Starting phenix.real_space_refine on Fri Feb 6 19:30:56 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9m9d_63730/02_2026/9m9d_63730_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9m9d_63730/02_2026/9m9d_63730.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.29 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9m9d_63730/02_2026/9m9d_63730.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9m9d_63730/02_2026/9m9d_63730.map" model { file = "/net/cci-nas-00/data/ceres_data/9m9d_63730/02_2026/9m9d_63730_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9m9d_63730/02_2026/9m9d_63730_neut.cif" } resolution = 3.29 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= -0.000 sd= 0.041 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 99 5.49 5 Mg 1 5.21 5 S 88 5.16 5 C 16543 2.51 5 N 4791 2.21 5 O 5342 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 26866 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 1658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1658 Classifications: {'peptide': 219} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 2, 'PTRANS': 12, 'TRANS': 204} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "B" Number of atoms: 1753 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1753 Classifications: {'peptide': 233} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 218} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 17 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "C" Number of atoms: 8520 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1123, 8520 Classifications: {'peptide': 1123} Incomplete info: {'truncation_to_alanine': 52} Link IDs: {'PCIS': 1, 'PTRANS': 61, 'TRANS': 1060} Unresolved non-hydrogen bonds: 199 Unresolved non-hydrogen angles: 247 Unresolved non-hydrogen dihedrals: 156 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'GLU:plan': 13, 'ASN:plan1': 4, 'ASP:plan': 5, 'ARG:plan': 8, 'GLN:plan1': 1, 'PHE:plan': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 136 Chain: "D" Number of atoms: 9769 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1260, 9769 Classifications: {'peptide': 1260} Incomplete info: {'truncation_to_alanine': 29} Link IDs: {'PCIS': 2, 'PTRANS': 58, 'TRANS': 1199} Chain breaks: 2 Unresolved non-hydrogen bonds: 123 Unresolved non-hydrogen angles: 153 Unresolved non-hydrogen dihedrals: 98 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 8, 'GLN:plan1': 2, 'ARG:plan': 6, 'ASP:plan': 6, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 101 Chain: "E" Number of atoms: 600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 600 Classifications: {'peptide': 76} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 69} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "F" Number of atoms: 1289 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1289 Classifications: {'peptide': 159} Link IDs: {'PTRANS': 9, 'TRANS': 149} Chain breaks: 1 Chain: "M" Number of atoms: 1234 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1234 Classifications: {'peptide': 159} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 154} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "G" Number of atoms: 954 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 954 Classifications: {'DNA': 47} Link IDs: {'rna3p': 46} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {' DT:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "H" Number of atoms: 945 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 945 Classifications: {'DNA': 47} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 46} Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {' DT:plan': 1, ' DG:plan': 1, ' DG:plan2': 1} Unresolved non-hydrogen planarities: 22 Chain: "I" Number of atoms: 141 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 141 Classifications: {'RNA': 7} Modifications used: {'5*END': 1, 'rna2p_pur': 1, 'rna3p_pur': 1, 'rna3p_pyr': 4} Link IDs: {'rna3p': 6} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "D" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 1, ' ZN': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 12409 SG CYS D 60 35.266 50.287 119.300 1.00174.83 S ATOM 12427 SG CYS D 62 35.587 47.229 121.337 1.00170.08 S ATOM 12536 SG CYS D 75 34.401 50.710 122.834 1.00176.15 S ATOM 12562 SG CYS D 78 37.850 50.225 122.338 1.00177.23 S ATOM 18971 SG CYS D 891 46.879 109.730 86.627 1.00139.00 S ATOM 19533 SG CYS D 968 48.851 106.761 88.105 1.00134.22 S ATOM 19575 SG CYS D 975 47.357 106.616 84.499 1.00128.63 S ATOM 19593 SG CYS D 978 50.251 108.612 85.169 1.00127.71 S Time building chain proxies: 6.40, per 1000 atoms: 0.24 Number of scatterers: 26866 At special positions: 0 Unit cell: (137.95, 142.4, 199.36, 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 88 16.00 P 99 15.00 Mg 1 11.99 O 5342 8.00 N 4791 7.00 C 16543 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 - 3.00 Amino acid : True - 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: 2.60 Conformation dependent library (CDL) restraints added in 1.3 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN D1402 " pdb="ZN ZN D1402 " - pdb=" SG CYS D 75 " pdb="ZN ZN D1402 " - pdb=" SG CYS D 60 " pdb="ZN ZN D1402 " - pdb=" SG CYS D 62 " pdb="ZN ZN D1402 " - pdb=" SG CYS D 78 " pdb=" ZN D1403 " pdb="ZN ZN D1403 " - pdb=" SG CYS D 978 " pdb="ZN ZN D1403 " - pdb=" SG CYS D 975 " pdb="ZN ZN D1403 " - pdb=" SG CYS D 968 " pdb="ZN ZN D1403 " - pdb=" SG CYS D 891 " Number of angles added : 12 6414 Ramachandran restraints generated. 3207 Oldfield, 0 Emsley, 3207 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5950 Finding SS restraints... Secondary structure from input PDB file: 121 helices and 40 sheets defined 42.5% alpha, 15.5% beta 32 base pairs and 70 stacking pairs defined. Time for finding SS restraints: 4.20 Creating SS restraints... Processing helix chain 'A' and resid 30 through 43 removed outlier: 3.511A pdb=" N LEU A 34 " --> pdb=" O PHE A 30 " (cutoff:3.500A) Processing helix chain 'A' and resid 72 through 82 removed outlier: 3.796A pdb=" N SER A 82 " --> pdb=" O LEU A 78 " (cutoff:3.500A) Processing helix chain 'A' and resid 108 through 110 No H-bonds generated for 'chain 'A' and resid 108 through 110' Processing helix chain 'A' and resid 203 through 220 Processing helix chain 'B' and resid 30 through 45 removed outlier: 3.758A pdb=" N SER B 37 " --> pdb=" O THR B 33 " (cutoff:3.500A) Processing helix chain 'B' and resid 72 through 82 Processing helix chain 'B' and resid 108 through 110 No H-bonds generated for 'chain 'B' and resid 108 through 110' Processing helix chain 'B' and resid 203 through 224 removed outlier: 3.670A pdb=" N ALA B 222 " --> pdb=" O LEU B 218 " (cutoff:3.500A) Processing helix chain 'C' and resid 54 through 66 removed outlier: 3.995A pdb=" N SER C 60 " --> pdb=" O VAL C 56 " (cutoff:3.500A) Processing helix chain 'C' and resid 67 through 78 Processing helix chain 'C' and resid 84 through 94 Processing helix chain 'C' and resid 118 through 126 Processing helix chain 'C' and resid 235 through 241 Processing helix chain 'C' and resid 244 through 252 Processing helix chain 'C' and resid 257 through 264 removed outlier: 3.560A pdb=" N LYS C 264 " --> pdb=" O SER C 260 " (cutoff:3.500A) Processing helix chain 'C' and resid 269 through 282 Processing helix chain 'C' and resid 288 through 301 Processing helix chain 'C' and resid 309 through 321 Processing helix chain 'C' and resid 334 through 351 Processing helix chain 'C' and resid 380 through 407 removed outlier: 3.583A pdb=" N LEU C 384 " --> pdb=" O THR C 380 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N THR C 405 " --> pdb=" O ARG C 401 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N THR C 406 " --> pdb=" O GLU C 402 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N GLN C 407 " --> pdb=" O ARG C 403 " (cutoff:3.500A) Processing helix chain 'C' and resid 413 through 418 Processing helix chain 'C' and resid 420 through 434 removed outlier: 3.544A pdb=" N VAL C 424 " --> pdb=" O ILE C 420 " (cutoff:3.500A) Processing helix chain 'C' and resid 444 through 453 Processing helix chain 'C' and resid 476 through 480 removed outlier: 3.570A pdb=" N TYR C 480 " --> pdb=" O PRO C 477 " (cutoff:3.500A) Processing helix chain 'C' and resid 532 through 539 removed outlier: 3.768A pdb=" N GLU C 536 " --> pdb=" O THR C 532 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N ASP C 537 " --> pdb=" O ALA C 533 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N ARG C 538 " --> pdb=" O ASP C 534 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N HIS C 539 " --> pdb=" O GLU C 535 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 532 through 539' Processing helix chain 'C' and resid 589 through 593 Processing helix chain 'C' and resid 596 through 600 Processing helix chain 'C' and resid 601 through 612 Processing helix chain 'C' and resid 630 through 639 removed outlier: 4.118A pdb=" N GLY C 639 " --> pdb=" O ALA C 635 " (cutoff:3.500A) Processing helix chain 'C' and resid 739 through 744 Processing helix chain 'C' and resid 777 through 782 removed outlier: 3.719A pdb=" N LEU C 781 " --> pdb=" O SER C 777 " (cutoff:3.500A) Processing helix chain 'C' and resid 815 through 826 removed outlier: 4.026A pdb=" N PHE C 825 " --> pdb=" O LEU C 821 " (cutoff:3.500A) Processing helix chain 'C' and resid 900 through 904 removed outlier: 3.777A pdb=" N MET C 904 " --> pdb=" O VAL C 901 " (cutoff:3.500A) Processing helix chain 'C' and resid 920 through 926 removed outlier: 4.579A pdb=" N ARG C 924 " --> pdb=" O HIS C 920 " (cutoff:3.500A) Processing helix chain 'C' and resid 928 through 943 Processing helix chain 'C' and resid 953 through 957 Processing helix chain 'C' and resid 960 through 963 Processing helix chain 'C' and resid 981 through 989 Processing helix chain 'C' and resid 990 through 992 No H-bonds generated for 'chain 'C' and resid 990 through 992' Processing helix chain 'C' and resid 1036 through 1040 Processing helix chain 'C' and resid 1069 through 1080 Processing helix chain 'C' and resid 1081 through 1091 Processing helix chain 'C' and resid 1095 through 1108 removed outlier: 4.127A pdb=" N VAL C1100 " --> pdb=" O THR C1096 " (cutoff:3.500A) Processing helix chain 'C' and resid 1118 through 1130 removed outlier: 3.897A pdb=" N LYS C1122 " --> pdb=" O PRO C1118 " (cutoff:3.500A) Processing helix chain 'D' and resid 17 through 24 removed outlier: 3.799A pdb=" N ARG D 21 " --> pdb=" O ALA D 17 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N SER D 24 " --> pdb=" O ILE D 20 " (cutoff:3.500A) 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: 3.657A pdb=" N VAL D 87 " --> pdb=" O ARG D 84 " (cutoff:3.500A) Processing helix chain 'D' and resid 104 through 109 Processing helix chain 'D' and resid 112 through 119 Processing helix chain 'D' and resid 121 through 130 removed outlier: 3.561A pdb=" N TYR D 130 " --> pdb=" O GLU D 126 " (cutoff:3.500A) Processing helix chain 'D' and resid 147 through 186 removed outlier: 4.168A pdb=" N GLU D 183 " --> pdb=" O ALA D 179 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N LEU D 184 " --> pdb=" O ASP D 180 " (cutoff:3.500A) Processing helix chain 'D' and resid 192 through 228 removed outlier: 3.922A pdb=" N VAL D 197 " --> pdb=" O ALA D 193 " (cutoff:3.500A) Processing helix chain 'D' and resid 237 through 248 Processing helix chain 'D' and resid 257 through 267 removed outlier: 3.581A pdb=" N ILE D 261 " --> pdb=" O GLY D 257 " (cutoff:3.500A) Processing helix chain 'D' and resid 270 through 283 Processing helix chain 'D' and resid 286 through 304 removed outlier: 3.573A pdb=" N LEU D 290 " --> pdb=" O GLY D 286 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N VAL D 298 " --> pdb=" O LYS D 294 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N ALA D 301 " --> pdb=" O LYS D 297 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N PHE D 302 " --> pdb=" O VAL D 298 " (cutoff:3.500A) Processing helix chain 'D' and resid 308 through 311 removed outlier: 3.560A pdb=" N GLY D 311 " --> pdb=" O SER D 308 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 308 through 311' Processing helix chain 'D' and resid 339 through 351 removed outlier: 4.363A pdb=" N LEU D 343 " --> pdb=" O ASP D 339 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N TYR D 344 " --> pdb=" O LEU D 340 " (cutoff:3.500A) Processing helix chain 'D' and resid 366 through 383 Processing helix chain 'D' and resid 401 through 406 Processing helix chain 'D' and resid 411 through 417 removed outlier: 3.722A pdb=" N LEU D 417 " --> pdb=" O PHE D 413 " (cutoff:3.500A) 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 477 Processing helix chain 'D' and resid 480 through 491 removed outlier: 3.965A pdb=" N TRP D 484 " --> pdb=" O ARG D 480 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N GLU D 488 " --> pdb=" O TRP D 484 " (cutoff:3.500A) removed outlier: 4.968A 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 527 No H-bonds generated for 'chain 'D' and resid 525 through 527' Processing helix chain 'D' and resid 528 through 533 Processing helix chain 'D' and resid 548 through 558 Processing helix chain 'D' and resid 560 through 564 Processing helix chain 'D' and resid 579 through 589 Processing helix chain 'D' and resid 614 through 623 Processing helix chain 'D' and resid 643 through 651 Processing helix chain 'D' and resid 668 through 677 removed outlier: 3.697A pdb=" N LEU D 676 " --> pdb=" O MET D 672 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N LEU D 677 " --> pdb=" O PHE D 673 " (cutoff:3.500A) Processing helix chain 'D' and resid 689 through 703 removed outlier: 3.518A pdb=" N ARG D 703 " --> pdb=" O ASP D 699 " (cutoff:3.500A) Processing helix chain 'D' and resid 705 through 726 removed outlier: 3.516A pdb=" N VAL D 709 " --> pdb=" O PRO D 705 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N ARG D 726 " --> pdb=" O TYR D 722 " (cutoff:3.500A) Processing helix chain 'D' and resid 741 through 762 removed outlier: 4.577A pdb=" N ARG D 752 " --> pdb=" O HIS D 748 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N ALA D 753 " --> pdb=" O TYR D 749 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ASP D 754 " --> pdb=" O GLU D 750 " (cutoff:3.500A) Processing helix chain 'D' and resid 766 through 793 removed outlier: 3.600A pdb=" N TYR D 793 " --> pdb=" O LEU D 789 " (cutoff:3.500A) Processing helix chain 'D' and resid 797 through 805 removed outlier: 3.719A pdb=" N VAL D 803 " --> pdb=" O ILE D 799 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N SER D 805 " --> pdb=" O THR D 801 " (cutoff:3.500A) Processing helix chain 'D' and resid 810 through 819 removed outlier: 3.809A pdb=" N THR D 814 " --> pdb=" O ASN D 810 " (cutoff:3.500A) Processing helix chain 'D' and resid 845 through 881 removed outlier: 3.746A pdb=" N THR D 853 " --> pdb=" O TYR D 849 " (cutoff:3.500A) removed outlier: 4.814A pdb=" N HIS D 854 " --> pdb=" O PHE D 850 " (cutoff:3.500A) removed outlier: 5.268A pdb=" N GLY D 855 " --> pdb=" O ILE D 851 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N ALA D 856 " --> pdb=" O ASN D 852 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N ALA D 868 " --> pdb=" O ALA D 864 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N GLY D 871 " --> pdb=" O THR D 867 " (cutoff:3.500A) Processing helix chain 'D' and resid 915 through 920 Processing helix chain 'D' and resid 944 through 955 removed outlier: 4.277A pdb=" N GLU D 948 " --> pdb=" O LEU D 944 " (cutoff:3.500A) Processing helix chain 'D' and resid 964 through 968 Processing helix chain 'D' and resid 975 through 980 Processing helix chain 'D' and resid 994 through 1005 removed outlier: 4.180A pdb=" N VAL D 998 " --> pdb=" O ALA D 994 " (cutoff:3.500A) Processing helix chain 'D' and resid 1006 through 1010 removed outlier: 3.666A pdb=" N GLN D1009 " --> pdb=" O PRO D1006 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N LEU D1010 " --> pdb=" O GLY D1007 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 1006 through 1010' Processing helix chain 'D' and resid 1027 through 1036 Processing helix chain 'D' and resid 1117 through 1125 Processing helix chain 'D' and resid 1126 through 1145 removed outlier: 3.792A pdb=" N VAL D1141 " --> pdb=" O GLU D1137 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N TYR D1142 " --> pdb=" O VAL D1138 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLN D1145 " --> pdb=" O VAL D1141 " (cutoff:3.500A) Processing helix chain 'D' and resid 1150 through 1160 removed outlier: 4.296A pdb=" N ILE D1154 " --> pdb=" O HIS D1150 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N GLN D1160 " --> pdb=" O VAL D1156 " (cutoff:3.500A) Processing helix chain 'D' and resid 1183 through 1190 Processing helix chain 'D' and resid 1209 through 1216 Processing helix chain 'D' and resid 1219 through 1225 removed outlier: 3.583A pdb=" N ALA D1223 " --> pdb=" O SER D1219 " (cutoff:3.500A) Processing helix chain 'D' and resid 1228 through 1240 removed outlier: 3.733A pdb=" N VAL D1232 " --> pdb=" O GLU D1228 " (cutoff:3.500A) Processing helix chain 'D' and resid 1247 through 1254 Processing helix chain 'D' and resid 1260 through 1263 Processing helix chain 'D' and resid 1264 through 1269 Processing helix chain 'D' and resid 1275 through 1281 removed outlier: 3.509A pdb=" N ALA D1281 " --> pdb=" O GLU D1277 " (cutoff:3.500A) Processing helix chain 'E' and resid 32 through 36 Processing helix chain 'E' and resid 38 through 43 Processing helix chain 'E' and resid 44 through 46 No H-bonds generated for 'chain 'E' and resid 44 through 46' Processing helix chain 'E' and resid 48 through 70 Processing helix chain 'E' and resid 89 through 101 removed outlier: 3.661A pdb=" N ILE E 93 " --> pdb=" O LYS E 89 " (cutoff:3.500A) Processing helix chain 'F' and resid 83 through 90 removed outlier: 4.359A pdb=" N GLN F 90 " --> pdb=" O GLU F 86 " (cutoff:3.500A) Processing helix chain 'F' and resid 91 through 104 removed outlier: 3.534A pdb=" N VAL F 95 " --> pdb=" O HIS F 91 " (cutoff:3.500A) Processing helix chain 'F' and resid 105 through 124 Processing helix chain 'F' and resid 125 through 127 No H-bonds generated for 'chain 'F' and resid 125 through 127' Processing helix chain 'F' and resid 131 through 153 Processing helix chain 'F' and resid 172 through 181 removed outlier: 3.720A pdb=" N ILE F 176 " --> pdb=" O ASN F 172 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N ARG F 181 " --> pdb=" O TYR F 177 " (cutoff:3.500A) Processing helix chain 'F' and resid 183 through 193 Processing helix chain 'F' and resid 194 through 206 Processing helix chain 'F' and resid 210 through 219 Processing helix chain 'F' and resid 221 through 240 removed outlier: 3.649A pdb=" N ARG F 231 " --> pdb=" O SER F 227 " (cutoff:3.500A) Processing helix chain 'M' and resid 52 through 57 removed outlier: 3.771A pdb=" N VAL M 56 " --> pdb=" O ASN M 52 " (cutoff:3.500A) Processing helix chain 'M' and resid 63 through 75 Processing helix chain 'M' and resid 84 through 98 Processing helix chain 'M' and resid 100 through 118 Processing helix chain 'M' and resid 121 through 144 Processing helix chain 'M' and resid 147 through 160 Processing sheet with id=AA1, first strand: chain 'A' and resid 8 through 15 removed outlier: 3.614A pdb=" N LEU A 14 " --> pdb=" O ARG A 18 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N ARG A 18 " --> pdb=" O LEU A 14 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N ASP A 190 " --> pdb=" O PRO A 25 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 93 through 100 removed outlier: 7.701A pdb=" N GLU A 135 " --> pdb=" O ILE A 56 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N ILE A 56 " --> pdb=" O GLU A 135 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N GLU A 137 " --> pdb=" O ILE A 54 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N ILE A 54 " --> pdb=" O GLU A 137 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N VAL A 139 " --> pdb=" O THR A 52 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ILE A 162 " --> pdb=" O ILE A 54 " (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 106 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 13 removed outlier: 3.699A pdb=" N ILE B 23 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N LEU B 192 " --> pdb=" O ILE B 23 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N ASP B 190 " --> pdb=" O PRO B 25 " (cutoff:3.500A) removed outlier: 5.803A pdb=" N THR B 181 " --> pdb=" O ASP B 188 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N ASP B 190 " --> pdb=" O ASP B 179 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N ASP B 179 " --> pdb=" O ASP B 190 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N LEU B 192 " --> pdb=" O LYS B 177 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N LYS B 177 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 4.788A pdb=" N LEU B 194 " --> pdb=" O THR B 175 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N THR B 175 " --> pdb=" O LEU B 194 " (cutoff:3.500A) removed outlier: 4.694A pdb=" N VAL B 196 " --> pdb=" O LYS B 173 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N LYS B 173 " --> pdb=" O VAL B 196 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N THR B 198 " --> pdb=" O VAL B 171 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N VAL B 171 " --> pdb=" O THR B 198 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 93 through 100 removed outlier: 7.827A pdb=" N GLU B 135 " --> pdb=" O ILE B 56 " (cutoff:3.500A) removed outlier: 4.755A pdb=" N ILE B 56 " --> pdb=" O GLU B 135 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N GLU B 137 " --> pdb=" O ILE B 54 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N ILE B 54 " --> pdb=" O GLU B 137 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N VAL B 139 " --> pdb=" O THR B 52 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ILE B 162 " --> pdb=" O ILE B 54 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 85 through 87 Processing sheet with id=AA9, first strand: chain 'B' and resid 103 through 106 Processing sheet with id=AB1, first strand: chain 'B' and resid 146 through 147 Processing sheet with id=AB2, first strand: chain 'C' and resid 39 through 40 removed outlier: 6.150A pdb=" N VAL C 39 " --> pdb=" O SER C 973 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 104 through 112 removed outlier: 6.443A pdb=" N LEU C 105 " --> pdb=" O ILE C 140 " (cutoff:3.500A) removed outlier: 7.419A pdb=" N ILE C 140 " --> pdb=" O LEU C 105 " (cutoff:3.500A) removed outlier: 5.580A pdb=" N PHE C 107 " --> pdb=" O GLU C 138 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N GLU C 138 " --> pdb=" O PHE C 107 " (cutoff:3.500A) removed outlier: 5.536A pdb=" N ASP C 109 " --> pdb=" O THR C 136 " (cutoff:3.500A) removed outlier: 4.604A pdb=" N THR C 136 " --> pdb=" O ASP C 109 " (cutoff:3.500A) removed outlier: 5.419A pdb=" N ALA C 131 " --> pdb=" O ASP C 156 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N ASP C 156 " --> pdb=" O ALA C 131 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N LEU C 133 " --> pdb=" O MET C 154 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N VAL M 36 " --> pdb=" O ALA M 21 " (cutoff:3.500A) removed outlier: 4.666A pdb=" N ALA M 21 " --> pdb=" O VAL M 36 " (cutoff:3.500A) removed outlier: 7.052A pdb=" N LYS M 38 " --> pdb=" O VAL M 19 " (cutoff:3.500A) removed outlier: 5.656A pdb=" N VAL M 19 " --> pdb=" O LYS M 38 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 166 through 168 Processing sheet with id=AB5, first strand: chain 'C' and resid 376 through 379 removed outlier: 3.745A pdb=" N SER C 177 " --> pdb=" O ARG C 454 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 184 through 190 removed outlier: 4.680A pdb=" N HIS C 200 " --> pdb=" O VAL C 216 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N LEU C 212 " --> pdb=" O VAL C 204 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 354 through 355 removed outlier: 3.719A pdb=" N MET C 355 " --> pdb=" O VAL C 363 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 505 through 506 removed outlier: 6.589A pdb=" N ILE C 512 " --> pdb=" O LEU C 531 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N LEU C 531 " --> pdb=" O ILE C 512 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N THR C 514 " --> pdb=" O VAL C 529 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N VAL C 529 " --> pdb=" O THR C 514 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N TYR C 516 " --> pdb=" O GLU C 527 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N GLU C 527 " --> pdb=" O TYR C 516 " (cutoff:3.500A) removed outlier: 4.983A pdb=" N LYS C 518 " --> pdb=" O SER C 525 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 505 through 506 removed outlier: 3.805A pdb=" N VAL C 541 " --> pdb=" O ARG C 562 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 642 through 643 removed outlier: 6.925A pdb=" N VAL C 642 " --> pdb=" O ILE C 702 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 667 through 671 removed outlier: 6.761A pdb=" N TYR C 657 " --> pdb=" O VAL C 653 " (cutoff:3.500A) removed outlier: 4.863A pdb=" N VAL C 653 " --> pdb=" O TYR C 657 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N THR C 659 " --> pdb=" O GLU C 651 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N GLY C 648 " --> pdb=" O VAL C 696 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 676 through 677 Processing sheet with id=AC4, first strand: chain 'C' and resid 708 through 709 Processing sheet with id=AC5, first strand: chain 'C' and resid 1007 through 1008 removed outlier: 3.771A pdb=" N ALA C 886 " --> pdb=" O MET C1031 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N ILE C 735 " --> pdb=" O LYS C 897 " (cutoff:3.500A) removed outlier: 7.934A pdb=" N LEU C 899 " --> pdb=" O ILE C 735 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N LEU C 737 " --> pdb=" O LEU C 899 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ILE C 736 " --> pdb=" O ILE C 916 " (cutoff:3.500A) removed outlier: 8.817A pdb=" N ILE C 915 " --> pdb=" O ASN C 718 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N LEU C 720 " --> pdb=" O ILE C 915 " (cutoff:3.500A) removed outlier: 7.804A pdb=" N LEU C 917 " --> pdb=" O LEU C 720 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N ALA C 722 " --> pdb=" O LEU C 917 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N THR C1024 " --> pdb=" O ILE C 723 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 749 through 760 removed outlier: 7.533A pdb=" N ASN C 866 " --> pdb=" O SER C 854 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N SER C 854 " --> pdb=" O ASN C 866 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N LEU C 868 " --> pdb=" O VAL C 852 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N VAL C 852 " --> pdb=" O LEU C 868 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N ARG C 870 " --> pdb=" O ILE C 850 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N ILE C 850 " --> pdb=" O ARG C 870 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N TYR C 872 " --> pdb=" O ILE C 848 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 768 through 769 Processing sheet with id=AC8, first strand: chain 'C' and resid 801 through 803 removed outlier: 3.569A pdb=" N LEU C 802 " --> pdb=" O LEU C 837 " (cutoff:3.500A) removed outlier: 7.524A pdb=" N LEU C 837 " --> pdb=" O LEU C 802 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC8 Processing sheet with id=AC9, first strand: chain 'C' and resid 944 through 945 Processing sheet with id=AD1, first strand: chain 'C' and resid 1042 through 1044 Processing sheet with id=AD2, first strand: chain 'C' and resid 1042 through 1044 removed outlier: 8.024A pdb=" N ILE D 522 " --> pdb=" O ARG D 427 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N VAL D 429 " --> pdb=" O ILE D 522 " (cutoff:3.500A) removed outlier: 7.791A pdb=" N LEU D 524 " --> pdb=" O VAL D 429 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N VAL D 431 " --> pdb=" O LEU D 524 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 1067 through 1068 Processing sheet with id=AD4, first strand: chain 'C' and resid 1133 through 1138 removed outlier: 3.616A pdb=" N ARG D 11 " --> pdb=" O GLU C1136 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'D' and resid 34 through 35 removed outlier: 3.633A pdb=" N LYS D 40 " --> pdb=" O ASN D 35 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'D' and resid 94 through 102 removed outlier: 10.206A pdb=" N LEU D 97 " --> pdb=" O PRO D 318 " (cutoff:3.500A) removed outlier: 10.760A pdb=" N ALA D 99 " --> pdb=" O ALA D 316 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N ALA D 316 " --> pdb=" O ALA D 99 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'D' and resid 611 through 612 Processing sheet with id=AD8, first strand: chain 'D' and resid 897 through 900 removed outlier: 4.689A pdb=" N THR D 924 " --> pdb=" O ARG D 963 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'D' and resid 902 through 904 Processing sheet with id=AE1, first strand: chain 'D' and resid 1075 through 1077 removed outlier: 4.173A pdb=" N GLY D1051 " --> pdb=" O VAL D1105 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N VAL D1105 " --> pdb=" O GLY D1051 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'D' and resid 1088 through 1090 Processing sheet with id=AE3, first strand: chain 'D' and resid 1180 through 1182 Processing sheet with id=AE4, first strand: chain 'D' and resid 1272 through 1274 1099 hydrogen bonds defined for protein. 3087 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 77 hydrogen bonds 154 hydrogen bond angles 0 basepair planarities 32 basepair parallelities 70 stacking parallelities Total time for adding SS restraints: 6.11 Time building geometry restraints manager: 3.54 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 6562 1.33 - 1.45: 5336 1.45 - 1.57: 15290 1.57 - 1.69: 192 1.69 - 1.81: 154 Bond restraints: 27534 Sorted by residual: bond pdb=" C LEU F 193 " pdb=" N PRO F 194 " ideal model delta sigma weight residual 1.329 1.502 -0.172 1.18e-02 7.18e+03 2.13e+02 bond pdb=" O3' DG G 37 " pdb=" P DT G 38 " ideal model delta sigma weight residual 1.607 1.463 0.144 1.50e-02 4.44e+03 9.16e+01 bond pdb=" O3' DC H 36 " pdb=" P DT H 37 " ideal model delta sigma weight residual 1.607 1.687 -0.080 1.50e-02 4.44e+03 2.82e+01 bond pdb=" O3' DC H 24 " pdb=" P DA H 25 " ideal model delta sigma weight residual 1.607 1.675 -0.068 1.50e-02 4.44e+03 2.08e+01 bond pdb=" C1' DG H 42 " pdb=" N9 DG H 42 " ideal model delta sigma weight residual 1.460 1.384 0.076 2.00e-02 2.50e+03 1.45e+01 ... (remaining 27529 not shown) Histogram of bond angle deviations from ideal: 0.00 - 16.40: 37753 16.40 - 32.80: 5 32.80 - 49.21: 3 49.21 - 65.61: 0 65.61 - 82.01: 1 Bond angle restraints: 37762 Sorted by residual: angle pdb=" O3' DG G 37 " pdb=" P DT G 38 " pdb=" OP1 DT G 38 " ideal model delta sigma weight residual 108.00 25.99 82.01 3.00e+00 1.11e-01 7.47e+02 angle pdb=" C3' DT H 31 " pdb=" O3' DT H 31 " pdb=" P DA H 32 " ideal model delta sigma weight residual 120.20 86.60 33.60 1.50e+00 4.44e-01 5.02e+02 angle pdb=" C LEU F 193 " pdb=" N PRO F 194 " pdb=" CA PRO F 194 " ideal model delta sigma weight residual 120.38 137.89 -17.51 1.03e+00 9.43e-01 2.89e+02 angle pdb=" O3' DG G 37 " pdb=" P DT G 38 " pdb=" O5' DT G 38 " ideal model delta sigma weight residual 104.00 128.62 -24.62 1.50e+00 4.44e-01 2.70e+02 angle pdb=" O3' DA H 25 " pdb=" C3' DA H 25 " pdb=" C2' DA H 25 " ideal model delta sigma weight residual 111.50 91.75 19.75 1.50e+00 4.44e-01 1.73e+02 ... (remaining 37757 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.89: 16010 35.89 - 71.78: 552 71.78 - 107.66: 19 107.66 - 143.55: 2 143.55 - 179.44: 5 Dihedral angle restraints: 16588 sinusoidal: 7342 harmonic: 9246 Sorted by residual: dihedral pdb=" CA TRP D 23 " pdb=" C TRP D 23 " pdb=" N SER D 24 " pdb=" CA SER D 24 " ideal model delta harmonic sigma weight residual 180.00 147.02 32.98 0 5.00e+00 4.00e-02 4.35e+01 dihedral pdb=" CA PRO D 322 " pdb=" C PRO D 322 " pdb=" N GLU D 323 " pdb=" CA GLU D 323 " ideal model delta harmonic sigma weight residual 180.00 147.28 32.72 0 5.00e+00 4.00e-02 4.28e+01 dihedral pdb=" C5' A I 7 " pdb=" C4' A I 7 " pdb=" C3' A I 7 " pdb=" O3' A I 7 " ideal model delta sinusoidal sigma weight residual 147.00 107.66 39.34 1 8.00e+00 1.56e-02 3.40e+01 ... (remaining 16585 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.097: 4042 0.097 - 0.194: 247 0.194 - 0.292: 23 0.292 - 0.389: 7 0.389 - 0.486: 4 Chirality restraints: 4323 Sorted by residual: chirality pdb=" C3' DC H 24 " pdb=" C4' DC H 24 " pdb=" O3' DC H 24 " pdb=" C2' DC H 24 " both_signs ideal model delta sigma weight residual False -2.66 -2.17 -0.49 2.00e-01 2.50e+01 5.91e+00 chirality pdb=" C3' DA H 25 " pdb=" C4' DA H 25 " pdb=" O3' DA H 25 " pdb=" C2' DA H 25 " both_signs ideal model delta sigma weight residual False -2.66 -3.14 0.48 2.00e-01 2.50e+01 5.77e+00 chirality pdb=" C3' DA G 29 " pdb=" C4' DA G 29 " pdb=" O3' DA G 29 " pdb=" C2' DA G 29 " both_signs ideal model delta sigma weight residual False -2.66 -2.20 -0.46 2.00e-01 2.50e+01 5.20e+00 ... (remaining 4320 not shown) Planarity restraints: 4622 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DA G 22 " -0.057 2.00e-02 2.50e+03 3.79e-02 3.95e+01 pdb=" N9 DA G 22 " 0.003 2.00e-02 2.50e+03 pdb=" C8 DA G 22 " 0.033 2.00e-02 2.50e+03 pdb=" N7 DA G 22 " -0.003 2.00e-02 2.50e+03 pdb=" C5 DA G 22 " -0.026 2.00e-02 2.50e+03 pdb=" C6 DA G 22 " -0.062 2.00e-02 2.50e+03 pdb=" N6 DA G 22 " 0.011 2.00e-02 2.50e+03 pdb=" N1 DA G 22 " 0.008 2.00e-02 2.50e+03 pdb=" C2 DA G 22 " 0.003 2.00e-02 2.50e+03 pdb=" N3 DA G 22 " 0.008 2.00e-02 2.50e+03 pdb=" C4 DA G 22 " 0.082 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DG G 25 " 0.050 2.00e-02 2.50e+03 2.67e-02 2.14e+01 pdb=" N9 DG G 25 " -0.066 2.00e-02 2.50e+03 pdb=" C8 DG G 25 " -0.003 2.00e-02 2.50e+03 pdb=" N7 DG G 25 " 0.005 2.00e-02 2.50e+03 pdb=" C5 DG G 25 " -0.011 2.00e-02 2.50e+03 pdb=" C6 DG G 25 " -0.003 2.00e-02 2.50e+03 pdb=" O6 DG G 25 " 0.009 2.00e-02 2.50e+03 pdb=" N1 DG G 25 " 0.025 2.00e-02 2.50e+03 pdb=" C2 DG G 25 " 0.009 2.00e-02 2.50e+03 pdb=" N2 DG G 25 " -0.025 2.00e-02 2.50e+03 pdb=" N3 DG G 25 " 0.004 2.00e-02 2.50e+03 pdb=" C4 DG G 25 " 0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DG H 33 " -0.023 2.00e-02 2.50e+03 2.64e-02 2.08e+01 pdb=" N9 DG H 33 " 0.069 2.00e-02 2.50e+03 pdb=" C8 DG H 33 " -0.047 2.00e-02 2.50e+03 pdb=" N7 DG H 33 " 0.002 2.00e-02 2.50e+03 pdb=" C5 DG H 33 " 0.005 2.00e-02 2.50e+03 pdb=" C6 DG H 33 " 0.004 2.00e-02 2.50e+03 pdb=" O6 DG H 33 " 0.002 2.00e-02 2.50e+03 pdb=" N1 DG H 33 " -0.013 2.00e-02 2.50e+03 pdb=" C2 DG H 33 " 0.016 2.00e-02 2.50e+03 pdb=" N2 DG H 33 " -0.016 2.00e-02 2.50e+03 pdb=" N3 DG H 33 " -0.002 2.00e-02 2.50e+03 pdb=" C4 DG H 33 " 0.004 2.00e-02 2.50e+03 ... (remaining 4619 not shown) Histogram of nonbonded interaction distances: 1.84 - 2.45: 127 2.45 - 3.07: 18088 3.07 - 3.68: 42113 3.68 - 4.29: 57812 4.29 - 4.90: 94160 Nonbonded interactions: 212300 Sorted by model distance: nonbonded pdb=" O3' A I 7 " pdb="MG MG D1401 " model vdw 1.843 2.170 nonbonded pdb=" C3' DG G 37 " pdb=" OP1 DT G 38 " model vdw 1.992 2.776 nonbonded pdb=" OD1 ASP D 537 " pdb="MG MG D1401 " model vdw 2.035 2.170 nonbonded pdb=" C2' DA G 19 " pdb=" C7 DT G 20 " model vdw 2.120 3.860 nonbonded pdb=" O TYR D 586 " pdb=" OG1 THR D 590 " model vdw 2.198 3.040 ... (remaining 212295 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 5 through 88 or (resid 89 through 91 and (name N or name C \ A or name C or name O or name CB )) or resid 92 through 130 or (resid 131 and (n \ ame N or name CA or name C or name O or name CB )) or resid 132 through 223)) selection = (chain 'B' and (resid 5 through 180 or (resid 181 and (name N or name CA or name \ C or name O or name CB )) or resid 182 through 185 or (resid 186 and (name N or \ name CA or name C or name O or name CB )) or resid 187 through 223)) } 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: 2.880 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.040 Extract box with map and model: 0.370 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 32.240 Find NCS groups from input model: 0.210 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: 0.010 Load rotamer database and sin/cos tables:1.520 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.450 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8312 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 0.172 27542 Z= 0.248 Angle : 0.981 82.011 37774 Z= 0.542 Chirality : 0.052 0.486 4323 Planarity : 0.004 0.071 4622 Dihedral : 16.751 179.440 10638 Min Nonbonded Distance : 1.843 Molprobity Statistics. All-atom Clashscore : 13.90 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.62 % Favored : 96.23 % Rotamer: Outliers : 0.46 % Allowed : 0.53 % Favored : 99.01 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 4.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.37 (0.15), residues: 3207 helix: 1.14 (0.16), residues: 1182 sheet: 0.29 (0.27), residues: 385 loop : -0.37 (0.16), residues: 1640 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 59 TYR 0.040 0.001 TYR E 55 PHE 0.017 0.001 PHE C 373 TRP 0.017 0.001 TRP D 723 HIS 0.006 0.001 HIS C 372 Details of bonding type rmsd covalent geometry : bond 0.00461 (27534) covalent geometry : angle 0.97489 (37762) hydrogen bonds : bond 0.17071 ( 1170) hydrogen bonds : angle 6.53154 ( 3241) metal coordination : bond 0.00868 ( 8) metal coordination : angle 6.01097 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6414 Ramachandran restraints generated. 3207 Oldfield, 0 Emsley, 3207 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6414 Ramachandran restraints generated. 3207 Oldfield, 0 Emsley, 3207 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 2722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 169 time to evaluate : 0.867 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 103 MET cc_start: 0.9107 (mpp) cc_final: 0.8586 (mpp) REVERT: C 258 MET cc_start: 0.8940 (ppp) cc_final: 0.8670 (ppp) REVERT: D 155 MET cc_start: 0.9531 (tpt) cc_final: 0.8819 (tpp) REVERT: D 256 MET cc_start: 0.8920 (tpt) cc_final: 0.8656 (tpt) REVERT: D 535 ASP cc_start: 0.8425 (t0) cc_final: 0.8086 (t0) REVERT: D 1112 MET cc_start: 0.7106 (tmm) cc_final: 0.6848 (tmm) REVERT: E 42 LEU cc_start: 0.8891 (tp) cc_final: 0.8670 (tp) REVERT: E 65 ASP cc_start: 0.8866 (m-30) cc_final: 0.8634 (m-30) REVERT: F 105 ASN cc_start: 0.8110 (t0) cc_final: 0.7728 (t0) REVERT: F 218 LEU cc_start: 0.8139 (OUTLIER) cc_final: 0.7836 (tp) REVERT: M 55 TYR cc_start: 0.9040 (m-80) cc_final: 0.8831 (m-80) REVERT: M 127 MET cc_start: 0.9411 (ppp) cc_final: 0.9174 (ppp) outliers start: 12 outliers final: 8 residues processed: 181 average time/residue: 0.1688 time to fit residues: 50.3618 Evaluate side-chains 157 residues out of total 2722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 148 time to evaluate : 1.038 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 230 ARG Chi-restraints excluded: chain F residue 138 ARG Chi-restraints excluded: chain F residue 193 LEU Chi-restraints excluded: chain F residue 202 VAL Chi-restraints excluded: chain F residue 217 THR Chi-restraints excluded: chain F residue 218 LEU Chi-restraints excluded: chain F residue 222 LEU Chi-restraints excluded: chain F residue 229 ILE Chi-restraints excluded: chain F residue 230 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 197 optimal weight: 9.9990 chunk 215 optimal weight: 20.0000 chunk 20 optimal weight: 3.9990 chunk 132 optimal weight: 1.9990 chunk 261 optimal weight: 3.9990 chunk 248 optimal weight: 0.0170 chunk 207 optimal weight: 8.9990 chunk 155 optimal weight: 0.0070 chunk 244 optimal weight: 9.9990 chunk 183 optimal weight: 10.0000 chunk 298 optimal weight: 4.9990 overall best weight: 2.0042 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 175 GLN D 267 ASN F 128 GLN M 72 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.054236 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2862 r_free = 0.2862 target = 0.037832 restraints weight = 139074.794| |-----------------------------------------------------------------------------| r_work (start): 0.2793 rms_B_bonded: 4.29 r_work (final): 0.2793 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2792 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2792 r_free = 0.2792 target_work(ls_wunit_k1) = 0.037 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2791 r_free = 0.2791 target_work(ls_wunit_k1) = 0.037 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2791 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8693 moved from start: 0.1011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 27542 Z= 0.144 Angle : 0.600 11.741 37774 Z= 0.318 Chirality : 0.043 0.209 4323 Planarity : 0.004 0.074 4622 Dihedral : 16.989 174.621 4694 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.62 % Favored : 96.29 % Rotamer: Outliers : 0.68 % Allowed : 6.62 % Favored : 92.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.49 (0.15), residues: 3207 helix: 1.27 (0.15), residues: 1207 sheet: 0.41 (0.27), residues: 384 loop : -0.37 (0.16), residues: 1616 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG F 237 TYR 0.029 0.001 TYR E 55 PHE 0.010 0.001 PHE D1226 TRP 0.013 0.001 TRP M 85 HIS 0.004 0.001 HIS C 755 Details of bonding type rmsd covalent geometry : bond 0.00319 (27534) covalent geometry : angle 0.59138 (37762) hydrogen bonds : bond 0.04708 ( 1170) hydrogen bonds : angle 4.75001 ( 3241) metal coordination : bond 0.01060 ( 8) metal coordination : angle 5.62943 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6414 Ramachandran restraints generated. 3207 Oldfield, 0 Emsley, 3207 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6414 Ramachandran restraints generated. 3207 Oldfield, 0 Emsley, 3207 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 2722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 160 time to evaluate : 0.988 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 103 MET cc_start: 0.9180 (mpp) cc_final: 0.8762 (mpp) REVERT: C 1051 MET cc_start: 0.9192 (pmm) cc_final: 0.8968 (pmm) REVERT: D 155 MET cc_start: 0.9489 (tpt) cc_final: 0.8859 (tpp) REVERT: D 404 ASP cc_start: 0.9088 (t70) cc_final: 0.8817 (t0) REVERT: D 535 ASP cc_start: 0.8585 (t0) cc_final: 0.8064 (t70) REVERT: D 749 TYR cc_start: 0.7685 (t80) cc_final: 0.7155 (t80) REVERT: D 1112 MET cc_start: 0.7368 (tmm) cc_final: 0.6856 (tmm) REVERT: E 89 LYS cc_start: 0.7540 (mttt) cc_final: 0.7250 (mtmt) REVERT: F 105 ASN cc_start: 0.8007 (t0) cc_final: 0.7561 (t0) REVERT: F 147 MET cc_start: 0.9500 (tmm) cc_final: 0.9242 (tmm) REVERT: F 218 LEU cc_start: 0.7963 (OUTLIER) cc_final: 0.7678 (tp) REVERT: M 43 ASP cc_start: 0.8760 (t0) cc_final: 0.8510 (t0) outliers start: 18 outliers final: 7 residues processed: 174 average time/residue: 0.1532 time to fit residues: 45.1697 Evaluate side-chains 157 residues out of total 2722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 149 time to evaluate : 0.969 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 72 GLU Chi-restraints excluded: chain C residue 402 GLU Chi-restraints excluded: chain C residue 1102 VAL Chi-restraints excluded: chain E residue 92 SER Chi-restraints excluded: chain E residue 103 LEU Chi-restraints excluded: chain F residue 202 VAL Chi-restraints excluded: chain F residue 218 LEU Chi-restraints excluded: chain F residue 229 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 321 optimal weight: 10.0000 chunk 163 optimal weight: 0.2980 chunk 294 optimal weight: 0.9990 chunk 323 optimal weight: 10.0000 chunk 193 optimal weight: 4.9990 chunk 204 optimal weight: 0.9980 chunk 68 optimal weight: 5.9990 chunk 154 optimal weight: 8.9990 chunk 108 optimal weight: 2.9990 chunk 220 optimal weight: 8.9990 chunk 146 optimal weight: 0.0980 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 267 ASN F 230 HIS ** M 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 133 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.054764 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2880 r_free = 0.2880 target = 0.038393 restraints weight = 137961.410| |-----------------------------------------------------------------------------| r_work (start): 0.2811 rms_B_bonded: 4.29 r_work: 0.2657 rms_B_bonded: 4.99 restraints_weight: 0.5000 r_work (final): 0.2657 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2648 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2648 r_free = 0.2648 target_work(ls_wunit_k1) = 0.033 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2648 r_free = 0.2648 target_work(ls_wunit_k1) = 0.033 | | occupancies: max = 1.00 min = 0.10 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.2648 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8806 moved from start: 0.1436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 27542 Z= 0.113 Angle : 0.550 10.779 37774 Z= 0.290 Chirality : 0.042 0.278 4323 Planarity : 0.004 0.047 4622 Dihedral : 16.919 169.659 4679 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.37 % Favored : 96.54 % Rotamer: Outliers : 1.10 % Allowed : 9.74 % Favored : 89.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.62 (0.15), residues: 3207 helix: 1.41 (0.15), residues: 1212 sheet: 0.50 (0.27), residues: 390 loop : -0.34 (0.16), residues: 1605 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 347 TYR 0.028 0.001 TYR E 55 PHE 0.012 0.001 PHE M 71 TRP 0.011 0.001 TRP C 938 HIS 0.004 0.001 HIS C 755 Details of bonding type rmsd covalent geometry : bond 0.00247 (27534) covalent geometry : angle 0.54334 (37762) hydrogen bonds : bond 0.03857 ( 1170) hydrogen bonds : angle 4.33806 ( 3241) metal coordination : bond 0.00762 ( 8) metal coordination : angle 4.68615 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6414 Ramachandran restraints generated. 3207 Oldfield, 0 Emsley, 3207 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6414 Ramachandran restraints generated. 3207 Oldfield, 0 Emsley, 3207 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 2722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 160 time to evaluate : 1.021 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 103 MET cc_start: 0.9403 (mpp) cc_final: 0.9039 (mpp) REVERT: C 402 GLU cc_start: 0.8676 (OUTLIER) cc_final: 0.8467 (pm20) REVERT: C 630 MET cc_start: 0.9160 (mmm) cc_final: 0.8684 (tpp) REVERT: D 155 MET cc_start: 0.9519 (tpt) cc_final: 0.8699 (tpp) REVERT: D 220 GLU cc_start: 0.9443 (OUTLIER) cc_final: 0.9212 (mm-30) REVERT: D 404 ASP cc_start: 0.9262 (t70) cc_final: 0.8989 (t0) REVERT: D 535 ASP cc_start: 0.9093 (t0) cc_final: 0.8480 (t70) REVERT: E 70 LEU cc_start: 0.9093 (mp) cc_final: 0.8594 (mp) REVERT: E 88 GLU cc_start: 0.7938 (mp0) cc_final: 0.7704 (mp0) REVERT: E 89 LYS cc_start: 0.7522 (mttt) cc_final: 0.7188 (mtmt) REVERT: F 105 ASN cc_start: 0.8134 (t0) cc_final: 0.7862 (t0) REVERT: F 147 MET cc_start: 0.9598 (tmm) cc_final: 0.9355 (tmm) REVERT: M 43 ASP cc_start: 0.8859 (t0) cc_final: 0.8529 (t0) outliers start: 29 outliers final: 12 residues processed: 180 average time/residue: 0.1478 time to fit residues: 45.0318 Evaluate side-chains 164 residues out of total 2722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 150 time to evaluate : 0.915 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 72 GLU Chi-restraints excluded: chain C residue 402 GLU Chi-restraints excluded: chain C residue 475 VAL Chi-restraints excluded: chain D residue 220 GLU Chi-restraints excluded: chain D residue 252 PHE Chi-restraints excluded: chain E residue 91 LEU Chi-restraints excluded: chain E residue 92 SER Chi-restraints excluded: chain E residue 103 LEU Chi-restraints excluded: chain F residue 222 LEU Chi-restraints excluded: chain F residue 224 THR Chi-restraints excluded: chain F residue 229 ILE Chi-restraints excluded: chain M residue 46 VAL Chi-restraints excluded: chain M residue 48 VAL Chi-restraints excluded: chain M residue 146 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 312 optimal weight: 3.9990 chunk 217 optimal weight: 2.9990 chunk 231 optimal weight: 1.9990 chunk 139 optimal weight: 10.0000 chunk 304 optimal weight: 2.9990 chunk 66 optimal weight: 1.9990 chunk 148 optimal weight: 7.9990 chunk 298 optimal weight: 5.9990 chunk 142 optimal weight: 10.0000 chunk 126 optimal weight: 10.0000 chunk 266 optimal weight: 1.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 64 GLN ** M 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.053890 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2847 r_free = 0.2847 target = 0.037475 restraints weight = 138742.102| |-----------------------------------------------------------------------------| r_work (start): 0.2778 rms_B_bonded: 4.28 r_work: 0.2619 rms_B_bonded: 5.00 restraints_weight: 0.5000 r_work (final): 0.2619 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2612 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2612 r_free = 0.2612 target_work(ls_wunit_k1) = 0.032 | | occupancies: max = 1.00 min = 0.10 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2612 r_free = 0.2612 target_work(ls_wunit_k1) = 0.032 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.2612 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8843 moved from start: 0.1623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 27542 Z= 0.146 Angle : 0.553 9.790 37774 Z= 0.291 Chirality : 0.042 0.296 4323 Planarity : 0.004 0.044 4622 Dihedral : 16.816 170.437 4676 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.52 % Favored : 96.38 % Rotamer: Outliers : 1.22 % Allowed : 11.87 % Favored : 86.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.73 (0.15), residues: 3207 helix: 1.56 (0.15), residues: 1213 sheet: 0.45 (0.27), residues: 390 loop : -0.30 (0.16), residues: 1604 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 347 TYR 0.027 0.001 TYR E 55 PHE 0.010 0.001 PHE D 131 TRP 0.010 0.001 TRP C 938 HIS 0.007 0.001 HIS C 755 Details of bonding type rmsd covalent geometry : bond 0.00327 (27534) covalent geometry : angle 0.54783 (37762) hydrogen bonds : bond 0.03909 ( 1170) hydrogen bonds : angle 4.21497 ( 3241) metal coordination : bond 0.00992 ( 8) metal coordination : angle 4.43447 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6414 Ramachandran restraints generated. 3207 Oldfield, 0 Emsley, 3207 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6414 Ramachandran restraints generated. 3207 Oldfield, 0 Emsley, 3207 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 2722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 157 time to evaluate : 0.850 Fit side-chains revert: symmetry clash REVERT: C 103 MET cc_start: 0.9408 (mpp) cc_final: 0.9057 (mpp) REVERT: C 402 GLU cc_start: 0.8697 (OUTLIER) cc_final: 0.8485 (pm20) REVERT: C 630 MET cc_start: 0.9196 (mmm) cc_final: 0.8726 (tpp) REVERT: C 1137 VAL cc_start: 0.9247 (OUTLIER) cc_final: 0.9045 (m) REVERT: D 155 MET cc_start: 0.9534 (tpt) cc_final: 0.8785 (tpp) REVERT: D 220 GLU cc_start: 0.9446 (OUTLIER) cc_final: 0.9233 (mm-30) REVERT: D 404 ASP cc_start: 0.9342 (t70) cc_final: 0.9040 (t0) REVERT: D 535 ASP cc_start: 0.9112 (t0) cc_final: 0.8560 (t70) REVERT: D 1036 GLU cc_start: 0.9028 (tm-30) cc_final: 0.8617 (tm-30) REVERT: D 1112 MET cc_start: 0.7589 (tmm) cc_final: 0.6936 (tmm) REVERT: E 34 ILE cc_start: 0.8561 (mm) cc_final: 0.8312 (mm) REVERT: E 88 GLU cc_start: 0.7968 (mp0) cc_final: 0.7634 (mp0) REVERT: E 89 LYS cc_start: 0.7548 (mttt) cc_final: 0.7174 (mtmt) REVERT: F 105 ASN cc_start: 0.8149 (t0) cc_final: 0.7868 (t0) REVERT: F 147 MET cc_start: 0.9591 (tmm) cc_final: 0.9335 (tmm) REVERT: M 43 ASP cc_start: 0.8981 (t0) cc_final: 0.8656 (t0) outliers start: 32 outliers final: 18 residues processed: 180 average time/residue: 0.1560 time to fit residues: 47.6893 Evaluate side-chains 170 residues out of total 2722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 149 time to evaluate : 1.061 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 VAL Chi-restraints excluded: chain B residue 13 VAL Chi-restraints excluded: chain B residue 177 LYS Chi-restraints excluded: chain C residue 72 GLU Chi-restraints excluded: chain C residue 402 GLU Chi-restraints excluded: chain C residue 475 VAL Chi-restraints excluded: chain C residue 520 VAL Chi-restraints excluded: chain C residue 1102 VAL Chi-restraints excluded: chain C residue 1137 VAL Chi-restraints excluded: chain D residue 220 GLU Chi-restraints excluded: chain D residue 252 PHE Chi-restraints excluded: chain D residue 666 THR Chi-restraints excluded: chain E residue 82 VAL Chi-restraints excluded: chain E residue 92 SER Chi-restraints excluded: chain E residue 103 LEU Chi-restraints excluded: chain F residue 224 THR Chi-restraints excluded: chain F residue 229 ILE Chi-restraints excluded: chain M residue 46 VAL Chi-restraints excluded: chain M residue 48 VAL Chi-restraints excluded: chain M residue 146 ASP Chi-restraints excluded: chain M residue 154 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 108 optimal weight: 0.9980 chunk 250 optimal weight: 5.9990 chunk 73 optimal weight: 3.9990 chunk 10 optimal weight: 0.5980 chunk 240 optimal weight: 9.9990 chunk 159 optimal weight: 9.9990 chunk 121 optimal weight: 6.9990 chunk 255 optimal weight: 0.9990 chunk 70 optimal weight: 6.9990 chunk 247 optimal weight: 3.9990 chunk 275 optimal weight: 10.0000 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 64 ASN M 72 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.053814 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2851 r_free = 0.2851 target = 0.037582 restraints weight = 136397.670| |-----------------------------------------------------------------------------| r_work (start): 0.2783 rms_B_bonded: 4.22 r_work: 0.2624 rms_B_bonded: 4.95 restraints_weight: 0.5000 r_work (final): 0.2624 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2614 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2614 r_free = 0.2614 target_work(ls_wunit_k1) = 0.032 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2614 r_free = 0.2614 target_work(ls_wunit_k1) = 0.032 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.2614 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8840 moved from start: 0.1811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 27542 Z= 0.131 Angle : 0.544 10.528 37774 Z= 0.284 Chirality : 0.042 0.273 4323 Planarity : 0.004 0.043 4622 Dihedral : 16.724 172.105 4676 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.52 % Favored : 96.38 % Rotamer: Outliers : 1.56 % Allowed : 12.70 % Favored : 85.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.74 (0.15), residues: 3207 helix: 1.61 (0.15), residues: 1217 sheet: 0.52 (0.28), residues: 372 loop : -0.35 (0.16), residues: 1618 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 161 TYR 0.026 0.001 TYR E 55 PHE 0.011 0.001 PHE D 131 TRP 0.010 0.001 TRP C 938 HIS 0.004 0.001 HIS C 755 Details of bonding type rmsd covalent geometry : bond 0.00299 (27534) covalent geometry : angle 0.53856 (37762) hydrogen bonds : bond 0.03730 ( 1170) hydrogen bonds : angle 4.16370 ( 3241) metal coordination : bond 0.00893 ( 8) metal coordination : angle 4.24719 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6414 Ramachandran restraints generated. 3207 Oldfield, 0 Emsley, 3207 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6414 Ramachandran restraints generated. 3207 Oldfield, 0 Emsley, 3207 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 2722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 156 time to evaluate : 1.005 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 95 MET cc_start: 0.8207 (tpp) cc_final: 0.7349 (tpp) REVERT: C 103 MET cc_start: 0.9405 (mpp) cc_final: 0.9049 (mpp) REVERT: C 1137 VAL cc_start: 0.9247 (OUTLIER) cc_final: 0.9040 (m) REVERT: D 155 MET cc_start: 0.9498 (tpt) cc_final: 0.8950 (tpp) REVERT: D 220 GLU cc_start: 0.9427 (OUTLIER) cc_final: 0.9211 (mm-30) REVERT: D 404 ASP cc_start: 0.9365 (t70) cc_final: 0.9060 (t0) REVERT: D 535 ASP cc_start: 0.9102 (t0) cc_final: 0.8512 (t0) REVERT: D 1112 MET cc_start: 0.7601 (tmm) cc_final: 0.6909 (tmm) REVERT: E 34 ILE cc_start: 0.8560 (mm) cc_final: 0.8311 (mm) REVERT: E 88 GLU cc_start: 0.8030 (mp0) cc_final: 0.7670 (mp0) REVERT: E 89 LYS cc_start: 0.7639 (mttt) cc_final: 0.7263 (mttt) REVERT: F 105 ASN cc_start: 0.8162 (t0) cc_final: 0.7876 (t0) REVERT: F 147 MET cc_start: 0.9581 (tmm) cc_final: 0.9326 (tmm) REVERT: M 43 ASP cc_start: 0.8993 (t0) cc_final: 0.8671 (t0) outliers start: 41 outliers final: 25 residues processed: 184 average time/residue: 0.1484 time to fit residues: 46.9034 Evaluate side-chains 174 residues out of total 2722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 147 time to evaluate : 0.886 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain B residue 13 VAL Chi-restraints excluded: chain B residue 177 LYS Chi-restraints excluded: chain C residue 72 GLU Chi-restraints excluded: chain C residue 402 GLU Chi-restraints excluded: chain C residue 475 VAL Chi-restraints excluded: chain C residue 841 HIS Chi-restraints excluded: chain C residue 1102 VAL Chi-restraints excluded: chain C residue 1137 VAL Chi-restraints excluded: chain D residue 220 GLU Chi-restraints excluded: chain D residue 252 PHE Chi-restraints excluded: chain D residue 666 THR Chi-restraints excluded: chain E residue 32 LEU Chi-restraints excluded: chain E residue 39 ILE Chi-restraints excluded: chain E residue 82 VAL Chi-restraints excluded: chain E residue 91 LEU Chi-restraints excluded: chain E residue 92 SER Chi-restraints excluded: chain E residue 103 LEU Chi-restraints excluded: chain F residue 154 ILE Chi-restraints excluded: chain F residue 202 VAL Chi-restraints excluded: chain F residue 224 THR Chi-restraints excluded: chain F residue 229 ILE Chi-restraints excluded: chain M residue 46 VAL Chi-restraints excluded: chain M residue 48 VAL Chi-restraints excluded: chain M residue 56 VAL Chi-restraints excluded: chain M residue 146 ASP Chi-restraints excluded: chain M residue 154 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 163 optimal weight: 20.0000 chunk 233 optimal weight: 2.9990 chunk 30 optimal weight: 6.9990 chunk 268 optimal weight: 3.9990 chunk 247 optimal weight: 2.9990 chunk 40 optimal weight: 9.9990 chunk 199 optimal weight: 9.9990 chunk 115 optimal weight: 5.9990 chunk 111 optimal weight: 8.9990 chunk 44 optimal weight: 0.0870 chunk 152 optimal weight: 10.0000 overall best weight: 3.2166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 679 ASN E 64 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.052936 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2820 r_free = 0.2820 target = 0.036673 restraints weight = 137346.000| |-----------------------------------------------------------------------------| r_work (start): 0.2754 rms_B_bonded: 4.22 r_work: 0.2597 rms_B_bonded: 4.88 restraints_weight: 0.5000 r_work (final): 0.2597 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2586 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2586 r_free = 0.2586 target_work(ls_wunit_k1) = 0.031 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2586 r_free = 0.2586 target_work(ls_wunit_k1) = 0.031 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.2586 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8867 moved from start: 0.1970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 27542 Z= 0.172 Angle : 0.573 9.771 37774 Z= 0.299 Chirality : 0.042 0.248 4323 Planarity : 0.004 0.044 4622 Dihedral : 16.720 172.567 4676 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.74 % Favored : 96.20 % Rotamer: Outliers : 1.86 % Allowed : 13.62 % Favored : 84.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.75 (0.15), residues: 3207 helix: 1.70 (0.15), residues: 1213 sheet: 0.33 (0.27), residues: 382 loop : -0.35 (0.16), residues: 1612 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 161 TYR 0.025 0.001 TYR E 55 PHE 0.013 0.001 PHE D 131 TRP 0.010 0.001 TRP D 723 HIS 0.004 0.001 HIS C 755 Details of bonding type rmsd covalent geometry : bond 0.00391 (27534) covalent geometry : angle 0.56823 (37762) hydrogen bonds : bond 0.04043 ( 1170) hydrogen bonds : angle 4.18551 ( 3241) metal coordination : bond 0.01175 ( 8) metal coordination : angle 4.27937 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6414 Ramachandran restraints generated. 3207 Oldfield, 0 Emsley, 3207 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6414 Ramachandran restraints generated. 3207 Oldfield, 0 Emsley, 3207 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 2722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 155 time to evaluate : 1.029 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 95 MET cc_start: 0.8437 (tpp) cc_final: 0.7683 (tpp) REVERT: C 103 MET cc_start: 0.9405 (mpp) cc_final: 0.9143 (mpp) REVERT: C 404 MET cc_start: 0.9278 (OUTLIER) cc_final: 0.8873 (ptm) REVERT: D 134 TYR cc_start: 0.8725 (OUTLIER) cc_final: 0.8507 (m-80) REVERT: D 155 MET cc_start: 0.9559 (tpt) cc_final: 0.9066 (tpp) REVERT: D 404 ASP cc_start: 0.9380 (t70) cc_final: 0.9064 (t0) REVERT: D 1112 MET cc_start: 0.7650 (tmm) cc_final: 0.6961 (tmm) REVERT: E 34 ILE cc_start: 0.8571 (mm) cc_final: 0.8321 (mm) REVERT: E 88 GLU cc_start: 0.8038 (mp0) cc_final: 0.7666 (mp0) REVERT: E 89 LYS cc_start: 0.7742 (mttt) cc_final: 0.7292 (mttt) REVERT: F 105 ASN cc_start: 0.8188 (t0) cc_final: 0.7878 (t0) REVERT: F 147 MET cc_start: 0.9586 (tmm) cc_final: 0.9319 (tmm) REVERT: M 43 ASP cc_start: 0.9090 (t0) cc_final: 0.8807 (t0) outliers start: 49 outliers final: 30 residues processed: 193 average time/residue: 0.1474 time to fit residues: 48.9440 Evaluate side-chains 177 residues out of total 2722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 145 time to evaluate : 1.026 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 VAL Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain B residue 13 VAL Chi-restraints excluded: chain B residue 177 LYS Chi-restraints excluded: chain B residue 184 GLU Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain C residue 311 VAL Chi-restraints excluded: chain C residue 402 GLU Chi-restraints excluded: chain C residue 404 MET Chi-restraints excluded: chain C residue 475 VAL Chi-restraints excluded: chain C residue 520 VAL Chi-restraints excluded: chain C residue 841 HIS Chi-restraints excluded: chain C residue 1102 VAL Chi-restraints excluded: chain D residue 134 TYR Chi-restraints excluded: chain D residue 252 PHE Chi-restraints excluded: chain D residue 666 THR Chi-restraints excluded: chain D residue 846 VAL Chi-restraints excluded: chain E residue 32 LEU Chi-restraints excluded: chain E residue 39 ILE Chi-restraints excluded: chain E residue 82 VAL Chi-restraints excluded: chain E residue 91 LEU Chi-restraints excluded: chain E residue 92 SER Chi-restraints excluded: chain E residue 103 LEU Chi-restraints excluded: chain F residue 154 ILE Chi-restraints excluded: chain F residue 202 VAL Chi-restraints excluded: chain F residue 224 THR Chi-restraints excluded: chain F residue 229 ILE Chi-restraints excluded: chain M residue 46 VAL Chi-restraints excluded: chain M residue 48 VAL Chi-restraints excluded: chain M residue 56 VAL Chi-restraints excluded: chain M residue 146 ASP Chi-restraints excluded: chain M residue 154 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 199 optimal weight: 6.9990 chunk 309 optimal weight: 5.9990 chunk 326 optimal weight: 10.0000 chunk 248 optimal weight: 8.9990 chunk 308 optimal weight: 0.8980 chunk 76 optimal weight: 0.6980 chunk 250 optimal weight: 6.9990 chunk 212 optimal weight: 3.9990 chunk 298 optimal weight: 4.9990 chunk 61 optimal weight: 2.9990 chunk 240 optimal weight: 7.9990 overall best weight: 2.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 20 GLN ** M 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.053087 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2825 r_free = 0.2825 target = 0.036821 restraints weight = 135793.830| |-----------------------------------------------------------------------------| r_work (start): 0.2758 rms_B_bonded: 4.19 r_work: 0.2599 rms_B_bonded: 4.91 restraints_weight: 0.5000 r_work (final): 0.2599 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2591 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2591 r_free = 0.2591 target_work(ls_wunit_k1) = 0.031 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2591 r_free = 0.2591 target_work(ls_wunit_k1) = 0.031 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.2591 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8864 moved from start: 0.2073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 27542 Z= 0.153 Angle : 0.562 9.807 37774 Z= 0.292 Chirality : 0.042 0.272 4323 Planarity : 0.004 0.045 4622 Dihedral : 16.683 173.164 4676 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.80 % Favored : 96.13 % Rotamer: Outliers : 1.56 % Allowed : 14.30 % Favored : 84.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.73 (0.15), residues: 3207 helix: 1.68 (0.15), residues: 1217 sheet: 0.20 (0.27), residues: 392 loop : -0.33 (0.16), residues: 1598 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 161 TYR 0.024 0.001 TYR E 55 PHE 0.012 0.001 PHE D1035 TRP 0.010 0.001 TRP D 723 HIS 0.003 0.001 HIS C 755 Details of bonding type rmsd covalent geometry : bond 0.00350 (27534) covalent geometry : angle 0.55659 (37762) hydrogen bonds : bond 0.03854 ( 1170) hydrogen bonds : angle 4.15870 ( 3241) metal coordination : bond 0.01007 ( 8) metal coordination : angle 4.23007 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6414 Ramachandran restraints generated. 3207 Oldfield, 0 Emsley, 3207 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6414 Ramachandran restraints generated. 3207 Oldfield, 0 Emsley, 3207 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 2722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 150 time to evaluate : 0.775 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 95 MET cc_start: 0.8417 (tpp) cc_final: 0.7746 (tpp) REVERT: B 123 MET cc_start: 0.9225 (ttp) cc_final: 0.9007 (ppp) REVERT: B 124 HIS cc_start: 0.9624 (OUTLIER) cc_final: 0.9317 (t70) REVERT: C 103 MET cc_start: 0.9397 (mpp) cc_final: 0.9131 (mpp) REVERT: C 159 MET cc_start: 0.9328 (mmm) cc_final: 0.9085 (tpp) REVERT: C 404 MET cc_start: 0.9283 (OUTLIER) cc_final: 0.8957 (ptm) REVERT: D 155 MET cc_start: 0.9431 (tpt) cc_final: 0.9168 (tpp) REVERT: D 404 ASP cc_start: 0.9382 (t70) cc_final: 0.9067 (t0) REVERT: D 820 MET cc_start: 0.9085 (ptm) cc_final: 0.8866 (ttp) REVERT: D 1035 PHE cc_start: 0.9237 (OUTLIER) cc_final: 0.8572 (t80) REVERT: D 1112 MET cc_start: 0.7668 (tmm) cc_final: 0.6955 (tmm) REVERT: E 34 ILE cc_start: 0.8598 (mm) cc_final: 0.8346 (mm) REVERT: E 88 GLU cc_start: 0.8001 (mp0) cc_final: 0.7615 (mp0) REVERT: E 89 LYS cc_start: 0.7686 (mttt) cc_final: 0.7227 (mttt) REVERT: F 105 ASN cc_start: 0.8183 (t0) cc_final: 0.7872 (t0) REVERT: F 147 MET cc_start: 0.9584 (tmm) cc_final: 0.9318 (tmm) REVERT: M 43 ASP cc_start: 0.9145 (t0) cc_final: 0.8903 (t0) outliers start: 41 outliers final: 28 residues processed: 178 average time/residue: 0.1518 time to fit residues: 45.9796 Evaluate side-chains 177 residues out of total 2722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 146 time to evaluate : 0.916 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 VAL Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain B residue 13 VAL Chi-restraints excluded: chain B residue 124 HIS Chi-restraints excluded: chain B residue 184 GLU Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain C residue 72 GLU Chi-restraints excluded: chain C residue 311 VAL Chi-restraints excluded: chain C residue 402 GLU Chi-restraints excluded: chain C residue 404 MET Chi-restraints excluded: chain C residue 475 VAL Chi-restraints excluded: chain C residue 520 VAL Chi-restraints excluded: chain C residue 841 HIS Chi-restraints excluded: chain C residue 1102 VAL Chi-restraints excluded: chain D residue 252 PHE Chi-restraints excluded: chain D residue 592 VAL Chi-restraints excluded: chain D residue 666 THR Chi-restraints excluded: chain D residue 1035 PHE Chi-restraints excluded: chain E residue 32 LEU Chi-restraints excluded: chain E residue 39 ILE Chi-restraints excluded: chain E residue 82 VAL Chi-restraints excluded: chain E residue 92 SER Chi-restraints excluded: chain E residue 103 LEU Chi-restraints excluded: chain F residue 154 ILE Chi-restraints excluded: chain F residue 224 THR Chi-restraints excluded: chain F residue 229 ILE Chi-restraints excluded: chain M residue 46 VAL Chi-restraints excluded: chain M residue 48 VAL Chi-restraints excluded: chain M residue 56 VAL Chi-restraints excluded: chain M residue 146 ASP Chi-restraints excluded: chain M residue 154 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 164 optimal weight: 9.9990 chunk 234 optimal weight: 10.0000 chunk 273 optimal weight: 6.9990 chunk 272 optimal weight: 3.9990 chunk 279 optimal weight: 9.9990 chunk 87 optimal weight: 9.9990 chunk 235 optimal weight: 0.8980 chunk 281 optimal weight: 1.9990 chunk 125 optimal weight: 7.9990 chunk 178 optimal weight: 6.9990 chunk 270 optimal weight: 0.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 494 HIS D 552 GLN ** M 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.052839 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2816 r_free = 0.2816 target = 0.036552 restraints weight = 137407.343| |-----------------------------------------------------------------------------| r_work (start): 0.2747 rms_B_bonded: 4.22 r_work: 0.2585 rms_B_bonded: 4.93 restraints_weight: 0.5000 r_work (final): 0.2585 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2576 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2576 r_free = 0.2576 target_work(ls_wunit_k1) = 0.031 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2576 r_free = 0.2576 target_work(ls_wunit_k1) = 0.031 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.2576 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8876 moved from start: 0.2179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 27542 Z= 0.163 Angle : 0.570 9.672 37774 Z= 0.296 Chirality : 0.042 0.245 4323 Planarity : 0.004 0.045 4622 Dihedral : 16.668 173.530 4676 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.84 % Favored : 96.10 % Rotamer: Outliers : 1.67 % Allowed : 14.83 % Favored : 83.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.74 (0.15), residues: 3207 helix: 1.70 (0.15), residues: 1219 sheet: 0.18 (0.27), residues: 391 loop : -0.33 (0.16), residues: 1597 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 161 TYR 0.024 0.001 TYR E 55 PHE 0.012 0.001 PHE D 131 TRP 0.010 0.001 TRP D 723 HIS 0.004 0.001 HIS C 755 Details of bonding type rmsd covalent geometry : bond 0.00370 (27534) covalent geometry : angle 0.56489 (37762) hydrogen bonds : bond 0.03934 ( 1170) hydrogen bonds : angle 4.16529 ( 3241) metal coordination : bond 0.01066 ( 8) metal coordination : angle 4.22898 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6414 Ramachandran restraints generated. 3207 Oldfield, 0 Emsley, 3207 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6414 Ramachandran restraints generated. 3207 Oldfield, 0 Emsley, 3207 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 2722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 154 time to evaluate : 1.073 Fit side-chains revert: symmetry clash REVERT: B 95 MET cc_start: 0.8386 (tpp) cc_final: 0.7771 (tpp) REVERT: B 123 MET cc_start: 0.9257 (ttp) cc_final: 0.9033 (ppp) REVERT: B 124 HIS cc_start: 0.9611 (OUTLIER) cc_final: 0.9307 (t70) REVERT: C 103 MET cc_start: 0.9394 (mpp) cc_final: 0.9115 (mpp) REVERT: C 404 MET cc_start: 0.9277 (OUTLIER) cc_final: 0.8954 (ptm) REVERT: D 155 MET cc_start: 0.9472 (tpt) cc_final: 0.9224 (tpp) REVERT: D 404 ASP cc_start: 0.9414 (t70) cc_final: 0.9096 (t0) REVERT: D 1035 PHE cc_start: 0.9229 (OUTLIER) cc_final: 0.8600 (t80) REVERT: D 1112 MET cc_start: 0.7657 (tmm) cc_final: 0.6973 (tmm) REVERT: E 34 ILE cc_start: 0.8586 (mm) cc_final: 0.8326 (mm) REVERT: E 40 ASP cc_start: 0.7484 (m-30) cc_final: 0.7211 (m-30) REVERT: E 89 LYS cc_start: 0.7859 (mttt) cc_final: 0.7321 (mttt) REVERT: F 105 ASN cc_start: 0.8145 (t0) cc_final: 0.7831 (t0) REVERT: F 147 MET cc_start: 0.9570 (tmm) cc_final: 0.9293 (tmm) REVERT: M 43 ASP cc_start: 0.9162 (t0) cc_final: 0.8947 (t0) outliers start: 44 outliers final: 30 residues processed: 186 average time/residue: 0.1480 time to fit residues: 47.1186 Evaluate side-chains 183 residues out of total 2722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 150 time to evaluate : 0.874 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 VAL Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain B residue 13 VAL Chi-restraints excluded: chain B residue 124 HIS Chi-restraints excluded: chain B residue 184 GLU Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain C residue 119 VAL Chi-restraints excluded: chain C residue 311 VAL Chi-restraints excluded: chain C residue 404 MET Chi-restraints excluded: chain C residue 475 VAL Chi-restraints excluded: chain C residue 520 VAL Chi-restraints excluded: chain C residue 841 HIS Chi-restraints excluded: chain C residue 1102 VAL Chi-restraints excluded: chain D residue 252 PHE Chi-restraints excluded: chain D residue 592 VAL Chi-restraints excluded: chain D residue 666 THR Chi-restraints excluded: chain D residue 793 TYR Chi-restraints excluded: chain D residue 846 VAL Chi-restraints excluded: chain D residue 1035 PHE Chi-restraints excluded: chain E residue 32 LEU Chi-restraints excluded: chain E residue 39 ILE Chi-restraints excluded: chain E residue 82 VAL Chi-restraints excluded: chain E residue 92 SER Chi-restraints excluded: chain E residue 103 LEU Chi-restraints excluded: chain F residue 131 THR Chi-restraints excluded: chain F residue 154 ILE Chi-restraints excluded: chain F residue 224 THR Chi-restraints excluded: chain F residue 229 ILE Chi-restraints excluded: chain M residue 46 VAL Chi-restraints excluded: chain M residue 48 VAL Chi-restraints excluded: chain M residue 56 VAL Chi-restraints excluded: chain M residue 146 ASP Chi-restraints excluded: chain M residue 154 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 317 optimal weight: 7.9990 chunk 141 optimal weight: 8.9990 chunk 286 optimal weight: 20.0000 chunk 18 optimal weight: 6.9990 chunk 66 optimal weight: 3.9990 chunk 69 optimal weight: 9.9990 chunk 320 optimal weight: 9.9990 chunk 241 optimal weight: 1.9990 chunk 36 optimal weight: 0.1980 chunk 122 optimal weight: 8.9990 chunk 262 optimal weight: 0.0570 overall best weight: 2.6504 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** M 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.052852 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2801 r_free = 0.2801 target = 0.036458 restraints weight = 136974.605| |-----------------------------------------------------------------------------| r_work (start): 0.2734 rms_B_bonded: 4.26 r_work (final): 0.2734 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2735 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2735 r_free = 0.2735 target_work(ls_wunit_k1) = 0.035 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2735 r_free = 0.2735 target_work(ls_wunit_k1) = 0.035 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.2735 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8739 moved from start: 0.2255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 27542 Z= 0.151 Angle : 0.576 13.025 37774 Z= 0.297 Chirality : 0.042 0.197 4323 Planarity : 0.004 0.045 4622 Dihedral : 16.645 173.859 4676 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.99 % Favored : 95.98 % Rotamer: Outliers : 1.45 % Allowed : 15.21 % Favored : 83.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.76 (0.15), residues: 3207 helix: 1.72 (0.15), residues: 1216 sheet: 0.20 (0.27), residues: 391 loop : -0.32 (0.16), residues: 1600 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 59 TYR 0.024 0.001 TYR E 55 PHE 0.010 0.001 PHE D1035 TRP 0.010 0.001 TRP C 938 HIS 0.003 0.001 HIS D 748 Details of bonding type rmsd covalent geometry : bond 0.00343 (27534) covalent geometry : angle 0.57149 (37762) hydrogen bonds : bond 0.03839 ( 1170) hydrogen bonds : angle 4.15192 ( 3241) metal coordination : bond 0.00993 ( 8) metal coordination : angle 4.18583 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6414 Ramachandran restraints generated. 3207 Oldfield, 0 Emsley, 3207 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6414 Ramachandran restraints generated. 3207 Oldfield, 0 Emsley, 3207 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 2722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 152 time to evaluate : 0.772 Fit side-chains revert: symmetry clash REVERT: B 95 MET cc_start: 0.8245 (tpp) cc_final: 0.7657 (tpp) REVERT: B 124 HIS cc_start: 0.9560 (OUTLIER) cc_final: 0.9335 (t70) REVERT: C 103 MET cc_start: 0.9183 (mpp) cc_final: 0.8921 (mpp) REVERT: C 159 MET cc_start: 0.9080 (tpp) cc_final: 0.7869 (mpp) REVERT: C 404 MET cc_start: 0.9093 (OUTLIER) cc_final: 0.8627 (ptm) REVERT: D 155 MET cc_start: 0.9417 (tpt) cc_final: 0.9136 (tpp) REVERT: D 404 ASP cc_start: 0.9257 (t70) cc_final: 0.8904 (t0) REVERT: D 475 MET cc_start: 0.9027 (ttp) cc_final: 0.8768 (ttp) REVERT: D 623 ASP cc_start: 0.8669 (p0) cc_final: 0.8266 (p0) REVERT: D 1035 PHE cc_start: 0.9142 (OUTLIER) cc_final: 0.8553 (t80) REVERT: D 1112 MET cc_start: 0.7470 (tmm) cc_final: 0.6853 (tmm) REVERT: E 34 ILE cc_start: 0.8402 (mm) cc_final: 0.8183 (mm) REVERT: E 89 LYS cc_start: 0.7875 (mttt) cc_final: 0.7530 (mttt) REVERT: F 105 ASN cc_start: 0.8061 (t0) cc_final: 0.7759 (t0) REVERT: F 147 MET cc_start: 0.9476 (tmm) cc_final: 0.9180 (tmm) REVERT: F 182 LEU cc_start: 0.8260 (OUTLIER) cc_final: 0.8032 (pp) REVERT: M 43 ASP cc_start: 0.9052 (t0) cc_final: 0.8809 (t0) outliers start: 38 outliers final: 29 residues processed: 180 average time/residue: 0.1482 time to fit residues: 45.4409 Evaluate side-chains 183 residues out of total 2722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 150 time to evaluate : 1.020 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 VAL Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain B residue 13 VAL Chi-restraints excluded: chain B residue 124 HIS Chi-restraints excluded: chain B residue 184 GLU Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain C residue 119 VAL Chi-restraints excluded: chain C residue 311 VAL Chi-restraints excluded: chain C residue 404 MET Chi-restraints excluded: chain C residue 475 VAL Chi-restraints excluded: chain C residue 520 VAL Chi-restraints excluded: chain C residue 841 HIS Chi-restraints excluded: chain C residue 1102 VAL Chi-restraints excluded: chain D residue 252 PHE Chi-restraints excluded: chain D residue 592 VAL Chi-restraints excluded: chain D residue 666 THR Chi-restraints excluded: chain D residue 793 TYR Chi-restraints excluded: chain D residue 846 VAL Chi-restraints excluded: chain D residue 1035 PHE Chi-restraints excluded: chain E residue 32 LEU Chi-restraints excluded: chain E residue 39 ILE Chi-restraints excluded: chain E residue 82 VAL Chi-restraints excluded: chain E residue 91 LEU Chi-restraints excluded: chain E residue 92 SER Chi-restraints excluded: chain F residue 131 THR Chi-restraints excluded: chain F residue 154 ILE Chi-restraints excluded: chain F residue 182 LEU Chi-restraints excluded: chain F residue 224 THR Chi-restraints excluded: chain M residue 46 VAL Chi-restraints excluded: chain M residue 48 VAL Chi-restraints excluded: chain M residue 56 VAL Chi-restraints excluded: chain M residue 146 ASP Chi-restraints excluded: chain M residue 154 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 291 optimal weight: 10.0000 chunk 258 optimal weight: 5.9990 chunk 20 optimal weight: 3.9990 chunk 61 optimal weight: 5.9990 chunk 110 optimal weight: 4.9990 chunk 35 optimal weight: 9.9990 chunk 214 optimal weight: 7.9990 chunk 0 optimal weight: 20.0000 chunk 160 optimal weight: 6.9990 chunk 91 optimal weight: 10.0000 chunk 36 optimal weight: 20.0000 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 90 GLN ** M 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.051627 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2750 r_free = 0.2750 target = 0.035215 restraints weight = 139380.743| |-----------------------------------------------------------------------------| r_work (start): 0.2677 rms_B_bonded: 4.21 r_work (final): 0.2677 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2678 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2678 r_free = 0.2678 target_work(ls_wunit_k1) = 0.033 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2678 r_free = 0.2678 target_work(ls_wunit_k1) = 0.033 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.2678 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8799 moved from start: 0.2421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.085 27542 Z= 0.271 Angle : 0.673 12.849 37774 Z= 0.348 Chirality : 0.044 0.215 4323 Planarity : 0.004 0.058 4622 Dihedral : 16.751 172.903 4674 Min Nonbonded Distance : 1.904 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 1.37 % Allowed : 15.44 % Favored : 83.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.51 (0.15), residues: 3207 helix: 1.49 (0.15), residues: 1221 sheet: -0.14 (0.26), residues: 406 loop : -0.40 (0.16), residues: 1580 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 347 TYR 0.023 0.002 TYR E 55 PHE 0.019 0.001 PHE D1035 TRP 0.013 0.002 TRP D 723 HIS 0.008 0.001 HIS D 145 Details of bonding type rmsd covalent geometry : bond 0.00612 (27534) covalent geometry : angle 0.66753 (37762) hydrogen bonds : bond 0.04967 ( 1170) hydrogen bonds : angle 4.44896 ( 3241) metal coordination : bond 0.01815 ( 8) metal coordination : angle 4.74549 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6414 Ramachandran restraints generated. 3207 Oldfield, 0 Emsley, 3207 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6414 Ramachandran restraints generated. 3207 Oldfield, 0 Emsley, 3207 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 2722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 152 time to evaluate : 0.949 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 95 MET cc_start: 0.8267 (tpp) cc_final: 0.8041 (tpp) REVERT: B 124 HIS cc_start: 0.9588 (OUTLIER) cc_final: 0.9353 (t70) REVERT: C 103 MET cc_start: 0.9168 (mpp) cc_final: 0.8928 (mpp) REVERT: C 122 CYS cc_start: 0.9384 (m) cc_final: 0.8734 (m) REVERT: C 404 MET cc_start: 0.9128 (OUTLIER) cc_final: 0.8698 (ptm) REVERT: D 155 MET cc_start: 0.9445 (tpt) cc_final: 0.9119 (tpp) REVERT: D 404 ASP cc_start: 0.9287 (t70) cc_final: 0.9066 (t0) REVERT: D 475 MET cc_start: 0.9029 (ttp) cc_final: 0.8763 (ttp) REVERT: D 820 MET cc_start: 0.9016 (ttp) cc_final: 0.8345 (ppp) REVERT: D 1035 PHE cc_start: 0.9218 (OUTLIER) cc_final: 0.8694 (t80) REVERT: E 89 LYS cc_start: 0.7942 (mttt) cc_final: 0.7538 (mttt) REVERT: F 105 ASN cc_start: 0.8224 (t0) cc_final: 0.7899 (t0) REVERT: F 147 MET cc_start: 0.9442 (tmm) cc_final: 0.9105 (tmm) REVERT: F 182 LEU cc_start: 0.8315 (OUTLIER) cc_final: 0.8045 (pp) outliers start: 36 outliers final: 28 residues processed: 177 average time/residue: 0.1544 time to fit residues: 46.5410 Evaluate side-chains 181 residues out of total 2722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 149 time to evaluate : 1.022 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 VAL Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain B residue 13 VAL Chi-restraints excluded: chain B residue 124 HIS Chi-restraints excluded: chain B residue 184 GLU Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain C residue 119 VAL Chi-restraints excluded: chain C residue 311 VAL Chi-restraints excluded: chain C residue 404 MET Chi-restraints excluded: chain C residue 475 VAL Chi-restraints excluded: chain C residue 520 VAL Chi-restraints excluded: chain C residue 841 HIS Chi-restraints excluded: chain C residue 1102 VAL Chi-restraints excluded: chain D residue 252 PHE Chi-restraints excluded: chain D residue 592 VAL Chi-restraints excluded: chain D residue 666 THR Chi-restraints excluded: chain D residue 793 TYR Chi-restraints excluded: chain D residue 846 VAL Chi-restraints excluded: chain D residue 1035 PHE Chi-restraints excluded: chain E residue 32 LEU Chi-restraints excluded: chain E residue 39 ILE Chi-restraints excluded: chain E residue 82 VAL Chi-restraints excluded: chain E residue 92 SER Chi-restraints excluded: chain F residue 131 THR Chi-restraints excluded: chain F residue 154 ILE Chi-restraints excluded: chain F residue 182 LEU Chi-restraints excluded: chain F residue 224 THR Chi-restraints excluded: chain M residue 46 VAL Chi-restraints excluded: chain M residue 48 VAL Chi-restraints excluded: chain M residue 56 VAL Chi-restraints excluded: chain M residue 146 ASP Chi-restraints excluded: chain M residue 154 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 69 optimal weight: 0.9980 chunk 287 optimal weight: 4.9990 chunk 296 optimal weight: 9.9990 chunk 144 optimal weight: 1.9990 chunk 244 optimal weight: 0.8980 chunk 162 optimal weight: 5.9990 chunk 88 optimal weight: 0.0040 chunk 155 optimal weight: 8.9990 chunk 271 optimal weight: 0.3980 chunk 206 optimal weight: 7.9990 chunk 196 optimal weight: 1.9990 overall best weight: 0.8594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.053249 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2813 r_free = 0.2813 target = 0.036806 restraints weight = 136154.791| |-----------------------------------------------------------------------------| r_work (start): 0.2746 rms_B_bonded: 4.28 r_work (final): 0.2746 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2745 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2745 r_free = 0.2745 target_work(ls_wunit_k1) = 0.035 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2745 r_free = 0.2745 target_work(ls_wunit_k1) = 0.035 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.2745 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8725 moved from start: 0.2434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 27542 Z= 0.115 Angle : 0.585 11.527 37774 Z= 0.301 Chirality : 0.042 0.219 4323 Planarity : 0.004 0.043 4622 Dihedral : 16.617 172.477 4674 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 1.10 % Allowed : 15.94 % Favored : 82.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.71 (0.15), residues: 3207 helix: 1.68 (0.15), residues: 1216 sheet: 0.18 (0.27), residues: 391 loop : -0.35 (0.16), residues: 1600 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 347 TYR 0.025 0.001 TYR E 55 PHE 0.010 0.001 PHE C 153 TRP 0.015 0.001 TRP C 938 HIS 0.003 0.001 HIS F 91 Details of bonding type rmsd covalent geometry : bond 0.00255 (27534) covalent geometry : angle 0.57972 (37762) hydrogen bonds : bond 0.03629 ( 1170) hydrogen bonds : angle 4.15130 ( 3241) metal coordination : bond 0.00738 ( 8) metal coordination : angle 4.55078 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5355.62 seconds wall clock time: 92 minutes 40.65 seconds (5560.65 seconds total)