Starting phenix.real_space_refine on Fri Aug 9 10:16:38 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ej3_28174/08_2024/8ej3_28174.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ej3_28174/08_2024/8ej3_28174.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.13 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ej3_28174/08_2024/8ej3_28174.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ej3_28174/08_2024/8ej3_28174.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ej3_28174/08_2024/8ej3_28174.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ej3_28174/08_2024/8ej3_28174.cif" } resolution = 3.13 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= 0.072 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: 7 Type Number sf(0) Gaussians Zn 2 6.06 5 P 81 5.49 5 Mg 2 5.21 5 S 89 5.16 5 C 15625 2.51 5 N 4495 2.21 5 O 5045 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 25339 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 1724 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1724 Classifications: {'peptide': 226} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 211} Chain: "B" Number of atoms: 1765 Number of conformers: 1 Conformer: "" Number of residues, atoms: 237, 1765 Classifications: {'peptide': 237} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 221} Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 43 Unresolved non-hydrogen dihedrals: 27 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 4, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 33 Chain: "C" Number of atoms: 8672 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1121, 8672 Classifications: {'peptide': 1121} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PCIS': 1, 'PTRANS': 60, 'TRANS': 1059} Chain breaks: 1 Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 17 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 17 Chain: "D" Number of atoms: 10010 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1281, 10010 Classifications: {'peptide': 1281} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PCIS': 2, 'PTRANS': 58, 'TRANS': 1220} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 38 Unresolved non-hydrogen dihedrals: 23 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 3, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 18 Chain: "E" Number of atoms: 649 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 649 Classifications: {'peptide': 83} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 76} Chain: "G" Number of atoms: 878 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 110, 869 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 6, 'TRANS': 103} Conformer: "B" Number of residues, atoms: 110, 869 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 6, 'TRANS': 103} bond proxies already assigned to first conformer: 877 Chain: "N" Number of atoms: 587 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 587 Classifications: {'DNA': 29} Link IDs: {'rna3p': 28} Chain breaks: 1 Chain: "R" Number of atoms: 369 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 369 Classifications: {'RNA': 17} Modifications used: {'rna2p_pur': 1, 'rna2p_pyr': 2, 'rna3p_pur': 10, 'rna3p_pyr': 4} Link IDs: {'rna2p': 3, 'rna3p': 13} Chain: "T" Number of atoms: 649 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 649 Classifications: {'DNA': 32} Link IDs: {'rna3p': 31} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'G2P': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' MG': 2, ' ZN': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 19212 SG CYS D 891 76.582 24.483 87.400 1.00 75.64 S ATOM 19779 SG CYS D 968 75.365 27.766 88.957 1.00 66.53 S ATOM 19821 SG CYS D 975 76.805 27.695 85.403 1.00 56.94 S ATOM 19839 SG CYS D 978 73.436 26.161 86.115 1.00 62.19 S ATOM 12668 SG CYS D 62 109.935 82.237 117.046 1.00151.09 S ATOM 12777 SG CYS D 75 110.795 79.173 118.788 1.00146.09 S ATOM 12803 SG CYS D 78 107.470 80.969 119.174 1.00145.63 S Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N AGLU G 15 " occ=0.50 ... (16 atoms not shown) pdb=" OE2BGLU G 15 " occ=0.50 Time building chain proxies: 16.74, per 1000 atoms: 0.66 Number of scatterers: 25339 At special positions: 0 Unit cell: (125.28, 133.11, 200.97, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 2 29.99 S 89 16.00 P 81 15.00 Mg 2 11.99 O 5045 8.00 N 4495 7.00 C 15625 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: 9.74 Conformation dependent library (CDL) restraints added in 5.0 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN D2003 " pdb="ZN ZN D2003 " - pdb=" SG CYS D 978 " pdb="ZN ZN D2003 " - pdb=" SG CYS D 891 " pdb="ZN ZN D2003 " - pdb=" SG CYS D 975 " pdb="ZN ZN D2003 " - pdb=" SG CYS D 968 " pdb=" ZN D2004 " pdb="ZN ZN D2004 " - pdb=" SG CYS D 62 " pdb="ZN ZN D2004 " - pdb=" SG CYS D 75 " pdb="ZN ZN D2004 " - pdb=" SG CYS D 78 " Number of angles added : 6 6094 Ramachandran restraints generated. 3047 Oldfield, 0 Emsley, 3047 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5612 Finding SS restraints... Secondary structure from input PDB file: 108 helices and 42 sheets defined 37.4% alpha, 15.1% beta 29 base pairs and 60 stacking pairs defined. Time for finding SS restraints: 8.31 Creating SS restraints... Processing helix chain 'A' and resid 31 through 43 removed outlier: 3.700A pdb=" N GLY A 35 " --> pdb=" O GLY A 31 " (cutoff:3.500A) Processing helix chain 'A' and resid 72 through 80 Processing helix chain 'A' and resid 151 through 155 Processing helix chain 'A' and resid 205 through 219 removed outlier: 3.763A pdb=" N SER A 210 " --> pdb=" O ASP A 206 " (cutoff:3.500A) Processing helix chain 'A' and resid 222 through 226 Processing helix chain 'B' and resid 34 through 44 Processing helix chain 'B' and resid 73 through 81 Processing helix chain 'B' and resid 154 through 158 Processing helix chain 'B' and resid 203 through 208 removed outlier: 3.833A pdb=" N LEU B 208 " --> pdb=" O PRO B 204 " (cutoff:3.500A) Processing helix chain 'B' and resid 212 through 217 removed outlier: 3.553A pdb=" N VAL B 216 " --> pdb=" O GLY B 212 " (cutoff:3.500A) Processing helix chain 'C' and resid 54 through 66 removed outlier: 4.262A pdb=" N SER C 60 " --> pdb=" O VAL C 56 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N PHE C 61 " --> pdb=" O GLN C 57 " (cutoff:3.500A) Processing helix chain 'C' and resid 67 through 77 removed outlier: 3.778A pdb=" N ARG C 77 " --> pdb=" O SER C 73 " (cutoff:3.500A) Processing helix chain 'C' and resid 86 through 94 Processing helix chain 'C' and resid 118 through 126 Processing helix chain 'C' and resid 226 through 229 Processing helix chain 'C' and resid 234 through 242 Processing helix chain 'C' and resid 244 through 252 Processing helix chain 'C' and resid 255 through 264 Processing helix chain 'C' and resid 269 through 282 removed outlier: 3.730A pdb=" N ARG C 282 " --> pdb=" O TYR C 278 " (cutoff:3.500A) Processing helix chain 'C' and resid 288 through 300 removed outlier: 3.911A pdb=" N PHE C 300 " --> pdb=" O LEU C 296 " (cutoff:3.500A) Processing helix chain 'C' and resid 309 through 317 Processing helix chain 'C' and resid 334 through 351 removed outlier: 3.665A pdb=" N ILE C 342 " --> pdb=" O VAL C 338 " (cutoff:3.500A) Processing helix chain 'C' and resid 380 through 403 removed outlier: 3.780A pdb=" N GLN C 388 " --> pdb=" O LEU C 384 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ARG C 398 " --> pdb=" O SER C 394 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N VAL C 399 " --> pdb=" O ARG C 395 " (cutoff:3.500A) Processing helix chain 'C' and resid 404 through 406 No H-bonds generated for 'chain 'C' and resid 404 through 406' Processing helix chain 'C' and resid 413 through 418 removed outlier: 3.535A pdb=" N LEU C 417 " --> pdb=" O THR C 413 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N ILE C 418 " --> pdb=" O PRO C 414 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 413 through 418' Processing helix chain 'C' and resid 420 through 432 removed outlier: 3.547A pdb=" N VAL C 424 " --> pdb=" O ILE C 420 " (cutoff:3.500A) Processing helix chain 'C' and resid 444 through 452 removed outlier: 3.751A pdb=" N LYS C 452 " --> pdb=" O GLY C 448 " (cutoff:3.500A) Processing helix chain 'C' and resid 476 through 480 removed outlier: 3.907A pdb=" N TYR C 480 " --> pdb=" O PRO C 477 " (cutoff:3.500A) Processing helix chain 'C' and resid 532 through 537 Processing helix chain 'C' and resid 590 through 594 removed outlier: 3.730A pdb=" N MET C 593 " --> pdb=" O ALA C 590 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ILE C 594 " --> pdb=" O THR C 591 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 590 through 594' Processing helix chain 'C' and resid 596 through 600 removed outlier: 3.583A pdb=" N HIS C 599 " --> pdb=" O PHE C 596 " (cutoff:3.500A) Processing helix chain 'C' and resid 601 through 612 Processing helix chain 'C' and resid 613 through 615 No H-bonds generated for 'chain 'C' and resid 613 through 615' Processing helix chain 'C' and resid 632 through 637 removed outlier: 3.568A pdb=" N ILE C 636 " --> pdb=" O LEU C 632 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ASP C 637 " --> pdb=" O ARG C 633 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 632 through 637' Processing helix chain 'C' and resid 739 through 744 Processing helix chain 'C' and resid 900 through 904 removed outlier: 3.581A pdb=" N MET C 904 " --> pdb=" O VAL C 901 " (cutoff:3.500A) Processing helix chain 'C' and resid 928 through 943 removed outlier: 3.544A pdb=" N LEU C 932 " --> pdb=" O ILE C 928 " (cutoff:3.500A) Processing helix chain 'C' and resid 953 through 957 removed outlier: 3.538A pdb=" N ALA C 957 " --> pdb=" O ASP C 954 " (cutoff:3.500A) Processing helix chain 'C' and resid 981 through 989 Processing helix chain 'C' and resid 1036 through 1040 removed outlier: 3.525A pdb=" N LYS C1040 " --> pdb=" O VAL C1037 " (cutoff:3.500A) Processing helix chain 'C' and resid 1069 through 1080 removed outlier: 3.541A pdb=" N CYS C1073 " --> pdb=" O GLY C1069 " (cutoff:3.500A) Processing helix chain 'C' and resid 1081 through 1090 removed outlier: 3.853A pdb=" N LEU C1085 " --> pdb=" O ALA C1081 " (cutoff:3.500A) Processing helix chain 'C' and resid 1095 through 1109 removed outlier: 4.654A pdb=" N VAL C1100 " --> pdb=" O THR C1096 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N LYS C1101 " --> pdb=" O VAL C1097 " (cutoff:3.500A) Processing helix chain 'C' and resid 1119 through 1131 Processing helix chain 'D' and resid 3 through 7 Processing helix chain 'D' and resid 16 through 24 Processing helix chain 'D' and resid 48 through 53 Processing helix chain 'D' and resid 67 through 71 Processing helix chain 'D' and resid 84 through 90 removed outlier: 3.831A pdb=" N VAL D 87 " --> pdb=" O ARG D 84 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ARG D 88 " --> pdb=" O ALA D 85 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ARG D 89 " --> pdb=" O LYS D 86 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLU D 90 " --> pdb=" O VAL D 87 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 84 through 90' Processing helix chain 'D' and resid 114 through 119 Processing helix chain 'D' and resid 121 through 130 Processing helix chain 'D' and resid 140 through 146 removed outlier: 4.046A pdb=" N ARG D 144 " --> pdb=" O ASP D 140 " (cutoff:3.500A) Processing helix chain 'D' and resid 147 through 185 removed outlier: 3.898A pdb=" N ALA D 161 " --> pdb=" O VAL D 157 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N VAL D 162 " --> pdb=" O GLU D 158 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N GLU D 163 " --> pdb=" O ARG D 159 " (cutoff:3.500A) Processing helix chain 'D' and resid 190 through 229 removed outlier: 4.324A pdb=" N LYS D 196 " --> pdb=" O ASP D 192 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N GLY D 201 " --> pdb=" O VAL D 197 " (cutoff:3.500A) Processing helix chain 'D' and resid 237 through 248 removed outlier: 3.700A pdb=" N TYR D 241 " --> pdb=" O ASP D 237 " (cutoff:3.500A) Processing helix chain 'D' and resid 257 through 267 removed outlier: 3.608A pdb=" N ASN D 267 " --> pdb=" O LYS D 263 " (cutoff:3.500A) Processing helix chain 'D' and resid 269 through 283 removed outlier: 3.650A pdb=" N GLU D 273 " --> pdb=" O ASP D 269 " (cutoff:3.500A) Processing helix chain 'D' and resid 286 through 305 removed outlier: 4.234A pdb=" N LEU D 290 " --> pdb=" O GLY D 286 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N VAL D 298 " --> pdb=" O LYS D 294 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N ALA D 301 " --> pdb=" O LYS D 297 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N SER D 305 " --> pdb=" O ALA D 301 " (cutoff:3.500A) Processing helix chain 'D' and resid 321 through 325 Processing helix chain 'D' and resid 339 through 361 removed outlier: 3.841A pdb=" N LEU D 343 " --> pdb=" O ASP D 339 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N TYR D 344 " --> pdb=" O LEU D 340 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ARG D 345 " --> pdb=" O ASN D 341 " (cutoff:3.500A) Processing helix chain 'D' and resid 363 through 383 removed outlier: 3.564A pdb=" N VAL D 367 " --> pdb=" O PRO D 363 " (cutoff:3.500A) Processing helix chain 'D' and resid 401 through 406 removed outlier: 3.930A pdb=" N LEU D 406 " --> pdb=" O SER D 403 " (cutoff:3.500A) Processing helix chain 'D' and resid 411 through 416 Processing helix chain 'D' and resid 445 through 452 Processing helix chain 'D' and resid 452 through 463 Processing helix chain 'D' and resid 468 through 478 Processing helix chain 'D' and resid 480 through 482 No H-bonds generated for 'chain 'D' and resid 480 through 482' Processing helix chain 'D' and resid 483 through 491 removed outlier: 3.634A pdb=" N LEU D 487 " --> pdb=" O VAL D 483 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N GLU D 488 " --> pdb=" O TRP D 484 " (cutoff:3.500A) removed outlier: 4.653A pdb=" N GLU D 489 " --> pdb=" O ASP D 485 " (cutoff:3.500A) Processing helix chain 'D' and resid 505 through 507 No H-bonds generated for 'chain 'D' and resid 505 through 507' Processing helix chain 'D' and resid 525 through 529 removed outlier: 3.603A pdb=" N CYS D 529 " --> pdb=" O PRO D 526 " (cutoff:3.500A) Processing helix chain 'D' and resid 548 through 558 Processing helix chain 'D' and resid 579 through 589 Processing helix chain 'D' and resid 614 through 625 removed outlier: 3.527A pdb=" N ARG D 624 " --> pdb=" O MET D 620 " (cutoff:3.500A) Processing helix chain 'D' and resid 643 through 651 Processing helix chain 'D' and resid 656 through 660 removed outlier: 3.667A pdb=" N GLY D 659 " --> pdb=" O TRP D 656 " (cutoff:3.500A) Processing helix chain 'D' and resid 667 through 675 Processing helix chain 'D' and resid 689 through 704 Processing helix chain 'D' and resid 705 through 728 removed outlier: 3.958A pdb=" N ASP D 714 " --> pdb=" O ALA D 710 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N LYS D 715 " --> pdb=" O GLN D 711 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N THR D 725 " --> pdb=" O PHE D 721 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N ARG D 726 " --> pdb=" O TYR D 722 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N GLY D 728 " --> pdb=" O ALA D 724 " (cutoff:3.500A) Processing helix chain 'D' and resid 742 through 763 removed outlier: 3.767A pdb=" N LYS D 755 " --> pdb=" O GLU D 751 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N VAL D 756 " --> pdb=" O ARG D 752 " (cutoff:3.500A) Processing helix chain 'D' and resid 766 through 793 removed outlier: 3.621A pdb=" N GLU D 776 " --> pdb=" O GLU D 772 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ASP D 783 " --> pdb=" O LYS D 779 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N GLU D 791 " --> pdb=" O GLN D 787 " (cutoff:3.500A) Processing helix chain 'D' and resid 797 through 805 removed outlier: 3.637A pdb=" N VAL D 803 " --> pdb=" O ILE D 799 " (cutoff:3.500A) Processing helix chain 'D' and resid 810 through 819 removed outlier: 3.744A pdb=" N THR D 814 " --> pdb=" O ASN D 810 " (cutoff:3.500A) Processing helix chain 'D' and resid 845 through 851 Processing helix chain 'D' and resid 853 through 858 removed outlier: 3.736A pdb=" N ARG D 857 " --> pdb=" O THR D 853 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N LYS D 858 " --> pdb=" O HIS D 854 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 853 through 858' Processing helix chain 'D' and resid 867 through 881 removed outlier: 3.696A pdb=" N LEU D 873 " --> pdb=" O ASP D 869 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N SER D 881 " --> pdb=" O LEU D 877 " (cutoff:3.500A) Processing helix chain 'D' and resid 945 through 956 Processing helix chain 'D' and resid 964 through 968 removed outlier: 3.619A pdb=" N THR D 967 " --> pdb=" O SER D 964 " (cutoff:3.500A) Processing helix chain 'D' and resid 976 through 980 Processing helix chain 'D' and resid 994 through 1013 removed outlier: 3.881A pdb=" N VAL D 998 " --> pdb=" O ALA D 994 " (cutoff:3.500A) Proline residue: D1006 - end of helix Processing helix chain 'D' and resid 1023 through 1037 Proline residue: D1029 - end of helix Processing helix chain 'D' and resid 1117 through 1125 Processing helix chain 'D' and resid 1126 through 1145 removed outlier: 3.871A pdb=" N VAL D1141 " --> pdb=" O GLU D1137 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N TYR D1142 " --> pdb=" O VAL D1138 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N GLN D1145 " --> pdb=" O VAL D1141 " (cutoff:3.500A) Processing helix chain 'D' and resid 1151 through 1162 removed outlier: 3.970A pdb=" N VAL D1156 " --> pdb=" O LYS D1152 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N ILE D1157 " --> pdb=" O HIS D1153 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LEU D1162 " --> pdb=" O VAL D1158 " (cutoff:3.500A) Processing helix chain 'D' and resid 1170 through 1174 removed outlier: 4.267A pdb=" N GLU D1174 " --> pdb=" O GLY D1171 " (cutoff:3.500A) Processing helix chain 'D' and resid 1183 through 1195 Processing helix chain 'D' and resid 1219 through 1227 removed outlier: 3.830A pdb=" N ALA D1223 " --> pdb=" O SER D1219 " (cutoff:3.500A) Processing helix chain 'D' and resid 1228 through 1240 Processing helix chain 'D' and resid 1247 through 1255 Processing helix chain 'D' and resid 1260 through 1263 removed outlier: 3.760A pdb=" N GLY D1263 " --> pdb=" O ALA D1260 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 1260 through 1263' Processing helix chain 'D' and resid 1264 through 1269 Processing helix chain 'D' and resid 1275 through 1282 Processing helix chain 'E' and resid 33 through 37 removed outlier: 3.574A pdb=" N THR E 36 " --> pdb=" O LEU E 33 " (cutoff:3.500A) Processing helix chain 'E' and resid 39 through 44 Processing helix chain 'E' and resid 49 through 70 removed outlier: 3.921A pdb=" N LEU E 53 " --> pdb=" O SER E 49 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N VAL E 54 " --> pdb=" O LYS E 50 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N ILE E 55 " --> pdb=" O TYR E 51 " (cutoff:3.500A) Processing helix chain 'E' and resid 90 through 101 Processing helix chain 'G' and resid 14 through 29 removed outlier: 3.721A pdb=" N GLU G 23 " --> pdb=" O LYS G 19 " (cutoff:3.500A) Processing helix chain 'G' and resid 73 through 81 Processing helix chain 'G' and resid 106 through 111 Processing sheet with id=AA1, first strand: chain 'A' and resid 18 through 26 removed outlier: 5.823A pdb=" N ASP A 190 " --> pdb=" O PRO A 25 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N LYS A 191 " --> pdb=" O ASP A 179 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N LYS A 173 " --> pdb=" O GLU A 197 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 93 through 100 removed outlier: 7.352A pdb=" N GLU A 135 " --> pdb=" O ILE A 56 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N ILE A 56 " --> pdb=" O GLU A 135 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N GLU A 137 " --> pdb=" O ILE A 54 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N ILE A 54 " --> pdb=" O GLU A 137 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N VAL A 139 " --> pdb=" O THR A 52 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 85 through 87 Processing sheet with id=AA4, first strand: chain 'A' and resid 103 through 105 removed outlier: 3.965A pdb=" N GLY A 103 " --> pdb=" O LEU A 128 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 146 through 147 Processing sheet with id=AA6, first strand: chain 'B' and resid 8 through 11 removed outlier: 3.599A pdb=" N VAL B 22 " --> pdb=" O SER B 10 " (cutoff:3.500A) removed outlier: 6.074A pdb=" N ASP B 190 " --> pdb=" O PRO B 25 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 8 through 11 removed outlier: 3.599A pdb=" N VAL B 22 " --> pdb=" O SER B 10 " (cutoff:3.500A) removed outlier: 6.074A pdb=" N ASP B 190 " --> pdb=" O PRO B 25 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 93 through 97 removed outlier: 3.821A pdb=" N VAL B 93 " --> pdb=" O VAL B 140 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N GLU B 137 " --> pdb=" O ILE B 54 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N ILE B 54 " --> pdb=" O GLU B 137 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N VAL B 139 " --> pdb=" O THR B 52 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 85 through 86 Processing sheet with id=AB1, first strand: chain 'B' and resid 103 through 106 Processing sheet with id=AB2, first strand: chain 'B' and resid 146 through 147 Processing sheet with id=AB3, first strand: chain 'C' and resid 39 through 40 removed outlier: 6.584A pdb=" N VAL C 39 " --> pdb=" O SER C 973 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 96 through 97 removed outlier: 6.682A pdb=" N PHE C 134 " --> pdb=" O PRO C 110 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N PHE C 112 " --> pdb=" O PRO C 132 " (cutoff:3.500A) removed outlier: 5.877A pdb=" N ALA C 131 " --> pdb=" O ASP C 156 " (cutoff:3.500A) removed outlier: 4.846A pdb=" N ASP C 156 " --> pdb=" O ALA C 131 " (cutoff:3.500A) removed outlier: 5.997A pdb=" N LEU C 133 " --> pdb=" O MET C 154 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LYS C 148 " --> pdb=" O PHE C 139 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 166 through 168 Processing sheet with id=AB6, first strand: chain 'C' and resid 376 through 379 removed outlier: 3.606A pdb=" N SER C 177 " --> pdb=" O ARG C 454 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 184 through 185 Processing sheet with id=AB8, first strand: chain 'C' and resid 188 through 189 Processing sheet with id=AB9, first strand: chain 'C' and resid 214 through 215 Processing sheet with id=AC1, first strand: chain 'C' and resid 354 through 355 removed outlier: 3.758A pdb=" N MET C 355 " --> pdb=" O VAL C 363 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 505 through 506 removed outlier: 5.331A pdb=" N GLU C 527 " --> pdb=" O LYS C 518 " (cutoff:3.500A) removed outlier: 7.498A pdb=" N VAL C 520 " --> pdb=" O SER C 525 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N SER C 525 " --> pdb=" O VAL C 520 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 505 through 506 removed outlier: 3.791A pdb=" N ASP C 580 " --> pdb=" O ALA C 542 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N GLU C 569 " --> pdb=" O VAL C 561 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 642 through 643 removed outlier: 6.596A pdb=" N VAL C 642 " --> pdb=" O ILE C 702 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 667 through 671 removed outlier: 7.083A pdb=" N TYR C 657 " --> pdb=" O VAL C 653 " (cutoff:3.500A) removed outlier: 5.095A pdb=" N VAL C 653 " --> pdb=" O TYR C 657 " (cutoff:3.500A) removed outlier: 7.062A pdb=" N THR C 659 " --> pdb=" O GLU C 651 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 676 through 677 Processing sheet with id=AC7, first strand: chain 'C' and resid 708 through 709 Processing sheet with id=AC8, first strand: chain 'C' and resid 1007 through 1008 removed outlier: 6.678A pdb=" N ILE C 735 " --> pdb=" O LYS C 897 " (cutoff:3.500A) removed outlier: 7.879A pdb=" N LEU C 899 " --> pdb=" O ILE C 735 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N LEU C 737 " --> pdb=" O LEU C 899 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ILE C 736 " --> pdb=" O ILE C 916 " (cutoff:3.500A) removed outlier: 8.807A pdb=" N ILE C 915 " --> pdb=" O ASN C 718 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N LEU C 720 " --> pdb=" O ILE C 915 " (cutoff:3.500A) removed outlier: 7.736A pdb=" N LEU C 917 " --> pdb=" O LEU C 720 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N ALA C 722 " --> pdb=" O LEU C 917 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N THR C1024 " --> pdb=" O ILE C 723 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 765 through 766 removed outlier: 3.525A pdb=" N THR C 762 " --> pdb=" O GLY C 765 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N GLU C 867 " --> pdb=" O ALA C 759 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N ASP C 761 " --> pdb=" O VAL C 865 " (cutoff:3.500A) removed outlier: 7.382A pdb=" N VAL C 865 " --> pdb=" O ASP C 761 " (cutoff:3.500A) removed outlier: 8.080A pdb=" N ASN C 866 " --> pdb=" O SER C 854 " (cutoff:3.500A) removed outlier: 5.033A pdb=" N SER C 854 " --> pdb=" O ASN C 866 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N LEU C 868 " --> pdb=" O VAL C 852 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N VAL C 852 " --> pdb=" O LEU C 868 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N ARG C 870 " --> pdb=" O ILE C 850 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N ILE C 850 " --> pdb=" O ARG C 870 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N TYR C 872 " --> pdb=" O ILE C 848 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 768 through 769 removed outlier: 3.805A pdb=" N GLU C 768 " --> pdb=" O VAL C 806 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N VAL C 806 " --> pdb=" O GLU C 768 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD1 Processing sheet with id=AD2, first strand: chain 'C' and resid 801 through 803 removed outlier: 6.512A pdb=" N LEU C 837 " --> pdb=" O LEU C 802 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 1042 through 1044 removed outlier: 3.522A pdb=" N SER D 428 " --> pdb=" O MET D 541 " (cutoff:3.500A) removed outlier: 7.964A pdb=" N ALA D 521 " --> pdb=" O PRO D 444 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 1066 through 1068 removed outlier: 3.806A pdb=" N GLN C1066 " --> pdb=" O VAL D 422 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 1136 through 1138 removed outlier: 3.887A pdb=" N GLU D 9 " --> pdb=" O LEU C1138 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'D' and resid 93 through 102 removed outlier: 7.047A pdb=" N ASP D 315 " --> pdb=" O LEU D 97 " (cutoff:3.500A) removed outlier: 11.028A pdb=" N ALA D 99 " --> pdb=" O VAL D 313 " (cutoff:3.500A) removed outlier: 10.247A pdb=" N VAL D 313 " --> pdb=" O ALA D 99 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'D' and resid 234 through 235 removed outlier: 7.303A pdb=" N THR D 253 " --> pdb=" O THR D 137 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'D' and resid 633 through 637 Processing sheet with id=AD9, first strand: chain 'D' and resid 886 through 888 Processing sheet with id=AE1, first strand: chain 'D' and resid 897 through 899 removed outlier: 3.937A pdb=" N VAL D 960 " --> pdb=" O VAL D 899 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'D' and resid 903 through 904 Processing sheet with id=AE3, first strand: chain 'D' and resid 1051 through 1052 removed outlier: 3.995A pdb=" N ARG D1052 " --> pdb=" O VAL D1067 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N VAL D1067 " --> pdb=" O ARG D1052 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE3 Processing sheet with id=AE4, first strand: chain 'D' and resid 1180 through 1182 removed outlier: 7.264A pdb=" N ALA D1202 " --> pdb=" O ILE D1168 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'D' and resid 1270 through 1274 removed outlier: 3.602A pdb=" N ALA D1271 " --> pdb=" O THR E 107 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'G' and resid 38 through 39 removed outlier: 7.744A pdb=" N VAL G 7 " --> pdb=" O PHE G 88 " (cutoff:3.500A) removed outlier: 5.262A pdb=" N PHE G 88 " --> pdb=" O VAL G 7 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N HIS G 9 " --> pdb=" O THR G 86 " (cutoff:3.500A) 887 hydrogen bonds defined for protein. 2463 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 78 hydrogen bonds 156 hydrogen bond angles 0 basepair planarities 29 basepair parallelities 60 stacking parallelities Total time for adding SS restraints: 11.28 Time building geometry restraints manager: 10.76 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 5409 1.33 - 1.46: 7590 1.46 - 1.59: 12620 1.59 - 1.72: 155 1.72 - 1.85: 159 Bond restraints: 25933 Sorted by residual: bond pdb=" C1' G2P C1201 " pdb=" O4' G2P C1201 " ideal model delta sigma weight residual 1.389 1.603 -0.214 2.00e-02 2.50e+03 1.14e+02 bond pdb=" C1' G2P C1201 " pdb=" C2' G2P C1201 " ideal model delta sigma weight residual 1.537 1.341 0.196 2.00e-02 2.50e+03 9.61e+01 bond pdb=" C2 G2P C1201 " pdb=" N3 G2P C1201 " ideal model delta sigma weight residual 1.305 1.460 -0.155 2.00e-02 2.50e+03 6.02e+01 bond pdb=" C4 G2P C1201 " pdb=" N3 G2P C1201 " ideal model delta sigma weight residual 1.345 1.492 -0.147 2.00e-02 2.50e+03 5.38e+01 bond pdb=" C5 G2P C1201 " pdb=" C6 G2P C1201 " ideal model delta sigma weight residual 1.420 1.550 -0.130 2.00e-02 2.50e+03 4.22e+01 ... (remaining 25928 not shown) Histogram of bond angle deviations from ideal: 99.32 - 106.26: 1182 106.26 - 113.20: 14118 113.20 - 120.14: 9188 120.14 - 127.08: 10602 127.08 - 134.02: 386 Bond angle restraints: 35476 Sorted by residual: angle pdb=" CA PRO D1029 " pdb=" N PRO D1029 " pdb=" CD PRO D1029 " ideal model delta sigma weight residual 112.00 105.41 6.59 1.40e+00 5.10e-01 2.22e+01 angle pdb=" C3A G2P C1201 " pdb=" PB G2P C1201 " pdb=" O3B G2P C1201 " ideal model delta sigma weight residual 99.71 110.23 -10.52 3.00e+00 1.11e-01 1.23e+01 angle pdb=" C3A G2P C1201 " pdb=" PA G2P C1201 " pdb=" O5' G2P C1201 " ideal model delta sigma weight residual 99.14 109.27 -10.13 3.00e+00 1.11e-01 1.14e+01 angle pdb=" C5 G2P C1201 " pdb=" C6 G2P C1201 " pdb=" N1 G2P C1201 " ideal model delta sigma weight residual 110.74 120.13 -9.39 3.00e+00 1.11e-01 9.80e+00 angle pdb=" N TYR D 793 " pdb=" CA TYR D 793 " pdb=" C TYR D 793 " ideal model delta sigma weight residual 109.57 113.26 -3.69 1.23e+00 6.61e-01 8.98e+00 ... (remaining 35471 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.31: 14293 35.31 - 70.62: 1345 70.62 - 105.93: 59 105.93 - 141.25: 1 141.25 - 176.56: 2 Dihedral angle restraints: 15700 sinusoidal: 6959 harmonic: 8741 Sorted by residual: dihedral pdb=" O4' A R 21 " pdb=" C1' A R 21 " pdb=" N9 A R 21 " pdb=" C4 A R 21 " ideal model delta sinusoidal sigma weight residual 254.00 164.62 89.38 1 1.70e+01 3.46e-03 3.29e+01 dihedral pdb=" C4' DC T 23 " pdb=" C3' DC T 23 " pdb=" O3' DC T 23 " pdb=" P DA T 24 " ideal model delta sinusoidal sigma weight residual -140.00 36.56 -176.56 1 3.50e+01 8.16e-04 1.57e+01 dihedral pdb=" O4' U R 15 " pdb=" C1' U R 15 " pdb=" N1 U R 15 " pdb=" C2 U R 15 " ideal model delta sinusoidal sigma weight residual -128.00 -72.32 -55.68 1 1.70e+01 3.46e-03 1.45e+01 ... (remaining 15697 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 2625 0.035 - 0.070: 953 0.070 - 0.105: 344 0.105 - 0.140: 119 0.140 - 0.175: 7 Chirality restraints: 4048 Sorted by residual: chirality pdb=" CA LEU D1028 " pdb=" N LEU D1028 " pdb=" C LEU D1028 " pdb=" CB LEU D1028 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.18 2.00e-01 2.50e+01 7.66e-01 chirality pdb=" CA ASP C 903 " pdb=" N ASP C 903 " pdb=" C ASP C 903 " pdb=" CB ASP C 903 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.42e-01 chirality pdb=" CB VAL G 40 " pdb=" CA VAL G 40 " pdb=" CG1 VAL G 40 " pdb=" CG2 VAL G 40 " both_signs ideal model delta sigma weight residual False -2.63 -2.47 -0.16 2.00e-01 2.50e+01 6.15e-01 ... (remaining 4045 not shown) Planarity restraints: 4391 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU D 746 " -0.016 2.00e-02 2.50e+03 3.17e-02 1.00e+01 pdb=" C LEU D 746 " 0.055 2.00e-02 2.50e+03 pdb=" O LEU D 746 " -0.020 2.00e-02 2.50e+03 pdb=" N ASP D 747 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU D1028 " 0.049 5.00e-02 4.00e+02 7.23e-02 8.36e+00 pdb=" N PRO D1029 " -0.125 5.00e-02 4.00e+02 pdb=" CA PRO D1029 " 0.036 5.00e-02 4.00e+02 pdb=" CD PRO D1029 " 0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASP B 206 " 0.014 2.00e-02 2.50e+03 2.88e-02 8.28e+00 pdb=" C ASP B 206 " -0.050 2.00e-02 2.50e+03 pdb=" O ASP B 206 " 0.019 2.00e-02 2.50e+03 pdb=" N ALA B 207 " 0.017 2.00e-02 2.50e+03 ... (remaining 4388 not shown) Histogram of nonbonded interaction distances: 2.02 - 2.60: 163 2.60 - 3.17: 19194 3.17 - 3.75: 36656 3.75 - 4.32: 50647 4.32 - 4.90: 86088 Nonbonded interactions: 192748 Sorted by model distance: nonbonded pdb=" O1B G2P C1201 " pdb="MG MG D2002 " model vdw 2.022 2.170 nonbonded pdb=" OD2 ASP D 535 " pdb="MG MG D2001 " model vdw 2.059 2.170 nonbonded pdb=" OD1 ASP D 535 " pdb="MG MG D2001 " model vdw 2.171 2.170 nonbonded pdb=" O SER B 37 " pdb=" OG1 THR B 41 " model vdw 2.195 3.040 nonbonded pdb=" OD1 ASP C 909 " pdb=" OG1 THR C 911 " model vdw 2.216 3.040 ... (remaining 192743 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 1 through 99 or (resid 100 and (name N or name CA or name \ C or name O or name CB )) or resid 101 through 129 or (resid 130 and (name N or \ name CA or name C or name O or name CB )) or resid 131 through 134 or (resid 135 \ and (name N or name CA or name C or name O or name CB )) or resid 136 through 1 \ 52 or (resid 153 through 154 and (name N or name CA or name C or name O or name \ CB )) or resid 155 through 157 or (resid 158 and (name N or name CA or name C or \ name O or name CB )) or resid 159 through 160 or (resid 161 and (name N or name \ CA or name C or name O or name CB )) or resid 162 through 183 or (resid 184 and \ (name N or name CA or name C or name O or name CB )) or resid 185 through 223 o \ r (resid 224 and (name N or name CA or name C or name O or name CB )) or resid 2 \ 25 through 226)) selection = (chain 'B' and resid 1 through 226) } 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=0.50 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: 8.460 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: 0.060 Extract box with map and model: 1.090 Check model and map are aligned: 0.200 Set scattering table: 0.260 Process input model: 82.000 Find NCS groups from input model: 0.520 Set up NCS constraints: 0.100 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:3.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 95.770 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8821 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 0.214 25933 Z= 0.291 Angle : 0.637 10.520 35476 Z= 0.338 Chirality : 0.043 0.175 4048 Planarity : 0.006 0.072 4391 Dihedral : 22.389 176.557 10088 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.89 % Allowed : 9.20 % Favored : 89.91 % Rotamer: Outliers : 15.79 % Allowed : 23.46 % Favored : 60.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.32 % 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: -2.87 (0.14), residues: 3047 helix: -1.23 (0.16), residues: 1018 sheet: -1.39 (0.25), residues: 410 loop : -2.55 (0.13), residues: 1619 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 223 HIS 0.009 0.001 HIS C 889 PHE 0.019 0.001 PHE C 439 TYR 0.016 0.001 TYR D 344 ARG 0.006 0.000 ARG E 46 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6094 Ramachandran restraints generated. 3047 Oldfield, 0 Emsley, 3047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6094 Ramachandran restraints generated. 3047 Oldfield, 0 Emsley, 3047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 565 residues out of total 2580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 404 poor density : 161 time to evaluate : 3.142 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 14 LEU cc_start: 0.8877 (OUTLIER) cc_final: 0.8616 (mt) REVERT: A 91 GLU cc_start: 0.8214 (OUTLIER) cc_final: 0.7967 (pm20) REVERT: A 151 GLN cc_start: 0.7984 (OUTLIER) cc_final: 0.7586 (mm-40) REVERT: B 55 ARG cc_start: 0.8846 (OUTLIER) cc_final: 0.8605 (ttm170) REVERT: B 105 VAL cc_start: 0.9219 (OUTLIER) cc_final: 0.8789 (m) REVERT: B 133 LYS cc_start: 0.8919 (OUTLIER) cc_final: 0.8695 (mmtt) REVERT: B 218 LEU cc_start: 0.9406 (OUTLIER) cc_final: 0.8953 (tt) REVERT: C 201 SER cc_start: 0.9152 (OUTLIER) cc_final: 0.8853 (p) REVERT: C 213 GLU cc_start: 0.8350 (OUTLIER) cc_final: 0.7479 (tm-30) REVERT: C 251 ARG cc_start: 0.8789 (OUTLIER) cc_final: 0.8331 (ttt180) REVERT: C 267 THR cc_start: 0.7848 (OUTLIER) cc_final: 0.7647 (p) REVERT: C 275 LEU cc_start: 0.9377 (tp) cc_final: 0.8364 (pp) REVERT: C 297 GLU cc_start: 0.7297 (OUTLIER) cc_final: 0.6902 (mp0) REVERT: C 304 LYS cc_start: 0.8807 (OUTLIER) cc_final: 0.8071 (tppp) REVERT: C 758 ASP cc_start: 0.8685 (OUTLIER) cc_final: 0.8428 (p0) REVERT: C 761 ASP cc_start: 0.9050 (OUTLIER) cc_final: 0.8812 (m-30) REVERT: C 773 ILE cc_start: 0.9434 (OUTLIER) cc_final: 0.9217 (mm) REVERT: C 805 LYS cc_start: 0.9015 (OUTLIER) cc_final: 0.8537 (ttpp) REVERT: C 1164 ILE cc_start: 0.5794 (OUTLIER) cc_final: 0.5593 (mt) REVERT: D 151 LEU cc_start: 0.9065 (OUTLIER) cc_final: 0.8635 (mt) REVERT: D 243 GLU cc_start: 0.8842 (OUTLIER) cc_final: 0.8564 (mp0) REVERT: D 1050 THR cc_start: 0.8195 (OUTLIER) cc_final: 0.7352 (t) REVERT: D 1107 VAL cc_start: 0.9164 (OUTLIER) cc_final: 0.8861 (p) REVERT: E 70 GLN cc_start: 0.8699 (tp40) cc_final: 0.8104 (tp40) REVERT: G 12 SER cc_start: 0.8395 (OUTLIER) cc_final: 0.8003 (p) REVERT: G 16 ASN cc_start: 0.9160 (OUTLIER) cc_final: 0.8707 (m-40) REVERT: G 31 MET cc_start: 0.7696 (mmp) cc_final: 0.7416 (mmp) REVERT: G 43 GLU cc_start: 0.7875 (OUTLIER) cc_final: 0.6501 (tp30) REVERT: G 57 LYS cc_start: 0.7431 (OUTLIER) cc_final: 0.7221 (pttt) outliers start: 404 outliers final: 114 residues processed: 528 average time/residue: 0.4497 time to fit residues: 351.2675 Evaluate side-chains 271 residues out of total 2580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 140 poor density : 131 time to evaluate : 2.922 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 SER Chi-restraints excluded: chain A residue 14 LEU Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 53 SER Chi-restraints excluded: chain A residue 56 ILE Chi-restraints excluded: chain A residue 62 GLU Chi-restraints excluded: chain A residue 72 ASP Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 90 ASP Chi-restraints excluded: chain A residue 91 GLU Chi-restraints excluded: chain A residue 120 ASN Chi-restraints excluded: chain A residue 123 MET Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 151 GLN Chi-restraints excluded: chain A residue 158 GLU Chi-restraints excluded: chain A residue 166 SER Chi-restraints excluded: chain A residue 205 ARG Chi-restraints excluded: chain A residue 217 GLU Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain B residue 3 ILE Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 46 ILE Chi-restraints excluded: chain B residue 55 ARG Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 72 ASP Chi-restraints excluded: chain B residue 90 ASP Chi-restraints excluded: chain B residue 105 VAL Chi-restraints excluded: chain B residue 109 ASP Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain B residue 127 THR Chi-restraints excluded: chain B residue 133 LYS Chi-restraints excluded: chain B residue 142 ARG Chi-restraints excluded: chain B residue 159 ILE Chi-restraints excluded: chain B residue 166 SER Chi-restraints excluded: chain B residue 175 THR Chi-restraints excluded: chain B residue 186 ARG Chi-restraints excluded: chain B residue 203 SER Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain C residue 151 THR Chi-restraints excluded: chain C residue 185 VAL Chi-restraints excluded: chain C residue 191 ILE Chi-restraints excluded: chain C residue 194 SER Chi-restraints excluded: chain C residue 201 SER Chi-restraints excluded: chain C residue 213 GLU Chi-restraints excluded: chain C residue 219 ARG Chi-restraints excluded: chain C residue 229 LYS Chi-restraints excluded: chain C residue 236 VAL Chi-restraints excluded: chain C residue 237 LEU Chi-restraints excluded: chain C residue 251 ARG Chi-restraints excluded: chain C residue 259 ARG Chi-restraints excluded: chain C residue 267 THR Chi-restraints excluded: chain C residue 270 THR Chi-restraints excluded: chain C residue 271 ASP Chi-restraints excluded: chain C residue 281 LEU Chi-restraints excluded: chain C residue 295 LEU Chi-restraints excluded: chain C residue 297 GLU Chi-restraints excluded: chain C residue 302 LYS Chi-restraints excluded: chain C residue 304 LYS Chi-restraints excluded: chain C residue 311 VAL Chi-restraints excluded: chain C residue 322 LEU Chi-restraints excluded: chain C residue 354 THR Chi-restraints excluded: chain C residue 366 GLU Chi-restraints excluded: chain C residue 367 THR Chi-restraints excluded: chain C residue 519 VAL Chi-restraints excluded: chain C residue 577 ASP Chi-restraints excluded: chain C residue 626 VAL Chi-restraints excluded: chain C residue 647 SER Chi-restraints excluded: chain C residue 702 ILE Chi-restraints excluded: chain C residue 757 ILE Chi-restraints excluded: chain C residue 758 ASP Chi-restraints excluded: chain C residue 761 ASP Chi-restraints excluded: chain C residue 762 THR Chi-restraints excluded: chain C residue 773 ILE Chi-restraints excluded: chain C residue 776 ILE Chi-restraints excluded: chain C residue 777 SER Chi-restraints excluded: chain C residue 780 VAL Chi-restraints excluded: chain C residue 789 ILE Chi-restraints excluded: chain C residue 803 VAL Chi-restraints excluded: chain C residue 805 LYS Chi-restraints excluded: chain C residue 806 VAL Chi-restraints excluded: chain C residue 847 VAL Chi-restraints excluded: chain C residue 850 ILE Chi-restraints excluded: chain C residue 891 ASN Chi-restraints excluded: chain C residue 898 ILE Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 992 THR Chi-restraints excluded: chain C residue 1107 VAL Chi-restraints excluded: chain C residue 1125 LEU Chi-restraints excluded: chain C residue 1147 LEU Chi-restraints excluded: chain C residue 1149 GLU Chi-restraints excluded: chain C residue 1154 ASP Chi-restraints excluded: chain C residue 1155 LEU Chi-restraints excluded: chain C residue 1162 LEU Chi-restraints excluded: chain C residue 1164 ILE Chi-restraints excluded: chain C residue 1167 SER Chi-restraints excluded: chain D residue 60 CYS Chi-restraints excluded: chain D residue 80 VAL Chi-restraints excluded: chain D residue 138 SER Chi-restraints excluded: chain D residue 149 SER Chi-restraints excluded: chain D residue 151 LEU Chi-restraints excluded: chain D residue 160 LYS Chi-restraints excluded: chain D residue 165 GLN Chi-restraints excluded: chain D residue 195 ARG Chi-restraints excluded: chain D residue 198 ARG Chi-restraints excluded: chain D residue 243 GLU Chi-restraints excluded: chain D residue 244 LEU Chi-restraints excluded: chain D residue 252 PHE Chi-restraints excluded: chain D residue 253 THR Chi-restraints excluded: chain D residue 320 ILE Chi-restraints excluded: chain D residue 468 ASN Chi-restraints excluded: chain D residue 486 VAL Chi-restraints excluded: chain D residue 738 VAL Chi-restraints excluded: chain D residue 775 VAL Chi-restraints excluded: chain D residue 796 ASP Chi-restraints excluded: chain D residue 866 ARG Chi-restraints excluded: chain D residue 966 LEU Chi-restraints excluded: chain D residue 997 ILE Chi-restraints excluded: chain D residue 1028 LEU Chi-restraints excluded: chain D residue 1046 ILE Chi-restraints excluded: chain D residue 1050 THR Chi-restraints excluded: chain D residue 1053 VAL Chi-restraints excluded: chain D residue 1060 ARG Chi-restraints excluded: chain D residue 1064 ILE Chi-restraints excluded: chain D residue 1080 ILE Chi-restraints excluded: chain D residue 1100 SER Chi-restraints excluded: chain D residue 1107 VAL Chi-restraints excluded: chain D residue 1115 SER Chi-restraints excluded: chain D residue 1272 VAL Chi-restraints excluded: chain E residue 68 TYR Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain G residue 12 SER Chi-restraints excluded: chain G residue 16 ASN Chi-restraints excluded: chain G residue 24 LYS Chi-restraints excluded: chain G residue 40 VAL Chi-restraints excluded: chain G residue 43 GLU Chi-restraints excluded: chain G residue 56 VAL Chi-restraints excluded: chain G residue 57 LYS Chi-restraints excluded: chain G residue 66 LEU Chi-restraints excluded: chain G residue 85 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 261 optimal weight: 0.0030 chunk 234 optimal weight: 1.9990 chunk 130 optimal weight: 3.9990 chunk 80 optimal weight: 0.8980 chunk 158 optimal weight: 5.9990 chunk 125 optimal weight: 0.8980 chunk 242 optimal weight: 4.9990 chunk 94 optimal weight: 8.9990 chunk 147 optimal weight: 0.9990 chunk 180 optimal weight: 8.9990 chunk 281 optimal weight: 4.9990 overall best weight: 0.9594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_failure.pdb'. Return code: -15 Dumping stderr: