Starting phenix.real_space_refine on Thu Mar 14 18:18:26 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jwi_36684/03_2024/8jwi_36684_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jwi_36684/03_2024/8jwi_36684.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.94 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jwi_36684/03_2024/8jwi_36684.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jwi_36684/03_2024/8jwi_36684.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jwi_36684/03_2024/8jwi_36684_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jwi_36684/03_2024/8jwi_36684_neut_updated.pdb" } resolution = 2.94 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.002 sd= 0.115 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 6 5.49 5 Mg 2 5.21 5 S 39 5.16 5 C 6102 2.51 5 N 1552 2.21 5 O 1730 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 575": "NH1" <-> "NH2" Residue "A ARG 614": "NH1" <-> "NH2" Residue "A ARG 627": "NH1" <-> "NH2" Residue "A ARG 1138": "NH1" <-> "NH2" Residue "A ARG 1176": "NH1" <-> "NH2" Residue "A ARG 1371": "NH1" <-> "NH2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 9431 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 9367 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1164, 9367 Classifications: {'peptide': 1164} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 26, 'TRANS': 1137} Chain breaks: 7 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "A" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 64 Unusual residues: {' MG': 2, 'ATP': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Time building chain proxies: 5.83, per 1000 atoms: 0.62 Number of scatterers: 9431 At special positions: 0 Unit cell: (72.6, 89.1, 145.2, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 39 16.00 P 6 15.00 Mg 2 11.99 O 1730 8.00 N 1552 7.00 C 6102 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.33 Conformation dependent library (CDL) restraints added in 1.9 seconds 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2208 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 46 helices and 4 sheets defined 59.4% alpha, 4.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.79 Creating SS restraints... Processing helix chain 'A' and resid 51 through 82 removed outlier: 4.010A pdb=" N LYS A 55 " --> pdb=" O ALA A 51 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N LEU A 56 " --> pdb=" O GLN A 52 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N ALA A 64 " --> pdb=" O SER A 60 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N VAL A 65 " --> pdb=" O PHE A 61 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N LEU A 66 " --> pdb=" O VAL A 62 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N SER A 67 " --> pdb=" O CYS A 63 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N THR A 70 " --> pdb=" O LEU A 66 " (cutoff:3.500A) removed outlier: 5.107A pdb=" N LEU A 71 " --> pdb=" O SER A 67 " (cutoff:3.500A) Proline residue: A 72 - end of helix removed outlier: 3.800A pdb=" N VAL A 80 " --> pdb=" O SER A 76 " (cutoff:3.500A) Processing helix chain 'A' and resid 92 through 133 removed outlier: 3.684A pdb=" N ILE A 111 " --> pdb=" O ILE A 107 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N SER A 112 " --> pdb=" O LEU A 108 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N SER A 113 " --> pdb=" O SER A 109 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N TYR A 114 " --> pdb=" O MET A 110 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N MET A 116 " --> pdb=" O SER A 112 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ASP A 117 " --> pdb=" O SER A 113 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N VAL A 118 " --> pdb=" O TYR A 114 " (cutoff:3.500A) removed outlier: 4.916A pdb=" N ILE A 119 " --> pdb=" O CYS A 115 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N SER A 121 " --> pdb=" O ASP A 117 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N LYS A 122 " --> pdb=" O VAL A 118 " (cutoff:3.500A) removed outlier: 5.257A pdb=" N LYS A 125 " --> pdb=" O SER A 121 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N LYS A 128 " --> pdb=" O LEU A 124 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N LEU A 132 " --> pdb=" O LYS A 128 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ARG A 133 " --> pdb=" O LEU A 129 " (cutoff:3.500A) Processing helix chain 'A' and resid 140 through 145 removed outlier: 3.779A pdb=" N ASN A 145 " --> pdb=" O GLN A 141 " (cutoff:3.500A) Processing helix chain 'A' and resid 148 through 165 removed outlier: 3.779A pdb=" N ARG A 152 " --> pdb=" O GLY A 148 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N SER A 153 " --> pdb=" O SER A 149 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ASP A 154 " --> pdb=" O LYS A 150 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N GLU A 160 " --> pdb=" O ASP A 156 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N GLN A 161 " --> pdb=" O PHE A 157 " (cutoff:3.500A) Processing helix chain 'A' and resid 168 through 184 removed outlier: 4.148A pdb=" N THR A 172 " --> pdb=" O LYS A 169 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N ILE A 173 " --> pdb=" O PHE A 170 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ALA A 177 " --> pdb=" O PHE A 174 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N SER A 178 " --> pdb=" O THR A 175 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N SER A 179 " --> pdb=" O TYR A 176 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N TYR A 184 " --> pdb=" O LEU A 181 " (cutoff:3.500A) Processing helix chain 'A' and resid 186 through 190 removed outlier: 4.215A pdb=" N LYS A 190 " --> pdb=" O TRP A 186 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 186 through 190' Processing helix chain 'A' and resid 202 through 239 removed outlier: 3.678A pdb=" N TYR A 206 " --> pdb=" O PHE A 202 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N VAL A 207 " --> pdb=" O PRO A 203 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N CYS A 208 " --> pdb=" O LEU A 204 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N GLY A 209 " --> pdb=" O ILE A 205 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N VAL A 210 " --> pdb=" O TYR A 206 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ILE A 211 " --> pdb=" O VAL A 207 " (cutoff:3.500A) removed outlier: 4.686A pdb=" N VAL A 216 " --> pdb=" O CYS A 212 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N LYS A 217 " --> pdb=" O ASN A 213 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N LEU A 218 " --> pdb=" O LYS A 214 " (cutoff:3.500A) removed outlier: 5.472A pdb=" N ASN A 219 " --> pdb=" O LYS A 215 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LEU A 225 " --> pdb=" O LYS A 221 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N TYR A 226 " --> pdb=" O THR A 222 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ILE A 233 " --> pdb=" O ASN A 229 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N ILE A 234 " --> pdb=" O THR A 230 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N GLU A 235 " --> pdb=" O MET A 231 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N GLU A 236 " --> pdb=" O SER A 232 " (cutoff:3.500A) Processing helix chain 'A' and resid 241 through 247 Processing helix chain 'A' and resid 252 through 307 removed outlier: 3.661A pdb=" N LYS A 256 " --> pdb=" O THR A 252 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N TYR A 264 " --> pdb=" O SER A 260 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N LYS A 266 " --> pdb=" O THR A 262 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N TYR A 267 " --> pdb=" O PHE A 263 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N PHE A 273 " --> pdb=" O LEU A 269 " (cutoff:3.500A) removed outlier: 4.611A pdb=" N VAL A 274 " --> pdb=" O LYS A 270 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N GLU A 275 " --> pdb=" O ALA A 271 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N ALA A 276 " --> pdb=" O ASN A 272 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N ILE A 279 " --> pdb=" O GLU A 275 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N GLY A 280 " --> pdb=" O ALA A 276 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ASN A 283 " --> pdb=" O ILE A 279 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N GLY A 284 " --> pdb=" O GLY A 280 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ARG A 299 " --> pdb=" O TRP A 295 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N ILE A 300 " --> pdb=" O TYR A 296 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N ILE A 301 " --> pdb=" O GLY A 297 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N THR A 306 " --> pdb=" O ILE A 302 " (cutoff:3.500A) Processing helix chain 'A' and resid 318 through 357 removed outlier: 3.869A pdb=" N ILE A 328 " --> pdb=" O LEU A 324 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N SER A 329 " --> pdb=" O GLY A 325 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N MET A 330 " --> pdb=" O VAL A 326 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ILE A 335 " --> pdb=" O PHE A 331 " (cutoff:3.500A) Proline residue: A 338 - end of helix removed outlier: 4.001A pdb=" N THR A 341 " --> pdb=" O LEU A 337 " (cutoff:3.500A) removed outlier: 5.028A pdb=" N GLU A 342 " --> pdb=" O PRO A 338 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N TYR A 343 " --> pdb=" O ASN A 339 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N ALA A 346 " --> pdb=" O GLU A 342 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N LEU A 347 " --> pdb=" O TYR A 343 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N GLU A 348 " --> pdb=" O MET A 344 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ALA A 349 " --> pdb=" O LYS A 345 " (cutoff:3.500A) Processing helix chain 'A' and resid 419 through 426 Processing helix chain 'A' and resid 445 through 447 No H-bonds generated for 'chain 'A' and resid 445 through 447' Processing helix chain 'A' and resid 450 through 454 Processing helix chain 'A' and resid 471 through 488 removed outlier: 4.678A pdb=" N SER A 478 " --> pdb=" O ASN A 474 " (cutoff:3.500A) removed outlier: 5.353A pdb=" N LEU A 479 " --> pdb=" O ILE A 475 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N TYR A 480 " --> pdb=" O LYS A 476 " (cutoff:3.500A) removed outlier: 4.805A pdb=" N SER A 481 " --> pdb=" O TYR A 477 " (cutoff:3.500A) removed outlier: 4.857A pdb=" N LEU A 482 " --> pdb=" O SER A 478 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N LEU A 485 " --> pdb=" O SER A 481 " (cutoff:3.500A) Processing helix chain 'A' and resid 520 through 526 removed outlier: 3.821A pdb=" N TYR A 524 " --> pdb=" O MET A 520 " (cutoff:3.500A) removed outlier: 5.314A pdb=" N GLN A 525 " --> pdb=" O LYS A 521 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N THR A 526 " --> pdb=" O LYS A 522 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 520 through 526' Processing helix chain 'A' and resid 531 through 539 removed outlier: 3.955A pdb=" N VAL A 539 " --> pdb=" O VAL A 535 " (cutoff:3.500A) Processing helix chain 'A' and resid 542 through 545 No H-bonds generated for 'chain 'A' and resid 542 through 545' Processing helix chain 'A' and resid 558 through 560 No H-bonds generated for 'chain 'A' and resid 558 through 560' Processing helix chain 'A' and resid 565 through 577 Processing helix chain 'A' and resid 595 through 607 removed outlier: 3.876A pdb=" N ASN A 607 " --> pdb=" O LYS A 603 " (cutoff:3.500A) Processing helix chain 'A' and resid 677 through 680 No H-bonds generated for 'chain 'A' and resid 677 through 680' Processing helix chain 'A' and resid 686 through 694 Processing helix chain 'A' and resid 774 through 784 removed outlier: 3.664A pdb=" N TYR A 779 " --> pdb=" O ARG A 776 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N LYS A 780 " --> pdb=" O ILE A 777 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N PHE A 783 " --> pdb=" O LYS A 780 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N SER A 784 " --> pdb=" O GLU A 781 " (cutoff:3.500A) Processing helix chain 'A' and resid 786 through 800 removed outlier: 3.840A pdb=" N ILE A 791 " --> pdb=" O LYS A 787 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ILE A 792 " --> pdb=" O ASP A 788 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N VAL A 798 " --> pdb=" O PHE A 794 " (cutoff:3.500A) Processing helix chain 'A' and resid 804 through 816 removed outlier: 3.811A pdb=" N TYR A 810 " --> pdb=" O ALA A 807 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N ARG A 812 " --> pdb=" O LEU A 809 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N SER A 815 " --> pdb=" O ARG A 812 " (cutoff:3.500A) Processing helix chain 'A' and resid 823 through 873 removed outlier: 3.734A pdb=" N SER A 831 " --> pdb=" O SER A 827 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ILE A 832 " --> pdb=" O ASN A 828 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ALA A 840 " --> pdb=" O LEU A 836 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N PHE A 842 " --> pdb=" O ALA A 838 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N ILE A 843 " --> pdb=" O ILE A 839 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N TYR A 851 " --> pdb=" O LEU A 847 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ASN A 852 " --> pdb=" O LYS A 848 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N ASN A 853 " --> pdb=" O ASN A 849 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N LYS A 858 " --> pdb=" O LYS A 854 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N VAL A 859 " --> pdb=" O ILE A 855 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N THR A 862 " --> pdb=" O LYS A 858 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N LEU A 867 " --> pdb=" O MET A 863 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N PHE A 868 " --> pdb=" O LYS A 864 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N TYR A 873 " --> pdb=" O GLU A 869 " (cutoff:3.500A) Processing helix chain 'A' and resid 877 through 880 No H-bonds generated for 'chain 'A' and resid 877 through 880' Processing helix chain 'A' and resid 886 through 926 removed outlier: 3.864A pdb=" N SER A 890 " --> pdb=" O PRO A 886 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N ALA A 891 " --> pdb=" O GLY A 887 " (cutoff:3.500A) removed outlier: 5.283A pdb=" N LEU A 900 " --> pdb=" O ASP A 896 " (cutoff:3.500A) removed outlier: 4.783A pdb=" N LYS A 901 " --> pdb=" O VAL A 897 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N THR A 902 " --> pdb=" O HIS A 898 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N VAL A 905 " --> pdb=" O LYS A 901 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N ILE A 908 " --> pdb=" O LEU A 904 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N VAL A 909 " --> pdb=" O VAL A 905 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N VAL A 923 " --> pdb=" O LEU A 919 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N PHE A 926 " --> pdb=" O MET A 922 " (cutoff:3.500A) Processing helix chain 'A' and resid 930 through 948 removed outlier: 4.240A pdb=" N PHE A 938 " --> pdb=" O ALA A 934 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N ILE A 939 " --> pdb=" O VAL A 935 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N PHE A 947 " --> pdb=" O ASN A 943 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N ALA A 948 " --> pdb=" O MET A 944 " (cutoff:3.500A) Processing helix chain 'A' and resid 982 through 998 removed outlier: 3.683A pdb=" N ASN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N HIS A 994 " --> pdb=" O PHE A 990 " (cutoff:3.500A) removed outlier: 7.169A pdb=" N THR A 995 " --> pdb=" O TYR A 991 " (cutoff:3.500A) Processing helix chain 'A' and resid 1003 through 1016 removed outlier: 3.542A pdb=" N GLU A1010 " --> pdb=" O CYS A1006 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N LYS A1011 " --> pdb=" O ASN A1007 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N ALA A1012 " --> pdb=" O LEU A1008 " (cutoff:3.500A) Processing helix chain 'A' and resid 1022 through 1036 removed outlier: 3.940A pdb=" N VAL A1026 " --> pdb=" O ARG A1022 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ASN A1027 " --> pdb=" O ARG A1023 " (cutoff:3.500A) Processing helix chain 'A' and resid 1039 through 1055 removed outlier: 3.508A pdb=" N PHE A1044 " --> pdb=" O PHE A1040 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N PHE A1051 " --> pdb=" O TRP A1047 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N LEU A1052 " --> pdb=" O PHE A1048 " (cutoff:3.500A) Processing helix chain 'A' and resid 1060 through 1081 removed outlier: 4.415A pdb=" N THR A1069 " --> pdb=" O LYS A1065 " (cutoff:3.500A) removed outlier: 4.783A pdb=" N PHE A1070 " --> pdb=" O SER A1066 " (cutoff:3.500A) removed outlier: 4.805A pdb=" N ILE A1071 " --> pdb=" O LEU A1067 " (cutoff:3.500A) removed outlier: 5.474A pdb=" N PHE A1072 " --> pdb=" O PHE A1068 " (cutoff:3.500A) removed outlier: 5.426A pdb=" N THR A1073 " --> pdb=" O THR A1069 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N ALA A1077 " --> pdb=" O THR A1073 " (cutoff:3.500A) removed outlier: 5.609A pdb=" N GLY A1078 " --> pdb=" O GLY A1074 " (cutoff:3.500A) removed outlier: 5.695A pdb=" N LYS A1079 " --> pdb=" O SER A1075 " (cutoff:3.500A) removed outlier: 4.646A pdb=" N LEU A1080 " --> pdb=" O TYR A1076 " (cutoff:3.500A) removed outlier: 4.840A pdb=" N MET A1081 " --> pdb=" O ALA A1077 " (cutoff:3.500A) Processing helix chain 'A' and resid 1085 through 1102 Proline residue: A1099 - end of helix Processing helix chain 'A' and resid 1167 through 1175 removed outlier: 4.196A pdb=" N MET A1171 " --> pdb=" O LYS A1167 " (cutoff:3.500A) removed outlier: 5.114A pdb=" N ASN A1172 " --> pdb=" O SER A1168 " (cutoff:3.500A) Processing helix chain 'A' and resid 1239 through 1241 No H-bonds generated for 'chain 'A' and resid 1239 through 1241' Processing helix chain 'A' and resid 1247 through 1250 No H-bonds generated for 'chain 'A' and resid 1247 through 1250' Processing helix chain 'A' and resid 1265 through 1269 Processing helix chain 'A' and resid 1278 through 1287 removed outlier: 3.709A pdb=" N LYS A1286 " --> pdb=" O LYS A1282 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N PHE A1287 " --> pdb=" O ARG A1283 " (cutoff:3.500A) Processing helix chain 'A' and resid 1294 through 1296 No H-bonds generated for 'chain 'A' and resid 1294 through 1296' Processing helix chain 'A' and resid 1307 through 1309 No H-bonds generated for 'chain 'A' and resid 1307 through 1309' Processing helix chain 'A' and resid 1314 through 1327 removed outlier: 3.563A pdb=" N ALA A1321 " --> pdb=" O LYS A1317 " (cutoff:3.500A) Processing helix chain 'A' and resid 1344 through 1359 Processing helix chain 'A' and resid 1372 through 1375 Processing helix chain 'A' and resid 1411 through 1416 removed outlier: 3.871A pdb=" N LYS A1416 " --> pdb=" O LYS A1412 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 407 through 411 removed outlier: 3.855A pdb=" N THR A 616 " --> pdb=" O LYS A 407 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N TYR A 409 " --> pdb=" O THR A 616 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N PHE A 411 " --> pdb=" O ILE A 618 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 1380 through 1383 removed outlier: 3.762A pdb=" N LYS A1380 " --> pdb=" O THR A1156 " (cutoff:3.500A) removed outlier: 7.306A pdb=" N ILE A1365 " --> pdb=" O THR A1157 " (cutoff:3.500A) removed outlier: 8.918A pdb=" N ILE A1159 " --> pdb=" O ILE A1365 " (cutoff:3.500A) removed outlier: 7.333A pdb=" N THR A1367 " --> pdb=" O ILE A1159 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 632 through 636 removed outlier: 3.650A pdb=" N GLY A 674 " --> pdb=" O ILE A 632 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N VAL A 634 " --> pdb=" O GLU A 672 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N GLU A 672 " --> pdb=" O VAL A 634 " (cutoff:3.500A) removed outlier: 6.078A pdb=" N SER A 636 " --> pdb=" O ILE A 670 " (cutoff:3.500A) removed outlier: 5.286A pdb=" N ILE A 670 " --> pdb=" O SER A 636 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 1126 through 1131 removed outlier: 3.820A pdb=" N LYS A1129 " --> pdb=" O GLU A1231 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N GLU A1231 " --> pdb=" O LYS A1129 " (cutoff:3.500A) 374 hydrogen bonds defined for protein. 1059 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.80 Time building geometry restraints manager: 3.64 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2919 1.34 - 1.46: 1925 1.46 - 1.58: 4690 1.58 - 1.69: 10 1.69 - 1.81: 65 Bond restraints: 9609 Sorted by residual: bond pdb=" C4 ATP A1502 " pdb=" C5 ATP A1502 " ideal model delta sigma weight residual 1.388 1.467 -0.079 1.00e-02 1.00e+04 6.21e+01 bond pdb=" C4 ATP A1501 " pdb=" C5 ATP A1501 " ideal model delta sigma weight residual 1.388 1.465 -0.077 1.00e-02 1.00e+04 5.93e+01 bond pdb=" C5 ATP A1502 " pdb=" C6 ATP A1502 " ideal model delta sigma weight residual 1.409 1.477 -0.068 1.00e-02 1.00e+04 4.68e+01 bond pdb=" C5 ATP A1501 " pdb=" C6 ATP A1501 " ideal model delta sigma weight residual 1.409 1.476 -0.067 1.00e-02 1.00e+04 4.49e+01 bond pdb=" C8 ATP A1502 " pdb=" N7 ATP A1502 " ideal model delta sigma weight residual 1.310 1.356 -0.046 1.00e-02 1.00e+04 2.14e+01 ... (remaining 9604 not shown) Histogram of bond angle deviations from ideal: 99.12 - 106.54: 170 106.54 - 113.95: 5449 113.95 - 121.37: 5137 121.37 - 128.78: 2164 128.78 - 136.19: 49 Bond angle restraints: 12969 Sorted by residual: angle pdb=" PB ATP A1501 " pdb=" O3B ATP A1501 " pdb=" PG ATP A1501 " ideal model delta sigma weight residual 139.87 119.67 20.20 1.00e+00 1.00e+00 4.08e+02 angle pdb=" PB ATP A1502 " pdb=" O3B ATP A1502 " pdb=" PG ATP A1502 " ideal model delta sigma weight residual 139.87 119.92 19.95 1.00e+00 1.00e+00 3.98e+02 angle pdb=" PA ATP A1502 " pdb=" O3A ATP A1502 " pdb=" PB ATP A1502 " ideal model delta sigma weight residual 136.83 119.71 17.12 1.00e+00 1.00e+00 2.93e+02 angle pdb=" PA ATP A1501 " pdb=" O3A ATP A1501 " pdb=" PB ATP A1501 " ideal model delta sigma weight residual 136.83 120.09 16.74 1.00e+00 1.00e+00 2.80e+02 angle pdb=" C5 ATP A1502 " pdb=" C4 ATP A1502 " pdb=" N3 ATP A1502 " ideal model delta sigma weight residual 126.80 118.61 8.19 1.00e+00 1.00e+00 6.71e+01 ... (remaining 12964 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.17: 5519 15.17 - 30.34: 241 30.34 - 45.51: 42 45.51 - 60.68: 8 60.68 - 75.85: 6 Dihedral angle restraints: 5816 sinusoidal: 2394 harmonic: 3422 Sorted by residual: dihedral pdb=" CA SER A 121 " pdb=" C SER A 121 " pdb=" N LYS A 122 " pdb=" CA LYS A 122 " ideal model delta harmonic sigma weight residual 180.00 155.01 24.99 0 5.00e+00 4.00e-02 2.50e+01 dihedral pdb=" CA ARG A 428 " pdb=" C ARG A 428 " pdb=" N LEU A 429 " pdb=" CA LEU A 429 " ideal model delta harmonic sigma weight residual 180.00 157.64 22.36 0 5.00e+00 4.00e-02 2.00e+01 dihedral pdb=" CA CYS A1151 " pdb=" C CYS A1151 " pdb=" N ASP A1152 " pdb=" CA ASP A1152 " ideal model delta harmonic sigma weight residual 180.00 -157.89 -22.11 0 5.00e+00 4.00e-02 1.96e+01 ... (remaining 5813 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 884 0.032 - 0.064: 411 0.064 - 0.096: 133 0.096 - 0.129: 49 0.129 - 0.161: 10 Chirality restraints: 1487 Sorted by residual: chirality pdb=" CA ASP A 441 " pdb=" N ASP A 441 " pdb=" C ASP A 441 " pdb=" CB ASP A 441 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.46e-01 chirality pdb=" CA ILE A1232 " pdb=" N ILE A1232 " pdb=" C ILE A1232 " pdb=" CB ILE A1232 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.38e-01 chirality pdb=" CA ILE A1368 " pdb=" N ILE A1368 " pdb=" C ILE A1368 " pdb=" CB ILE A1368 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.29e-01 ... (remaining 1484 not shown) Planarity restraints: 1599 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE A 893 " 0.012 2.00e-02 2.50e+03 2.44e-02 5.96e+00 pdb=" C ILE A 893 " -0.042 2.00e-02 2.50e+03 pdb=" O ILE A 893 " 0.016 2.00e-02 2.50e+03 pdb=" N ASN A 894 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN A 440 " 0.010 2.00e-02 2.50e+03 2.06e-02 4.24e+00 pdb=" C ASN A 440 " -0.036 2.00e-02 2.50e+03 pdb=" O ASN A 440 " 0.014 2.00e-02 2.50e+03 pdb=" N ASP A 441 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR A 902 " 0.009 2.00e-02 2.50e+03 1.89e-02 3.58e+00 pdb=" C THR A 902 " -0.033 2.00e-02 2.50e+03 pdb=" O THR A 902 " 0.012 2.00e-02 2.50e+03 pdb=" N GLY A 903 " 0.011 2.00e-02 2.50e+03 ... (remaining 1596 not shown) Histogram of nonbonded interaction distances: 2.04 - 2.61: 59 2.61 - 3.18: 8418 3.18 - 3.75: 12693 3.75 - 4.33: 18282 4.33 - 4.90: 30361 Nonbonded interactions: 69813 Sorted by model distance: nonbonded pdb=" O2B ATP A1501 " pdb="MG MG A1504 " model vdw 2.035 2.170 nonbonded pdb=" O2G ATP A1502 " pdb="MG MG A1503 " model vdw 2.039 2.170 nonbonded pdb=" OE1 GLN A1256 " pdb="MG MG A1503 " model vdw 2.041 2.170 nonbonded pdb=" OE1 GLN A 462 " pdb="MG MG A1504 " model vdw 2.049 2.170 nonbonded pdb=" O3G ATP A1501 " pdb="MG MG A1504 " model vdw 2.111 2.170 ... (remaining 69808 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.720 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 3.950 Check model and map are aligned: 0.170 Set scattering table: 0.100 Process input model: 28.760 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.030 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:12.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.830 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7517 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 : 0.005 0.079 9609 Z= 0.321 Angle : 0.811 20.195 12969 Z= 0.540 Chirality : 0.043 0.161 1487 Planarity : 0.003 0.041 1599 Dihedral : 9.607 75.850 3608 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 1.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.71 % Favored : 93.29 % Rotamer: Outliers : 0.00 % Allowed : 0.95 % Favored : 99.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.73 (0.21), residues: 1148 helix: -2.05 (0.17), residues: 681 sheet: -1.44 (0.62), residues: 68 loop : -3.21 (0.26), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 452 HIS 0.007 0.002 HIS A 278 PHE 0.025 0.002 PHE A 911 TYR 0.018 0.002 TYR A 158 ARG 0.004 0.001 ARG A1176 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1051 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 194 time to evaluate : 1.110 Fit side-chains revert: symmetry clash REVERT: A 63 CYS cc_start: 0.7871 (m) cc_final: 0.7525 (m) REVERT: A 608 LEU cc_start: 0.7798 (tp) cc_final: 0.7570 (tp) REVERT: A 688 HIS cc_start: 0.6712 (t70) cc_final: 0.6311 (t-90) REVERT: A 841 MET cc_start: 0.6964 (tpt) cc_final: 0.6585 (tpt) REVERT: A 916 MET cc_start: 0.7473 (mmm) cc_final: 0.7239 (mmt) REVERT: A 941 PHE cc_start: 0.7771 (t80) cc_final: 0.7480 (t80) REVERT: A 1352 LYS cc_start: 0.8296 (ttmt) cc_final: 0.8013 (ttpt) outliers start: 0 outliers final: 1 residues processed: 194 average time/residue: 1.1405 time to fit residues: 237.4432 Evaluate side-chains 108 residues out of total 1051 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 107 time to evaluate : 1.105 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 426 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 97 optimal weight: 0.0670 chunk 87 optimal weight: 0.0570 chunk 48 optimal weight: 0.9990 chunk 30 optimal weight: 2.9990 chunk 59 optimal weight: 5.9990 chunk 46 optimal weight: 9.9990 chunk 90 optimal weight: 4.9990 chunk 35 optimal weight: 0.0170 chunk 55 optimal weight: 4.9990 chunk 67 optimal weight: 0.9990 chunk 105 optimal weight: 0.9980 overall best weight: 0.4276 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 191 ASN A 303 ASN A 443 HIS A 559 ASN A 892 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7586 moved from start: 0.1785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 9609 Z= 0.133 Angle : 0.517 6.895 12969 Z= 0.271 Chirality : 0.041 0.148 1487 Planarity : 0.003 0.031 1599 Dihedral : 6.784 78.781 1328 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 2.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.84 % Favored : 94.16 % Rotamer: Outliers : 2.48 % Allowed : 9.24 % Favored : 88.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.30 (0.23), residues: 1148 helix: -0.90 (0.19), residues: 686 sheet: 1.02 (0.73), residues: 55 loop : -2.91 (0.27), residues: 407 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A1047 HIS 0.006 0.001 HIS A 892 PHE 0.023 0.001 PHE A1048 TYR 0.030 0.001 TYR A1097 ARG 0.007 0.000 ARG A1377 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1051 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 125 time to evaluate : 1.046 Fit side-chains revert: symmetry clash REVERT: A 1171 MET cc_start: 0.8061 (OUTLIER) cc_final: 0.6294 (mmm) REVERT: A 1259 MET cc_start: 0.8034 (OUTLIER) cc_final: 0.7176 (ttt) outliers start: 26 outliers final: 8 residues processed: 139 average time/residue: 1.0850 time to fit residues: 163.0727 Evaluate side-chains 110 residues out of total 1051 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 100 time to evaluate : 1.136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 109 SER Chi-restraints excluded: chain A residue 195 THR Chi-restraints excluded: chain A residue 392 ASP Chi-restraints excluded: chain A residue 690 MET Chi-restraints excluded: chain A residue 882 ASP Chi-restraints excluded: chain A residue 1064 MET Chi-restraints excluded: chain A residue 1171 MET Chi-restraints excluded: chain A residue 1250 LEU Chi-restraints excluded: chain A residue 1259 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 58 optimal weight: 6.9990 chunk 32 optimal weight: 4.9990 chunk 87 optimal weight: 5.9990 chunk 71 optimal weight: 2.9990 chunk 29 optimal weight: 0.0980 chunk 105 optimal weight: 0.7980 chunk 114 optimal weight: 0.8980 chunk 93 optimal weight: 10.0000 chunk 104 optimal weight: 0.9990 chunk 35 optimal weight: 4.9990 chunk 84 optimal weight: 6.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 303 ASN A 559 ASN A 688 HIS A 892 HIS A 992 ASN A1146 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7743 moved from start: 0.2562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9609 Z= 0.182 Angle : 0.528 6.505 12969 Z= 0.279 Chirality : 0.042 0.142 1487 Planarity : 0.003 0.026 1599 Dihedral : 6.921 84.271 1326 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 3.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.45 % Favored : 93.55 % Rotamer: Outliers : 3.05 % Allowed : 11.62 % Favored : 85.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.62 (0.24), residues: 1148 helix: -0.37 (0.20), residues: 674 sheet: 0.64 (0.72), residues: 66 loop : -2.53 (0.28), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A1047 HIS 0.005 0.001 HIS A 278 PHE 0.029 0.001 PHE A1068 TYR 0.018 0.001 TYR A1097 ARG 0.005 0.000 ARG A1273 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 1051 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 113 time to evaluate : 1.102 Fit side-chains revert: symmetry clash REVERT: A 463 ASP cc_start: 0.8205 (OUTLIER) cc_final: 0.7789 (p0) REVERT: A 941 PHE cc_start: 0.7720 (t80) cc_final: 0.7386 (t80) REVERT: A 1022 ARG cc_start: 0.7360 (ttt-90) cc_final: 0.7119 (ttm-80) REVERT: A 1064 MET cc_start: 0.6657 (OUTLIER) cc_final: 0.6286 (ttp) REVERT: A 1171 MET cc_start: 0.7964 (OUTLIER) cc_final: 0.6332 (mmm) REVERT: A 1259 MET cc_start: 0.8364 (OUTLIER) cc_final: 0.7526 (ttt) REVERT: A 1273 ARG cc_start: 0.6894 (mpt-90) cc_final: 0.6407 (mtm180) outliers start: 32 outliers final: 10 residues processed: 134 average time/residue: 1.2007 time to fit residues: 172.9296 Evaluate side-chains 119 residues out of total 1051 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 105 time to evaluate : 1.110 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 109 SER Chi-restraints excluded: chain A residue 392 ASP Chi-restraints excluded: chain A residue 463 ASP Chi-restraints excluded: chain A residue 520 MET Chi-restraints excluded: chain A residue 882 ASP Chi-restraints excluded: chain A residue 892 HIS Chi-restraints excluded: chain A residue 1048 PHE Chi-restraints excluded: chain A residue 1064 MET Chi-restraints excluded: chain A residue 1143 ILE Chi-restraints excluded: chain A residue 1171 MET Chi-restraints excluded: chain A residue 1250 LEU Chi-restraints excluded: chain A residue 1259 MET Chi-restraints excluded: chain A residue 1277 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 104 optimal weight: 1.9990 chunk 79 optimal weight: 3.9990 chunk 54 optimal weight: 8.9990 chunk 11 optimal weight: 0.8980 chunk 50 optimal weight: 1.9990 chunk 70 optimal weight: 3.9990 chunk 105 optimal weight: 4.9990 chunk 112 optimal weight: 1.9990 chunk 55 optimal weight: 0.9980 chunk 100 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 303 ASN A 559 ASN A 870 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7799 moved from start: 0.3002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9609 Z= 0.218 Angle : 0.540 6.544 12969 Z= 0.287 Chirality : 0.043 0.156 1487 Planarity : 0.003 0.027 1599 Dihedral : 7.105 87.078 1326 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 3.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.88 % Favored : 93.12 % Rotamer: Outliers : 3.62 % Allowed : 12.48 % Favored : 83.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.42 (0.25), residues: 1148 helix: -0.23 (0.20), residues: 676 sheet: 0.61 (0.66), residues: 76 loop : -2.45 (0.29), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 295 HIS 0.018 0.002 HIS A 892 PHE 0.026 0.001 PHE A 202 TYR 0.021 0.001 TYR A 206 ARG 0.005 0.000 ARG A 627 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 1051 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 107 time to evaluate : 1.198 Fit side-chains revert: symmetry clash REVERT: A 463 ASP cc_start: 0.8233 (OUTLIER) cc_final: 0.7832 (p0) REVERT: A 941 PHE cc_start: 0.7770 (t80) cc_final: 0.7400 (t80) REVERT: A 1171 MET cc_start: 0.7846 (OUTLIER) cc_final: 0.6255 (mmm) REVERT: A 1259 MET cc_start: 0.8467 (OUTLIER) cc_final: 0.7620 (ttt) REVERT: A 1273 ARG cc_start: 0.6850 (mpt-90) cc_final: 0.6451 (mtm180) REVERT: A 1337 GLN cc_start: 0.8899 (OUTLIER) cc_final: 0.8172 (mt0) outliers start: 38 outliers final: 12 residues processed: 134 average time/residue: 1.1342 time to fit residues: 163.6871 Evaluate side-chains 116 residues out of total 1051 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 100 time to evaluate : 1.173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 109 SER Chi-restraints excluded: chain A residue 337 LEU Chi-restraints excluded: chain A residue 392 ASP Chi-restraints excluded: chain A residue 463 ASP Chi-restraints excluded: chain A residue 805 VAL Chi-restraints excluded: chain A residue 882 ASP Chi-restraints excluded: chain A residue 1048 PHE Chi-restraints excluded: chain A residue 1064 MET Chi-restraints excluded: chain A residue 1143 ILE Chi-restraints excluded: chain A residue 1171 MET Chi-restraints excluded: chain A residue 1250 LEU Chi-restraints excluded: chain A residue 1253 ILE Chi-restraints excluded: chain A residue 1259 MET Chi-restraints excluded: chain A residue 1277 THR Chi-restraints excluded: chain A residue 1337 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 93 optimal weight: 0.5980 chunk 63 optimal weight: 3.9990 chunk 1 optimal weight: 5.9990 chunk 83 optimal weight: 3.9990 chunk 46 optimal weight: 9.9990 chunk 95 optimal weight: 6.9990 chunk 77 optimal weight: 0.0470 chunk 0 optimal weight: 3.9990 chunk 57 optimal weight: 7.9990 chunk 100 optimal weight: 0.9980 chunk 28 optimal weight: 1.9990 overall best weight: 1.5282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 303 ASN A 386 HIS A 559 ASN A 569 GLN A 870 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7829 moved from start: 0.3403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9609 Z= 0.213 Angle : 0.552 7.651 12969 Z= 0.292 Chirality : 0.043 0.165 1487 Planarity : 0.003 0.033 1599 Dihedral : 7.285 87.604 1326 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 3.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.32 % Favored : 92.68 % Rotamer: Outliers : 4.10 % Allowed : 12.86 % Favored : 83.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.19 (0.25), residues: 1148 helix: -0.10 (0.20), residues: 674 sheet: 2.24 (0.72), residues: 56 loop : -2.36 (0.28), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 295 HIS 0.005 0.001 HIS A 913 PHE 0.028 0.001 PHE A1068 TYR 0.025 0.001 TYR A 206 ARG 0.007 0.001 ARG A 627 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1051 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 113 time to evaluate : 1.086 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 941 PHE cc_start: 0.7826 (t80) cc_final: 0.7464 (t80) REVERT: A 1171 MET cc_start: 0.7886 (OUTLIER) cc_final: 0.6438 (mmm) REVERT: A 1259 MET cc_start: 0.8532 (OUTLIER) cc_final: 0.7717 (ttt) REVERT: A 1273 ARG cc_start: 0.6825 (mpt-90) cc_final: 0.6550 (mtm180) REVERT: A 1337 GLN cc_start: 0.8874 (OUTLIER) cc_final: 0.8215 (mt0) REVERT: A 1380 LYS cc_start: 0.7975 (OUTLIER) cc_final: 0.7361 (ptmm) outliers start: 43 outliers final: 15 residues processed: 143 average time/residue: 1.0812 time to fit residues: 167.2538 Evaluate side-chains 120 residues out of total 1051 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 101 time to evaluate : 1.156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 109 SER Chi-restraints excluded: chain A residue 337 LEU Chi-restraints excluded: chain A residue 392 ASP Chi-restraints excluded: chain A residue 436 ASP Chi-restraints excluded: chain A residue 805 VAL Chi-restraints excluded: chain A residue 839 ILE Chi-restraints excluded: chain A residue 882 ASP Chi-restraints excluded: chain A residue 1048 PHE Chi-restraints excluded: chain A residue 1064 MET Chi-restraints excluded: chain A residue 1143 ILE Chi-restraints excluded: chain A residue 1171 MET Chi-restraints excluded: chain A residue 1250 LEU Chi-restraints excluded: chain A residue 1259 MET Chi-restraints excluded: chain A residue 1277 THR Chi-restraints excluded: chain A residue 1284 VAL Chi-restraints excluded: chain A residue 1337 GLN Chi-restraints excluded: chain A residue 1380 LYS Chi-restraints excluded: chain A residue 1397 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 37 optimal weight: 3.9990 chunk 100 optimal weight: 2.9990 chunk 22 optimal weight: 0.4980 chunk 65 optimal weight: 3.9990 chunk 27 optimal weight: 0.9990 chunk 112 optimal weight: 4.9990 chunk 93 optimal weight: 4.9990 chunk 51 optimal weight: 5.9990 chunk 9 optimal weight: 0.5980 chunk 58 optimal weight: 8.9990 chunk 108 optimal weight: 4.9990 overall best weight: 1.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 303 ASN A 559 ASN A 688 HIS A 870 ASN A1395 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7854 moved from start: 0.3587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 9609 Z= 0.244 Angle : 0.569 12.399 12969 Z= 0.298 Chirality : 0.044 0.184 1487 Planarity : 0.003 0.027 1599 Dihedral : 7.433 87.738 1326 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 3.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.49 % Favored : 92.51 % Rotamer: Outliers : 3.71 % Allowed : 14.67 % Favored : 81.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.23 (0.25), residues: 1148 helix: -0.09 (0.20), residues: 677 sheet: 1.00 (0.72), residues: 66 loop : -2.35 (0.29), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 295 HIS 0.006 0.001 HIS A 913 PHE 0.031 0.001 PHE A1068 TYR 0.024 0.002 TYR A 206 ARG 0.003 0.000 ARG A 627 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 1051 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 104 time to evaluate : 1.113 Fit side-chains revert: symmetry clash REVERT: A 132 LEU cc_start: 0.9152 (OUTLIER) cc_final: 0.8707 (pp) REVERT: A 941 PHE cc_start: 0.7916 (t80) cc_final: 0.7520 (t80) REVERT: A 943 ASN cc_start: 0.7629 (m110) cc_final: 0.6723 (t0) REVERT: A 1101 MET cc_start: 0.8193 (ttm) cc_final: 0.7989 (ttp) REVERT: A 1171 MET cc_start: 0.7893 (OUTLIER) cc_final: 0.6423 (mmm) REVERT: A 1259 MET cc_start: 0.8602 (OUTLIER) cc_final: 0.7794 (ttt) REVERT: A 1273 ARG cc_start: 0.6871 (mpt-90) cc_final: 0.6606 (mtm180) REVERT: A 1337 GLN cc_start: 0.8859 (OUTLIER) cc_final: 0.8233 (mt0) REVERT: A 1380 LYS cc_start: 0.7959 (OUTLIER) cc_final: 0.7356 (ptmm) outliers start: 39 outliers final: 19 residues processed: 132 average time/residue: 1.0800 time to fit residues: 154.1331 Evaluate side-chains 127 residues out of total 1051 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 103 time to evaluate : 1.113 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 109 SER Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 250 GLU Chi-restraints excluded: chain A residue 337 LEU Chi-restraints excluded: chain A residue 392 ASP Chi-restraints excluded: chain A residue 436 ASP Chi-restraints excluded: chain A residue 437 ILE Chi-restraints excluded: chain A residue 679 LEU Chi-restraints excluded: chain A residue 805 VAL Chi-restraints excluded: chain A residue 839 ILE Chi-restraints excluded: chain A residue 882 ASP Chi-restraints excluded: chain A residue 1048 PHE Chi-restraints excluded: chain A residue 1064 MET Chi-restraints excluded: chain A residue 1143 ILE Chi-restraints excluded: chain A residue 1171 MET Chi-restraints excluded: chain A residue 1250 LEU Chi-restraints excluded: chain A residue 1253 ILE Chi-restraints excluded: chain A residue 1259 MET Chi-restraints excluded: chain A residue 1277 THR Chi-restraints excluded: chain A residue 1284 VAL Chi-restraints excluded: chain A residue 1337 GLN Chi-restraints excluded: chain A residue 1380 LYS Chi-restraints excluded: chain A residue 1397 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 12 optimal weight: 0.8980 chunk 63 optimal weight: 2.9990 chunk 81 optimal weight: 0.4980 chunk 94 optimal weight: 4.9990 chunk 62 optimal weight: 0.7980 chunk 111 optimal weight: 0.8980 chunk 69 optimal weight: 2.9990 chunk 68 optimal weight: 0.6980 chunk 51 optimal weight: 5.9990 chunk 44 optimal weight: 5.9990 chunk 66 optimal weight: 3.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 303 ASN A 559 ASN A 688 HIS A 870 ASN A1345 ASN A1390 ASN A1395 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7800 moved from start: 0.3660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 9609 Z= 0.147 Angle : 0.511 11.298 12969 Z= 0.267 Chirality : 0.041 0.177 1487 Planarity : 0.003 0.027 1599 Dihedral : 7.253 81.514 1326 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 3.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.88 % Favored : 93.12 % Rotamer: Outliers : 3.33 % Allowed : 14.95 % Favored : 81.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.86 (0.25), residues: 1148 helix: 0.18 (0.21), residues: 681 sheet: 2.33 (0.73), residues: 56 loop : -2.29 (0.28), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 295 HIS 0.003 0.001 HIS A 278 PHE 0.032 0.001 PHE A1068 TYR 0.024 0.001 TYR A 206 ARG 0.003 0.000 ARG A 776 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1051 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 114 time to evaluate : 1.096 Fit side-chains revert: symmetry clash REVERT: A 412 VAL cc_start: 0.8356 (t) cc_final: 0.8051 (m) REVERT: A 941 PHE cc_start: 0.7846 (t80) cc_final: 0.7411 (t80) REVERT: A 943 ASN cc_start: 0.7492 (m110) cc_final: 0.6722 (t0) REVERT: A 1064 MET cc_start: 0.6650 (OUTLIER) cc_final: 0.6222 (ttp) REVERT: A 1171 MET cc_start: 0.7885 (OUTLIER) cc_final: 0.6331 (mmm) REVERT: A 1259 MET cc_start: 0.8498 (OUTLIER) cc_final: 0.7696 (ttt) REVERT: A 1273 ARG cc_start: 0.6838 (mpt-90) cc_final: 0.6568 (mtm180) REVERT: A 1377 ARG cc_start: 0.8534 (mmm160) cc_final: 0.8238 (mmm-85) REVERT: A 1380 LYS cc_start: 0.7857 (OUTLIER) cc_final: 0.7276 (ptmm) outliers start: 35 outliers final: 16 residues processed: 136 average time/residue: 1.0397 time to fit residues: 153.6892 Evaluate side-chains 128 residues out of total 1051 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 108 time to evaluate : 1.132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 175 THR Chi-restraints excluded: chain A residue 250 GLU Chi-restraints excluded: chain A residue 337 LEU Chi-restraints excluded: chain A residue 366 ASN Chi-restraints excluded: chain A residue 392 ASP Chi-restraints excluded: chain A residue 436 ASP Chi-restraints excluded: chain A residue 679 LEU Chi-restraints excluded: chain A residue 805 VAL Chi-restraints excluded: chain A residue 842 PHE Chi-restraints excluded: chain A residue 882 ASP Chi-restraints excluded: chain A residue 904 LEU Chi-restraints excluded: chain A residue 1048 PHE Chi-restraints excluded: chain A residue 1064 MET Chi-restraints excluded: chain A residue 1106 ASN Chi-restraints excluded: chain A residue 1143 ILE Chi-restraints excluded: chain A residue 1171 MET Chi-restraints excluded: chain A residue 1253 ILE Chi-restraints excluded: chain A residue 1259 MET Chi-restraints excluded: chain A residue 1277 THR Chi-restraints excluded: chain A residue 1380 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 33 optimal weight: 4.9990 chunk 21 optimal weight: 2.9990 chunk 71 optimal weight: 0.6980 chunk 76 optimal weight: 3.9990 chunk 55 optimal weight: 5.9990 chunk 10 optimal weight: 0.9980 chunk 87 optimal weight: 1.9990 chunk 101 optimal weight: 3.9990 chunk 107 optimal weight: 0.2980 chunk 97 optimal weight: 3.9990 chunk 104 optimal weight: 2.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 303 ASN A 559 ASN A 688 HIS A 870 ASN A1345 ASN A1390 ASN A1395 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7841 moved from start: 0.3785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9609 Z= 0.203 Angle : 0.547 11.602 12969 Z= 0.287 Chirality : 0.042 0.181 1487 Planarity : 0.003 0.028 1599 Dihedral : 7.357 82.592 1326 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 3.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.14 % Favored : 92.86 % Rotamer: Outliers : 3.14 % Allowed : 16.38 % Favored : 80.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.84 (0.25), residues: 1148 helix: 0.20 (0.21), residues: 683 sheet: 2.29 (0.73), residues: 56 loop : -2.27 (0.29), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 295 HIS 0.004 0.001 HIS A 913 PHE 0.033 0.001 PHE A1068 TYR 0.025 0.001 TYR A 206 ARG 0.003 0.000 ARG A 627 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 1051 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 103 time to evaluate : 1.020 Fit side-chains revert: symmetry clash REVERT: A 52 GLN cc_start: 0.7502 (tm-30) cc_final: 0.7224 (tm-30) REVERT: A 412 VAL cc_start: 0.8420 (t) cc_final: 0.8107 (m) REVERT: A 463 ASP cc_start: 0.8192 (OUTLIER) cc_final: 0.7725 (p0) REVERT: A 941 PHE cc_start: 0.7881 (t80) cc_final: 0.7490 (t80) REVERT: A 943 ASN cc_start: 0.7490 (m110) cc_final: 0.6731 (t0) REVERT: A 1171 MET cc_start: 0.7885 (OUTLIER) cc_final: 0.6383 (mmm) REVERT: A 1259 MET cc_start: 0.8539 (OUTLIER) cc_final: 0.7741 (ttt) REVERT: A 1273 ARG cc_start: 0.6859 (mpt-90) cc_final: 0.6607 (mtm180) REVERT: A 1337 GLN cc_start: 0.8800 (OUTLIER) cc_final: 0.8145 (mt0) REVERT: A 1351 GLU cc_start: 0.8196 (mm-30) cc_final: 0.7965 (tp30) REVERT: A 1377 ARG cc_start: 0.8511 (mmm160) cc_final: 0.8180 (mmm-85) REVERT: A 1380 LYS cc_start: 0.7906 (OUTLIER) cc_final: 0.7333 (ptmm) outliers start: 33 outliers final: 19 residues processed: 125 average time/residue: 1.1221 time to fit residues: 151.2871 Evaluate side-chains 124 residues out of total 1051 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 100 time to evaluate : 1.143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 175 THR Chi-restraints excluded: chain A residue 250 GLU Chi-restraints excluded: chain A residue 337 LEU Chi-restraints excluded: chain A residue 366 ASN Chi-restraints excluded: chain A residue 392 ASP Chi-restraints excluded: chain A residue 436 ASP Chi-restraints excluded: chain A residue 463 ASP Chi-restraints excluded: chain A residue 679 LEU Chi-restraints excluded: chain A residue 805 VAL Chi-restraints excluded: chain A residue 842 PHE Chi-restraints excluded: chain A residue 882 ASP Chi-restraints excluded: chain A residue 904 LEU Chi-restraints excluded: chain A residue 1048 PHE Chi-restraints excluded: chain A residue 1064 MET Chi-restraints excluded: chain A residue 1106 ASN Chi-restraints excluded: chain A residue 1143 ILE Chi-restraints excluded: chain A residue 1171 MET Chi-restraints excluded: chain A residue 1253 ILE Chi-restraints excluded: chain A residue 1259 MET Chi-restraints excluded: chain A residue 1277 THR Chi-restraints excluded: chain A residue 1284 VAL Chi-restraints excluded: chain A residue 1337 GLN Chi-restraints excluded: chain A residue 1380 LYS Chi-restraints excluded: chain A residue 1397 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 107 optimal weight: 0.0770 chunk 62 optimal weight: 0.9990 chunk 45 optimal weight: 7.9990 chunk 81 optimal weight: 0.3980 chunk 31 optimal weight: 0.8980 chunk 94 optimal weight: 3.9990 chunk 98 optimal weight: 6.9990 chunk 103 optimal weight: 0.1980 chunk 68 optimal weight: 2.9990 chunk 110 optimal weight: 3.9990 chunk 67 optimal weight: 0.7980 overall best weight: 0.4738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 303 ASN A 559 ASN A 688 HIS A 870 ASN A1345 ASN A1390 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7769 moved from start: 0.3834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 9609 Z= 0.126 Angle : 0.502 11.295 12969 Z= 0.261 Chirality : 0.040 0.176 1487 Planarity : 0.003 0.027 1599 Dihedral : 7.181 86.350 1326 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 3.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.71 % Favored : 93.29 % Rotamer: Outliers : 2.57 % Allowed : 17.05 % Favored : 80.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.47 (0.26), residues: 1148 helix: 0.49 (0.21), residues: 677 sheet: 2.37 (0.73), residues: 56 loop : -2.07 (0.29), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 295 HIS 0.002 0.001 HIS A1400 PHE 0.033 0.001 PHE A1068 TYR 0.024 0.001 TYR A 206 ARG 0.003 0.000 ARG A1273 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 1051 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 111 time to evaluate : 1.104 Fit side-chains REVERT: A 52 GLN cc_start: 0.7464 (tm-30) cc_final: 0.7178 (tm-30) REVERT: A 412 VAL cc_start: 0.8344 (t) cc_final: 0.8044 (m) REVERT: A 941 PHE cc_start: 0.7951 (t80) cc_final: 0.7509 (t80) REVERT: A 943 ASN cc_start: 0.7372 (m110) cc_final: 0.6729 (t0) REVERT: A 1064 MET cc_start: 0.6715 (OUTLIER) cc_final: 0.6311 (ttp) REVERT: A 1171 MET cc_start: 0.7831 (OUTLIER) cc_final: 0.7506 (mtt) REVERT: A 1259 MET cc_start: 0.8432 (OUTLIER) cc_final: 0.7643 (ttt) REVERT: A 1351 GLU cc_start: 0.8176 (mm-30) cc_final: 0.7973 (tp30) REVERT: A 1377 ARG cc_start: 0.8510 (mmm160) cc_final: 0.8164 (mmm-85) outliers start: 27 outliers final: 12 residues processed: 128 average time/residue: 1.1003 time to fit residues: 151.9836 Evaluate side-chains 118 residues out of total 1051 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 103 time to evaluate : 1.034 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 175 THR Chi-restraints excluded: chain A residue 250 GLU Chi-restraints excluded: chain A residue 366 ASN Chi-restraints excluded: chain A residue 392 ASP Chi-restraints excluded: chain A residue 436 ASP Chi-restraints excluded: chain A residue 679 LEU Chi-restraints excluded: chain A residue 842 PHE Chi-restraints excluded: chain A residue 882 ASP Chi-restraints excluded: chain A residue 1048 PHE Chi-restraints excluded: chain A residue 1064 MET Chi-restraints excluded: chain A residue 1171 MET Chi-restraints excluded: chain A residue 1250 LEU Chi-restraints excluded: chain A residue 1259 MET Chi-restraints excluded: chain A residue 1277 THR Chi-restraints excluded: chain A residue 1397 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 52 optimal weight: 3.9990 chunk 76 optimal weight: 3.9990 chunk 115 optimal weight: 8.9990 chunk 106 optimal weight: 2.9990 chunk 92 optimal weight: 5.9990 chunk 9 optimal weight: 4.9990 chunk 71 optimal weight: 1.9990 chunk 56 optimal weight: 3.9990 chunk 73 optimal weight: 0.8980 chunk 98 optimal weight: 4.9990 chunk 28 optimal weight: 0.6980 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 303 ASN A 559 ASN A 688 HIS A 870 ASN A1345 ASN A1390 ASN A1395 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7872 moved from start: 0.3970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 9609 Z= 0.282 Angle : 0.616 12.697 12969 Z= 0.320 Chirality : 0.044 0.190 1487 Planarity : 0.003 0.029 1599 Dihedral : 7.447 83.972 1326 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 3.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.49 % Favored : 92.51 % Rotamer: Outliers : 2.10 % Allowed : 18.19 % Favored : 79.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.84 (0.25), residues: 1148 helix: 0.20 (0.20), residues: 683 sheet: 1.08 (0.72), residues: 66 loop : -2.15 (0.29), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 295 HIS 0.007 0.001 HIS A 913 PHE 0.035 0.002 PHE A1068 TYR 0.026 0.002 TYR A 206 ARG 0.003 0.000 ARG A 454 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 1051 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 104 time to evaluate : 1.118 Fit side-chains revert: symmetry clash REVERT: A 52 GLN cc_start: 0.7533 (tm-30) cc_final: 0.7273 (tm-30) REVERT: A 404 LYS cc_start: 0.7511 (mtpt) cc_final: 0.7309 (mptm) REVERT: A 941 PHE cc_start: 0.8004 (t80) cc_final: 0.7571 (t80) REVERT: A 943 ASN cc_start: 0.7502 (m110) cc_final: 0.6740 (t0) REVERT: A 1259 MET cc_start: 0.8630 (OUTLIER) cc_final: 0.7861 (ttt) REVERT: A 1377 ARG cc_start: 0.8535 (mmm160) cc_final: 0.8171 (mmm-85) outliers start: 22 outliers final: 13 residues processed: 117 average time/residue: 1.1505 time to fit residues: 144.9257 Evaluate side-chains 115 residues out of total 1051 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 101 time to evaluate : 1.086 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 175 THR Chi-restraints excluded: chain A residue 250 GLU Chi-restraints excluded: chain A residue 392 ASP Chi-restraints excluded: chain A residue 436 ASP Chi-restraints excluded: chain A residue 679 LEU Chi-restraints excluded: chain A residue 805 VAL Chi-restraints excluded: chain A residue 882 ASP Chi-restraints excluded: chain A residue 1048 PHE Chi-restraints excluded: chain A residue 1064 MET Chi-restraints excluded: chain A residue 1250 LEU Chi-restraints excluded: chain A residue 1259 MET Chi-restraints excluded: chain A residue 1277 THR Chi-restraints excluded: chain A residue 1284 VAL Chi-restraints excluded: chain A residue 1397 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 84 optimal weight: 2.9990 chunk 13 optimal weight: 2.9990 chunk 25 optimal weight: 0.9990 chunk 92 optimal weight: 0.9980 chunk 38 optimal weight: 4.9990 chunk 94 optimal weight: 5.9990 chunk 11 optimal weight: 0.9990 chunk 16 optimal weight: 5.9990 chunk 80 optimal weight: 4.9990 chunk 5 optimal weight: 0.9990 chunk 66 optimal weight: 2.9990 overall best weight: 1.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 303 ASN A 559 ASN A 870 ASN A1345 ASN A1395 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.141793 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.109793 restraints weight = 12846.423| |-----------------------------------------------------------------------------| r_work (start): 0.3436 rms_B_bonded: 2.35 r_work: 0.3294 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.3167 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.3167 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8072 moved from start: 0.3996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9609 Z= 0.207 Angle : 0.577 12.177 12969 Z= 0.300 Chirality : 0.042 0.188 1487 Planarity : 0.003 0.029 1599 Dihedral : 7.501 87.184 1326 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.49 % Favored : 92.51 % Rotamer: Outliers : 1.81 % Allowed : 18.29 % Favored : 79.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.75 (0.25), residues: 1148 helix: 0.25 (0.20), residues: 683 sheet: 1.82 (0.68), residues: 66 loop : -2.22 (0.29), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 295 HIS 0.004 0.001 HIS A 913 PHE 0.034 0.001 PHE A1068 TYR 0.025 0.001 TYR A 206 ARG 0.003 0.000 ARG A 627 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3369.58 seconds wall clock time: 60 minutes 23.52 seconds (3623.52 seconds total)