Starting phenix.real_space_refine on Thu Aug 6 16:17:11 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ne7_49300/08_2026/9ne7_49300.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ne7_49300/08_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 { model { file = "/net/cci-nas-00/data/ceres_data/9ne7_49300/08_2026/9ne7_49300.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ne7_49300/08_2026/9ne7_49300.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9ne7_49300/08_2026/9ne7_49300.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ne7_49300/08_2026/9ne7_49300.map" } 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-2.2rc3-6140/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: 2.51, per 1000 atoms: 0.16 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: 0.91 Conformation dependent library (CDL) restraints added in 572.1 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: 1.56 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: 3.00 Time building geometry restraints manager: 1.24 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: 772 3.78 - 5.67: 95 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: 2.670 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: 0.250 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 15.030 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:0.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.060 ------------------------------------------------------------------------------- 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 : 0.846 14.598 22532 Z= 0.473 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 0.82417 / 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 : 0.460 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: 0.0995 time to fit residues: 50.0903 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 : 0.510 ------------------------------------------------------------------------------- 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 D 131 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4275 r_free = 0.4275 target = 0.171659 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.130922 restraints weight = 26731.942| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.135220 restraints weight = 13842.135| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.138062 restraints weight = 9102.856| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 52)----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.139896 restraints weight = 6977.084| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.141015 restraints weight = 5915.688| |-----------------------------------------------------------------------------| r_work (final): 0.3898 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7304 moved from start: 0.1341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 16541 Z= 0.169 Angle : 0.711 15.362 22532 Z= 0.363 Chirality : 0.046 0.221 2511 Planarity : 0.005 0.072 2762 Dihedral : 15.707 142.622 2535 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 11.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 1.48 % Allowed : 8.51 % Favored : 90.02 % 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: -0.93 (0.18), residues: 1911 helix: -0.03 (0.21), residues: 591 sheet: -0.11 (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 0.025 0.002 TYR A 224 PHE 0.024 0.002 PHE C 215 TRP 0.023 0.002 TRP A1166 HIS 0.013 0.001 HIS A 511 Details of bonding type rmsd/Z covalent geometry : bond 0.00381 / 0.17 (16537) covalent geometry : angle 0.68887 / 0.36 (22520) hydrogen bonds : bond 0.04765 / 3.07 ( 726) hydrogen bonds : angle 6.02059 / 4.19 ( 2028) metal coordination : bond 0.00983 / 0.46 ( 4) metal coordination : angle 7.74283 / 4.79 ( 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 262 residues out of total 1693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 237 time to evaluate : 0.422 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 132 GLU cc_start: 0.6937 (pm20) cc_final: 0.6217 (pm20) REVERT: A 294 MET cc_start: 0.5466 (pmm) cc_final: 0.4844 (ptt) REVERT: A 299 MET cc_start: 0.6291 (mmt) cc_final: 0.5827 (mmp) REVERT: A 549 SER cc_start: 0.8706 (m) cc_final: 0.8438 (p) REVERT: A 689 GLN cc_start: 0.8895 (tm-30) cc_final: 0.8586 (tt0) REVERT: A 850 ILE cc_start: 0.8584 (mm) cc_final: 0.8150 (mt) REVERT: A 906 THR cc_start: 0.8951 (m) cc_final: 0.8487 (p) REVERT: A 979 LEU cc_start: 0.6743 (mm) cc_final: 0.5771 (tt) REVERT: A 1039 MET cc_start: 0.5825 (pmm) cc_final: 0.4852 (ptt) REVERT: A 1083 LYS cc_start: 0.6152 (pttp) cc_final: 0.5391 (tppt) REVERT: B 12 LEU cc_start: 0.7313 (tp) cc_final: 0.7056 (tp) REVERT: B 199 MET cc_start: 0.6121 (tpt) cc_final: 0.4869 (tpt) REVERT: C 95 ASN cc_start: 0.6240 (m-40) cc_final: 0.5722 (m-40) REVERT: D 17 GLU cc_start: 0.8623 (pt0) cc_final: 0.7979 (pt0) outliers start: 25 outliers final: 17 residues processed: 251 average time/residue: 0.1007 time to fit residues: 39.4472 Evaluate side-chains 232 residues out of total 1693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 215 time to evaluate : 0.474 ------------------------------------------------------------------------------- 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: 0.4980 chunk 143 optimal weight: 10.0000 chunk 171 optimal weight: 9.9990 chunk 134 optimal weight: 0.7980 chunk 146 optimal weight: 0.0670 chunk 8 optimal weight: 3.9990 chunk 160 optimal weight: 0.0970 chunk 22 optimal weight: 5.9990 chunk 172 optimal weight: 3.9990 chunk 56 optimal weight: 0.9990 chunk 164 optimal weight: 20.0000 overall best weight: 0.4918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 986 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 44 HIS 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 = 0.4297 r_free = 0.4297 target = 0.173903 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.133151 restraints weight = 27102.173| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.137589 restraints weight = 13896.084| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.140461 restraints weight = 9047.749| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.142338 restraints weight = 6899.861| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.143252 restraints weight = 5833.852| |-----------------------------------------------------------------------------| r_work (final): 0.3923 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7253 moved from start: 0.1502 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= 0.120 Angle : 0.637 12.232 22532 Z= 0.324 Chirality : 0.043 0.227 2511 Planarity : 0.004 0.061 2762 Dihedral : 15.603 142.407 2535 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 10.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 1.83 % Allowed : 10.34 % Favored : 87.83 % 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: -0.62 (0.19), residues: 1911 helix: 0.33 (0.21), residues: 592 sheet: 0.21 (0.24), residues: 478 loop : -1.29 (0.20), residues: 841 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 5 TYR 0.013 0.001 TYR A 726 PHE 0.024 0.002 PHE C 215 TRP 0.026 0.002 TRP A1166 HIS 0.005 0.001 HIS A 511 Details of bonding type rmsd/Z covalent geometry : bond 0.00258 / 0.12 (16537) covalent geometry : angle 0.61934 / 0.32 (22520) hydrogen bonds : bond 0.04282 / 2.77 ( 726) hydrogen bonds : angle 5.59956 / 3.89 ( 2028) metal coordination : bond 0.00440 / 0.22 ( 4) metal coordination : angle 6.46209 / 4.06 ( 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 274 residues out of total 1693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 243 time to evaluate : 0.440 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 36 GLU cc_start: 0.7157 (mp0) cc_final: 0.6945 (mp0) REVERT: A 223 GLU cc_start: 0.7820 (OUTLIER) cc_final: 0.7583 (pt0) REVERT: A 294 MET cc_start: 0.5247 (pmm) cc_final: 0.4781 (ptt) REVERT: A 549 SER cc_start: 0.8608 (m) cc_final: 0.8399 (p) REVERT: A 689 GLN cc_start: 0.8834 (tm-30) cc_final: 0.8529 (tt0) REVERT: A 850 ILE cc_start: 0.8507 (mm) cc_final: 0.8031 (mt) REVERT: A 1039 MET cc_start: 0.5807 (pmm) cc_final: 0.4930 (ptt) REVERT: A 1083 LYS cc_start: 0.6178 (pttp) cc_final: 0.5442 (tppt) REVERT: B 12 LEU cc_start: 0.7211 (tp) cc_final: 0.7002 (tp) REVERT: B 116 MET cc_start: 0.7595 (pmm) cc_final: 0.7273 (ppp) REVERT: B 199 MET cc_start: 0.5947 (tpt) cc_final: 0.4681 (tpt) REVERT: B 244 MET cc_start: 0.8515 (tmm) cc_final: 0.8248 (tmm) REVERT: C 95 ASN cc_start: 0.6226 (m-40) cc_final: 0.5754 (m-40) REVERT: C 150 ASP cc_start: 0.6919 (m-30) cc_final: 0.6415 (t0) REVERT: C 248 LYS cc_start: 0.8555 (mmtm) cc_final: 0.8290 (mmtm) REVERT: D 1 MET cc_start: 0.6283 (tpp) cc_final: 0.6064 (tpp) REVERT: D 17 GLU cc_start: 0.8646 (pt0) cc_final: 0.8010 (pt0) REVERT: D 150 ASP cc_start: 0.7616 (t0) cc_final: 0.7394 (t70) REVERT: D 204 GLN cc_start: 0.8374 (mm-40) cc_final: 0.7927 (mm-40) REVERT: D 210 ARG cc_start: 0.7427 (tpm170) cc_final: 0.7020 (tpm170) outliers start: 31 outliers final: 18 residues processed: 256 average time/residue: 0.0969 time to fit residues: 38.2294 Evaluate side-chains 240 residues out of total 1693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 221 time to evaluate : 0.457 ------------------------------------------------------------------------------- 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 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 44 HIS Chi-restraints excluded: chain B residue 115 GLU Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain D residue 128 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: 0.0050 chunk 0 optimal weight: 20.0000 chunk 46 optimal weight: 9.9990 chunk 104 optimal weight: 7.9990 chunk 100 optimal weight: 5.9990 chunk 21 optimal weight: 1.9990 chunk 123 optimal weight: 0.0970 chunk 98 optimal weight: 3.9990 chunk 13 optimal weight: 2.9990 chunk 175 optimal weight: 0.4980 chunk 187 optimal weight: 5.9990 overall best weight: 1.1196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 927 ASN ** B 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 44 HIS B 131 GLN B 204 GLN ** B 246 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 246 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4285 r_free = 0.4285 target = 0.172259 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.131484 restraints weight = 27070.381| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.135796 restraints weight = 13926.305| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.138665 restraints weight = 9126.075| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.140466 restraints weight = 7003.403| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.141621 restraints weight = 5946.620| |-----------------------------------------------------------------------------| r_work (final): 0.3907 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7287 moved from start: 0.1727 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= 0.133 Angle : 0.629 12.855 22532 Z= 0.320 Chirality : 0.043 0.228 2511 Planarity : 0.004 0.062 2762 Dihedral : 15.574 142.248 2535 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 11.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 2.07 % Allowed : 11.40 % Favored : 86.53 % 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: -0.55 (0.19), residues: 1911 helix: 0.45 (0.21), residues: 595 sheet: 0.21 (0.24), residues: 487 loop : -1.28 (0.20), residues: 829 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 579 TYR 0.014 0.001 TYR A 458 PHE 0.023 0.002 PHE C 215 TRP 0.024 0.001 TRP A 369 HIS 0.012 0.001 HIS B 44 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.13 (16537) covalent geometry : angle 0.61019 / 0.32 (22520) hydrogen bonds : bond 0.04003 / 2.61 ( 726) hydrogen bonds : angle 5.37436 / 3.73 ( 2028) metal coordination : bond 0.00645 / 0.31 ( 4) metal coordination : angle 6.57599 / 4.10 ( 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 271 residues out of total 1693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 236 time to evaluate : 0.507 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 36 GLU cc_start: 0.7186 (mp0) cc_final: 0.6949 (mp0) REVERT: A 223 GLU cc_start: 0.7983 (OUTLIER) cc_final: 0.7696 (pt0) REVERT: A 294 MET cc_start: 0.5304 (pmm) cc_final: 0.4958 (ptm) REVERT: A 299 MET cc_start: 0.6411 (mmt) cc_final: 0.5925 (mmp) REVERT: A 549 SER cc_start: 0.8603 (m) cc_final: 0.8389 (p) REVERT: A 689 GLN cc_start: 0.8845 (tm-30) cc_final: 0.8543 (tt0) REVERT: A 850 ILE cc_start: 0.8508 (mm) cc_final: 0.8020 (mt) REVERT: A 1024 MET cc_start: 0.6659 (ppp) cc_final: 0.6329 (ppp) REVERT: A 1039 MET cc_start: 0.5872 (pmm) cc_final: 0.5068 (ptt) REVERT: A 1083 LYS cc_start: 0.6270 (pttp) cc_final: 0.5497 (tppt) REVERT: B 12 LEU cc_start: 0.7290 (tp) cc_final: 0.7075 (tp) REVERT: B 116 MET cc_start: 0.7567 (pmm) cc_final: 0.7292 (ppp) REVERT: B 199 MET cc_start: 0.6025 (tpt) cc_final: 0.4753 (tpt) REVERT: C 47 LEU cc_start: 0.7452 (pp) cc_final: 0.7058 (tt) REVERT: C 95 ASN cc_start: 0.6246 (m-40) cc_final: 0.5803 (m-40) REVERT: C 149 ARG cc_start: 0.7762 (tmt170) cc_final: 0.6666 (ttp80) REVERT: C 150 ASP cc_start: 0.6944 (m-30) cc_final: 0.6417 (t70) REVERT: D 1 MET cc_start: 0.6307 (tpp) cc_final: 0.6074 (tpp) REVERT: D 17 GLU cc_start: 0.8627 (pt0) cc_final: 0.7903 (pt0) REVERT: D 150 ASP cc_start: 0.7569 (t0) cc_final: 0.7361 (t0) REVERT: D 204 GLN cc_start: 0.8390 (mm-40) cc_final: 0.7888 (mm-40) REVERT: D 210 ARG cc_start: 0.7439 (tpm170) cc_final: 0.7008 (tpm170) outliers start: 35 outliers final: 28 residues processed: 254 average time/residue: 0.1039 time to fit residues: 40.1720 Evaluate side-chains 250 residues out of total 1693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 221 time to evaluate : 0.422 ------------------------------------------------------------------------------- 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 232 LEU Chi-restraints excluded: chain A residue 424 LEU Chi-restraints excluded: chain A residue 481 LEU Chi-restraints excluded: chain A residue 514 ILE 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 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 115 GLU 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 241 ILE Chi-restraints excluded: chain D residue 23 ILE Chi-restraints excluded: chain D residue 128 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: 1.9990 chunk 15 optimal weight: 7.9990 chunk 191 optimal weight: 50.0000 chunk 142 optimal weight: 9.9990 chunk 81 optimal weight: 0.8980 chunk 91 optimal weight: 3.9990 chunk 160 optimal weight: 0.8980 chunk 104 optimal weight: 3.9990 chunk 105 optimal weight: 1.9990 chunk 14 optimal weight: 10.0000 chunk 174 optimal weight: 8.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** B 204 GLN ** B 246 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 200 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4248 r_free = 0.4248 target = 0.169379 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.128058 restraints weight = 27106.233| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.132989 restraints weight = 14654.030| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.134563 restraints weight = 8895.402| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.135308 restraints weight = 7551.544| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.135505 restraints weight = 7477.503| |-----------------------------------------------------------------------------| r_work (final): 0.3811 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7422 moved from start: 0.1971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 16541 Z= 0.174 Angle : 0.674 18.184 22532 Z= 0.336 Chirality : 0.044 0.228 2511 Planarity : 0.005 0.082 2762 Dihedral : 15.585 142.215 2535 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 12.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 2.24 % Allowed : 13.29 % Favored : 84.47 % 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: -0.50 (0.19), residues: 1911 helix: 0.47 (0.21), residues: 595 sheet: 0.20 (0.24), residues: 481 loop : -1.19 (0.20), residues: 835 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 346 TYR 0.015 0.002 TYR A 228 PHE 0.023 0.002 PHE C 215 TRP 0.030 0.002 TRP A 369 HIS 0.007 0.001 HIS B 153 Details of bonding type rmsd/Z covalent geometry : bond 0.00402 / 0.17 (16537) covalent geometry : angle 0.64183 / 0.34 (22520) hydrogen bonds : bond 0.04094 / 2.70 ( 726) hydrogen bonds : angle 5.28819 / 3.66 ( 2028) metal coordination : bond 0.01170 / 0.54 ( 4) metal coordination : angle 8.96925 / 5.48 ( 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 266 residues out of total 1693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 228 time to evaluate : 0.534 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 36 GLU cc_start: 0.7359 (mp0) cc_final: 0.7078 (mp0) REVERT: A 223 GLU cc_start: 0.8169 (OUTLIER) cc_final: 0.7262 (pt0) REVERT: A 299 MET cc_start: 0.6535 (mmt) cc_final: 0.5977 (mmp) REVERT: A 446 ARG cc_start: 0.6791 (tmm160) cc_final: 0.6440 (mmt180) REVERT: A 447 MET cc_start: 0.8699 (tpp) cc_final: 0.8482 (tpp) REVERT: A 549 SER cc_start: 0.8693 (m) cc_final: 0.8439 (p) REVERT: A 647 ASP cc_start: 0.7465 (t70) cc_final: 0.7254 (t70) REVERT: A 689 GLN cc_start: 0.8940 (tm-30) cc_final: 0.8620 (tt0) REVERT: A 850 ILE cc_start: 0.8598 (mm) cc_final: 0.8106 (mt) REVERT: A 906 THR cc_start: 0.9113 (m) cc_final: 0.8665 (p) REVERT: A 1039 MET cc_start: 0.5974 (pmm) cc_final: 0.5375 (ptt) REVERT: A 1083 LYS cc_start: 0.6308 (pttp) cc_final: 0.5499 (tppt) REVERT: A 1183 ILE cc_start: 0.6444 (OUTLIER) cc_final: 0.6076 (mm) REVERT: B 12 LEU cc_start: 0.7367 (tp) cc_final: 0.7152 (tp) REVERT: B 116 MET cc_start: 0.7666 (pmm) cc_final: 0.7260 (ppp) REVERT: B 199 MET cc_start: 0.6201 (tpt) cc_final: 0.4815 (tpt) REVERT: C 47 LEU cc_start: 0.7553 (pp) cc_final: 0.7194 (tt) REVERT: C 139 MET cc_start: 0.6876 (tpp) cc_final: 0.6634 (tpp) REVERT: C 150 ASP cc_start: 0.7027 (m-30) cc_final: 0.6572 (t70) REVERT: D 1 MET cc_start: 0.6289 (tpp) cc_final: 0.6042 (tpp) REVERT: D 17 GLU cc_start: 0.8652 (pt0) cc_final: 0.7924 (pt0) REVERT: D 150 ASP cc_start: 0.7633 (t0) cc_final: 0.7413 (t0) REVERT: D 204 GLN cc_start: 0.8443 (mm-40) cc_final: 0.7879 (mm-40) REVERT: D 210 ARG cc_start: 0.7461 (tpm170) cc_final: 0.7075 (tpm170) outliers start: 38 outliers final: 28 residues processed: 250 average time/residue: 0.0978 time to fit residues: 37.8364 Evaluate side-chains 243 residues out of total 1693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 213 time to evaluate : 0.402 ------------------------------------------------------------------------------- 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 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 514 ILE 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 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 162 optimal weight: 2.9990 chunk 165 optimal weight: 4.9990 chunk 92 optimal weight: 0.8980 chunk 24 optimal weight: 1.9990 chunk 0 optimal weight: 20.0000 chunk 67 optimal weight: 4.9990 chunk 141 optimal weight: 1.9990 chunk 127 optimal weight: 0.8980 chunk 86 optimal weight: 7.9990 chunk 91 optimal weight: 0.9990 chunk 121 optimal weight: 7.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** B 204 GLN ** B 246 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 200 ASN ** C 246 HIS ** 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 = 0.169868 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.128469 restraints weight = 27061.582| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.133486 restraints weight = 14954.214| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.135547 restraints weight = 9024.279| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.135992 restraints weight = 7198.495| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.136298 restraints weight = 7267.267| |-----------------------------------------------------------------------------| r_work (final): 0.3820 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7406 moved from start: 0.2124 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= 0.145 Angle : 0.657 18.095 22532 Z= 0.326 Chirality : 0.044 0.227 2511 Planarity : 0.004 0.072 2762 Dihedral : 15.560 142.184 2535 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 11.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 2.30 % Allowed : 14.47 % Favored : 83.23 % 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: -0.45 (0.19), residues: 1911 helix: 0.56 (0.21), residues: 597 sheet: 0.16 (0.24), residues: 482 loop : -1.16 (0.21), residues: 832 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 64 TYR 0.024 0.002 TYR A 244 PHE 0.023 0.002 PHE C 215 TRP 0.031 0.002 TRP A 369 HIS 0.004 0.001 HIS A 475 Details of bonding type rmsd/Z covalent geometry : bond 0.00333 / 0.14 (16537) covalent geometry : angle 0.62476 / 0.33 (22520) hydrogen bonds : bond 0.03898 / 2.56 ( 726) hydrogen bonds : angle 5.15183 / 3.57 ( 2028) metal coordination : bond 0.00783 / 0.36 ( 4) metal coordination : angle 8.81439 / 5.40 ( 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 269 residues out of total 1693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 230 time to evaluate : 0.453 Fit side-chains revert: symmetry clash REVERT: A 36 GLU cc_start: 0.7351 (mp0) cc_final: 0.7060 (mp0) REVERT: A 223 GLU cc_start: 0.7989 (OUTLIER) cc_final: 0.7587 (pt0) REVERT: A 446 ARG cc_start: 0.6911 (tmm160) cc_final: 0.6563 (mmt180) REVERT: A 549 SER cc_start: 0.8664 (m) cc_final: 0.8412 (p) REVERT: A 684 HIS cc_start: 0.8769 (OUTLIER) cc_final: 0.8274 (t-90) REVERT: A 689 GLN cc_start: 0.8933 (tm-30) cc_final: 0.8624 (tt0) REVERT: A 850 ILE cc_start: 0.8589 (mm) cc_final: 0.8096 (mt) REVERT: A 897 LEU cc_start: 0.8108 (OUTLIER) cc_final: 0.7776 (mm) REVERT: A 906 THR cc_start: 0.9111 (m) cc_final: 0.8606 (p) REVERT: A 1039 MET cc_start: 0.5946 (pmm) cc_final: 0.5182 (ptm) REVERT: A 1083 LYS cc_start: 0.6264 (pttp) cc_final: 0.5482 (tppt) REVERT: A 1183 ILE cc_start: 0.6439 (OUTLIER) cc_final: 0.6097 (mm) REVERT: B 12 LEU cc_start: 0.7351 (tp) cc_final: 0.7103 (tp) REVERT: B 116 MET cc_start: 0.7724 (pmm) cc_final: 0.7444 (ppp) REVERT: B 199 MET cc_start: 0.6175 (tpt) cc_final: 0.4777 (tpt) REVERT: B 244 MET cc_start: 0.8623 (tmm) cc_final: 0.8336 (tmm) REVERT: C 47 LEU cc_start: 0.7609 (pp) cc_final: 0.7251 (tt) REVERT: C 139 MET cc_start: 0.6899 (tpp) cc_final: 0.6626 (tpp) REVERT: C 150 ASP cc_start: 0.7054 (m-30) cc_final: 0.6627 (t70) REVERT: D 1 MET cc_start: 0.6273 (tpp) cc_final: 0.6022 (tpp) REVERT: D 17 GLU cc_start: 0.8655 (pt0) cc_final: 0.7942 (pt0) REVERT: D 40 MET cc_start: 0.5085 (tpp) cc_final: 0.4739 (tpt) REVERT: D 150 ASP cc_start: 0.7592 (t0) cc_final: 0.7368 (t0) REVERT: D 204 GLN cc_start: 0.8438 (mm-40) cc_final: 0.7856 (mm-40) REVERT: D 210 ARG cc_start: 0.7435 (tpm170) cc_final: 0.7051 (tpm170) outliers start: 39 outliers final: 27 residues processed: 253 average time/residue: 0.0988 time to fit residues: 38.5296 Evaluate side-chains 246 residues out of total 1693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 215 time to evaluate : 0.413 ------------------------------------------------------------------------------- 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 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 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 29 ASP 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 221 LEU 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: 0.8980 chunk 35 optimal weight: 0.0030 chunk 166 optimal weight: 1.9990 chunk 4 optimal weight: 0.9990 chunk 189 optimal weight: 0.9990 chunk 39 optimal weight: 0.6980 chunk 64 optimal weight: 0.0170 chunk 184 optimal weight: 0.3980 chunk 92 optimal weight: 2.9990 chunk 164 optimal weight: 10.0000 chunk 3 optimal weight: 0.7980 overall best weight: 0.3828 ------------------------------------------------------------------------------- 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 200 ASN ** 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 = 0.4276 r_free = 0.4276 target = 0.171992 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.131168 restraints weight = 26561.819| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.135463 restraints weight = 13684.439| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.138305 restraints weight = 8946.154| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.140105 restraints weight = 6868.815| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.141268 restraints weight = 5833.576| |-----------------------------------------------------------------------------| r_work (final): 0.3897 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7279 moved from start: 0.2193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 16541 Z= 0.116 Angle : 0.635 13.226 22532 Z= 0.321 Chirality : 0.043 0.226 2511 Planarity : 0.004 0.065 2762 Dihedral : 15.499 141.988 2535 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 10.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 1.71 % Allowed : 16.13 % Favored : 82.16 % 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: -0.38 (0.19), residues: 1911 helix: 0.63 (0.21), residues: 595 sheet: 0.20 (0.24), residues: 476 loop : -1.13 (0.21), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG A 579 TYR 0.019 0.002 TYR A 458 PHE 0.025 0.001 PHE C 215 TRP 0.024 0.001 TRP A 369 HIS 0.003 0.001 HIS D 246 Details of bonding type rmsd/Z covalent geometry : bond 0.00253 / 0.12 (16537) covalent geometry : angle 0.61747 / 0.32 (22520) hydrogen bonds : bond 0.03616 / 2.36 ( 726) hydrogen bonds : angle 5.01018 / 3.48 ( 2028) metal coordination : bond 0.00311 / 0.15 ( 4) metal coordination : angle 6.53145 / 4.10 ( 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 264 residues out of total 1693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 235 time to evaluate : 0.612 Fit side-chains revert: symmetry clash REVERT: A 36 GLU cc_start: 0.7215 (mp0) cc_final: 0.6994 (mp0) REVERT: A 282 PRO cc_start: 0.8029 (Cg_exo) cc_final: 0.7791 (Cg_endo) REVERT: A 294 MET cc_start: 0.4147 (ptt) cc_final: 0.3931 (ptt) REVERT: A 684 HIS cc_start: 0.8705 (OUTLIER) cc_final: 0.8190 (t-90) REVERT: A 689 GLN cc_start: 0.8864 (tm-30) cc_final: 0.8564 (tt0) REVERT: A 897 LEU cc_start: 0.8043 (OUTLIER) cc_final: 0.7745 (mm) REVERT: A 906 THR cc_start: 0.9061 (m) cc_final: 0.8560 (p) REVERT: A 1024 MET cc_start: 0.6179 (ppp) cc_final: 0.5313 (ppp) REVERT: A 1039 MET cc_start: 0.5924 (pmm) cc_final: 0.5407 (ptp) REVERT: A 1083 LYS cc_start: 0.6276 (pttp) cc_final: 0.5496 (tppt) REVERT: A 1183 ILE cc_start: 0.6368 (OUTLIER) cc_final: 0.6074 (mm) REVERT: B 12 LEU cc_start: 0.7316 (tp) cc_final: 0.7076 (tp) REVERT: B 116 MET cc_start: 0.7770 (pmm) cc_final: 0.7457 (ppp) REVERT: B 199 MET cc_start: 0.5929 (tpt) cc_final: 0.4647 (tpt) REVERT: B 244 MET cc_start: 0.8592 (tmm) cc_final: 0.8291 (tmm) REVERT: C 47 LEU cc_start: 0.7601 (OUTLIER) cc_final: 0.7266 (tt) REVERT: C 108 GLN cc_start: 0.7459 (mm-40) cc_final: 0.6464 (tp40) REVERT: C 139 MET cc_start: 0.6762 (tpp) cc_final: 0.6451 (tpp) REVERT: C 150 ASP cc_start: 0.6996 (m-30) cc_final: 0.6605 (t70) REVERT: C 248 LYS cc_start: 0.8535 (mmtm) cc_final: 0.8255 (mmtm) REVERT: D 1 MET cc_start: 0.6346 (tpp) cc_final: 0.6096 (tpp) REVERT: D 17 GLU cc_start: 0.8568 (pt0) cc_final: 0.7876 (pt0) REVERT: D 40 MET cc_start: 0.5219 (tpp) cc_final: 0.4962 (tpt) REVERT: D 53 ARG cc_start: 0.8218 (mpp80) cc_final: 0.7944 (mtm110) REVERT: D 150 ASP cc_start: 0.7615 (t0) cc_final: 0.7384 (t0) REVERT: D 204 GLN cc_start: 0.8397 (mm-40) cc_final: 0.7824 (mm-40) REVERT: D 210 ARG cc_start: 0.7337 (tpm170) cc_final: 0.6918 (tpm170) outliers start: 29 outliers final: 17 residues processed: 251 average time/residue: 0.0971 time to fit residues: 38.1066 Evaluate side-chains 236 residues out of total 1693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 215 time to evaluate : 0.597 ------------------------------------------------------------------------------- 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 1172 LEU Chi-restraints excluded: chain A residue 1183 ILE 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 221 LEU Chi-restraints excluded: chain D residue 236 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 58 optimal weight: 3.9990 chunk 46 optimal weight: 5.9990 chunk 18 optimal weight: 0.6980 chunk 162 optimal weight: 0.2980 chunk 158 optimal weight: 6.9990 chunk 81 optimal weight: 0.9990 chunk 124 optimal weight: 6.9990 chunk 131 optimal weight: 0.0970 chunk 33 optimal weight: 0.6980 chunk 146 optimal weight: 6.9990 chunk 7 optimal weight: 2.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- 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 108 GLN C 200 ASN ** C 246 HIS ** 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 = 0.4286 r_free = 0.4286 target = 0.172845 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.131341 restraints weight = 26991.674| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.135723 restraints weight = 14036.661| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.138637 restraints weight = 9258.757| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.140494 restraints weight = 7131.861| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.141630 restraints weight = 6073.451| |-----------------------------------------------------------------------------| r_work (final): 0.3890 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7293 moved from start: 0.2300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 16541 Z= 0.116 Angle : 0.625 11.670 22532 Z= 0.316 Chirality : 0.043 0.226 2511 Planarity : 0.004 0.065 2762 Dihedral : 15.457 141.785 2535 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 11.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 1.65 % Allowed : 16.77 % Favored : 81.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.68 (0.21), residues: 595 sheet: 0.28 (0.23), residues: 499 loop : -1.13 (0.21), residues: 817 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 579 TYR 0.025 0.002 TYR A 244 PHE 0.018 0.002 PHE C 215 TRP 0.032 0.001 TRP A 369 HIS 0.004 0.001 HIS B 153 Details of bonding type rmsd/Z covalent geometry : bond 0.00259 / 0.12 (16537) covalent geometry : angle 0.61074 / 0.32 (22520) hydrogen bonds : bond 0.03582 / 2.34 ( 726) hydrogen bonds : angle 4.91636 / 3.40 ( 2028) metal coordination : bond 0.00344 / 0.17 ( 4) metal coordination : angle 5.74125 / 3.60 ( 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 260 residues out of total 1693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 232 time to evaluate : 0.372 Fit side-chains revert: symmetry clash REVERT: A 36 GLU cc_start: 0.7215 (mp0) cc_final: 0.6996 (mp0) REVERT: A 282 PRO cc_start: 0.7980 (Cg_exo) cc_final: 0.7753 (Cg_endo) REVERT: A 299 MET cc_start: 0.6403 (mmt) cc_final: 0.6168 (mmp) REVERT: A 359 MET cc_start: 0.6271 (ptt) cc_final: 0.6026 (ptt) REVERT: A 495 LYS cc_start: 0.7054 (OUTLIER) cc_final: 0.6533 (ptpp) REVERT: A 684 HIS cc_start: 0.8696 (OUTLIER) cc_final: 0.8184 (t-90) REVERT: A 689 GLN cc_start: 0.8902 (tm-30) cc_final: 0.8607 (tt0) REVERT: A 897 LEU cc_start: 0.8065 (OUTLIER) cc_final: 0.7772 (mm) REVERT: A 906 THR cc_start: 0.9053 (m) cc_final: 0.8560 (p) REVERT: A 1024 MET cc_start: 0.6249 (ppp) cc_final: 0.5287 (ppp) REVERT: A 1039 MET cc_start: 0.5888 (pmm) cc_final: 0.5397 (ptp) REVERT: A 1083 LYS cc_start: 0.6286 (pttp) cc_final: 0.5535 (tppt) REVERT: A 1183 ILE cc_start: 0.6391 (OUTLIER) cc_final: 0.6133 (mm) REVERT: B 12 LEU cc_start: 0.7326 (tp) cc_final: 0.7090 (tp) REVERT: B 116 MET cc_start: 0.7705 (pmm) cc_final: 0.7241 (ppp) REVERT: B 199 MET cc_start: 0.5893 (tpt) cc_final: 0.4634 (tpt) REVERT: B 244 MET cc_start: 0.8619 (tmm) cc_final: 0.8275 (tmm) REVERT: C 47 LEU cc_start: 0.7615 (OUTLIER) cc_final: 0.7263 (tt) REVERT: C 248 LYS cc_start: 0.8483 (mmtm) cc_final: 0.8180 (mmtm) REVERT: D 1 MET cc_start: 0.6362 (tpp) cc_final: 0.6113 (tpp) REVERT: D 17 GLU cc_start: 0.8577 (pt0) cc_final: 0.7851 (pt0) REVERT: D 150 ASP cc_start: 0.7647 (t0) cc_final: 0.7406 (t0) REVERT: D 204 GLN cc_start: 0.8395 (mm-40) cc_final: 0.7812 (mm-40) REVERT: D 210 ARG cc_start: 0.7372 (tpm170) cc_final: 0.6971 (tpm170) outliers start: 28 outliers final: 23 residues processed: 246 average time/residue: 0.0983 time to fit residues: 37.7090 Evaluate side-chains 243 residues out of total 1693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 215 time to evaluate : 0.409 ------------------------------------------------------------------------------- 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 495 LYS 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 1141 ILE 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 B residue 115 GLU Chi-restraints excluded: chain B residue 224 THR 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 C residue 191 GLU 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 5 optimal weight: 0.6980 chunk 184 optimal weight: 6.9990 chunk 42 optimal weight: 0.0010 chunk 4 optimal weight: 2.9990 chunk 153 optimal weight: 0.9980 chunk 168 optimal weight: 7.9990 chunk 188 optimal weight: 0.9990 chunk 60 optimal weight: 3.9990 chunk 173 optimal weight: 0.2980 chunk 170 optimal weight: 4.9990 chunk 160 optimal weight: 0.0570 overall best weight: 0.4104 ------------------------------------------------------------------------------- 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 200 ASN ** 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 = 0.4289 r_free = 0.4289 target = 0.173166 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.132391 restraints weight = 26842.726| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.136739 restraints weight = 13736.261| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.139638 restraints weight = 8963.583| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.141478 restraints weight = 6848.169| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.142642 restraints weight = 5809.786| |-----------------------------------------------------------------------------| r_work (final): 0.3910 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7252 moved from start: 0.2365 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 : 0.621 10.842 22532 Z= 0.315 Chirality : 0.043 0.226 2511 Planarity : 0.004 0.066 2762 Dihedral : 15.396 141.501 2535 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 10.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 1.54 % Allowed : 17.07 % Favored : 81.39 % 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: -0.29 (0.19), residues: 1911 helix: 0.71 (0.21), residues: 593 sheet: 0.21 (0.23), residues: 505 loop : -1.07 (0.21), residues: 813 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 579 TYR 0.020 0.001 TYR A 458 PHE 0.018 0.001 PHE B 207 TRP 0.033 0.001 TRP A 369 HIS 0.004 0.001 HIS D 246 Details of bonding type rmsd/Z covalent geometry : bond 0.00246 / 0.11 (16537) covalent geometry : angle 0.60971 / 0.31 (22520) hydrogen bonds : bond 0.03472 / 2.27 ( 726) hydrogen bonds : angle 4.86868 / 3.35 ( 2028) metal coordination : bond 0.00327 / 0.16 ( 4) metal coordination : angle 5.10021 / 3.20 ( 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 255 residues out of total 1693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 229 time to evaluate : 0.439 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 36 GLU cc_start: 0.7263 (mp0) cc_final: 0.7055 (mp0) REVERT: A 119 PHE cc_start: 0.8362 (t80) cc_final: 0.8072 (t80) REVERT: A 282 PRO cc_start: 0.8017 (Cg_exo) cc_final: 0.7800 (Cg_endo) REVERT: A 299 MET cc_start: 0.6351 (mmt) cc_final: 0.6120 (mmt) REVERT: A 359 MET cc_start: 0.6248 (ptt) cc_final: 0.5993 (ptt) REVERT: A 372 VAL cc_start: 0.3424 (m) cc_final: 0.2923 (p) REVERT: A 684 HIS cc_start: 0.8697 (OUTLIER) cc_final: 0.8197 (t-90) REVERT: A 689 GLN cc_start: 0.8905 (tm-30) cc_final: 0.8613 (tt0) REVERT: A 831 MET cc_start: 0.6973 (mmt) cc_final: 0.6716 (mmt) REVERT: A 897 LEU cc_start: 0.8012 (OUTLIER) cc_final: 0.7729 (mm) REVERT: A 906 THR cc_start: 0.9054 (m) cc_final: 0.8560 (p) REVERT: A 1024 MET cc_start: 0.6181 (ppp) cc_final: 0.5207 (ppp) REVERT: A 1039 MET cc_start: 0.5931 (pmm) cc_final: 0.5308 (ptm) REVERT: A 1083 LYS cc_start: 0.6320 (pttp) cc_final: 0.5572 (tppt) REVERT: A 1183 ILE cc_start: 0.6381 (OUTLIER) cc_final: 0.6144 (mm) REVERT: B 12 LEU cc_start: 0.7325 (tp) cc_final: 0.7086 (tp) REVERT: B 116 MET cc_start: 0.7632 (pmm) cc_final: 0.7258 (ppp) REVERT: B 199 MET cc_start: 0.5936 (tpt) cc_final: 0.4675 (tpt) REVERT: C 47 LEU cc_start: 0.7640 (OUTLIER) cc_final: 0.7275 (tt) REVERT: C 248 LYS cc_start: 0.8430 (mmtm) cc_final: 0.8153 (mmtm) REVERT: D 17 GLU cc_start: 0.8569 (pt0) cc_final: 0.7837 (pt0) REVERT: D 150 ASP cc_start: 0.7640 (t0) cc_final: 0.7399 (t0) REVERT: D 204 GLN cc_start: 0.8401 (mm-40) cc_final: 0.7817 (mm-40) REVERT: D 210 ARG cc_start: 0.7359 (tpm170) cc_final: 0.6967 (tpm170) outliers start: 26 outliers final: 19 residues processed: 242 average time/residue: 0.1046 time to fit residues: 39.1869 Evaluate side-chains 243 residues out of total 1693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 220 time to evaluate : 0.463 ------------------------------------------------------------------------------- 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 676 MET Chi-restraints excluded: chain A residue 684 HIS 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 1141 ILE Chi-restraints excluded: chain A residue 1172 LEU Chi-restraints excluded: chain A residue 1183 ILE Chi-restraints excluded: chain B residue 81 CYS 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 221 LEU 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 83 optimal weight: 4.9990 chunk 190 optimal weight: 0.8980 chunk 91 optimal weight: 7.9990 chunk 29 optimal weight: 3.9990 chunk 71 optimal weight: 4.9990 chunk 155 optimal weight: 6.9990 chunk 40 optimal weight: 7.9990 chunk 175 optimal weight: 0.9990 chunk 176 optimal weight: 0.9990 chunk 161 optimal weight: 0.9990 chunk 184 optimal weight: 6.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 451 GLN A 688 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** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4259 r_free = 0.4259 target = 0.170421 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.131036 restraints weight = 26963.980| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.133361 restraints weight = 14103.126| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.135370 restraints weight = 9546.777| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.136339 restraints weight = 7888.867| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.136678 restraints weight = 7632.653| |-----------------------------------------------------------------------------| r_work (final): 0.3823 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7400 moved from start: 0.2472 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= 0.155 Angle : 0.649 13.553 22532 Z= 0.328 Chirality : 0.044 0.226 2511 Planarity : 0.004 0.070 2762 Dihedral : 15.414 141.501 2535 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 12.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 1.59 % Allowed : 17.31 % Favored : 81.10 % 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: -0.29 (0.19), residues: 1911 helix: 0.72 (0.21), residues: 595 sheet: 0.19 (0.23), residues: 500 loop : -1.06 (0.21), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 310 TYR 0.019 0.002 TYR A 458 PHE 0.031 0.002 PHE A 516 TRP 0.036 0.002 TRP A 369 HIS 0.005 0.001 HIS D 246 Details of bonding type rmsd/Z covalent geometry : bond 0.00361 / 0.15 (16537) covalent geometry : angle 0.63060 / 0.33 (22520) hydrogen bonds : bond 0.03695 / 2.43 ( 726) hydrogen bonds : angle 4.89612 / 3.37 ( 2028) metal coordination : bond 0.00856 / 0.39 ( 4) metal coordination : angle 6.76522 / 4.17 ( 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 241 residues out of total 1693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 214 time to evaluate : 0.513 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 36 GLU cc_start: 0.7357 (mp0) cc_final: 0.7089 (mp0) REVERT: A 299 MET cc_start: 0.6459 (mmt) cc_final: 0.6218 (mmt) REVERT: A 495 LYS cc_start: 0.7162 (OUTLIER) cc_final: 0.6651 (ptpp) REVERT: A 684 HIS cc_start: 0.8710 (OUTLIER) cc_final: 0.8253 (t-90) REVERT: A 689 GLN cc_start: 0.8939 (tm-30) cc_final: 0.8642 (tt0) REVERT: A 897 LEU cc_start: 0.8156 (OUTLIER) cc_final: 0.7822 (mm) REVERT: A 906 THR cc_start: 0.9086 (m) cc_final: 0.8620 (p) REVERT: A 1024 MET cc_start: 0.6366 (ppp) cc_final: 0.5333 (ppp) REVERT: A 1039 MET cc_start: 0.6039 (pmm) cc_final: 0.5471 (ptm) REVERT: A 1083 LYS cc_start: 0.6326 (pttp) cc_final: 0.5591 (tppt) REVERT: A 1183 ILE cc_start: 0.6486 (OUTLIER) cc_final: 0.6227 (mm) REVERT: B 116 MET cc_start: 0.7735 (pmm) cc_final: 0.7342 (ppp) REVERT: C 47 LEU cc_start: 0.7627 (OUTLIER) cc_final: 0.7294 (tt) REVERT: C 116 MET cc_start: 0.6084 (tpt) cc_final: 0.5864 (tpt) REVERT: C 248 LYS cc_start: 0.8433 (mmtm) cc_final: 0.8175 (mmtm) REVERT: D 17 GLU cc_start: 0.8533 (pt0) cc_final: 0.7835 (pt0) REVERT: D 204 GLN cc_start: 0.8458 (mm-40) cc_final: 0.7863 (mm-40) REVERT: D 210 ARG cc_start: 0.7431 (tpm170) cc_final: 0.7045 (tpm170) outliers start: 27 outliers final: 19 residues processed: 230 average time/residue: 0.1091 time to fit residues: 38.0139 Evaluate side-chains 229 residues out of total 1693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 205 time to evaluate : 0.445 ------------------------------------------------------------------------------- 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 495 LYS 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 1172 LEU Chi-restraints excluded: chain A residue 1183 ILE Chi-restraints excluded: chain B residue 81 CYS 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 221 LEU 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: 0.7980 chunk 41 optimal weight: 0.9980 chunk 153 optimal weight: 0.9980 chunk 122 optimal weight: 6.9990 chunk 128 optimal weight: 5.9990 chunk 145 optimal weight: 10.0000 chunk 143 optimal weight: 0.1980 chunk 116 optimal weight: 3.9990 chunk 157 optimal weight: 8.9990 chunk 189 optimal weight: 0.9990 chunk 176 optimal weight: 9.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4275 r_free = 0.4275 target = 0.171905 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.130757 restraints weight = 26674.768| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.135072 restraints weight = 13807.958| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.137863 restraints weight = 9071.331| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.139745 restraints weight = 6987.331| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.140886 restraints weight = 5924.918| |-----------------------------------------------------------------------------| r_work (final): 0.3883 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7297 moved from start: 0.2536 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= 0.122 Angle : 0.640 12.948 22532 Z= 0.321 Chirality : 0.043 0.226 2511 Planarity : 0.004 0.070 2762 Dihedral : 15.386 141.495 2535 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 11.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 1.65 % Allowed : 17.66 % Favored : 80.69 % 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: -0.32 (0.19), residues: 1911 helix: 0.72 (0.21), residues: 595 sheet: 0.11 (0.23), residues: 506 loop : -1.07 (0.21), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 64 TYR 0.021 0.002 TYR A 458 PHE 0.037 0.002 PHE B 207 TRP 0.038 0.002 TRP A1130 HIS 0.005 0.001 HIS A 511 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.12 (16537) covalent geometry : angle 0.62245 / 0.32 (22520) hydrogen bonds : bond 0.03521 / 2.30 ( 726) hydrogen bonds : angle 4.87239 / 3.35 ( 2028) metal coordination : bond 0.00517 / 0.25 ( 4) metal coordination : angle 6.46743 / 4.04 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2372.33 seconds wall clock time: 41 minutes 52.25 seconds (2512.25 seconds total)