Starting phenix.real_space_refine on Sat Sep 28 04:08:11 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9bf1_44486/09_2024/9bf1_44486.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9bf1_44486/09_2024/9bf1_44486.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9bf1_44486/09_2024/9bf1_44486.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9bf1_44486/09_2024/9bf1_44486.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9bf1_44486/09_2024/9bf1_44486.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9bf1_44486/09_2024/9bf1_44486.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.034 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 46 5.16 5 C 11484 2.51 5 N 3192 2.21 5 O 3436 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 18158 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 9079 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1122, 9079 Classifications: {'peptide': 1122} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 32, 'TRANS': 1088} Chain breaks: 3 Chain: "B" Number of atoms: 9079 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1122, 9079 Classifications: {'peptide': 1122} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 32, 'TRANS': 1088} Chain breaks: 3 Time building chain proxies: 11.24, per 1000 atoms: 0.62 Number of scatterers: 18158 At special positions: 0 Unit cell: (121.9, 132.5, 136.21, 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 46 16.00 O 3436 8.00 N 3192 7.00 C 11484 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.45 Conformation dependent library (CDL) restraints added in 2.3 seconds 4456 Ramachandran restraints generated. 2228 Oldfield, 0 Emsley, 2228 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4284 Finding SS restraints... Secondary structure from input PDB file: 95 helices and 20 sheets defined 54.5% alpha, 9.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.28 Creating SS restraints... Processing helix chain 'A' and resid 4 through 9 removed outlier: 3.718A pdb=" N THR A 9 " --> pdb=" O GLU A 6 " (cutoff:3.500A) Processing helix chain 'A' and resid 20 through 37 Proline residue: A 29 - end of helix Processing helix chain 'A' and resid 54 through 78 Processing helix chain 'A' and resid 79 through 81 No H-bonds generated for 'chain 'A' and resid 79 through 81' Processing helix chain 'A' and resid 96 through 112 removed outlier: 3.511A pdb=" N SER A 100 " --> pdb=" O ASP A 96 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ALA A 101 " --> pdb=" O ASN A 97 " (cutoff:3.500A) removed outlier: 6.139A pdb=" N LYS A 102 " --> pdb=" O VAL A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 121 through 130 Processing helix chain 'A' and resid 137 through 145 Processing helix chain 'A' and resid 146 through 157 removed outlier: 3.575A pdb=" N LEU A 150 " --> pdb=" O SER A 146 " (cutoff:3.500A) Processing helix chain 'A' and resid 162 through 178 removed outlier: 3.565A pdb=" N GLN A 166 " --> pdb=" O GLU A 162 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N HIS A 178 " --> pdb=" O GLY A 174 " (cutoff:3.500A) Processing helix chain 'A' and resid 181 through 207 removed outlier: 3.805A pdb=" N SER A 187 " --> pdb=" O GLU A 183 " (cutoff:3.500A) Processing helix chain 'A' and resid 217 through 227 Processing helix chain 'A' and resid 227 through 235 removed outlier: 4.028A pdb=" N LYS A 231 " --> pdb=" O LEU A 227 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ILE A 232 " --> pdb=" O PRO A 228 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N GLY A 235 " --> pdb=" O LYS A 231 " (cutoff:3.500A) Processing helix chain 'A' and resid 244 through 250 Processing helix chain 'A' and resid 259 through 263 Processing helix chain 'A' and resid 276 through 286 Processing helix chain 'A' and resid 293 through 304 removed outlier: 3.577A pdb=" N ILE A 297 " --> pdb=" O LEU A 293 " (cutoff:3.500A) Processing helix chain 'A' and resid 322 through 337 removed outlier: 3.544A pdb=" N GLU A 331 " --> pdb=" O GLU A 327 " (cutoff:3.500A) Processing helix chain 'A' and resid 401 through 435 Processing helix chain 'A' and resid 443 through 459 removed outlier: 3.699A pdb=" N THR A 447 " --> pdb=" O SER A 443 " (cutoff:3.500A) removed outlier: 4.820A pdb=" N GLN A 449 " --> pdb=" O GLU A 445 " (cutoff:3.500A) removed outlier: 5.058A pdb=" N GLU A 450 " --> pdb=" O GLY A 446 " (cutoff:3.500A) Processing helix chain 'A' and resid 461 through 463 No H-bonds generated for 'chain 'A' and resid 461 through 463' Processing helix chain 'A' and resid 464 through 471 Processing helix chain 'A' and resid 475 through 479 removed outlier: 3.965A pdb=" N GLN A 479 " --> pdb=" O GLY A 476 " (cutoff:3.500A) Processing helix chain 'A' and resid 493 through 497 removed outlier: 3.590A pdb=" N HIS A 496 " --> pdb=" O SER A 493 " (cutoff:3.500A) Processing helix chain 'A' and resid 524 through 536 removed outlier: 3.530A pdb=" N GLY A 536 " --> pdb=" O MET A 532 " (cutoff:3.500A) Processing helix chain 'A' and resid 556 through 565 Processing helix chain 'A' and resid 572 through 587 Processing helix chain 'A' and resid 604 through 616 Processing helix chain 'A' and resid 621 through 629 removed outlier: 4.412A pdb=" N ILE A 625 " --> pdb=" O SER A 621 " (cutoff:3.500A) Processing helix chain 'A' and resid 635 through 657 removed outlier: 4.631A pdb=" N PHE A 639 " --> pdb=" O SER A 635 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ALA A 649 " --> pdb=" O SER A 645 " (cutoff:3.500A) Processing helix chain 'A' and resid 672 through 691 removed outlier: 3.755A pdb=" N ILE A 678 " --> pdb=" O THR A 674 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N LYS A 688 " --> pdb=" O PHE A 684 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N LYS A 691 " --> pdb=" O ASP A 687 " (cutoff:3.500A) Processing helix chain 'A' and resid 789 through 808 removed outlier: 3.750A pdb=" N ASN A 793 " --> pdb=" O SER A 789 " (cutoff:3.500A) Processing helix chain 'A' and resid 811 through 825 Processing helix chain 'A' and resid 827 through 837 removed outlier: 4.075A pdb=" N GLN A 837 " --> pdb=" O GLN A 833 " (cutoff:3.500A) Processing helix chain 'A' and resid 838 through 855 removed outlier: 3.878A pdb=" N GLN A 842 " --> pdb=" O THR A 838 " (cutoff:3.500A) Processing helix chain 'A' and resid 874 through 880 Processing helix chain 'A' and resid 889 through 901 removed outlier: 3.687A pdb=" N SER A 901 " --> pdb=" O ASN A 897 " (cutoff:3.500A) Processing helix chain 'A' and resid 909 through 937 removed outlier: 3.970A pdb=" N ARG A 913 " --> pdb=" O ASP A 909 " (cutoff:3.500A) Processing helix chain 'A' and resid 943 through 960 Processing helix chain 'A' and resid 970 through 972 No H-bonds generated for 'chain 'A' and resid 970 through 972' Processing helix chain 'A' and resid 992 through 996 removed outlier: 3.732A pdb=" N PHE A 996 " --> pdb=" O PRO A 993 " (cutoff:3.500A) Processing helix chain 'A' and resid 1000 through 1002 No H-bonds generated for 'chain 'A' and resid 1000 through 1002' Processing helix chain 'A' and resid 1014 through 1019 Processing helix chain 'A' and resid 1023 through 1032 removed outlier: 3.708A pdb=" N TRP A1027 " --> pdb=" O TYR A1023 " (cutoff:3.500A) Processing helix chain 'A' and resid 1045 through 1068 Processing helix chain 'A' and resid 1110 through 1127 Processing helix chain 'A' and resid 1176 through 1189 Processing helix chain 'B' and resid 4 through 9 Processing helix chain 'B' and resid 20 through 37 removed outlier: 3.700A pdb=" N ILE B 26 " --> pdb=" O LEU B 22 " (cutoff:3.500A) Proline residue: B 29 - end of helix Processing helix chain 'B' and resid 54 through 78 Processing helix chain 'B' and resid 79 through 81 No H-bonds generated for 'chain 'B' and resid 79 through 81' Processing helix chain 'B' and resid 95 through 98 Processing helix chain 'B' and resid 99 through 112 Processing helix chain 'B' and resid 121 through 130 Processing helix chain 'B' and resid 137 through 145 Processing helix chain 'B' and resid 146 through 158 Processing helix chain 'B' and resid 162 through 178 removed outlier: 3.615A pdb=" N HIS B 178 " --> pdb=" O GLY B 174 " (cutoff:3.500A) Processing helix chain 'B' and resid 181 through 207 removed outlier: 3.632A pdb=" N SER B 187 " --> pdb=" O GLU B 183 " (cutoff:3.500A) Processing helix chain 'B' and resid 217 through 227 Processing helix chain 'B' and resid 227 through 234 removed outlier: 3.874A pdb=" N LYS B 231 " --> pdb=" O LEU B 227 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ILE B 232 " --> pdb=" O PRO B 228 " (cutoff:3.500A) Processing helix chain 'B' and resid 244 through 250 Processing helix chain 'B' and resid 273 through 286 removed outlier: 3.694A pdb=" N GLN B 277 " --> pdb=" O GLU B 273 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N ASN B 278 " --> pdb=" O ILE B 274 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N GLN B 279 " --> pdb=" O ASP B 275 " (cutoff:3.500A) Processing helix chain 'B' and resid 293 through 304 Processing helix chain 'B' and resid 312 through 316 Processing helix chain 'B' and resid 322 through 337 Processing helix chain 'B' and resid 401 through 435 Processing helix chain 'B' and resid 436 through 438 No H-bonds generated for 'chain 'B' and resid 436 through 438' Processing helix chain 'B' and resid 443 through 460 removed outlier: 4.501A pdb=" N GLN B 449 " --> pdb=" O GLU B 445 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N GLU B 450 " --> pdb=" O GLY B 446 " (cutoff:3.500A) Processing helix chain 'B' and resid 461 through 463 No H-bonds generated for 'chain 'B' and resid 461 through 463' Processing helix chain 'B' and resid 464 through 471 Processing helix chain 'B' and resid 493 through 497 Processing helix chain 'B' and resid 524 through 536 removed outlier: 3.663A pdb=" N GLY B 536 " --> pdb=" O MET B 532 " (cutoff:3.500A) Processing helix chain 'B' and resid 558 through 565 removed outlier: 3.637A pdb=" N GLU B 562 " --> pdb=" O LYS B 558 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LEU B 564 " --> pdb=" O LEU B 560 " (cutoff:3.500A) Processing helix chain 'B' and resid 566 through 568 No H-bonds generated for 'chain 'B' and resid 566 through 568' Processing helix chain 'B' and resid 572 through 587 Processing helix chain 'B' and resid 604 through 616 removed outlier: 3.859A pdb=" N LYS B 616 " --> pdb=" O LEU B 612 " (cutoff:3.500A) Processing helix chain 'B' and resid 621 through 629 removed outlier: 3.554A pdb=" N ILE B 625 " --> pdb=" O SER B 621 " (cutoff:3.500A) Processing helix chain 'B' and resid 633 through 657 removed outlier: 4.257A pdb=" N ALA B 638 " --> pdb=" O GLU B 634 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N PHE B 639 " --> pdb=" O SER B 635 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N LYS B 646 " --> pdb=" O SER B 642 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N ALA B 649 " --> pdb=" O SER B 645 " (cutoff:3.500A) Processing helix chain 'B' and resid 675 through 691 removed outlier: 3.558A pdb=" N LYS B 691 " --> pdb=" O ASP B 687 " (cutoff:3.500A) Processing helix chain 'B' and resid 789 through 808 removed outlier: 3.643A pdb=" N ASN B 793 " --> pdb=" O SER B 789 " (cutoff:3.500A) Processing helix chain 'B' and resid 811 through 824 Processing helix chain 'B' and resid 827 through 836 Processing helix chain 'B' and resid 838 through 856 removed outlier: 4.048A pdb=" N GLN B 842 " --> pdb=" O THR B 838 " (cutoff:3.500A) Processing helix chain 'B' and resid 873 through 879 removed outlier: 4.450A pdb=" N ILE B 877 " --> pdb=" O GLY B 873 " (cutoff:3.500A) Processing helix chain 'B' and resid 889 through 902 Processing helix chain 'B' and resid 909 through 938 removed outlier: 4.362A pdb=" N ARG B 913 " --> pdb=" O ASP B 909 " (cutoff:3.500A) Processing helix chain 'B' and resid 943 through 960 Processing helix chain 'B' and resid 970 through 972 No H-bonds generated for 'chain 'B' and resid 970 through 972' Processing helix chain 'B' and resid 1000 through 1002 No H-bonds generated for 'chain 'B' and resid 1000 through 1002' Processing helix chain 'B' and resid 1009 through 1014 removed outlier: 3.586A pdb=" N SER B1014 " --> pdb=" O GLU B1010 " (cutoff:3.500A) Processing helix chain 'B' and resid 1014 through 1019 Processing helix chain 'B' and resid 1023 through 1032 Processing helix chain 'B' and resid 1045 through 1068 Processing helix chain 'B' and resid 1077 through 1081 removed outlier: 3.826A pdb=" N ILE B1080 " --> pdb=" O PRO B1077 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N TYR B1081 " --> pdb=" O ASN B1078 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1077 through 1081' Processing helix chain 'B' and resid 1110 through 1127 Processing helix chain 'B' and resid 1176 through 1190 Processing sheet with id=AA1, first strand: chain 'A' and resid 43 through 44 removed outlier: 5.937A pdb=" N ALA A 43 " --> pdb=" O ILE A 539 " (cutoff:3.500A) removed outlier: 7.187A pdb=" N GLY A 541 " --> pdb=" O ALA A 43 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N ALA A 267 " --> pdb=" O VAL A 538 " (cutoff:3.500A) removed outlier: 7.494A pdb=" N LEU A 540 " --> pdb=" O ALA A 267 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N LEU A 269 " --> pdb=" O LEU A 540 " (cutoff:3.500A) removed outlier: 7.713A pdb=" N ILE A 542 " --> pdb=" O LEU A 269 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N ILE A 271 " --> pdb=" O ILE A 542 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N LEU A 88 " --> pdb=" O ALA A 240 " (cutoff:3.500A) removed outlier: 7.625A pdb=" N LEU A 242 " --> pdb=" O LEU A 88 " (cutoff:3.500A) removed outlier: 5.609A pdb=" N TYR A 90 " --> pdb=" O LEU A 242 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 113 through 114 Processing sheet with id=AA3, first strand: chain 'A' and resid 251 through 252 Processing sheet with id=AA4, first strand: chain 'A' and resid 291 through 292 Processing sheet with id=AA5, first strand: chain 'A' and resid 342 through 344 removed outlier: 6.916A pdb=" N ASN A 343 " --> pdb=" O ILE A 385 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 595 through 601 removed outlier: 3.704A pdb=" N VAL A 870 " --> pdb=" O LYS A 599 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 974 through 975 Processing sheet with id=AA8, first strand: chain 'A' and resid 997 through 998 Processing sheet with id=AA9, first strand: chain 'A' and resid 1072 through 1074 Processing sheet with id=AB1, first strand: chain 'A' and resid 1097 through 1099 removed outlier: 6.542A pdb=" N PHE A1131 " --> pdb=" O ILE A1162 " (cutoff:3.500A) removed outlier: 8.138A pdb=" N ILE A1164 " --> pdb=" O PHE A1131 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N TYR A1133 " --> pdb=" O ILE A1164 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N ARG A1145 " --> pdb=" O GLU A1163 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 43 through 47 removed outlier: 5.875A pdb=" N ALA B 43 " --> pdb=" O ILE B 539 " (cutoff:3.500A) removed outlier: 7.384A pdb=" N GLY B 541 " --> pdb=" O ALA B 43 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N LEU B 45 " --> pdb=" O GLY B 541 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N ALA B 267 " --> pdb=" O VAL B 538 " (cutoff:3.500A) removed outlier: 7.460A pdb=" N LEU B 540 " --> pdb=" O ALA B 267 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N LEU B 269 " --> pdb=" O LEU B 540 " (cutoff:3.500A) removed outlier: 7.705A pdb=" N ILE B 542 " --> pdb=" O LEU B 269 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N ILE B 271 " --> pdb=" O ILE B 542 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N LEU B 88 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.602A pdb=" N LEU B 242 " --> pdb=" O LEU B 88 " (cutoff:3.500A) removed outlier: 5.567A pdb=" N TYR B 90 " --> pdb=" O LEU B 242 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N VAL B 133 " --> pdb=" O PHE B 241 " (cutoff:3.500A) removed outlier: 8.856A pdb=" N THR B 243 " --> pdb=" O VAL B 133 " (cutoff:3.500A) removed outlier: 8.440A pdb=" N LEU B 135 " --> pdb=" O THR B 243 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 113 through 114 Processing sheet with id=AB4, first strand: chain 'B' and resid 251 through 252 Processing sheet with id=AB5, first strand: chain 'B' and resid 291 through 292 Processing sheet with id=AB6, first strand: chain 'B' and resid 342 through 344 Processing sheet with id=AB7, first strand: chain 'B' and resid 595 through 601 removed outlier: 6.754A pdb=" N LEU B 664 " --> pdb=" O TYR B 775 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 974 through 975 Processing sheet with id=AB9, first strand: chain 'B' and resid 997 through 998 Processing sheet with id=AC1, first strand: chain 'B' and resid 1072 through 1074 removed outlier: 4.256A pdb=" N ASN B1086 " --> pdb=" O LEU B1099 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N LEU B1099 " --> pdb=" O ASN B1086 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N ILE B1097 " --> pdb=" O VAL B1088 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N TRP B1098 " --> pdb=" O ILE B1132 " (cutoff:3.500A) removed outlier: 7.915A pdb=" N VAL B1134 " --> pdb=" O TRP B1098 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N ASP B1100 " --> pdb=" O VAL B1134 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N ARG B1145 " --> pdb=" O GLU B1163 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 1137 through 1138 removed outlier: 4.457A pdb=" N GLY B1138 " --> pdb=" O ILE B1168 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 934 hydrogen bonds defined for protein. 2676 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: 6.59 Time building geometry restraints manager: 5.22 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 6079 1.34 - 1.46: 3127 1.46 - 1.57: 9242 1.57 - 1.69: 0 1.69 - 1.81: 72 Bond restraints: 18520 Sorted by residual: bond pdb=" C THR A1045 " pdb=" N PRO A1046 " ideal model delta sigma weight residual 1.335 1.357 -0.022 1.38e-02 5.25e+03 2.53e+00 bond pdb=" CG LEU B 142 " pdb=" CD1 LEU B 142 " ideal model delta sigma weight residual 1.521 1.479 0.042 3.30e-02 9.18e+02 1.58e+00 bond pdb=" CA ASP B1070 " pdb=" CB ASP B1070 " ideal model delta sigma weight residual 1.527 1.541 -0.014 1.61e-02 3.86e+03 7.90e-01 bond pdb=" CA ASN A1042 " pdb=" C ASN A1042 " ideal model delta sigma weight residual 1.529 1.520 0.009 1.04e-02 9.25e+03 7.63e-01 bond pdb=" CB VAL A 502 " pdb=" CG1 VAL A 502 " ideal model delta sigma weight residual 1.521 1.492 0.029 3.30e-02 9.18e+02 7.49e-01 ... (remaining 18515 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.09: 24810 2.09 - 4.17: 185 4.17 - 6.26: 23 6.26 - 8.34: 1 8.34 - 10.43: 1 Bond angle restraints: 25020 Sorted by residual: angle pdb=" C PHE B 999 " pdb=" CA PHE B 999 " pdb=" CB PHE B 999 " ideal model delta sigma weight residual 116.34 109.81 6.53 1.40e+00 5.10e-01 2.17e+01 angle pdb=" N PHE B 999 " pdb=" CA PHE B 999 " pdb=" C PHE B 999 " ideal model delta sigma weight residual 108.00 113.24 -5.24 1.48e+00 4.57e-01 1.25e+01 angle pdb=" CA LEU A 135 " pdb=" CB LEU A 135 " pdb=" CG LEU A 135 " ideal model delta sigma weight residual 116.30 126.73 -10.43 3.50e+00 8.16e-02 8.88e+00 angle pdb=" C PHE A1069 " pdb=" N ASP A1070 " pdb=" CA ASP A1070 " ideal model delta sigma weight residual 122.82 126.76 -3.94 1.42e+00 4.96e-01 7.71e+00 angle pdb=" C PHE B1069 " pdb=" N ASP B1070 " pdb=" CA ASP B1070 " ideal model delta sigma weight residual 122.82 126.63 -3.81 1.42e+00 4.96e-01 7.21e+00 ... (remaining 25015 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.65: 10027 17.65 - 35.30: 964 35.30 - 52.96: 131 52.96 - 70.61: 63 70.61 - 88.26: 27 Dihedral angle restraints: 11212 sinusoidal: 4612 harmonic: 6600 Sorted by residual: dihedral pdb=" CA VAL B 98 " pdb=" C VAL B 98 " pdb=" N VAL B 99 " pdb=" CA VAL B 99 " ideal model delta harmonic sigma weight residual 180.00 152.30 27.70 0 5.00e+00 4.00e-02 3.07e+01 dihedral pdb=" CA VAL A 98 " pdb=" C VAL A 98 " pdb=" N VAL A 99 " pdb=" CA VAL A 99 " ideal model delta harmonic sigma weight residual 180.00 153.35 26.65 0 5.00e+00 4.00e-02 2.84e+01 dihedral pdb=" CA ARG B 675 " pdb=" C ARG B 675 " pdb=" N GLN B 676 " pdb=" CA GLN B 676 " ideal model delta harmonic sigma weight residual 180.00 162.80 17.20 0 5.00e+00 4.00e-02 1.18e+01 ... (remaining 11209 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 1936 0.037 - 0.074: 625 0.074 - 0.111: 152 0.111 - 0.148: 28 0.148 - 0.185: 5 Chirality restraints: 2746 Sorted by residual: chirality pdb=" CG LEU A 135 " pdb=" CB LEU A 135 " pdb=" CD1 LEU A 135 " pdb=" CD2 LEU A 135 " both_signs ideal model delta sigma weight residual False -2.59 -2.40 -0.19 2.00e-01 2.50e+01 8.57e-01 chirality pdb=" CA ASP A1070 " pdb=" N ASP A1070 " pdb=" C ASP A1070 " pdb=" CB ASP A1070 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.53e-01 chirality pdb=" CA ASP B1070 " pdb=" N ASP B1070 " pdb=" C ASP B1070 " pdb=" CB ASP B1070 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.29e-01 ... (remaining 2743 not shown) Planarity restraints: 3256 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE A1049 " -0.013 2.00e-02 2.50e+03 2.54e-02 6.48e+00 pdb=" C PHE A1049 " 0.044 2.00e-02 2.50e+03 pdb=" O PHE A1049 " -0.016 2.00e-02 2.50e+03 pdb=" N THR A1050 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE B1049 " 0.012 2.00e-02 2.50e+03 2.43e-02 5.92e+00 pdb=" C PHE B1049 " -0.042 2.00e-02 2.50e+03 pdb=" O PHE B1049 " 0.016 2.00e-02 2.50e+03 pdb=" N THR B1050 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR A1050 " -0.010 2.00e-02 2.50e+03 1.99e-02 3.96e+00 pdb=" C THR A1050 " 0.034 2.00e-02 2.50e+03 pdb=" O THR A1050 " -0.013 2.00e-02 2.50e+03 pdb=" N ASN A1051 " -0.012 2.00e-02 2.50e+03 ... (remaining 3253 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 596 2.72 - 3.26: 18403 3.26 - 3.81: 29519 3.81 - 4.35: 35368 4.35 - 4.90: 60769 Nonbonded interactions: 144655 Sorted by model distance: nonbonded pdb=" OG1 THR A 121 " pdb=" OE1 GLN A 124 " model vdw 2.174 3.040 nonbonded pdb=" OG SER A 311 " pdb=" O LEU B 379 " model vdw 2.178 3.040 nonbonded pdb=" OH TYR A 494 " pdb=" ND1 HIS A 799 " model vdw 2.199 3.120 nonbonded pdb=" OH TYR B 427 " pdb=" OE2 GLU B 450 " model vdw 2.227 3.040 nonbonded pdb=" OE1 GLU A 77 " pdb=" OG1 THR A 80 " model vdw 2.232 3.040 ... (remaining 144650 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' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 23.840 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: 0.000 Extract box with map and model: 0.280 Check model and map are aligned: 0.150 Set scattering table: 0.200 Process input model: 41.580 Find NCS groups from input model: 0.460 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 69.380 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2759 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 0.042 18520 Z= 0.207 Angle : 0.482 10.429 25020 Z= 0.262 Chirality : 0.040 0.185 2746 Planarity : 0.004 0.048 3256 Dihedral : 14.853 88.261 6928 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.25 % Favored : 94.75 % Rotamer: Outliers : 0.00 % Allowed : 0.25 % Favored : 99.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.71 (0.18), residues: 2228 helix: 1.72 (0.16), residues: 1084 sheet: -0.12 (0.31), residues: 302 loop : -0.95 (0.21), residues: 842 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 336 HIS 0.006 0.001 HIS B 836 PHE 0.009 0.001 PHE A 157 TYR 0.021 0.001 TYR A1115 ARG 0.004 0.000 ARG B 72 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4456 Ramachandran restraints generated. 2228 Oldfield, 0 Emsley, 2228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4456 Ramachandran restraints generated. 2228 Oldfield, 0 Emsley, 2228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 160 time to evaluate : 1.900 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 298 ARG cc_start: 0.3167 (mtp180) cc_final: 0.2653 (ttm-80) REVERT: A 978 MET cc_start: 0.2048 (mmt) cc_final: 0.1783 (mmt) REVERT: B 500 LYS cc_start: 0.2382 (ttpt) cc_final: 0.1674 (ttpt) REVERT: B 613 GLU cc_start: 0.7680 (mt-10) cc_final: 0.7348 (mt-10) REVERT: B 1102 LYS cc_start: 0.7104 (mmtt) cc_final: 0.6862 (mmtt) outliers start: 0 outliers final: 0 residues processed: 160 average time/residue: 0.3653 time to fit residues: 87.0812 Evaluate side-chains 130 residues out of total 1996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 130 time to evaluate : 1.883 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 189 optimal weight: 1.9990 chunk 169 optimal weight: 0.7980 chunk 94 optimal weight: 2.9990 chunk 57 optimal weight: 9.9990 chunk 114 optimal weight: 1.9990 chunk 90 optimal weight: 1.9990 chunk 175 optimal weight: 3.9990 chunk 67 optimal weight: 1.9990 chunk 106 optimal weight: 5.9990 chunk 130 optimal weight: 4.9990 chunk 203 optimal weight: 3.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 70 GLN A 125 GLN A 131 GLN ** A 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 151 ASN ** A 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 253 ASN A 495 HIS A 637 GLN A 679 ASN A 794 GLN A 799 HIS A 800 GLN A 805 GLN A 834 GLN A 935 HIS A1060 GLN A1188 HIS B 131 GLN B 141 GLN ** B 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 279 GLN ** B 307 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 458 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 460 ASN ** B 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 637 GLN B 668 ASN B 790 HIS ** B 807 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 935 HIS B 994 ASN B1060 GLN B1078 ASN Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5750 moved from start: 0.8317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.135 18520 Z= 0.493 Angle : 1.016 19.136 25020 Z= 0.536 Chirality : 0.055 0.281 2746 Planarity : 0.008 0.079 3256 Dihedral : 6.156 25.791 2460 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 16.05 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.01 % Favored : 93.94 % Rotamer: Outliers : 1.60 % Allowed : 9.22 % Favored : 89.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.26 (0.16), residues: 2228 helix: -0.12 (0.14), residues: 1119 sheet: -0.83 (0.34), residues: 232 loop : -1.68 (0.19), residues: 877 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.003 TRP B 336 HIS 0.019 0.003 HIS B 458 PHE 0.035 0.004 PHE B 241 TYR 0.053 0.004 TYR A1115 ARG 0.015 0.001 ARG A 969 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4456 Ramachandran restraints generated. 2228 Oldfield, 0 Emsley, 2228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4456 Ramachandran restraints generated. 2228 Oldfield, 0 Emsley, 2228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 1996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 227 time to evaluate : 3.006 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 271 ILE cc_start: 0.5293 (mt) cc_final: 0.4904 (pt) REVERT: A 327 GLU cc_start: 0.7157 (mp0) cc_final: 0.6509 (mp0) REVERT: A 450 GLU cc_start: 0.7438 (tt0) cc_final: 0.6565 (tt0) REVERT: A 463 GLU cc_start: 0.7607 (mp0) cc_final: 0.7099 (mp0) REVERT: A 522 ASN cc_start: 0.6397 (m-40) cc_final: 0.5959 (m110) REVERT: A 1047 ILE cc_start: 0.6979 (OUTLIER) cc_final: 0.6605 (tp) REVERT: B 172 ILE cc_start: 0.6132 (mm) cc_final: 0.5464 (mm) REVERT: B 318 ILE cc_start: 0.8023 (OUTLIER) cc_final: 0.7745 (mt) REVERT: B 408 GLU cc_start: 0.6914 (mt-10) cc_final: 0.6271 (tt0) REVERT: B 469 TYR cc_start: 0.6871 (m-10) cc_final: 0.6546 (m-10) REVERT: B 493 SER cc_start: 0.8520 (t) cc_final: 0.8306 (m) REVERT: B 576 LYS cc_start: 0.6518 (mtmm) cc_final: 0.6273 (mtpp) REVERT: B 613 GLU cc_start: 0.7921 (mt-10) cc_final: 0.7585 (mt-10) REVERT: B 646 LYS cc_start: 0.5382 (mttt) cc_final: 0.5069 (mttt) REVERT: B 786 ASP cc_start: 0.7404 (OUTLIER) cc_final: 0.6859 (t0) REVERT: B 824 MET cc_start: 0.6748 (mpp) cc_final: 0.6484 (mpp) REVERT: B 829 GLU cc_start: 0.6624 (mp0) cc_final: 0.6209 (mp0) REVERT: B 983 TYR cc_start: 0.6911 (p90) cc_final: 0.5879 (p90) REVERT: B 984 ARG cc_start: 0.5819 (OUTLIER) cc_final: 0.5248 (mtm-85) REVERT: B 1011 GLU cc_start: 0.5838 (tp30) cc_final: 0.5511 (tp30) REVERT: B 1059 GLU cc_start: 0.7047 (pt0) cc_final: 0.6803 (pt0) outliers start: 32 outliers final: 11 residues processed: 250 average time/residue: 0.3163 time to fit residues: 122.6721 Evaluate side-chains 194 residues out of total 1996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 179 time to evaluate : 1.840 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 494 TYR Chi-restraints excluded: chain A residue 502 VAL Chi-restraints excluded: chain A residue 639 PHE Chi-restraints excluded: chain A residue 871 ASP Chi-restraints excluded: chain A residue 1047 ILE Chi-restraints excluded: chain A residue 1057 LEU Chi-restraints excluded: chain B residue 98 VAL Chi-restraints excluded: chain B residue 318 ILE Chi-restraints excluded: chain B residue 733 TYR Chi-restraints excluded: chain B residue 786 ASP Chi-restraints excluded: chain B residue 962 THR Chi-restraints excluded: chain B residue 984 ARG Chi-restraints excluded: chain B residue 1023 TYR Chi-restraints excluded: chain B residue 1047 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 113 optimal weight: 0.2980 chunk 63 optimal weight: 10.0000 chunk 169 optimal weight: 0.6980 chunk 138 optimal weight: 1.9990 chunk 56 optimal weight: 1.9990 chunk 203 optimal weight: 0.9990 chunk 220 optimal weight: 7.9990 chunk 181 optimal weight: 0.5980 chunk 202 optimal weight: 2.9990 chunk 69 optimal weight: 3.9990 chunk 163 optimal weight: 1.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 37 ASN A 160 ASN A 449 GLN A 460 ASN A 637 GLN A 822 GLN A 938 HIS A 956 GLN B 70 GLN B 131 GLN B 144 GLN ** B 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 279 GLN B 307 HIS B 335 ASN B 637 GLN B 668 ASN B 805 GLN B 817 ASN B 821 GLN B1051 ASN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6276 moved from start: 0.9452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.078 18520 Z= 0.267 Angle : 0.599 11.846 25020 Z= 0.314 Chirality : 0.043 0.212 2746 Planarity : 0.005 0.061 3256 Dihedral : 4.471 27.451 2460 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 8.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 1.45 % Allowed : 11.17 % Favored : 87.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.12 (0.17), residues: 2228 helix: 0.95 (0.15), residues: 1127 sheet: -0.47 (0.31), residues: 276 loop : -1.34 (0.21), residues: 825 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A1037 HIS 0.008 0.001 HIS A 496 PHE 0.021 0.002 PHE A 472 TYR 0.026 0.002 TYR A1115 ARG 0.008 0.001 ARG A 478 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4456 Ramachandran restraints generated. 2228 Oldfield, 0 Emsley, 2228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4456 Ramachandran restraints generated. 2228 Oldfield, 0 Emsley, 2228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 1996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 218 time to evaluate : 1.886 Fit side-chains revert: symmetry clash REVERT: A 50 GLN cc_start: 0.6457 (mp10) cc_final: 0.5810 (mp10) REVERT: A 74 GLU cc_start: 0.6293 (tp30) cc_final: 0.5518 (mm-30) REVERT: A 201 ASP cc_start: 0.7381 (t70) cc_final: 0.7159 (t0) REVERT: A 230 GLU cc_start: 0.6697 (tp30) cc_final: 0.6057 (tp30) REVERT: A 278 ASN cc_start: 0.7678 (t0) cc_final: 0.7305 (t0) REVERT: A 463 GLU cc_start: 0.8207 (mp0) cc_final: 0.7501 (mp0) REVERT: A 816 GLU cc_start: 0.6299 (tp30) cc_final: 0.5844 (tp30) REVERT: A 928 LEU cc_start: 0.7456 (OUTLIER) cc_final: 0.7045 (mp) REVERT: A 1028 PHE cc_start: 0.5926 (m-10) cc_final: 0.5207 (m-10) REVERT: B 14 GLN cc_start: 0.6772 (tm-30) cc_final: 0.6238 (tm-30) REVERT: B 105 LEU cc_start: 0.7190 (OUTLIER) cc_final: 0.6977 (tp) REVERT: B 271 ILE cc_start: 0.8354 (mt) cc_final: 0.7787 (mp) REVERT: B 273 GLU cc_start: 0.7036 (mt-10) cc_final: 0.6701 (mt-10) REVERT: B 366 SER cc_start: 0.8312 (p) cc_final: 0.8085 (m) REVERT: B 521 LEU cc_start: 0.8314 (tp) cc_final: 0.8037 (tt) REVERT: B 613 GLU cc_start: 0.7914 (mt-10) cc_final: 0.7574 (mt-10) REVERT: B 797 GLN cc_start: 0.8388 (mp10) cc_final: 0.8154 (mp10) REVERT: B 807 ASN cc_start: 0.6697 (t0) cc_final: 0.6114 (t0) REVERT: B 820 ARG cc_start: 0.6943 (ttp-170) cc_final: 0.5947 (ttp-170) REVERT: B 824 MET cc_start: 0.7088 (mpp) cc_final: 0.5942 (mpp) REVERT: B 829 GLU cc_start: 0.6914 (mp0) cc_final: 0.6452 (mp0) REVERT: B 980 LYS cc_start: 0.7352 (mttt) cc_final: 0.7120 (mttt) REVERT: B 983 TYR cc_start: 0.6958 (p90) cc_final: 0.5750 (p90) REVERT: B 984 ARG cc_start: 0.5915 (OUTLIER) cc_final: 0.5282 (mtm-85) REVERT: B 986 GLN cc_start: 0.7052 (tp40) cc_final: 0.6610 (tp40) REVERT: B 1008 VAL cc_start: 0.6595 (t) cc_final: 0.6291 (t) REVERT: B 1029 GLU cc_start: 0.7694 (mt-10) cc_final: 0.7396 (mt-10) REVERT: B 1044 MET cc_start: 0.7048 (ptp) cc_final: 0.6520 (ptm) REVERT: B 1059 GLU cc_start: 0.7074 (pt0) cc_final: 0.6842 (pt0) outliers start: 29 outliers final: 13 residues processed: 239 average time/residue: 0.3230 time to fit residues: 116.8142 Evaluate side-chains 202 residues out of total 1996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 186 time to evaluate : 2.013 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 232 ILE Chi-restraints excluded: chain A residue 259 SER Chi-restraints excluded: chain A residue 363 THR Chi-restraints excluded: chain A residue 374 LEU Chi-restraints excluded: chain A residue 639 PHE Chi-restraints excluded: chain A residue 674 THR Chi-restraints excluded: chain A residue 928 LEU Chi-restraints excluded: chain A residue 938 HIS Chi-restraints excluded: chain A residue 1072 THR Chi-restraints excluded: chain A residue 1099 LEU Chi-restraints excluded: chain B residue 25 VAL Chi-restraints excluded: chain B residue 27 THR Chi-restraints excluded: chain B residue 105 LEU Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 784 LEU Chi-restraints excluded: chain B residue 984 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 201 optimal weight: 0.7980 chunk 153 optimal weight: 0.8980 chunk 105 optimal weight: 0.9990 chunk 22 optimal weight: 0.8980 chunk 97 optimal weight: 0.9990 chunk 136 optimal weight: 0.9990 chunk 204 optimal weight: 0.6980 chunk 216 optimal weight: 40.0000 chunk 106 optimal weight: 3.9990 chunk 193 optimal weight: 6.9990 chunk 58 optimal weight: 3.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 112 GLN A 131 GLN A 799 HIS ** A 800 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 939 ASN B 97 ASN B 131 GLN B 141 GLN ** B 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 522 ASN ** B 799 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 807 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 923 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6664 moved from start: 1.1491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.097 18520 Z= 0.252 Angle : 0.573 7.734 25020 Z= 0.303 Chirality : 0.042 0.376 2746 Planarity : 0.005 0.071 3256 Dihedral : 4.302 23.248 2460 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 9.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % Rotamer: Outliers : 2.61 % Allowed : 13.03 % Favored : 84.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.10 (0.18), residues: 2228 helix: 1.20 (0.15), residues: 1131 sheet: -0.41 (0.33), residues: 252 loop : -1.33 (0.20), residues: 845 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 415 HIS 0.046 0.002 HIS A 938 PHE 0.018 0.002 PHE A 120 TYR 0.034 0.002 TYR A1115 ARG 0.008 0.001 ARG A 921 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4456 Ramachandran restraints generated. 2228 Oldfield, 0 Emsley, 2228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4456 Ramachandran restraints generated. 2228 Oldfield, 0 Emsley, 2228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 1996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 232 time to evaluate : 2.154 Fit side-chains revert: symmetry clash REVERT: A 50 GLN cc_start: 0.7582 (mp10) cc_final: 0.6942 (mp10) REVERT: A 91 VAL cc_start: 0.8210 (m) cc_final: 0.8006 (t) REVERT: A 254 THR cc_start: 0.7991 (m) cc_final: 0.7775 (p) REVERT: A 259 SER cc_start: 0.6868 (OUTLIER) cc_final: 0.6661 (p) REVERT: A 271 ILE cc_start: 0.7408 (mt) cc_final: 0.6909 (mt) REVERT: A 278 ASN cc_start: 0.8344 (t0) cc_final: 0.8099 (t0) REVERT: A 335 ASN cc_start: 0.8031 (t0) cc_final: 0.7819 (t0) REVERT: A 380 ARG cc_start: 0.8125 (ttm170) cc_final: 0.7887 (ttp-110) REVERT: A 814 SER cc_start: 0.8709 (t) cc_final: 0.8313 (m) REVERT: A 824 MET cc_start: 0.7568 (mmt) cc_final: 0.7340 (mmt) REVERT: A 990 ASP cc_start: 0.5386 (p0) cc_final: 0.5134 (p0) REVERT: A 1028 PHE cc_start: 0.6563 (m-10) cc_final: 0.5559 (m-10) REVERT: A 1044 MET cc_start: 0.4743 (tpp) cc_final: 0.4105 (ttt) REVERT: B 1 MET cc_start: -0.1862 (OUTLIER) cc_final: -0.2452 (ptm) REVERT: B 14 GLN cc_start: 0.7129 (tm-30) cc_final: 0.6860 (tm-30) REVERT: B 55 LYS cc_start: 0.7302 (OUTLIER) cc_final: 0.6882 (mtmt) REVERT: B 232 ILE cc_start: 0.7625 (mt) cc_final: 0.7347 (tt) REVERT: B 273 GLU cc_start: 0.7290 (mt-10) cc_final: 0.7050 (mt-10) REVERT: B 366 SER cc_start: 0.8033 (p) cc_final: 0.7798 (m) REVERT: B 420 MET cc_start: 0.8370 (tpp) cc_final: 0.8114 (tpp) REVERT: B 469 TYR cc_start: 0.7548 (m-10) cc_final: 0.7211 (m-10) REVERT: B 552 ILE cc_start: 0.8161 (mm) cc_final: 0.7458 (tt) REVERT: B 578 ARG cc_start: 0.7441 (mtt180) cc_final: 0.6951 (mtt-85) REVERT: B 613 GLU cc_start: 0.7979 (mt-10) cc_final: 0.7646 (mt-10) REVERT: B 797 GLN cc_start: 0.8310 (mp10) cc_final: 0.8076 (mp10) REVERT: B 807 ASN cc_start: 0.7049 (t0) cc_final: 0.6463 (t0) REVERT: B 820 ARG cc_start: 0.6899 (ttp-170) cc_final: 0.5955 (ttp-170) REVERT: B 824 MET cc_start: 0.6735 (mpp) cc_final: 0.5914 (mpp) REVERT: B 980 LYS cc_start: 0.7375 (mttt) cc_final: 0.7056 (mttt) REVERT: B 983 TYR cc_start: 0.7105 (p90) cc_final: 0.5737 (p90) REVERT: B 984 ARG cc_start: 0.5923 (OUTLIER) cc_final: 0.5246 (mtm-85) REVERT: B 1008 VAL cc_start: 0.6828 (t) cc_final: 0.6197 (t) REVERT: B 1029 GLU cc_start: 0.7768 (mt-10) cc_final: 0.7473 (mt-10) REVERT: B 1044 MET cc_start: 0.7464 (ptp) cc_final: 0.7142 (ptp) REVERT: B 1057 LEU cc_start: 0.8826 (OUTLIER) cc_final: 0.8578 (mp) outliers start: 52 outliers final: 26 residues processed: 270 average time/residue: 0.3193 time to fit residues: 131.0778 Evaluate side-chains 245 residues out of total 1996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 214 time to evaluate : 1.955 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 232 ILE Chi-restraints excluded: chain A residue 245 SER Chi-restraints excluded: chain A residue 259 SER Chi-restraints excluded: chain A residue 363 THR Chi-restraints excluded: chain A residue 374 LEU Chi-restraints excluded: chain A residue 639 PHE Chi-restraints excluded: chain A residue 674 THR Chi-restraints excluded: chain A residue 676 GLN Chi-restraints excluded: chain A residue 733 TYR Chi-restraints excluded: chain A residue 930 ILE Chi-restraints excluded: chain A residue 1072 THR Chi-restraints excluded: chain A residue 1134 VAL Chi-restraints excluded: chain A residue 1144 ILE Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 24 LEU Chi-restraints excluded: chain B residue 25 VAL Chi-restraints excluded: chain B residue 55 LYS Chi-restraints excluded: chain B residue 109 ILE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 379 LEU Chi-restraints excluded: chain B residue 522 ASN Chi-restraints excluded: chain B residue 550 THR Chi-restraints excluded: chain B residue 784 LEU Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 874 LEU Chi-restraints excluded: chain B residue 984 ARG Chi-restraints excluded: chain B residue 1023 TYR Chi-restraints excluded: chain B residue 1040 GLU Chi-restraints excluded: chain B residue 1045 THR Chi-restraints excluded: chain B residue 1047 ILE Chi-restraints excluded: chain B residue 1057 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 180 optimal weight: 2.9990 chunk 122 optimal weight: 0.9980 chunk 3 optimal weight: 4.9990 chunk 161 optimal weight: 1.9990 chunk 89 optimal weight: 3.9990 chunk 184 optimal weight: 1.9990 chunk 149 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 chunk 110 optimal weight: 0.9980 chunk 194 optimal weight: 2.9990 chunk 54 optimal weight: 0.8980 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 33 HIS A 66 GLN A 506 HIS A 507 ASN A 553 HIS A 566 ASN ** A 800 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 144 GLN B 181 ASN B 337 ASN B 460 ASN B 479 GLN B 522 ASN B 628 HIS B 668 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6951 moved from start: 1.3301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 18520 Z= 0.339 Angle : 0.629 9.110 25020 Z= 0.327 Chirality : 0.044 0.265 2746 Planarity : 0.005 0.051 3256 Dihedral : 4.478 26.689 2460 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 9.94 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.71 % Favored : 95.24 % Rotamer: Outliers : 2.30 % Allowed : 14.63 % Favored : 83.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.14 (0.18), residues: 2228 helix: 1.23 (0.15), residues: 1118 sheet: -0.37 (0.32), residues: 268 loop : -1.29 (0.20), residues: 842 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 336 HIS 0.007 0.001 HIS A 836 PHE 0.029 0.002 PHE B 970 TYR 0.024 0.002 TYR A1115 ARG 0.011 0.001 ARG A 972 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4456 Ramachandran restraints generated. 2228 Oldfield, 0 Emsley, 2228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4456 Ramachandran restraints generated. 2228 Oldfield, 0 Emsley, 2228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 1996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 252 time to evaluate : 1.939 Fit side-chains revert: symmetry clash REVERT: A 194 TYR cc_start: 0.7304 (t80) cc_final: 0.7085 (t80) REVERT: A 262 ARG cc_start: 0.7810 (tpp80) cc_final: 0.7536 (tpp80) REVERT: A 271 ILE cc_start: 0.7821 (mt) cc_final: 0.7372 (mm) REVERT: A 806 GLU cc_start: 0.7185 (OUTLIER) cc_final: 0.6964 (mp0) REVERT: A 831 SER cc_start: 0.6598 (OUTLIER) cc_final: 0.6173 (t) REVERT: A 834 GLN cc_start: 0.6987 (OUTLIER) cc_final: 0.6633 (mm-40) REVERT: A 956 GLN cc_start: 0.7823 (OUTLIER) cc_final: 0.7257 (tt0) REVERT: A 970 PHE cc_start: 0.8199 (m-80) cc_final: 0.7728 (m-80) REVERT: A 1028 PHE cc_start: 0.6992 (m-10) cc_final: 0.6137 (m-10) REVERT: B 273 GLU cc_start: 0.7203 (mt-10) cc_final: 0.6953 (mt-10) REVERT: B 289 GLN cc_start: 0.7754 (mm-40) cc_final: 0.7471 (mt0) REVERT: B 380 ARG cc_start: 0.8231 (mtm110) cc_final: 0.8014 (ttm170) REVERT: B 521 LEU cc_start: 0.8556 (tp) cc_final: 0.8283 (tt) REVERT: B 551 VAL cc_start: 0.8203 (p) cc_final: 0.8002 (p) REVERT: B 552 ILE cc_start: 0.8152 (mm) cc_final: 0.7648 (tt) REVERT: B 613 GLU cc_start: 0.8031 (mt-10) cc_final: 0.7706 (mt-10) REVERT: B 797 GLN cc_start: 0.8382 (OUTLIER) cc_final: 0.8041 (mp10) REVERT: B 807 ASN cc_start: 0.7022 (t0) cc_final: 0.6523 (t0) REVERT: B 824 MET cc_start: 0.6765 (mpp) cc_final: 0.5963 (mpp) REVERT: B 984 ARG cc_start: 0.6105 (OUTLIER) cc_final: 0.5340 (mtm-85) REVERT: B 986 GLN cc_start: 0.7286 (tp40) cc_final: 0.7080 (tp40) REVERT: B 1029 GLU cc_start: 0.7814 (mt-10) cc_final: 0.7511 (mt-10) REVERT: B 1057 LEU cc_start: 0.8789 (OUTLIER) cc_final: 0.8469 (mp) outliers start: 46 outliers final: 20 residues processed: 282 average time/residue: 0.3390 time to fit residues: 139.7114 Evaluate side-chains 260 residues out of total 1996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 233 time to evaluate : 1.782 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 259 SER Chi-restraints excluded: chain A residue 363 THR Chi-restraints excluded: chain A residue 374 LEU Chi-restraints excluded: chain A residue 499 LEU Chi-restraints excluded: chain A residue 639 PHE Chi-restraints excluded: chain A residue 733 TYR Chi-restraints excluded: chain A residue 806 GLU Chi-restraints excluded: chain A residue 831 SER Chi-restraints excluded: chain A residue 834 GLN Chi-restraints excluded: chain A residue 956 GLN Chi-restraints excluded: chain A residue 1072 THR Chi-restraints excluded: chain A residue 1099 LEU Chi-restraints excluded: chain B residue 25 VAL Chi-restraints excluded: chain B residue 449 GLN Chi-restraints excluded: chain B residue 522 ASN Chi-restraints excluded: chain B residue 550 THR Chi-restraints excluded: chain B residue 784 LEU Chi-restraints excluded: chain B residue 794 GLN Chi-restraints excluded: chain B residue 797 GLN Chi-restraints excluded: chain B residue 874 LEU Chi-restraints excluded: chain B residue 934 VAL Chi-restraints excluded: chain B residue 958 LEU Chi-restraints excluded: chain B residue 984 ARG Chi-restraints excluded: chain B residue 1057 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 72 optimal weight: 0.9990 chunk 194 optimal weight: 4.9990 chunk 42 optimal weight: 0.6980 chunk 127 optimal weight: 3.9990 chunk 53 optimal weight: 1.9990 chunk 216 optimal weight: 40.0000 chunk 179 optimal weight: 6.9990 chunk 100 optimal weight: 2.9990 chunk 18 optimal weight: 1.9990 chunk 71 optimal weight: 1.9990 chunk 113 optimal weight: 0.0870 overall best weight: 1.1564 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 234 ASN A 449 GLN A 495 HIS A 553 HIS A 566 ASN A 797 GLN ** A 800 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 938 HIS B 97 ASN B 584 HIS ** B 799 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6999 moved from start: 1.3928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 18520 Z= 0.272 Angle : 0.540 7.113 25020 Z= 0.282 Chirality : 0.042 0.177 2746 Planarity : 0.004 0.052 3256 Dihedral : 4.177 21.824 2460 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 2.66 % Allowed : 15.03 % Favored : 82.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.24 (0.18), residues: 2228 helix: 1.36 (0.15), residues: 1122 sheet: -0.51 (0.32), residues: 267 loop : -1.25 (0.21), residues: 839 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 336 HIS 0.005 0.001 HIS A 134 PHE 0.019 0.001 PHE B 251 TYR 0.027 0.002 TYR A1115 ARG 0.007 0.001 ARG A 119 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4456 Ramachandran restraints generated. 2228 Oldfield, 0 Emsley, 2228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4456 Ramachandran restraints generated. 2228 Oldfield, 0 Emsley, 2228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 1996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 239 time to evaluate : 2.073 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 GLU cc_start: 0.6778 (tp30) cc_final: 0.6526 (tp30) REVERT: A 262 ARG cc_start: 0.7722 (tpp80) cc_final: 0.7254 (mpp80) REVERT: A 271 ILE cc_start: 0.7868 (mt) cc_final: 0.7312 (mm) REVERT: A 824 MET cc_start: 0.8201 (mmt) cc_final: 0.7918 (mmt) REVERT: A 831 SER cc_start: 0.7355 (OUTLIER) cc_final: 0.6943 (m) REVERT: A 1059 GLU cc_start: 0.6125 (pt0) cc_final: 0.5762 (pt0) REVERT: B 74 GLU cc_start: 0.7826 (tp30) cc_final: 0.7567 (tp30) REVERT: B 117 GLU cc_start: 0.7925 (mm-30) cc_final: 0.7651 (tp30) REVERT: B 187 SER cc_start: 0.8467 (m) cc_final: 0.8229 (p) REVERT: B 255 ARG cc_start: 0.8171 (ttm-80) cc_final: 0.7738 (mtm-85) REVERT: B 273 GLU cc_start: 0.7343 (mt-10) cc_final: 0.7114 (mt-10) REVERT: B 366 SER cc_start: 0.8060 (p) cc_final: 0.7808 (m) REVERT: B 380 ARG cc_start: 0.8290 (mtm110) cc_final: 0.8088 (ttm170) REVERT: B 470 GLU cc_start: 0.6993 (mp0) cc_final: 0.6776 (mp0) REVERT: B 551 VAL cc_start: 0.8166 (OUTLIER) cc_final: 0.7933 (p) REVERT: B 552 ILE cc_start: 0.8194 (mm) cc_final: 0.7632 (tt) REVERT: B 613 GLU cc_start: 0.8030 (mt-10) cc_final: 0.7733 (mt-10) REVERT: B 797 GLN cc_start: 0.8378 (OUTLIER) cc_final: 0.8109 (mp10) REVERT: B 807 ASN cc_start: 0.7104 (t0) cc_final: 0.6556 (t0) REVERT: B 824 MET cc_start: 0.6581 (mpp) cc_final: 0.5830 (mpp) REVERT: B 983 TYR cc_start: 0.7040 (p90) cc_final: 0.5535 (p90) REVERT: B 984 ARG cc_start: 0.6033 (OUTLIER) cc_final: 0.5274 (mtm-85) REVERT: B 1044 MET cc_start: 0.7495 (OUTLIER) cc_final: 0.7156 (ptm) outliers start: 53 outliers final: 31 residues processed: 274 average time/residue: 0.3377 time to fit residues: 135.4384 Evaluate side-chains 257 residues out of total 1996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 221 time to evaluate : 1.893 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 40 LYS Chi-restraints excluded: chain A residue 66 GLN Chi-restraints excluded: chain A residue 93 ASP Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 135 LEU Chi-restraints excluded: chain A residue 137 ASN Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 232 ILE Chi-restraints excluded: chain A residue 363 THR Chi-restraints excluded: chain A residue 374 LEU Chi-restraints excluded: chain A residue 499 LEU Chi-restraints excluded: chain A residue 676 GLN Chi-restraints excluded: chain A residue 733 TYR Chi-restraints excluded: chain A residue 831 SER Chi-restraints excluded: chain A residue 1072 THR Chi-restraints excluded: chain A residue 1099 LEU Chi-restraints excluded: chain A residue 1132 ILE Chi-restraints excluded: chain A residue 1164 ILE Chi-restraints excluded: chain B residue 5 ILE Chi-restraints excluded: chain B residue 24 LEU Chi-restraints excluded: chain B residue 25 VAL Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 379 LEU Chi-restraints excluded: chain B residue 510 THR Chi-restraints excluded: chain B residue 550 THR Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 784 LEU Chi-restraints excluded: chain B residue 794 GLN Chi-restraints excluded: chain B residue 797 GLN Chi-restraints excluded: chain B residue 874 LEU Chi-restraints excluded: chain B residue 934 VAL Chi-restraints excluded: chain B residue 984 ARG Chi-restraints excluded: chain B residue 1040 GLU Chi-restraints excluded: chain B residue 1044 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 208 optimal weight: 4.9990 chunk 24 optimal weight: 0.8980 chunk 123 optimal weight: 0.0970 chunk 158 optimal weight: 0.4980 chunk 122 optimal weight: 0.6980 chunk 182 optimal weight: 6.9990 chunk 121 optimal weight: 0.6980 chunk 215 optimal weight: 20.0000 chunk 135 optimal weight: 0.9980 chunk 131 optimal weight: 2.9990 chunk 99 optimal weight: 0.7980 overall best weight: 0.5578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 37 ASN ** A 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 449 GLN A 566 ASN ** A 800 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 920 GLN A 938 HIS A1022 GLN B 131 GLN B 805 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6974 moved from start: 1.4167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 18520 Z= 0.173 Angle : 0.488 5.953 25020 Z= 0.257 Chirality : 0.039 0.160 2746 Planarity : 0.004 0.047 3256 Dihedral : 3.957 23.742 2460 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 2.25 % Allowed : 15.83 % Favored : 81.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.51 (0.18), residues: 2228 helix: 1.58 (0.15), residues: 1126 sheet: -0.39 (0.32), residues: 267 loop : -1.12 (0.21), residues: 835 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP B1027 HIS 0.003 0.000 HIS A 33 PHE 0.030 0.001 PHE A 195 TYR 0.026 0.001 TYR A1115 ARG 0.008 0.000 ARG A 954 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4456 Ramachandran restraints generated. 2228 Oldfield, 0 Emsley, 2228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4456 Ramachandran restraints generated. 2228 Oldfield, 0 Emsley, 2228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 1996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 236 time to evaluate : 1.913 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 824 MET cc_start: 0.8193 (mmt) cc_final: 0.7893 (mmt) REVERT: A 831 SER cc_start: 0.7267 (OUTLIER) cc_final: 0.6866 (m) REVERT: A 954 ARG cc_start: 0.7839 (mtp85) cc_final: 0.7273 (mtt-85) REVERT: A 978 MET cc_start: 0.6782 (mmt) cc_final: 0.6572 (mmt) REVERT: A 1059 GLU cc_start: 0.5985 (pt0) cc_final: 0.5614 (pt0) REVERT: B 74 GLU cc_start: 0.7815 (tp30) cc_final: 0.7526 (tp30) REVERT: B 98 VAL cc_start: 0.7169 (m) cc_final: 0.6966 (p) REVERT: B 117 GLU cc_start: 0.7906 (mm-30) cc_final: 0.7694 (tp30) REVERT: B 187 SER cc_start: 0.8456 (m) cc_final: 0.8231 (p) REVERT: B 255 ARG cc_start: 0.8148 (ttm-80) cc_final: 0.7755 (mtm-85) REVERT: B 273 GLU cc_start: 0.7251 (mt-10) cc_final: 0.7031 (mt-10) REVERT: B 289 GLN cc_start: 0.7804 (mm-40) cc_final: 0.7531 (mt0) REVERT: B 366 SER cc_start: 0.7980 (p) cc_final: 0.7751 (m) REVERT: B 470 GLU cc_start: 0.6925 (mp0) cc_final: 0.6713 (mp0) REVERT: B 551 VAL cc_start: 0.8184 (OUTLIER) cc_final: 0.7950 (p) REVERT: B 552 ILE cc_start: 0.8153 (mm) cc_final: 0.7666 (tt) REVERT: B 613 GLU cc_start: 0.8005 (mt-10) cc_final: 0.7697 (mt-10) REVERT: B 663 MET cc_start: 0.4205 (OUTLIER) cc_final: 0.3898 (ppp) REVERT: B 797 GLN cc_start: 0.8358 (OUTLIER) cc_final: 0.8025 (mp10) REVERT: B 803 SER cc_start: 0.8454 (t) cc_final: 0.8083 (p) REVERT: B 807 ASN cc_start: 0.7077 (t0) cc_final: 0.6574 (t0) REVERT: B 824 MET cc_start: 0.6550 (mpp) cc_final: 0.5822 (mpp) REVERT: B 983 TYR cc_start: 0.7014 (p90) cc_final: 0.5397 (p90) REVERT: B 984 ARG cc_start: 0.6001 (OUTLIER) cc_final: 0.5287 (mtm-85) REVERT: B 986 GLN cc_start: 0.7314 (tp40) cc_final: 0.7028 (tp40) REVERT: B 1044 MET cc_start: 0.7374 (ptp) cc_final: 0.7134 (ptm) outliers start: 45 outliers final: 28 residues processed: 265 average time/residue: 0.3502 time to fit residues: 138.3823 Evaluate side-chains 254 residues out of total 1996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 221 time to evaluate : 2.142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 LEU Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 194 TYR Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 232 ILE Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 245 SER Chi-restraints excluded: chain A residue 363 THR Chi-restraints excluded: chain A residue 374 LEU Chi-restraints excluded: chain A residue 379 LEU Chi-restraints excluded: chain A residue 499 LEU Chi-restraints excluded: chain A residue 663 MET Chi-restraints excluded: chain A residue 676 GLN Chi-restraints excluded: chain A residue 733 TYR Chi-restraints excluded: chain A residue 831 SER Chi-restraints excluded: chain A residue 989 LEU Chi-restraints excluded: chain A residue 1072 THR Chi-restraints excluded: chain A residue 1132 ILE Chi-restraints excluded: chain A residue 1144 ILE Chi-restraints excluded: chain B residue 25 VAL Chi-restraints excluded: chain B residue 379 LEU Chi-restraints excluded: chain B residue 510 THR Chi-restraints excluded: chain B residue 550 THR Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 663 MET Chi-restraints excluded: chain B residue 784 LEU Chi-restraints excluded: chain B residue 794 GLN Chi-restraints excluded: chain B residue 797 GLN Chi-restraints excluded: chain B residue 874 LEU Chi-restraints excluded: chain B residue 984 ARG Chi-restraints excluded: chain B residue 1018 LEU Chi-restraints excluded: chain B residue 1040 GLU Chi-restraints excluded: chain B residue 1115 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 133 optimal weight: 5.9990 chunk 86 optimal weight: 3.9990 chunk 128 optimal weight: 5.9990 chunk 65 optimal weight: 4.9990 chunk 42 optimal weight: 0.6980 chunk 41 optimal weight: 0.9990 chunk 137 optimal weight: 0.7980 chunk 147 optimal weight: 2.9990 chunk 106 optimal weight: 0.9980 chunk 20 optimal weight: 0.8980 chunk 169 optimal weight: 2.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 37 ASN ** A 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 449 GLN ** A 800 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 938 HIS ** B 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 799 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7031 moved from start: 1.4570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 18520 Z= 0.231 Angle : 0.514 6.783 25020 Z= 0.269 Chirality : 0.041 0.193 2746 Planarity : 0.004 0.047 3256 Dihedral : 4.029 23.293 2460 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 2.35 % Allowed : 15.93 % Favored : 81.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.58 (0.18), residues: 2228 helix: 1.59 (0.15), residues: 1125 sheet: -0.35 (0.32), residues: 262 loop : -1.02 (0.21), residues: 841 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 336 HIS 0.004 0.001 HIS B 238 PHE 0.028 0.001 PHE A 970 TYR 0.025 0.002 TYR A1115 ARG 0.009 0.000 ARG A 954 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4456 Ramachandran restraints generated. 2228 Oldfield, 0 Emsley, 2228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4456 Ramachandran restraints generated. 2228 Oldfield, 0 Emsley, 2228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 1996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 233 time to evaluate : 2.031 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 32 ASN cc_start: 0.7576 (t0) cc_final: 0.7236 (t0) REVERT: A 195 PHE cc_start: 0.6464 (t80) cc_final: 0.6154 (t80) REVERT: A 824 MET cc_start: 0.8175 (mmt) cc_final: 0.7931 (mmt) REVERT: A 831 SER cc_start: 0.7453 (OUTLIER) cc_final: 0.7096 (t) REVERT: A 954 ARG cc_start: 0.7924 (mtp85) cc_final: 0.7259 (mtt-85) REVERT: A 1059 GLU cc_start: 0.6072 (pt0) cc_final: 0.5710 (pt0) REVERT: B 14 GLN cc_start: 0.7554 (pm20) cc_final: 0.7288 (pm20) REVERT: B 117 GLU cc_start: 0.7934 (mm-30) cc_final: 0.7719 (tp30) REVERT: B 187 SER cc_start: 0.8479 (m) cc_final: 0.8275 (p) REVERT: B 230 GLU cc_start: 0.7065 (OUTLIER) cc_final: 0.6842 (tp30) REVERT: B 273 GLU cc_start: 0.7304 (mt-10) cc_final: 0.7088 (mt-10) REVERT: B 366 SER cc_start: 0.8032 (p) cc_final: 0.7788 (m) REVERT: B 457 THR cc_start: 0.8279 (m) cc_final: 0.7852 (p) REVERT: B 470 GLU cc_start: 0.6995 (mp0) cc_final: 0.6746 (mp0) REVERT: B 551 VAL cc_start: 0.8202 (OUTLIER) cc_final: 0.7957 (p) REVERT: B 552 ILE cc_start: 0.8187 (mm) cc_final: 0.7652 (tt) REVERT: B 613 GLU cc_start: 0.8021 (mt-10) cc_final: 0.7721 (mt-10) REVERT: B 797 GLN cc_start: 0.8313 (OUTLIER) cc_final: 0.8049 (mp10) REVERT: B 807 ASN cc_start: 0.7095 (t0) cc_final: 0.6566 (t0) REVERT: B 824 MET cc_start: 0.6558 (mpp) cc_final: 0.5824 (mpp) REVERT: B 983 TYR cc_start: 0.7010 (p90) cc_final: 0.5423 (p90) REVERT: B 984 ARG cc_start: 0.6017 (OUTLIER) cc_final: 0.5320 (mtm-85) REVERT: B 986 GLN cc_start: 0.7300 (tp40) cc_final: 0.6986 (tp40) outliers start: 47 outliers final: 31 residues processed: 264 average time/residue: 0.3319 time to fit residues: 130.1894 Evaluate side-chains 262 residues out of total 1996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 226 time to evaluate : 1.826 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 LEU Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 194 TYR Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 232 ILE Chi-restraints excluded: chain A residue 363 THR Chi-restraints excluded: chain A residue 374 LEU Chi-restraints excluded: chain A residue 379 LEU Chi-restraints excluded: chain A residue 472 PHE Chi-restraints excluded: chain A residue 499 LEU Chi-restraints excluded: chain A residue 670 THR Chi-restraints excluded: chain A residue 831 SER Chi-restraints excluded: chain A residue 1072 THR Chi-restraints excluded: chain A residue 1132 ILE Chi-restraints excluded: chain A residue 1144 ILE Chi-restraints excluded: chain B residue 25 VAL Chi-restraints excluded: chain B residue 132 ILE Chi-restraints excluded: chain B residue 203 LEU Chi-restraints excluded: chain B residue 230 GLU Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 306 ASP Chi-restraints excluded: chain B residue 379 LEU Chi-restraints excluded: chain B residue 510 THR Chi-restraints excluded: chain B residue 514 VAL Chi-restraints excluded: chain B residue 522 ASN Chi-restraints excluded: chain B residue 550 THR Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 784 LEU Chi-restraints excluded: chain B residue 794 GLN Chi-restraints excluded: chain B residue 797 GLN Chi-restraints excluded: chain B residue 874 LEU Chi-restraints excluded: chain B residue 984 ARG Chi-restraints excluded: chain B residue 1018 LEU Chi-restraints excluded: chain B residue 1040 GLU Chi-restraints excluded: chain B residue 1047 ILE Chi-restraints excluded: chain B residue 1115 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 196 optimal weight: 2.9990 chunk 206 optimal weight: 3.9990 chunk 188 optimal weight: 0.6980 chunk 201 optimal weight: 0.9990 chunk 121 optimal weight: 1.9990 chunk 87 optimal weight: 0.3980 chunk 157 optimal weight: 0.9980 chunk 61 optimal weight: 0.7980 chunk 181 optimal weight: 6.9990 chunk 190 optimal weight: 0.8980 chunk 200 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 449 GLN A 453 GLN ** A 800 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 938 HIS B 131 GLN ** B 479 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 799 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7027 moved from start: 1.4852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 18520 Z= 0.203 Angle : 0.500 7.165 25020 Z= 0.263 Chirality : 0.040 0.180 2746 Planarity : 0.004 0.045 3256 Dihedral : 3.953 24.483 2460 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 1.95 % Allowed : 16.98 % Favored : 81.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.65 (0.18), residues: 2228 helix: 1.67 (0.16), residues: 1118 sheet: -0.25 (0.33), residues: 260 loop : -1.00 (0.21), residues: 850 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A1186 HIS 0.007 0.001 HIS B 238 PHE 0.018 0.001 PHE B 251 TYR 0.025 0.001 TYR A1115 ARG 0.006 0.000 ARG A 954 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4456 Ramachandran restraints generated. 2228 Oldfield, 0 Emsley, 2228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4456 Ramachandran restraints generated. 2228 Oldfield, 0 Emsley, 2228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 1996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 237 time to evaluate : 1.799 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 32 ASN cc_start: 0.7617 (t0) cc_final: 0.7276 (t0) REVERT: A 74 GLU cc_start: 0.6836 (tp30) cc_final: 0.6619 (tp30) REVERT: A 247 PHE cc_start: 0.8446 (t80) cc_final: 0.8033 (t80) REVERT: A 255 ARG cc_start: 0.7446 (tpp-160) cc_final: 0.7188 (mmt-90) REVERT: A 824 MET cc_start: 0.8139 (mmt) cc_final: 0.7905 (mmt) REVERT: A 831 SER cc_start: 0.7379 (OUTLIER) cc_final: 0.6975 (m) REVERT: A 954 ARG cc_start: 0.7821 (mtp85) cc_final: 0.7179 (mtt-85) REVERT: A 970 PHE cc_start: 0.8140 (m-80) cc_final: 0.7757 (m-80) REVERT: A 978 MET cc_start: 0.6971 (mmt) cc_final: 0.6722 (mmt) REVERT: A 1059 GLU cc_start: 0.6061 (pt0) cc_final: 0.5671 (pt0) REVERT: B 14 GLN cc_start: 0.7550 (pm20) cc_final: 0.7260 (pm20) REVERT: B 273 GLU cc_start: 0.7233 (mt-10) cc_final: 0.7021 (mt-10) REVERT: B 366 SER cc_start: 0.7990 (p) cc_final: 0.7762 (m) REVERT: B 457 THR cc_start: 0.8260 (m) cc_final: 0.7831 (p) REVERT: B 470 GLU cc_start: 0.6992 (mp0) cc_final: 0.6723 (mp0) REVERT: B 551 VAL cc_start: 0.8214 (OUTLIER) cc_final: 0.7972 (p) REVERT: B 552 ILE cc_start: 0.8185 (mm) cc_final: 0.7675 (tt) REVERT: B 575 GLN cc_start: 0.7278 (mt0) cc_final: 0.6990 (mt0) REVERT: B 613 GLU cc_start: 0.8018 (mt-10) cc_final: 0.7701 (mt-10) REVERT: B 797 GLN cc_start: 0.8298 (OUTLIER) cc_final: 0.8041 (mp10) REVERT: B 807 ASN cc_start: 0.7115 (t0) cc_final: 0.6592 (t0) REVERT: B 824 MET cc_start: 0.6504 (mpp) cc_final: 0.5823 (mpp) REVERT: B 984 ARG cc_start: 0.5978 (OUTLIER) cc_final: 0.5312 (mtm-85) REVERT: B 986 GLN cc_start: 0.7304 (tp40) cc_final: 0.7005 (tp40) outliers start: 39 outliers final: 28 residues processed: 261 average time/residue: 0.3722 time to fit residues: 146.2863 Evaluate side-chains 260 residues out of total 1996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 228 time to evaluate : 2.164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 LEU Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 194 TYR Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 232 ILE Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 363 THR Chi-restraints excluded: chain A residue 374 LEU Chi-restraints excluded: chain A residue 379 LEU Chi-restraints excluded: chain A residue 472 PHE Chi-restraints excluded: chain A residue 499 LEU Chi-restraints excluded: chain A residue 663 MET Chi-restraints excluded: chain A residue 670 THR Chi-restraints excluded: chain A residue 676 GLN Chi-restraints excluded: chain A residue 831 SER Chi-restraints excluded: chain A residue 1072 THR Chi-restraints excluded: chain A residue 1144 ILE Chi-restraints excluded: chain B residue 25 VAL Chi-restraints excluded: chain B residue 306 ASP Chi-restraints excluded: chain B residue 379 LEU Chi-restraints excluded: chain B residue 510 THR Chi-restraints excluded: chain B residue 550 THR Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 784 LEU Chi-restraints excluded: chain B residue 794 GLN Chi-restraints excluded: chain B residue 797 GLN Chi-restraints excluded: chain B residue 874 LEU Chi-restraints excluded: chain B residue 984 ARG Chi-restraints excluded: chain B residue 1018 LEU Chi-restraints excluded: chain B residue 1040 GLU Chi-restraints excluded: chain B residue 1047 ILE Chi-restraints excluded: chain B residue 1115 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 132 optimal weight: 0.9980 chunk 212 optimal weight: 0.9980 chunk 129 optimal weight: 2.9990 chunk 100 optimal weight: 0.7980 chunk 147 optimal weight: 1.9990 chunk 223 optimal weight: 4.9990 chunk 205 optimal weight: 0.9990 chunk 177 optimal weight: 1.9990 chunk 18 optimal weight: 0.7980 chunk 137 optimal weight: 0.2980 chunk 108 optimal weight: 1.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 449 GLN ** A 800 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 938 HIS B 131 GLN ** B 479 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 799 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7047 moved from start: 1.5129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 18520 Z= 0.214 Angle : 0.519 14.567 25020 Z= 0.269 Chirality : 0.040 0.191 2746 Planarity : 0.004 0.047 3256 Dihedral : 3.991 24.092 2460 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 9.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 1.95 % Allowed : 16.93 % Favored : 81.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.68 (0.18), residues: 2228 helix: 1.66 (0.15), residues: 1124 sheet: -0.19 (0.33), residues: 261 loop : -0.97 (0.21), residues: 843 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 336 HIS 0.006 0.001 HIS B 238 PHE 0.018 0.001 PHE B 251 TYR 0.024 0.001 TYR A1115 ARG 0.005 0.000 ARG A 954 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4456 Ramachandran restraints generated. 2228 Oldfield, 0 Emsley, 2228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4456 Ramachandran restraints generated. 2228 Oldfield, 0 Emsley, 2228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 1996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 241 time to evaluate : 2.198 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 32 ASN cc_start: 0.7651 (t0) cc_final: 0.7322 (t0) REVERT: A 124 GLN cc_start: 0.8084 (mp10) cc_final: 0.7789 (mp10) REVERT: A 194 TYR cc_start: 0.7020 (OUTLIER) cc_final: 0.6637 (m-80) REVERT: A 195 PHE cc_start: 0.6578 (t80) cc_final: 0.6158 (t80) REVERT: A 450 GLU cc_start: 0.8335 (tt0) cc_final: 0.7630 (tt0) REVERT: A 824 MET cc_start: 0.8125 (mmt) cc_final: 0.7883 (mmt) REVERT: A 831 SER cc_start: 0.7458 (OUTLIER) cc_final: 0.7052 (m) REVERT: A 954 ARG cc_start: 0.7841 (mtp85) cc_final: 0.7186 (mtt-85) REVERT: A 978 MET cc_start: 0.6935 (mmt) cc_final: 0.6701 (mmt) REVERT: A 1028 PHE cc_start: 0.7147 (m-10) cc_final: 0.6910 (m-10) REVERT: A 1038 GLN cc_start: 0.7170 (mp10) cc_final: 0.6904 (mp10) REVERT: A 1059 GLU cc_start: 0.6104 (pt0) cc_final: 0.5743 (pt0) REVERT: B 230 GLU cc_start: 0.7047 (OUTLIER) cc_final: 0.6822 (tp30) REVERT: B 273 GLU cc_start: 0.7281 (mt-10) cc_final: 0.6914 (mt-10) REVERT: B 314 ARG cc_start: 0.8020 (ttm-80) cc_final: 0.7264 (ttm-80) REVERT: B 366 SER cc_start: 0.7984 (p) cc_final: 0.7753 (m) REVERT: B 470 GLU cc_start: 0.6998 (mp0) cc_final: 0.6738 (mp0) REVERT: B 551 VAL cc_start: 0.8211 (OUTLIER) cc_final: 0.7974 (p) REVERT: B 552 ILE cc_start: 0.8185 (mm) cc_final: 0.7667 (tt) REVERT: B 613 GLU cc_start: 0.8022 (mt-10) cc_final: 0.7711 (mt-10) REVERT: B 797 GLN cc_start: 0.8293 (OUTLIER) cc_final: 0.8032 (mp10) REVERT: B 807 ASN cc_start: 0.7103 (t0) cc_final: 0.6587 (t0) REVERT: B 824 MET cc_start: 0.6508 (mpp) cc_final: 0.5829 (mpp) REVERT: B 984 ARG cc_start: 0.5965 (OUTLIER) cc_final: 0.5324 (mtm-85) outliers start: 39 outliers final: 28 residues processed: 268 average time/residue: 0.3609 time to fit residues: 142.7371 Evaluate side-chains 264 residues out of total 1996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 230 time to evaluate : 2.028 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 LEU Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 194 TYR Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 232 ILE Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 363 THR Chi-restraints excluded: chain A residue 374 LEU Chi-restraints excluded: chain A residue 379 LEU Chi-restraints excluded: chain A residue 472 PHE Chi-restraints excluded: chain A residue 499 LEU Chi-restraints excluded: chain A residue 670 THR Chi-restraints excluded: chain A residue 676 GLN Chi-restraints excluded: chain A residue 831 SER Chi-restraints excluded: chain A residue 1072 THR Chi-restraints excluded: chain A residue 1144 ILE Chi-restraints excluded: chain B residue 25 VAL Chi-restraints excluded: chain B residue 230 GLU Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 306 ASP Chi-restraints excluded: chain B residue 379 LEU Chi-restraints excluded: chain B residue 510 THR Chi-restraints excluded: chain B residue 514 VAL Chi-restraints excluded: chain B residue 550 THR Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 784 LEU Chi-restraints excluded: chain B residue 794 GLN Chi-restraints excluded: chain B residue 797 GLN Chi-restraints excluded: chain B residue 874 LEU Chi-restraints excluded: chain B residue 984 ARG Chi-restraints excluded: chain B residue 1018 LEU Chi-restraints excluded: chain B residue 1040 GLU Chi-restraints excluded: chain B residue 1047 ILE Chi-restraints excluded: chain B residue 1115 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 141 optimal weight: 1.9990 chunk 189 optimal weight: 0.9980 chunk 54 optimal weight: 0.3980 chunk 163 optimal weight: 1.9990 chunk 26 optimal weight: 2.9990 chunk 49 optimal weight: 0.9980 chunk 177 optimal weight: 0.2980 chunk 74 optimal weight: 1.9990 chunk 182 optimal weight: 0.9990 chunk 22 optimal weight: 1.9990 chunk 32 optimal weight: 0.6980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 160 ASN A 449 GLN ** A 800 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 938 HIS B 131 GLN ** B 479 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 799 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4379 r_free = 0.4379 target = 0.192926 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.154855 restraints weight = 25307.096| |-----------------------------------------------------------------------------| r_work (start): 0.3922 rms_B_bonded: 2.45 r_work: 0.3784 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work (final): 0.3784 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6980 moved from start: 1.5290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 18520 Z= 0.194 Angle : 0.511 14.078 25020 Z= 0.264 Chirality : 0.040 0.220 2746 Planarity : 0.004 0.045 3256 Dihedral : 3.928 24.180 2460 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 9.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 1.95 % Allowed : 17.03 % Favored : 81.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.67 (0.18), residues: 2228 helix: 1.65 (0.15), residues: 1128 sheet: -0.20 (0.32), residues: 266 loop : -1.00 (0.21), residues: 834 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A1186 HIS 0.004 0.001 HIS B 238 PHE 0.017 0.001 PHE B 970 TYR 0.025 0.001 TYR A1115 ARG 0.005 0.000 ARG A 954 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5145.18 seconds wall clock time: 93 minutes 36.31 seconds (5616.31 seconds total)