Starting phenix.real_space_refine (version: 1.21rc1) on Wed Oct 4 19:38:04 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jwi_36684/10_2023/8jwi_36684_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jwi_36684/10_2023/8jwi_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_36684/10_2023/8jwi_36684.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jwi_36684/10_2023/8jwi_36684.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jwi_36684/10_2023/8jwi_36684_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jwi_36684/10_2023/8jwi_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-1.21rc1-5097/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: 5.19, per 1000 atoms: 0.55 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: 3.63 Conformation dependent library (CDL) restraints added in 1.4 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: 2.13 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: 2.67 Time building geometry restraints manager: 3.90 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 - 14.50: 5454 14.50 - 29.00: 252 29.00 - 43.50: 41 43.50 - 58.00: 3 58.00 - 72.50: 4 Dihedral angle restraints: 5754 sinusoidal: 2332 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 5751 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: 0.760 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 4.000 Check model and map are aligned: 0.140 Set scattering table: 0.090 Process input model: 26.930 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.150 ------------------------------------------------------------------------------- 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 : 9.004 72.504 3546 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 *********************** 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 : 1.111 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 1 residues processed: 194 average time/residue: 1.1612 time to fit residues: 241.6203 Evaluate side-chains 106 residues out of total 1051 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 105 time to evaluate : 1.075 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 1 residues processed: 0 time to fit residues: 1.4507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 688 HIS A 892 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7585 moved from start: 0.1811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 9609 Z= 0.131 Angle : 0.520 7.111 12969 Z= 0.272 Chirality : 0.041 0.150 1487 Planarity : 0.003 0.031 1599 Dihedral : 4.975 62.887 1264 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 2.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.84 % Favored : 94.16 % Rotamer: Outliers : 2.48 % Allowed : 9.43 % Favored : 88.10 % 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: -2.27 (0.23), residues: 1148 helix: -0.88 (0.19), residues: 686 sheet: 1.04 (0.73), residues: 55 loop : -2.90 (0.27), residues: 407 *********************** 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 : 1.050 Fit side-chains revert: symmetry clash outliers start: 26 outliers final: 7 residues processed: 139 average time/residue: 1.1167 time to fit residues: 167.8244 Evaluate side-chains 106 residues out of total 1051 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 99 time to evaluate : 1.103 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 4 residues processed: 3 average time/residue: 0.5562 time to fit residues: 3.4612 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 58 optimal weight: 8.9990 chunk 32 optimal weight: 0.2980 chunk 87 optimal weight: 5.9990 chunk 71 optimal weight: 5.9990 chunk 29 optimal weight: 0.7980 chunk 105 optimal weight: 3.9990 chunk 114 optimal weight: 0.0670 chunk 93 optimal weight: 3.9990 chunk 104 optimal weight: 3.9990 chunk 35 optimal weight: 6.9990 chunk 84 optimal weight: 6.9990 overall best weight: 1.8322 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** A 892 HIS A 992 ASN A1146 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7824 moved from start: 0.2919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 9609 Z= 0.250 Angle : 0.593 7.681 12969 Z= 0.314 Chirality : 0.045 0.156 1487 Planarity : 0.003 0.028 1599 Dihedral : 5.192 52.489 1264 Min Nonbonded Distance : 1.877 Molprobity Statistics. All-atom Clashscore : 3.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.97 % Favored : 93.03 % Rotamer: Outliers : 3.43 % Allowed : 11.14 % Favored : 85.43 % 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: -1.87 (0.24), residues: 1148 helix: -0.57 (0.20), residues: 675 sheet: 0.34 (0.66), residues: 76 loop : -2.66 (0.28), residues: 397 *********************** 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: 36 poor density : 109 time to evaluate : 1.083 Fit side-chains revert: symmetry clash outliers start: 36 outliers final: 11 residues processed: 135 average time/residue: 1.1200 time to fit residues: 163.3552 Evaluate side-chains 112 residues out of total 1051 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 101 time to evaluate : 1.093 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 7 residues processed: 4 average time/residue: 0.4890 time to fit residues: 3.7247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 104 optimal weight: 6.9990 chunk 79 optimal weight: 4.9990 chunk 54 optimal weight: 9.9990 chunk 11 optimal weight: 0.8980 chunk 50 optimal weight: 0.9990 chunk 70 optimal weight: 5.9990 chunk 105 optimal weight: 3.9990 chunk 112 optimal weight: 4.9990 chunk 55 optimal weight: 1.9990 chunk 100 optimal weight: 0.9990 chunk 30 optimal weight: 0.9980 overall best weight: 1.1786 ------------------------------------------------------------------------------- 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: 0.7800 moved from start: 0.3174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 9609 Z= 0.180 Angle : 0.520 7.637 12969 Z= 0.276 Chirality : 0.042 0.166 1487 Planarity : 0.003 0.026 1599 Dihedral : 4.901 47.656 1264 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 3.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.97 % Favored : 93.03 % Rotamer: Outliers : 2.95 % Allowed : 13.24 % Favored : 83.81 % 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: -1.41 (0.25), residues: 1148 helix: -0.25 (0.20), residues: 674 sheet: 1.57 (0.67), residues: 66 loop : -2.50 (0.28), residues: 408 *********************** 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 142 residues out of total 1051 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 111 time to evaluate : 0.993 Fit side-chains revert: symmetry clash outliers start: 31 outliers final: 12 residues processed: 134 average time/residue: 1.0189 time to fit residues: 148.3605 Evaluate side-chains 109 residues out of total 1051 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 97 time to evaluate : 1.082 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 10 residues processed: 2 average time/residue: 0.2496 time to fit residues: 2.2587 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 93 optimal weight: 5.9990 chunk 63 optimal weight: 2.9990 chunk 1 optimal weight: 4.9990 chunk 83 optimal weight: 7.9990 chunk 46 optimal weight: 8.9990 chunk 95 optimal weight: 0.6980 chunk 77 optimal weight: 0.6980 chunk 0 optimal weight: 3.9990 chunk 57 optimal weight: 6.9990 chunk 100 optimal weight: 0.0980 chunk 28 optimal weight: 0.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- 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 569 GLN A 688 HIS A 870 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7805 moved from start: 0.3385 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= 0.173 Angle : 0.531 12.000 12969 Z= 0.278 Chirality : 0.042 0.185 1487 Planarity : 0.003 0.026 1599 Dihedral : 4.708 42.953 1264 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 2.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.97 % Favored : 93.03 % Rotamer: Outliers : 3.52 % Allowed : 14.00 % Favored : 82.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.16 (0.25), residues: 1148 helix: -0.07 (0.20), residues: 679 sheet: 2.31 (0.72), residues: 56 loop : -2.40 (0.28), residues: 413 *********************** 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 141 residues out of total 1051 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 104 time to evaluate : 1.002 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 37 outliers final: 17 residues processed: 131 average time/residue: 1.1166 time to fit residues: 158.7497 Evaluate side-chains 112 residues out of total 1051 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 95 time to evaluate : 2.099 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 13 residues processed: 4 average time/residue: 0.2152 time to fit residues: 2.9280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.6980 chunk 22 optimal weight: 2.9990 chunk 65 optimal weight: 3.9990 chunk 27 optimal weight: 1.9990 chunk 112 optimal weight: 7.9990 chunk 93 optimal weight: 9.9990 chunk 51 optimal weight: 7.9990 chunk 9 optimal weight: 1.9990 chunk 58 optimal weight: 7.9990 chunk 108 optimal weight: 5.9990 overall best weight: 2.3388 ------------------------------------------------------------------------------- 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 569 GLN A 688 HIS ** A 849 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 870 ASN A1390 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7883 moved from start: 0.3701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 9609 Z= 0.303 Angle : 0.609 12.835 12969 Z= 0.320 Chirality : 0.045 0.185 1487 Planarity : 0.003 0.027 1599 Dihedral : 5.028 44.535 1264 Min Nonbonded Distance : 1.876 Molprobity Statistics. All-atom Clashscore : 3.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.58 % Favored : 92.42 % Rotamer: Outliers : 3.71 % Allowed : 14.29 % Favored : 82.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.34 (0.25), residues: 1148 helix: -0.19 (0.20), residues: 677 sheet: 0.75 (0.67), residues: 76 loop : -2.40 (0.29), residues: 395 *********************** 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 140 residues out of total 1051 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 101 time to evaluate : 1.146 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 39 outliers final: 18 residues processed: 130 average time/residue: 0.9991 time to fit residues: 141.4716 Evaluate side-chains 111 residues out of total 1051 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 93 time to evaluate : 1.040 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 15 residues processed: 3 average time/residue: 0.2157 time to fit residues: 2.3534 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.6980 chunk 81 optimal weight: 0.9990 chunk 94 optimal weight: 1.9990 chunk 62 optimal weight: 0.9990 chunk 111 optimal weight: 3.9990 chunk 69 optimal weight: 3.9990 chunk 68 optimal weight: 1.9990 chunk 51 optimal weight: 3.9990 chunk 44 optimal weight: 9.9990 chunk 66 optimal weight: 0.7980 overall best weight: 0.8784 ------------------------------------------------------------------------------- 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 569 GLN A 688 HIS A 870 ASN A1345 ASN A1397 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7816 moved from start: 0.3771 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= 0.159 Angle : 0.520 10.903 12969 Z= 0.274 Chirality : 0.041 0.182 1487 Planarity : 0.003 0.027 1599 Dihedral : 4.706 38.903 1264 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 3.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.79 % Favored : 93.21 % Rotamer: Outliers : 3.52 % Allowed : 15.14 % Favored : 81.33 % 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: -0.90 (0.25), residues: 1148 helix: 0.15 (0.21), residues: 681 sheet: 1.90 (0.67), residues: 66 loop : -2.33 (0.29), residues: 401 *********************** 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 146 residues out of total 1051 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 109 time to evaluate : 1.171 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 37 outliers final: 20 residues processed: 139 average time/residue: 1.0399 time to fit residues: 157.9284 Evaluate side-chains 121 residues out of total 1051 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 101 time to evaluate : 1.098 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 17 residues processed: 3 average time/residue: 0.1898 time to fit residues: 2.3425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.8980 chunk 76 optimal weight: 4.9990 chunk 55 optimal weight: 0.4980 chunk 10 optimal weight: 0.0670 chunk 87 optimal weight: 5.9990 chunk 101 optimal weight: 3.9990 chunk 107 optimal weight: 0.5980 chunk 97 optimal weight: 6.9990 chunk 104 optimal weight: 5.9990 overall best weight: 1.0120 ------------------------------------------------------------------------------- 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 569 GLN A 688 HIS A 870 ASN A1345 ASN A1390 ASN A1397 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7822 moved from start: 0.3853 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= 0.172 Angle : 0.548 12.418 12969 Z= 0.285 Chirality : 0.041 0.185 1487 Planarity : 0.003 0.028 1599 Dihedral : 4.618 37.305 1264 Min Nonbonded Distance : 1.908 Molprobity Statistics. All-atom Clashscore : 3.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.79 % Favored : 93.21 % Rotamer: Outliers : 2.67 % Allowed : 17.52 % Favored : 79.81 % 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: -0.74 (0.25), residues: 1148 helix: 0.29 (0.21), residues: 681 sheet: 2.37 (0.72), residues: 56 loop : -2.24 (0.29), residues: 411 *********************** 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 129 residues out of total 1051 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 101 time to evaluate : 1.093 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 28 outliers final: 20 residues processed: 123 average time/residue: 1.0808 time to fit residues: 144.7155 Evaluate side-chains 120 residues out of total 1051 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 100 time to evaluate : 1.142 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 17 residues processed: 3 average time/residue: 0.2058 time to fit residues: 2.4345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 107 optimal weight: 0.0060 chunk 62 optimal weight: 0.0050 chunk 45 optimal weight: 9.9990 chunk 81 optimal weight: 6.9990 chunk 31 optimal weight: 2.9990 chunk 94 optimal weight: 6.9990 chunk 98 optimal weight: 6.9990 chunk 103 optimal weight: 5.9990 chunk 68 optimal weight: 2.9990 chunk 110 optimal weight: 1.9990 chunk 67 optimal weight: 0.8980 overall best weight: 1.1814 ------------------------------------------------------------------------------- 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 569 GLN A 688 HIS A 870 ASN A1345 ASN A1390 ASN A1397 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7831 moved from start: 0.3934 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= 0.186 Angle : 0.554 12.284 12969 Z= 0.287 Chirality : 0.042 0.190 1487 Planarity : 0.003 0.028 1599 Dihedral : 4.630 36.597 1264 Min Nonbonded Distance : 1.895 Molprobity Statistics. All-atom Clashscore : 3.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.23 % Favored : 92.77 % Rotamer: Outliers : 2.67 % Allowed : 16.86 % 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: -0.70 (0.25), residues: 1148 helix: 0.30 (0.21), residues: 683 sheet: 2.34 (0.73), residues: 56 loop : -2.19 (0.29), residues: 409 *********************** 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 128 residues out of total 1051 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 100 time to evaluate : 1.013 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 28 outliers final: 22 residues processed: 120 average time/residue: 1.0583 time to fit residues: 138.0798 Evaluate side-chains 121 residues out of total 1051 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 99 time to evaluate : 1.110 Switching outliers to nearest non-outliers outliers start: 22 outliers final: 18 residues processed: 4 average time/residue: 0.2272 time to fit residues: 2.7600 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.7980 chunk 115 optimal weight: 20.0000 chunk 106 optimal weight: 2.9990 chunk 92 optimal weight: 4.9990 chunk 9 optimal weight: 3.9990 chunk 71 optimal weight: 0.9980 chunk 56 optimal weight: 7.9990 chunk 73 optimal weight: 1.9990 chunk 98 optimal weight: 4.9990 chunk 28 optimal weight: 1.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- 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 569 GLN A 688 HIS A 870 ASN A1345 ASN A1390 ASN A1397 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7868 moved from start: 0.4042 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 9609 Z= 0.244 Angle : 0.600 12.697 12969 Z= 0.312 Chirality : 0.043 0.191 1487 Planarity : 0.003 0.030 1599 Dihedral : 4.813 37.999 1264 Min Nonbonded Distance : 1.868 Molprobity Statistics. All-atom Clashscore : 3.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.32 % Favored : 92.68 % Rotamer: Outliers : 2.57 % Allowed : 17.24 % Favored : 80.19 % 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: -0.82 (0.25), residues: 1148 helix: 0.20 (0.20), residues: 677 sheet: 1.99 (0.68), residues: 65 loop : -2.25 (0.29), residues: 406 ********************** 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 128 residues out of total 1051 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 101 time to evaluate : 1.182 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 27 outliers final: 19 residues processed: 123 average time/residue: 1.0596 time to fit residues: 141.3135 Evaluate side-chains 115 residues out of total 1051 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 96 time to evaluate : 0.974 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 17 residues processed: 2 average time/residue: 0.1629 time to fit residues: 1.8356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 84 optimal weight: 1.9990 chunk 13 optimal weight: 3.9990 chunk 25 optimal weight: 0.8980 chunk 92 optimal weight: 0.2980 chunk 38 optimal weight: 2.9990 chunk 94 optimal weight: 4.9990 chunk 11 optimal weight: 0.7980 chunk 16 optimal weight: 5.9990 chunk 80 optimal weight: 4.9990 chunk 5 optimal weight: 0.9980 chunk 66 optimal weight: 1.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- 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 569 GLN A 688 HIS A 692 ASN A 870 ASN A1345 ASN A1390 ASN A1397 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.143001 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.110959 restraints weight = 12883.420| |-----------------------------------------------------------------------------| r_work (start): 0.3451 rms_B_bonded: 2.37 r_work: 0.3315 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.3190 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.3190 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8058 moved from start: 0.4047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9609 Z= 0.175 Angle : 0.565 12.004 12969 Z= 0.293 Chirality : 0.041 0.189 1487 Planarity : 0.003 0.036 1599 Dihedral : 4.678 37.113 1264 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 3.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.32 % Favored : 92.68 % Rotamer: Outliers : 2.48 % Allowed : 17.52 % Favored : 80.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.65 (0.25), residues: 1148 helix: 0.33 (0.21), residues: 681 sheet: 2.02 (0.68), residues: 65 loop : -2.17 (0.29), residues: 402 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3262.53 seconds wall clock time: 58 minutes 42.83 seconds (3522.83 seconds total)