9990 chunk 216 optimal weight: 40.0000 chunk 39 optimal weight: 8.9990 chunk 82 optimal weight: 0.7980 chunk 36 optimal weight: 1.9990 chunk 181 optimal weight: 5.9990 chunk 185 optimal weight: 4.9990 overall best weight: 3.5588 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.077571 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2903 r_free = 0.2903 target = 0.052483 restraints weight = 73917.400| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.2949 r_free = 0.2949 target = 0.054215 restraints weight = 40471.516| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 60)----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.055199 restraints weight = 29477.254| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.055767 restraints weight = 24980.484| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.056010 restraints weight = 22914.539| |-----------------------------------------------------------------------------| r_work (final): 0.2972 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8386 moved from start: 0.1743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 18933 Z= 0.231 Angle : 0.599 8.214 25599 Z= 0.302 Chirality : 0.044 0.274 2725 Planarity : 0.004 0.045 3289 Dihedral : 4.022 18.055 2479 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 9.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Rotamer: Outliers : 1.47 % Allowed : 12.73 % Favored : 85.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.00 (0.18), residues: 2222 helix: 1.55 (0.17), residues: 981 sheet: -0.25 (0.31), residues: 276 loop : 0.14 (0.21), residues: 965 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 69 TYR 0.015 0.001 TYR C 841 PHE 0.013 0.001 PHE A 248 TRP 0.017 0.002 TRP E 110 HIS 0.005 0.001 HIS C 334 Details of bonding type rmsd covalent geometry : bond 0.00507 (18933) covalent geometry : angle 0.59893 (25599) hydrogen bonds : bond 0.04194 ( 824) hydrogen bonds : angle 4.87238 ( 2328) *********************** 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 153 residues out of total 2035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 123 time to evaluate : 0.813 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 110 MET cc_start: 0.8947 (pmm) cc_final: 0.8567 (pmm) REVERT: A 113 GLN cc_start: 0.9265 (OUTLIER) cc_final: 0.8851 (pm20) REVERT: A 205 GLU cc_start: 0.7936 (pm20) cc_final: 0.7671 (pm20) REVERT: A 380 GLU cc_start: 0.8700 (tp30) cc_final: 0.8455 (tp30) REVERT: A 624 GLN cc_start: 0.8616 (tm-30) cc_final: 0.8367 (tm-30) REVERT: A 645 MET cc_start: 0.7778 (OUTLIER) cc_final: 0.6778 (tmm) REVERT: A 838 PHE cc_start: 0.7252 (m-80) cc_final: 0.6843 (m-80) REVERT: B 53 ASP cc_start: 0.8292 (m-30) cc_final: 0.7937 (m-30) REVERT: C 76 MET cc_start: 0.9016 (ptt) cc_final: 0.8355 (ppp) REVERT: C 167 MET cc_start: 0.8078 (mmp) cc_final: 0.7566 (mmm) REVERT: C 356 LEU cc_start: 0.9744 (OUTLIER) cc_final: 0.9478 (mt) REVERT: C 360 LYS cc_start: 0.8637 (ptmt) cc_final: 0.8142 (tppt) REVERT: C 655 PHE cc_start: 0.8812 (m-10) cc_final: 0.8612 (m-10) REVERT: C 783 MET cc_start: 0.7919 (mtp) cc_final: 0.7674 (mtm) REVERT: D 53 ASP cc_start: 0.8844 (m-30) cc_final: 0.8551 (m-30) REVERT: E 69 ARG cc_start: 0.7968 (ttm-80) cc_final: 0.7728 (ttm-80) REVERT: E 72 ARG cc_start: 0.7866 (mtp85) cc_final: 0.6683 (ptt-90) REVERT: E 80 PHE cc_start: 0.9122 (m-80) cc_final: 0.8878 (m-80) outliers start: 30 outliers final: 16 residues processed: 147 average time/residue: 0.1283 time to fit residues: 30.7459 Evaluate side-chains 136 residues out of total 2035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 117 time to evaluate : 0.790 ------------------------------------------------------------------------------- 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 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 574 VAL Chi-restraints excluded: chain C residue 669 VAL Chi-restraints excluded: chain C residue 719 HIS Chi-restraints excluded: chain D residue 100 THR 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 E residue 20 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 109 optimal weight: 6.9990 chunk 169 optimal weight: 0.3980 chunk 190 optimal weight: 0.9980 chunk 108 optimal weight: 20.0000 chunk 88 optimal weight: 5.9990 chunk 82 optimal weight: 9.9990 chunk 121 optimal weight: 0.8980 chunk 105 optimal weight: 6.9990 chunk 48 optimal weight: 9.9990 chunk 165 optimal weight: 8.9990 chunk 164 optimal weight: 3.9990 overall best weight: 2.4584 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.078269 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2925 r_free = 0.2925 target = 0.053347 restraints weight = 73511.625| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2973 r_free = 0.2973 target = 0.055128 restraints weight = 39853.070| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.056120 restraints weight = 28874.441| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.056715 restraints weight = 24340.672| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 16)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.056918 restraints weight = 22280.138| |-----------------------------------------------------------------------------| r_work (final): 0.2994 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8358 moved from start: 0.1838 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= 0.167 Angle : 0.564 9.343 25599 Z= 0.282 Chirality : 0.043 0.262 2725 Planarity : 0.004 0.046 3289 Dihedral : 3.940 19.734 2479 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 1.62 % Allowed : 13.32 % Favored : 85.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.05 (0.18), residues: 2222 helix: 1.60 (0.17), residues: 979 sheet: -0.22 (0.31), residues: 276 loop : 0.16 (0.21), residues: 967 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 69 TYR 0.020 0.001 TYR C 841 PHE 0.012 0.001 PHE D 158 TRP 0.016 0.002 TRP E 110 HIS 0.003 0.001 HIS A 805 Details of bonding type rmsd covalent geometry : bond 0.00370 (18933) covalent geometry : angle 0.56358 (25599) hydrogen bonds : bond 0.03938 ( 824) hydrogen bonds : angle 4.73435 ( 2328) *********************** 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: 33 poor density : 126 time to evaluate : 0.769 Fit side-chains REVERT: A 110 MET cc_start: 0.8877 (pmm) cc_final: 0.8523 (pmm) REVERT: A 113 GLN cc_start: 0.9268 (OUTLIER) cc_final: 0.8924 (pm20) REVERT: A 205 GLU cc_start: 0.8005 (pm20) cc_final: 0.7733 (pm20) REVERT: A 380 GLU cc_start: 0.8679 (tp30) cc_final: 0.8418 (tp30) REVERT: A 566 MET cc_start: 0.7932 (tmm) cc_final: 0.7443 (tmm) REVERT: A 645 MET cc_start: 0.8182 (tmm) cc_final: 0.7248 (tmm) REVERT: A 838 PHE cc_start: 0.7242 (m-80) cc_final: 0.6790 (m-80) REVERT: B 53 ASP cc_start: 0.8249 (m-30) cc_final: 0.7885 (m-30) REVERT: B 252 LEU cc_start: 0.9606 (OUTLIER) cc_final: 0.9303 (mm) REVERT: C 76 MET cc_start: 0.9000 (ptt) cc_final: 0.8341 (ppp) REVERT: C 167 MET cc_start: 0.8109 (mmp) cc_final: 0.7588 (mmm) REVERT: C 360 LYS cc_start: 0.8657 (ptmt) cc_final: 0.8145 (tppt) REVERT: C 655 PHE cc_start: 0.8771 (m-10) cc_final: 0.8568 (m-10) REVERT: D 53 ASP cc_start: 0.8822 (m-30) cc_final: 0.8532 (m-30) REVERT: E 69 ARG cc_start: 0.7930 (ttm-80) cc_final: 0.7704 (ttm-80) REVERT: E 72 ARG cc_start: 0.7876 (mtp85) cc_final: 0.6688 (ptt-90) REVERT: E 80 PHE cc_start: 0.9089 (m-80) cc_final: 0.8854 (m-80) outliers start: 33 outliers final: 21 residues processed: 153 average time/residue: 0.1191 time to fit residues: 30.1356 Evaluate side-chains 143 residues out of total 2035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 120 time to evaluate : 0.470 ------------------------------------------------------------------------------- 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 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 B residue 252 LEU Chi-restraints excluded: chain C residue 236 LEU Chi-restraints excluded: chain C residue 239 LEU Chi-restraints excluded: chain C residue 669 VAL Chi-restraints excluded: chain C residue 697 THR Chi-restraints excluded: chain C residue 719 HIS Chi-restraints excluded: chain C residue 797 MET Chi-restraints excluded: chain D residue 60 VAL Chi-restraints excluded: chain D residue 100 THR 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 D residue 334 LEU Chi-restraints excluded: chain E residue 20 ILE Chi-restraints excluded: chain E residue 95 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 112 optimal weight: 0.9980 chunk 208 optimal weight: 10.0000 chunk 195 optimal weight: 0.0010 chunk 15 optimal weight: 0.7980 chunk 100 optimal weight: 8.9990 chunk 169 optimal weight: 2.9990 chunk 198 optimal weight: 3.9990 chunk 197 optimal weight: 3.9990 chunk 155 optimal weight: 9.9990 chunk 75 optimal weight: 1.9990 chunk 37 optimal weight: 0.9990 overall best weight: 0.9590 ------------------------------------------------------------------------------- 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 = 0.3557 r_free = 0.3557 target = 0.079536 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2963 r_free = 0.2963 target = 0.054606 restraints weight = 72729.993| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.056482 restraints weight = 37302.392| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.057610 restraints weight = 26194.088| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.058243 restraints weight = 21793.309| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 49)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.058573 restraints weight = 19799.059| |-----------------------------------------------------------------------------| r_work (final): 0.3038 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8306 moved from start: 0.1977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 18933 Z= 0.106 Angle : 0.544 11.342 25599 Z= 0.268 Chirality : 0.043 0.338 2725 Planarity : 0.003 0.045 3289 Dihedral : 3.755 18.523 2479 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 1.28 % Allowed : 14.05 % Favored : 84.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.17 (0.18), residues: 2222 helix: 1.68 (0.17), residues: 981 sheet: -0.03 (0.31), residues: 278 loop : 0.19 (0.21), residues: 963 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 69 TYR 0.019 0.001 TYR C 841 PHE 0.011 0.001 PHE D 158 TRP 0.017 0.001 TRP C 9 HIS 0.003 0.001 HIS A 221 Details of bonding type rmsd covalent geometry : bond 0.00232 (18933) covalent geometry : angle 0.54358 (25599) hydrogen bonds : bond 0.03639 ( 824) hydrogen bonds : angle 4.55839 ( 2328) *********************** 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 160 residues out of total 2035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 134 time to evaluate : 0.797 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 110 MET cc_start: 0.8823 (pmm) cc_final: 0.8614 (pmm) REVERT: A 113 GLN cc_start: 0.9242 (OUTLIER) cc_final: 0.8926 (pm20) REVERT: A 318 ASP cc_start: 0.8769 (m-30) cc_final: 0.8509 (m-30) REVERT: A 380 GLU cc_start: 0.8670 (tp30) cc_final: 0.8339 (tp30) REVERT: A 566 MET cc_start: 0.7628 (tmm) cc_final: 0.7080 (tmm) REVERT: A 626 MET cc_start: 0.8967 (ttp) cc_final: 0.8106 (tmm) REVERT: A 645 MET cc_start: 0.8160 (OUTLIER) cc_final: 0.7187 (tmm) REVERT: A 838 PHE cc_start: 0.7096 (m-80) cc_final: 0.6686 (m-80) REVERT: B 53 ASP cc_start: 0.8327 (m-30) cc_final: 0.7991 (m-30) REVERT: B 252 LEU cc_start: 0.9572 (OUTLIER) cc_final: 0.9256 (mm) REVERT: C 76 MET cc_start: 0.8986 (ptt) cc_final: 0.8363 (ppp) REVERT: C 110 MET cc_start: 0.8493 (mmp) cc_final: 0.8214 (mmp) REVERT: C 360 LYS cc_start: 0.8705 (ptmt) cc_final: 0.8197 (tppt) REVERT: D 53 ASP cc_start: 0.8778 (m-30) cc_final: 0.8508 (m-30) REVERT: E 69 ARG cc_start: 0.7879 (ttm-80) cc_final: 0.7661 (ttm-80) REVERT: E 72 ARG cc_start: 0.7950 (mtp85) cc_final: 0.6687 (ptt-90) REVERT: E 80 PHE cc_start: 0.9083 (m-80) cc_final: 0.8845 (m-80) outliers start: 26 outliers final: 16 residues processed: 154 average time/residue: 0.1346 time to fit residues: 33.9793 Evaluate side-chains 144 residues out of total 2035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 125 time to evaluate : 0.788 ------------------------------------------------------------------------------- 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 652 ILE Chi-restraints excluded: chain A residue 686 LEU Chi-restraints excluded: chain B residue 64 HIS Chi-restraints excluded: chain B residue 252 LEU 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 719 HIS Chi-restraints excluded: chain D residue 60 VAL Chi-restraints excluded: chain D residue 252 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 32 optimal weight: 0.7980 chunk 218 optimal weight: 6.9990 chunk 119 optimal weight: 7.9990 chunk 113 optimal weight: 4.9990 chunk 38 optimal weight: 4.9990 chunk 65 optimal weight: 7.9990 chunk 55 optimal weight: 0.7980 chunk 34 optimal weight: 0.8980 chunk 149 optimal weight: 0.4980 chunk 180 optimal weight: 0.7980 chunk 183 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 = 0.3571 r_free = 0.3571 target = 0.080153 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2980 r_free = 0.2980 target = 0.055228 restraints weight = 72810.418| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.057099 restraints weight = 38490.225| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 58)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.058194 restraints weight = 27346.610| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.058810 restraints weight = 22904.494| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.059030 restraints weight = 20910.820| |-----------------------------------------------------------------------------| r_work (final): 0.3051 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8309 moved from start: 0.2126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 18933 Z= 0.099 Angle : 0.560 12.235 25599 Z= 0.272 Chirality : 0.043 0.352 2725 Planarity : 0.003 0.043 3289 Dihedral : 3.645 18.288 2479 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 1.18 % Allowed : 14.50 % Favored : 84.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.25 (0.18), residues: 2222 helix: 1.72 (0.17), residues: 990 sheet: 0.12 (0.31), residues: 278 loop : 0.21 (0.21), residues: 954 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 69 TYR 0.018 0.001 TYR C 841 PHE 0.017 0.001 PHE C 655 TRP 0.015 0.001 TRP C 9 HIS 0.003 0.001 HIS A 221 Details of bonding type rmsd covalent geometry : bond 0.00217 (18933) covalent geometry : angle 0.56012 (25599) hydrogen bonds : bond 0.03440 ( 824) hydrogen bonds : angle 4.44235 ( 2328) *********************** 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 162 residues out of total 2035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 138 time to evaluate : 0.797 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 110 MET cc_start: 0.8893 (OUTLIER) cc_final: 0.8664 (pmm) REVERT: A 113 GLN cc_start: 0.9198 (OUTLIER) cc_final: 0.8895 (pm20) REVERT: A 318 ASP cc_start: 0.8551 (m-30) cc_final: 0.8330 (m-30) REVERT: A 380 GLU cc_start: 0.8647 (tp30) cc_final: 0.8296 (tp30) REVERT: A 566 MET cc_start: 0.7593 (tmm) cc_final: 0.7092 (tmm) REVERT: A 626 MET cc_start: 0.8936 (ttp) cc_final: 0.8207 (tmm) REVERT: A 645 MET cc_start: 0.8177 (OUTLIER) cc_final: 0.7231 (tmm) REVERT: A 656 TYR cc_start: 0.8352 (m-80) cc_final: 0.8071 (m-80) REVERT: A 838 PHE cc_start: 0.7049 (m-80) cc_final: 0.6652 (m-80) REVERT: B 53 ASP cc_start: 0.8293 (m-30) cc_final: 0.7960 (m-30) REVERT: B 252 LEU cc_start: 0.9546 (OUTLIER) cc_final: 0.9211 (mm) REVERT: C 76 MET cc_start: 0.8951 (ptt) cc_final: 0.8361 (ppp) REVERT: C 110 MET cc_start: 0.8382 (mmp) cc_final: 0.8142 (mmp) REVERT: C 167 MET cc_start: 0.8176 (mmp) cc_final: 0.7471 (mmm) REVERT: C 360 LYS cc_start: 0.8714 (ptmt) cc_final: 0.8263 (tppt) REVERT: C 625 LEU cc_start: 0.8942 (mt) cc_final: 0.8494 (mt) REVERT: D 1 MET cc_start: 0.6684 (ppp) cc_final: 0.6213 (ppp) REVERT: D 53 ASP cc_start: 0.8730 (m-30) cc_final: 0.8473 (m-30) REVERT: D 105 MET cc_start: 0.9124 (mmm) cc_final: 0.8857 (mmm) REVERT: E 69 ARG cc_start: 0.7854 (ttm-80) cc_final: 0.7645 (ttm-80) REVERT: E 72 ARG cc_start: 0.7801 (mtp85) cc_final: 0.6552 (ptt-90) REVERT: E 80 PHE cc_start: 0.9084 (m-80) cc_final: 0.8838 (m-80) outliers start: 24 outliers final: 15 residues processed: 155 average time/residue: 0.1258 time to fit residues: 31.9723 Evaluate side-chains 148 residues out of total 2035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 129 time to evaluate : 0.685 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 HIS Chi-restraints excluded: chain A residue 110 MET Chi-restraints excluded: chain A residue 113 GLN Chi-restraints excluded: chain A residue 548 GLU Chi-restraints excluded: chain A residue 645 MET Chi-restraints excluded: chain B residue 64 HIS Chi-restraints excluded: chain B residue 100 THR Chi-restraints excluded: chain B residue 252 LEU 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 697 THR Chi-restraints excluded: chain C residue 719 HIS Chi-restraints excluded: chain D residue 60 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 133 optimal weight: 4.9990 chunk 125 optimal weight: 0.0030 chunk 171 optimal weight: 3.9990 chunk 126 optimal weight: 0.6980 chunk 162 optimal weight: 0.6980 chunk 22 optimal weight: 7.9990 chunk 174 optimal weight: 9.9990 chunk 187 optimal weight: 6.9990 chunk 141 optimal weight: 1.9990 chunk 190 optimal weight: 0.8980 chunk 50 optimal weight: 10.0000 overall best weight: 0.8592 ------------------------------------------------------------------------------- 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 = 0.3575 r_free = 0.3575 target = 0.080308 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.055432 restraints weight = 73257.064| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.057324 restraints weight = 38624.507| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.058435 restraints weight = 27417.771| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.059054 restraints weight = 22930.619| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.059324 restraints weight = 20912.615| |-----------------------------------------------------------------------------| r_work (final): 0.3060 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8303 moved from start: 0.2211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 18933 Z= 0.100 Angle : 0.556 11.895 25599 Z= 0.269 Chirality : 0.043 0.357 2725 Planarity : 0.003 0.042 3289 Dihedral : 3.585 20.029 2479 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 1.38 % Allowed : 14.84 % Favored : 83.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.31 (0.18), residues: 2222 helix: 1.77 (0.17), residues: 990 sheet: 0.11 (0.31), residues: 287 loop : 0.27 (0.21), residues: 945 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 69 TYR 0.017 0.001 TYR C 841 PHE 0.020 0.001 PHE C 655 TRP 0.016 0.001 TRP A 177 HIS 0.003 0.001 HIS A 221 Details of bonding type rmsd covalent geometry : bond 0.00219 (18933) covalent geometry : angle 0.55610 (25599) hydrogen bonds : bond 0.03364 ( 824) hydrogen bonds : angle 4.36765 ( 2328) *********************** 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: 28 poor density : 128 time to evaluate : 0.813 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 110 MET cc_start: 0.8893 (OUTLIER) cc_final: 0.8653 (pmm) REVERT: A 113 GLN cc_start: 0.9191 (OUTLIER) cc_final: 0.8873 (pm20) REVERT: A 318 ASP cc_start: 0.8543 (m-30) cc_final: 0.8310 (m-30) REVERT: A 380 GLU cc_start: 0.8657 (tp30) cc_final: 0.8296 (tp30) REVERT: A 566 MET cc_start: 0.7644 (tmm) cc_final: 0.7129 (tmm) REVERT: A 626 MET cc_start: 0.8928 (ttp) cc_final: 0.8208 (tmm) REVERT: A 645 MET cc_start: 0.8190 (OUTLIER) cc_final: 0.7179 (tmm) REVERT: A 656 TYR cc_start: 0.8373 (m-80) cc_final: 0.8112 (m-80) REVERT: A 838 PHE cc_start: 0.7023 (m-80) cc_final: 0.6649 (m-80) REVERT: B 53 ASP cc_start: 0.8295 (m-30) cc_final: 0.7961 (m-30) REVERT: B 252 LEU cc_start: 0.9546 (OUTLIER) cc_final: 0.9214 (mm) REVERT: C 76 MET cc_start: 0.8955 (ptt) cc_final: 0.8364 (ppp) REVERT: C 110 MET cc_start: 0.8396 (mmp) cc_final: 0.8163 (mmp) REVERT: C 167 MET cc_start: 0.8094 (mmp) cc_final: 0.7367 (mmm) REVERT: C 360 LYS cc_start: 0.8715 (ptmt) cc_final: 0.8231 (tppt) REVERT: C 625 LEU cc_start: 0.8965 (mt) cc_final: 0.8499 (mt) REVERT: D 1 MET cc_start: 0.6679 (ppp) cc_final: 0.6403 (ppp) REVERT: D 53 ASP cc_start: 0.8723 (m-30) cc_final: 0.8470 (m-30) REVERT: D 105 MET cc_start: 0.9136 (mmm) cc_final: 0.8861 (mmm) REVERT: E 69 ARG cc_start: 0.7787 (ttm-80) cc_final: 0.7587 (ttm-80) REVERT: E 72 ARG cc_start: 0.7800 (mtp85) cc_final: 0.6548 (ptt-90) REVERT: E 80 PHE cc_start: 0.9079 (m-80) cc_final: 0.8829 (m-80) outliers start: 28 outliers final: 17 residues processed: 149 average time/residue: 0.1285 time to fit residues: 31.4385 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 : 0.780 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 MET Chi-restraints excluded: chain A residue 113 GLN Chi-restraints excluded: chain A residue 548 GLU Chi-restraints excluded: chain A residue 645 MET Chi-restraints excluded: chain B residue 64 HIS Chi-restraints excluded: chain B residue 100 THR Chi-restraints excluded: chain B residue 252 LEU 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 697 THR Chi-restraints excluded: chain D residue 60 VAL Chi-restraints excluded: chain D residue 100 THR Chi-restraints excluded: chain D residue 109 LEU 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 D residue 334 LEU Chi-restraints excluded: chain E residue 20 ILE 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 159 optimal weight: 4.9990 chunk 177 optimal weight: 5.9990 chunk 108 optimal weight: 20.0000 chunk 22 optimal weight: 3.9990 chunk 98 optimal weight: 8.9990 chunk 106 optimal weight: 7.9990 chunk 34 optimal weight: 0.6980 chunk 125 optimal weight: 0.0870 chunk 139 optimal weight: 0.9980 chunk 55 optimal weight: 0.5980 chunk 150 optimal weight: 6.9990 overall best weight: 1.2760 ------------------------------------------------------------------------------- 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 376 ASN ** E 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.079966 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.2975 r_free = 0.2975 target = 0.055131 restraints weight = 73276.467| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.056960 restraints weight = 39345.729| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.058030 restraints weight = 28241.430| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.058660 restraints weight = 23747.925| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 49)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.058975 restraints weight = 21632.844| |-----------------------------------------------------------------------------| r_work (final): 0.3051 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8306 moved from start: 0.2250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 18933 Z= 0.112 Angle : 0.567 13.277 25599 Z= 0.273 Chirality : 0.043 0.349 2725 Planarity : 0.003 0.044 3289 Dihedral : 3.601 19.366 2479 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 1.18 % Allowed : 14.94 % Favored : 83.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.33 (0.18), residues: 2222 helix: 1.80 (0.17), residues: 990 sheet: 0.16 (0.31), residues: 285 loop : 0.24 (0.21), residues: 947 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 69 TYR 0.017 0.001 TYR C 841 PHE 0.019 0.001 PHE C 655 TRP 0.013 0.001 TRP A 352 HIS 0.004 0.001 HIS A 59 Details of bonding type rmsd covalent geometry : bond 0.00249 (18933) covalent geometry : angle 0.56696 (25599) hydrogen bonds : bond 0.03374 ( 824) hydrogen bonds : angle 4.34761 ( 2328) ********************** 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 151 residues out of total 2035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 127 time to evaluate : 0.925 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 110 MET cc_start: 0.8906 (OUTLIER) cc_final: 0.8646 (pmm) REVERT: A 113 GLN cc_start: 0.9204 (OUTLIER) cc_final: 0.8878 (pm20) REVERT: A 318 ASP cc_start: 0.8564 (m-30) cc_final: 0.8351 (m-30) REVERT: A 380 GLU cc_start: 0.8679 (tp30) cc_final: 0.8321 (tp30) REVERT: A 626 MET cc_start: 0.8958 (ttp) cc_final: 0.8232 (tmm) REVERT: A 645 MET cc_start: 0.8094 (OUTLIER) cc_final: 0.7088 (tmm) REVERT: A 656 TYR cc_start: 0.8378 (m-80) cc_final: 0.8131 (m-80) REVERT: A 838 PHE cc_start: 0.7027 (m-80) cc_final: 0.6655 (m-80) REVERT: B 53 ASP cc_start: 0.8317 (m-30) cc_final: 0.7980 (m-30) REVERT: B 252 LEU cc_start: 0.9554 (OUTLIER) cc_final: 0.9220 (mm) REVERT: C 76 MET cc_start: 0.8973 (ptt) cc_final: 0.8376 (ppp) REVERT: C 167 MET cc_start: 0.8094 (mmp) cc_final: 0.7373 (mmm) REVERT: C 324 CYS cc_start: 0.8170 (m) cc_final: 0.7569 (m) REVERT: C 360 LYS cc_start: 0.8737 (ptmt) cc_final: 0.8265 (tppt) REVERT: C 625 LEU cc_start: 0.8957 (mt) cc_final: 0.8489 (mt) REVERT: D 53 ASP cc_start: 0.8734 (m-30) cc_final: 0.8488 (m-30) REVERT: D 105 MET cc_start: 0.9154 (mmm) cc_final: 0.8873 (mmm) REVERT: E 72 ARG cc_start: 0.7799 (mtp85) cc_final: 0.6501 (ptt-90) REVERT: E 80 PHE cc_start: 0.9081 (m-80) cc_final: 0.8828 (m-80) outliers start: 24 outliers final: 19 residues processed: 145 average time/residue: 0.1262 time to fit residues: 30.2257 Evaluate side-chains 149 residues out of total 2035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 126 time to evaluate : 0.546 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 HIS Chi-restraints excluded: chain A residue 110 MET Chi-restraints excluded: chain A residue 113 GLN 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 100 THR Chi-restraints excluded: chain B residue 252 LEU 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 697 THR Chi-restraints excluded: chain D residue 60 VAL Chi-restraints excluded: chain D residue 100 THR Chi-restraints excluded: chain D residue 109 LEU 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 D residue 334 LEU Chi-restraints excluded: chain E residue 20 ILE 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 136 optimal weight: 3.9990 chunk 115 optimal weight: 4.9990 chunk 92 optimal weight: 0.9980 chunk 65 optimal weight: 20.0000 chunk 86 optimal weight: 4.9990 chunk 44 optimal weight: 7.9990 chunk 153 optimal weight: 3.9990 chunk 3 optimal weight: 5.9990 chunk 187 optimal weight: 4.9990 chunk 10 optimal weight: 5.9990 chunk 146 optimal weight: 0.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- 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 = 0.3531 r_free = 0.3531 target = 0.078379 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.2926 r_free = 0.2926 target = 0.053458 restraints weight = 73954.694| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.2972 r_free = 0.2972 target = 0.055218 restraints weight = 40095.365| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 62)----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.056261 restraints weight = 28923.321| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.056830 restraints weight = 24334.253| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.057092 restraints weight = 22258.297| |-----------------------------------------------------------------------------| r_work (final): 0.2999 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8358 moved from start: 0.2157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 18933 Z= 0.202 Angle : 0.621 12.120 25599 Z= 0.304 Chirality : 0.044 0.340 2725 Planarity : 0.004 0.042 3289 Dihedral : 3.856 24.866 2479 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 9.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer: Outliers : 1.23 % Allowed : 14.89 % Favored : 83.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.20 (0.19), residues: 2222 helix: 1.76 (0.17), residues: 987 sheet: -0.17 (0.30), residues: 293 loop : 0.19 (0.21), residues: 942 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 69 TYR 0.026 0.001 TYR C 841 PHE 0.017 0.001 PHE C 655 TRP 0.012 0.001 TRP D 332 HIS 0.005 0.001 HIS C 719 Details of bonding type rmsd covalent geometry : bond 0.00446 (18933) covalent geometry : angle 0.62065 (25599) hydrogen bonds : bond 0.03756 ( 824) hydrogen bonds : angle 4.52061 ( 2328) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3181.62 seconds wall clock time: 55 minutes 54.73 seconds (3354.73 seconds total)