Starting phenix.real_space_refine on Wed Jan 14 00:07:49 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7mge_23827/01_2026/7mge_23827.cif Found real_map, /net/cci-nas-00/data/ceres_data/7mge_23827/01_2026/7mge_23827.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.94 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7mge_23827/01_2026/7mge_23827.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7mge_23827/01_2026/7mge_23827.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7mge_23827/01_2026/7mge_23827.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7mge_23827/01_2026/7mge_23827.map" } resolution = 3.94 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.036 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 1840 atoms to isotropic. 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: 8 Type Number sf(0) Gaussians P 2 5.49 5 Mg 1 5.21 5 S 37 5.16 5 Be 1 3.05 5 C 5700 2.51 5 N 1586 2.21 5 O 1680 1.98 5 F 3 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5927/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 9010 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 2080 Number of conformers: 1 Conformer: "" Number of residues, atoms: 349, 2080 Classifications: {'peptide': 349} Incomplete info: {'truncation_to_alanine': 204} Link IDs: {'PTRANS': 5, 'TRANS': 343} Chain breaks: 7 Unresolved non-hydrogen bonds: 750 Unresolved non-hydrogen angles: 967 Unresolved non-hydrogen dihedrals: 596 Unresolved non-hydrogen chiralities: 86 Planarities with less than four sites: {'GLN:plan1': 12, 'ASN:plan1': 12, 'GLU:plan': 18, 'HIS:plan': 5, 'ASP:plan': 20, 'TYR:plan': 2, 'ARG:plan': 16, 'TRP:plan': 5, 'PHE:plan': 6} Unresolved non-hydrogen planarities: 414 Chain: "B" Number of atoms: 3189 Number of conformers: 1 Conformer: "" Number of residues, atoms: 442, 3189 Classifications: {'peptide': 442} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 106} Link IDs: {'CIS': 1, 'PTRANS': 14, 'TRANS': 426} Chain breaks: 11 Unresolved non-hydrogen bonds: 416 Unresolved non-hydrogen angles: 523 Unresolved non-hydrogen dihedrals: 345 Unresolved non-hydrogen chiralities: 35 Planarities with less than four sites: {'PHE:plan': 8, 'ASP:plan': 8, 'ASN:plan1': 3, 'TYR:plan': 4, 'ARG:plan': 9, 'HIS:plan': 4, 'GLU:plan': 11, 'GLN:plan1': 5} Unresolved non-hydrogen planarities: 238 Chain: "C" Number of atoms: 2381 Number of conformers: 1 Conformer: "" Number of residues, atoms: 365, 2381 Classifications: {'peptide': 365} Incomplete info: {'truncation_to_alanine': 135} Link IDs: {'PTRANS': 15, 'TRANS': 349} Chain breaks: 5 Unresolved non-hydrogen bonds: 475 Unresolved non-hydrogen angles: 593 Unresolved non-hydrogen dihedrals: 376 Unresolved non-hydrogen chiralities: 47 Planarities with less than four sites: {'GLU:plan': 15, 'HIS:plan': 1, 'ASP:plan': 17, 'ASN:plan1': 5, 'ARG:plan': 11, 'GLN:plan1': 6, 'TRP:plan': 1, 'TYR:plan': 2, 'PHE:plan': 2} Unresolved non-hydrogen planarities: 245 Chain: "E" Number of atoms: 1355 Number of conformers: 1 Conformer: "" Number of residues, atoms: 167, 1355 Unusual residues: {'GDP': 1} Classifications: {'peptide': 166, 'undetermined': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 3, 'TRANS': 162, None: 1} Not linked: pdbres="GLN E 180 " pdbres="GDP E 200 " Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "E" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 5 Unusual residues: {' MG': 1, 'BEF': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 2.02, per 1000 atoms: 0.22 Number of scatterers: 9010 At special positions: 0 Unit cell: (78.96, 116.56, 177.66, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) S 37 16.00 P 2 15.00 Mg 1 11.99 F 3 9.00 O 1680 8.00 N 1586 7.00 C 5700 6.00 Be 1 4.00 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.84 Conformation dependent library (CDL) restraints added in 381.7 milliseconds 2536 Ramachandran restraints generated. 1268 Oldfield, 0 Emsley, 1268 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2504 Finding SS restraints... Secondary structure from input PDB file: 44 helices and 15 sheets defined 38.8% alpha, 14.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.21 Creating SS restraints... Processing helix chain 'A' and resid 434 through 443 removed outlier: 3.759A pdb=" N LEU A 440 " --> pdb=" O ARG A 436 " (cutoff:3.500A) Processing helix chain 'A' and resid 445 through 453 removed outlier: 3.518A pdb=" N GLU A 450 " --> pdb=" O PHE A 446 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N GLU A 451 " --> pdb=" O GLN A 447 " (cutoff:3.500A) Processing helix chain 'B' and resid 98 through 105 Processing helix chain 'B' and resid 161 through 219 removed outlier: 4.248A pdb=" N ILE B 165 " --> pdb=" O ASP B 161 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N MET B 166 " --> pdb=" O GLN B 162 " (cutoff:3.500A) removed outlier: 5.320A pdb=" N GLN B 170 " --> pdb=" O MET B 166 " (cutoff:3.500A) removed outlier: 6.031A pdb=" N GLU B 171 " --> pdb=" O GLN B 167 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N ALA B 174 " --> pdb=" O GLN B 170 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N GLU B 175 " --> pdb=" O GLU B 171 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N PHE B 176 " --> pdb=" O LEU B 172 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ARG B 188 " --> pdb=" O LYS B 184 " (cutoff:3.500A) removed outlier: 4.765A pdb=" N LYS B 189 " --> pdb=" O THR B 185 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N GLU B 214 " --> pdb=" O HIS B 210 " (cutoff:3.500A) Processing helix chain 'B' and resid 226 through 252 removed outlier: 4.062A pdb=" N GLN B 252 " --> pdb=" O ASP B 248 " (cutoff:3.500A) Processing helix chain 'B' and resid 330 through 344 removed outlier: 3.896A pdb=" N MET B 344 " --> pdb=" O HIS B 340 " (cutoff:3.500A) Processing helix chain 'B' and resid 348 through 363 removed outlier: 3.798A pdb=" N THR B 354 " --> pdb=" O CYS B 350 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N ARG B 359 " --> pdb=" O SER B 355 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N LYS B 363 " --> pdb=" O ARG B 359 " (cutoff:3.500A) Processing helix chain 'B' and resid 367 through 371 removed outlier: 4.127A pdb=" N PHE B 370 " --> pdb=" O ILE B 367 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N LEU B 371 " --> pdb=" O THR B 368 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 367 through 371' Processing helix chain 'B' and resid 707 through 714 Processing helix chain 'B' and resid 720 through 730 removed outlier: 3.841A pdb=" N ILE B 724 " --> pdb=" O ALA B 720 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N TYR B 725 " --> pdb=" O HIS B 721 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N GLY B 730 " --> pdb=" O SER B 726 " (cutoff:3.500A) Processing helix chain 'B' and resid 739 through 750 removed outlier: 3.929A pdb=" N THR B 748 " --> pdb=" O ARG B 744 " (cutoff:3.500A) Processing helix chain 'B' and resid 751 through 754 removed outlier: 3.564A pdb=" N VAL B 754 " --> pdb=" O ALA B 751 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 751 through 754' Processing helix chain 'B' and resid 774 through 778 Processing helix chain 'B' and resid 796 through 801 Processing helix chain 'B' and resid 802 through 804 No H-bonds generated for 'chain 'B' and resid 802 through 804' Processing helix chain 'B' and resid 825 through 831 removed outlier: 4.042A pdb=" N ARG B 829 " --> pdb=" O THR B 825 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LEU B 830 " --> pdb=" O LEU B 826 " (cutoff:3.500A) Processing helix chain 'B' and resid 840 through 863 removed outlier: 3.627A pdb=" N TYR B 844 " --> pdb=" O GLY B 840 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N THR B 852 " --> pdb=" O GLN B 848 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N GLN B 853 " --> pdb=" O SER B 849 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N LEU B 854 " --> pdb=" O MET B 850 " (cutoff:3.500A) Processing helix chain 'B' and resid 864 through 869 removed outlier: 4.014A pdb=" N HIS B 868 " --> pdb=" O CYS B 864 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LEU B 869 " --> pdb=" O HIS B 865 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 864 through 869' Processing helix chain 'B' and resid 877 through 891 removed outlier: 3.936A pdb=" N LEU B 888 " --> pdb=" O GLN B 884 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N LYS B 889 " --> pdb=" O MET B 885 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LEU B 890 " --> pdb=" O SER B 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 895 through 898 Processing helix chain 'B' and resid 899 through 915 removed outlier: 3.793A pdb=" N GLN B 903 " --> pdb=" O VAL B 899 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N MET B 914 " --> pdb=" O LYS B 910 " (cutoff:3.500A) Processing helix chain 'C' and resid 55 through 68 removed outlier: 3.760A pdb=" N ILE C 59 " --> pdb=" O SER C 55 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N THR C 60 " --> pdb=" O ASP C 56 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N HIS C 65 " --> pdb=" O PHE C 61 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N THR C 66 " --> pdb=" O LEU C 62 " (cutoff:3.500A) Processing helix chain 'C' and resid 124 through 126 No H-bonds generated for 'chain 'C' and resid 124 through 126' Processing helix chain 'C' and resid 127 through 148 removed outlier: 3.878A pdb=" N ASP C 133 " --> pdb=" O ARG C 129 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ILE C 144 " --> pdb=" O ARG C 140 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N HIS C 147 " --> pdb=" O ARG C 143 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N LYS C 148 " --> pdb=" O ILE C 144 " (cutoff:3.500A) Processing helix chain 'C' and resid 173 through 179 Processing helix chain 'C' and resid 180 through 190 removed outlier: 3.639A pdb=" N LEU C 187 " --> pdb=" O VAL C 183 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N SER C 188 " --> pdb=" O MET C 184 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N MET C 190 " --> pdb=" O LEU C 186 " (cutoff:3.500A) Processing helix chain 'C' and resid 191 through 193 No H-bonds generated for 'chain 'C' and resid 191 through 193' Processing helix chain 'C' and resid 213 through 230 Processing helix chain 'C' and resid 241 through 252 Processing helix chain 'C' and resid 253 through 255 No H-bonds generated for 'chain 'C' and resid 253 through 255' Processing helix chain 'C' and resid 256 through 261 removed outlier: 4.273A pdb=" N LYS C 261 " --> pdb=" O PRO C 257 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 300 Processing helix chain 'C' and resid 375 through 385 removed outlier: 4.344A pdb=" N PHE C 385 " --> pdb=" O LEU C 381 " (cutoff:3.500A) Processing helix chain 'C' and resid 392 through 419 removed outlier: 3.687A pdb=" N THR C 396 " --> pdb=" O SER C 392 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N PHE C 397 " --> pdb=" O LEU C 393 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N LEU C 398 " --> pdb=" O ARG C 394 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N ALA C 399 " --> pdb=" O SER C 395 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N GLN C 400 " --> pdb=" O THR C 396 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N PHE C 401 " --> pdb=" O PHE C 397 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N LEU C 402 " --> pdb=" O LEU C 398 " (cutoff:3.500A) Processing helix chain 'C' and resid 430 through 437 removed outlier: 3.604A pdb=" N LEU C 437 " --> pdb=" O LEU C 433 " (cutoff:3.500A) Processing helix chain 'C' and resid 441 through 454 removed outlier: 3.610A pdb=" N LEU C 451 " --> pdb=" O ILE C 447 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N ALA C 452 " --> pdb=" O ILE C 448 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N GLU C 453 " --> pdb=" O MET C 449 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N LYS C 454 " --> pdb=" O ALA C 450 " (cutoff:3.500A) Processing helix chain 'C' and resid 458 through 465 Processing helix chain 'E' and resid 29 through 39 Processing helix chain 'E' and resid 74 through 82 removed outlier: 3.756A pdb=" N TRP E 78 " --> pdb=" O ARG E 75 " (cutoff:3.500A) removed outlier: 5.337A pdb=" N ARG E 79 " --> pdb=" O PRO E 76 " (cutoff:3.500A) Processing helix chain 'E' and resid 99 through 112 Processing helix chain 'E' and resid 113 through 117 Processing helix chain 'E' and resid 135 through 144 removed outlier: 4.646A pdb=" N ILE E 139 " --> pdb=" O ASN E 135 " (cutoff:3.500A) Processing helix chain 'E' and resid 145 through 148 removed outlier: 3.544A pdb=" N LEU E 148 " --> pdb=" O LEU E 145 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 145 through 148' Processing helix chain 'E' and resid 165 through 178 Processing sheet with id=AA1, first strand: chain 'A' and resid 35 through 39 removed outlier: 3.753A pdb=" N GLU A 35 " --> pdb=" O LYS A 432 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N LEU A 37 " --> pdb=" O LEU A 430 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N ILE A 429 " --> pdb=" O THR A 421 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 87 through 91 removed outlier: 6.650A pdb=" N ALA A 109 " --> pdb=" O THR A 88 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N ILE A 90 " --> pdb=" O LEU A 107 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N LEU A 107 " --> pdb=" O ILE A 90 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N THR A 108 " --> pdb=" O ILE A 116 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 140 through 142 removed outlier: 3.597A pdb=" N THR A 140 " --> pdb=" O LEU A 149 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N TRP A 148 " --> pdb=" O TRP A 158 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 180 through 182 removed outlier: 3.506A pdb=" N CYS A 186 " --> pdb=" O ILE A 182 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N VAL A 187 " --> pdb=" O PHE A 198 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ALA A 189 " --> pdb=" O ILE A 196 " (cutoff:3.500A) removed outlier: 7.357A pdb=" N LEU A 195 " --> pdb=" O ARG A 217 " (cutoff:3.500A) removed outlier: 4.867A pdb=" N ARG A 217 " --> pdb=" O LEU A 195 " (cutoff:3.500A) removed outlier: 7.108A pdb=" N ILE A 197 " --> pdb=" O VAL A 215 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 230 through 231 removed outlier: 3.548A pdb=" N VAL A 231 " --> pdb=" O SER A 235 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N SER A 235 " --> pdb=" O VAL A 231 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 289 through 291 Processing sheet with id=AA7, first strand: chain 'A' and resid 326 through 332 removed outlier: 3.687A pdb=" N HIS A 328 " --> pdb=" O CYS A 340 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N GLN A 336 " --> pdb=" O LEU A 332 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N SER A 341 " --> pdb=" O SER A 345 " (cutoff:3.500A) removed outlier: 4.806A pdb=" N SER A 345 " --> pdb=" O SER A 341 " (cutoff:3.500A) removed outlier: 7.068A pdb=" N VAL A 346 " --> pdb=" O ASP A 400 " (cutoff:3.500A) removed outlier: 5.031A pdb=" N ASP A 400 " --> pdb=" O VAL A 346 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N ILE A 348 " --> pdb=" O ILE A 398 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N GLU A 350 " --> pdb=" O GLU A 396 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N GLU A 396 " --> pdb=" O GLU A 350 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 131 through 138 removed outlier: 3.973A pdb=" N PHE B 133 " --> pdb=" O TYR B 157 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N TYR B 135 " --> pdb=" O MET B 155 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 784 through 785 removed outlier: 7.919A pdb=" N LEU B 785 " --> pdb=" O LEU B 733 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N VAL B 735 " --> pdb=" O LEU B 785 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 15 through 17 removed outlier: 4.042A pdb=" N ALA C 46 " --> pdb=" O THR C 15 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ILE C 17 " --> pdb=" O ALA C 46 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'C' and resid 27 through 29 removed outlier: 3.827A pdb=" N ALA C 27 " --> pdb=" O ILE C 115 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ILE C 115 " --> pdb=" O ALA C 27 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N SER C 96 " --> pdb=" O LYS C 83 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ILE C 98 " --> pdb=" O ASP C 81 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ASP C 81 " --> pdb=" O ILE C 98 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 27 through 29 removed outlier: 3.827A pdb=" N ALA C 27 " --> pdb=" O ILE C 115 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ILE C 115 " --> pdb=" O ALA C 27 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 263 through 264 removed outlier: 6.403A pdb=" N ARG C 264 " --> pdb=" O GLY C 282 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N GLN C 281 " --> pdb=" O SER C 234 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N ILE C 308 " --> pdb=" O VAL C 235 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 17 through 20 removed outlier: 6.024A pdb=" N MET E 18 " --> pdb=" O THR E 64 " (cutoff:3.500A) removed outlier: 7.336A pdb=" N TRP E 66 " --> pdb=" O MET E 18 " (cutoff:3.500A) removed outlier: 7.161A pdb=" N ILE E 20 " --> pdb=" O TRP E 66 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 23 through 24 removed outlier: 6.408A pdb=" N VAL E 23 " --> pdb=" O VAL E 91 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N LEU E 122 " --> pdb=" O LEU E 88 " (cutoff:3.500A) 382 hydrogen bonds defined for protein. 1071 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: 1.36 Time building geometry restraints manager: 1.09 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1633 1.32 - 1.45: 2283 1.45 - 1.57: 5182 1.57 - 1.69: 7 1.69 - 1.81: 56 Bond restraints: 9161 Sorted by residual: bond pdb=" N TRP C 33 " pdb=" CA TRP C 33 " ideal model delta sigma weight residual 1.457 1.540 -0.082 1.29e-02 6.01e+03 4.07e+01 bond pdb=" N ALA C 31 " pdb=" CA ALA C 31 " ideal model delta sigma weight residual 1.455 1.520 -0.065 1.23e-02 6.61e+03 2.76e+01 bond pdb=" CA TRP C 33 " pdb=" C TRP C 33 " ideal model delta sigma weight residual 1.523 1.584 -0.061 1.34e-02 5.57e+03 2.08e+01 bond pdb=" CA ALA C 31 " pdb=" C ALA C 31 " ideal model delta sigma weight residual 1.521 1.576 -0.055 1.28e-02 6.10e+03 1.86e+01 bond pdb=" N PHE C 30 " pdb=" CA PHE C 30 " ideal model delta sigma weight residual 1.457 1.512 -0.055 1.29e-02 6.01e+03 1.82e+01 ... (remaining 9156 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.59: 12274 2.59 - 5.18: 189 5.18 - 7.78: 35 7.78 - 10.37: 13 10.37 - 12.96: 3 Bond angle restraints: 12514 Sorted by residual: angle pdb=" C LEU B 199 " pdb=" N LYS B 200 " pdb=" CA LYS B 200 " ideal model delta sigma weight residual 120.28 109.95 10.33 1.34e+00 5.57e-01 5.94e+01 angle pdb=" N ALA C 31 " pdb=" CA ALA C 31 " pdb=" C ALA C 31 " ideal model delta sigma weight residual 108.76 120.54 -11.78 1.58e+00 4.01e-01 5.56e+01 angle pdb=" N THR C 29 " pdb=" CA THR C 29 " pdb=" C THR C 29 " ideal model delta sigma weight residual 108.19 117.73 -9.54 1.29e+00 6.01e-01 5.47e+01 angle pdb=" N LEU B 199 " pdb=" CA LEU B 199 " pdb=" C LEU B 199 " ideal model delta sigma weight residual 111.28 104.04 7.24 1.09e+00 8.42e-01 4.41e+01 angle pdb=" C LYS B 251 " pdb=" N GLN B 252 " pdb=" CA GLN B 252 " ideal model delta sigma weight residual 121.54 133.80 -12.26 1.91e+00 2.74e-01 4.12e+01 ... (remaining 12509 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.67: 4981 17.67 - 35.33: 298 35.33 - 53.00: 56 53.00 - 70.67: 11 70.67 - 88.33: 7 Dihedral angle restraints: 5353 sinusoidal: 1521 harmonic: 3832 Sorted by residual: dihedral pdb=" C THR C 29 " pdb=" N THR C 29 " pdb=" CA THR C 29 " pdb=" CB THR C 29 " ideal model delta harmonic sigma weight residual -122.00 -136.30 14.30 0 2.50e+00 1.60e-01 3.27e+01 dihedral pdb=" N THR C 29 " pdb=" C THR C 29 " pdb=" CA THR C 29 " pdb=" CB THR C 29 " ideal model delta harmonic sigma weight residual 123.40 135.61 -12.21 0 2.50e+00 1.60e-01 2.39e+01 dihedral pdb=" CA VAL C 86 " pdb=" C VAL C 86 " pdb=" N LEU C 87 " pdb=" CA LEU C 87 " ideal model delta harmonic sigma weight residual 180.00 -156.25 -23.75 0 5.00e+00 4.00e-02 2.26e+01 ... (remaining 5350 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.102: 1451 0.102 - 0.204: 62 0.204 - 0.306: 5 0.306 - 0.408: 0 0.408 - 0.510: 1 Chirality restraints: 1519 Sorted by residual: chirality pdb=" CA THR C 29 " pdb=" N THR C 29 " pdb=" C THR C 29 " pdb=" CB THR C 29 " both_signs ideal model delta sigma weight residual False 2.53 2.02 0.51 2.00e-01 2.50e+01 6.50e+00 chirality pdb=" CA TYR C 32 " pdb=" N TYR C 32 " pdb=" C TYR C 32 " pdb=" CB TYR C 32 " both_signs ideal model delta sigma weight residual False 2.51 2.77 -0.26 2.00e-01 2.50e+01 1.66e+00 chirality pdb=" CA LEU B 199 " pdb=" N LEU B 199 " pdb=" C LEU B 199 " pdb=" CB LEU B 199 " both_signs ideal model delta sigma weight residual False 2.51 2.76 -0.25 2.00e-01 2.50e+01 1.59e+00 ... (remaining 1516 not shown) Planarity restraints: 1614 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA C 31 " -0.021 2.00e-02 2.50e+03 4.28e-02 1.83e+01 pdb=" C ALA C 31 " 0.074 2.00e-02 2.50e+03 pdb=" O ALA C 31 " -0.028 2.00e-02 2.50e+03 pdb=" N TYR C 32 " -0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA C 27 " 0.021 2.00e-02 2.50e+03 4.05e-02 1.64e+01 pdb=" C ALA C 27 " -0.070 2.00e-02 2.50e+03 pdb=" O ALA C 27 " 0.027 2.00e-02 2.50e+03 pdb=" N ALA C 28 " 0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU B 250 " 0.019 2.00e-02 2.50e+03 3.76e-02 1.41e+01 pdb=" C LEU B 250 " -0.065 2.00e-02 2.50e+03 pdb=" O LEU B 250 " 0.024 2.00e-02 2.50e+03 pdb=" N LYS B 251 " 0.022 2.00e-02 2.50e+03 ... (remaining 1611 not shown) Histogram of nonbonded interaction distances: 1.35 - 2.06: 7 2.06 - 2.77: 1843 2.77 - 3.48: 12619 3.48 - 4.19: 18046 4.19 - 4.90: 30954 Nonbonded interactions: 63469 Sorted by model distance: nonbonded pdb=" CG2 THR C 29 " pdb=" CA HIS C 43 " model vdw 1.353 3.890 nonbonded pdb=" CG2 THR C 29 " pdb=" N HIS C 43 " model vdw 1.460 3.540 nonbonded pdb=" F3 BEF E 201 " pdb="MG MG E 202 " model vdw 1.850 2.120 nonbonded pdb=" O3A GDP E 200 " pdb="MG MG E 202 " model vdw 1.891 2.170 nonbonded pdb=" F2 BEF E 201 " pdb="MG MG E 202 " model vdw 1.894 2.120 ... (remaining 63464 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.140 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.030 Construct map_model_manager: 0.000 Extract box with map and model: 0.150 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 9.380 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.110 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7403 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.085 9163 Z= 0.264 Angle : 0.835 12.960 12514 Z= 0.473 Chirality : 0.050 0.510 1519 Planarity : 0.005 0.052 1614 Dihedral : 13.066 88.333 2849 Min Nonbonded Distance : 1.353 Molprobity Statistics. All-atom Clashscore : 12.44 Ramachandran Plot: Outliers : 0.79 % Allowed : 12.15 % Favored : 87.07 % Rotamer: Outliers : 0.84 % Allowed : 0.42 % Favored : 98.75 % Cbeta Deviations : 0.16 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.04 (0.23), residues: 1268 helix: 0.35 (0.27), residues: 414 sheet: -1.00 (0.37), residues: 208 loop : -2.74 (0.22), residues: 646 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 346 TYR 0.016 0.001 TYR A 413 PHE 0.018 0.002 PHE A 262 TRP 0.024 0.002 TRP E 172 HIS 0.008 0.001 HIS B 366 Details of bonding type rmsd covalent geometry : bond 0.00429 ( 9161) covalent geometry : angle 0.83495 (12514) hydrogen bonds : bond 0.21848 ( 376) hydrogen bonds : angle 8.20662 ( 1071) Misc. bond : bond 0.00315 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2536 Ramachandran restraints generated. 1268 Oldfield, 0 Emsley, 1268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2536 Ramachandran restraints generated. 1268 Oldfield, 0 Emsley, 1268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 1172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 274 time to evaluate : 0.341 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 334 ASN cc_start: 0.8053 (p0) cc_final: 0.7619 (p0) REVERT: A 410 MET cc_start: 0.6909 (ppp) cc_final: 0.6530 (ppp) REVERT: A 436 ARG cc_start: 0.8417 (OUTLIER) cc_final: 0.8152 (ttp80) REVERT: B 155 MET cc_start: 0.7025 (mpp) cc_final: 0.6452 (mpp) REVERT: B 342 GLU cc_start: 0.8145 (tm-30) cc_final: 0.7838 (tm-30) REVERT: B 345 PHE cc_start: 0.8006 (m-80) cc_final: 0.7672 (m-10) REVERT: B 363 LYS cc_start: 0.8172 (ptpp) cc_final: 0.7865 (ptpp) REVERT: B 781 LYS cc_start: 0.8202 (tmtt) cc_final: 0.7973 (tmtt) REVERT: B 814 ASN cc_start: 0.9075 (m110) cc_final: 0.8656 (m110) REVERT: B 887 PHE cc_start: 0.8333 (t80) cc_final: 0.7947 (t80) REVERT: B 892 LEU cc_start: 0.8706 (mm) cc_final: 0.8437 (mm) REVERT: B 904 TYR cc_start: 0.8746 (t80) cc_final: 0.8326 (t80) REVERT: B 908 LEU cc_start: 0.8754 (mm) cc_final: 0.8529 (mm) REVERT: B 910 LYS cc_start: 0.8079 (ptpp) cc_final: 0.7854 (ptpp) REVERT: C 121 LEU cc_start: 0.8891 (tp) cc_final: 0.8677 (tp) REVERT: E 18 MET cc_start: 0.5678 (tpt) cc_final: 0.5069 (tpt) REVERT: E 63 PHE cc_start: 0.7616 (m-80) cc_final: 0.7212 (m-80) REVERT: E 106 GLU cc_start: 0.8142 (tm-30) cc_final: 0.7453 (tm-30) REVERT: E 164 ASP cc_start: 0.8012 (p0) cc_final: 0.7742 (p0) outliers start: 6 outliers final: 4 residues processed: 279 average time/residue: 0.0902 time to fit residues: 34.9132 Evaluate side-chains 261 residues out of total 1172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 256 time to evaluate : 0.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 436 ARG Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 30 PHE Chi-restraints excluded: chain C residue 32 TYR Chi-restraints excluded: chain C residue 33 TRP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 98 optimal weight: 0.9980 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 8.9990 chunk 66 optimal weight: 4.9990 chunk 124 optimal weight: 10.0000 chunk 103 optimal weight: 4.9990 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 0.8980 chunk 91 optimal weight: 4.9990 chunk 55 optimal weight: 0.9980 chunk 129 optimal weight: 3.9990 overall best weight: 1.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 170 HIS B 365 GLN B 366 HIS B 865 HIS B 866 HIS C 307 HIS C 446 ASN E 71 GLN E 156 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.111829 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.091801 restraints weight = 19651.408| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.095057 restraints weight = 11738.548| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.097325 restraints weight = 7947.197| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.098951 restraints weight = 5886.993| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.100149 restraints weight = 4646.301| |-----------------------------------------------------------------------------| r_work (final): 0.3471 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7425 moved from start: 0.1651 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 9163 Z= 0.227 Angle : 0.749 11.260 12514 Z= 0.386 Chirality : 0.047 0.156 1519 Planarity : 0.005 0.057 1614 Dihedral : 6.720 79.096 1379 Min Nonbonded Distance : 1.448 Molprobity Statistics. All-atom Clashscore : 11.36 Ramachandran Plot: Outliers : 0.39 % Allowed : 12.54 % Favored : 87.07 % Rotamer: Outliers : 2.37 % Allowed : 16.02 % Favored : 81.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.34 (0.23), residues: 1268 helix: 0.12 (0.25), residues: 432 sheet: -1.44 (0.35), residues: 221 loop : -2.93 (0.22), residues: 615 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 346 TYR 0.026 0.002 TYR A 33 PHE 0.026 0.002 PHE C 397 TRP 0.015 0.002 TRP E 172 HIS 0.013 0.001 HIS B 866 Details of bonding type rmsd covalent geometry : bond 0.00449 ( 9161) covalent geometry : angle 0.74869 (12514) hydrogen bonds : bond 0.04897 ( 376) hydrogen bonds : angle 6.11981 ( 1071) Misc. bond : bond 0.00162 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2536 Ramachandran restraints generated. 1268 Oldfield, 0 Emsley, 1268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2536 Ramachandran restraints generated. 1268 Oldfield, 0 Emsley, 1268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 1172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 266 time to evaluate : 0.338 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 410 MET cc_start: 0.6969 (ppp) cc_final: 0.6759 (ppp) REVERT: A 436 ARG cc_start: 0.8028 (OUTLIER) cc_final: 0.7572 (ttp80) REVERT: B 136 VAL cc_start: 0.9016 (t) cc_final: 0.8812 (m) REVERT: B 155 MET cc_start: 0.7086 (mpp) cc_final: 0.6433 (mpp) REVERT: B 342 GLU cc_start: 0.8173 (tm-30) cc_final: 0.7885 (tm-30) REVERT: B 345 PHE cc_start: 0.8249 (m-80) cc_final: 0.7710 (m-10) REVERT: B 346 ARG cc_start: 0.7589 (mtm-85) cc_final: 0.6627 (mtt-85) REVERT: B 363 LYS cc_start: 0.8227 (ptpp) cc_final: 0.7911 (ptpp) REVERT: B 781 LYS cc_start: 0.8245 (tmtt) cc_final: 0.7991 (tmtt) REVERT: B 814 ASN cc_start: 0.9076 (m110) cc_final: 0.8745 (m110) REVERT: B 838 LYS cc_start: 0.8786 (mptt) cc_final: 0.8297 (mmtt) REVERT: B 887 PHE cc_start: 0.8409 (t80) cc_final: 0.8062 (t80) REVERT: B 890 LEU cc_start: 0.9065 (mm) cc_final: 0.8805 (mp) REVERT: B 892 LEU cc_start: 0.8732 (mm) cc_final: 0.8495 (mm) REVERT: B 903 GLN cc_start: 0.9059 (pm20) cc_final: 0.8822 (pm20) REVERT: B 904 TYR cc_start: 0.8851 (t80) cc_final: 0.8571 (t80) REVERT: B 908 LEU cc_start: 0.8692 (mm) cc_final: 0.8431 (mm) REVERT: B 910 LYS cc_start: 0.8088 (ptpp) cc_final: 0.7830 (ptpp) REVERT: C 316 LYS cc_start: 0.8474 (tppt) cc_final: 0.8207 (tppt) REVERT: E 18 MET cc_start: 0.6050 (tpt) cc_final: 0.5394 (tpt) REVERT: E 63 PHE cc_start: 0.7170 (m-80) cc_final: 0.6920 (m-80) REVERT: E 106 GLU cc_start: 0.8140 (tm-30) cc_final: 0.7745 (tm-30) REVERT: E 122 LEU cc_start: 0.7823 (tt) cc_final: 0.7502 (tt) REVERT: E 164 ASP cc_start: 0.8137 (p0) cc_final: 0.7893 (p0) outliers start: 17 outliers final: 14 residues processed: 275 average time/residue: 0.0934 time to fit residues: 35.7308 Evaluate side-chains 278 residues out of total 1172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 263 time to evaluate : 0.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 436 ARG Chi-restraints excluded: chain B residue 798 HIS Chi-restraints excluded: chain B residue 809 ILE Chi-restraints excluded: chain B residue 852 THR Chi-restraints excluded: chain B residue 865 HIS Chi-restraints excluded: chain B residue 866 HIS Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 30 PHE Chi-restraints excluded: chain C residue 32 TYR Chi-restraints excluded: chain C residue 33 TRP Chi-restraints excluded: chain C residue 110 TYR Chi-restraints excluded: chain C residue 135 LEU Chi-restraints excluded: chain C residue 225 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 106 optimal weight: 4.9990 chunk 79 optimal weight: 0.9980 chunk 127 optimal weight: 8.9990 chunk 121 optimal weight: 4.9990 chunk 115 optimal weight: 5.9990 chunk 80 optimal weight: 0.9980 chunk 21 optimal weight: 6.9990 chunk 29 optimal weight: 7.9990 chunk 27 optimal weight: 6.9990 chunk 19 optimal weight: 3.9990 chunk 63 optimal weight: 0.9980 overall best weight: 2.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 170 HIS ** B 365 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 366 HIS C 307 HIS C 446 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.110206 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.090529 restraints weight = 19756.801| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.093697 restraints weight = 11891.392| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.095904 restraints weight = 8087.085| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.097501 restraints weight = 6013.778| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.098589 restraints weight = 4767.142| |-----------------------------------------------------------------------------| r_work (final): 0.3447 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7464 moved from start: 0.2173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 9163 Z= 0.268 Angle : 0.761 11.320 12514 Z= 0.398 Chirality : 0.048 0.183 1519 Planarity : 0.005 0.060 1614 Dihedral : 6.817 80.170 1379 Min Nonbonded Distance : 1.365 Molprobity Statistics. All-atom Clashscore : 12.93 Ramachandran Plot: Outliers : 0.39 % Allowed : 13.72 % Favored : 85.88 % Rotamer: Outliers : 4.87 % Allowed : 18.25 % Favored : 76.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.55 (0.22), residues: 1268 helix: -0.08 (0.25), residues: 438 sheet: -1.58 (0.36), residues: 204 loop : -3.03 (0.21), residues: 626 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 731 TYR 0.024 0.002 TYR A 33 PHE 0.025 0.002 PHE A 446 TRP 0.018 0.002 TRP B 780 HIS 0.023 0.002 HIS B 866 Details of bonding type rmsd covalent geometry : bond 0.00527 ( 9161) covalent geometry : angle 0.76135 (12514) hydrogen bonds : bond 0.04870 ( 376) hydrogen bonds : angle 6.05648 ( 1071) Misc. bond : bond 0.00180 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2536 Ramachandran restraints generated. 1268 Oldfield, 0 Emsley, 1268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2536 Ramachandran restraints generated. 1268 Oldfield, 0 Emsley, 1268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 1172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 266 time to evaluate : 0.358 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 413 TYR cc_start: 0.8018 (t80) cc_final: 0.7803 (t80) REVERT: A 436 ARG cc_start: 0.8052 (OUTLIER) cc_final: 0.7594 (ttp80) REVERT: B 99 TYR cc_start: 0.8483 (t80) cc_final: 0.8175 (t80) REVERT: B 155 MET cc_start: 0.7125 (mpp) cc_final: 0.6441 (mpp) REVERT: B 342 GLU cc_start: 0.8102 (tm-30) cc_final: 0.7722 (tm-30) REVERT: B 345 PHE cc_start: 0.8271 (m-80) cc_final: 0.7682 (m-10) REVERT: B 359 ARG cc_start: 0.7672 (ttm110) cc_final: 0.7080 (ttm110) REVERT: B 363 LYS cc_start: 0.8234 (ptpp) cc_final: 0.7921 (ptpp) REVERT: B 779 LYS cc_start: 0.7470 (pptt) cc_final: 0.7091 (pptt) REVERT: B 781 LYS cc_start: 0.8269 (tmtt) cc_final: 0.7915 (tmtt) REVERT: B 803 TYR cc_start: 0.8007 (OUTLIER) cc_final: 0.7755 (m-10) REVERT: B 814 ASN cc_start: 0.9078 (m110) cc_final: 0.8808 (m110) REVERT: B 838 LYS cc_start: 0.8820 (mptt) cc_final: 0.8307 (mmtt) REVERT: B 887 PHE cc_start: 0.8409 (t80) cc_final: 0.7999 (t80) REVERT: B 892 LEU cc_start: 0.8749 (mm) cc_final: 0.8433 (mm) REVERT: B 894 LEU cc_start: 0.7911 (mt) cc_final: 0.7655 (mp) REVERT: B 903 GLN cc_start: 0.9079 (pm20) cc_final: 0.8863 (pm20) REVERT: B 904 TYR cc_start: 0.8845 (t80) cc_final: 0.8569 (t80) REVERT: B 908 LEU cc_start: 0.8737 (mm) cc_final: 0.8507 (mm) REVERT: B 910 LYS cc_start: 0.8021 (ptpp) cc_final: 0.7763 (ptpp) REVERT: C 115 ILE cc_start: 0.8729 (mm) cc_final: 0.8502 (mm) REVERT: C 179 GLU cc_start: 0.7638 (mp0) cc_final: 0.7069 (mp0) REVERT: E 18 MET cc_start: 0.6029 (tpt) cc_final: 0.5321 (tpt) REVERT: E 106 GLU cc_start: 0.8257 (tm-30) cc_final: 0.7546 (tm-30) REVERT: E 108 MET cc_start: 0.8829 (OUTLIER) cc_final: 0.8594 (mpp) REVERT: E 122 LEU cc_start: 0.7958 (tt) cc_final: 0.7584 (tt) REVERT: E 164 ASP cc_start: 0.8110 (p0) cc_final: 0.7901 (p0) REVERT: E 173 LEU cc_start: 0.9264 (tp) cc_final: 0.8894 (tp) outliers start: 35 outliers final: 20 residues processed: 282 average time/residue: 0.0901 time to fit residues: 35.4646 Evaluate side-chains 288 residues out of total 1172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 265 time to evaluate : 0.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 57 PHE Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 336 GLN Chi-restraints excluded: chain A residue 436 ARG Chi-restraints excluded: chain B residue 798 HIS Chi-restraints excluded: chain B residue 803 TYR Chi-restraints excluded: chain B residue 806 TYR Chi-restraints excluded: chain B residue 852 THR Chi-restraints excluded: chain B residue 865 HIS Chi-restraints excluded: chain C residue 26 LEU Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 30 PHE Chi-restraints excluded: chain C residue 32 TYR Chi-restraints excluded: chain C residue 33 TRP Chi-restraints excluded: chain C residue 92 VAL Chi-restraints excluded: chain C residue 110 TYR Chi-restraints excluded: chain C residue 225 SER Chi-restraints excluded: chain C residue 228 LEU Chi-restraints excluded: chain C residue 378 LYS Chi-restraints excluded: chain E residue 30 LYS Chi-restraints excluded: chain E residue 108 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 22 optimal weight: 1.9990 chunk 48 optimal weight: 0.3980 chunk 79 optimal weight: 0.8980 chunk 126 optimal weight: 2.9990 chunk 44 optimal weight: 4.9990 chunk 68 optimal weight: 2.9990 chunk 47 optimal weight: 0.9980 chunk 50 optimal weight: 0.9990 chunk 4 optimal weight: 0.0270 chunk 84 optimal weight: 3.9990 chunk 51 optimal weight: 7.9990 overall best weight: 0.6640 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 366 HIS B 866 HIS C 64 ASN C 307 HIS C 446 ASN C 460 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.114511 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.094492 restraints weight = 19972.386| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.097808 restraints weight = 11871.819| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.100130 restraints weight = 8004.657| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.101766 restraints weight = 5912.273| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.102989 restraints weight = 4662.382| |-----------------------------------------------------------------------------| r_work (final): 0.3521 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7365 moved from start: 0.2397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 9163 Z= 0.123 Angle : 0.693 11.234 12514 Z= 0.344 Chirality : 0.044 0.183 1519 Planarity : 0.004 0.053 1614 Dihedral : 6.196 73.314 1379 Min Nonbonded Distance : 1.444 Molprobity Statistics. All-atom Clashscore : 9.12 Ramachandran Plot: Outliers : 0.39 % Allowed : 9.54 % Favored : 90.06 % Rotamer: Outliers : 4.18 % Allowed : 24.23 % Favored : 71.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.02 (0.23), residues: 1268 helix: 0.71 (0.26), residues: 429 sheet: -1.57 (0.35), residues: 219 loop : -2.86 (0.23), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 900 TYR 0.026 0.001 TYR B 843 PHE 0.025 0.002 PHE C 397 TRP 0.016 0.001 TRP B 780 HIS 0.013 0.001 HIS B 866 Details of bonding type rmsd covalent geometry : bond 0.00262 ( 9161) covalent geometry : angle 0.69268 (12514) hydrogen bonds : bond 0.03343 ( 376) hydrogen bonds : angle 5.19894 ( 1071) Misc. bond : bond 0.00073 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2536 Ramachandran restraints generated. 1268 Oldfield, 0 Emsley, 1268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2536 Ramachandran restraints generated. 1268 Oldfield, 0 Emsley, 1268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 1172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 261 time to evaluate : 0.279 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 412 LEU cc_start: 0.7897 (OUTLIER) cc_final: 0.7651 (tt) REVERT: A 436 ARG cc_start: 0.8000 (OUTLIER) cc_final: 0.7786 (ttm110) REVERT: B 99 TYR cc_start: 0.8413 (t80) cc_final: 0.8127 (t80) REVERT: B 155 MET cc_start: 0.7179 (mpp) cc_final: 0.6465 (mpp) REVERT: B 176 PHE cc_start: 0.8056 (m-80) cc_final: 0.7818 (m-80) REVERT: B 345 PHE cc_start: 0.8178 (m-80) cc_final: 0.7661 (m-10) REVERT: B 346 ARG cc_start: 0.7769 (mtm-85) cc_final: 0.6863 (mtm-85) REVERT: B 359 ARG cc_start: 0.7660 (ttm110) cc_final: 0.7081 (ttm110) REVERT: B 363 LYS cc_start: 0.8192 (ptpp) cc_final: 0.7872 (ptpp) REVERT: B 780 TRP cc_start: 0.7911 (m-90) cc_final: 0.7671 (m-90) REVERT: B 781 LYS cc_start: 0.8238 (tmtt) cc_final: 0.7944 (tmtt) REVERT: B 803 TYR cc_start: 0.7838 (m-10) cc_final: 0.7484 (m-10) REVERT: B 814 ASN cc_start: 0.9060 (m110) cc_final: 0.8780 (m110) REVERT: B 838 LYS cc_start: 0.8638 (mptt) cc_final: 0.8191 (mmtt) REVERT: B 887 PHE cc_start: 0.8340 (t80) cc_final: 0.8083 (t80) REVERT: B 890 LEU cc_start: 0.8995 (mm) cc_final: 0.8770 (mp) REVERT: B 903 GLN cc_start: 0.9012 (pm20) cc_final: 0.8747 (pm20) REVERT: B 904 TYR cc_start: 0.8804 (t80) cc_final: 0.8596 (t80) REVERT: B 908 LEU cc_start: 0.8636 (mm) cc_final: 0.8416 (mm) REVERT: B 910 LYS cc_start: 0.7881 (ptpp) cc_final: 0.7601 (ptpp) REVERT: B 925 LEU cc_start: 0.7885 (OUTLIER) cc_final: 0.7389 (tt) REVERT: C 179 GLU cc_start: 0.7672 (mp0) cc_final: 0.7095 (mp0) REVERT: E 18 MET cc_start: 0.6161 (tpt) cc_final: 0.5414 (tpt) REVERT: E 106 GLU cc_start: 0.8148 (tm-30) cc_final: 0.7685 (tm-30) REVERT: E 108 MET cc_start: 0.8809 (OUTLIER) cc_final: 0.8608 (mpp) REVERT: E 122 LEU cc_start: 0.7559 (tt) cc_final: 0.7135 (tt) REVERT: E 164 ASP cc_start: 0.8067 (p0) cc_final: 0.7855 (p0) outliers start: 30 outliers final: 19 residues processed: 272 average time/residue: 0.0925 time to fit residues: 34.5948 Evaluate side-chains 282 residues out of total 1172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 259 time to evaluate : 0.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 HIS Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 213 LEU Chi-restraints excluded: chain A residue 349 TRP Chi-restraints excluded: chain A residue 412 LEU Chi-restraints excluded: chain A residue 436 ARG Chi-restraints excluded: chain B residue 798 HIS Chi-restraints excluded: chain B residue 809 ILE Chi-restraints excluded: chain B residue 852 THR Chi-restraints excluded: chain B residue 865 HIS Chi-restraints excluded: chain B residue 866 HIS Chi-restraints excluded: chain B residue 925 LEU Chi-restraints excluded: chain C residue 30 PHE Chi-restraints excluded: chain C residue 32 TYR Chi-restraints excluded: chain C residue 33 TRP Chi-restraints excluded: chain C residue 92 VAL Chi-restraints excluded: chain C residue 110 TYR Chi-restraints excluded: chain C residue 122 SER Chi-restraints excluded: chain C residue 135 LEU Chi-restraints excluded: chain C residue 225 SER Chi-restraints excluded: chain C residue 228 LEU Chi-restraints excluded: chain E residue 63 PHE Chi-restraints excluded: chain E residue 108 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 60 optimal weight: 0.7980 chunk 82 optimal weight: 3.9990 chunk 17 optimal weight: 10.0000 chunk 55 optimal weight: 5.9990 chunk 9 optimal weight: 10.0000 chunk 8 optimal weight: 10.0000 chunk 5 optimal weight: 10.0000 chunk 25 optimal weight: 7.9990 chunk 100 optimal weight: 0.0030 chunk 112 optimal weight: 7.9990 chunk 127 optimal weight: 1.9990 overall best weight: 2.5596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 170 HIS ** B 365 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 366 HIS ** B 865 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 866 HIS C 307 HIS C 383 GLN C 446 ASN C 460 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.109397 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.089823 restraints weight = 19953.470| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.093000 restraints weight = 11940.155| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.095250 restraints weight = 8091.414| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.096856 restraints weight = 5978.320| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.098010 restraints weight = 4720.518| |-----------------------------------------------------------------------------| r_work (final): 0.3436 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7471 moved from start: 0.2697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 9163 Z= 0.280 Angle : 0.777 12.249 12514 Z= 0.402 Chirality : 0.048 0.209 1519 Planarity : 0.005 0.065 1614 Dihedral : 6.645 84.745 1378 Min Nonbonded Distance : 1.273 Molprobity Statistics. All-atom Clashscore : 12.75 Ramachandran Plot: Outliers : 0.47 % Allowed : 14.27 % Favored : 85.25 % Rotamer: Outliers : 5.71 % Allowed : 25.07 % Favored : 69.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.47 (0.23), residues: 1268 helix: 0.08 (0.25), residues: 431 sheet: -1.68 (0.36), residues: 204 loop : -2.97 (0.22), residues: 633 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 787 TYR 0.022 0.002 TYR B 843 PHE 0.030 0.002 PHE B 927 TRP 0.024 0.002 TRP A 148 HIS 0.027 0.002 HIS B 866 Details of bonding type rmsd covalent geometry : bond 0.00550 ( 9161) covalent geometry : angle 0.77734 (12514) hydrogen bonds : bond 0.04700 ( 376) hydrogen bonds : angle 5.90204 ( 1071) Misc. bond : bond 0.00166 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2536 Ramachandran restraints generated. 1268 Oldfield, 0 Emsley, 1268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2536 Ramachandran restraints generated. 1268 Oldfield, 0 Emsley, 1268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 318 residues out of total 1172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 277 time to evaluate : 0.354 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 410 MET cc_start: 0.7325 (ppp) cc_final: 0.6749 (ppp) REVERT: A 412 LEU cc_start: 0.8281 (OUTLIER) cc_final: 0.8005 (tt) REVERT: A 431 TRP cc_start: 0.8029 (m100) cc_final: 0.7549 (m-10) REVERT: B 136 VAL cc_start: 0.9005 (t) cc_final: 0.8794 (m) REVERT: B 155 MET cc_start: 0.7231 (mpp) cc_final: 0.6496 (mpp) REVERT: B 176 PHE cc_start: 0.8072 (m-80) cc_final: 0.7820 (m-80) REVERT: B 345 PHE cc_start: 0.8334 (m-80) cc_final: 0.7659 (m-10) REVERT: B 346 ARG cc_start: 0.7966 (mtm-85) cc_final: 0.7316 (mtm-85) REVERT: B 359 ARG cc_start: 0.7652 (ttm110) cc_final: 0.7070 (ttm110) REVERT: B 363 LYS cc_start: 0.8238 (ptpp) cc_final: 0.7920 (ptpp) REVERT: B 779 LYS cc_start: 0.7391 (pptt) cc_final: 0.7073 (pptt) REVERT: B 781 LYS cc_start: 0.8263 (tmtt) cc_final: 0.7962 (tmtt) REVERT: B 803 TYR cc_start: 0.8023 (OUTLIER) cc_final: 0.7783 (m-10) REVERT: B 848 GLN cc_start: 0.8454 (tp40) cc_final: 0.8117 (tp-100) REVERT: B 865 HIS cc_start: 0.7989 (OUTLIER) cc_final: 0.7673 (m170) REVERT: B 887 PHE cc_start: 0.8400 (t80) cc_final: 0.8082 (t80) REVERT: B 890 LEU cc_start: 0.9062 (mm) cc_final: 0.8790 (mp) REVERT: B 892 LEU cc_start: 0.8765 (mm) cc_final: 0.8518 (mm) REVERT: B 894 LEU cc_start: 0.7882 (mt) cc_final: 0.7611 (mp) REVERT: B 903 GLN cc_start: 0.9018 (pm20) cc_final: 0.8764 (pm20) REVERT: B 904 TYR cc_start: 0.8873 (t80) cc_final: 0.8642 (t80) REVERT: B 908 LEU cc_start: 0.8763 (mm) cc_final: 0.8511 (mm) REVERT: B 910 LYS cc_start: 0.8061 (ptpp) cc_final: 0.7780 (ptpp) REVERT: B 925 LEU cc_start: 0.7964 (OUTLIER) cc_final: 0.7417 (tt) REVERT: C 179 GLU cc_start: 0.7668 (mp0) cc_final: 0.7103 (mp0) REVERT: E 18 MET cc_start: 0.6212 (tpt) cc_final: 0.5531 (tpt) REVERT: E 106 GLU cc_start: 0.8298 (tm-30) cc_final: 0.7649 (tm-30) REVERT: E 108 MET cc_start: 0.8834 (OUTLIER) cc_final: 0.8625 (mpp) REVERT: E 122 LEU cc_start: 0.7898 (tt) cc_final: 0.7504 (tt) REVERT: E 171 ASP cc_start: 0.8603 (m-30) cc_final: 0.8333 (m-30) outliers start: 41 outliers final: 26 residues processed: 293 average time/residue: 0.0849 time to fit residues: 34.6672 Evaluate side-chains 303 residues out of total 1172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 272 time to evaluate : 0.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 HIS Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 213 LEU Chi-restraints excluded: chain A residue 336 GLN Chi-restraints excluded: chain A residue 412 LEU Chi-restraints excluded: chain B residue 332 THR Chi-restraints excluded: chain B residue 798 HIS Chi-restraints excluded: chain B residue 803 TYR Chi-restraints excluded: chain B residue 809 ILE Chi-restraints excluded: chain B residue 845 LEU Chi-restraints excluded: chain B residue 850 MET Chi-restraints excluded: chain B residue 852 THR Chi-restraints excluded: chain B residue 865 HIS Chi-restraints excluded: chain B residue 866 HIS Chi-restraints excluded: chain B residue 925 LEU Chi-restraints excluded: chain C residue 26 LEU Chi-restraints excluded: chain C residue 30 PHE Chi-restraints excluded: chain C residue 32 TYR Chi-restraints excluded: chain C residue 33 TRP Chi-restraints excluded: chain C residue 92 VAL Chi-restraints excluded: chain C residue 99 PHE Chi-restraints excluded: chain C residue 110 TYR Chi-restraints excluded: chain C residue 147 HIS Chi-restraints excluded: chain C residue 181 ILE Chi-restraints excluded: chain C residue 225 SER Chi-restraints excluded: chain C residue 228 LEU Chi-restraints excluded: chain C residue 254 PHE Chi-restraints excluded: chain E residue 30 LYS Chi-restraints excluded: chain E residue 63 PHE Chi-restraints excluded: chain E residue 108 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 129 optimal weight: 6.9990 chunk 9 optimal weight: 10.0000 chunk 23 optimal weight: 9.9990 chunk 7 optimal weight: 9.9990 chunk 121 optimal weight: 0.3980 chunk 66 optimal weight: 1.9990 chunk 31 optimal weight: 4.9990 chunk 45 optimal weight: 4.9990 chunk 114 optimal weight: 1.9990 chunk 95 optimal weight: 2.9990 chunk 13 optimal weight: 0.9980 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 170 HIS B 366 HIS B 866 HIS B 903 GLN ** C 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 307 HIS C 446 ASN C 460 HIS E 128 GLN E 156 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.111095 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.091390 restraints weight = 19922.845| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.094656 restraints weight = 11910.488| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.096934 restraints weight = 8050.193| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.098557 restraints weight = 5934.667| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.099746 restraints weight = 4668.366| |-----------------------------------------------------------------------------| r_work (final): 0.3464 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7428 moved from start: 0.2878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 9163 Z= 0.196 Angle : 0.735 12.475 12514 Z= 0.376 Chirality : 0.046 0.191 1519 Planarity : 0.004 0.058 1614 Dihedral : 6.281 80.346 1374 Min Nonbonded Distance : 1.285 Molprobity Statistics. All-atom Clashscore : 11.42 Ramachandran Plot: Outliers : 0.39 % Allowed : 11.99 % Favored : 87.62 % Rotamer: Outliers : 5.85 % Allowed : 28.97 % Favored : 65.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.42 (0.23), residues: 1268 helix: 0.29 (0.25), residues: 431 sheet: -1.74 (0.35), residues: 218 loop : -3.06 (0.22), residues: 619 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 79 TYR 0.019 0.001 TYR B 843 PHE 0.024 0.002 PHE B 927 TRP 0.017 0.002 TRP A 148 HIS 0.020 0.001 HIS B 866 Details of bonding type rmsd covalent geometry : bond 0.00398 ( 9161) covalent geometry : angle 0.73533 (12514) hydrogen bonds : bond 0.04035 ( 376) hydrogen bonds : angle 5.59270 ( 1071) Misc. bond : bond 0.00116 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2536 Ramachandran restraints generated. 1268 Oldfield, 0 Emsley, 1268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2536 Ramachandran restraints generated. 1268 Oldfield, 0 Emsley, 1268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 1172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 271 time to evaluate : 0.374 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 194 GLU cc_start: 0.6436 (tm-30) cc_final: 0.5790 (tm-30) REVERT: A 410 MET cc_start: 0.7131 (ppp) cc_final: 0.6629 (ppp) REVERT: A 412 LEU cc_start: 0.8112 (OUTLIER) cc_final: 0.7829 (tt) REVERT: A 431 TRP cc_start: 0.8004 (m100) cc_final: 0.7403 (m-10) REVERT: B 155 MET cc_start: 0.7228 (mpp) cc_final: 0.6461 (mpp) REVERT: B 176 PHE cc_start: 0.8095 (m-80) cc_final: 0.7642 (m-80) REVERT: B 345 PHE cc_start: 0.8332 (m-80) cc_final: 0.7677 (m-10) REVERT: B 346 ARG cc_start: 0.8138 (mtm-85) cc_final: 0.7487 (mtm-85) REVERT: B 359 ARG cc_start: 0.7667 (ttm110) cc_final: 0.7083 (ttm110) REVERT: B 363 LYS cc_start: 0.8228 (ptpp) cc_final: 0.7887 (ptpp) REVERT: B 779 LYS cc_start: 0.7370 (pptt) cc_final: 0.7046 (pptt) REVERT: B 781 LYS cc_start: 0.8246 (tmtt) cc_final: 0.7946 (tmtt) REVERT: B 803 TYR cc_start: 0.7978 (OUTLIER) cc_final: 0.7669 (m-10) REVERT: B 845 LEU cc_start: 0.7348 (OUTLIER) cc_final: 0.6941 (tt) REVERT: B 848 GLN cc_start: 0.8483 (tp40) cc_final: 0.8127 (tp-100) REVERT: B 887 PHE cc_start: 0.8361 (t80) cc_final: 0.7997 (t80) REVERT: B 890 LEU cc_start: 0.9055 (mm) cc_final: 0.8783 (mp) REVERT: B 892 LEU cc_start: 0.8764 (mm) cc_final: 0.8518 (mm) REVERT: B 894 LEU cc_start: 0.7827 (mt) cc_final: 0.7546 (mp) REVERT: B 903 GLN cc_start: 0.9015 (OUTLIER) cc_final: 0.8742 (mp10) REVERT: B 904 TYR cc_start: 0.8871 (t80) cc_final: 0.8655 (t80) REVERT: B 908 LEU cc_start: 0.8748 (mm) cc_final: 0.8510 (mm) REVERT: B 910 LYS cc_start: 0.7986 (ptpp) cc_final: 0.7708 (ptpp) REVERT: B 925 LEU cc_start: 0.7922 (OUTLIER) cc_final: 0.7440 (tt) REVERT: C 179 GLU cc_start: 0.7692 (mp0) cc_final: 0.7090 (mp0) REVERT: E 18 MET cc_start: 0.6253 (tpt) cc_final: 0.5550 (tpt) REVERT: E 36 LYS cc_start: 0.8943 (mmpt) cc_final: 0.8583 (mmpt) REVERT: E 106 GLU cc_start: 0.8204 (tm-30) cc_final: 0.7758 (tm-30) REVERT: E 108 MET cc_start: 0.8859 (OUTLIER) cc_final: 0.8623 (mpp) REVERT: E 122 LEU cc_start: 0.7779 (tt) cc_final: 0.7443 (tt) REVERT: E 171 ASP cc_start: 0.8580 (m-30) cc_final: 0.8328 (m-30) outliers start: 42 outliers final: 25 residues processed: 288 average time/residue: 0.1016 time to fit residues: 40.4086 Evaluate side-chains 303 residues out of total 1172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 272 time to evaluate : 0.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 HIS Chi-restraints excluded: chain A residue 57 PHE Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 213 LEU Chi-restraints excluded: chain A residue 215 VAL Chi-restraints excluded: chain A residue 336 GLN Chi-restraints excluded: chain A residue 412 LEU Chi-restraints excluded: chain B residue 798 HIS Chi-restraints excluded: chain B residue 803 TYR Chi-restraints excluded: chain B residue 845 LEU Chi-restraints excluded: chain B residue 850 MET Chi-restraints excluded: chain B residue 852 THR Chi-restraints excluded: chain B residue 865 HIS Chi-restraints excluded: chain B residue 903 GLN Chi-restraints excluded: chain B residue 925 LEU Chi-restraints excluded: chain C residue 26 LEU Chi-restraints excluded: chain C residue 30 PHE Chi-restraints excluded: chain C residue 32 TYR Chi-restraints excluded: chain C residue 33 TRP Chi-restraints excluded: chain C residue 92 VAL Chi-restraints excluded: chain C residue 110 TYR Chi-restraints excluded: chain C residue 122 SER Chi-restraints excluded: chain C residue 135 LEU Chi-restraints excluded: chain C residue 181 ILE Chi-restraints excluded: chain C residue 201 ILE Chi-restraints excluded: chain C residue 225 SER Chi-restraints excluded: chain C residue 228 LEU Chi-restraints excluded: chain E residue 30 LYS Chi-restraints excluded: chain E residue 63 PHE Chi-restraints excluded: chain E residue 108 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 70 optimal weight: 0.6980 chunk 94 optimal weight: 6.9990 chunk 58 optimal weight: 0.4980 chunk 6 optimal weight: 0.2980 chunk 2 optimal weight: 2.9990 chunk 42 optimal weight: 6.9990 chunk 105 optimal weight: 0.6980 chunk 52 optimal weight: 5.9990 chunk 48 optimal weight: 5.9990 chunk 117 optimal weight: 0.7980 chunk 38 optimal weight: 5.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 366 HIS B 778 GLN B 866 HIS C 64 ASN C 307 HIS C 446 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.114773 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.094782 restraints weight = 19602.527| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.098154 restraints weight = 11683.346| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.100518 restraints weight = 7875.648| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.102177 restraints weight = 5778.620| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.103414 restraints weight = 4541.021| |-----------------------------------------------------------------------------| r_work (final): 0.3524 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7360 moved from start: 0.2996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 9163 Z= 0.121 Angle : 0.710 13.901 12514 Z= 0.348 Chirality : 0.045 0.205 1519 Planarity : 0.004 0.052 1614 Dihedral : 5.754 74.582 1374 Min Nonbonded Distance : 1.372 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.39 % Allowed : 10.88 % Favored : 88.72 % Rotamer: Outliers : 5.15 % Allowed : 30.50 % Favored : 64.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.00 (0.24), residues: 1268 helix: 0.79 (0.26), residues: 431 sheet: -1.71 (0.36), residues: 211 loop : -2.83 (0.23), residues: 626 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 744 TYR 0.017 0.001 TYR B 843 PHE 0.017 0.001 PHE E 51 TRP 0.015 0.001 TRP A 148 HIS 0.013 0.001 HIS B 866 Details of bonding type rmsd covalent geometry : bond 0.00257 ( 9161) covalent geometry : angle 0.70955 (12514) hydrogen bonds : bond 0.03174 ( 376) hydrogen bonds : angle 5.00234 ( 1071) Misc. bond : bond 0.00051 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2536 Ramachandran restraints generated. 1268 Oldfield, 0 Emsley, 1268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2536 Ramachandran restraints generated. 1268 Oldfield, 0 Emsley, 1268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 1172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 262 time to evaluate : 0.335 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 155 MET cc_start: 0.7266 (mpp) cc_final: 0.6537 (mpp) REVERT: B 167 GLN cc_start: 0.8798 (mt0) cc_final: 0.8571 (mt0) REVERT: B 176 PHE cc_start: 0.7966 (m-80) cc_final: 0.7683 (m-80) REVERT: B 345 PHE cc_start: 0.8236 (m-80) cc_final: 0.7679 (m-10) REVERT: B 346 ARG cc_start: 0.8216 (mtm-85) cc_final: 0.7517 (mtm-85) REVERT: B 359 ARG cc_start: 0.7637 (ttm110) cc_final: 0.7081 (ttm110) REVERT: B 363 LYS cc_start: 0.8191 (ptpp) cc_final: 0.7844 (ptpp) REVERT: B 736 LEU cc_start: 0.6720 (mt) cc_final: 0.6323 (mt) REVERT: B 781 LYS cc_start: 0.8194 (tmtt) cc_final: 0.7952 (tmtt) REVERT: B 803 TYR cc_start: 0.7869 (m-10) cc_final: 0.7533 (m-10) REVERT: B 845 LEU cc_start: 0.7218 (OUTLIER) cc_final: 0.6787 (tt) REVERT: B 848 GLN cc_start: 0.8413 (tp40) cc_final: 0.8004 (tp-100) REVERT: B 887 PHE cc_start: 0.8300 (t80) cc_final: 0.8065 (t80) REVERT: B 890 LEU cc_start: 0.9019 (OUTLIER) cc_final: 0.8764 (mp) REVERT: B 903 GLN cc_start: 0.8907 (OUTLIER) cc_final: 0.8622 (pm20) REVERT: B 904 TYR cc_start: 0.8845 (t80) cc_final: 0.8637 (t80) REVERT: B 908 LEU cc_start: 0.8632 (mm) cc_final: 0.8424 (mm) REVERT: B 910 LYS cc_start: 0.7913 (ptpp) cc_final: 0.7613 (ptpp) REVERT: B 925 LEU cc_start: 0.7844 (OUTLIER) cc_final: 0.7379 (tt) REVERT: E 18 MET cc_start: 0.6149 (tpt) cc_final: 0.5455 (tpt) REVERT: E 36 LYS cc_start: 0.8971 (mmpt) cc_final: 0.8650 (mmpt) REVERT: E 106 GLU cc_start: 0.8185 (tm-30) cc_final: 0.7713 (tm-30) REVERT: E 108 MET cc_start: 0.8856 (mpp) cc_final: 0.8627 (mpp) outliers start: 37 outliers final: 23 residues processed: 276 average time/residue: 0.0955 time to fit residues: 36.5437 Evaluate side-chains 289 residues out of total 1172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 262 time to evaluate : 0.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 HIS Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 213 LEU Chi-restraints excluded: chain A residue 336 GLN Chi-restraints excluded: chain A residue 349 TRP Chi-restraints excluded: chain B residue 798 HIS Chi-restraints excluded: chain B residue 837 ILE Chi-restraints excluded: chain B residue 845 LEU Chi-restraints excluded: chain B residue 850 MET Chi-restraints excluded: chain B residue 852 THR Chi-restraints excluded: chain B residue 865 HIS Chi-restraints excluded: chain B residue 890 LEU Chi-restraints excluded: chain B residue 902 VAL Chi-restraints excluded: chain B residue 903 GLN Chi-restraints excluded: chain B residue 925 LEU Chi-restraints excluded: chain C residue 26 LEU Chi-restraints excluded: chain C residue 32 TYR Chi-restraints excluded: chain C residue 33 TRP Chi-restraints excluded: chain C residue 92 VAL Chi-restraints excluded: chain C residue 110 TYR Chi-restraints excluded: chain C residue 122 SER Chi-restraints excluded: chain C residue 135 LEU Chi-restraints excluded: chain C residue 225 SER Chi-restraints excluded: chain C residue 228 LEU Chi-restraints excluded: chain C residue 280 VAL Chi-restraints excluded: chain E residue 30 LYS Chi-restraints excluded: chain E residue 63 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 27 optimal weight: 5.9990 chunk 13 optimal weight: 0.7980 chunk 15 optimal weight: 9.9990 chunk 89 optimal weight: 3.9990 chunk 5 optimal weight: 4.9990 chunk 129 optimal weight: 0.0020 chunk 75 optimal weight: 0.0470 chunk 109 optimal weight: 2.9990 chunk 24 optimal weight: 5.9990 chunk 116 optimal weight: 0.6980 chunk 77 optimal weight: 3.9990 overall best weight: 0.9088 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 170 HIS B 366 HIS B 866 HIS C 207 ASN C 307 HIS C 446 ASN C 460 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.114102 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.094162 restraints weight = 19657.306| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.097538 restraints weight = 11689.690| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.099915 restraints weight = 7869.217| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.101614 restraints weight = 5770.487| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.102832 restraints weight = 4515.186| |-----------------------------------------------------------------------------| r_work (final): 0.3518 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7371 moved from start: 0.3158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 9163 Z= 0.136 Angle : 0.730 12.694 12514 Z= 0.359 Chirality : 0.045 0.236 1519 Planarity : 0.004 0.051 1614 Dihedral : 5.622 78.949 1372 Min Nonbonded Distance : 1.325 Molprobity Statistics. All-atom Clashscore : 9.48 Ramachandran Plot: Outliers : 0.39 % Allowed : 11.67 % Favored : 87.93 % Rotamer: Outliers : 5.01 % Allowed : 30.92 % Favored : 64.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.93 (0.24), residues: 1268 helix: 0.90 (0.26), residues: 427 sheet: -1.65 (0.36), residues: 210 loop : -2.83 (0.23), residues: 631 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG B 787 TYR 0.016 0.001 TYR B 99 PHE 0.023 0.001 PHE B 927 TRP 0.033 0.001 TRP A 148 HIS 0.013 0.001 HIS B 866 Details of bonding type rmsd covalent geometry : bond 0.00291 ( 9161) covalent geometry : angle 0.73048 (12514) hydrogen bonds : bond 0.03253 ( 376) hydrogen bonds : angle 4.93500 ( 1071) Misc. bond : bond 0.00060 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2536 Ramachandran restraints generated. 1268 Oldfield, 0 Emsley, 1268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2536 Ramachandran restraints generated. 1268 Oldfield, 0 Emsley, 1268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 1172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 264 time to evaluate : 0.360 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 194 GLU cc_start: 0.8463 (pm20) cc_final: 0.7705 (tp30) REVERT: B 155 MET cc_start: 0.7322 (mpp) cc_final: 0.6552 (mpp) REVERT: B 167 GLN cc_start: 0.8801 (mt0) cc_final: 0.8566 (mt0) REVERT: B 176 PHE cc_start: 0.7983 (m-80) cc_final: 0.7611 (m-80) REVERT: B 345 PHE cc_start: 0.8308 (m-80) cc_final: 0.7826 (m-10) REVERT: B 346 ARG cc_start: 0.8203 (mtm-85) cc_final: 0.7479 (mtm-85) REVERT: B 359 ARG cc_start: 0.7643 (ttm110) cc_final: 0.7116 (ttm110) REVERT: B 363 LYS cc_start: 0.8184 (ptpp) cc_final: 0.7829 (ptpp) REVERT: B 736 LEU cc_start: 0.6567 (mt) cc_final: 0.6263 (mt) REVERT: B 781 LYS cc_start: 0.8201 (tmtt) cc_final: 0.7924 (tmtt) REVERT: B 838 LYS cc_start: 0.8636 (mptt) cc_final: 0.8143 (mmtt) REVERT: B 845 LEU cc_start: 0.7224 (OUTLIER) cc_final: 0.6875 (tt) REVERT: B 887 PHE cc_start: 0.8314 (t80) cc_final: 0.8084 (t80) REVERT: B 890 LEU cc_start: 0.8999 (mm) cc_final: 0.8737 (mp) REVERT: B 904 TYR cc_start: 0.8879 (t80) cc_final: 0.8615 (t80) REVERT: B 908 LEU cc_start: 0.8655 (mm) cc_final: 0.8432 (mm) REVERT: B 910 LYS cc_start: 0.7912 (ptpp) cc_final: 0.7592 (ptpp) REVERT: B 925 LEU cc_start: 0.7853 (OUTLIER) cc_final: 0.7387 (tt) REVERT: C 179 GLU cc_start: 0.7732 (mp0) cc_final: 0.7111 (mp0) REVERT: E 18 MET cc_start: 0.6171 (tpt) cc_final: 0.5501 (tpt) REVERT: E 36 LYS cc_start: 0.8972 (mmpt) cc_final: 0.8659 (mmpt) REVERT: E 106 GLU cc_start: 0.8197 (tm-30) cc_final: 0.7757 (tm-30) REVERT: E 108 MET cc_start: 0.8835 (OUTLIER) cc_final: 0.8601 (mpp) outliers start: 36 outliers final: 24 residues processed: 280 average time/residue: 0.0944 time to fit residues: 36.8754 Evaluate side-chains 291 residues out of total 1172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 264 time to evaluate : 0.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 HIS Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 213 LEU Chi-restraints excluded: chain A residue 336 GLN Chi-restraints excluded: chain A residue 349 TRP Chi-restraints excluded: chain A residue 438 SER Chi-restraints excluded: chain B residue 797 LEU Chi-restraints excluded: chain B residue 798 HIS Chi-restraints excluded: chain B residue 837 ILE Chi-restraints excluded: chain B residue 845 LEU Chi-restraints excluded: chain B residue 850 MET Chi-restraints excluded: chain B residue 852 THR Chi-restraints excluded: chain B residue 865 HIS Chi-restraints excluded: chain B residue 925 LEU Chi-restraints excluded: chain C residue 26 LEU Chi-restraints excluded: chain C residue 32 TYR Chi-restraints excluded: chain C residue 33 TRP Chi-restraints excluded: chain C residue 92 VAL Chi-restraints excluded: chain C residue 110 TYR Chi-restraints excluded: chain C residue 122 SER Chi-restraints excluded: chain C residue 127 LEU Chi-restraints excluded: chain C residue 135 LEU Chi-restraints excluded: chain C residue 225 SER Chi-restraints excluded: chain C residue 307 HIS Chi-restraints excluded: chain E residue 30 LYS Chi-restraints excluded: chain E residue 63 PHE Chi-restraints excluded: chain E residue 108 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 79 optimal weight: 0.8980 chunk 32 optimal weight: 0.8980 chunk 65 optimal weight: 0.0770 chunk 66 optimal weight: 6.9990 chunk 0 optimal weight: 2.9990 chunk 43 optimal weight: 4.9990 chunk 26 optimal weight: 4.9990 chunk 120 optimal weight: 2.9990 chunk 67 optimal weight: 2.9990 chunk 56 optimal weight: 2.9990 chunk 13 optimal weight: 0.9980 overall best weight: 1.1740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 170 HIS B 366 HIS B 866 HIS C 307 HIS C 446 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.115337 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.094589 restraints weight = 19031.205| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.097875 restraints weight = 11756.691| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.100176 restraints weight = 8133.327| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.101850 restraints weight = 6096.354| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.103062 restraints weight = 4852.165| |-----------------------------------------------------------------------------| r_work (final): 0.3504 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7404 moved from start: 0.3201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 9163 Z= 0.152 Angle : 0.750 13.693 12514 Z= 0.367 Chirality : 0.046 0.231 1519 Planarity : 0.004 0.051 1614 Dihedral : 5.623 79.874 1372 Min Nonbonded Distance : 1.328 Molprobity Statistics. All-atom Clashscore : 10.27 Ramachandran Plot: Outliers : 0.39 % Allowed : 11.75 % Favored : 87.85 % Rotamer: Outliers : 4.46 % Allowed : 32.45 % Favored : 63.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.94 (0.24), residues: 1268 helix: 0.85 (0.26), residues: 428 sheet: -1.60 (0.36), residues: 208 loop : -2.82 (0.23), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 731 TYR 0.017 0.001 TYR B 99 PHE 0.023 0.001 PHE B 169 TRP 0.035 0.001 TRP A 148 HIS 0.014 0.001 HIS B 866 Details of bonding type rmsd covalent geometry : bond 0.00319 ( 9161) covalent geometry : angle 0.74980 (12514) hydrogen bonds : bond 0.03397 ( 376) hydrogen bonds : angle 4.98486 ( 1071) Misc. bond : bond 0.00071 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2536 Ramachandran restraints generated. 1268 Oldfield, 0 Emsley, 1268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2536 Ramachandran restraints generated. 1268 Oldfield, 0 Emsley, 1268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 1172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 265 time to evaluate : 0.384 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 410 MET cc_start: 0.7180 (ppp) cc_final: 0.6337 (ppp) REVERT: B 155 MET cc_start: 0.7310 (mpp) cc_final: 0.6656 (mpp) REVERT: B 167 GLN cc_start: 0.8785 (mt0) cc_final: 0.8557 (mt0) REVERT: B 176 PHE cc_start: 0.8002 (m-80) cc_final: 0.7665 (m-80) REVERT: B 345 PHE cc_start: 0.8272 (m-80) cc_final: 0.7821 (m-10) REVERT: B 346 ARG cc_start: 0.8198 (mtm-85) cc_final: 0.7494 (mtm-85) REVERT: B 363 LYS cc_start: 0.8198 (ptpp) cc_final: 0.7864 (ptpp) REVERT: B 736 LEU cc_start: 0.6649 (mt) cc_final: 0.6239 (mt) REVERT: B 781 LYS cc_start: 0.8144 (tmtt) cc_final: 0.7916 (tmtt) REVERT: B 887 PHE cc_start: 0.8332 (t80) cc_final: 0.8101 (t80) REVERT: B 890 LEU cc_start: 0.9014 (mm) cc_final: 0.8748 (mp) REVERT: B 904 TYR cc_start: 0.8843 (t80) cc_final: 0.8612 (t80) REVERT: B 908 LEU cc_start: 0.8664 (mm) cc_final: 0.8444 (mm) REVERT: B 910 LYS cc_start: 0.7925 (ptpp) cc_final: 0.7604 (ptpp) REVERT: B 925 LEU cc_start: 0.7894 (OUTLIER) cc_final: 0.7443 (tt) REVERT: E 18 MET cc_start: 0.6147 (tpt) cc_final: 0.5506 (tpt) REVERT: E 36 LYS cc_start: 0.8977 (mmpt) cc_final: 0.8653 (mmpt) REVERT: E 106 GLU cc_start: 0.8152 (tm-30) cc_final: 0.7731 (tm-30) REVERT: E 108 MET cc_start: 0.8809 (OUTLIER) cc_final: 0.8596 (mpp) outliers start: 32 outliers final: 27 residues processed: 280 average time/residue: 0.0939 time to fit residues: 36.5398 Evaluate side-chains 294 residues out of total 1172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 265 time to evaluate : 0.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 HIS Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 213 LEU Chi-restraints excluded: chain A residue 349 TRP Chi-restraints excluded: chain A residue 438 SER Chi-restraints excluded: chain B residue 797 LEU Chi-restraints excluded: chain B residue 798 HIS Chi-restraints excluded: chain B residue 837 ILE Chi-restraints excluded: chain B residue 845 LEU Chi-restraints excluded: chain B residue 850 MET Chi-restraints excluded: chain B residue 852 THR Chi-restraints excluded: chain B residue 865 HIS Chi-restraints excluded: chain B residue 925 LEU Chi-restraints excluded: chain B residue 933 PHE Chi-restraints excluded: chain C residue 26 LEU Chi-restraints excluded: chain C residue 30 PHE Chi-restraints excluded: chain C residue 32 TYR Chi-restraints excluded: chain C residue 33 TRP Chi-restraints excluded: chain C residue 92 VAL Chi-restraints excluded: chain C residue 110 TYR Chi-restraints excluded: chain C residue 122 SER Chi-restraints excluded: chain C residue 135 LEU Chi-restraints excluded: chain C residue 225 SER Chi-restraints excluded: chain C residue 280 VAL Chi-restraints excluded: chain C residue 312 VAL Chi-restraints excluded: chain E residue 30 LYS Chi-restraints excluded: chain E residue 63 PHE Chi-restraints excluded: chain E residue 108 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 42 optimal weight: 6.9990 chunk 16 optimal weight: 0.8980 chunk 79 optimal weight: 0.5980 chunk 46 optimal weight: 5.9990 chunk 60 optimal weight: 0.5980 chunk 110 optimal weight: 0.9990 chunk 61 optimal weight: 0.2980 chunk 58 optimal weight: 0.6980 chunk 19 optimal weight: 4.9990 chunk 51 optimal weight: 7.9990 chunk 118 optimal weight: 4.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 866 HIS C 207 ASN C 446 ASN C 460 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.116047 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.096423 restraints weight = 19619.164| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.099768 restraints weight = 11703.463| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.102145 restraints weight = 7892.527| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.103814 restraints weight = 5776.286| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.105029 restraints weight = 4525.999| |-----------------------------------------------------------------------------| r_work (final): 0.3550 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7340 moved from start: 0.3347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 9163 Z= 0.123 Angle : 0.730 12.184 12514 Z= 0.359 Chirality : 0.045 0.227 1519 Planarity : 0.004 0.050 1614 Dihedral : 5.394 75.429 1372 Min Nonbonded Distance : 1.392 Molprobity Statistics. All-atom Clashscore : 9.79 Ramachandran Plot: Outliers : 0.39 % Allowed : 9.94 % Favored : 89.67 % Rotamer: Outliers : 4.32 % Allowed : 32.87 % Favored : 62.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.77 (0.24), residues: 1268 helix: 1.06 (0.26), residues: 422 sheet: -1.73 (0.35), residues: 221 loop : -2.67 (0.23), residues: 625 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG B 787 TYR 0.018 0.001 TYR B 99 PHE 0.021 0.001 PHE B 169 TRP 0.035 0.001 TRP A 148 HIS 0.013 0.001 HIS B 866 Details of bonding type rmsd covalent geometry : bond 0.00267 ( 9161) covalent geometry : angle 0.72987 (12514) hydrogen bonds : bond 0.03013 ( 376) hydrogen bonds : angle 4.72972 ( 1071) Misc. bond : bond 0.00054 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2536 Ramachandran restraints generated. 1268 Oldfield, 0 Emsley, 1268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2536 Ramachandran restraints generated. 1268 Oldfield, 0 Emsley, 1268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 1172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 262 time to evaluate : 0.334 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 194 GLU cc_start: 0.8434 (pm20) cc_final: 0.7588 (tp30) REVERT: A 410 MET cc_start: 0.7052 (ppp) cc_final: 0.6199 (ppp) REVERT: B 155 MET cc_start: 0.7354 (mpp) cc_final: 0.6618 (mpp) REVERT: B 167 GLN cc_start: 0.8782 (mt0) cc_final: 0.8538 (mt0) REVERT: B 176 PHE cc_start: 0.7929 (m-80) cc_final: 0.7553 (m-80) REVERT: B 345 PHE cc_start: 0.8199 (m-80) cc_final: 0.7815 (m-10) REVERT: B 346 ARG cc_start: 0.8204 (mtm-85) cc_final: 0.7483 (mtm-85) REVERT: B 363 LYS cc_start: 0.8161 (ptpp) cc_final: 0.7816 (ptpp) REVERT: B 781 LYS cc_start: 0.8145 (tmtt) cc_final: 0.7915 (tmtt) REVERT: B 787 ARG cc_start: 0.7278 (ttm110) cc_final: 0.7052 (ptp-110) REVERT: B 814 ASN cc_start: 0.9052 (m110) cc_final: 0.8737 (m110) REVERT: B 838 LYS cc_start: 0.8591 (mptt) cc_final: 0.8336 (mptt) REVERT: B 887 PHE cc_start: 0.8284 (t80) cc_final: 0.8048 (t80) REVERT: B 890 LEU cc_start: 0.8993 (mm) cc_final: 0.8726 (mp) REVERT: B 904 TYR cc_start: 0.8854 (t80) cc_final: 0.8584 (t80) REVERT: B 908 LEU cc_start: 0.8635 (mm) cc_final: 0.8415 (mm) REVERT: B 910 LYS cc_start: 0.7889 (ptpp) cc_final: 0.7551 (ptpp) REVERT: B 925 LEU cc_start: 0.7811 (OUTLIER) cc_final: 0.7375 (tt) REVERT: C 316 LYS cc_start: 0.8340 (tppt) cc_final: 0.8123 (tppt) REVERT: E 18 MET cc_start: 0.6132 (tpt) cc_final: 0.5450 (tpt) REVERT: E 36 LYS cc_start: 0.8967 (mmpt) cc_final: 0.8642 (mmpt) REVERT: E 106 GLU cc_start: 0.8141 (tm-30) cc_final: 0.7703 (tm-30) REVERT: E 108 MET cc_start: 0.8864 (OUTLIER) cc_final: 0.8629 (mpp) outliers start: 31 outliers final: 26 residues processed: 275 average time/residue: 0.0904 time to fit residues: 34.7903 Evaluate side-chains 289 residues out of total 1172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 261 time to evaluate : 0.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 HIS Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 213 LEU Chi-restraints excluded: chain A residue 349 TRP Chi-restraints excluded: chain A residue 438 SER Chi-restraints excluded: chain B residue 797 LEU Chi-restraints excluded: chain B residue 798 HIS Chi-restraints excluded: chain B residue 837 ILE Chi-restraints excluded: chain B residue 845 LEU Chi-restraints excluded: chain B residue 850 MET Chi-restraints excluded: chain B residue 852 THR Chi-restraints excluded: chain B residue 865 HIS Chi-restraints excluded: chain B residue 925 LEU Chi-restraints excluded: chain B residue 933 PHE Chi-restraints excluded: chain C residue 26 LEU Chi-restraints excluded: chain C residue 30 PHE Chi-restraints excluded: chain C residue 33 TRP Chi-restraints excluded: chain C residue 92 VAL Chi-restraints excluded: chain C residue 110 TYR Chi-restraints excluded: chain C residue 122 SER Chi-restraints excluded: chain C residue 135 LEU Chi-restraints excluded: chain C residue 225 SER Chi-restraints excluded: chain C residue 280 VAL Chi-restraints excluded: chain C residue 312 VAL Chi-restraints excluded: chain E residue 30 LYS Chi-restraints excluded: chain E residue 63 PHE Chi-restraints excluded: chain E residue 108 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 16 optimal weight: 3.9990 chunk 41 optimal weight: 0.4980 chunk 121 optimal weight: 0.9980 chunk 98 optimal weight: 3.9990 chunk 89 optimal weight: 3.9990 chunk 59 optimal weight: 0.6980 chunk 61 optimal weight: 0.9990 chunk 46 optimal weight: 5.9990 chunk 29 optimal weight: 7.9990 chunk 78 optimal weight: 4.9990 chunk 17 optimal weight: 10.0000 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 170 HIS ** A 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 866 HIS C 446 ASN C 460 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.114778 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.094043 restraints weight = 18826.625| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.097281 restraints weight = 11744.107| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.099555 restraints weight = 8168.511| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.101190 restraints weight = 6144.873| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.102395 restraints weight = 4918.267| |-----------------------------------------------------------------------------| r_work (final): 0.3494 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7419 moved from start: 0.3395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 9163 Z= 0.178 Angle : 0.771 13.473 12514 Z= 0.382 Chirality : 0.046 0.229 1519 Planarity : 0.004 0.052 1614 Dihedral : 5.631 82.179 1370 Min Nonbonded Distance : 1.318 Molprobity Statistics. All-atom Clashscore : 11.17 Ramachandran Plot: Outliers : 0.39 % Allowed : 12.30 % Favored : 87.30 % Rotamer: Outliers : 4.74 % Allowed : 33.43 % Favored : 61.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.95 (0.23), residues: 1268 helix: 0.80 (0.26), residues: 429 sheet: -1.59 (0.37), residues: 198 loop : -2.80 (0.23), residues: 641 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG B 787 TYR 0.016 0.001 TYR B 843 PHE 0.024 0.001 PHE B 927 TRP 0.040 0.002 TRP A 148 HIS 0.014 0.001 HIS B 866 Details of bonding type rmsd covalent geometry : bond 0.00369 ( 9161) covalent geometry : angle 0.77075 (12514) hydrogen bonds : bond 0.03600 ( 376) hydrogen bonds : angle 5.02673 ( 1071) Misc. bond : bond 0.00085 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1900.96 seconds wall clock time: 33 minutes 18.35 seconds (1998.35 seconds total)