Starting phenix.real_space_refine on Thu Mar 14 20:36:36 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jvh_36674/03_2024/8jvh_36674_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jvh_36674/03_2024/8jvh_36674.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.19 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jvh_36674/03_2024/8jvh_36674.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jvh_36674/03_2024/8jvh_36674.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jvh_36674/03_2024/8jvh_36674_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jvh_36674/03_2024/8jvh_36674_neut.pdb" } resolution = 3.19 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= -0.003 sd= 0.077 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 40 5.16 5 C 6289 2.51 5 N 1599 2.21 5 O 1771 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 401": "CD1" <-> "CD2" "CE1" <-> "CE2" 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: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 9699 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 9699 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1205, 9699 Classifications: {'peptide': 1205} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 26, 'TRANS': 1178} Chain breaks: 6 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Time building chain proxies: 5.28, per 1000 atoms: 0.54 Number of scatterers: 9699 At special positions: 0 Unit cell: (72.6, 119.9, 144.1, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 40 16.00 O 1771 8.00 N 1599 7.00 C 6289 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: 3.55 Conformation dependent library (CDL) restraints added in 1.8 seconds 2382 Ramachandran restraints generated. 1191 Oldfield, 0 Emsley, 1191 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2288 Finding SS restraints... Secondary structure from input PDB file: 57 helices and 7 sheets defined 62.7% alpha, 3.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.16 Creating SS restraints... Processing helix chain 'A' and resid 14 through 24 removed outlier: 3.645A pdb=" N GLU A 22 " --> pdb=" O GLU A 18 " (cutoff:3.500A) Processing helix chain 'A' and resid 27 through 37 removed outlier: 3.694A pdb=" N ARG A 33 " --> pdb=" O ALA A 29 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N ASN A 37 " --> pdb=" O ARG A 33 " (cutoff:3.500A) Processing helix chain 'A' and resid 44 through 48 removed outlier: 3.622A pdb=" N LYS A 47 " --> pdb=" O LEU A 44 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N CYS A 48 " --> pdb=" O PRO A 45 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 44 through 48' Processing helix chain 'A' and resid 55 through 66 removed outlier: 3.668A pdb=" N ALA A 64 " --> pdb=" O SER A 60 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N LEU A 66 " --> pdb=" O VAL A 62 " (cutoff:3.500A) Processing helix chain 'A' and resid 67 through 69 No H-bonds generated for 'chain 'A' and resid 67 through 69' Processing helix chain 'A' and resid 70 through 86 removed outlier: 3.823A pdb=" N SER A 76 " --> pdb=" O PRO A 72 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N GLY A 79 " --> pdb=" O ILE A 75 " (cutoff:3.500A) removed outlier: 4.774A pdb=" N VAL A 80 " --> pdb=" O SER A 76 " (cutoff:3.500A) Processing helix chain 'A' and resid 91 through 137 removed outlier: 4.102A pdb=" N SER A 100 " --> pdb=" O LEU A 96 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N ILE A 101 " --> pdb=" O SER A 97 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N GLY A 102 " --> pdb=" O LEU A 98 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N SER A 112 " --> pdb=" O LEU A 108 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N SER A 113 " --> pdb=" O SER A 109 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N TYR A 114 " --> pdb=" O MET A 110 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N VAL A 118 " --> pdb=" O TYR A 114 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N ILE A 119 " --> pdb=" O CYS A 115 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N LYS A 128 " --> pdb=" O LEU A 124 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N ARG A 133 " --> pdb=" O LEU A 129 " (cutoff:3.500A) Processing helix chain 'A' and resid 140 through 146 removed outlier: 3.915A pdb=" N ASN A 145 " --> pdb=" O GLN A 141 " (cutoff:3.500A) Processing helix chain 'A' and resid 147 through 149 No H-bonds generated for 'chain 'A' and resid 147 through 149' Processing helix chain 'A' and resid 150 through 159 removed outlier: 4.017A pdb=" N ASP A 156 " --> pdb=" O ARG A 152 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N PHE A 157 " --> pdb=" O SER A 153 " (cutoff:3.500A) Processing helix chain 'A' and resid 167 through 170 removed outlier: 3.894A pdb=" N PHE A 170 " --> pdb=" O GLY A 167 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 167 through 170' Processing helix chain 'A' and resid 171 through 191 removed outlier: 3.790A pdb=" N THR A 175 " --> pdb=" O ILE A 171 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N TYR A 176 " --> pdb=" O THR A 172 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ASN A 191 " --> pdb=" O SER A 187 " (cutoff:3.500A) Processing helix chain 'A' and resid 191 through 197 removed outlier: 3.887A pdb=" N THR A 195 " --> pdb=" O ASN A 191 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N CYS A 197 " --> pdb=" O ARG A 193 " (cutoff:3.500A) Processing helix chain 'A' and resid 202 through 240 removed outlier: 3.975A pdb=" N LYS A 214 " --> pdb=" O VAL A 210 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N LYS A 215 " --> pdb=" O ILE A 211 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ASN A 219 " --> pdb=" O LYS A 215 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N THR A 222 " --> pdb=" O LEU A 218 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N TYR A 226 " --> pdb=" O THR A 222 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ASN A 227 " --> pdb=" O SER A 223 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ASN A 228 " --> pdb=" O LEU A 224 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N ASN A 229 " --> pdb=" O LEU A 225 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N THR A 230 " --> pdb=" O TYR A 226 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N GLY A 240 " --> pdb=" O GLU A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 241 through 246 removed outlier: 3.858A pdb=" N SER A 246 " --> pdb=" O ARG A 242 " (cutoff:3.500A) Processing helix chain 'A' and resid 253 through 303 removed outlier: 3.682A pdb=" N THR A 262 " --> pdb=" O ASN A 258 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N PHE A 263 " --> pdb=" O LEU A 259 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N TYR A 264 " --> pdb=" O SER A 260 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N VAL A 274 " --> pdb=" O LYS A 270 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N HIS A 278 " --> pdb=" O VAL A 274 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N ILE A 279 " --> pdb=" O GLU A 275 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N GLY A 280 " --> pdb=" O ALA A 276 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N ILE A 286 " --> pdb=" O ILE A 282 " (cutoff:3.500A) removed outlier: 5.193A pdb=" N LEU A 287 " --> pdb=" O ASN A 283 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N VAL A 288 " --> pdb=" O GLY A 284 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ARG A 299 " --> pdb=" O TRP A 295 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N ILE A 302 " --> pdb=" O THR A 298 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ASN A 303 " --> pdb=" O ARG A 299 " (cutoff:3.500A) Processing helix chain 'A' and resid 315 through 318 removed outlier: 3.681A pdb=" N SER A 318 " --> pdb=" O ASN A 315 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 315 through 318' Processing helix chain 'A' and resid 319 through 334 removed outlier: 3.797A pdb=" N LEU A 323 " --> pdb=" O VAL A 319 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N LEU A 324 " --> pdb=" O ILE A 320 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N MET A 330 " --> pdb=" O VAL A 326 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N PHE A 331 " --> pdb=" O LEU A 327 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N MET A 332 " --> pdb=" O ILE A 328 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N LEU A 333 " --> pdb=" O SER A 329 " (cutoff:3.500A) Processing helix chain 'A' and resid 336 through 351 removed outlier: 3.565A pdb=" N ILE A 340 " --> pdb=" O ILE A 336 " (cutoff:3.500A) Processing helix chain 'A' and resid 418 through 427 Processing helix chain 'A' and resid 444 through 448 removed outlier: 3.552A 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 471 through 477 removed outlier: 3.842A pdb=" N ILE A 475 " --> pdb=" O ILE A 471 " (cutoff:3.500A) Processing helix chain 'A' and resid 479 through 488 removed outlier: 3.894A pdb=" N LEU A 485 " --> pdb=" O SER A 481 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N GLU A 486 " --> pdb=" O LEU A 482 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N ALA A 487 " --> pdb=" O LYS A 483 " (cutoff:3.500A) removed outlier: 4.541A pdb=" N MET A 488 " --> pdb=" O ASP A 484 " (cutoff:3.500A) Processing helix chain 'A' and resid 522 through 527 Processing helix chain 'A' and resid 529 through 539 removed outlier: 3.697A pdb=" N VAL A 533 " --> pdb=" O ASP A 529 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ASP A 534 " --> pdb=" O SER A 530 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N VAL A 539 " --> pdb=" O VAL A 535 " (cutoff:3.500A) Processing helix chain 'A' and resid 541 through 548 removed outlier: 3.775A pdb=" N LEU A 548 " --> pdb=" O PHE A 544 " (cutoff:3.500A) Processing helix chain 'A' and resid 564 through 579 removed outlier: 4.558A pdb=" N ARG A 579 " --> pdb=" O ARG A 575 " (cutoff:3.500A) Processing helix chain 'A' and resid 594 through 607 removed outlier: 3.688A pdb=" N GLU A 598 " --> pdb=" O ASP A 594 " (cutoff:3.500A) Processing helix chain 'A' and resid 685 through 694 removed outlier: 3.547A pdb=" N LEU A 689 " --> pdb=" O GLY A 685 " (cutoff:3.500A) Processing helix chain 'A' and resid 772 through 783 removed outlier: 3.837A pdb=" N ILE A 778 " --> pdb=" O ASN A 774 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N PHE A 783 " --> pdb=" O TYR A 779 " (cutoff:3.500A) Processing helix chain 'A' and resid 785 through 803 removed outlier: 3.761A pdb=" N VAL A 789 " --> pdb=" O TYR A 785 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N THR A 790 " --> pdb=" O LYS A 786 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N ILE A 791 " --> pdb=" O LYS A 787 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N ILE A 792 " --> pdb=" O ASP A 788 " (cutoff:3.500A) Processing helix chain 'A' and resid 804 through 815 removed outlier: 3.837A pdb=" N LEU A 808 " --> pdb=" O PRO A 804 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N ARG A 812 " --> pdb=" O LEU A 808 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N TYR A 813 " --> pdb=" O LEU A 809 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N VAL A 814 " --> pdb=" O TYR A 810 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N SER A 815 " --> pdb=" O ALA A 811 " (cutoff:3.500A) Processing helix chain 'A' and resid 822 through 873 removed outlier: 3.746A pdb=" N ASN A 826 " --> pdb=" O ASN A 822 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N ILE A 832 " --> pdb=" O ASN A 828 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N TYR A 833 " --> pdb=" O LYS A 829 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N ILE A 834 " --> pdb=" O TYR A 830 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ILE A 843 " --> pdb=" O ILE A 839 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N TYR A 851 " --> pdb=" O LEU A 847 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ASN A 852 " --> pdb=" O LYS A 848 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N ASN A 853 " --> pdb=" O ASN A 849 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N LYS A 858 " --> pdb=" O LYS A 854 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N VAL A 859 " --> pdb=" O ILE A 855 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N GLU A 860 " --> pdb=" O GLY A 856 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N ARG A 865 " --> pdb=" O LYS A 861 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N ARG A 866 " --> pdb=" O THR A 862 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N LEU A 872 " --> pdb=" O PHE A 868 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N TYR A 873 " --> pdb=" O GLU A 869 " (cutoff:3.500A) Processing helix chain 'A' and resid 875 through 881 removed outlier: 4.115A pdb=" N PHE A 879 " --> pdb=" O GLU A 875 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N GLN A 881 " --> pdb=" O SER A 877 " (cutoff:3.500A) Processing helix chain 'A' and resid 885 through 903 removed outlier: 4.001A pdb=" N ILE A 893 " --> pdb=" O LEU A 889 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N ASN A 894 " --> pdb=" O SER A 890 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N VAL A 897 " --> pdb=" O ILE A 893 " (cutoff:3.500A) Processing helix chain 'A' and resid 903 through 927 removed outlier: 5.210A pdb=" N VAL A 909 " --> pdb=" O VAL A 905 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N VAL A 920 " --> pdb=" O MET A 916 " (cutoff:3.500A) Processing helix chain 'A' and resid 929 through 945 removed outlier: 3.768A pdb=" N ALA A 933 " --> pdb=" O CYS A 929 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ALA A 934 " --> pdb=" O PRO A 930 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N VAL A 935 " --> pdb=" O ILE A 931 " (cutoff:3.500A) Processing helix chain 'A' and resid 948 through 963 removed outlier: 4.068A pdb=" N ILE A 959 " --> pdb=" O LYS A 955 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N GLU A 960 " --> pdb=" O SER A 956 " (cutoff:3.500A) Processing helix chain 'A' and resid 986 through 991 removed outlier: 3.715A pdb=" N PHE A 990 " --> pdb=" O ILE A 986 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N TYR A 991 " --> pdb=" O GLN A 987 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 986 through 991' Processing helix chain 'A' and resid 992 through 997 removed outlier: 3.783A pdb=" N VAL A 996 " --> pdb=" O ASN A 992 " (cutoff:3.500A) Processing helix chain 'A' and resid 1007 through 1014 Processing helix chain 'A' and resid 1016 through 1036 removed outlier: 4.364A pdb=" N ARG A1022 " --> pdb=" O LYS A1018 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N ALA A1029 " --> pdb=" O ILE A1025 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N TRP A1031 " --> pdb=" O ASN A1027 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N PHE A1033 " --> pdb=" O ALA A1029 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N SER A1034 " --> pdb=" O LEU A1030 " (cutoff:3.500A) Processing helix chain 'A' and resid 1037 through 1054 removed outlier: 4.006A pdb=" N LYS A1054 " --> pdb=" O SER A1050 " (cutoff:3.500A) Processing helix chain 'A' and resid 1060 through 1081 removed outlier: 3.799A pdb=" N PHE A1068 " --> pdb=" O MET A1064 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N THR A1069 " --> pdb=" O LYS A1065 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N PHE A1070 " --> pdb=" O SER A1066 " (cutoff:3.500A) Processing helix chain 'A' and resid 1086 through 1097 removed outlier: 3.998A pdb=" N ALA A1090 " --> pdb=" O ASP A1086 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N LYS A1091 " --> pdb=" O SER A1087 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N PHE A1094 " --> pdb=" O ALA A1090 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N GLU A1095 " --> pdb=" O LYS A1091 " (cutoff:3.500A) Processing helix chain 'A' and resid 1169 through 1175 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 1264 through 1270 removed outlier: 3.532A pdb=" N LYS A1270 " --> pdb=" O TYR A1266 " (cutoff:3.500A) Processing helix chain 'A' and resid 1277 through 1288 removed outlier: 3.846A pdb=" N VAL A1281 " --> pdb=" O THR A1277 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N PHE A1287 " --> pdb=" O ARG A1283 " (cutoff:3.500A) Processing helix chain 'A' and resid 1293 through 1297 removed outlier: 3.928A pdb=" N LEU A1297 " --> pdb=" O ILE A1294 " (cutoff:3.500A) Processing helix chain 'A' and resid 1299 through 1303 removed outlier: 4.001A pdb=" N THR A1303 " --> pdb=" O LYS A1300 " (cutoff:3.500A) Processing helix chain 'A' and resid 1306 through 1310 Processing helix chain 'A' and resid 1313 through 1327 removed outlier: 3.823A pdb=" N GLN A1318 " --> pdb=" O GLY A1314 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N ARG A1319 " --> pdb=" O GLY A1315 " (cutoff:3.500A) Processing helix chain 'A' and resid 1343 through 1358 Processing helix chain 'A' and resid 1371 through 1378 removed outlier: 4.403A pdb=" N ARG A1377 " --> pdb=" O ALA A1373 " (cutoff:3.500A) Processing helix chain 'A' and resid 1410 through 1417 Processing sheet with id=AA1, first strand: chain 'A' and resid 378 through 379 Processing sheet with id=AA2, first strand: chain 'A' and resid 409 through 411 removed outlier: 4.016A pdb=" N ILE A 618 " --> pdb=" O TYR A 409 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 457 through 460 removed outlier: 6.082A pdb=" N GLY A 458 " --> pdb=" O ILE A 585 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 635 through 636 removed outlier: 4.613A pdb=" N SER A 636 " --> pdb=" O TYR A 669 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N TYR A 669 " --> pdb=" O SER A 636 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 1149 through 1151 removed outlier: 6.319A pdb=" N GLU A1231 " --> pdb=" O LYS A1129 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 1158 through 1161 removed outlier: 6.618A pdb=" N ALA A1158 " --> pdb=" O VAL A1382 " (cutoff:3.500A) removed outlier: 7.783A pdb=" N PHE A1384 " --> pdb=" O ALA A1158 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N VAL A1160 " --> pdb=" O PHE A1384 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ASN A1385 " --> pdb=" O PHE A1393 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N PHE A1393 " --> pdb=" O ASN A1385 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'A' and resid 1251 through 1254 421 hydrogen bonds defined for protein. 1227 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: 3.02 Time building geometry restraints manager: 3.88 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: 3013 1.34 - 1.46: 1987 1.46 - 1.58: 4809 1.58 - 1.70: 0 1.70 - 1.82: 67 Bond restraints: 9876 Sorted by residual: bond pdb=" CB ASP A 441 " pdb=" CG ASP A 441 " ideal model delta sigma weight residual 1.516 1.551 -0.035 2.50e-02 1.60e+03 2.00e+00 bond pdb=" CG LEU A1080 " pdb=" CD2 LEU A1080 " ideal model delta sigma weight residual 1.521 1.475 0.046 3.30e-02 9.18e+02 1.97e+00 bond pdb=" CA LEU A 362 " pdb=" C LEU A 362 " ideal model delta sigma weight residual 1.523 1.543 -0.021 1.49e-02 4.50e+03 1.92e+00 bond pdb=" C ILE A 328 " pdb=" N SER A 329 " ideal model delta sigma weight residual 1.335 1.353 -0.018 1.31e-02 5.83e+03 1.89e+00 bond pdb=" CB ASN A1106 " pdb=" CG ASN A1106 " ideal model delta sigma weight residual 1.516 1.549 -0.033 2.50e-02 1.60e+03 1.74e+00 ... (remaining 9871 not shown) Histogram of bond angle deviations from ideal: 99.24 - 106.21: 142 106.21 - 113.17: 5305 113.17 - 120.14: 3840 120.14 - 127.11: 3960 127.11 - 134.08: 58 Bond angle restraints: 13305 Sorted by residual: angle pdb=" C SER A1105 " pdb=" N ASN A1106 " pdb=" CA ASN A1106 " ideal model delta sigma weight residual 121.54 131.63 -10.09 1.91e+00 2.74e-01 2.79e+01 angle pdb=" C ASN A 440 " pdb=" N ASP A 441 " pdb=" CA ASP A 441 " ideal model delta sigma weight residual 121.54 128.60 -7.06 1.91e+00 2.74e-01 1.37e+01 angle pdb=" C ALA A 821 " pdb=" N ASN A 822 " pdb=" CA ASN A 822 " ideal model delta sigma weight residual 121.54 127.58 -6.04 1.91e+00 2.74e-01 9.99e+00 angle pdb=" CA ASN A1106 " pdb=" CB ASN A1106 " pdb=" CG ASN A1106 " ideal model delta sigma weight residual 112.60 115.68 -3.08 1.00e+00 1.00e+00 9.50e+00 angle pdb=" C PRO A 361 " pdb=" N LEU A 362 " pdb=" CA LEU A 362 " ideal model delta sigma weight residual 123.91 128.78 -4.87 1.66e+00 3.63e-01 8.62e+00 ... (remaining 13300 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.07: 5645 15.07 - 30.15: 274 30.15 - 45.22: 51 45.22 - 60.30: 1 60.30 - 75.37: 3 Dihedral angle restraints: 5974 sinusoidal: 2431 harmonic: 3543 Sorted by residual: dihedral pdb=" CA VAL A 905 " pdb=" C VAL A 905 " pdb=" N ASN A 906 " pdb=" CA ASN A 906 " ideal model delta harmonic sigma weight residual 180.00 154.25 25.75 0 5.00e+00 4.00e-02 2.65e+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 -155.65 -24.35 0 5.00e+00 4.00e-02 2.37e+01 dihedral pdb=" CA LYS A1016 " pdb=" C LYS A1016 " pdb=" N ASN A1017 " pdb=" CA ASN A1017 " ideal model delta harmonic sigma weight residual -180.00 -156.32 -23.68 0 5.00e+00 4.00e-02 2.24e+01 ... (remaining 5971 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 987 0.039 - 0.079: 401 0.079 - 0.118: 116 0.118 - 0.157: 22 0.157 - 0.196: 3 Chirality restraints: 1529 Sorted by residual: chirality pdb=" CB ILE A 437 " pdb=" CA ILE A 437 " pdb=" CG1 ILE A 437 " pdb=" CG2 ILE A 437 " both_signs ideal model delta sigma weight residual False 2.64 2.84 -0.20 2.00e-01 2.50e+01 9.63e-01 chirality pdb=" CA ASN A1106 " pdb=" N ASN A1106 " pdb=" C ASN A1106 " pdb=" CB ASN A1106 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.18 2.00e-01 2.50e+01 7.67e-01 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 2.34 0.17 2.00e-01 2.50e+01 7.18e-01 ... (remaining 1526 not shown) Planarity restraints: 1654 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE A 437 " -0.010 2.00e-02 2.50e+03 2.07e-02 4.29e+00 pdb=" C ILE A 437 " 0.036 2.00e-02 2.50e+03 pdb=" O ILE A 437 " -0.014 2.00e-02 2.50e+03 pdb=" N ILE A 438 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLU A1257 " 0.033 5.00e-02 4.00e+02 4.98e-02 3.97e+00 pdb=" N PRO A1258 " -0.086 5.00e-02 4.00e+02 pdb=" CA PRO A1258 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO A1258 " 0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASN A 440 " -0.010 2.00e-02 2.50e+03 1.96e-02 3.83e+00 pdb=" C ASN A 440 " 0.034 2.00e-02 2.50e+03 pdb=" O ASN A 440 " -0.013 2.00e-02 2.50e+03 pdb=" N ASP A 441 " -0.011 2.00e-02 2.50e+03 ... (remaining 1651 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 610 2.74 - 3.28: 10110 3.28 - 3.82: 13912 3.82 - 4.36: 17111 4.36 - 4.90: 29368 Nonbonded interactions: 71111 Sorted by model distance: nonbonded pdb=" O ILE A 286 " pdb=" OG SER A 289 " model vdw 2.195 2.440 nonbonded pdb=" O ILE A1375 " pdb=" OG SER A1378 " model vdw 2.244 2.440 nonbonded pdb=" OD2 ASP A 144 " pdb=" OH TYR A 430 " model vdw 2.253 2.440 nonbonded pdb=" O PRO A 338 " pdb=" OG1 THR A 341 " model vdw 2.255 2.440 nonbonded pdb=" ND2 ASN A 774 " pdb=" OE1 GLU A1095 " model vdw 2.264 2.520 ... (remaining 71106 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: 0.680 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: 4.010 Check model and map are aligned: 0.130 Set scattering table: 0.080 Process input model: 28.110 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.050 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:3.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.470 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7042 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 0.052 9876 Z= 0.337 Angle : 0.785 10.087 13305 Z= 0.442 Chirality : 0.046 0.196 1529 Planarity : 0.004 0.050 1654 Dihedral : 9.557 75.370 3686 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 2.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.65 % Favored : 91.35 % Rotamer: Outliers : 0.18 % Allowed : 2.21 % Favored : 97.61 % 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: -4.48 (0.19), residues: 1191 helix: -2.45 (0.16), residues: 713 sheet: -3.43 (0.53), residues: 56 loop : -3.61 (0.24), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 186 HIS 0.011 0.002 HIS A 892 PHE 0.030 0.002 PHE A 294 TYR 0.027 0.002 TYR A 940 ARG 0.007 0.001 ARG A1176 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2382 Ramachandran restraints generated. 1191 Oldfield, 0 Emsley, 1191 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2382 Ramachandran restraints generated. 1191 Oldfield, 0 Emsley, 1191 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1089 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 197 time to evaluate : 1.035 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 28 THR cc_start: 0.8516 (p) cc_final: 0.8294 (m) REVERT: A 153 SER cc_start: 0.8701 (t) cc_final: 0.8091 (p) REVERT: A 160 GLU cc_start: 0.7203 (pp20) cc_final: 0.6774 (pp20) REVERT: A 251 LYS cc_start: 0.8219 (ttmm) cc_final: 0.7973 (mptt) REVERT: A 776 ARG cc_start: 0.6492 (ptp90) cc_final: 0.6186 (mmm-85) REVERT: A 924 MET cc_start: 0.8738 (ptt) cc_final: 0.8474 (ptt) REVERT: A 955 LYS cc_start: 0.8459 (ttpt) cc_final: 0.8216 (ttpt) REVERT: A 1092 LEU cc_start: 0.8725 (tp) cc_final: 0.8468 (tp) outliers start: 2 outliers final: 0 residues processed: 197 average time/residue: 0.2883 time to fit residues: 74.2293 Evaluate side-chains 99 residues out of total 1089 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 99 time to evaluate : 1.108 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 101 optimal weight: 3.9990 chunk 90 optimal weight: 1.9990 chunk 50 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 chunk 61 optimal weight: 0.5980 chunk 48 optimal weight: 6.9990 chunk 94 optimal weight: 5.9990 chunk 36 optimal weight: 3.9990 chunk 57 optimal weight: 5.9990 chunk 70 optimal weight: 0.6980 chunk 108 optimal weight: 0.0870 overall best weight: 1.0762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 283 ASN ** A 606 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 894 ASN A 992 ASN A1256 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7223 moved from start: 0.2513 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9876 Z= 0.210 Angle : 0.623 9.798 13305 Z= 0.325 Chirality : 0.044 0.166 1529 Planarity : 0.004 0.043 1654 Dihedral : 5.210 23.984 1301 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.55 % Favored : 93.45 % Rotamer: Outliers : 1.56 % Allowed : 7.64 % Favored : 90.80 % 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: -3.08 (0.22), residues: 1191 helix: -1.33 (0.18), residues: 721 sheet: -2.87 (0.59), residues: 61 loop : -3.06 (0.26), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A1047 HIS 0.008 0.002 HIS A 676 PHE 0.016 0.002 PHE A 294 TYR 0.020 0.002 TYR A1266 ARG 0.005 0.000 ARG A1283 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2382 Ramachandran restraints generated. 1191 Oldfield, 0 Emsley, 1191 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2382 Ramachandran restraints generated. 1191 Oldfield, 0 Emsley, 1191 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1089 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 122 time to evaluate : 1.113 Fit side-chains revert: symmetry clash REVERT: A 153 SER cc_start: 0.8696 (t) cc_final: 0.8065 (p) REVERT: A 160 GLU cc_start: 0.7266 (pp20) cc_final: 0.6742 (pp20) REVERT: A 185 ILE cc_start: 0.8376 (OUTLIER) cc_final: 0.8104 (mt) REVERT: A 231 MET cc_start: 0.7442 (mtp) cc_final: 0.7207 (mtm) REVERT: A 251 LYS cc_start: 0.8340 (ttmm) cc_final: 0.8058 (mptt) REVERT: A 348 GLU cc_start: 0.7367 (pp20) cc_final: 0.6982 (pp20) REVERT: A 382 ASN cc_start: 0.6529 (m110) cc_final: 0.5972 (p0) REVERT: A 437 ILE cc_start: 0.7971 (mm) cc_final: 0.7706 (mm) REVERT: A 955 LYS cc_start: 0.8495 (ttpt) cc_final: 0.8277 (ttmt) REVERT: A 1080 LEU cc_start: 0.8111 (OUTLIER) cc_final: 0.7664 (pt) REVERT: A 1256 GLN cc_start: 0.7359 (tp-100) cc_final: 0.6707 (mm110) outliers start: 17 outliers final: 12 residues processed: 134 average time/residue: 0.2371 time to fit residues: 43.8506 Evaluate side-chains 107 residues out of total 1089 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 93 time to evaluate : 1.086 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 MET Chi-restraints excluded: chain A residue 89 ASP Chi-restraints excluded: chain A residue 185 ILE Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 199 THR Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain A residue 1070 PHE Chi-restraints excluded: chain A residue 1080 LEU Chi-restraints excluded: chain A residue 1107 ILE Chi-restraints excluded: chain A residue 1127 ASP Chi-restraints excluded: chain A residue 1263 MET Chi-restraints excluded: chain A residue 1284 VAL Chi-restraints excluded: chain A residue 1294 ILE Chi-restraints excluded: chain A residue 1367 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 60 optimal weight: 9.9990 chunk 33 optimal weight: 1.9990 chunk 90 optimal weight: 2.9990 chunk 74 optimal weight: 0.7980 chunk 30 optimal weight: 0.8980 chunk 109 optimal weight: 7.9990 chunk 117 optimal weight: 9.9990 chunk 97 optimal weight: 0.0020 chunk 108 optimal weight: 0.3980 chunk 37 optimal weight: 7.9990 chunk 87 optimal weight: 0.5980 overall best weight: 0.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 606 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 998 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7212 moved from start: 0.3073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 9876 Z= 0.139 Angle : 0.524 9.325 13305 Z= 0.274 Chirality : 0.041 0.147 1529 Planarity : 0.003 0.040 1654 Dihedral : 4.647 21.937 1301 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.30 % Favored : 93.70 % Rotamer: Outliers : 1.56 % Allowed : 9.20 % Favored : 89.24 % 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: -2.29 (0.23), residues: 1191 helix: -0.67 (0.19), residues: 720 sheet: -2.77 (0.58), residues: 71 loop : -2.73 (0.26), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A1047 HIS 0.005 0.001 HIS A1400 PHE 0.010 0.001 PHE A 633 TYR 0.016 0.001 TYR A1266 ARG 0.005 0.000 ARG A1283 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2382 Ramachandran restraints generated. 1191 Oldfield, 0 Emsley, 1191 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2382 Ramachandran restraints generated. 1191 Oldfield, 0 Emsley, 1191 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 1089 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 100 time to evaluate : 1.369 Fit side-chains revert: symmetry clash REVERT: A 160 GLU cc_start: 0.7251 (pp20) cc_final: 0.6852 (pp20) REVERT: A 185 ILE cc_start: 0.8351 (tp) cc_final: 0.8103 (mp) REVERT: A 251 LYS cc_start: 0.8401 (ttmm) cc_final: 0.8115 (mptt) REVERT: A 382 ASN cc_start: 0.6548 (m110) cc_final: 0.6055 (p0) REVERT: A 437 ILE cc_start: 0.8011 (mm) cc_final: 0.7647 (mm) REVERT: A 446 LYS cc_start: 0.8619 (mttt) cc_final: 0.8330 (mttp) REVERT: A 955 LYS cc_start: 0.8474 (ttpt) cc_final: 0.8262 (ttmt) REVERT: A 1249 ASN cc_start: 0.8973 (OUTLIER) cc_final: 0.8660 (t0) REVERT: A 1274 GLU cc_start: 0.8319 (pt0) cc_final: 0.8104 (mt-10) outliers start: 17 outliers final: 9 residues processed: 111 average time/residue: 0.2318 time to fit residues: 36.3705 Evaluate side-chains 98 residues out of total 1089 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 88 time to evaluate : 1.041 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 ASP Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain A residue 616 THR Chi-restraints excluded: chain A residue 1025 ILE Chi-restraints excluded: chain A residue 1070 PHE Chi-restraints excluded: chain A residue 1127 ASP Chi-restraints excluded: chain A residue 1171 MET Chi-restraints excluded: chain A residue 1249 ASN Chi-restraints excluded: chain A residue 1294 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 107 optimal weight: 2.9990 chunk 82 optimal weight: 3.9990 chunk 56 optimal weight: 10.0000 chunk 12 optimal weight: 4.9990 chunk 52 optimal weight: 7.9990 chunk 73 optimal weight: 0.9990 chunk 109 optimal weight: 2.9990 chunk 115 optimal weight: 2.9990 chunk 57 optimal weight: 5.9990 chunk 103 optimal weight: 3.9990 chunk 31 optimal weight: 0.7980 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 606 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1020 GLN A1256 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7393 moved from start: 0.3759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.075 9876 Z= 0.327 Angle : 0.653 9.147 13305 Z= 0.346 Chirality : 0.047 0.169 1529 Planarity : 0.004 0.045 1654 Dihedral : 5.063 23.361 1301 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.72 % Favored : 92.28 % Rotamer: Outliers : 2.21 % Allowed : 10.21 % Favored : 87.58 % 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: -2.43 (0.22), residues: 1191 helix: -0.83 (0.18), residues: 736 sheet: -2.21 (0.66), residues: 61 loop : -2.88 (0.26), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A1047 HIS 0.006 0.002 HIS A1400 PHE 0.022 0.002 PHE A 842 TYR 0.020 0.002 TYR A 851 ARG 0.004 0.001 ARG A 454 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2382 Ramachandran restraints generated. 1191 Oldfield, 0 Emsley, 1191 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2382 Ramachandran restraints generated. 1191 Oldfield, 0 Emsley, 1191 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 1089 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 95 time to evaluate : 1.145 Fit side-chains revert: symmetry clash REVERT: A 160 GLU cc_start: 0.7513 (pp20) cc_final: 0.7136 (pp20) REVERT: A 185 ILE cc_start: 0.8404 (tp) cc_final: 0.8132 (mt) REVERT: A 251 LYS cc_start: 0.8502 (ttmm) cc_final: 0.8081 (mptt) REVERT: A 382 ASN cc_start: 0.6593 (m110) cc_final: 0.6012 (p0) REVERT: A 437 ILE cc_start: 0.8066 (mm) cc_final: 0.7747 (mm) REVERT: A 955 LYS cc_start: 0.8365 (ttpt) cc_final: 0.8151 (ttmt) REVERT: A 1134 ARG cc_start: 0.7615 (ttm-80) cc_final: 0.7288 (ttm-80) REVERT: A 1249 ASN cc_start: 0.9133 (OUTLIER) cc_final: 0.8772 (t0) REVERT: A 1274 GLU cc_start: 0.8417 (pt0) cc_final: 0.8139 (mt-10) outliers start: 24 outliers final: 15 residues processed: 114 average time/residue: 0.2519 time to fit residues: 39.8231 Evaluate side-chains 100 residues out of total 1089 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 84 time to evaluate : 1.072 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 89 ASP Chi-restraints excluded: chain A residue 111 ILE Chi-restraints excluded: chain A residue 171 ILE Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 199 THR Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain A residue 535 VAL Chi-restraints excluded: chain A residue 616 THR Chi-restraints excluded: chain A residue 635 LEU Chi-restraints excluded: chain A residue 1025 ILE Chi-restraints excluded: chain A residue 1070 PHE Chi-restraints excluded: chain A residue 1249 ASN Chi-restraints excluded: chain A residue 1263 MET Chi-restraints excluded: chain A residue 1294 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 96 optimal weight: 5.9990 chunk 65 optimal weight: 0.8980 chunk 1 optimal weight: 5.9990 chunk 86 optimal weight: 4.9990 chunk 47 optimal weight: 0.4980 chunk 98 optimal weight: 1.9990 chunk 80 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 59 optimal weight: 0.9990 chunk 104 optimal weight: 0.9990 chunk 29 optimal weight: 1.9990 overall best weight: 1.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 374 ASN ** A 606 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1020 GLN A1256 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7345 moved from start: 0.3996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9876 Z= 0.190 Angle : 0.538 8.549 13305 Z= 0.286 Chirality : 0.042 0.150 1529 Planarity : 0.003 0.047 1654 Dihedral : 4.751 22.652 1301 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.63 % Favored : 93.37 % Rotamer: Outliers : 2.30 % Allowed : 11.50 % Favored : 86.20 % 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: -1.97 (0.23), residues: 1191 helix: -0.43 (0.19), residues: 731 sheet: -2.08 (0.66), residues: 63 loop : -2.73 (0.26), residues: 397 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A1047 HIS 0.005 0.001 HIS A1400 PHE 0.020 0.001 PHE A1293 TYR 0.015 0.001 TYR A 290 ARG 0.003 0.000 ARG A1283 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2382 Ramachandran restraints generated. 1191 Oldfield, 0 Emsley, 1191 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2382 Ramachandran restraints generated. 1191 Oldfield, 0 Emsley, 1191 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 1089 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 94 time to evaluate : 0.902 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 160 GLU cc_start: 0.7508 (pp20) cc_final: 0.7151 (pp20) REVERT: A 166 ILE cc_start: 0.8811 (OUTLIER) cc_final: 0.8541 (tp) REVERT: A 185 ILE cc_start: 0.8341 (tp) cc_final: 0.8085 (mp) REVERT: A 231 MET cc_start: 0.7541 (mtm) cc_final: 0.7307 (mtm) REVERT: A 239 MET cc_start: 0.7753 (tpp) cc_final: 0.7276 (mpp) REVERT: A 251 LYS cc_start: 0.8442 (ttmm) cc_final: 0.8089 (mptt) REVERT: A 382 ASN cc_start: 0.6612 (m110) cc_final: 0.6107 (p0) REVERT: A 437 ILE cc_start: 0.8120 (mm) cc_final: 0.7827 (mm) REVERT: A 582 LYS cc_start: 0.6715 (mttm) cc_final: 0.6290 (mttp) REVERT: A 955 LYS cc_start: 0.8336 (ttpt) cc_final: 0.8106 (ttmt) REVERT: A 1134 ARG cc_start: 0.7564 (ttm-80) cc_final: 0.7261 (ttm-80) REVERT: A 1249 ASN cc_start: 0.9080 (OUTLIER) cc_final: 0.8694 (t0) REVERT: A 1274 GLU cc_start: 0.8374 (pt0) cc_final: 0.8095 (mt-10) outliers start: 25 outliers final: 11 residues processed: 114 average time/residue: 0.2385 time to fit residues: 37.3202 Evaluate side-chains 101 residues out of total 1089 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 88 time to evaluate : 1.012 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 89 ASP Chi-restraints excluded: chain A residue 166 ILE Chi-restraints excluded: chain A residue 199 THR Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain A residue 616 THR Chi-restraints excluded: chain A residue 635 LEU Chi-restraints excluded: chain A residue 1025 ILE Chi-restraints excluded: chain A residue 1070 PHE Chi-restraints excluded: chain A residue 1073 THR Chi-restraints excluded: chain A residue 1127 ASP Chi-restraints excluded: chain A residue 1249 ASN Chi-restraints excluded: chain A residue 1294 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 39 optimal weight: 7.9990 chunk 104 optimal weight: 0.0770 chunk 22 optimal weight: 2.9990 chunk 68 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 chunk 116 optimal weight: 6.9990 chunk 96 optimal weight: 5.9990 chunk 53 optimal weight: 2.9990 chunk 9 optimal weight: 0.8980 chunk 38 optimal weight: 5.9990 chunk 60 optimal weight: 9.9990 overall best weight: 1.7944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 143 HIS ** A 606 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 881 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7408 moved from start: 0.4299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 9876 Z= 0.285 Angle : 0.610 8.471 13305 Z= 0.323 Chirality : 0.045 0.147 1529 Planarity : 0.004 0.048 1654 Dihedral : 4.905 23.081 1301 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.98 % Favored : 92.02 % Rotamer: Outliers : 2.12 % Allowed : 12.14 % Favored : 85.74 % 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: -2.04 (0.23), residues: 1191 helix: -0.46 (0.19), residues: 726 sheet: -2.22 (0.66), residues: 63 loop : -2.78 (0.26), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 186 HIS 0.005 0.001 HIS A 278 PHE 0.020 0.002 PHE A 842 TYR 0.017 0.002 TYR A1097 ARG 0.003 0.000 ARG A 454 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2382 Ramachandran restraints generated. 1191 Oldfield, 0 Emsley, 1191 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2382 Ramachandran restraints generated. 1191 Oldfield, 0 Emsley, 1191 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 1089 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 86 time to evaluate : 1.084 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 160 GLU cc_start: 0.7653 (pp20) cc_final: 0.7334 (pp20) REVERT: A 185 ILE cc_start: 0.8344 (tp) cc_final: 0.8066 (mp) REVERT: A 231 MET cc_start: 0.7480 (mtm) cc_final: 0.7229 (mtm) REVERT: A 239 MET cc_start: 0.7779 (tpp) cc_final: 0.7295 (tpp) REVERT: A 251 LYS cc_start: 0.8524 (ttmm) cc_final: 0.8122 (mptt) REVERT: A 332 MET cc_start: 0.8318 (mmt) cc_final: 0.7288 (mmt) REVERT: A 382 ASN cc_start: 0.6662 (m110) cc_final: 0.6123 (p0) REVERT: A 446 LYS cc_start: 0.8807 (mttt) cc_final: 0.8575 (mptt) REVERT: A 955 LYS cc_start: 0.8357 (ttpt) cc_final: 0.8134 (ttmt) REVERT: A 1249 ASN cc_start: 0.9171 (OUTLIER) cc_final: 0.8759 (t0) REVERT: A 1274 GLU cc_start: 0.8387 (pt0) cc_final: 0.8176 (mt-10) REVERT: A 1376 LYS cc_start: 0.8308 (tmmt) cc_final: 0.8081 (mttp) outliers start: 23 outliers final: 17 residues processed: 105 average time/residue: 0.2395 time to fit residues: 35.0312 Evaluate side-chains 100 residues out of total 1089 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 82 time to evaluate : 1.077 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 89 ASP Chi-restraints excluded: chain A residue 111 ILE Chi-restraints excluded: chain A residue 171 ILE Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 199 THR Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain A residue 616 THR Chi-restraints excluded: chain A residue 635 LEU Chi-restraints excluded: chain A residue 1025 ILE Chi-restraints excluded: chain A residue 1070 PHE Chi-restraints excluded: chain A residue 1107 ILE Chi-restraints excluded: chain A residue 1127 ASP Chi-restraints excluded: chain A residue 1160 VAL Chi-restraints excluded: chain A residue 1249 ASN Chi-restraints excluded: chain A residue 1263 MET Chi-restraints excluded: chain A residue 1294 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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-5265/modules/cctbx_project/iotbx/cli_parser.py", line 944, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/programs/real_space_refine.py", line 189, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 700, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 764, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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-5265/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-5265/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-5265/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-5265/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-5265/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-5265/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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-5265/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-5265/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-5265/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-5265/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: 62.3252 > 50: distance: 13 - 17: 13.429 distance: 17 - 18: 12.037 distance: 18 - 21: 9.095 distance: 19 - 20: 13.284 distance: 19 - 25: 12.247 distance: 21 - 22: 13.964 distance: 22 - 23: 9.215 distance: 25 - 26: 5.971 distance: 26 - 27: 7.197 distance: 26 - 29: 9.396 distance: 27 - 28: 25.205 distance: 27 - 32: 7.100 distance: 28 - 55: 15.293 distance: 29 - 30: 4.472 distance: 29 - 31: 14.614 distance: 32 - 33: 7.817 distance: 33 - 34: 5.555 distance: 33 - 36: 15.037 distance: 34 - 35: 6.322 distance: 34 - 39: 11.341 distance: 35 - 66: 35.151 distance: 36 - 37: 25.785 distance: 36 - 38: 16.276 distance: 39 - 40: 6.000 distance: 40 - 41: 7.977 distance: 40 - 43: 8.597 distance: 41 - 42: 4.258 distance: 41 - 47: 6.739 distance: 42 - 77: 44.114 distance: 43 - 44: 3.367 distance: 43 - 45: 6.509 distance: 44 - 46: 17.643 distance: 47 - 48: 3.971 distance: 48 - 49: 9.053 distance: 48 - 51: 14.138 distance: 49 - 50: 5.206 distance: 50 - 83: 37.437 distance: 51 - 52: 15.738 distance: 51 - 53: 20.856 distance: 52 - 54: 7.635 distance: 55 - 56: 5.547 distance: 56 - 57: 11.541 distance: 56 - 59: 11.020 distance: 57 - 58: 35.327 distance: 57 - 66: 29.763 distance: 58 - 91: 18.975 distance: 59 - 60: 6.790 distance: 60 - 61: 14.149 distance: 60 - 62: 5.591 distance: 61 - 63: 7.170 distance: 62 - 64: 10.191 distance: 63 - 65: 6.681 distance: 64 - 65: 11.950 distance: 66 - 67: 31.452 distance: 67 - 68: 18.762 distance: 67 - 70: 16.204 distance: 68 - 69: 5.422 distance: 68 - 77: 10.854 distance: 69 - 99: 21.018 distance: 70 - 71: 20.933 distance: 71 - 72: 35.078 distance: 71 - 73: 25.048 distance: 72 - 74: 7.665 distance: 73 - 75: 9.022 distance: 74 - 76: 32.774 distance: 75 - 76: 31.267 distance: 77 - 78: 8.370 distance: 78 - 79: 9.307 distance: 78 - 81: 17.239 distance: 79 - 80: 4.562 distance: 80 - 106: 21.973 distance: 81 - 82: 7.036 distance: 83 - 84: 9.186 distance: 84 - 85: 12.603 distance: 84 - 87: 7.199 distance: 85 - 86: 16.313 distance: 85 - 91: 6.419 distance: 86 - 111: 30.258 distance: 87 - 88: 12.197 distance: 87 - 89: 10.559 distance: 88 - 90: 4.815 distance: 92 - 93: 14.605 distance: 92 - 95: 13.192 distance: 93 - 94: 8.777 distance: 93 - 99: 6.180 distance: 94 - 115: 8.171 distance: 95 - 96: 14.462 distance: 96 - 97: 19.564 distance: 96 - 98: 21.082 distance: 102 - 119: 3.014