Starting phenix.real_space_refine on Fri Jul 3 20:47:26 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ne7_49300/07_2026/9ne7_49300.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ne7_49300/07_2026/9ne7_49300.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.53 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9ne7_49300/07_2026/9ne7_49300.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ne7_49300/07_2026/9ne7_49300.map" model { file = "/net/cci-nas-00/data/ceres_data/9ne7_49300/07_2026/9ne7_49300.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ne7_49300/07_2026/9ne7_49300.cif" } resolution = 3.53 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= 0.001 sd= 0.023 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Fe 4 7.16 5 P 41 5.49 5 S 102 5.16 5 C 10097 2.51 5 N 2715 2.21 5 O 3179 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 16138 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 9265 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1138, 9265 Classifications: {'peptide': 1138} Link IDs: {'PTRANS': 58, 'TRANS': 1079} Chain breaks: 1 Chain: "B" Number of atoms: 2008 Number of conformers: 1 Conformer: "" Number of residues, atoms: 261, 2008 Classifications: {'peptide': 261} Link IDs: {'PTRANS': 7, 'TRANS': 253} Chain: "C" Number of atoms: 2008 Number of conformers: 1 Conformer: "" Number of residues, atoms: 261, 2008 Classifications: {'peptide': 261} Link IDs: {'PTRANS': 7, 'TRANS': 253} Chain: "D" Number of atoms: 2008 Number of conformers: 1 Conformer: "" Number of residues, atoms: 261, 2008 Classifications: {'peptide': 261} Link IDs: {'PTRANS': 7, 'TRANS': 253} Chain: "P" Number of atoms: 412 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 412 Classifications: {'DNA': 20} Link IDs: {'rna3p': 19} Chain: "T" Number of atoms: 429 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 429 Classifications: {'DNA': 21} Link IDs: {'rna3p': 20} Chain: "A" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 8 Unusual residues: {'SF4': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 4815 SG CYS A 651 42.278 85.068 91.366 1.00 90.05 S ATOM 4831 SG CYS A 654 40.866 87.199 97.141 1.00 90.00 S ATOM 4897 SG CYS A 663 46.576 89.069 94.280 1.00 84.84 S ATOM 5621 SG CYS A 747 45.831 83.259 96.161 1.00 65.79 S Time building chain proxies: 3.02, per 1000 atoms: 0.19 Number of scatterers: 16138 At special positions: 0 Unit cell: (103.5, 110.124, 142.416, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Fe 4 26.01 S 102 16.00 P 41 15.00 O 3179 8.00 N 2715 7.00 C 10097 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: 1.09 Conformation dependent library (CDL) restraints added in 568.9 milliseconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" SF4 A1301 " pdb="FE4 SF4 A1301 " - pdb=" SG CYS A 747 " pdb="FE3 SF4 A1301 " - pdb=" SG CYS A 663 " pdb="FE2 SF4 A1301 " - pdb=" SG CYS A 654 " pdb="FE1 SF4 A1301 " - pdb=" SG CYS A 651 " Number of angles added : 12 3822 Ramachandran restraints generated. 1911 Oldfield, 0 Emsley, 1911 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3656 Finding SS restraints... Secondary structure from input PDB file: 54 helices and 20 sheets defined 34.4% alpha, 21.3% beta 18 base pairs and 33 stacking pairs defined. Time for finding SS restraints: 1.54 Creating SS restraints... Processing helix chain 'A' and resid 30 through 47 removed outlier: 5.232A pdb=" N GLU A 36 " --> pdb=" O LEU A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 112 through 122 Processing helix chain 'A' and resid 159 through 181 Proline residue: A 172 - end of helix removed outlier: 3.628A pdb=" N ASP A 181 " --> pdb=" O ASN A 177 " (cutoff:3.500A) Processing helix chain 'A' and resid 214 through 216 No H-bonds generated for 'chain 'A' and resid 214 through 216' Processing helix chain 'A' and resid 227 through 236 Processing helix chain 'A' and resid 339 through 355 Processing helix chain 'A' and resid 368 through 379 Processing helix chain 'A' and resid 407 through 414 Processing helix chain 'A' and resid 418 through 422 Processing helix chain 'A' and resid 425 through 431 Processing helix chain 'A' and resid 440 through 451 removed outlier: 3.559A pdb=" N MET A 444 " --> pdb=" O ASP A 440 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N CYS A 445 " --> pdb=" O PRO A 441 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N ARG A 446 " --> pdb=" O GLU A 442 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N THR A 449 " --> pdb=" O CYS A 445 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N GLU A 450 " --> pdb=" O ARG A 446 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N GLN A 451 " --> pdb=" O MET A 447 " (cutoff:3.500A) Processing helix chain 'A' and resid 452 through 473 removed outlier: 3.607A pdb=" N TYR A 473 " --> pdb=" O LEU A 469 " (cutoff:3.500A) Processing helix chain 'A' and resid 473 through 482 Processing helix chain 'A' and resid 488 through 495 removed outlier: 3.620A pdb=" N LYS A 495 " --> pdb=" O GLU A 491 " (cutoff:3.500A) Processing helix chain 'A' and resid 496 through 512 removed outlier: 3.627A pdb=" N LEU A 500 " --> pdb=" O GLY A 496 " (cutoff:3.500A) Processing helix chain 'A' and resid 563 through 572 Processing helix chain 'A' and resid 573 through 585 Processing helix chain 'A' and resid 589 through 593 removed outlier: 4.271A pdb=" N GLN A 592 " --> pdb=" O PRO A 589 " (cutoff:3.500A) Processing helix chain 'A' and resid 595 through 612 Processing helix chain 'A' and resid 629 through 638 Processing helix chain 'A' and resid 647 through 652 removed outlier: 3.563A pdb=" N CYS A 651 " --> pdb=" O ASP A 647 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ALA A 652 " --> pdb=" O GLU A 648 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 647 through 652' Processing helix chain 'A' and resid 679 through 690 Processing helix chain 'A' and resid 711 through 731 removed outlier: 3.920A pdb=" N LYS A 729 " --> pdb=" O ASP A 725 " (cutoff:3.500A) Processing helix chain 'A' and resid 753 through 786 Processing helix chain 'A' and resid 787 through 820 removed outlier: 4.616A pdb=" N TYR A 816 " --> pdb=" O LEU A 812 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N GLY A 817 " --> pdb=" O ASN A 813 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N VAL A 819 " --> pdb=" O PHE A 815 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N MET A 820 " --> pdb=" O TYR A 816 " (cutoff:3.500A) Processing helix chain 'A' and resid 828 through 854 removed outlier: 3.889A pdb=" N ALA A 832 " --> pdb=" O SER A 828 " (cutoff:3.500A) Processing helix chain 'A' and resid 892 through 905 Processing helix chain 'A' and resid 982 through 993 Processing helix chain 'A' and resid 998 through 1019 removed outlier: 3.838A pdb=" N TYR A1012 " --> pdb=" O LYS A1008 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N TRP A1013 " --> pdb=" O VAL A1009 " (cutoff:3.500A) Processing helix chain 'A' and resid 1028 through 1034 Processing helix chain 'A' and resid 1052 through 1062 Processing helix chain 'A' and resid 1065 through 1069 removed outlier: 3.970A pdb=" N MET A1068 " --> pdb=" O GLY A1065 " (cutoff:3.500A) Processing helix chain 'A' and resid 1102 through 1114 removed outlier: 3.811A pdb=" N LEU A1114 " --> pdb=" O LEU A1110 " (cutoff:3.500A) Processing helix chain 'A' and resid 1123 through 1128 removed outlier: 4.018A pdb=" N LEU A1128 " --> pdb=" O ILE A1124 " (cutoff:3.500A) Processing helix chain 'A' and resid 1129 through 1145 removed outlier: 3.598A pdb=" N TYR A1133 " --> pdb=" O ASP A1129 " (cutoff:3.500A) Processing helix chain 'A' and resid 1145 through 1152 Processing helix chain 'A' and resid 1164 through 1176 Processing helix chain 'B' and resid 9 through 19 removed outlier: 3.919A pdb=" N LEU B 19 " --> pdb=" O VAL B 15 " (cutoff:3.500A) Processing helix chain 'B' and resid 71 through 82 removed outlier: 3.630A pdb=" N MET B 75 " --> pdb=" O ASN B 71 " (cutoff:3.500A) Processing helix chain 'B' and resid 141 through 155 Processing helix chain 'B' and resid 209 through 217 Processing helix chain 'B' and resid 218 through 222 removed outlier: 3.833A pdb=" N SER B 222 " --> pdb=" O THR B 219 " (cutoff:3.500A) Processing helix chain 'C' and resid 9 through 23 removed outlier: 3.538A pdb=" N LYS C 13 " --> pdb=" O GLY C 9 " (cutoff:3.500A) removed outlier: 5.113A pdb=" N ASP C 21 " --> pdb=" O GLU C 17 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N LEU C 22 " --> pdb=" O ALA C 18 " (cutoff:3.500A) Processing helix chain 'C' and resid 55 through 57 No H-bonds generated for 'chain 'C' and resid 55 through 57' Processing helix chain 'C' and resid 71 through 80 removed outlier: 3.772A pdb=" N MET C 75 " --> pdb=" O ASN C 71 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N LYS C 77 " --> pdb=" O THR C 73 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ILE C 78 " --> pdb=" O SER C 74 " (cutoff:3.500A) Processing helix chain 'C' and resid 141 through 153 removed outlier: 3.514A pdb=" N HIS C 153 " --> pdb=" O ARG C 149 " (cutoff:3.500A) Processing helix chain 'C' and resid 209 through 216 Processing helix chain 'C' and resid 217 through 222 Proline residue: C 220 - end of helix No H-bonds generated for 'chain 'C' and resid 217 through 222' Processing helix chain 'D' and resid 9 through 20 removed outlier: 3.576A pdb=" N LYS D 13 " --> pdb=" O GLY D 9 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 57 No H-bonds generated for 'chain 'D' and resid 55 through 57' Processing helix chain 'D' and resid 72 through 80 Processing helix chain 'D' and resid 141 through 153 removed outlier: 3.910A pdb=" N HIS D 153 " --> pdb=" O ARG D 149 " (cutoff:3.500A) Processing helix chain 'D' and resid 208 through 217 removed outlier: 3.723A pdb=" N LEU D 212 " --> pdb=" O ALA D 208 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N LYS D 217 " --> pdb=" O ASN D 213 " (cutoff:3.500A) Processing helix chain 'D' and resid 218 through 222 Processing sheet with id=AA1, first strand: chain 'A' and resid 68 through 70 Processing sheet with id=AA2, first strand: chain 'A' and resid 68 through 70 removed outlier: 3.827A pdb=" N ASN A 65 " --> pdb=" O TYR A 85 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N ILE A 87 " --> pdb=" O LEU A 63 " (cutoff:3.500A) removed outlier: 5.517A pdb=" N LEU A 63 " --> pdb=" O ILE A 87 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N TRP A 243 " --> pdb=" O ARG A 260 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 130 through 136 removed outlier: 3.826A pdb=" N LYS A 130 " --> pdb=" O SER A 156 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N LYS A 136 " --> pdb=" O ARG A 150 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ARG A 150 " --> pdb=" O LYS A 136 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N ASN A 151 " --> pdb=" O THR A 108 " (cutoff:3.500A) removed outlier: 5.041A pdb=" N THR A 108 " --> pdb=" O ASN A 151 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N LEU A 155 " --> pdb=" O PHE A 104 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N PHE A 104 " --> pdb=" O LEU A 155 " (cutoff:3.500A) removed outlier: 7.060A pdb=" N TYR A 105 " --> pdb=" O MET A 221 " (cutoff:3.500A) removed outlier: 4.599A pdb=" N MET A 221 " --> pdb=" O TYR A 105 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N ALA A 107 " --> pdb=" O VAL A 219 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 273 through 278 removed outlier: 3.741A pdb=" N SER A 297 " --> pdb=" O ALA A 275 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N ALA A 277 " --> pdb=" O MET A 295 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N MET A 295 " --> pdb=" O ALA A 277 " (cutoff:3.500A) removed outlier: 6.086A pdb=" N MET A 294 " --> pdb=" O ASN A 309 " (cutoff:3.500A) removed outlier: 7.857A pdb=" N PHE A 335 " --> pdb=" O GLY A 304 " (cutoff:3.500A) removed outlier: 6.142A pdb=" N LEU A 306 " --> pdb=" O PHE A 335 " (cutoff:3.500A) removed outlier: 7.301A pdb=" N GLU A 337 " --> pdb=" O LEU A 306 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N THR A 308 " --> pdb=" O GLU A 337 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 358 through 361 Processing sheet with id=AA6, first strand: chain 'A' and resid 390 through 391 removed outlier: 3.906A pdb=" N GLN A 390 " --> pdb=" O LYS A 398 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N LYS A 398 " --> pdb=" O GLN A 390 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'A' and resid 534 through 539 removed outlier: 6.763A pdb=" N GLU A 674 " --> pdb=" O ASP A 535 " (cutoff:3.500A) removed outlier: 5.008A pdb=" N GLU A 537 " --> pdb=" O ARG A 672 " (cutoff:3.500A) removed outlier: 7.291A pdb=" N ARG A 672 " --> pdb=" O GLU A 537 " (cutoff:3.500A) removed outlier: 5.145A pdb=" N TYR A 539 " --> pdb=" O GLN A 670 " (cutoff:3.500A) removed outlier: 7.298A pdb=" N GLN A 670 " --> pdb=" O TYR A 539 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N MET A 667 " --> pdb=" O THR A 744 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N THR A 744 " --> pdb=" O MET A 667 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 545 through 546 removed outlier: 3.502A pdb=" N ARG A 855 " --> pdb=" O VAL A 867 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N TRP A 865 " --> pdb=" O LEU A 857 " (cutoff:3.500A) removed outlier: 5.160A pdb=" N LEU A 859 " --> pdb=" O GLY A 863 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N GLY A 863 " --> pdb=" O LEU A 859 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 550 through 553 removed outlier: 4.123A pdb=" N ALA A 939 " --> pdb=" O PHE A 959 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 875 through 879 Processing sheet with id=AB2, first strand: chain 'A' and resid 911 through 915 removed outlier: 7.428A pdb=" N THR A 920 " --> pdb=" O ALA A 914 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 1079 through 1080 removed outlier: 3.550A pdb=" N ILE A1079 " --> pdb=" O ILE A1094 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ILE A1094 " --> pdb=" O ILE A1079 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'A' and resid 1189 through 1191 removed outlier: 4.041A pdb=" N GLY A1191 " --> pdb=" O GLN D 125 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N GLN D 125 " --> pdb=" O GLY A1191 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'B' and resid 59 through 61 removed outlier: 3.619A pdb=" N ALA B 4 " --> pdb=" O LEU B 90 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N VAL C 167 " --> pdb=" O LEU C 182 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N SER C 172 " --> pdb=" O ALA C 157 " (cutoff:3.500A) removed outlier: 5.220A pdb=" N ALA C 157 " --> pdb=" O SER C 172 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LEU C 205 " --> pdb=" O ILE C 160 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 66 through 68 removed outlier: 3.819A pdb=" N SER B 39 " --> pdb=" O VAL B 48 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N VAL B 48 " --> pdb=" O SER B 39 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N GLN B 49 " --> pdb=" O LYS B 248 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LEU B 247 " --> pdb=" O TYR B 239 " (cutoff:3.500A) removed outlier: 4.606A pdb=" N LYS B 240 " --> pdb=" O THR B 224 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N THR B 224 " --> pdb=" O LYS B 240 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N MET B 229 " --> pdb=" O CYS B 135 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N VAL B 136 " --> pdb=" O GLU B 198 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 204 through 208 removed outlier: 3.654A pdb=" N LEU B 205 " --> pdb=" O ILE B 160 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N VAL B 158 " --> pdb=" O PHE B 207 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N ALA B 157 " --> pdb=" O SER B 172 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N SER B 172 " --> pdb=" O ALA B 157 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ASP D 113 " --> pdb=" O ASN B 179 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N ILE D 88 " --> pdb=" O LEU D 6 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 59 through 61 removed outlier: 4.356A pdb=" N THR C 59 " --> pdb=" O ARG C 5 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLU C 3 " --> pdb=" O ARG C 61 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N LEU C 99 " --> pdb=" O MET C 116 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ASN D 177 " --> pdb=" O GLU C 115 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N VAL D 167 " --> pdb=" O LEU D 182 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N SER D 172 " --> pdb=" O ALA D 157 " (cutoff:3.500A) removed outlier: 4.873A pdb=" N ALA D 157 " --> pdb=" O SER D 172 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N LEU D 205 " --> pdb=" O ILE D 160 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 66 through 67 removed outlier: 3.516A pdb=" N TYR C 250 " --> pdb=" O LEU C 47 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N THR C 51 " --> pdb=" O HIS C 246 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N TYR C 249 " --> pdb=" O VAL C 237 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N LEU C 251 " --> pdb=" O LEU C 235 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N LEU C 235 " --> pdb=" O LEU C 251 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LEU C 227 " --> pdb=" O VAL C 137 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 66 through 71 Processing sheet with id=AC2, first strand: chain 'D' and resid 196 through 198 removed outlier: 3.619A pdb=" N THR D 196 " --> pdb=" O LYS D 138 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N THR D 226 " --> pdb=" O GLU D 238 " (cutoff:3.500A) 686 hydrogen bonds defined for protein. 1944 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 42 hydrogen bonds 84 hydrogen bond angles 0 basepair planarities 18 basepair parallelities 33 stacking parallelities Total time for adding SS restraints: 3.44 Time building geometry restraints manager: 1.41 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.43: 6929 1.43 - 1.64: 9438 1.64 - 1.86: 158 1.86 - 2.07: 0 2.07 - 2.28: 12 Bond restraints: 16537 Sorted by residual: bond pdb=" C3' DT T 14 " pdb=" C2' DT T 14 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 9.39e+00 bond pdb=" C3' DT P 33 " pdb=" C2' DT P 33 " ideal model delta sigma weight residual 1.516 1.539 -0.023 8.00e-03 1.56e+04 8.50e+00 bond pdb=" C3' DT P 22 " pdb=" C2' DT P 22 " ideal model delta sigma weight residual 1.516 1.539 -0.023 8.00e-03 1.56e+04 8.43e+00 bond pdb=" C3' DT T 14 " pdb=" O3' DT T 14 " ideal model delta sigma weight residual 1.435 1.467 -0.032 1.30e-02 5.92e+03 6.08e+00 bond pdb=" C1' DT P 29 " pdb=" N1 DT P 29 " ideal model delta sigma weight residual 1.468 1.502 -0.034 1.40e-02 5.10e+03 5.74e+00 ... (remaining 16532 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.89: 21605 1.89 - 3.78: 773 3.78 - 5.67: 94 5.67 - 7.56: 36 7.56 - 9.44: 12 Bond angle restraints: 22520 Sorted by residual: angle pdb=" C ALA A1022 " pdb=" CA ALA A1022 " pdb=" CB ALA A1022 " ideal model delta sigma weight residual 116.63 110.20 6.43 1.16e+00 7.43e-01 3.08e+01 angle pdb=" N ASP B 243 " pdb=" CA ASP B 243 " pdb=" C ASP B 243 " ideal model delta sigma weight residual 110.44 104.10 6.34 1.20e+00 6.94e-01 2.79e+01 angle pdb=" C LEU A 424 " pdb=" N LYS A 425 " pdb=" CA LYS A 425 " ideal model delta sigma weight residual 121.54 130.32 -8.78 1.91e+00 2.74e-01 2.11e+01 angle pdb=" N3 DT P 22 " pdb=" C4 DT P 22 " pdb=" O4 DT P 22 " ideal model delta sigma weight residual 119.90 122.54 -2.64 6.00e-01 2.78e+00 1.93e+01 angle pdb=" N3 DT P 23 " pdb=" C4 DT P 23 " pdb=" O4 DT P 23 " ideal model delta sigma weight residual 119.90 122.49 -2.59 6.00e-01 2.78e+00 1.87e+01 ... (remaining 22515 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.62: 9420 28.62 - 57.24: 524 57.24 - 85.86: 66 85.86 - 114.48: 4 114.48 - 143.10: 1 Dihedral angle restraints: 10015 sinusoidal: 4374 harmonic: 5641 Sorted by residual: dihedral pdb=" CA MET A 359 " pdb=" C MET A 359 " pdb=" N VAL A 360 " pdb=" CA VAL A 360 " ideal model delta harmonic sigma weight residual -180.00 -154.12 -25.88 0 5.00e+00 4.00e-02 2.68e+01 dihedral pdb=" CA PRO D 253 " pdb=" C PRO D 253 " pdb=" N LYS D 254 " pdb=" CA LYS D 254 " ideal model delta harmonic sigma weight residual 180.00 156.45 23.55 0 5.00e+00 4.00e-02 2.22e+01 dihedral pdb=" CA ASN C 71 " pdb=" C ASN C 71 " pdb=" N LEU C 72 " pdb=" CA LEU C 72 " ideal model delta harmonic sigma weight residual 180.00 -159.14 -20.86 0 5.00e+00 4.00e-02 1.74e+01 ... (remaining 10012 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 1890 0.053 - 0.106: 517 0.106 - 0.159: 92 0.159 - 0.212: 9 0.212 - 0.265: 3 Chirality restraints: 2511 Sorted by residual: chirality pdb=" CB THR A 528 " pdb=" CA THR A 528 " pdb=" OG1 THR A 528 " pdb=" CG2 THR A 528 " both_signs ideal model delta sigma weight residual False 2.55 2.29 0.27 2.00e-01 2.50e+01 1.76e+00 chirality pdb=" CB ILE A 296 " pdb=" CA ILE A 296 " pdb=" CG1 ILE A 296 " pdb=" CG2 ILE A 296 " both_signs ideal model delta sigma weight residual False 2.64 2.40 0.24 2.00e-01 2.50e+01 1.44e+00 chirality pdb=" CA THR C 219 " pdb=" N THR C 219 " pdb=" C THR C 219 " pdb=" CB THR C 219 " both_signs ideal model delta sigma weight residual False 2.53 2.31 0.22 2.00e-01 2.50e+01 1.18e+00 ... (remaining 2508 not shown) Planarity restraints: 2762 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS A 425 " 0.017 2.00e-02 2.50e+03 3.42e-02 1.17e+01 pdb=" C LYS A 425 " -0.059 2.00e-02 2.50e+03 pdb=" O LYS A 425 " 0.022 2.00e-02 2.50e+03 pdb=" N ALA A 426 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL A 613 " 0.044 5.00e-02 4.00e+02 6.68e-02 7.14e+00 pdb=" N PRO A 614 " -0.116 5.00e-02 4.00e+02 pdb=" CA PRO A 614 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO A 614 " 0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY A 330 " -0.040 5.00e-02 4.00e+02 6.01e-02 5.78e+00 pdb=" N PRO A 331 " 0.104 5.00e-02 4.00e+02 pdb=" CA PRO A 331 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO A 331 " -0.033 5.00e-02 4.00e+02 ... (remaining 2759 not shown) Histogram of nonbonded interaction distances: 2.60 - 3.06: 9825 3.06 - 3.52: 17086 3.52 - 3.98: 24841 3.98 - 4.44: 28659 4.44 - 4.90: 44839 Nonbonded interactions: 125250 Sorted by model distance: nonbonded pdb=" N1 DG P 26 " pdb=" C4 DG P 26 " model vdw 2.600 2.672 nonbonded pdb=" N1 DG T 15 " pdb=" C4 DG T 15 " model vdw 2.602 2.672 nonbonded pdb=" N1 DG P 14 " pdb=" C4 DG P 14 " model vdw 2.602 2.672 nonbonded pdb=" N1 DG P 17 " pdb=" C4 DG P 17 " model vdw 2.602 2.672 nonbonded pdb=" N1 DG P 20 " pdb=" C4 DG P 20 " model vdw 2.603 2.672 ... (remaining 125245 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 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.960 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.310 Check model and map are aligned: 0.070 Set scattering table: 0.050 Process input model: 17.290 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.970 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7144 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 : 0.004 0.047 16541 Z= 0.238 Angle : 0.845 14.598 22532 Z= 0.472 Chirality : 0.050 0.265 2511 Planarity : 0.006 0.067 2762 Dihedral : 16.927 143.101 6359 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 0.00 % Allowed : 0.24 % Favored : 99.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -1.45 (0.18), residues: 1911 helix: -0.63 (0.20), residues: 579 sheet: -0.42 (0.24), residues: 485 loop : -1.44 (0.19), residues: 847 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 375 TYR 0.018 0.002 TYR A 362 PHE 0.030 0.002 PHE A 815 TRP 0.037 0.002 TRP A 369 HIS 0.008 0.001 HIS B 153 Details of bonding type rmsd/Z covalent geometry : bond 0.00422 / 0.24 (16537) covalent geometry : angle 0.82335 / 0.47 (22520) hydrogen bonds : bond 0.18832 / 12.16 ( 726) hydrogen bonds : angle 7.98847 / 5.60 ( 2028) metal coordination : bond 0.01113 / 0.54 ( 4) metal coordination : angle 8.25920 / 5.13 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3822 Ramachandran restraints generated. 1911 Oldfield, 0 Emsley, 1911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3822 Ramachandran restraints generated. 1911 Oldfield, 0 Emsley, 1911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 334 residues out of total 1693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 334 time to evaluate : 0.641 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 LEU cc_start: 0.7853 (mp) cc_final: 0.7472 (pp) REVERT: A 132 GLU cc_start: 0.6843 (pm20) cc_final: 0.6384 (pm20) REVERT: A 223 GLU cc_start: 0.7690 (pm20) cc_final: 0.6267 (pm20) REVERT: A 294 MET cc_start: 0.5687 (pmm) cc_final: 0.4570 (ptm) REVERT: A 446 ARG cc_start: 0.6898 (tmm160) cc_final: 0.6498 (mmt180) REVERT: A 689 GLN cc_start: 0.8835 (tm-30) cc_final: 0.8490 (pt0) REVERT: A 740 GLU cc_start: 0.6992 (pt0) cc_final: 0.6699 (pp20) REVERT: A 850 ILE cc_start: 0.8568 (mm) cc_final: 0.8129 (mt) REVERT: A 1039 MET cc_start: 0.5900 (pmm) cc_final: 0.4753 (ptt) REVERT: A 1074 LEU cc_start: 0.8422 (pt) cc_final: 0.8177 (pt) REVERT: A 1083 LYS cc_start: 0.6144 (pttp) cc_final: 0.5449 (tppt) REVERT: B 24 ASN cc_start: 0.8235 (t0) cc_final: 0.8006 (t0) REVERT: C 95 ASN cc_start: 0.6152 (m-40) cc_final: 0.5545 (m-40) REVERT: D 1 MET cc_start: 0.6510 (tpp) cc_final: 0.6157 (tpp) REVERT: D 17 GLU cc_start: 0.8450 (pt0) cc_final: 0.8072 (pt0) outliers start: 0 outliers final: 0 residues processed: 334 average time/residue: 0.1225 time to fit residues: 61.0758 Evaluate side-chains 228 residues out of total 1693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 228 time to evaluate : 0.586 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 98 optimal weight: 0.1980 chunk 194 optimal weight: 40.0000 chunk 107 optimal weight: 4.9990 chunk 10 optimal weight: 8.9990 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 7.9990 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 10.0000 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 6.9990 chunk 91 optimal weight: 0.9990 overall best weight: 1.6388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 239 HIS ** B 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 44 HIS B 204 GLN ** B 246 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 108 GLN ** C 246 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 131 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4274 r_free = 0.4274 target = 0.171657 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.130851 restraints weight = 26833.844| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.135153 restraints weight = 13904.045| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.137996 restraints weight = 9144.145| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.139822 restraints weight = 7016.021| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.140868 restraints weight = 5952.620| |-----------------------------------------------------------------------------| r_work (final): 0.3896 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7307 moved from start: 0.1298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 16541 Z= 0.171 Angle : 0.708 15.310 22532 Z= 0.361 Chirality : 0.045 0.216 2511 Planarity : 0.005 0.075 2762 Dihedral : 15.716 143.255 2535 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 11.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 1.42 % Allowed : 8.86 % Favored : 89.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -0.96 (0.18), residues: 1911 helix: -0.07 (0.21), residues: 591 sheet: -0.14 (0.23), residues: 491 loop : -1.29 (0.20), residues: 829 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 5 TYR 0.023 0.002 TYR A 224 PHE 0.023 0.002 PHE C 215 TRP 0.020 0.002 TRP A1166 HIS 0.012 0.001 HIS A 511 Details of bonding type rmsd/Z covalent geometry : bond 0.00382 / 0.17 (16537) covalent geometry : angle 0.68526 / 0.36 (22520) hydrogen bonds : bond 0.05136 / 3.31 ( 726) hydrogen bonds : angle 6.10283 / 4.25 ( 2028) metal coordination : bond 0.00988 / 0.47 ( 4) metal coordination : angle 7.75273 / 4.80 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3822 Ramachandran restraints generated. 1911 Oldfield, 0 Emsley, 1911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3822 Ramachandran restraints generated. 1911 Oldfield, 0 Emsley, 1911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 1693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 236 time to evaluate : 0.493 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 132 GLU cc_start: 0.6943 (pm20) cc_final: 0.6239 (pm20) REVERT: A 294 MET cc_start: 0.5469 (pmm) cc_final: 0.4825 (ptt) REVERT: A 299 MET cc_start: 0.6332 (mmt) cc_final: 0.5870 (mmp) REVERT: A 549 SER cc_start: 0.8724 (m) cc_final: 0.8470 (p) REVERT: A 689 GLN cc_start: 0.8894 (tm-30) cc_final: 0.8585 (tt0) REVERT: A 850 ILE cc_start: 0.8593 (mm) cc_final: 0.8157 (mt) REVERT: A 906 THR cc_start: 0.8945 (m) cc_final: 0.8487 (p) REVERT: A 979 LEU cc_start: 0.6692 (mm) cc_final: 0.5758 (tt) REVERT: A 1039 MET cc_start: 0.5822 (pmm) cc_final: 0.4850 (ptt) REVERT: A 1083 LYS cc_start: 0.6169 (pttp) cc_final: 0.5397 (tppt) REVERT: B 12 LEU cc_start: 0.7303 (tp) cc_final: 0.7043 (tp) REVERT: B 199 MET cc_start: 0.6112 (tpt) cc_final: 0.4861 (tpt) REVERT: C 95 ASN cc_start: 0.6235 (m-40) cc_final: 0.5710 (m-40) REVERT: D 1 MET cc_start: 0.6366 (tpp) cc_final: 0.6132 (tpp) REVERT: D 17 GLU cc_start: 0.8624 (pt0) cc_final: 0.7981 (pt0) outliers start: 24 outliers final: 17 residues processed: 249 average time/residue: 0.1106 time to fit residues: 42.4544 Evaluate side-chains 231 residues out of total 1693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 214 time to evaluate : 0.493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 424 LEU Chi-restraints excluded: chain A residue 528 THR Chi-restraints excluded: chain A residue 684 HIS Chi-restraints excluded: chain A residue 690 LEU Chi-restraints excluded: chain A residue 708 HIS Chi-restraints excluded: chain A residue 736 ILE Chi-restraints excluded: chain A residue 1018 TYR Chi-restraints excluded: chain A residue 1053 SER Chi-restraints excluded: chain B residue 72 LEU Chi-restraints excluded: chain B residue 224 THR Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 191 GLU Chi-restraints excluded: chain C residue 251 LEU Chi-restraints excluded: chain D residue 23 ILE Chi-restraints excluded: chain D residue 221 LEU Chi-restraints excluded: chain D residue 251 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 156 optimal weight: 5.9990 chunk 143 optimal weight: 2.9990 chunk 171 optimal weight: 7.9990 chunk 134 optimal weight: 0.8980 chunk 146 optimal weight: 0.7980 chunk 8 optimal weight: 7.9990 chunk 160 optimal weight: 5.9990 chunk 22 optimal weight: 3.9990 chunk 172 optimal weight: 1.9990 chunk 56 optimal weight: 0.9990 chunk 164 optimal weight: 10.0000 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 44 HIS ** B 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 71 ASN ** B 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 204 GLN ** B 246 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 246 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4268 r_free = 0.4268 target = 0.170848 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.130895 restraints weight = 27392.732| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.134465 restraints weight = 14104.240| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.136908 restraints weight = 9048.615| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.136972 restraints weight = 7612.448| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.137057 restraints weight = 7191.894| |-----------------------------------------------------------------------------| r_work (final): 0.3833 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7386 moved from start: 0.1592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 16541 Z= 0.155 Angle : 0.674 17.096 22532 Z= 0.339 Chirality : 0.044 0.211 2511 Planarity : 0.004 0.062 2762 Dihedral : 15.661 143.113 2535 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 11.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 2.24 % Allowed : 10.45 % Favored : 87.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -0.64 (0.19), residues: 1911 helix: 0.29 (0.21), residues: 593 sheet: 0.25 (0.24), residues: 468 loop : -1.29 (0.20), residues: 850 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 5 TYR 0.013 0.002 TYR A 397 PHE 0.024 0.002 PHE C 215 TRP 0.030 0.002 TRP A1166 HIS 0.006 0.001 HIS A 511 Details of bonding type rmsd/Z covalent geometry : bond 0.00352 / 0.16 (16537) covalent geometry : angle 0.64608 / 0.34 (22520) hydrogen bonds : bond 0.04425 / 2.87 ( 726) hydrogen bonds : angle 5.59610 / 3.88 ( 2028) metal coordination : bond 0.00995 / 0.47 ( 4) metal coordination : angle 8.41362 / 5.22 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3822 Ramachandran restraints generated. 1911 Oldfield, 0 Emsley, 1911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3822 Ramachandran restraints generated. 1911 Oldfield, 0 Emsley, 1911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 1693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 240 time to evaluate : 0.504 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 36 GLU cc_start: 0.7348 (mp0) cc_final: 0.7066 (mp0) REVERT: A 223 GLU cc_start: 0.7995 (OUTLIER) cc_final: 0.7646 (pt0) REVERT: A 294 MET cc_start: 0.5398 (pmm) cc_final: 0.5061 (ptt) REVERT: A 549 SER cc_start: 0.8662 (m) cc_final: 0.8406 (p) REVERT: A 689 GLN cc_start: 0.8913 (tm-30) cc_final: 0.8609 (tt0) REVERT: A 850 ILE cc_start: 0.8564 (mm) cc_final: 0.8108 (mt) REVERT: A 979 LEU cc_start: 0.6651 (mm) cc_final: 0.5762 (tt) REVERT: A 986 GLN cc_start: 0.5482 (pt0) cc_final: 0.5250 (pp30) REVERT: A 1039 MET cc_start: 0.5937 (pmm) cc_final: 0.5219 (ptt) REVERT: A 1083 LYS cc_start: 0.6237 (pttp) cc_final: 0.5457 (tppt) REVERT: B 12 LEU cc_start: 0.7341 (tp) cc_final: 0.7130 (tp) REVERT: B 199 MET cc_start: 0.6505 (tpt) cc_final: 0.5152 (tpt) REVERT: C 47 LEU cc_start: 0.7464 (pp) cc_final: 0.7057 (tt) REVERT: C 133 TYR cc_start: 0.7662 (m-10) cc_final: 0.7429 (m-10) REVERT: C 139 MET cc_start: 0.6864 (tpp) cc_final: 0.6631 (tpp) REVERT: C 149 ARG cc_start: 0.7715 (tmt170) cc_final: 0.6746 (ttp80) REVERT: C 150 ASP cc_start: 0.6997 (m-30) cc_final: 0.6336 (t0) REVERT: D 1 MET cc_start: 0.6226 (tpp) cc_final: 0.6018 (tpp) REVERT: D 17 GLU cc_start: 0.8642 (pt0) cc_final: 0.7949 (pt0) REVERT: D 204 GLN cc_start: 0.8434 (mm-40) cc_final: 0.7944 (mm-40) REVERT: D 210 ARG cc_start: 0.7474 (tpm170) cc_final: 0.7079 (tpm170) REVERT: D 244 MET cc_start: 0.7167 (mmm) cc_final: 0.6890 (tpt) outliers start: 38 outliers final: 24 residues processed: 259 average time/residue: 0.1083 time to fit residues: 42.5176 Evaluate side-chains 247 residues out of total 1693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 222 time to evaluate : 0.527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 SER Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 223 GLU Chi-restraints excluded: chain A residue 424 LEU Chi-restraints excluded: chain A residue 481 LEU Chi-restraints excluded: chain A residue 528 THR Chi-restraints excluded: chain A residue 676 MET Chi-restraints excluded: chain A residue 684 HIS Chi-restraints excluded: chain A residue 690 LEU Chi-restraints excluded: chain A residue 708 HIS Chi-restraints excluded: chain A residue 736 ILE Chi-restraints excluded: chain A residue 1053 SER Chi-restraints excluded: chain B residue 15 VAL Chi-restraints excluded: chain B residue 44 HIS Chi-restraints excluded: chain B residue 72 LEU Chi-restraints excluded: chain B residue 115 GLU Chi-restraints excluded: chain B residue 137 VAL Chi-restraints excluded: chain B residue 224 THR Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain D residue 23 ILE Chi-restraints excluded: chain D residue 221 LEU Chi-restraints excluded: chain D residue 235 LEU Chi-restraints excluded: chain D residue 236 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 133 optimal weight: 2.9990 chunk 0 optimal weight: 20.0000 chunk 46 optimal weight: 2.9990 chunk 104 optimal weight: 2.9990 chunk 100 optimal weight: 0.0870 chunk 21 optimal weight: 3.9990 chunk 123 optimal weight: 0.0000 chunk 98 optimal weight: 10.0000 chunk 13 optimal weight: 7.9990 chunk 175 optimal weight: 5.9990 chunk 187 optimal weight: 6.9990 overall best weight: 1.8168 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 44 HIS ** B 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 204 GLN ** B 246 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 246 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4247 r_free = 0.4247 target = 0.169237 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.128149 restraints weight = 27101.567| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.132559 restraints weight = 15887.306| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.134594 restraints weight = 9383.409| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.135632 restraints weight = 7519.455| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.135966 restraints weight = 7287.115| |-----------------------------------------------------------------------------| r_work (final): 0.3819 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7419 moved from start: 0.1863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 16541 Z= 0.168 Angle : 0.678 19.383 22532 Z= 0.336 Chirality : 0.044 0.217 2511 Planarity : 0.004 0.064 2762 Dihedral : 15.655 143.148 2535 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 11.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 2.72 % Allowed : 11.22 % Favored : 86.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -0.56 (0.19), residues: 1911 helix: 0.39 (0.21), residues: 595 sheet: 0.20 (0.24), residues: 485 loop : -1.23 (0.20), residues: 831 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 579 TYR 0.013 0.002 TYR A 726 PHE 0.023 0.002 PHE C 215 TRP 0.027 0.002 TRP A 369 HIS 0.015 0.001 HIS B 44 Details of bonding type rmsd/Z covalent geometry : bond 0.00385 / 0.17 (16537) covalent geometry : angle 0.64168 / 0.34 (22520) hydrogen bonds : bond 0.04171 / 2.73 ( 726) hydrogen bonds : angle 5.39841 / 3.74 ( 2028) metal coordination : bond 0.01009 / 0.46 ( 4) metal coordination : angle 9.51853 / 5.82 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3822 Ramachandran restraints generated. 1911 Oldfield, 0 Emsley, 1911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3822 Ramachandran restraints generated. 1911 Oldfield, 0 Emsley, 1911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 1693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 235 time to evaluate : 0.564 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 36 GLU cc_start: 0.7251 (mp0) cc_final: 0.6982 (mp0) REVERT: A 223 GLU cc_start: 0.8066 (OUTLIER) cc_final: 0.7210 (pt0) REVERT: A 294 MET cc_start: 0.5440 (pmm) cc_final: 0.5219 (ptt) REVERT: A 446 ARG cc_start: 0.6896 (tmm160) cc_final: 0.6515 (mmt180) REVERT: A 549 SER cc_start: 0.8694 (m) cc_final: 0.8452 (p) REVERT: A 689 GLN cc_start: 0.8931 (tm-30) cc_final: 0.8613 (tt0) REVERT: A 850 ILE cc_start: 0.8632 (mm) cc_final: 0.8193 (mt) REVERT: A 906 THR cc_start: 0.8944 (m) cc_final: 0.8491 (p) REVERT: A 979 LEU cc_start: 0.6837 (mm) cc_final: 0.5901 (tt) REVERT: A 986 GLN cc_start: 0.5568 (pt0) cc_final: 0.5306 (pp30) REVERT: A 1039 MET cc_start: 0.5960 (pmm) cc_final: 0.5286 (ptt) REVERT: A 1083 LYS cc_start: 0.6291 (pttp) cc_final: 0.5505 (tppt) REVERT: B 12 LEU cc_start: 0.7373 (tp) cc_final: 0.7151 (tp) REVERT: B 116 MET cc_start: 0.7634 (pmm) cc_final: 0.7297 (ppp) REVERT: B 199 MET cc_start: 0.6200 (tpt) cc_final: 0.4886 (tpt) REVERT: C 47 LEU cc_start: 0.7454 (pp) cc_final: 0.7044 (tt) REVERT: C 149 ARG cc_start: 0.7716 (tmt170) cc_final: 0.6771 (ttp80) REVERT: C 150 ASP cc_start: 0.6958 (m-30) cc_final: 0.6420 (t0) REVERT: D 1 MET cc_start: 0.6257 (tpp) cc_final: 0.6046 (tpp) REVERT: D 17 GLU cc_start: 0.8622 (pt0) cc_final: 0.7923 (pt0) REVERT: D 204 GLN cc_start: 0.8455 (mm-40) cc_final: 0.7888 (mm-40) REVERT: D 210 ARG cc_start: 0.7503 (tpm170) cc_final: 0.7097 (tpm170) REVERT: D 244 MET cc_start: 0.7045 (mmm) cc_final: 0.6595 (tpt) outliers start: 46 outliers final: 32 residues processed: 259 average time/residue: 0.1035 time to fit residues: 40.9684 Evaluate side-chains 253 residues out of total 1693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 220 time to evaluate : 0.452 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 SER Chi-restraints excluded: chain A residue 87 ILE Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 218 ILE Chi-restraints excluded: chain A residue 223 GLU Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain A residue 317 ILE Chi-restraints excluded: chain A residue 424 LEU Chi-restraints excluded: chain A residue 481 LEU Chi-restraints excluded: chain A residue 528 THR Chi-restraints excluded: chain A residue 684 HIS Chi-restraints excluded: chain A residue 690 LEU Chi-restraints excluded: chain A residue 708 HIS Chi-restraints excluded: chain A residue 736 ILE Chi-restraints excluded: chain A residue 843 ILE Chi-restraints excluded: chain A residue 1018 TYR Chi-restraints excluded: chain A residue 1053 SER Chi-restraints excluded: chain A residue 1172 LEU Chi-restraints excluded: chain B residue 15 VAL Chi-restraints excluded: chain B residue 72 LEU Chi-restraints excluded: chain B residue 137 VAL Chi-restraints excluded: chain B residue 224 THR Chi-restraints excluded: chain C residue 29 ASP Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain C residue 72 LEU Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 191 GLU Chi-restraints excluded: chain C residue 241 ILE Chi-restraints excluded: chain D residue 23 ILE Chi-restraints excluded: chain D residue 135 CYS Chi-restraints excluded: chain D residue 221 LEU Chi-restraints excluded: chain D residue 236 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 10 optimal weight: 0.0030 chunk 15 optimal weight: 0.0770 chunk 191 optimal weight: 50.0000 chunk 142 optimal weight: 9.9990 chunk 81 optimal weight: 1.9990 chunk 91 optimal weight: 0.9990 chunk 160 optimal weight: 0.3980 chunk 104 optimal weight: 8.9990 chunk 105 optimal weight: 1.9990 chunk 14 optimal weight: 0.6980 chunk 174 optimal weight: 8.9990 overall best weight: 0.4350 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 131 GLN B 204 GLN ** B 246 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 200 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4277 r_free = 0.4277 target = 0.172115 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.130830 restraints weight = 26838.862| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.135222 restraints weight = 13567.495| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.138128 restraints weight = 8790.816| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.140039 restraints weight = 6693.238| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.141265 restraints weight = 5634.698| |-----------------------------------------------------------------------------| r_work (final): 0.3895 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7288 moved from start: 0.1925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 16541 Z= 0.113 Angle : 0.622 14.129 22532 Z= 0.312 Chirality : 0.043 0.209 2511 Planarity : 0.004 0.066 2762 Dihedral : 15.572 142.830 2535 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 10.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 1.89 % Allowed : 13.94 % Favored : 84.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -0.43 (0.19), residues: 1911 helix: 0.59 (0.21), residues: 594 sheet: 0.17 (0.23), residues: 494 loop : -1.17 (0.21), residues: 823 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG A 579 TYR 0.017 0.001 TYR A 458 PHE 0.024 0.002 PHE C 215 TRP 0.026 0.001 TRP A 369 HIS 0.007 0.001 HIS B 153 Details of bonding type rmsd/Z covalent geometry : bond 0.00245 / 0.11 (16537) covalent geometry : angle 0.59976 / 0.31 (22520) hydrogen bonds : bond 0.03734 / 2.43 ( 726) hydrogen bonds : angle 5.17112 / 3.60 ( 2028) metal coordination : bond 0.00352 / 0.17 ( 4) metal coordination : angle 7.10612 / 4.46 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3822 Ramachandran restraints generated. 1911 Oldfield, 0 Emsley, 1911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3822 Ramachandran restraints generated. 1911 Oldfield, 0 Emsley, 1911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 1693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 244 time to evaluate : 0.545 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 36 GLU cc_start: 0.7165 (mp0) cc_final: 0.6933 (mp0) REVERT: A 76 LYS cc_start: 0.5922 (tptp) cc_final: 0.5607 (tptt) REVERT: A 223 GLU cc_start: 0.7862 (OUTLIER) cc_final: 0.7576 (pt0) REVERT: A 294 MET cc_start: 0.5360 (pmm) cc_final: 0.4950 (ptp) REVERT: A 299 MET cc_start: 0.6410 (mmt) cc_final: 0.6109 (mmp) REVERT: A 684 HIS cc_start: 0.8679 (OUTLIER) cc_final: 0.8166 (t-90) REVERT: A 689 GLN cc_start: 0.8848 (tm-30) cc_final: 0.8546 (tt0) REVERT: A 850 ILE cc_start: 0.8536 (mm) cc_final: 0.8041 (mt) REVERT: A 897 LEU cc_start: 0.8048 (OUTLIER) cc_final: 0.7777 (mm) REVERT: A 906 THR cc_start: 0.8905 (m) cc_final: 0.8482 (p) REVERT: A 1024 MET cc_start: 0.6244 (ppp) cc_final: 0.5338 (ppp) REVERT: A 1039 MET cc_start: 0.5927 (pmm) cc_final: 0.5260 (ptt) REVERT: A 1083 LYS cc_start: 0.6263 (pttp) cc_final: 0.5498 (tppt) REVERT: A 1183 ILE cc_start: 0.6412 (OUTLIER) cc_final: 0.6109 (mm) REVERT: B 12 LEU cc_start: 0.7302 (tp) cc_final: 0.7059 (tp) REVERT: B 115 GLU cc_start: 0.6484 (pm20) cc_final: 0.6217 (pp20) REVERT: B 116 MET cc_start: 0.7630 (pmm) cc_final: 0.7141 (ppp) REVERT: B 199 MET cc_start: 0.5862 (tpt) cc_final: 0.4571 (tpt) REVERT: B 244 MET cc_start: 0.8587 (tmm) cc_final: 0.8315 (tmm) REVERT: C 47 LEU cc_start: 0.7500 (pp) cc_final: 0.7199 (tt) REVERT: C 150 ASP cc_start: 0.6980 (m-30) cc_final: 0.6536 (t70) REVERT: D 17 GLU cc_start: 0.8638 (pt0) cc_final: 0.7927 (pt0) REVERT: D 150 ASP cc_start: 0.7267 (t0) cc_final: 0.7058 (t70) REVERT: D 204 GLN cc_start: 0.8374 (mm-40) cc_final: 0.7849 (mm-40) REVERT: D 210 ARG cc_start: 0.7347 (tpm170) cc_final: 0.6959 (tpm170) REVERT: D 244 MET cc_start: 0.7055 (mmm) cc_final: 0.6800 (tpt) outliers start: 32 outliers final: 17 residues processed: 259 average time/residue: 0.1082 time to fit residues: 43.1397 Evaluate side-chains 241 residues out of total 1693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 220 time to evaluate : 0.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 223 GLU Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain A residue 424 LEU Chi-restraints excluded: chain A residue 528 THR Chi-restraints excluded: chain A residue 538 THR Chi-restraints excluded: chain A residue 684 HIS Chi-restraints excluded: chain A residue 690 LEU Chi-restraints excluded: chain A residue 708 HIS Chi-restraints excluded: chain A residue 736 ILE Chi-restraints excluded: chain A residue 897 LEU Chi-restraints excluded: chain A residue 1018 TYR Chi-restraints excluded: chain A residue 1172 LEU Chi-restraints excluded: chain A residue 1183 ILE Chi-restraints excluded: chain B residue 72 LEU Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain D residue 135 CYS Chi-restraints excluded: chain D residue 236 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 162 optimal weight: 0.6980 chunk 165 optimal weight: 7.9990 chunk 92 optimal weight: 2.9990 chunk 24 optimal weight: 0.9980 chunk 0 optimal weight: 20.0000 chunk 67 optimal weight: 6.9990 chunk 141 optimal weight: 0.0040 chunk 127 optimal weight: 1.9990 chunk 86 optimal weight: 9.9990 chunk 91 optimal weight: 0.0980 chunk 121 optimal weight: 0.6980 overall best weight: 0.4992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 451 GLN ** B 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 131 GLN B 204 GLN ** B 246 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 246 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4279 r_free = 0.4279 target = 0.172182 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.131488 restraints weight = 26881.399| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.136360 restraints weight = 14509.282| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.138228 restraints weight = 8646.383| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.138575 restraints weight = 7509.261| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.138848 restraints weight = 6738.588| |-----------------------------------------------------------------------------| r_work (final): 0.3851 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7335 moved from start: 0.2055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 16541 Z= 0.115 Angle : 0.610 12.443 22532 Z= 0.308 Chirality : 0.042 0.209 2511 Planarity : 0.004 0.064 2762 Dihedral : 15.528 142.598 2535 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 10.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 2.07 % Allowed : 15.53 % Favored : 82.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -0.30 (0.19), residues: 1911 helix: 0.67 (0.21), residues: 597 sheet: 0.24 (0.23), residues: 500 loop : -1.09 (0.21), residues: 814 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 579 TYR 0.028 0.001 TYR A 244 PHE 0.024 0.002 PHE D 207 TRP 0.019 0.001 TRP A 369 HIS 0.003 0.001 HIS D 246 Details of bonding type rmsd/Z covalent geometry : bond 0.00255 / 0.11 (16537) covalent geometry : angle 0.59343 / 0.31 (22520) hydrogen bonds : bond 0.03641 / 2.37 ( 726) hydrogen bonds : angle 5.05834 / 3.51 ( 2028) metal coordination : bond 0.00274 / 0.14 ( 4) metal coordination : angle 6.12036 / 3.85 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3822 Ramachandran restraints generated. 1911 Oldfield, 0 Emsley, 1911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3822 Ramachandran restraints generated. 1911 Oldfield, 0 Emsley, 1911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 1693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 240 time to evaluate : 0.663 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 36 GLU cc_start: 0.7338 (mp0) cc_final: 0.7046 (mp0) REVERT: A 294 MET cc_start: 0.5345 (pmm) cc_final: 0.4972 (ptp) REVERT: A 299 MET cc_start: 0.6373 (mmt) cc_final: 0.6117 (mmt) REVERT: A 446 ARG cc_start: 0.6786 (tmm160) cc_final: 0.6369 (mmt180) REVERT: A 684 HIS cc_start: 0.8766 (OUTLIER) cc_final: 0.8254 (t-90) REVERT: A 689 GLN cc_start: 0.8861 (tm-30) cc_final: 0.8555 (tt0) REVERT: A 897 LEU cc_start: 0.8032 (OUTLIER) cc_final: 0.7733 (mm) REVERT: A 906 THR cc_start: 0.8929 (m) cc_final: 0.8485 (p) REVERT: A 1024 MET cc_start: 0.6719 (ppp) cc_final: 0.5780 (ppp) REVERT: A 1039 MET cc_start: 0.5964 (pmm) cc_final: 0.5189 (ptm) REVERT: A 1083 LYS cc_start: 0.6264 (pttp) cc_final: 0.5498 (tppt) REVERT: A 1183 ILE cc_start: 0.6355 (OUTLIER) cc_final: 0.6072 (mm) REVERT: B 12 LEU cc_start: 0.7318 (tp) cc_final: 0.7072 (tp) REVERT: B 115 GLU cc_start: 0.6549 (pm20) cc_final: 0.6314 (pm20) REVERT: B 116 MET cc_start: 0.7634 (pmm) cc_final: 0.7344 (ppp) REVERT: B 199 MET cc_start: 0.6141 (tpt) cc_final: 0.4745 (tpt) REVERT: B 244 MET cc_start: 0.8584 (tmm) cc_final: 0.8244 (tmm) REVERT: C 47 LEU cc_start: 0.7576 (pp) cc_final: 0.7246 (tt) REVERT: C 150 ASP cc_start: 0.6992 (m-30) cc_final: 0.6574 (t70) REVERT: D 17 GLU cc_start: 0.8616 (pt0) cc_final: 0.7891 (pt0) REVERT: D 204 GLN cc_start: 0.8386 (mm-40) cc_final: 0.7841 (mm-40) REVERT: D 210 ARG cc_start: 0.7369 (tpm170) cc_final: 0.6976 (tpm170) REVERT: D 244 MET cc_start: 0.7149 (mmm) cc_final: 0.6820 (tpt) outliers start: 35 outliers final: 19 residues processed: 257 average time/residue: 0.1198 time to fit residues: 46.8596 Evaluate side-chains 239 residues out of total 1693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 217 time to evaluate : 0.577 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain A residue 424 LEU Chi-restraints excluded: chain A residue 481 LEU Chi-restraints excluded: chain A residue 528 THR Chi-restraints excluded: chain A residue 538 THR Chi-restraints excluded: chain A residue 684 HIS Chi-restraints excluded: chain A residue 690 LEU Chi-restraints excluded: chain A residue 708 HIS Chi-restraints excluded: chain A residue 736 ILE Chi-restraints excluded: chain A residue 897 LEU Chi-restraints excluded: chain A residue 1018 TYR Chi-restraints excluded: chain A residue 1053 SER Chi-restraints excluded: chain A residue 1172 LEU Chi-restraints excluded: chain A residue 1183 ILE Chi-restraints excluded: chain B residue 15 VAL Chi-restraints excluded: chain B residue 137 VAL Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 191 GLU Chi-restraints excluded: chain D residue 135 CYS Chi-restraints excluded: chain D residue 236 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 69 optimal weight: 2.9990 chunk 35 optimal weight: 0.8980 chunk 166 optimal weight: 1.9990 chunk 4 optimal weight: 3.9990 chunk 189 optimal weight: 2.9990 chunk 39 optimal weight: 0.7980 chunk 64 optimal weight: 4.9990 chunk 184 optimal weight: 1.9990 chunk 92 optimal weight: 2.9990 chunk 164 optimal weight: 0.8980 chunk 3 optimal weight: 1.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 511 HIS ** B 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 131 GLN B 204 GLN ** B 246 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 246 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4262 r_free = 0.4262 target = 0.170530 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.129218 restraints weight = 26782.383| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.134055 restraints weight = 14821.028| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.135524 restraints weight = 8869.857| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.136790 restraints weight = 7562.206| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.136816 restraints weight = 7286.968| |-----------------------------------------------------------------------------| r_work (final): 0.3823 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7379 moved from start: 0.2167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 16541 Z= 0.140 Angle : 0.633 13.567 22532 Z= 0.318 Chirality : 0.043 0.210 2511 Planarity : 0.004 0.090 2762 Dihedral : 15.530 142.498 2535 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 11.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 2.13 % Allowed : 15.77 % Favored : 82.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.34 (0.19), residues: 1911 helix: 0.60 (0.21), residues: 597 sheet: 0.26 (0.23), residues: 505 loop : -1.11 (0.21), residues: 809 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.000 ARG A 579 TYR 0.018 0.002 TYR A 244 PHE 0.023 0.002 PHE C 215 TRP 0.020 0.001 TRP A 369 HIS 0.004 0.001 HIS A 475 Details of bonding type rmsd/Z covalent geometry : bond 0.00321 / 0.14 (16537) covalent geometry : angle 0.61333 / 0.32 (22520) hydrogen bonds : bond 0.03720 / 2.43 ( 726) hydrogen bonds : angle 5.02713 / 3.49 ( 2028) metal coordination : bond 0.00739 / 0.35 ( 4) metal coordination : angle 6.85495 / 4.24 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3822 Ramachandran restraints generated. 1911 Oldfield, 0 Emsley, 1911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3822 Ramachandran restraints generated. 1911 Oldfield, 0 Emsley, 1911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 1693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 222 time to evaluate : 0.681 Fit side-chains revert: symmetry clash REVERT: A 36 GLU cc_start: 0.7362 (mp0) cc_final: 0.7092 (mp0) REVERT: A 294 MET cc_start: 0.5421 (pmm) cc_final: 0.5174 (ptp) REVERT: A 446 ARG cc_start: 0.6755 (tmm160) cc_final: 0.6499 (mmt180) REVERT: A 684 HIS cc_start: 0.8774 (OUTLIER) cc_final: 0.8295 (t-90) REVERT: A 689 GLN cc_start: 0.8927 (tm-30) cc_final: 0.8617 (tt0) REVERT: A 897 LEU cc_start: 0.8089 (OUTLIER) cc_final: 0.7748 (mm) REVERT: A 900 MET cc_start: 0.8702 (tmm) cc_final: 0.8114 (ttt) REVERT: A 906 THR cc_start: 0.8951 (m) cc_final: 0.8506 (p) REVERT: A 986 GLN cc_start: 0.5525 (pt0) cc_final: 0.5282 (pp30) REVERT: A 1039 MET cc_start: 0.5930 (pmm) cc_final: 0.5470 (ptp) REVERT: A 1083 LYS cc_start: 0.6265 (pttp) cc_final: 0.5501 (tppt) REVERT: A 1132 TYR cc_start: 0.6993 (t80) cc_final: 0.6793 (t80) REVERT: A 1183 ILE cc_start: 0.6398 (OUTLIER) cc_final: 0.6135 (mm) REVERT: B 12 LEU cc_start: 0.7340 (tp) cc_final: 0.7110 (tp) REVERT: B 116 MET cc_start: 0.7686 (pmm) cc_final: 0.7361 (ppp) REVERT: B 199 MET cc_start: 0.6301 (tpt) cc_final: 0.4923 (tpt) REVERT: C 47 LEU cc_start: 0.7649 (pp) cc_final: 0.7298 (tt) REVERT: C 139 MET cc_start: 0.6825 (tpp) cc_final: 0.6477 (tpp) REVERT: C 150 ASP cc_start: 0.7056 (m-30) cc_final: 0.6621 (t70) REVERT: D 17 GLU cc_start: 0.8671 (pt0) cc_final: 0.7938 (pt0) REVERT: D 204 GLN cc_start: 0.8415 (mm-40) cc_final: 0.7850 (mm-40) REVERT: D 210 ARG cc_start: 0.7391 (tpm170) cc_final: 0.7005 (tpm170) REVERT: D 244 MET cc_start: 0.7180 (mmm) cc_final: 0.6715 (tpt) outliers start: 36 outliers final: 23 residues processed: 243 average time/residue: 0.1246 time to fit residues: 46.1434 Evaluate side-chains 238 residues out of total 1693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 212 time to evaluate : 0.566 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain A residue 424 LEU Chi-restraints excluded: chain A residue 481 LEU Chi-restraints excluded: chain A residue 528 THR Chi-restraints excluded: chain A residue 538 THR Chi-restraints excluded: chain A residue 684 HIS Chi-restraints excluded: chain A residue 690 LEU Chi-restraints excluded: chain A residue 708 HIS Chi-restraints excluded: chain A residue 736 ILE Chi-restraints excluded: chain A residue 897 LEU Chi-restraints excluded: chain A residue 1018 TYR Chi-restraints excluded: chain A residue 1053 SER Chi-restraints excluded: chain A residue 1172 LEU Chi-restraints excluded: chain A residue 1183 ILE Chi-restraints excluded: chain B residue 15 VAL Chi-restraints excluded: chain B residue 72 LEU Chi-restraints excluded: chain B residue 137 VAL Chi-restraints excluded: chain B residue 224 THR Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 191 GLU Chi-restraints excluded: chain D residue 23 ILE Chi-restraints excluded: chain D residue 135 CYS Chi-restraints excluded: chain D residue 236 VAL Chi-restraints excluded: chain D residue 251 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 58 optimal weight: 0.1980 chunk 46 optimal weight: 4.9990 chunk 18 optimal weight: 0.8980 chunk 162 optimal weight: 0.2980 chunk 158 optimal weight: 9.9990 chunk 81 optimal weight: 2.9990 chunk 124 optimal weight: 8.9990 chunk 131 optimal weight: 0.0060 chunk 33 optimal weight: 0.7980 chunk 146 optimal weight: 6.9990 chunk 7 optimal weight: 0.9990 overall best weight: 0.4396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 131 GLN B 204 GLN ** B 246 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 246 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 125 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 = 0.4281 r_free = 0.4281 target = 0.172324 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.131567 restraints weight = 26672.858| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.135867 restraints weight = 13598.269| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.138723 restraints weight = 8859.808| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.140516 restraints weight = 6786.065| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.141588 restraints weight = 5762.115| |-----------------------------------------------------------------------------| r_work (final): 0.3898 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7266 moved from start: 0.2260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 16541 Z= 0.112 Angle : 0.623 11.767 22532 Z= 0.314 Chirality : 0.042 0.209 2511 Planarity : 0.004 0.078 2762 Dihedral : 15.469 142.259 2535 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 10.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 1.59 % Allowed : 16.60 % Favored : 81.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.28 (0.19), residues: 1911 helix: 0.70 (0.21), residues: 594 sheet: 0.26 (0.23), residues: 507 loop : -1.10 (0.21), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 579 TYR 0.019 0.001 TYR A 458 PHE 0.024 0.002 PHE C 215 TRP 0.022 0.001 TRP A 369 HIS 0.004 0.001 HIS B 153 Details of bonding type rmsd/Z covalent geometry : bond 0.00245 / 0.11 (16537) covalent geometry : angle 0.60830 / 0.31 (22520) hydrogen bonds : bond 0.03509 / 2.29 ( 726) hydrogen bonds : angle 4.92269 / 3.41 ( 2028) metal coordination : bond 0.00329 / 0.16 ( 4) metal coordination : angle 5.80924 / 3.66 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3822 Ramachandran restraints generated. 1911 Oldfield, 0 Emsley, 1911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3822 Ramachandran restraints generated. 1911 Oldfield, 0 Emsley, 1911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 1693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 231 time to evaluate : 0.614 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 36 GLU cc_start: 0.7236 (mp0) cc_final: 0.7021 (mp0) REVERT: A 238 ILE cc_start: 0.8822 (mm) cc_final: 0.8437 (mm) REVERT: A 684 HIS cc_start: 0.8695 (OUTLIER) cc_final: 0.8189 (t-90) REVERT: A 689 GLN cc_start: 0.8864 (tm-30) cc_final: 0.8565 (tt0) REVERT: A 897 LEU cc_start: 0.8040 (OUTLIER) cc_final: 0.7729 (mm) REVERT: A 900 MET cc_start: 0.8691 (tmm) cc_final: 0.8091 (ttt) REVERT: A 906 THR cc_start: 0.8897 (m) cc_final: 0.8458 (p) REVERT: A 1039 MET cc_start: 0.5889 (pmm) cc_final: 0.5411 (ptp) REVERT: A 1083 LYS cc_start: 0.6280 (pttp) cc_final: 0.5537 (tppt) REVERT: A 1183 ILE cc_start: 0.6382 (OUTLIER) cc_final: 0.6157 (mm) REVERT: B 12 LEU cc_start: 0.7306 (tp) cc_final: 0.7070 (tp) REVERT: B 116 MET cc_start: 0.7694 (pmm) cc_final: 0.7385 (ppp) REVERT: B 199 MET cc_start: 0.5918 (tpt) cc_final: 0.4606 (tpt) REVERT: C 47 LEU cc_start: 0.7642 (pp) cc_final: 0.7325 (tt) REVERT: D 17 GLU cc_start: 0.8582 (pt0) cc_final: 0.7870 (pt0) REVERT: D 204 GLN cc_start: 0.8357 (mm-40) cc_final: 0.7792 (mm-40) REVERT: D 210 ARG cc_start: 0.7344 (tpm170) cc_final: 0.6967 (tpm170) REVERT: D 244 MET cc_start: 0.7177 (mmm) cc_final: 0.6807 (tpt) outliers start: 27 outliers final: 19 residues processed: 244 average time/residue: 0.1097 time to fit residues: 41.8898 Evaluate side-chains 234 residues out of total 1693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 212 time to evaluate : 0.605 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain A residue 424 LEU Chi-restraints excluded: chain A residue 481 LEU Chi-restraints excluded: chain A residue 528 THR Chi-restraints excluded: chain A residue 538 THR Chi-restraints excluded: chain A residue 684 HIS Chi-restraints excluded: chain A residue 690 LEU Chi-restraints excluded: chain A residue 708 HIS Chi-restraints excluded: chain A residue 736 ILE Chi-restraints excluded: chain A residue 897 LEU Chi-restraints excluded: chain A residue 1018 TYR Chi-restraints excluded: chain A residue 1172 LEU Chi-restraints excluded: chain A residue 1183 ILE Chi-restraints excluded: chain B residue 137 VAL Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 191 GLU Chi-restraints excluded: chain D residue 135 CYS Chi-restraints excluded: chain D residue 197 ILE Chi-restraints excluded: chain D residue 236 VAL Chi-restraints excluded: chain D residue 251 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 5 optimal weight: 0.6980 chunk 184 optimal weight: 5.9990 chunk 42 optimal weight: 1.9990 chunk 4 optimal weight: 3.9990 chunk 153 optimal weight: 0.5980 chunk 168 optimal weight: 9.9990 chunk 188 optimal weight: 0.7980 chunk 60 optimal weight: 5.9990 chunk 173 optimal weight: 0.0010 chunk 170 optimal weight: 10.0000 chunk 160 optimal weight: 0.9980 overall best weight: 0.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 131 GLN B 204 GLN ** B 246 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 246 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 125 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 = 0.4285 r_free = 0.4285 target = 0.172595 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.131274 restraints weight = 26839.603| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.135627 restraints weight = 13865.387| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.138521 restraints weight = 9091.720| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.140319 restraints weight = 6978.172| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.141494 restraints weight = 5933.873| |-----------------------------------------------------------------------------| r_work (final): 0.3895 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7281 moved from start: 0.2337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 16541 Z= 0.117 Angle : 0.627 11.327 22532 Z= 0.316 Chirality : 0.043 0.209 2511 Planarity : 0.004 0.086 2762 Dihedral : 15.444 142.133 2535 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 11.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 1.59 % Allowed : 17.07 % Favored : 81.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.30 (0.19), residues: 1911 helix: 0.70 (0.21), residues: 595 sheet: 0.20 (0.23), residues: 510 loop : -1.10 (0.21), residues: 806 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 579 TYR 0.019 0.001 TYR A 458 PHE 0.022 0.002 PHE A 516 TRP 0.025 0.001 TRP A 369 HIS 0.005 0.001 HIS D 246 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.12 (16537) covalent geometry : angle 0.61373 / 0.32 (22520) hydrogen bonds : bond 0.03509 / 2.29 ( 726) hydrogen bonds : angle 4.90370 / 3.39 ( 2028) metal coordination : bond 0.00374 / 0.18 ( 4) metal coordination : angle 5.51282 / 3.45 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3822 Ramachandran restraints generated. 1911 Oldfield, 0 Emsley, 1911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3822 Ramachandran restraints generated. 1911 Oldfield, 0 Emsley, 1911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 1693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 224 time to evaluate : 0.647 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 36 GLU cc_start: 0.7206 (mp0) cc_final: 0.7002 (mp0) REVERT: A 119 PHE cc_start: 0.8349 (t80) cc_final: 0.8083 (t80) REVERT: A 238 ILE cc_start: 0.8796 (mm) cc_final: 0.8408 (mm) REVERT: A 282 PRO cc_start: 0.7962 (Cg_exo) cc_final: 0.7721 (Cg_endo) REVERT: A 444 MET cc_start: 0.6531 (ppp) cc_final: 0.6300 (tmm) REVERT: A 684 HIS cc_start: 0.8672 (OUTLIER) cc_final: 0.8179 (t-90) REVERT: A 689 GLN cc_start: 0.8903 (tm-30) cc_final: 0.8609 (tt0) REVERT: A 897 LEU cc_start: 0.8060 (OUTLIER) cc_final: 0.7757 (mm) REVERT: A 906 THR cc_start: 0.8859 (m) cc_final: 0.8451 (p) REVERT: A 986 GLN cc_start: 0.5475 (pt0) cc_final: 0.5254 (pp30) REVERT: A 1024 MET cc_start: 0.5693 (ppp) cc_final: 0.5092 (ppp) REVERT: A 1039 MET cc_start: 0.5884 (pmm) cc_final: 0.5413 (ptp) REVERT: A 1083 LYS cc_start: 0.6291 (pttp) cc_final: 0.5559 (tppt) REVERT: A 1183 ILE cc_start: 0.6435 (OUTLIER) cc_final: 0.6220 (mm) REVERT: B 12 LEU cc_start: 0.7339 (tp) cc_final: 0.7095 (tp) REVERT: B 116 MET cc_start: 0.7723 (pmm) cc_final: 0.7420 (ppp) REVERT: C 47 LEU cc_start: 0.7641 (pp) cc_final: 0.7306 (tt) REVERT: C 108 GLN cc_start: 0.7464 (mm-40) cc_final: 0.6468 (tp40) REVERT: C 248 LYS cc_start: 0.8501 (mmtm) cc_final: 0.8195 (mmtm) REVERT: D 17 GLU cc_start: 0.8571 (pt0) cc_final: 0.7873 (pt0) REVERT: D 204 GLN cc_start: 0.8352 (mm-40) cc_final: 0.7809 (mm-40) REVERT: D 210 ARG cc_start: 0.7398 (tpm170) cc_final: 0.7028 (tpm170) REVERT: D 244 MET cc_start: 0.7325 (mmm) cc_final: 0.6728 (tpt) outliers start: 27 outliers final: 21 residues processed: 241 average time/residue: 0.1149 time to fit residues: 42.9930 Evaluate side-chains 238 residues out of total 1693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 214 time to evaluate : 0.626 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain A residue 424 LEU Chi-restraints excluded: chain A residue 481 LEU Chi-restraints excluded: chain A residue 528 THR Chi-restraints excluded: chain A residue 538 THR Chi-restraints excluded: chain A residue 676 MET Chi-restraints excluded: chain A residue 684 HIS Chi-restraints excluded: chain A residue 690 LEU Chi-restraints excluded: chain A residue 708 HIS Chi-restraints excluded: chain A residue 736 ILE Chi-restraints excluded: chain A residue 897 LEU Chi-restraints excluded: chain A residue 1018 TYR Chi-restraints excluded: chain A residue 1053 SER Chi-restraints excluded: chain A residue 1172 LEU Chi-restraints excluded: chain A residue 1183 ILE Chi-restraints excluded: chain B residue 15 VAL Chi-restraints excluded: chain B residue 81 CYS Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 191 GLU Chi-restraints excluded: chain D residue 135 CYS Chi-restraints excluded: chain D residue 236 VAL Chi-restraints excluded: chain D residue 251 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 83 optimal weight: 5.9990 chunk 190 optimal weight: 5.9990 chunk 91 optimal weight: 0.4980 chunk 29 optimal weight: 3.9990 chunk 71 optimal weight: 3.9990 chunk 155 optimal weight: 7.9990 chunk 40 optimal weight: 0.8980 chunk 175 optimal weight: 0.9990 chunk 176 optimal weight: 9.9990 chunk 161 optimal weight: 6.9990 chunk 184 optimal weight: 5.9990 overall best weight: 2.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 688 HIS ** B 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 131 GLN B 204 GLN ** B 246 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 108 GLN ** C 246 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4239 r_free = 0.4239 target = 0.168406 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.128658 restraints weight = 26901.203| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.131562 restraints weight = 14155.569| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.132738 restraints weight = 9212.755| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.132887 restraints weight = 8057.913| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.133074 restraints weight = 8208.522| |-----------------------------------------------------------------------------| r_work (final): 0.3779 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7449 moved from start: 0.2497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 16541 Z= 0.186 Angle : 0.697 17.813 22532 Z= 0.345 Chirality : 0.045 0.209 2511 Planarity : 0.005 0.090 2762 Dihedral : 15.504 142.264 2535 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 12.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 1.59 % Allowed : 17.48 % Favored : 80.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -0.44 (0.19), residues: 1911 helix: 0.58 (0.21), residues: 594 sheet: 0.07 (0.23), residues: 508 loop : -1.13 (0.21), residues: 809 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 579 TYR 0.019 0.002 TYR A 458 PHE 0.022 0.002 PHE A 516 TRP 0.033 0.002 TRP A 369 HIS 0.006 0.001 HIS A 475 Details of bonding type rmsd/Z covalent geometry : bond 0.00432 / 0.19 (16537) covalent geometry : angle 0.66684 / 0.34 (22520) hydrogen bonds : bond 0.03900 / 2.57 ( 726) hydrogen bonds : angle 5.00154 / 3.45 ( 2028) metal coordination : bond 0.01100 / 0.50 ( 4) metal coordination : angle 8.75031 / 5.30 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3822 Ramachandran restraints generated. 1911 Oldfield, 0 Emsley, 1911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3822 Ramachandran restraints generated. 1911 Oldfield, 0 Emsley, 1911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 1693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 217 time to evaluate : 0.672 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 36 GLU cc_start: 0.7447 (mp0) cc_final: 0.7122 (mp0) REVERT: A 446 ARG cc_start: 0.6981 (tmm160) cc_final: 0.6749 (mmt180) REVERT: A 684 HIS cc_start: 0.8755 (OUTLIER) cc_final: 0.8311 (t-90) REVERT: A 685 ARG cc_start: 0.8169 (mtp-110) cc_final: 0.7714 (ttt-90) REVERT: A 689 GLN cc_start: 0.8948 (tm-30) cc_final: 0.8596 (tt0) REVERT: A 897 LEU cc_start: 0.8137 (OUTLIER) cc_final: 0.7803 (mm) REVERT: A 906 THR cc_start: 0.8933 (m) cc_final: 0.8542 (p) REVERT: A 979 LEU cc_start: 0.6985 (mm) cc_final: 0.6123 (tt) REVERT: A 986 GLN cc_start: 0.5705 (pt0) cc_final: 0.5420 (pp30) REVERT: A 1039 MET cc_start: 0.6118 (pmm) cc_final: 0.5782 (ptp) REVERT: A 1083 LYS cc_start: 0.6393 (pttp) cc_final: 0.5606 (tppt) REVERT: B 12 LEU cc_start: 0.7443 (tp) cc_final: 0.7175 (tp) REVERT: B 116 MET cc_start: 0.7709 (pmm) cc_final: 0.7195 (ppp) REVERT: C 8 GLN cc_start: 0.8103 (mm-40) cc_final: 0.7838 (mm-40) REVERT: C 47 LEU cc_start: 0.7669 (OUTLIER) cc_final: 0.7269 (tt) REVERT: C 139 MET cc_start: 0.7028 (tpp) cc_final: 0.6627 (tpp) REVERT: C 248 LYS cc_start: 0.8503 (mmtm) cc_final: 0.8209 (mmtm) REVERT: D 17 GLU cc_start: 0.8597 (pt0) cc_final: 0.7907 (pt0) REVERT: D 204 GLN cc_start: 0.8474 (mm-40) cc_final: 0.7899 (mm-40) REVERT: D 210 ARG cc_start: 0.7448 (tpm170) cc_final: 0.7075 (tpm170) REVERT: D 244 MET cc_start: 0.7445 (mmm) cc_final: 0.6709 (tpt) outliers start: 27 outliers final: 20 residues processed: 235 average time/residue: 0.1271 time to fit residues: 45.4703 Evaluate side-chains 232 residues out of total 1693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 209 time to evaluate : 1.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 ILE Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain A residue 424 LEU Chi-restraints excluded: chain A residue 481 LEU Chi-restraints excluded: chain A residue 528 THR Chi-restraints excluded: chain A residue 538 THR Chi-restraints excluded: chain A residue 684 HIS Chi-restraints excluded: chain A residue 690 LEU Chi-restraints excluded: chain A residue 708 HIS Chi-restraints excluded: chain A residue 736 ILE Chi-restraints excluded: chain A residue 897 LEU Chi-restraints excluded: chain A residue 1018 TYR Chi-restraints excluded: chain A residue 1053 SER Chi-restraints excluded: chain A residue 1172 LEU Chi-restraints excluded: chain B residue 15 VAL Chi-restraints excluded: chain B residue 81 CYS Chi-restraints excluded: chain B residue 137 VAL Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain C residue 47 LEU Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain D residue 135 CYS Chi-restraints excluded: chain D residue 236 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 16 optimal weight: 1.9990 chunk 41 optimal weight: 0.6980 chunk 153 optimal weight: 4.9990 chunk 122 optimal weight: 0.9980 chunk 128 optimal weight: 5.9990 chunk 145 optimal weight: 10.0000 chunk 143 optimal weight: 10.0000 chunk 116 optimal weight: 2.9990 chunk 157 optimal weight: 6.9990 chunk 189 optimal weight: 0.8980 chunk 176 optimal weight: 0.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 131 GLN B 204 GLN ** B 246 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 246 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 125 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 = 0.4254 r_free = 0.4254 target = 0.169875 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.128405 restraints weight = 26833.875| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.132646 restraints weight = 13966.089| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.135421 restraints weight = 9208.510| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.137213 restraints weight = 7102.370| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.138338 restraints weight = 6053.404| |-----------------------------------------------------------------------------| r_work (final): 0.3853 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7343 moved from start: 0.2504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 16541 Z= 0.137 Angle : 0.661 17.010 22532 Z= 0.327 Chirality : 0.043 0.208 2511 Planarity : 0.004 0.088 2762 Dihedral : 15.475 142.365 2535 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 11.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 1.48 % Allowed : 18.07 % Favored : 80.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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 (0.19), residues: 1911 helix: 0.63 (0.21), residues: 595 sheet: 0.11 (0.23), residues: 509 loop : -1.08 (0.21), residues: 807 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 579 TYR 0.020 0.002 TYR A 458 PHE 0.024 0.002 PHE B 207 TRP 0.032 0.002 TRP A 369 HIS 0.004 0.001 HIS D 246 Details of bonding type rmsd/Z covalent geometry : bond 0.00314 / 0.14 (16537) covalent geometry : angle 0.63326 / 0.33 (22520) hydrogen bonds : bond 0.03635 / 2.38 ( 726) hydrogen bonds : angle 4.94944 / 3.43 ( 2028) metal coordination : bond 0.00691 / 0.33 ( 4) metal coordination : angle 8.20855 / 5.04 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2632.89 seconds wall clock time: 46 minutes 25.49 seconds (2785.49 seconds total)