Starting phenix.real_space_refine on Sun Aug 4 03:56:17 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jwi_36684/08_2024/8jwi_36684_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jwi_36684/08_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_36684/08_2024/8jwi_36684.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jwi_36684/08_2024/8jwi_36684.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jwi_36684/08_2024/8jwi_36684_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jwi_36684/08_2024/8jwi_36684_neut.cif" } 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-5409/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: 5.53, per 1000 atoms: 0.59 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: 3.51 Conformation dependent library (CDL) restraints added in 1.6 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... Secondary structure from input PDB file: 55 helices and 4 sheets defined 65.1% alpha, 5.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.08 Creating SS restraints... Processing helix chain 'A' and resid 50 through 69 removed outlier: 3.646A pdb=" N ARG A 54 " --> pdb=" O PRO A 50 " (cutoff:3.500A) 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) Processing helix chain 'A' and resid 70 through 83 removed outlier: 3.800A pdb=" N VAL A 80 " --> pdb=" O SER A 76 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N LYS A 83 " --> pdb=" O GLY A 79 " (cutoff:3.500A) Processing helix chain 'A' and resid 92 through 132 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) Processing helix chain 'A' and resid 139 through 146 removed outlier: 3.783A pdb=" N HIS A 143 " --> pdb=" O ASP A 139 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ASN A 145 " --> pdb=" O GLN A 141 " (cutoff:3.500A) Processing helix chain 'A' and resid 147 through 164 removed outlier: 3.757A pdb=" N LEU A 151 " --> pdb=" O PRO A 147 " (cutoff:3.500A) 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 165 through 167 No H-bonds generated for 'chain 'A' and resid 165 through 167' Processing helix chain 'A' and resid 168 through 185 removed outlier: 3.690A pdb=" N THR A 172 " --> pdb=" O THR A 168 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N ILE A 173 " --> pdb=" O LYS A 169 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N PHE A 174 " --> pdb=" O PHE A 170 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N SER A 178 " --> pdb=" O PHE A 174 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N SER A 179 " --> pdb=" O THR A 175 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N PHE A 180 " --> pdb=" O TYR A 176 " (cutoff:3.500A) Processing helix chain 'A' and resid 185 through 191 removed outlier: 3.662A pdb=" N ILE A 189 " --> pdb=" O ILE A 185 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N LYS A 190 " --> pdb=" O TRP A 186 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N ASN A 191 " --> pdb=" O SER A 187 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 185 through 191' Processing helix chain 'A' and resid 201 through 240 removed outlier: 3.637A pdb=" N ILE A 205 " --> pdb=" O VAL A 201 " (cutoff:3.500A) 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) removed outlier: 3.595A pdb=" N GLY A 240 " --> pdb=" O GLU A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 240 through 248 Processing helix chain 'A' and resid 251 through 272 removed outlier: 3.592A pdb=" N ASN A 255 " --> pdb=" O LYS A 251 " (cutoff:3.500A) 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) Processing helix chain 'A' and resid 273 through 308 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 317 through 337 removed outlier: 3.667A pdb=" N SER A 321 " --> pdb=" O ALA A 317 " (cutoff:3.500A) 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) Processing helix chain 'A' and resid 339 through 358 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 418 through 427 removed outlier: 3.936A pdb=" N GLU A 427 " --> pdb=" O LEU A 423 " (cutoff:3.500A) Processing helix chain 'A' and resid 444 through 448 removed outlier: 3.674A pdb=" N ILE A 448 " --> pdb=" O LEU A 445 " (cutoff:3.500A) Processing helix chain 'A' and resid 449 through 454 Processing helix chain 'A' and resid 470 through 477 removed outlier: 3.709A pdb=" N ASN A 474 " --> pdb=" O SER A 470 " (cutoff:3.500A) Processing helix chain 'A' and resid 479 through 489 removed outlier: 3.645A pdb=" N LEU A 485 " --> pdb=" O SER A 481 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N GLU A 489 " --> pdb=" O LEU A 485 " (cutoff:3.500A) Processing helix chain 'A' and resid 519 through 524 removed outlier: 4.025A pdb=" N GLU A 523 " --> pdb=" O GLU A 519 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N TYR A 524 " --> pdb=" O MET A 520 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 519 through 524' Processing helix chain 'A' and resid 525 through 527 No H-bonds generated for 'chain 'A' and resid 525 through 527' Processing helix chain 'A' and resid 530 through 538 removed outlier: 3.583A pdb=" N ASP A 534 " --> pdb=" O SER A 530 " (cutoff:3.500A) Processing helix chain 'A' and resid 541 through 546 Processing helix chain 'A' and resid 557 through 561 Processing helix chain 'A' and resid 564 through 578 Processing helix chain 'A' and resid 594 through 606 Processing helix chain 'A' and resid 676 through 681 removed outlier: 3.805A pdb=" N MET A 680 " --> pdb=" O HIS A 676 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N LYS A 681 " --> pdb=" O ASP A 677 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 676 through 681' Processing helix chain 'A' and resid 685 through 695 Processing helix chain 'A' and resid 775 through 783 removed outlier: 3.508A pdb=" N TYR A 779 " --> pdb=" O LEU A 775 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N GLU A 781 " --> pdb=" O ILE A 777 " (cutoff:3.500A) Processing helix chain 'A' and resid 785 through 801 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) removed outlier: 3.964A pdb=" N GLY A 801 " --> pdb=" O LEU A 797 " (cutoff:3.500A) Processing helix chain 'A' and resid 805 through 815 removed outlier: 3.614A pdb=" N LEU A 809 " --> pdb=" O VAL A 805 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N TYR A 813 " --> pdb=" O LEU A 809 " (cutoff:3.500A) Processing helix chain 'A' and resid 822 through 872 removed outlier: 3.953A pdb=" N ASN A 826 " --> pdb=" O ASN A 822 " (cutoff:3.500A) 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) Processing helix chain 'A' and resid 876 through 881 removed outlier: 3.643A pdb=" N GLN A 881 " --> pdb=" O SER A 877 " (cutoff:3.500A) Processing helix chain 'A' and resid 885 through 927 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) removed outlier: 3.733A pdb=" N TYR A 927 " --> pdb=" O VAL A 923 " (cutoff:3.500A) Processing helix chain 'A' and resid 929 through 949 removed outlier: 4.002A pdb=" N ALA A 933 " --> pdb=" O CYS A 929 " (cutoff:3.500A) 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) removed outlier: 3.721A pdb=" N VAL A 949 " --> pdb=" O ARG A 945 " (cutoff:3.500A) Processing helix chain 'A' and resid 981 through 992 removed outlier: 3.953A pdb=" N LEU A 985 " --> pdb=" O ASP A 981 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ASN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) Processing helix chain 'A' and resid 992 through 999 Processing helix chain 'A' and resid 1002 through 1017 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 1021 through 1037 removed outlier: 4.305A pdb=" N ILE A1025 " --> pdb=" O LYS A1021 " (cutoff:3.500A) 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 1038 through 1056 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 1059 through 1068 removed outlier: 3.726A pdb=" N PHE A1063 " --> pdb=" O LEU A1059 " (cutoff:3.500A) Processing helix chain 'A' and resid 1070 through 1076 Processing helix chain 'A' and resid 1077 through 1082 removed outlier: 3.801A pdb=" N MET A1081 " --> pdb=" O GLY A1078 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N SER A1082 " --> pdb=" O LYS A1079 " (cutoff:3.500A) Processing helix chain 'A' and resid 1084 through 1103 Proline residue: A1099 - end of helix Processing helix chain 'A' and resid 1166 through 1175 removed outlier: 3.908A pdb=" N PHE A1170 " --> pdb=" O GLY A1166 " (cutoff:3.500A) 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 1240 through 1242 No H-bonds generated for 'chain 'A' and resid 1240 through 1242' Processing helix chain 'A' and resid 1246 through 1250 removed outlier: 3.681A pdb=" N LEU A1250 " --> pdb=" O ASP A1246 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1246 through 1250' Processing helix chain 'A' and resid 1264 through 1270 Processing helix chain 'A' and resid 1277 through 1288 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) removed outlier: 3.851A pdb=" N ALA A1288 " --> pdb=" O VAL A1284 " (cutoff:3.500A) Processing helix chain 'A' and resid 1293 through 1297 removed outlier: 3.587A pdb=" N LEU A1297 " --> pdb=" O ILE A1294 " (cutoff:3.500A) Processing helix chain 'A' and resid 1306 through 1310 Processing helix chain 'A' and resid 1313 through 1328 removed outlier: 3.563A pdb=" N ALA A1321 " --> pdb=" O LYS A1317 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N ARG A1328 " --> pdb=" O ARG A1324 " (cutoff:3.500A) Processing helix chain 'A' and resid 1343 through 1360 removed outlier: 3.844A pdb=" N LYS A1360 " --> pdb=" O ASP A1356 " (cutoff:3.500A) Processing helix chain 'A' and resid 1371 through 1375 removed outlier: 3.574A pdb=" N SER A1374 " --> pdb=" O ARG A1371 " (cutoff:3.500A) Processing helix chain 'A' and resid 1410 through 1417 removed outlier: 3.871A pdb=" N LYS A1416 " --> pdb=" O LYS A1412 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 378 through 383 removed outlier: 5.794A pdb=" N GLU A 379 " --> pdb=" O LEU A 403 " (cutoff:3.500A) removed outlier: 7.741A pdb=" N LEU A 403 " --> pdb=" O GLU A 379 " (cutoff:3.500A) removed outlier: 5.627A pdb=" N LYS A 381 " --> pdb=" O PHE A 401 " (cutoff:3.500A) removed outlier: 8.068A pdb=" N PHE A 401 " --> pdb=" O LYS A 381 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N LEU A 399 " --> pdb=" O VAL A 383 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 457 through 460 removed outlier: 6.774A pdb=" N LYS A 407 " --> pdb=" O THR A 616 " (cutoff:3.500A) removed outlier: 8.138A pdb=" N ILE A 618 " --> pdb=" O LYS A 407 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N TYR A 409 " --> pdb=" O ILE A 618 " (cutoff:3.500A) removed outlier: 8.418A pdb=" N PHE A 633 " --> pdb=" O THR A 408 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N ALA A 410 " --> pdb=" O PHE A 633 " (cutoff:3.500A) removed outlier: 8.211A pdb=" N LEU A 635 " --> pdb=" O ALA A 410 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N VAL A 412 " --> pdb=" O LEU A 635 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N ILE A 632 " --> pdb=" O GLN A 673 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N GLN A 673 " --> pdb=" O ILE A 632 " (cutoff:3.500A) removed outlier: 7.053A pdb=" N VAL A 634 " --> pdb=" O ILE A 671 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 1150 through 1151 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) Processing sheet with id=AA4, first strand: chain 'A' and resid 1251 through 1254 removed outlier: 6.247A pdb=" N SER A1252 " --> pdb=" O LEU A1334 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N THR A1157 " --> pdb=" O THR A1367 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N LYS A1380 " --> pdb=" O THR A1156 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N ILE A1381 " --> pdb=" O HIS A1397 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N HIS A1397 " --> pdb=" O ILE A1381 " (cutoff:3.500A) removed outlier: 7.026A pdb=" N VAL A1383 " --> pdb=" O GLN A1395 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLN A1395 " --> pdb=" O VAL A1383 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ASN A1385 " --> pdb=" O PHE A1393 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N PHE A1393 " --> pdb=" O ASN A1385 " (cutoff:3.500A) 413 hydrogen bonds defined for protein. 1206 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: 2.93 Time building geometry restraints manager: 3.87 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: 58 2.61 - 3.18: 8400 3.18 - 3.75: 12673 3.75 - 4.33: 18189 4.33 - 4.90: 30337 Nonbonded interactions: 69657 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 69652 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: 1.040 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.360 Check model and map are aligned: 0.060 Set scattering table: 0.090 Process input model: 27.510 Find NCS groups from input model: 0.200 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: 0.010 Load rotamer database and sin/cos tables:10.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.910 ------------------------------------------------------------------------------- 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 : 0.939 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: 1.1373 time to fit residues: 236.5508 Evaluate side-chains 108 residues out of total 1051 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 107 time to evaluate : 1.038 ------------------------------------------------------------------------------- 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: 6.9990 chunk 87 optimal weight: 4.9990 chunk 48 optimal weight: 1.9990 chunk 30 optimal weight: 0.7980 chunk 59 optimal weight: 0.1980 chunk 46 optimal weight: 8.9990 chunk 90 optimal weight: 5.9990 chunk 35 optimal weight: 6.9990 chunk 55 optimal weight: 4.9990 chunk 67 optimal weight: 1.9990 chunk 105 optimal weight: 0.9980 overall best weight: 1.1984 ------------------------------------------------------------------------------- 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: 0.7677 moved from start: 0.1859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9609 Z= 0.195 Angle : 0.570 7.278 12969 Z= 0.301 Chirality : 0.043 0.166 1487 Planarity : 0.003 0.031 1599 Dihedral : 7.025 83.080 1328 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 1.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.71 % Favored : 93.29 % Rotamer: Outliers : 2.29 % Allowed : 9.71 % Favored : 88.00 % 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: -2.35 (0.23), residues: 1148 helix: -0.93 (0.19), residues: 693 sheet: 0.53 (0.66), residues: 63 loop : -2.95 (0.28), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A1047 HIS 0.005 0.001 HIS A 892 PHE 0.023 0.001 PHE A1048 TYR 0.026 0.002 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 142 residues out of total 1051 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 118 time to evaluate : 1.107 Fit side-chains revert: symmetry clash REVERT: A 571 ILE cc_start: 0.8210 (OUTLIER) cc_final: 0.7929 (mp) REVERT: A 841 MET cc_start: 0.6992 (tpt) cc_final: 0.6755 (tpt) REVERT: A 1022 ARG cc_start: 0.7181 (ttt-90) cc_final: 0.6934 (ttm-80) REVERT: A 1171 MET cc_start: 0.7981 (OUTLIER) cc_final: 0.6601 (mmm) REVERT: A 1259 MET cc_start: 0.8141 (OUTLIER) cc_final: 0.7263 (ttt) outliers start: 24 outliers final: 6 residues processed: 131 average time/residue: 1.1961 time to fit residues: 168.7781 Evaluate side-chains 109 residues out of total 1051 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 100 time to evaluate : 1.099 ------------------------------------------------------------------------------- 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 571 ILE 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: 2.9990 chunk 87 optimal weight: 4.9990 chunk 71 optimal weight: 3.9990 chunk 29 optimal weight: 0.6980 chunk 105 optimal weight: 3.9990 chunk 114 optimal weight: 8.9990 chunk 93 optimal weight: 5.9990 chunk 104 optimal weight: 1.9990 chunk 35 optimal weight: 4.9990 chunk 84 optimal weight: 6.9990 overall best weight: 2.7388 ------------------------------------------------------------------------------- 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 688 HIS A1146 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7881 moved from start: 0.3206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 9609 Z= 0.344 Angle : 0.670 8.795 12969 Z= 0.358 Chirality : 0.048 0.177 1487 Planarity : 0.004 0.031 1599 Dihedral : 7.787 88.987 1326 Min Nonbonded Distance : 1.857 Molprobity Statistics. All-atom Clashscore : 2.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.49 % Favored : 92.51 % 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: -2.07 (0.24), residues: 1148 helix: -0.66 (0.19), residues: 688 sheet: 0.31 (0.67), residues: 73 loop : -2.95 (0.27), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A1047 HIS 0.010 0.001 HIS A 913 PHE 0.029 0.002 PHE A1068 TYR 0.025 0.002 TYR A 430 ARG 0.007 0.001 ARG A 454 *********************** 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 150 residues out of total 1051 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 114 time to evaluate : 2.564 Fit side-chains revert: symmetry clash REVERT: A 571 ILE cc_start: 0.8314 (OUTLIER) cc_final: 0.7899 (mp) REVERT: A 614 ARG cc_start: 0.8128 (OUTLIER) cc_final: 0.7333 (ptp90) REVERT: A 941 PHE cc_start: 0.7750 (t80) cc_final: 0.7401 (t80) REVERT: A 1171 MET cc_start: 0.7909 (OUTLIER) cc_final: 0.6590 (mmm) REVERT: A 1259 MET cc_start: 0.8590 (OUTLIER) cc_final: 0.7722 (ttt) REVERT: A 1337 GLN cc_start: 0.8977 (OUTLIER) cc_final: 0.8389 (mt0) outliers start: 36 outliers final: 12 residues processed: 140 average time/residue: 1.1663 time to fit residues: 176.0572 Evaluate side-chains 121 residues out of total 1051 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 104 time to evaluate : 0.925 ------------------------------------------------------------------------------- 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 520 MET Chi-restraints excluded: chain A residue 571 ILE Chi-restraints excluded: chain A residue 614 ARG Chi-restraints excluded: chain A residue 805 VAL 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 1236 ASP 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 104 optimal weight: 5.9990 chunk 79 optimal weight: 0.2980 chunk 54 optimal weight: 3.9990 chunk 11 optimal weight: 0.9980 chunk 50 optimal weight: 0.6980 chunk 70 optimal weight: 0.7980 chunk 105 optimal weight: 1.9990 chunk 112 optimal weight: 3.9990 chunk 55 optimal weight: 5.9990 chunk 100 optimal weight: 0.5980 chunk 30 optimal weight: 1.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 303 ASN A 559 ASN A 688 HIS A1390 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7793 moved from start: 0.3320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 9609 Z= 0.146 Angle : 0.509 5.622 12969 Z= 0.274 Chirality : 0.041 0.147 1487 Planarity : 0.003 0.030 1599 Dihedral : 7.423 88.537 1326 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 2.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.71 % Favored : 93.29 % Rotamer: Outliers : 3.24 % Allowed : 12.29 % Favored : 84.48 % 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: -1.37 (0.25), residues: 1148 helix: -0.15 (0.20), residues: 697 sheet: 1.64 (0.69), residues: 66 loop : -2.76 (0.28), residues: 385 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 0.027 0.001 PHE A1068 TYR 0.019 0.001 TYR A1097 ARG 0.004 0.000 ARG A1273 *********************** 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 144 residues out of total 1051 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 110 time to evaluate : 1.255 Fit side-chains revert: symmetry clash REVERT: A 412 VAL cc_start: 0.8362 (t) cc_final: 0.8070 (m) REVERT: A 434 GLU cc_start: 0.7860 (OUTLIER) cc_final: 0.7600 (mp0) REVERT: A 571 ILE cc_start: 0.8181 (OUTLIER) cc_final: 0.7960 (mp) REVERT: A 614 ARG cc_start: 0.8055 (OUTLIER) cc_final: 0.7555 (ptp90) REVERT: A 941 PHE cc_start: 0.7782 (t80) cc_final: 0.7420 (t80) REVERT: A 943 ASN cc_start: 0.7546 (m110) cc_final: 0.6520 (t0) REVERT: A 1171 MET cc_start: 0.7958 (OUTLIER) cc_final: 0.6345 (mmm) REVERT: A 1259 MET cc_start: 0.8438 (OUTLIER) cc_final: 0.7619 (ttt) REVERT: A 1273 ARG cc_start: 0.7001 (mmt90) cc_final: 0.6350 (mtm180) REVERT: A 1337 GLN cc_start: 0.8827 (OUTLIER) cc_final: 0.8222 (mt0) outliers start: 34 outliers final: 8 residues processed: 132 average time/residue: 1.1716 time to fit residues: 167.5391 Evaluate side-chains 116 residues out of total 1051 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 102 time to evaluate : 1.128 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 392 ASP Chi-restraints excluded: chain A residue 434 GLU Chi-restraints excluded: chain A residue 571 ILE Chi-restraints excluded: chain A residue 614 ARG 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 1171 MET Chi-restraints excluded: chain A residue 1250 LEU Chi-restraints excluded: chain A residue 1259 MET Chi-restraints excluded: chain A residue 1284 VAL Chi-restraints excluded: chain A residue 1337 GLN Chi-restraints excluded: chain A residue 1390 ASN Chi-restraints excluded: chain A residue 1397 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 93 optimal weight: 0.4980 chunk 63 optimal weight: 1.9990 chunk 1 optimal weight: 6.9990 chunk 83 optimal weight: 5.9990 chunk 46 optimal weight: 0.4980 chunk 95 optimal weight: 4.9990 chunk 77 optimal weight: 4.9990 chunk 0 optimal weight: 3.9990 chunk 57 optimal weight: 1.9990 chunk 100 optimal weight: 0.9980 chunk 28 optimal weight: 2.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- 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 A1390 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7815 moved from start: 0.3453 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= 0.179 Angle : 0.533 9.261 12969 Z= 0.283 Chirality : 0.042 0.292 1487 Planarity : 0.003 0.029 1599 Dihedral : 7.366 88.124 1326 Min Nonbonded Distance : 1.906 Molprobity Statistics. All-atom Clashscore : 2.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.79 % Favored : 93.21 % Rotamer: Outliers : 3.62 % Allowed : 12.76 % Favored : 83.62 % 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: -1.06 (0.25), residues: 1148 helix: 0.08 (0.20), residues: 691 sheet: 1.85 (0.69), residues: 66 loop : -2.59 (0.29), residues: 391 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 295 HIS 0.004 0.001 HIS A 278 PHE 0.029 0.001 PHE A1068 TYR 0.024 0.001 TYR A 206 ARG 0.003 0.000 ARG A1273 *********************** 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 145 residues out of total 1051 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 107 time to evaluate : 1.201 Fit side-chains revert: symmetry clash REVERT: A 412 VAL cc_start: 0.8444 (t) cc_final: 0.8154 (m) REVERT: A 434 GLU cc_start: 0.7888 (OUTLIER) cc_final: 0.7630 (mp0) REVERT: A 571 ILE cc_start: 0.8211 (OUTLIER) cc_final: 0.7963 (mp) REVERT: A 614 ARG cc_start: 0.8074 (OUTLIER) cc_final: 0.7438 (ptp90) REVERT: A 941 PHE cc_start: 0.7822 (t80) cc_final: 0.7433 (t80) REVERT: A 943 ASN cc_start: 0.7461 (m110) cc_final: 0.6537 (t0) REVERT: A 1171 MET cc_start: 0.7892 (OUTLIER) cc_final: 0.6309 (mmm) REVERT: A 1259 MET cc_start: 0.8462 (OUTLIER) cc_final: 0.7639 (ttt) REVERT: A 1273 ARG cc_start: 0.7057 (mmt90) cc_final: 0.6421 (mtm180) REVERT: A 1337 GLN cc_start: 0.8806 (OUTLIER) cc_final: 0.8275 (mt0) REVERT: A 1380 LYS cc_start: 0.7923 (OUTLIER) cc_final: 0.7335 (ptmm) outliers start: 38 outliers final: 13 residues processed: 136 average time/residue: 1.1184 time to fit residues: 164.1244 Evaluate side-chains 121 residues out of total 1051 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 101 time to evaluate : 1.126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 434 GLU Chi-restraints excluded: chain A residue 571 ILE Chi-restraints excluded: chain A residue 614 ARG Chi-restraints excluded: chain A residue 805 VAL Chi-restraints excluded: chain A residue 839 ILE 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 1390 ASN 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: 2.9990 chunk 100 optimal weight: 2.9990 chunk 22 optimal weight: 0.9990 chunk 65 optimal weight: 4.9990 chunk 27 optimal weight: 0.9980 chunk 112 optimal weight: 3.9990 chunk 93 optimal weight: 0.0570 chunk 51 optimal weight: 7.9990 chunk 9 optimal weight: 3.9990 chunk 58 optimal weight: 6.9990 chunk 108 optimal weight: 0.9990 overall best weight: 1.2104 ------------------------------------------------------------------------------- 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 684 ASN A 892 HIS A1390 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7823 moved from start: 0.3602 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= 0.182 Angle : 0.533 11.932 12969 Z= 0.282 Chirality : 0.042 0.193 1487 Planarity : 0.003 0.028 1599 Dihedral : 7.369 88.020 1326 Min Nonbonded Distance : 1.902 Molprobity Statistics. All-atom Clashscore : 2.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.79 % Favored : 93.21 % Rotamer: Outliers : 3.81 % Allowed : 13.62 % Favored : 82.57 % 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: -0.88 (0.25), residues: 1148 helix: 0.22 (0.20), residues: 692 sheet: 1.92 (0.69), residues: 66 loop : -2.52 (0.29), residues: 390 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 0.030 0.001 PHE A1068 TYR 0.026 0.001 TYR A 206 ARG 0.003 0.000 ARG A1273 *********************** 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: 40 poor density : 103 time to evaluate : 1.033 Fit side-chains revert: symmetry clash REVERT: A 412 VAL cc_start: 0.8437 (t) cc_final: 0.8143 (m) REVERT: A 434 GLU cc_start: 0.7878 (OUTLIER) cc_final: 0.7602 (mp0) REVERT: A 571 ILE cc_start: 0.8209 (OUTLIER) cc_final: 0.7968 (mp) REVERT: A 614 ARG cc_start: 0.8055 (OUTLIER) cc_final: 0.7394 (ptp90) REVERT: A 941 PHE cc_start: 0.7886 (t80) cc_final: 0.7498 (t80) REVERT: A 943 ASN cc_start: 0.7506 (m110) cc_final: 0.6536 (t0) REVERT: A 1064 MET cc_start: 0.6779 (OUTLIER) cc_final: 0.6456 (ttp) REVERT: A 1171 MET cc_start: 0.7892 (OUTLIER) cc_final: 0.6338 (mmm) REVERT: A 1259 MET cc_start: 0.8492 (OUTLIER) cc_final: 0.7665 (ttt) REVERT: A 1273 ARG cc_start: 0.7041 (mmt90) cc_final: 0.6416 (mtm180) REVERT: A 1337 GLN cc_start: 0.8788 (OUTLIER) cc_final: 0.8260 (mt0) REVERT: A 1377 ARG cc_start: 0.8444 (mmm160) cc_final: 0.8200 (mmm-85) REVERT: A 1380 LYS cc_start: 0.7899 (OUTLIER) cc_final: 0.7327 (ptmm) outliers start: 40 outliers final: 12 residues processed: 135 average time/residue: 1.0790 time to fit residues: 157.6372 Evaluate side-chains 112 residues out of total 1051 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 92 time to evaluate : 1.012 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 104 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 434 GLU Chi-restraints excluded: chain A residue 571 ILE Chi-restraints excluded: chain A residue 614 ARG Chi-restraints excluded: chain A residue 805 VAL Chi-restraints excluded: chain A residue 839 ILE Chi-restraints excluded: chain A residue 892 HIS 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 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 ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/programs/real_space_refine.py", line 200, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 766, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 61.1769 > 50: distance: 32 - 57: 13.289 distance: 38 - 66: 25.904 distance: 42 - 74: 25.879 distance: 48 - 57: 15.027 distance: 49 - 82: 28.336 distance: 57 - 58: 24.674 distance: 58 - 59: 19.781 distance: 58 - 61: 20.512 distance: 59 - 60: 8.843 distance: 59 - 66: 9.947 distance: 61 - 62: 22.666 distance: 62 - 63: 37.045 distance: 63 - 64: 9.508 distance: 63 - 65: 18.114 distance: 66 - 67: 10.432 distance: 67 - 68: 14.370 distance: 67 - 70: 23.634 distance: 68 - 69: 6.316 distance: 68 - 74: 8.981 distance: 70 - 71: 41.649 distance: 71 - 72: 26.555 distance: 71 - 73: 6.184 distance: 74 - 75: 46.093 distance: 75 - 76: 25.718 distance: 75 - 78: 9.126 distance: 76 - 77: 5.408 distance: 76 - 82: 11.737 distance: 78 - 79: 41.106 distance: 78 - 80: 26.891 distance: 79 - 81: 27.626 distance: 82 - 83: 41.301 distance: 83 - 84: 45.658 distance: 83 - 86: 25.194 distance: 84 - 85: 38.602 distance: 84 - 90: 21.926 distance: 86 - 87: 32.344 distance: 87 - 88: 22.385 distance: 87 - 89: 10.830 distance: 90 - 91: 19.245 distance: 91 - 92: 25.938 distance: 91 - 94: 46.478 distance: 92 - 93: 59.731 distance: 92 - 102: 34.456 distance: 95 - 96: 22.111 distance: 95 - 97: 26.381 distance: 96 - 98: 42.477 distance: 97 - 99: 17.428 distance: 98 - 100: 12.305 distance: 99 - 100: 42.036 distance: 102 - 103: 3.943 distance: 103 - 104: 46.125 distance: 103 - 106: 28.176 distance: 104 - 105: 13.276 distance: 104 - 111: 23.363 distance: 106 - 107: 12.772 distance: 107 - 108: 35.400 distance: 108 - 109: 6.803 distance: 108 - 110: 38.371 distance: 111 - 112: 24.714 distance: 112 - 113: 24.813 distance: 112 - 115: 28.714 distance: 113 - 114: 4.911 distance: 113 - 120: 30.892 distance: 115 - 116: 9.319 distance: 116 - 117: 4.444 distance: 117 - 118: 29.188 distance: 117 - 119: 3.320 distance: 120 - 121: 11.051 distance: 121 - 122: 37.100 distance: 121 - 124: 37.737 distance: 122 - 123: 27.920 distance: 122 - 128: 40.706 distance: 123 - 156: 18.876 distance: 124 - 125: 10.914 distance: 125 - 126: 34.232 distance: 126 - 127: 26.207 distance: 128 - 129: 9.475 distance: 129 - 130: 19.319 distance: 129 - 132: 9.644 distance: 130 - 131: 31.645 distance: 130 - 134: 18.497 distance: 132 - 133: 8.959 distance: 134 - 135: 43.281 distance: 135 - 136: 15.589 distance: 135 - 138: 18.251 distance: 136 - 137: 36.932 distance: 136 - 145: 32.477 distance: 138 - 139: 33.425 distance: 139 - 140: 32.070 distance: 140 - 142: 15.414 distance: 142 - 144: 29.683