Starting phenix.real_space_refine on Wed May 6 00:18:57 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9qu9_53375/05_2026/9qu9_53375.cif Found real_map, /net/cci-nas-00/data/ceres_data/9qu9_53375/05_2026/9qu9_53375.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9qu9_53375/05_2026/9qu9_53375.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9qu9_53375/05_2026/9qu9_53375.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9qu9_53375/05_2026/9qu9_53375.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9qu9_53375/05_2026/9qu9_53375.map" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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: 5 Type Number sf(0) Gaussians P 8 5.49 5 S 204 5.16 5 C 21161 2.51 5 N 5678 2.21 5 O 6247 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 152 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 33298 Number of models: 1 Model: "" Number of chains: 12 Chain: "P" Number of atoms: 565 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 565 Classifications: {'peptide': 74} Link IDs: {'TRANS': 73} Chain: "Q" Number of atoms: 576 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 576 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 1, 'TRANS': 74} Chain: "R" Number of atoms: 565 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 565 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain: "S" Number of atoms: 558 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 558 Classifications: {'peptide': 73} Link IDs: {'TRANS': 72} Chain: "A" Number of atoms: 7722 Number of conformers: 1 Conformer: "" Number of residues, atoms: 971, 7722 Classifications: {'peptide': 971} Link IDs: {'PTRANS': 34, 'TRANS': 936} Chain breaks: 1 Chain: "B" Number of atoms: 7737 Number of conformers: 1 Conformer: "" Number of residues, atoms: 974, 7737 Classifications: {'peptide': 974} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 34, 'TRANS': 939} Chain breaks: 1 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'ARG:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 8 Chain: "C" Number of atoms: 7722 Number of conformers: 1 Conformer: "" Number of residues, atoms: 971, 7722 Classifications: {'peptide': 971} Link IDs: {'CIS': 1, 'PTRANS': 34, 'TRANS': 935} Chain breaks: 1 Chain: "D" Number of atoms: 7745 Number of conformers: 1 Conformer: "" Number of residues, atoms: 974, 7745 Classifications: {'peptide': 974} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 34, 'TRANS': 939} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "A" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 7.19, per 1000 atoms: 0.22 Number of scatterers: 33298 At special positions: 0 Unit cell: (193.752, 194.58, 139.932, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 204 16.00 P 8 15.00 O 6247 8.00 N 5678 7.00 C 21161 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS P 43 " - pdb=" SG CYS P 81 " distance=2.03 Simple disulfide: pdb=" SG CYS S 40 " - pdb=" SG CYS S 87 " distance=2.03 Simple disulfide: pdb=" SG CYS S 43 " - pdb=" SG CYS S 81 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.74 Conformation dependent library (CDL) restraints added in 1.4 seconds 8326 Ramachandran restraints generated. 4163 Oldfield, 0 Emsley, 4163 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7948 Finding SS restraints... Secondary structure from input PDB file: 131 helices and 28 sheets defined 34.5% alpha, 10.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.13 Creating SS restraints... Processing helix chain 'P' and resid 35 through 47 Processing helix chain 'P' and resid 70 through 76 Processing helix chain 'Q' and resid 33 through 49 removed outlier: 4.066A pdb=" N LEU Q 37 " --> pdb=" O SER Q 33 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N SER Q 38 " --> pdb=" O ARG Q 34 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ALA Q 42 " --> pdb=" O SER Q 38 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LEU Q 45 " --> pdb=" O GLN Q 41 " (cutoff:3.500A) Processing helix chain 'Q' and resid 70 through 76 Processing helix chain 'R' and resid 34 through 45 removed outlier: 4.549A pdb=" N SER R 38 " --> pdb=" O ARG R 34 " (cutoff:3.500A) Processing helix chain 'R' and resid 70 through 76 Processing helix chain 'S' and resid 35 through 40 removed outlier: 4.118A pdb=" N LEU S 39 " --> pdb=" O ASN S 35 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N CYS S 40 " --> pdb=" O SER S 36 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 35 through 40' Processing helix chain 'S' and resid 42 through 47 removed outlier: 3.590A pdb=" N LYS S 47 " --> pdb=" O CYS S 43 " (cutoff:3.500A) Processing helix chain 'S' and resid 70 through 76 removed outlier: 3.536A pdb=" N ALA S 75 " --> pdb=" O ASP S 71 " (cutoff:3.500A) Processing helix chain 'A' and resid 20 through 25 Processing helix chain 'A' and resid 27 through 40 removed outlier: 3.767A pdb=" N HIS A 31 " --> pdb=" O LYS A 27 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 65 removed outlier: 3.643A pdb=" N GLY A 64 " --> pdb=" O LYS A 60 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLU A 65 " --> pdb=" O LYS A 61 " (cutoff:3.500A) Processing helix chain 'A' and resid 76 through 79 Processing helix chain 'A' and resid 80 through 97 Processing helix chain 'A' and resid 109 through 115 Processing helix chain 'A' and resid 120 through 128 Processing helix chain 'A' and resid 132 through 148 Processing helix chain 'A' and resid 155 through 157 No H-bonds generated for 'chain 'A' and resid 155 through 157' Processing helix chain 'A' and resid 159 through 177 removed outlier: 3.787A pdb=" N VAL A 177 " --> pdb=" O THR A 173 " (cutoff:3.500A) Processing helix chain 'A' and resid 188 through 201 removed outlier: 3.804A pdb=" N HIS A 192 " --> pdb=" O GLY A 188 " (cutoff:3.500A) Processing helix chain 'A' and resid 219 through 232 Processing helix chain 'A' and resid 245 through 250 Processing helix chain 'A' and resid 254 through 271 Processing helix chain 'A' and resid 281 through 288 removed outlier: 3.674A pdb=" N ASP A 285 " --> pdb=" O SER A 281 " (cutoff:3.500A) Processing helix chain 'A' and resid 301 through 309 removed outlier: 3.797A pdb=" N LEU A 305 " --> pdb=" O SER A 301 " (cutoff:3.500A) Processing helix chain 'A' and resid 326 through 333 removed outlier: 4.278A pdb=" N LEU A 330 " --> pdb=" O ASN A 326 " (cutoff:3.500A) Processing helix chain 'A' and resid 345 through 358 Processing helix chain 'A' and resid 367 through 379 Processing helix chain 'A' and resid 381 through 392 Processing helix chain 'A' and resid 396 through 410 Proline residue: A 405 - end of helix removed outlier: 3.749A pdb=" N ASN A 409 " --> pdb=" O PRO A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 424 removed outlier: 4.025A pdb=" N VAL A 420 " --> pdb=" O SER A 416 " (cutoff:3.500A) removed outlier: 4.835A pdb=" N GLY A 421 " --> pdb=" O VAL A 417 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N PHE A 422 " --> pdb=" O LEU A 418 " (cutoff:3.500A) Processing helix chain 'A' and resid 426 through 439 Processing helix chain 'A' and resid 444 through 452 Processing helix chain 'A' and resid 458 through 469 Processing helix chain 'A' and resid 485 through 499 Processing helix chain 'A' and resid 499 through 505 removed outlier: 4.007A pdb=" N SER A 504 " --> pdb=" O LYS A 500 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N GLN A 505 " --> pdb=" O PRO A 501 " (cutoff:3.500A) Processing helix chain 'A' and resid 509 through 520 Processing helix chain 'A' and resid 642 through 646 removed outlier: 4.540A pdb=" N ASN A 645 " --> pdb=" O ASP A 642 " (cutoff:3.500A) Processing helix chain 'A' and resid 664 through 670 Processing helix chain 'A' and resid 776 through 783 removed outlier: 4.540A pdb=" N ILE A 780 " --> pdb=" O THR A 776 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N LYS A 781 " --> pdb=" O GLU A 777 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N GLY A 782 " --> pdb=" O ASP A 778 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N LEU A 783 " --> pdb=" O CYS A 779 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 776 through 783' Processing helix chain 'A' and resid 841 through 851 removed outlier: 4.058A pdb=" N GLN A 851 " --> pdb=" O ALA A 847 " (cutoff:3.500A) Processing helix chain 'B' and resid 20 through 25 Processing helix chain 'B' and resid 27 through 40 removed outlier: 3.768A pdb=" N HIS B 31 " --> pdb=" O LYS B 27 " (cutoff:3.500A) Processing helix chain 'B' and resid 76 through 78 No H-bonds generated for 'chain 'B' and resid 76 through 78' Processing helix chain 'B' and resid 80 through 96 Processing helix chain 'B' and resid 109 through 115 removed outlier: 3.777A pdb=" N VAL B 113 " --> pdb=" O ASP B 109 " (cutoff:3.500A) Processing helix chain 'B' and resid 117 through 130 removed outlier: 3.600A pdb=" N GLY B 121 " --> pdb=" O THR B 117 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N ALA B 123 " --> pdb=" O ASP B 119 " (cutoff:3.500A) Processing helix chain 'B' and resid 132 through 149 removed outlier: 3.748A pdb=" N ARG B 136 " --> pdb=" O THR B 132 " (cutoff:3.500A) Processing helix chain 'B' and resid 159 through 175 Processing helix chain 'B' and resid 188 through 201 removed outlier: 3.647A pdb=" N HIS B 192 " --> pdb=" O GLY B 188 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N SER B 198 " --> pdb=" O LYS B 194 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N LEU B 199 " --> pdb=" O GLU B 195 " (cutoff:3.500A) Processing helix chain 'B' and resid 219 through 232 Processing helix chain 'B' and resid 245 through 250 removed outlier: 3.742A pdb=" N ILE B 250 " --> pdb=" O GLU B 246 " (cutoff:3.500A) Processing helix chain 'B' and resid 254 through 271 Processing helix chain 'B' and resid 281 through 287 Processing helix chain 'B' and resid 288 through 290 No H-bonds generated for 'chain 'B' and resid 288 through 290' Processing helix chain 'B' and resid 301 through 309 removed outlier: 3.826A pdb=" N LEU B 305 " --> pdb=" O SER B 301 " (cutoff:3.500A) Processing helix chain 'B' and resid 326 through 333 removed outlier: 3.832A pdb=" N LEU B 330 " --> pdb=" O ASN B 326 " (cutoff:3.500A) Processing helix chain 'B' and resid 345 through 358 Processing helix chain 'B' and resid 367 through 379 Processing helix chain 'B' and resid 381 through 392 Processing helix chain 'B' and resid 396 through 410 Proline residue: B 405 - end of helix removed outlier: 4.064A pdb=" N ASN B 409 " --> pdb=" O PRO B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 414 through 424 removed outlier: 3.952A pdb=" N VAL B 420 " --> pdb=" O SER B 416 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N GLY B 421 " --> pdb=" O VAL B 417 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N PHE B 422 " --> pdb=" O LEU B 418 " (cutoff:3.500A) Processing helix chain 'B' and resid 426 through 440 Processing helix chain 'B' and resid 444 through 452 Processing helix chain 'B' and resid 458 through 469 Processing helix chain 'B' and resid 485 through 499 Processing helix chain 'B' and resid 499 through 504 removed outlier: 3.950A pdb=" N SER B 504 " --> pdb=" O LYS B 500 " (cutoff:3.500A) Processing helix chain 'B' and resid 509 through 520 Processing helix chain 'B' and resid 664 through 670 removed outlier: 3.515A pdb=" N ASN B 669 " --> pdb=" O SER B 666 " (cutoff:3.500A) Processing helix chain 'B' and resid 776 through 782 removed outlier: 4.529A pdb=" N ILE B 780 " --> pdb=" O THR B 776 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N LYS B 781 " --> pdb=" O GLU B 777 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N GLY B 782 " --> pdb=" O ASP B 778 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 776 through 782' Processing helix chain 'B' and resid 841 through 851 Processing helix chain 'C' and resid 20 through 25 removed outlier: 3.881A pdb=" N VAL C 24 " --> pdb=" O HIS C 20 " (cutoff:3.500A) Processing helix chain 'C' and resid 27 through 40 removed outlier: 3.950A pdb=" N HIS C 31 " --> pdb=" O LYS C 27 " (cutoff:3.500A) Processing helix chain 'C' and resid 55 through 65 removed outlier: 3.780A pdb=" N GLY C 64 " --> pdb=" O LYS C 60 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N GLU C 65 " --> pdb=" O LYS C 61 " (cutoff:3.500A) Processing helix chain 'C' and resid 76 through 79 Processing helix chain 'C' and resid 80 through 98 removed outlier: 3.521A pdb=" N GLU C 95 " --> pdb=" O LEU C 91 " (cutoff:3.500A) Processing helix chain 'C' and resid 109 through 115 Processing helix chain 'C' and resid 120 through 128 Processing helix chain 'C' and resid 132 through 149 Processing helix chain 'C' and resid 155 through 157 No H-bonds generated for 'chain 'C' and resid 155 through 157' Processing helix chain 'C' and resid 159 through 177 removed outlier: 3.785A pdb=" N VAL C 177 " --> pdb=" O THR C 173 " (cutoff:3.500A) Processing helix chain 'C' and resid 188 through 201 removed outlier: 3.761A pdb=" N HIS C 192 " --> pdb=" O GLY C 188 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLU C 195 " --> pdb=" O ARG C 191 " (cutoff:3.500A) Processing helix chain 'C' and resid 219 through 232 Processing helix chain 'C' and resid 245 through 250 Processing helix chain 'C' and resid 254 through 271 Processing helix chain 'C' and resid 281 through 288 removed outlier: 3.647A pdb=" N ASP C 285 " --> pdb=" O SER C 281 " (cutoff:3.500A) Processing helix chain 'C' and resid 301 through 309 removed outlier: 3.803A pdb=" N LEU C 305 " --> pdb=" O SER C 301 " (cutoff:3.500A) Processing helix chain 'C' and resid 326 through 334 removed outlier: 4.059A pdb=" N LEU C 330 " --> pdb=" O ASN C 326 " (cutoff:3.500A) Processing helix chain 'C' and resid 345 through 358 Processing helix chain 'C' and resid 367 through 379 Processing helix chain 'C' and resid 381 through 392 Processing helix chain 'C' and resid 396 through 410 Proline residue: C 405 - end of helix removed outlier: 3.790A pdb=" N ASN C 409 " --> pdb=" O PRO C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 414 through 424 removed outlier: 3.853A pdb=" N VAL C 420 " --> pdb=" O SER C 416 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N GLY C 421 " --> pdb=" O VAL C 417 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N PHE C 422 " --> pdb=" O LEU C 418 " (cutoff:3.500A) Processing helix chain 'C' and resid 426 through 439 Processing helix chain 'C' and resid 444 through 452 Processing helix chain 'C' and resid 458 through 469 Processing helix chain 'C' and resid 485 through 499 Processing helix chain 'C' and resid 499 through 505 removed outlier: 3.783A pdb=" N SER C 504 " --> pdb=" O LYS C 500 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N GLN C 505 " --> pdb=" O PRO C 501 " (cutoff:3.500A) Processing helix chain 'C' and resid 509 through 519 Processing helix chain 'C' and resid 642 through 646 removed outlier: 4.347A pdb=" N ASN C 645 " --> pdb=" O ASP C 642 " (cutoff:3.500A) Processing helix chain 'C' and resid 664 through 670 removed outlier: 3.636A pdb=" N GLY C 668 " --> pdb=" O SER C 665 " (cutoff:3.500A) Processing helix chain 'C' and resid 747 through 751 removed outlier: 3.652A pdb=" N ASN C 750 " --> pdb=" O GLY C 747 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LEU C 751 " --> pdb=" O SER C 748 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 747 through 751' Processing helix chain 'C' and resid 841 through 851 Processing helix chain 'D' and resid 27 through 40 Processing helix chain 'D' and resid 56 through 63 removed outlier: 4.168A pdb=" N LYS D 60 " --> pdb=" O ALA D 56 " (cutoff:3.500A) Processing helix chain 'D' and resid 80 through 97 removed outlier: 3.581A pdb=" N GLU D 95 " --> pdb=" O LEU D 91 " (cutoff:3.500A) Processing helix chain 'D' and resid 109 through 115 removed outlier: 3.553A pdb=" N VAL D 113 " --> pdb=" O ASP D 109 " (cutoff:3.500A) Processing helix chain 'D' and resid 117 through 130 removed outlier: 3.641A pdb=" N GLY D 121 " --> pdb=" O THR D 117 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N ALA D 123 " --> pdb=" O ASP D 119 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N HIS D 130 " --> pdb=" O GLU D 126 " (cutoff:3.500A) Processing helix chain 'D' and resid 132 through 149 Processing helix chain 'D' and resid 159 through 175 Processing helix chain 'D' and resid 188 through 201 removed outlier: 3.808A pdb=" N HIS D 192 " --> pdb=" O GLY D 188 " (cutoff:3.500A) Processing helix chain 'D' and resid 219 through 232 Processing helix chain 'D' and resid 245 through 250 removed outlier: 3.693A pdb=" N ILE D 250 " --> pdb=" O GLU D 246 " (cutoff:3.500A) Processing helix chain 'D' and resid 254 through 271 Processing helix chain 'D' and resid 281 through 287 Processing helix chain 'D' and resid 301 through 309 removed outlier: 3.826A pdb=" N LEU D 305 " --> pdb=" O SER D 301 " (cutoff:3.500A) Processing helix chain 'D' and resid 326 through 333 removed outlier: 4.239A pdb=" N LEU D 330 " --> pdb=" O ASN D 326 " (cutoff:3.500A) Processing helix chain 'D' and resid 345 through 358 Processing helix chain 'D' and resid 367 through 379 Processing helix chain 'D' and resid 381 through 392 Processing helix chain 'D' and resid 396 through 410 Proline residue: D 405 - end of helix removed outlier: 4.115A pdb=" N ASN D 409 " --> pdb=" O PRO D 405 " (cutoff:3.500A) Processing helix chain 'D' and resid 414 through 424 removed outlier: 3.765A pdb=" N VAL D 420 " --> pdb=" O SER D 416 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N GLY D 421 " --> pdb=" O VAL D 417 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N PHE D 422 " --> pdb=" O LEU D 418 " (cutoff:3.500A) Processing helix chain 'D' and resid 426 through 439 Processing helix chain 'D' and resid 444 through 452 Processing helix chain 'D' and resid 458 through 469 Processing helix chain 'D' and resid 485 through 499 Processing helix chain 'D' and resid 499 through 504 removed outlier: 4.069A pdb=" N SER D 504 " --> pdb=" O LYS D 500 " (cutoff:3.500A) Processing helix chain 'D' and resid 509 through 520 Processing helix chain 'D' and resid 664 through 670 Processing helix chain 'D' and resid 776 through 782 removed outlier: 4.251A pdb=" N ILE D 780 " --> pdb=" O THR D 776 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N LYS D 781 " --> pdb=" O GLU D 777 " (cutoff:3.500A) Processing helix chain 'D' and resid 841 through 851 removed outlier: 3.534A pdb=" N GLN D 851 " --> pdb=" O ALA D 847 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'P' and resid 24 through 29 removed outlier: 3.560A pdb=" N GLY P 24 " --> pdb=" O ILE P 67 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ILE P 28 " --> pdb=" O ALA P 63 " (cutoff:3.500A) removed outlier: 7.065A pdb=" N VAL P 62 " --> pdb=" O ASP P 58 " (cutoff:3.500A) removed outlier: 5.138A pdb=" N ASP P 58 " --> pdb=" O VAL P 62 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N THR P 64 " --> pdb=" O ILE P 56 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'Q' and resid 27 through 29 removed outlier: 3.900A pdb=" N LYS Q 66 " --> pdb=" O LYS Q 54 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N LYS Q 54 " --> pdb=" O LYS Q 66 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N THR Q 68 " --> pdb=" O ARG Q 52 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'R' and resid 52 through 58 removed outlier: 3.736A pdb=" N ILE R 56 " --> pdb=" O THR R 64 " (cutoff:3.500A) removed outlier: 7.382A pdb=" N THR R 64 " --> pdb=" O ILE R 56 " (cutoff:3.500A) removed outlier: 5.858A pdb=" N ASP R 58 " --> pdb=" O VAL R 62 " (cutoff:3.500A) removed outlier: 7.047A pdb=" N VAL R 62 " --> pdb=" O ASP R 58 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'S' and resid 25 through 29 Processing sheet with id=AA5, first strand: chain 'A' and resid 13 through 16 removed outlier: 6.217A pdb=" N ASN A 14 " --> pdb=" O VAL A 68 " (cutoff:3.500A) removed outlier: 7.178A pdb=" N ILE A 70 " --> pdb=" O ASN A 14 " (cutoff:3.500A) removed outlier: 6.094A pdb=" N PHE A 16 " --> pdb=" O ILE A 70 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N LEU A 72 " --> pdb=" O PHE A 16 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 237 through 241 removed outlier: 6.799A pdb=" N HIS A 237 " --> pdb=" O LEU A 293 " (cutoff:3.500A) removed outlier: 7.942A pdb=" N ILE A 295 " --> pdb=" O HIS A 237 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N CYS A 239 " --> pdb=" O ILE A 295 " (cutoff:3.500A) removed outlier: 7.548A pdb=" N ASP A 297 " --> pdb=" O CYS A 239 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N VAL A 241 " --> pdb=" O ASP A 297 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N VAL A 299 " --> pdb=" O VAL A 241 " (cutoff:3.500A) removed outlier: 6.958A pdb=" N MET A 209 " --> pdb=" O ASP A 337 " (cutoff:3.500A) removed outlier: 8.286A pdb=" N TYR A 339 " --> pdb=" O MET A 209 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N GLY A 211 " --> pdb=" O TYR A 339 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 473 through 475 Processing sheet with id=AA8, first strand: chain 'A' and resid 506 through 507 removed outlier: 6.288A pdb=" N LEU A 507 " --> pdb=" O SER A 530 " (cutoff:3.500A) removed outlier: 7.231A pdb=" N ASP A 532 " --> pdb=" O LEU A 507 " (cutoff:3.500A) removed outlier: 5.915A pdb=" N VAL A 529 " --> pdb=" O LYS A 556 " (cutoff:3.500A) removed outlier: 7.222A pdb=" N TYR A 558 " --> pdb=" O VAL A 529 " (cutoff:3.500A) removed outlier: 6.064A pdb=" N PHE A 531 " --> pdb=" O TYR A 558 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N PHE A 584 " --> pdb=" O ASN A 607 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N VAL A 606 " --> pdb=" O ASP A 630 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N ILE A 629 " --> pdb=" O TYR A 653 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N VAL A 720 " --> pdb=" O LYS A 744 " (cutoff:3.500A) removed outlier: 7.689A pdb=" N SER A 746 " --> pdb=" O VAL A 720 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N VAL A 722 " --> pdb=" O SER A 746 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 799 through 800 removed outlier: 3.978A pdb=" N LEU A 800 " --> pdb=" O SER A 820 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'A' and resid 857 through 859 removed outlier: 3.590A pdb=" N ALA A 858 " --> pdb=" O ILE A 949 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N HIS A 946 " --> pdb=" O MET A 894 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 912 through 915 removed outlier: 8.737A pdb=" N TRP A 913 " --> pdb=" O VAL A 920 " (cutoff:3.500A) removed outlier: 8.303A pdb=" N VAL A 920 " --> pdb=" O TRP A 913 " (cutoff:3.500A) removed outlier: 4.687A pdb=" N VAL A 915 " --> pdb=" O ASP A 918 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 15 through 18 Processing sheet with id=AB4, first strand: chain 'B' and resid 237 through 241 removed outlier: 6.403A pdb=" N HIS B 237 " --> pdb=" O LEU B 293 " (cutoff:3.500A) removed outlier: 7.965A pdb=" N ILE B 295 " --> pdb=" O HIS B 237 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N CYS B 239 " --> pdb=" O ILE B 295 " (cutoff:3.500A) removed outlier: 7.370A pdb=" N ASP B 297 " --> pdb=" O CYS B 239 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N VAL B 241 " --> pdb=" O ASP B 297 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N VAL B 299 " --> pdb=" O VAL B 241 " (cutoff:3.500A) removed outlier: 6.242A pdb=" N VAL B 292 " --> pdb=" O ARG B 319 " (cutoff:3.500A) removed outlier: 7.529A pdb=" N ILE B 321 " --> pdb=" O VAL B 292 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N ILE B 294 " --> pdb=" O ILE B 321 " (cutoff:3.500A) removed outlier: 7.644A pdb=" N THR B 323 " --> pdb=" O ILE B 294 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N LEU B 296 " --> pdb=" O THR B 323 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N MET B 209 " --> pdb=" O ASP B 337 " (cutoff:3.500A) removed outlier: 8.363A pdb=" N TYR B 339 " --> pdb=" O MET B 209 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N GLY B 211 " --> pdb=" O TYR B 339 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 472 through 475 Processing sheet with id=AB6, first strand: chain 'B' and resid 530 through 532 removed outlier: 6.238A pdb=" N PHE B 531 " --> pdb=" O TYR B 558 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N VAL B 606 " --> pdb=" O ASP B 630 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N ILE B 629 " --> pdb=" O TYR B 653 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N THR B 725 " --> pdb=" O LYS B 703 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N SER B 705 " --> pdb=" O THR B 725 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 13 through 16 removed outlier: 6.181A pdb=" N ASN C 14 " --> pdb=" O VAL C 68 " (cutoff:3.500A) removed outlier: 7.127A pdb=" N ILE C 70 " --> pdb=" O ASN C 14 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N PHE C 16 " --> pdb=" O ILE C 70 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N LEU C 72 " --> pdb=" O PHE C 16 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N ARG C 67 " --> pdb=" O ILE C 100 " (cutoff:3.500A) removed outlier: 7.313A pdb=" N MET C 102 " --> pdb=" O ARG C 67 " (cutoff:3.500A) removed outlier: 5.646A pdb=" N ALA C 69 " --> pdb=" O MET C 102 " (cutoff:3.500A) removed outlier: 7.007A pdb=" N VAL C 104 " --> pdb=" O ALA C 69 " (cutoff:3.500A) removed outlier: 6.178A pdb=" N VAL C 71 " --> pdb=" O VAL C 104 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 237 through 241 removed outlier: 6.562A pdb=" N HIS C 237 " --> pdb=" O LEU C 293 " (cutoff:3.500A) removed outlier: 7.949A pdb=" N ILE C 295 " --> pdb=" O HIS C 237 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N CYS C 239 " --> pdb=" O ILE C 295 " (cutoff:3.500A) removed outlier: 7.109A pdb=" N MET C 209 " --> pdb=" O ASP C 337 " (cutoff:3.500A) removed outlier: 8.492A pdb=" N TYR C 339 " --> pdb=" O MET C 209 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N GLY C 211 " --> pdb=" O TYR C 339 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 472 through 475 Processing sheet with id=AC1, first strand: chain 'C' and resid 506 through 507 removed outlier: 6.249A pdb=" N LEU C 507 " --> pdb=" O SER C 530 " (cutoff:3.500A) removed outlier: 7.286A pdb=" N ASP C 532 " --> pdb=" O LEU C 507 " (cutoff:3.500A) removed outlier: 5.921A pdb=" N VAL C 529 " --> pdb=" O LYS C 556 " (cutoff:3.500A) removed outlier: 7.464A pdb=" N TYR C 558 " --> pdb=" O VAL C 529 " (cutoff:3.500A) removed outlier: 6.124A pdb=" N PHE C 531 " --> pdb=" O TYR C 558 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N PHE C 584 " --> pdb=" O ASN C 607 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N VAL C 606 " --> pdb=" O ASP C 630 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N ILE C 629 " --> pdb=" O TYR C 653 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N LEU C 652 " --> pdb=" O MET C 677 " (cutoff:3.500A) removed outlier: 7.839A pdb=" N TYR C 679 " --> pdb=" O LEU C 652 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ASN C 702 " --> pdb=" O MET C 678 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 831 through 833 removed outlier: 6.650A pdb=" N LEU C 832 " --> pdb=" O LEU C 859 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N HIS C 946 " --> pdb=" O MET C 894 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ASP C 983 " --> pdb=" O SER C 895 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 831 through 833 removed outlier: 6.650A pdb=" N LEU C 832 " --> pdb=" O LEU C 859 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N HIS C 946 " --> pdb=" O MET C 894 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N GLY C 988 " --> pdb=" O CYS C 891 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 910 through 913 Processing sheet with id=AC5, first strand: chain 'D' and resid 15 through 19 Processing sheet with id=AC6, first strand: chain 'D' and resid 237 through 241 removed outlier: 6.333A pdb=" N HIS D 237 " --> pdb=" O LEU D 293 " (cutoff:3.500A) removed outlier: 7.875A pdb=" N ILE D 295 " --> pdb=" O HIS D 237 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N CYS D 239 " --> pdb=" O ILE D 295 " (cutoff:3.500A) removed outlier: 7.290A pdb=" N ASP D 297 " --> pdb=" O CYS D 239 " (cutoff:3.500A) removed outlier: 6.094A pdb=" N VAL D 241 " --> pdb=" O ASP D 297 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N VAL D 299 " --> pdb=" O VAL D 241 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N VAL D 292 " --> pdb=" O ARG D 319 " (cutoff:3.500A) removed outlier: 7.516A pdb=" N ILE D 321 " --> pdb=" O VAL D 292 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N ILE D 294 " --> pdb=" O ILE D 321 " (cutoff:3.500A) removed outlier: 7.619A pdb=" N THR D 323 " --> pdb=" O ILE D 294 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N LEU D 296 " --> pdb=" O THR D 323 " (cutoff:3.500A) removed outlier: 8.430A pdb=" N TYR D 339 " --> pdb=" O MET D 209 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N GLY D 211 " --> pdb=" O TYR D 339 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'D' and resid 472 through 475 Processing sheet with id=AC8, first strand: chain 'D' and resid 530 through 532 removed outlier: 6.616A pdb=" N VAL D 606 " --> pdb=" O ASP D 630 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N ILE D 629 " --> pdb=" O TYR D 653 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N LEU D 652 " --> pdb=" O MET D 677 " (cutoff:3.500A) removed outlier: 7.810A pdb=" N TYR D 679 " --> pdb=" O LEU D 652 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N ILE D 676 " --> pdb=" O ASN D 700 " (cutoff:3.500A) removed outlier: 7.853A pdb=" N ASN D 702 " --> pdb=" O ILE D 676 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N MET D 678 " --> pdb=" O ASN D 702 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N GLN D 721 " --> pdb=" O LEU D 699 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'D' and resid 858 through 860 removed outlier: 3.984A pdb=" N LEU D 947 " --> pdb=" O LEU D 860 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'D' and resid 871 through 873 removed outlier: 3.692A pdb=" N CYS D 987 " --> pdb=" O ALA D 873 " (cutoff:3.500A) 1034 hydrogen bonds defined for protein. 2991 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.38 Time building geometry restraints manager: 3.70 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.15 - 1.29: 5583 1.29 - 1.42: 8339 1.42 - 1.56: 19735 1.56 - 1.69: 12 1.69 - 1.83: 284 Bond restraints: 33953 Sorted by residual: bond pdb=" C VAL C 529 " pdb=" O VAL C 529 " ideal model delta sigma weight residual 1.238 1.153 0.085 1.10e-02 8.26e+03 5.95e+01 bond pdb=" C ARG B 25 " pdb=" N ILE B 26 " ideal model delta sigma weight residual 1.334 1.244 0.090 1.26e-02 6.30e+03 5.05e+01 bond pdb=" C ARG B 25 " pdb=" O ARG B 25 " ideal model delta sigma weight residual 1.236 1.158 0.079 1.18e-02 7.18e+03 4.47e+01 bond pdb=" C SER A 530 " pdb=" N PHE A 531 " ideal model delta sigma weight residual 1.331 1.236 0.095 1.44e-02 4.82e+03 4.37e+01 bond pdb=" C SER C 530 " pdb=" O SER C 530 " ideal model delta sigma weight residual 1.236 1.161 0.075 1.14e-02 7.69e+03 4.34e+01 ... (remaining 33948 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.35: 44714 2.35 - 4.69: 1034 4.69 - 7.04: 144 7.04 - 9.39: 22 9.39 - 11.73: 12 Bond angle restraints: 45926 Sorted by residual: angle pdb=" N GLU D 65 " pdb=" CA GLU D 65 " pdb=" C GLU D 65 " ideal model delta sigma weight residual 111.28 100.33 10.95 1.09e+00 8.42e-01 1.01e+02 angle pdb=" CA PHE C 531 " pdb=" CB PHE C 531 " pdb=" CG PHE C 531 " ideal model delta sigma weight residual 113.80 122.84 -9.04 1.00e+00 1.00e+00 8.17e+01 angle pdb=" N GLU B 65 " pdb=" CA GLU B 65 " pdb=" C GLU B 65 " ideal model delta sigma weight residual 111.11 100.41 10.70 1.20e+00 6.94e-01 7.95e+01 angle pdb=" C GLN A 741 " pdb=" CA GLN A 741 " pdb=" CB GLN A 741 " ideal model delta sigma weight residual 116.63 107.42 9.21 1.16e+00 7.43e-01 6.30e+01 angle pdb=" N ASP C 936 " pdb=" CA ASP C 936 " pdb=" C ASP C 936 " ideal model delta sigma weight residual 111.28 102.73 8.55 1.09e+00 8.42e-01 6.15e+01 ... (remaining 45921 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.68: 19739 35.68 - 71.37: 802 71.37 - 107.05: 39 107.05 - 142.74: 3 142.74 - 178.42: 1 Dihedral angle restraints: 20584 sinusoidal: 8369 harmonic: 12215 Sorted by residual: dihedral pdb=" CB CYS P 43 " pdb=" SG CYS P 43 " pdb=" SG CYS P 81 " pdb=" CB CYS P 81 " ideal model delta sinusoidal sigma weight residual 93.00 157.36 -64.36 1 1.00e+01 1.00e-02 5.45e+01 dihedral pdb=" C2' ADP A1301 " pdb=" C1' ADP A1301 " pdb=" N9 ADP A1301 " pdb=" C4 ADP A1301 " ideal model delta sinusoidal sigma weight residual 91.55 -86.87 178.42 1 2.00e+01 2.50e-03 4.80e+01 dihedral pdb=" CA TRP B 11 " pdb=" C TRP B 11 " pdb=" N ARG B 12 " pdb=" CA ARG B 12 " ideal model delta harmonic sigma weight residual -180.00 -150.31 -29.69 0 5.00e+00 4.00e-02 3.53e+01 ... (remaining 20581 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.090: 4846 0.090 - 0.180: 386 0.180 - 0.271: 25 0.271 - 0.361: 1 0.361 - 0.451: 2 Chirality restraints: 5260 Sorted by residual: chirality pdb=" CB VAL A 529 " pdb=" CA VAL A 529 " pdb=" CG1 VAL A 529 " pdb=" CG2 VAL A 529 " both_signs ideal model delta sigma weight residual False -2.63 -2.18 -0.45 2.00e-01 2.50e+01 5.08e+00 chirality pdb=" CB VAL C 529 " pdb=" CA VAL C 529 " pdb=" CG1 VAL C 529 " pdb=" CG2 VAL C 529 " both_signs ideal model delta sigma weight residual False -2.63 -2.22 -0.41 2.00e-01 2.50e+01 4.23e+00 chirality pdb=" CA VAL B 762 " pdb=" N VAL B 762 " pdb=" C VAL B 762 " pdb=" CB VAL B 762 " both_signs ideal model delta sigma weight residual False 2.44 2.73 -0.29 2.00e-01 2.50e+01 2.11e+00 ... (remaining 5257 not shown) Planarity restraints: 5818 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE B 765 " -0.025 2.00e-02 2.50e+03 5.10e-02 2.60e+01 pdb=" C ILE B 765 " 0.088 2.00e-02 2.50e+03 pdb=" O ILE B 765 " -0.033 2.00e-02 2.50e+03 pdb=" N ASN B 766 " -0.030 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN B 76 " 0.015 2.00e-02 2.50e+03 3.22e-02 1.04e+01 pdb=" C ASN B 76 " -0.056 2.00e-02 2.50e+03 pdb=" O ASN B 76 " 0.021 2.00e-02 2.50e+03 pdb=" N TYR B 77 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA HIS C 928 " 0.014 2.00e-02 2.50e+03 2.86e-02 8.18e+00 pdb=" C HIS C 928 " -0.049 2.00e-02 2.50e+03 pdb=" O HIS C 928 " 0.018 2.00e-02 2.50e+03 pdb=" N LEU C 929 " 0.017 2.00e-02 2.50e+03 ... (remaining 5815 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 5674 2.76 - 3.30: 32735 3.30 - 3.83: 55423 3.83 - 4.37: 65726 4.37 - 4.90: 112366 Nonbonded interactions: 271924 Sorted by model distance: nonbonded pdb=" ND2 ASN D 897 " pdb=" O LEU D 942 " model vdw 2.231 3.120 nonbonded pdb=" O THR B 694 " pdb=" OG SER B 716 " model vdw 2.234 3.040 nonbonded pdb=" NZ LYS P 30 " pdb=" O ASP P 59 " model vdw 2.237 3.120 nonbonded pdb=" OG1 THR C 914 " pdb=" O MET C 972 " model vdw 2.237 3.040 nonbonded pdb=" O LEU B 569 " pdb=" OG SER B 590 " model vdw 2.237 3.040 ... (remaining 271919 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and resid 11 through 1301) selection = chain 'C' selection = (chain 'D' and resid 11 through 1301) } ncs_group { reference = (chain 'P' and resid 21 through 93) selection = (chain 'Q' and resid 21 through 93) selection = (chain 'R' and resid 21 through 93) selection = chain 'S' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 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: 4.130 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: 0.020 Extract box with map and model: 0.590 Check model and map are aligned: 0.080 Set scattering table: 0.090 Process input model: 28.930 Find NCS groups from input model: 0.650 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.960 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8278 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.095 33956 Z= 0.301 Angle : 0.850 11.731 45932 Z= 0.523 Chirality : 0.048 0.451 5260 Planarity : 0.004 0.069 5818 Dihedral : 18.258 178.420 12627 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 16.32 Ramachandran Plot: Outliers : 0.29 % Allowed : 6.94 % Favored : 92.77 % Rotamer: Outliers : 4.31 % Allowed : 29.03 % Favored : 66.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.02 % 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: -1.10 (0.13), residues: 4163 helix: 1.06 (0.15), residues: 1283 sheet: -1.01 (0.24), residues: 523 loop : -1.76 (0.12), residues: 2357 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 169 TYR 0.025 0.001 TYR C 979 PHE 0.029 0.002 PHE C 531 TRP 0.034 0.002 TRP A 617 HIS 0.012 0.001 HIS D 946 Details of bonding type rmsd covalent geometry : bond 0.00471 (33953) covalent geometry : angle 0.85000 (45926) SS BOND : bond 0.00395 ( 3) SS BOND : angle 1.72855 ( 6) hydrogen bonds : bond 0.18281 ( 1027) hydrogen bonds : angle 7.16490 ( 2991) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8326 Ramachandran restraints generated. 4163 Oldfield, 0 Emsley, 4163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8326 Ramachandran restraints generated. 4163 Oldfield, 0 Emsley, 4163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 455 residues out of total 3762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 162 poor density : 293 time to evaluate : 1.267 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 41 GLN cc_start: 0.8393 (tt0) cc_final: 0.8146 (tp40) REVERT: A 379 ASP cc_start: 0.8767 (t0) cc_final: 0.8412 (t70) REVERT: A 404 LEU cc_start: 0.8770 (OUTLIER) cc_final: 0.8404 (mp) REVERT: A 521 THR cc_start: 0.8675 (p) cc_final: 0.8431 (p) REVERT: A 601 GLU cc_start: 0.7694 (OUTLIER) cc_final: 0.7297 (mm-30) REVERT: A 872 ARG cc_start: 0.6102 (OUTLIER) cc_final: 0.5864 (tmt-80) REVERT: A 893 VAL cc_start: 0.5348 (OUTLIER) cc_final: 0.5140 (m) REVERT: A 932 MET cc_start: 0.5795 (OUTLIER) cc_final: 0.4423 (pp-130) REVERT: B 758 LEU cc_start: 0.8319 (OUTLIER) cc_final: 0.8065 (mp) REVERT: B 825 LEU cc_start: 0.5515 (OUTLIER) cc_final: 0.4793 (tt) REVERT: B 833 TYR cc_start: 0.6234 (OUTLIER) cc_final: 0.5952 (m-80) REVERT: B 834 PHE cc_start: 0.5426 (OUTLIER) cc_final: 0.5048 (p90) REVERT: C 362 SER cc_start: 0.8777 (OUTLIER) cc_final: 0.8364 (p) REVERT: C 614 GLN cc_start: 0.8042 (OUTLIER) cc_final: 0.7633 (mt0) REVERT: C 643 LEU cc_start: 0.8711 (OUTLIER) cc_final: 0.8472 (mt) REVERT: C 712 ASP cc_start: 0.6430 (OUTLIER) cc_final: 0.5987 (p0) REVERT: C 857 TRP cc_start: 0.5906 (p-90) cc_final: 0.5487 (p-90) REVERT: C 894 MET cc_start: 0.4758 (tpp) cc_final: 0.4480 (tpt) REVERT: C 927 PHE cc_start: 0.4473 (OUTLIER) cc_final: 0.3858 (m-80) REVERT: C 932 MET cc_start: 0.4998 (ppp) cc_final: 0.4051 (ppp) REVERT: D 267 SER cc_start: 0.8886 (m) cc_final: 0.8440 (p) REVERT: D 569 LEU cc_start: 0.7495 (mt) cc_final: 0.7034 (mp) REVERT: D 949 ILE cc_start: 0.6294 (OUTLIER) cc_final: 0.5932 (mt) outliers start: 162 outliers final: 82 residues processed: 423 average time/residue: 0.2136 time to fit residues: 147.5657 Evaluate side-chains 356 residues out of total 3762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 259 time to evaluate : 1.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 28 ILE Chi-restraints excluded: chain Q residue 71 ASP Chi-restraints excluded: chain R residue 28 ILE Chi-restraints excluded: chain S residue 39 LEU Chi-restraints excluded: chain S residue 85 ASN Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 185 ASP Chi-restraints excluded: chain A residue 207 VAL Chi-restraints excluded: chain A residue 369 ASP Chi-restraints excluded: chain A residue 404 LEU Chi-restraints excluded: chain A residue 410 CYS Chi-restraints excluded: chain A residue 414 ILE Chi-restraints excluded: chain A residue 557 VAL Chi-restraints excluded: chain A residue 601 GLU Chi-restraints excluded: chain A residue 648 ASN Chi-restraints excluded: chain A residue 690 LEU Chi-restraints excluded: chain A residue 697 THR Chi-restraints excluded: chain A residue 713 ILE Chi-restraints excluded: chain A residue 746 SER Chi-restraints excluded: chain A residue 786 LEU Chi-restraints excluded: chain A residue 787 HIS Chi-restraints excluded: chain A residue 827 THR Chi-restraints excluded: chain A residue 829 ASN Chi-restraints excluded: chain A residue 872 ARG Chi-restraints excluded: chain A residue 893 VAL Chi-restraints excluded: chain A residue 896 LEU Chi-restraints excluded: chain A residue 932 MET Chi-restraints excluded: chain B residue 67 ARG Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain B residue 120 PHE Chi-restraints excluded: chain B residue 136 ARG Chi-restraints excluded: chain B residue 159 ASP Chi-restraints excluded: chain B residue 182 ASP Chi-restraints excluded: chain B residue 398 THR Chi-restraints excluded: chain B residue 410 CYS Chi-restraints excluded: chain B residue 458 ASN Chi-restraints excluded: chain B residue 481 ARG Chi-restraints excluded: chain B residue 616 LEU Chi-restraints excluded: chain B residue 621 GLN Chi-restraints excluded: chain B residue 712 ASP Chi-restraints excluded: chain B residue 742 THR Chi-restraints excluded: chain B residue 748 SER Chi-restraints excluded: chain B residue 753 ILE Chi-restraints excluded: chain B residue 754 PHE Chi-restraints excluded: chain B residue 757 GLU Chi-restraints excluded: chain B residue 758 LEU Chi-restraints excluded: chain B residue 825 LEU Chi-restraints excluded: chain B residue 831 GLU Chi-restraints excluded: chain B residue 832 LEU Chi-restraints excluded: chain B residue 833 TYR Chi-restraints excluded: chain B residue 834 PHE Chi-restraints excluded: chain B residue 926 THR Chi-restraints excluded: chain B residue 942 LEU Chi-restraints excluded: chain B residue 952 SER Chi-restraints excluded: chain B residue 972 MET Chi-restraints excluded: chain C residue 79 SER Chi-restraints excluded: chain C residue 234 THR Chi-restraints excluded: chain C residue 362 SER Chi-restraints excluded: chain C residue 369 ASP Chi-restraints excluded: chain C residue 414 ILE Chi-restraints excluded: chain C residue 526 ILE Chi-restraints excluded: chain C residue 614 GLN Chi-restraints excluded: chain C residue 643 LEU Chi-restraints excluded: chain C residue 690 LEU Chi-restraints excluded: chain C residue 692 ASN Chi-restraints excluded: chain C residue 712 ASP Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 783 LEU Chi-restraints excluded: chain C residue 827 THR Chi-restraints excluded: chain C residue 829 ASN Chi-restraints excluded: chain C residue 834 PHE Chi-restraints excluded: chain C residue 839 LYS Chi-restraints excluded: chain C residue 851 GLN Chi-restraints excluded: chain C residue 927 PHE Chi-restraints excluded: chain C residue 933 PHE Chi-restraints excluded: chain C residue 936 ASP Chi-restraints excluded: chain C residue 946 HIS Chi-restraints excluded: chain C residue 950 PHE Chi-restraints excluded: chain D residue 63 ILE Chi-restraints excluded: chain D residue 70 ILE Chi-restraints excluded: chain D residue 74 SER Chi-restraints excluded: chain D residue 119 ASP Chi-restraints excluded: chain D residue 136 ARG Chi-restraints excluded: chain D residue 182 ASP Chi-restraints excluded: chain D residue 311 MET Chi-restraints excluded: chain D residue 414 ILE Chi-restraints excluded: chain D residue 580 THR Chi-restraints excluded: chain D residue 616 LEU Chi-restraints excluded: chain D residue 699 LEU Chi-restraints excluded: chain D residue 717 ILE Chi-restraints excluded: chain D residue 742 THR Chi-restraints excluded: chain D residue 743 ILE Chi-restraints excluded: chain D residue 810 LEU Chi-restraints excluded: chain D residue 813 ASP Chi-restraints excluded: chain D residue 928 HIS Chi-restraints excluded: chain D residue 949 ILE Chi-restraints excluded: chain D residue 985 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 416 random chunks: chunk 197 optimal weight: 4.9990 chunk 388 optimal weight: 10.0000 chunk 215 optimal weight: 0.9980 chunk 20 optimal weight: 0.0980 chunk 132 optimal weight: 1.9990 chunk 261 optimal weight: 2.9990 chunk 248 optimal weight: 5.9990 chunk 207 optimal weight: 20.0000 chunk 401 optimal weight: 8.9990 chunk 155 optimal weight: 1.9990 chunk 244 optimal weight: 0.7980 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Q 76 ASN ** A 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 897 ASN ** A 946 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 148 ASN B 721 GLN B 741 GLN B 822 ASN B 836 ASN C 53 GLN C 908 ASN ** C 939 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 946 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 951 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 951 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.144752 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.089631 restraints weight = 56944.099| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.091634 restraints weight = 36115.539| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.092018 restraints weight = 24131.399| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.092329 restraints weight = 19905.418| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.092569 restraints weight = 19790.137| |-----------------------------------------------------------------------------| r_work (final): 0.3183 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8278 moved from start: 0.0937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 33956 Z= 0.150 Angle : 0.645 11.558 45932 Z= 0.329 Chirality : 0.044 0.173 5260 Planarity : 0.004 0.048 5818 Dihedral : 9.225 178.748 4680 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 11.06 Ramachandran Plot: Outliers : 0.14 % Allowed : 6.32 % Favored : 93.54 % Rotamer: Outliers : 5.32 % Allowed : 26.32 % Favored : 68.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -1.06 (0.13), residues: 4163 helix: 1.17 (0.15), residues: 1299 sheet: -1.25 (0.23), residues: 541 loop : -1.74 (0.12), residues: 2323 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 12 TYR 0.011 0.001 TYR C 979 PHE 0.018 0.001 PHE B 754 TRP 0.028 0.002 TRP A 617 HIS 0.009 0.001 HIS C 931 Details of bonding type rmsd covalent geometry : bond 0.00351 (33953) covalent geometry : angle 0.64446 (45926) SS BOND : bond 0.00338 ( 3) SS BOND : angle 1.60055 ( 6) hydrogen bonds : bond 0.04225 ( 1027) hydrogen bonds : angle 5.57691 ( 2991) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8326 Ramachandran restraints generated. 4163 Oldfield, 0 Emsley, 4163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8326 Ramachandran restraints generated. 4163 Oldfield, 0 Emsley, 4163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 464 residues out of total 3762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 200 poor density : 264 time to evaluate : 1.301 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 53 MET cc_start: 0.2918 (ppp) cc_final: 0.2391 (ppp) REVERT: R 41 GLN cc_start: 0.8233 (tt0) cc_final: 0.7982 (tt0) REVERT: S 51 SER cc_start: 0.8090 (OUTLIER) cc_final: 0.7611 (p) REVERT: A 379 ASP cc_start: 0.8842 (t0) cc_final: 0.8386 (t70) REVERT: A 404 LEU cc_start: 0.8712 (OUTLIER) cc_final: 0.8306 (mp) REVERT: A 521 THR cc_start: 0.8757 (p) cc_final: 0.8497 (p) REVERT: A 563 HIS cc_start: 0.8165 (OUTLIER) cc_final: 0.7935 (p90) REVERT: A 743 ILE cc_start: 0.7117 (OUTLIER) cc_final: 0.6903 (mp) REVERT: A 932 MET cc_start: 0.5730 (OUTLIER) cc_final: 0.4399 (pp-130) REVERT: B 486 ARG cc_start: 0.8752 (OUTLIER) cc_final: 0.8503 (ttp80) REVERT: B 712 ASP cc_start: 0.7233 (OUTLIER) cc_final: 0.6986 (p0) REVERT: B 725 THR cc_start: 0.7075 (OUTLIER) cc_final: 0.6710 (m) REVERT: B 758 LEU cc_start: 0.8558 (OUTLIER) cc_final: 0.8264 (mp) REVERT: B 825 LEU cc_start: 0.5341 (OUTLIER) cc_final: 0.4639 (tt) REVERT: B 833 TYR cc_start: 0.6503 (OUTLIER) cc_final: 0.5960 (m-80) REVERT: B 834 PHE cc_start: 0.6361 (OUTLIER) cc_final: 0.5752 (p90) REVERT: C 67 ARG cc_start: 0.7941 (OUTLIER) cc_final: 0.7683 (ttt180) REVERT: C 535 GLU cc_start: 0.8269 (mp0) cc_final: 0.8058 (mp0) REVERT: C 614 GLN cc_start: 0.8090 (OUTLIER) cc_final: 0.7631 (mp10) REVERT: C 643 LEU cc_start: 0.8560 (OUTLIER) cc_final: 0.8350 (mt) REVERT: C 894 MET cc_start: 0.5005 (tpp) cc_final: 0.4763 (tpt) REVERT: C 932 MET cc_start: 0.4899 (ppp) cc_final: 0.4284 (ptm) REVERT: D 569 LEU cc_start: 0.7652 (mt) cc_final: 0.7219 (mp) REVERT: D 574 ASP cc_start: 0.7814 (p0) cc_final: 0.7453 (t70) REVERT: D 787 HIS cc_start: 0.7167 (m-70) cc_final: 0.6769 (m-70) REVERT: D 840 LEU cc_start: 0.3442 (OUTLIER) cc_final: 0.3005 (tt) REVERT: D 932 MET cc_start: 0.4010 (tpt) cc_final: 0.3697 (tpt) REVERT: D 949 ILE cc_start: 0.5712 (OUTLIER) cc_final: 0.5458 (mt) outliers start: 200 outliers final: 89 residues processed: 441 average time/residue: 0.2108 time to fit residues: 153.8895 Evaluate side-chains 344 residues out of total 3762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 238 time to evaluate : 1.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 28 ILE Chi-restraints excluded: chain Q residue 28 ILE Chi-restraints excluded: chain Q residue 40 CYS Chi-restraints excluded: chain Q residue 43 CYS Chi-restraints excluded: chain Q residue 71 ASP Chi-restraints excluded: chain R residue 28 ILE Chi-restraints excluded: chain S residue 40 CYS Chi-restraints excluded: chain S residue 45 LEU Chi-restraints excluded: chain S residue 51 SER Chi-restraints excluded: chain S residue 71 ASP Chi-restraints excluded: chain S residue 85 ASN Chi-restraints excluded: chain A residue 52 SER Chi-restraints excluded: chain A residue 54 ILE Chi-restraints excluded: chain A residue 79 SER Chi-restraints excluded: chain A residue 207 VAL Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 404 LEU Chi-restraints excluded: chain A residue 424 SER Chi-restraints excluded: chain A residue 557 VAL Chi-restraints excluded: chain A residue 563 HIS Chi-restraints excluded: chain A residue 580 THR Chi-restraints excluded: chain A residue 647 THR Chi-restraints excluded: chain A residue 690 LEU Chi-restraints excluded: chain A residue 713 ILE Chi-restraints excluded: chain A residue 729 GLU Chi-restraints excluded: chain A residue 743 ILE Chi-restraints excluded: chain A residue 786 LEU Chi-restraints excluded: chain A residue 819 GLU Chi-restraints excluded: chain A residue 827 THR Chi-restraints excluded: chain A residue 932 MET Chi-restraints excluded: chain B residue 54 ILE Chi-restraints excluded: chain B residue 66 SER Chi-restraints excluded: chain B residue 136 ARG Chi-restraints excluded: chain B residue 182 ASP Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 362 SER Chi-restraints excluded: chain B residue 437 THR Chi-restraints excluded: chain B residue 486 ARG Chi-restraints excluded: chain B residue 536 ILE Chi-restraints excluded: chain B residue 652 LEU Chi-restraints excluded: chain B residue 663 LEU Chi-restraints excluded: chain B residue 712 ASP Chi-restraints excluded: chain B residue 725 THR Chi-restraints excluded: chain B residue 748 SER Chi-restraints excluded: chain B residue 754 PHE Chi-restraints excluded: chain B residue 757 GLU Chi-restraints excluded: chain B residue 758 LEU Chi-restraints excluded: chain B residue 818 LEU Chi-restraints excluded: chain B residue 825 LEU Chi-restraints excluded: chain B residue 831 GLU Chi-restraints excluded: chain B residue 832 LEU Chi-restraints excluded: chain B residue 833 TYR Chi-restraints excluded: chain B residue 834 PHE Chi-restraints excluded: chain B residue 891 CYS Chi-restraints excluded: chain B residue 926 THR Chi-restraints excluded: chain B residue 942 LEU Chi-restraints excluded: chain C residue 67 ARG Chi-restraints excluded: chain C residue 117 THR Chi-restraints excluded: chain C residue 132 THR Chi-restraints excluded: chain C residue 185 ASP Chi-restraints excluded: chain C residue 234 THR Chi-restraints excluded: chain C residue 391 SER Chi-restraints excluded: chain C residue 410 CYS Chi-restraints excluded: chain C residue 526 ILE Chi-restraints excluded: chain C residue 594 LEU Chi-restraints excluded: chain C residue 614 GLN Chi-restraints excluded: chain C residue 643 LEU Chi-restraints excluded: chain C residue 671 HIS Chi-restraints excluded: chain C residue 678 MET Chi-restraints excluded: chain C residue 690 LEU Chi-restraints excluded: chain C residue 803 LEU Chi-restraints excluded: chain C residue 827 THR Chi-restraints excluded: chain C residue 839 LYS Chi-restraints excluded: chain C residue 933 PHE Chi-restraints excluded: chain C residue 948 PHE Chi-restraints excluded: chain C residue 951 HIS Chi-restraints excluded: chain D residue 11 TRP Chi-restraints excluded: chain D residue 26 ILE Chi-restraints excluded: chain D residue 63 ILE Chi-restraints excluded: chain D residue 89 GLU Chi-restraints excluded: chain D residue 102 MET Chi-restraints excluded: chain D residue 119 ASP Chi-restraints excluded: chain D residue 172 SER Chi-restraints excluded: chain D residue 182 ASP Chi-restraints excluded: chain D residue 187 VAL Chi-restraints excluded: chain D residue 368 MET Chi-restraints excluded: chain D residue 396 SER Chi-restraints excluded: chain D residue 404 LEU Chi-restraints excluded: chain D residue 469 ARG Chi-restraints excluded: chain D residue 493 ILE Chi-restraints excluded: chain D residue 579 ARG Chi-restraints excluded: chain D residue 647 THR Chi-restraints excluded: chain D residue 661 VAL Chi-restraints excluded: chain D residue 717 ILE Chi-restraints excluded: chain D residue 740 LEU Chi-restraints excluded: chain D residue 742 THR Chi-restraints excluded: chain D residue 772 ILE Chi-restraints excluded: chain D residue 810 LEU Chi-restraints excluded: chain D residue 813 ASP Chi-restraints excluded: chain D residue 840 LEU Chi-restraints excluded: chain D residue 854 VAL Chi-restraints excluded: chain D residue 897 ASN Chi-restraints excluded: chain D residue 949 ILE Chi-restraints excluded: chain D residue 985 LEU Chi-restraints excluded: chain D residue 987 CYS Chi-restraints excluded: chain D residue 989 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 416 random chunks: chunk 191 optimal weight: 8.9990 chunk 349 optimal weight: 1.9990 chunk 120 optimal weight: 20.0000 chunk 164 optimal weight: 0.4980 chunk 308 optimal weight: 3.9990 chunk 9 optimal weight: 20.0000 chunk 403 optimal weight: 9.9990 chunk 392 optimal weight: 9.9990 chunk 105 optimal weight: 10.0000 chunk 39 optimal weight: 1.9990 chunk 287 optimal weight: 0.8980 overall best weight: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 648 ASN ** A 787 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 946 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 247 ASN B 721 GLN C 908 ASN ** C 951 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 951 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 = 0.3970 r_free = 0.3970 target = 0.142597 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.088559 restraints weight = 56928.921| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.090023 restraints weight = 39422.403| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.089507 restraints weight = 27737.878| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.090225 restraints weight = 24210.167| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.090460 restraints weight = 21715.368| |-----------------------------------------------------------------------------| r_work (final): 0.3140 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8334 moved from start: 0.1421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 33956 Z= 0.190 Angle : 0.630 9.994 45932 Z= 0.320 Chirality : 0.044 0.173 5260 Planarity : 0.004 0.044 5818 Dihedral : 8.259 178.180 4574 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 10.58 Ramachandran Plot: Outliers : 0.14 % Allowed : 6.85 % Favored : 93.01 % Rotamer: Outliers : 5.72 % Allowed : 25.55 % Favored : 68.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -1.12 (0.13), residues: 4163 helix: 1.13 (0.15), residues: 1300 sheet: -1.40 (0.22), residues: 589 loop : -1.75 (0.12), residues: 2274 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 67 TYR 0.022 0.001 TYR C 833 PHE 0.020 0.001 PHE C 710 TRP 0.024 0.002 TRP A 617 HIS 0.015 0.001 HIS A 899 Details of bonding type rmsd covalent geometry : bond 0.00460 (33953) covalent geometry : angle 0.62975 (45926) SS BOND : bond 0.00369 ( 3) SS BOND : angle 1.73504 ( 6) hydrogen bonds : bond 0.03961 ( 1027) hydrogen bonds : angle 5.18915 ( 2991) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8326 Ramachandran restraints generated. 4163 Oldfield, 0 Emsley, 4163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8326 Ramachandran restraints generated. 4163 Oldfield, 0 Emsley, 4163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 466 residues out of total 3762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 215 poor density : 251 time to evaluate : 1.295 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 53 MET cc_start: 0.2786 (ppp) cc_final: 0.2255 (ppp) REVERT: P 74 PHE cc_start: 0.7718 (m-80) cc_final: 0.7517 (m-10) REVERT: R 41 GLN cc_start: 0.8171 (tt0) cc_final: 0.7814 (tt0) REVERT: R 74 PHE cc_start: 0.7851 (m-80) cc_final: 0.7329 (m-80) REVERT: S 40 CYS cc_start: 0.2772 (OUTLIER) cc_final: 0.2408 (p) REVERT: S 51 SER cc_start: 0.8243 (OUTLIER) cc_final: 0.7769 (p) REVERT: A 50 GLU cc_start: 0.6958 (OUTLIER) cc_final: 0.4549 (mp0) REVERT: A 97 ILE cc_start: 0.8843 (tt) cc_final: 0.8500 (pt) REVERT: A 362 SER cc_start: 0.8878 (OUTLIER) cc_final: 0.8445 (p) REVERT: A 379 ASP cc_start: 0.8920 (t0) cc_final: 0.8402 (t70) REVERT: A 404 LEU cc_start: 0.8756 (OUTLIER) cc_final: 0.8364 (mp) REVERT: A 521 THR cc_start: 0.8895 (p) cc_final: 0.8621 (p) REVERT: A 743 ILE cc_start: 0.7068 (OUTLIER) cc_final: 0.6855 (mp) REVERT: A 809 ILE cc_start: 0.7745 (OUTLIER) cc_final: 0.7071 (mp) REVERT: A 932 MET cc_start: 0.5712 (OUTLIER) cc_final: 0.4573 (pp-130) REVERT: B 486 ARG cc_start: 0.8849 (OUTLIER) cc_final: 0.8529 (ttp80) REVERT: B 712 ASP cc_start: 0.7220 (OUTLIER) cc_final: 0.6926 (p0) REVERT: B 758 LEU cc_start: 0.8546 (mt) cc_final: 0.8341 (mp) REVERT: B 825 LEU cc_start: 0.5225 (OUTLIER) cc_final: 0.4526 (tt) REVERT: B 834 PHE cc_start: 0.6532 (OUTLIER) cc_final: 0.5714 (p90) REVERT: C 535 GLU cc_start: 0.8325 (mp0) cc_final: 0.8061 (mp0) REVERT: C 614 GLN cc_start: 0.8190 (OUTLIER) cc_final: 0.7716 (mp10) REVERT: C 713 ILE cc_start: 0.8413 (OUTLIER) cc_final: 0.8115 (pp) REVERT: C 734 LEU cc_start: 0.8579 (tt) cc_final: 0.8100 (pt) REVERT: C 894 MET cc_start: 0.5072 (tpp) cc_final: 0.4751 (tpt) REVERT: C 908 ASN cc_start: 0.3103 (OUTLIER) cc_final: 0.2884 (p0) REVERT: C 927 PHE cc_start: 0.4474 (OUTLIER) cc_final: 0.3867 (m-80) REVERT: C 990 GLN cc_start: 0.5095 (OUTLIER) cc_final: 0.4892 (pp30) REVERT: D 11 TRP cc_start: 0.4430 (OUTLIER) cc_final: 0.3146 (m100) REVERT: D 569 LEU cc_start: 0.7678 (mt) cc_final: 0.7235 (mp) REVERT: D 574 ASP cc_start: 0.7894 (p0) cc_final: 0.7469 (t70) REVERT: D 709 ARG cc_start: 0.7164 (ttm110) cc_final: 0.6745 (ptp-170) REVERT: D 787 HIS cc_start: 0.7232 (m-70) cc_final: 0.6988 (m-70) REVERT: D 840 LEU cc_start: 0.3337 (OUTLIER) cc_final: 0.2883 (tt) REVERT: D 932 MET cc_start: 0.4117 (tpt) cc_final: 0.3826 (tpt) REVERT: D 949 ILE cc_start: 0.5970 (OUTLIER) cc_final: 0.5637 (mt) outliers start: 215 outliers final: 108 residues processed: 441 average time/residue: 0.2149 time to fit residues: 156.9846 Evaluate side-chains 361 residues out of total 3762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 128 poor density : 233 time to evaluate : 1.442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 28 ILE Chi-restraints excluded: chain P residue 68 THR Chi-restraints excluded: chain P residue 79 VAL Chi-restraints excluded: chain Q residue 28 ILE Chi-restraints excluded: chain Q residue 40 CYS Chi-restraints excluded: chain Q residue 43 CYS Chi-restraints excluded: chain Q residue 71 ASP Chi-restraints excluded: chain R residue 23 SER Chi-restraints excluded: chain R residue 28 ILE Chi-restraints excluded: chain R residue 55 LEU Chi-restraints excluded: chain S residue 40 CYS Chi-restraints excluded: chain S residue 45 LEU Chi-restraints excluded: chain S residue 51 SER Chi-restraints excluded: chain S residue 71 ASP Chi-restraints excluded: chain S residue 85 ASN Chi-restraints excluded: chain A residue 50 GLU Chi-restraints excluded: chain A residue 52 SER Chi-restraints excluded: chain A residue 54 ILE Chi-restraints excluded: chain A residue 79 SER Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 207 VAL Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 362 SER Chi-restraints excluded: chain A residue 404 LEU Chi-restraints excluded: chain A residue 410 CYS Chi-restraints excluded: chain A residue 424 SER Chi-restraints excluded: chain A residue 557 VAL Chi-restraints excluded: chain A residue 563 HIS Chi-restraints excluded: chain A residue 580 THR Chi-restraints excluded: chain A residue 690 LEU Chi-restraints excluded: chain A residue 713 ILE Chi-restraints excluded: chain A residue 729 GLU Chi-restraints excluded: chain A residue 743 ILE Chi-restraints excluded: chain A residue 786 LEU Chi-restraints excluded: chain A residue 809 ILE Chi-restraints excluded: chain A residue 819 GLU Chi-restraints excluded: chain A residue 827 THR Chi-restraints excluded: chain A residue 932 MET Chi-restraints excluded: chain B residue 41 ILE Chi-restraints excluded: chain B residue 54 ILE Chi-restraints excluded: chain B residue 66 SER Chi-restraints excluded: chain B residue 136 ARG Chi-restraints excluded: chain B residue 182 ASP Chi-restraints excluded: chain B residue 209 MET Chi-restraints excluded: chain B residue 210 VAL Chi-restraints excluded: chain B residue 362 SER Chi-restraints excluded: chain B residue 404 LEU Chi-restraints excluded: chain B residue 410 CYS Chi-restraints excluded: chain B residue 437 THR Chi-restraints excluded: chain B residue 486 ARG Chi-restraints excluded: chain B residue 493 ILE Chi-restraints excluded: chain B residue 508 VAL Chi-restraints excluded: chain B residue 663 LEU Chi-restraints excluded: chain B residue 697 THR Chi-restraints excluded: chain B residue 712 ASP Chi-restraints excluded: chain B residue 742 THR Chi-restraints excluded: chain B residue 748 SER Chi-restraints excluded: chain B residue 754 PHE Chi-restraints excluded: chain B residue 757 GLU Chi-restraints excluded: chain B residue 818 LEU Chi-restraints excluded: chain B residue 825 LEU Chi-restraints excluded: chain B residue 831 GLU Chi-restraints excluded: chain B residue 832 LEU Chi-restraints excluded: chain B residue 834 PHE Chi-restraints excluded: chain B residue 854 VAL Chi-restraints excluded: chain B residue 926 THR Chi-restraints excluded: chain B residue 942 LEU Chi-restraints excluded: chain C residue 117 THR Chi-restraints excluded: chain C residue 132 THR Chi-restraints excluded: chain C residue 185 ASP Chi-restraints excluded: chain C residue 234 THR Chi-restraints excluded: chain C residue 410 CYS Chi-restraints excluded: chain C residue 594 LEU Chi-restraints excluded: chain C residue 614 GLN Chi-restraints excluded: chain C residue 643 LEU Chi-restraints excluded: chain C residue 671 HIS Chi-restraints excluded: chain C residue 678 MET Chi-restraints excluded: chain C residue 690 LEU Chi-restraints excluded: chain C residue 713 ILE Chi-restraints excluded: chain C residue 803 LEU Chi-restraints excluded: chain C residue 827 THR Chi-restraints excluded: chain C residue 829 ASN Chi-restraints excluded: chain C residue 839 LYS Chi-restraints excluded: chain C residue 908 ASN Chi-restraints excluded: chain C residue 927 PHE Chi-restraints excluded: chain C residue 948 PHE Chi-restraints excluded: chain C residue 951 HIS Chi-restraints excluded: chain C residue 990 GLN Chi-restraints excluded: chain D residue 11 TRP Chi-restraints excluded: chain D residue 17 THR Chi-restraints excluded: chain D residue 41 ILE Chi-restraints excluded: chain D residue 54 ILE Chi-restraints excluded: chain D residue 63 ILE Chi-restraints excluded: chain D residue 89 GLU Chi-restraints excluded: chain D residue 90 ILE Chi-restraints excluded: chain D residue 96 TYR Chi-restraints excluded: chain D residue 102 MET Chi-restraints excluded: chain D residue 117 THR Chi-restraints excluded: chain D residue 172 SER Chi-restraints excluded: chain D residue 182 ASP Chi-restraints excluded: chain D residue 187 VAL Chi-restraints excluded: chain D residue 368 MET Chi-restraints excluded: chain D residue 369 ASP Chi-restraints excluded: chain D residue 396 SER Chi-restraints excluded: chain D residue 414 ILE Chi-restraints excluded: chain D residue 437 THR Chi-restraints excluded: chain D residue 469 ARG Chi-restraints excluded: chain D residue 493 ILE Chi-restraints excluded: chain D residue 579 ARG Chi-restraints excluded: chain D residue 616 LEU Chi-restraints excluded: chain D residue 647 THR Chi-restraints excluded: chain D residue 658 THR Chi-restraints excluded: chain D residue 663 LEU Chi-restraints excluded: chain D residue 697 THR Chi-restraints excluded: chain D residue 717 ILE Chi-restraints excluded: chain D residue 742 THR Chi-restraints excluded: chain D residue 790 CYS Chi-restraints excluded: chain D residue 810 LEU Chi-restraints excluded: chain D residue 813 ASP Chi-restraints excluded: chain D residue 840 LEU Chi-restraints excluded: chain D residue 854 VAL Chi-restraints excluded: chain D residue 897 ASN Chi-restraints excluded: chain D residue 905 VAL Chi-restraints excluded: chain D residue 949 ILE Chi-restraints excluded: chain D residue 954 LEU Chi-restraints excluded: chain D residue 985 LEU Chi-restraints excluded: chain D residue 987 CYS Chi-restraints excluded: chain D residue 989 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 416 random chunks: chunk 182 optimal weight: 2.9990 chunk 104 optimal weight: 6.9990 chunk 360 optimal weight: 2.9990 chunk 415 optimal weight: 0.3980 chunk 275 optimal weight: 0.2980 chunk 18 optimal weight: 10.0000 chunk 111 optimal weight: 30.0000 chunk 66 optimal weight: 3.9990 chunk 57 optimal weight: 0.6980 chunk 5 optimal weight: 9.9990 chunk 122 optimal weight: 7.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Q 76 ASN ** A 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 441 ASN A 648 ASN A 675 HIS ** A 787 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 934 ASN C 333 HIS ** C 951 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 148 ASN ** D 951 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.142971 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.087119 restraints weight = 56685.654| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.090200 restraints weight = 34449.105| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.090805 restraints weight = 21643.630| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.091340 restraints weight = 18829.044| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.091387 restraints weight = 17301.718| |-----------------------------------------------------------------------------| r_work (final): 0.3169 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8301 moved from start: 0.1626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 33956 Z= 0.158 Angle : 0.604 9.946 45932 Z= 0.305 Chirality : 0.044 0.549 5260 Planarity : 0.004 0.044 5818 Dihedral : 8.042 177.709 4564 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 10.23 Ramachandran Plot: Outliers : 0.14 % Allowed : 6.49 % Favored : 93.37 % Rotamer: Outliers : 4.87 % Allowed : 26.48 % Favored : 68.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.02 % 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: -1.09 (0.13), residues: 4163 helix: 1.18 (0.15), residues: 1302 sheet: -1.48 (0.22), residues: 584 loop : -1.72 (0.12), residues: 2277 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG R 52 TYR 0.013 0.001 TYR C 833 PHE 0.023 0.001 PHE C 710 TRP 0.023 0.002 TRP A 617 HIS 0.007 0.001 HIS C 928 Details of bonding type rmsd covalent geometry : bond 0.00379 (33953) covalent geometry : angle 0.60392 (45926) SS BOND : bond 0.00377 ( 3) SS BOND : angle 1.70446 ( 6) hydrogen bonds : bond 0.03532 ( 1027) hydrogen bonds : angle 5.01155 ( 2991) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8326 Ramachandran restraints generated. 4163 Oldfield, 0 Emsley, 4163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8326 Ramachandran restraints generated. 4163 Oldfield, 0 Emsley, 4163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 423 residues out of total 3762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 183 poor density : 240 time to evaluate : 1.244 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 53 MET cc_start: 0.2747 (ppp) cc_final: 0.2287 (ppp) REVERT: P 74 PHE cc_start: 0.7668 (m-80) cc_final: 0.7431 (m-10) REVERT: R 41 GLN cc_start: 0.8198 (tt0) cc_final: 0.7948 (tt0) REVERT: R 74 PHE cc_start: 0.7885 (m-80) cc_final: 0.7432 (m-80) REVERT: S 52 ARG cc_start: 0.5956 (tpm170) cc_final: 0.5639 (tpm170) REVERT: A 97 ILE cc_start: 0.8822 (tt) cc_final: 0.8543 (pt) REVERT: A 362 SER cc_start: 0.8860 (OUTLIER) cc_final: 0.8444 (p) REVERT: A 379 ASP cc_start: 0.8844 (t0) cc_final: 0.8408 (t70) REVERT: A 404 LEU cc_start: 0.8743 (OUTLIER) cc_final: 0.8347 (mp) REVERT: A 521 THR cc_start: 0.8859 (OUTLIER) cc_final: 0.8577 (p) REVERT: A 614 GLN cc_start: 0.8432 (OUTLIER) cc_final: 0.8092 (mt0) REVERT: A 743 ILE cc_start: 0.7140 (OUTLIER) cc_final: 0.6890 (mp) REVERT: A 894 MET cc_start: 0.3060 (mmp) cc_final: 0.2169 (ptp) REVERT: A 932 MET cc_start: 0.5439 (OUTLIER) cc_final: 0.4271 (pp-130) REVERT: B 486 ARG cc_start: 0.8836 (OUTLIER) cc_final: 0.8519 (ttp80) REVERT: B 712 ASP cc_start: 0.7230 (OUTLIER) cc_final: 0.6904 (p0) REVERT: B 758 LEU cc_start: 0.8520 (mt) cc_final: 0.8268 (mp) REVERT: B 825 LEU cc_start: 0.5246 (OUTLIER) cc_final: 0.4504 (tp) REVERT: B 834 PHE cc_start: 0.6683 (OUTLIER) cc_final: 0.5660 (p90) REVERT: C 535 GLU cc_start: 0.8188 (mp0) cc_final: 0.7969 (mp0) REVERT: C 614 GLN cc_start: 0.8192 (OUTLIER) cc_final: 0.7606 (mp10) REVERT: C 713 ILE cc_start: 0.8388 (OUTLIER) cc_final: 0.8097 (pp) REVERT: C 734 LEU cc_start: 0.8474 (tt) cc_final: 0.7990 (pt) REVERT: C 894 MET cc_start: 0.5285 (tpp) cc_final: 0.4957 (tpt) REVERT: C 927 PHE cc_start: 0.4416 (OUTLIER) cc_final: 0.3945 (m-80) REVERT: D 469 ARG cc_start: 0.8873 (OUTLIER) cc_final: 0.8064 (mtm-85) REVERT: D 574 ASP cc_start: 0.7736 (p0) cc_final: 0.7390 (t70) REVERT: D 709 ARG cc_start: 0.7080 (ttm110) cc_final: 0.6636 (ptp-170) REVERT: D 840 LEU cc_start: 0.3243 (OUTLIER) cc_final: 0.2790 (tt) REVERT: D 932 MET cc_start: 0.4004 (tpt) cc_final: 0.3711 (tpt) REVERT: D 949 ILE cc_start: 0.5916 (OUTLIER) cc_final: 0.5568 (mt) outliers start: 183 outliers final: 107 residues processed: 398 average time/residue: 0.2093 time to fit residues: 139.3184 Evaluate side-chains 356 residues out of total 3762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 123 poor density : 233 time to evaluate : 1.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 28 ILE Chi-restraints excluded: chain P residue 68 THR Chi-restraints excluded: chain P residue 79 VAL Chi-restraints excluded: chain P residue 84 VAL Chi-restraints excluded: chain Q residue 28 ILE Chi-restraints excluded: chain Q residue 31 THR Chi-restraints excluded: chain Q residue 40 CYS Chi-restraints excluded: chain Q residue 43 CYS Chi-restraints excluded: chain Q residue 71 ASP Chi-restraints excluded: chain R residue 23 SER Chi-restraints excluded: chain R residue 28 ILE Chi-restraints excluded: chain R residue 32 ASP Chi-restraints excluded: chain S residue 45 LEU Chi-restraints excluded: chain S residue 71 ASP Chi-restraints excluded: chain S residue 85 ASN Chi-restraints excluded: chain A residue 52 SER Chi-restraints excluded: chain A residue 54 ILE Chi-restraints excluded: chain A residue 79 SER Chi-restraints excluded: chain A residue 178 THR Chi-restraints excluded: chain A residue 207 VAL Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 362 SER Chi-restraints excluded: chain A residue 404 LEU Chi-restraints excluded: chain A residue 414 ILE Chi-restraints excluded: chain A residue 424 SER Chi-restraints excluded: chain A residue 469 ARG Chi-restraints excluded: chain A residue 521 THR Chi-restraints excluded: chain A residue 557 VAL Chi-restraints excluded: chain A residue 580 THR Chi-restraints excluded: chain A residue 614 GLN Chi-restraints excluded: chain A residue 648 ASN Chi-restraints excluded: chain A residue 690 LEU Chi-restraints excluded: chain A residue 713 ILE Chi-restraints excluded: chain A residue 729 GLU Chi-restraints excluded: chain A residue 733 SER Chi-restraints excluded: chain A residue 743 ILE Chi-restraints excluded: chain A residue 786 LEU Chi-restraints excluded: chain A residue 819 GLU Chi-restraints excluded: chain A residue 827 THR Chi-restraints excluded: chain A residue 932 MET Chi-restraints excluded: chain A residue 938 VAL Chi-restraints excluded: chain B residue 17 THR Chi-restraints excluded: chain B residue 41 ILE Chi-restraints excluded: chain B residue 54 ILE Chi-restraints excluded: chain B residue 66 SER Chi-restraints excluded: chain B residue 136 ARG Chi-restraints excluded: chain B residue 182 ASP Chi-restraints excluded: chain B residue 209 MET Chi-restraints excluded: chain B residue 362 SER Chi-restraints excluded: chain B residue 404 LEU Chi-restraints excluded: chain B residue 486 ARG Chi-restraints excluded: chain B residue 616 LEU Chi-restraints excluded: chain B residue 647 THR Chi-restraints excluded: chain B residue 663 LEU Chi-restraints excluded: chain B residue 712 ASP Chi-restraints excluded: chain B residue 754 PHE Chi-restraints excluded: chain B residue 757 GLU Chi-restraints excluded: chain B residue 818 LEU Chi-restraints excluded: chain B residue 825 LEU Chi-restraints excluded: chain B residue 834 PHE Chi-restraints excluded: chain B residue 868 GLU Chi-restraints excluded: chain B residue 916 ILE Chi-restraints excluded: chain B residue 926 THR Chi-restraints excluded: chain B residue 932 MET Chi-restraints excluded: chain B residue 942 LEU Chi-restraints excluded: chain C residue 17 THR Chi-restraints excluded: chain C residue 117 THR Chi-restraints excluded: chain C residue 132 THR Chi-restraints excluded: chain C residue 185 ASP Chi-restraints excluded: chain C residue 391 SER Chi-restraints excluded: chain C residue 410 CYS Chi-restraints excluded: chain C residue 540 MET Chi-restraints excluded: chain C residue 594 LEU Chi-restraints excluded: chain C residue 614 GLN Chi-restraints excluded: chain C residue 643 LEU Chi-restraints excluded: chain C residue 671 HIS Chi-restraints excluded: chain C residue 690 LEU Chi-restraints excluded: chain C residue 701 MET Chi-restraints excluded: chain C residue 713 ILE Chi-restraints excluded: chain C residue 803 LEU Chi-restraints excluded: chain C residue 827 THR Chi-restraints excluded: chain C residue 829 ASN Chi-restraints excluded: chain C residue 926 THR Chi-restraints excluded: chain C residue 927 PHE Chi-restraints excluded: chain C residue 933 PHE Chi-restraints excluded: chain C residue 948 PHE Chi-restraints excluded: chain C residue 951 HIS Chi-restraints excluded: chain D residue 41 ILE Chi-restraints excluded: chain D residue 54 ILE Chi-restraints excluded: chain D residue 63 ILE Chi-restraints excluded: chain D residue 71 VAL Chi-restraints excluded: chain D residue 89 GLU Chi-restraints excluded: chain D residue 96 TYR Chi-restraints excluded: chain D residue 102 MET Chi-restraints excluded: chain D residue 172 SER Chi-restraints excluded: chain D residue 182 ASP Chi-restraints excluded: chain D residue 187 VAL Chi-restraints excluded: chain D residue 368 MET Chi-restraints excluded: chain D residue 369 ASP Chi-restraints excluded: chain D residue 414 ILE Chi-restraints excluded: chain D residue 469 ARG Chi-restraints excluded: chain D residue 493 ILE Chi-restraints excluded: chain D residue 499 GLN Chi-restraints excluded: chain D residue 563 HIS Chi-restraints excluded: chain D residue 579 ARG Chi-restraints excluded: chain D residue 647 THR Chi-restraints excluded: chain D residue 663 LEU Chi-restraints excluded: chain D residue 666 SER Chi-restraints excluded: chain D residue 697 THR Chi-restraints excluded: chain D residue 717 ILE Chi-restraints excluded: chain D residue 723 THR Chi-restraints excluded: chain D residue 748 SER Chi-restraints excluded: chain D residue 790 CYS Chi-restraints excluded: chain D residue 810 LEU Chi-restraints excluded: chain D residue 813 ASP Chi-restraints excluded: chain D residue 840 LEU Chi-restraints excluded: chain D residue 854 VAL Chi-restraints excluded: chain D residue 905 VAL Chi-restraints excluded: chain D residue 949 ILE Chi-restraints excluded: chain D residue 954 LEU Chi-restraints excluded: chain D residue 985 LEU Chi-restraints excluded: chain D residue 987 CYS Chi-restraints excluded: chain D residue 989 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 416 random chunks: chunk 255 optimal weight: 0.9990 chunk 78 optimal weight: 3.9990 chunk 76 optimal weight: 2.9990 chunk 332 optimal weight: 0.8980 chunk 243 optimal weight: 0.5980 chunk 405 optimal weight: 9.9990 chunk 194 optimal weight: 4.9990 chunk 279 optimal weight: 2.9990 chunk 216 optimal weight: 20.0000 chunk 30 optimal weight: 3.9990 chunk 57 optimal weight: 0.1980 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 787 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 766 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 908 ASN ** C 951 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 951 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.143401 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.087254 restraints weight = 56802.868| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.090617 restraints weight = 33590.786| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.091478 restraints weight = 21416.723| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.092070 restraints weight = 16040.287| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.092375 restraints weight = 17044.399| |-----------------------------------------------------------------------------| r_work (final): 0.3186 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8277 moved from start: 0.1778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 33956 Z= 0.135 Angle : 0.588 10.993 45932 Z= 0.296 Chirality : 0.043 0.325 5260 Planarity : 0.004 0.040 5818 Dihedral : 7.812 177.907 4552 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 10.01 Ramachandran Plot: Outliers : 0.14 % Allowed : 6.58 % Favored : 93.27 % Rotamer: Outliers : 4.92 % Allowed : 26.40 % Favored : 68.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.02 % 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: -1.05 (0.13), residues: 4163 helix: 1.25 (0.15), residues: 1304 sheet: -1.55 (0.22), residues: 572 loop : -1.69 (0.12), residues: 2287 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG R 52 TYR 0.016 0.001 TYR C 833 PHE 0.020 0.001 PHE C 710 TRP 0.021 0.001 TRP A 617 HIS 0.006 0.001 HIS D 946 Details of bonding type rmsd covalent geometry : bond 0.00320 (33953) covalent geometry : angle 0.58518 (45926) SS BOND : bond 0.00395 ( 3) SS BOND : angle 5.08931 ( 6) hydrogen bonds : bond 0.03294 ( 1027) hydrogen bonds : angle 4.86576 ( 2991) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8326 Ramachandran restraints generated. 4163 Oldfield, 0 Emsley, 4163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8326 Ramachandran restraints generated. 4163 Oldfield, 0 Emsley, 4163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 432 residues out of total 3762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 185 poor density : 247 time to evaluate : 1.399 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: P 53 MET cc_start: 0.2604 (ppp) cc_final: 0.2171 (ppp) REVERT: P 74 PHE cc_start: 0.7604 (m-80) cc_final: 0.7293 (m-10) REVERT: R 45 LEU cc_start: 0.8493 (OUTLIER) cc_final: 0.8227 (mm) REVERT: R 74 PHE cc_start: 0.7858 (m-80) cc_final: 0.7456 (m-80) REVERT: A 23 ASP cc_start: 0.8443 (OUTLIER) cc_final: 0.8234 (t0) REVERT: A 97 ILE cc_start: 0.8763 (tt) cc_final: 0.8492 (pt) REVERT: A 362 SER cc_start: 0.8836 (OUTLIER) cc_final: 0.8420 (p) REVERT: A 379 ASP cc_start: 0.8839 (t0) cc_final: 0.8407 (t70) REVERT: A 404 LEU cc_start: 0.8715 (OUTLIER) cc_final: 0.8328 (mp) REVERT: A 521 THR cc_start: 0.8892 (OUTLIER) cc_final: 0.8604 (p) REVERT: A 563 HIS cc_start: 0.8142 (OUTLIER) cc_final: 0.7817 (p-80) REVERT: A 593 ARG cc_start: 0.7788 (ptt180) cc_final: 0.7487 (ttp-170) REVERT: A 614 GLN cc_start: 0.8426 (OUTLIER) cc_final: 0.8061 (mt0) REVERT: A 743 ILE cc_start: 0.7127 (OUTLIER) cc_final: 0.6871 (mp) REVERT: A 809 ILE cc_start: 0.7727 (OUTLIER) cc_final: 0.7079 (mp) REVERT: A 894 MET cc_start: 0.3073 (mmp) cc_final: 0.2275 (ptp) REVERT: A 932 MET cc_start: 0.5370 (OUTLIER) cc_final: 0.4324 (pp-130) REVERT: B 97 ILE cc_start: 0.8453 (tp) cc_final: 0.8167 (pt) REVERT: B 469 ARG cc_start: 0.8810 (OUTLIER) cc_final: 0.7786 (mtm-85) REVERT: B 486 ARG cc_start: 0.8820 (OUTLIER) cc_final: 0.8500 (ttp80) REVERT: B 599 PHE cc_start: 0.8311 (t80) cc_final: 0.8002 (t80) REVERT: B 712 ASP cc_start: 0.7173 (OUTLIER) cc_final: 0.6843 (p0) REVERT: B 825 LEU cc_start: 0.5218 (OUTLIER) cc_final: 0.4492 (tp) REVERT: B 834 PHE cc_start: 0.6663 (OUTLIER) cc_final: 0.5659 (p90) REVERT: C 362 SER cc_start: 0.8835 (OUTLIER) cc_final: 0.8421 (p) REVERT: C 614 GLN cc_start: 0.8190 (OUTLIER) cc_final: 0.7648 (mp10) REVERT: C 713 ILE cc_start: 0.8452 (OUTLIER) cc_final: 0.8162 (pp) REVERT: C 734 LEU cc_start: 0.8414 (tt) cc_final: 0.7979 (pt) REVERT: C 894 MET cc_start: 0.5326 (tpp) cc_final: 0.5038 (tpt) REVERT: D 469 ARG cc_start: 0.8868 (OUTLIER) cc_final: 0.8048 (mtm-85) REVERT: D 574 ASP cc_start: 0.7692 (p0) cc_final: 0.7325 (t70) REVERT: D 627 LYS cc_start: 0.7960 (OUTLIER) cc_final: 0.7585 (mttp) REVERT: D 709 ARG cc_start: 0.7076 (ttm110) cc_final: 0.6711 (ptp-170) REVERT: D 840 LEU cc_start: 0.3220 (OUTLIER) cc_final: 0.2790 (tt) REVERT: D 932 MET cc_start: 0.4000 (tpt) cc_final: 0.3758 (tpt) REVERT: D 949 ILE cc_start: 0.6093 (OUTLIER) cc_final: 0.5752 (mt) outliers start: 185 outliers final: 121 residues processed: 407 average time/residue: 0.2118 time to fit residues: 143.8577 Evaluate side-chains 372 residues out of total 3762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 143 poor density : 229 time to evaluate : 1.450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 28 ILE Chi-restraints excluded: chain P residue 68 THR Chi-restraints excluded: chain P residue 77 LEU Chi-restraints excluded: chain P residue 79 VAL Chi-restraints excluded: chain P residue 84 VAL Chi-restraints excluded: chain Q residue 28 ILE Chi-restraints excluded: chain Q residue 31 THR Chi-restraints excluded: chain Q residue 40 CYS Chi-restraints excluded: chain Q residue 43 CYS Chi-restraints excluded: chain Q residue 71 ASP Chi-restraints excluded: chain R residue 23 SER Chi-restraints excluded: chain R residue 28 ILE Chi-restraints excluded: chain R residue 45 LEU Chi-restraints excluded: chain S residue 38 SER Chi-restraints excluded: chain S residue 45 LEU Chi-restraints excluded: chain S residue 73 VAL Chi-restraints excluded: chain S residue 85 ASN Chi-restraints excluded: chain A residue 23 ASP Chi-restraints excluded: chain A residue 52 SER Chi-restraints excluded: chain A residue 54 ILE Chi-restraints excluded: chain A residue 79 SER Chi-restraints excluded: chain A residue 178 THR Chi-restraints excluded: chain A residue 207 VAL Chi-restraints excluded: chain A residue 267 SER Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 362 SER Chi-restraints excluded: chain A residue 404 LEU Chi-restraints excluded: chain A residue 410 CYS Chi-restraints excluded: chain A residue 414 ILE Chi-restraints excluded: chain A residue 469 ARG Chi-restraints excluded: chain A residue 521 THR Chi-restraints excluded: chain A residue 557 VAL Chi-restraints excluded: chain A residue 563 HIS Chi-restraints excluded: chain A residue 580 THR Chi-restraints excluded: chain A residue 614 GLN Chi-restraints excluded: chain A residue 647 THR Chi-restraints excluded: chain A residue 690 LEU Chi-restraints excluded: chain A residue 713 ILE Chi-restraints excluded: chain A residue 729 GLU Chi-restraints excluded: chain A residue 733 SER Chi-restraints excluded: chain A residue 743 ILE Chi-restraints excluded: chain A residue 786 LEU Chi-restraints excluded: chain A residue 809 ILE Chi-restraints excluded: chain A residue 819 GLU Chi-restraints excluded: chain A residue 827 THR Chi-restraints excluded: chain A residue 932 MET Chi-restraints excluded: chain A residue 938 VAL Chi-restraints excluded: chain B residue 41 ILE Chi-restraints excluded: chain B residue 54 ILE Chi-restraints excluded: chain B residue 66 SER Chi-restraints excluded: chain B residue 90 ILE Chi-restraints excluded: chain B residue 136 ARG Chi-restraints excluded: chain B residue 182 ASP Chi-restraints excluded: chain B residue 209 MET Chi-restraints excluded: chain B residue 302 LEU Chi-restraints excluded: chain B residue 362 SER Chi-restraints excluded: chain B residue 404 LEU Chi-restraints excluded: chain B residue 437 THR Chi-restraints excluded: chain B residue 469 ARG Chi-restraints excluded: chain B residue 486 ARG Chi-restraints excluded: chain B residue 508 VAL Chi-restraints excluded: chain B residue 513 ILE Chi-restraints excluded: chain B residue 616 LEU Chi-restraints excluded: chain B residue 647 THR Chi-restraints excluded: chain B residue 663 LEU Chi-restraints excluded: chain B residue 712 ASP Chi-restraints excluded: chain B residue 754 PHE Chi-restraints excluded: chain B residue 757 GLU Chi-restraints excluded: chain B residue 818 LEU Chi-restraints excluded: chain B residue 825 LEU Chi-restraints excluded: chain B residue 834 PHE Chi-restraints excluded: chain B residue 854 VAL Chi-restraints excluded: chain B residue 868 GLU Chi-restraints excluded: chain B residue 916 ILE Chi-restraints excluded: chain B residue 926 THR Chi-restraints excluded: chain B residue 932 MET Chi-restraints excluded: chain B residue 942 LEU Chi-restraints excluded: chain B residue 984 ILE Chi-restraints excluded: chain C residue 17 THR Chi-restraints excluded: chain C residue 178 THR Chi-restraints excluded: chain C residue 185 ASP Chi-restraints excluded: chain C residue 234 THR Chi-restraints excluded: chain C residue 362 SER Chi-restraints excluded: chain C residue 391 SER Chi-restraints excluded: chain C residue 410 CYS Chi-restraints excluded: chain C residue 414 ILE Chi-restraints excluded: chain C residue 540 MET Chi-restraints excluded: chain C residue 594 LEU Chi-restraints excluded: chain C residue 614 GLN Chi-restraints excluded: chain C residue 643 LEU Chi-restraints excluded: chain C residue 671 HIS Chi-restraints excluded: chain C residue 678 MET Chi-restraints excluded: chain C residue 690 LEU Chi-restraints excluded: chain C residue 701 MET Chi-restraints excluded: chain C residue 713 ILE Chi-restraints excluded: chain C residue 803 LEU Chi-restraints excluded: chain C residue 827 THR Chi-restraints excluded: chain C residue 829 ASN Chi-restraints excluded: chain C residue 926 THR Chi-restraints excluded: chain C residue 933 PHE Chi-restraints excluded: chain C residue 951 HIS Chi-restraints excluded: chain D residue 41 ILE Chi-restraints excluded: chain D residue 54 ILE Chi-restraints excluded: chain D residue 63 ILE Chi-restraints excluded: chain D residue 89 GLU Chi-restraints excluded: chain D residue 96 TYR Chi-restraints excluded: chain D residue 102 MET Chi-restraints excluded: chain D residue 117 THR Chi-restraints excluded: chain D residue 172 SER Chi-restraints excluded: chain D residue 182 ASP Chi-restraints excluded: chain D residue 187 VAL Chi-restraints excluded: chain D residue 368 MET Chi-restraints excluded: chain D residue 369 ASP Chi-restraints excluded: chain D residue 396 SER Chi-restraints excluded: chain D residue 404 LEU Chi-restraints excluded: chain D residue 414 ILE Chi-restraints excluded: chain D residue 469 ARG Chi-restraints excluded: chain D residue 493 ILE Chi-restraints excluded: chain D residue 499 GLN Chi-restraints excluded: chain D residue 513 ILE Chi-restraints excluded: chain D residue 563 HIS Chi-restraints excluded: chain D residue 579 ARG Chi-restraints excluded: chain D residue 616 LEU Chi-restraints excluded: chain D residue 622 CYS Chi-restraints excluded: chain D residue 627 LYS Chi-restraints excluded: chain D residue 654 VAL Chi-restraints excluded: chain D residue 663 LEU Chi-restraints excluded: chain D residue 666 SER Chi-restraints excluded: chain D residue 697 THR Chi-restraints excluded: chain D residue 717 ILE Chi-restraints excluded: chain D residue 748 SER Chi-restraints excluded: chain D residue 790 CYS Chi-restraints excluded: chain D residue 810 LEU Chi-restraints excluded: chain D residue 813 ASP Chi-restraints excluded: chain D residue 840 LEU Chi-restraints excluded: chain D residue 854 VAL Chi-restraints excluded: chain D residue 905 VAL Chi-restraints excluded: chain D residue 928 HIS Chi-restraints excluded: chain D residue 949 ILE Chi-restraints excluded: chain D residue 954 LEU Chi-restraints excluded: chain D residue 985 LEU Chi-restraints excluded: chain D residue 987 CYS Chi-restraints excluded: chain D residue 989 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 416 random chunks: chunk 160 optimal weight: 3.9990 chunk 59 optimal weight: 3.9990 chunk 145 optimal weight: 3.9990 chunk 333 optimal weight: 1.9990 chunk 385 optimal weight: 2.9990 chunk 379 optimal weight: 5.9990 chunk 126 optimal weight: 8.9990 chunk 141 optimal weight: 0.7980 chunk 305 optimal weight: 5.9990 chunk 388 optimal weight: 1.9990 chunk 2 optimal weight: 0.6980 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 648 ASN ** A 787 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 928 HIS ** C 928 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 951 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 871 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.142359 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.086296 restraints weight = 56621.737| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.089598 restraints weight = 33289.181| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.090451 restraints weight = 21104.957| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.091496 restraints weight = 15831.295| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.091578 restraints weight = 15893.122| |-----------------------------------------------------------------------------| r_work (final): 0.3182 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8301 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 0.037 33956 Z= 0.172 Angle : 0.598 10.362 45932 Z= 0.302 Chirality : 0.044 0.280 5260 Planarity : 0.004 0.047 5818 Dihedral : 7.816 178.054 4552 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 10.25 Ramachandran Plot: Outliers : 0.14 % Allowed : 6.75 % Favored : 93.11 % Rotamer: Outliers : 5.91 % Allowed : 25.68 % Favored : 68.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.02 % 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: -1.11 (0.13), residues: 4163 helix: 1.15 (0.15), residues: 1316 sheet: -1.62 (0.21), residues: 592 loop : -1.69 (0.12), residues: 2255 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 706 TYR 0.015 0.001 TYR C 833 PHE 0.020 0.001 PHE C 933 TRP 0.022 0.002 TRP A 617 HIS 0.005 0.001 HIS D 946 Details of bonding type rmsd covalent geometry : bond 0.00417 (33953) covalent geometry : angle 0.59763 (45926) SS BOND : bond 0.00374 ( 3) SS BOND : angle 2.59034 ( 6) hydrogen bonds : bond 0.03464 ( 1027) hydrogen bonds : angle 4.79931 ( 2991) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8326 Ramachandran restraints generated. 4163 Oldfield, 0 Emsley, 4163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8326 Ramachandran restraints generated. 4163 Oldfield, 0 Emsley, 4163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 464 residues out of total 3762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 222 poor density : 242 time to evaluate : 1.182 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 53 MET cc_start: 0.2542 (ppp) cc_final: 0.2097 (ppp) REVERT: P 74 PHE cc_start: 0.7606 (m-80) cc_final: 0.7275 (m-10) REVERT: R 45 LEU cc_start: 0.8378 (OUTLIER) cc_final: 0.8175 (mm) REVERT: R 74 PHE cc_start: 0.7849 (m-80) cc_final: 0.7412 (m-80) REVERT: A 23 ASP cc_start: 0.8475 (OUTLIER) cc_final: 0.8257 (t0) REVERT: A 50 GLU cc_start: 0.7234 (OUTLIER) cc_final: 0.4690 (mp0) REVERT: A 97 ILE cc_start: 0.8773 (tt) cc_final: 0.8542 (pt) REVERT: A 362 SER cc_start: 0.8848 (OUTLIER) cc_final: 0.8430 (p) REVERT: A 379 ASP cc_start: 0.8839 (t0) cc_final: 0.8393 (t70) REVERT: A 404 LEU cc_start: 0.8762 (OUTLIER) cc_final: 0.8345 (mp) REVERT: A 521 THR cc_start: 0.8941 (OUTLIER) cc_final: 0.8665 (p) REVERT: A 593 ARG cc_start: 0.7852 (ptt180) cc_final: 0.7554 (ttp-170) REVERT: A 614 GLN cc_start: 0.8440 (OUTLIER) cc_final: 0.8047 (mt0) REVERT: A 743 ILE cc_start: 0.7115 (OUTLIER) cc_final: 0.6859 (mp) REVERT: A 809 ILE cc_start: 0.7774 (OUTLIER) cc_final: 0.7130 (mp) REVERT: A 894 MET cc_start: 0.3044 (mmp) cc_final: 0.2052 (ptp) REVERT: A 932 MET cc_start: 0.5429 (OUTLIER) cc_final: 0.4404 (pp-130) REVERT: B 469 ARG cc_start: 0.8816 (OUTLIER) cc_final: 0.7779 (mtm-85) REVERT: B 486 ARG cc_start: 0.8867 (OUTLIER) cc_final: 0.8525 (ttp80) REVERT: B 599 PHE cc_start: 0.8290 (t80) cc_final: 0.7959 (t80) REVERT: B 709 ARG cc_start: 0.7003 (tpp-160) cc_final: 0.6795 (tpp-160) REVERT: B 712 ASP cc_start: 0.7181 (OUTLIER) cc_final: 0.6846 (p0) REVERT: B 825 LEU cc_start: 0.5245 (OUTLIER) cc_final: 0.4535 (tp) REVERT: B 834 PHE cc_start: 0.6722 (OUTLIER) cc_final: 0.5639 (p90) REVERT: B 947 LEU cc_start: 0.4071 (OUTLIER) cc_final: 0.3867 (mm) REVERT: C 126 GLU cc_start: 0.7434 (OUTLIER) cc_final: 0.7021 (mp0) REVERT: C 362 SER cc_start: 0.8830 (OUTLIER) cc_final: 0.8418 (p) REVERT: C 713 ILE cc_start: 0.8445 (OUTLIER) cc_final: 0.8146 (pp) REVERT: C 734 LEU cc_start: 0.8379 (tt) cc_final: 0.7971 (pt) REVERT: C 894 MET cc_start: 0.5238 (tpp) cc_final: 0.4944 (tpt) REVERT: C 927 PHE cc_start: 0.4560 (OUTLIER) cc_final: 0.3915 (m-80) REVERT: D 627 LYS cc_start: 0.8021 (OUTLIER) cc_final: 0.7662 (mttp) REVERT: D 787 HIS cc_start: 0.7057 (m-70) cc_final: 0.6634 (m-70) REVERT: D 840 LEU cc_start: 0.3301 (OUTLIER) cc_final: 0.2838 (tt) REVERT: D 932 MET cc_start: 0.4001 (tpt) cc_final: 0.3773 (tpt) REVERT: D 949 ILE cc_start: 0.6053 (OUTLIER) cc_final: 0.5543 (mt) outliers start: 222 outliers final: 141 residues processed: 432 average time/residue: 0.2039 time to fit residues: 147.6951 Evaluate side-chains 395 residues out of total 3762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 164 poor density : 231 time to evaluate : 1.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 28 ILE Chi-restraints excluded: chain P residue 68 THR Chi-restraints excluded: chain P residue 77 LEU Chi-restraints excluded: chain P residue 79 VAL Chi-restraints excluded: chain P residue 84 VAL Chi-restraints excluded: chain Q residue 28 ILE Chi-restraints excluded: chain Q residue 31 THR Chi-restraints excluded: chain Q residue 40 CYS Chi-restraints excluded: chain Q residue 43 CYS Chi-restraints excluded: chain Q residue 71 ASP Chi-restraints excluded: chain R residue 23 SER Chi-restraints excluded: chain R residue 28 ILE Chi-restraints excluded: chain R residue 45 LEU Chi-restraints excluded: chain R residue 68 THR Chi-restraints excluded: chain S residue 45 LEU Chi-restraints excluded: chain S residue 71 ASP Chi-restraints excluded: chain S residue 73 VAL Chi-restraints excluded: chain S residue 85 ASN Chi-restraints excluded: chain A residue 23 ASP Chi-restraints excluded: chain A residue 50 GLU Chi-restraints excluded: chain A residue 52 SER Chi-restraints excluded: chain A residue 54 ILE Chi-restraints excluded: chain A residue 79 SER Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 178 THR Chi-restraints excluded: chain A residue 207 VAL Chi-restraints excluded: chain A residue 213 SER Chi-restraints excluded: chain A residue 267 SER Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 362 SER Chi-restraints excluded: chain A residue 404 LEU Chi-restraints excluded: chain A residue 410 CYS Chi-restraints excluded: chain A residue 457 LEU Chi-restraints excluded: chain A residue 469 ARG Chi-restraints excluded: chain A residue 521 THR Chi-restraints excluded: chain A residue 557 VAL Chi-restraints excluded: chain A residue 563 HIS Chi-restraints excluded: chain A residue 580 THR Chi-restraints excluded: chain A residue 614 GLN Chi-restraints excluded: chain A residue 647 THR Chi-restraints excluded: chain A residue 690 LEU Chi-restraints excluded: chain A residue 713 ILE Chi-restraints excluded: chain A residue 729 GLU Chi-restraints excluded: chain A residue 733 SER Chi-restraints excluded: chain A residue 743 ILE Chi-restraints excluded: chain A residue 786 LEU Chi-restraints excluded: chain A residue 809 ILE Chi-restraints excluded: chain A residue 819 GLU Chi-restraints excluded: chain A residue 827 THR Chi-restraints excluded: chain A residue 932 MET Chi-restraints excluded: chain A residue 938 VAL Chi-restraints excluded: chain B residue 17 THR Chi-restraints excluded: chain B residue 41 ILE Chi-restraints excluded: chain B residue 66 SER Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 89 GLU Chi-restraints excluded: chain B residue 136 ARG Chi-restraints excluded: chain B residue 182 ASP Chi-restraints excluded: chain B residue 209 MET Chi-restraints excluded: chain B residue 298 ASP Chi-restraints excluded: chain B residue 302 LEU Chi-restraints excluded: chain B residue 362 SER Chi-restraints excluded: chain B residue 398 THR Chi-restraints excluded: chain B residue 404 LEU Chi-restraints excluded: chain B residue 410 CYS Chi-restraints excluded: chain B residue 437 THR Chi-restraints excluded: chain B residue 469 ARG Chi-restraints excluded: chain B residue 486 ARG Chi-restraints excluded: chain B residue 493 ILE Chi-restraints excluded: chain B residue 508 VAL Chi-restraints excluded: chain B residue 513 ILE Chi-restraints excluded: chain B residue 563 HIS Chi-restraints excluded: chain B residue 616 LEU Chi-restraints excluded: chain B residue 647 THR Chi-restraints excluded: chain B residue 652 LEU Chi-restraints excluded: chain B residue 663 LEU Chi-restraints excluded: chain B residue 697 THR Chi-restraints excluded: chain B residue 712 ASP Chi-restraints excluded: chain B residue 754 PHE Chi-restraints excluded: chain B residue 757 GLU Chi-restraints excluded: chain B residue 818 LEU Chi-restraints excluded: chain B residue 825 LEU Chi-restraints excluded: chain B residue 834 PHE Chi-restraints excluded: chain B residue 854 VAL Chi-restraints excluded: chain B residue 916 ILE Chi-restraints excluded: chain B residue 926 THR Chi-restraints excluded: chain B residue 932 MET Chi-restraints excluded: chain B residue 942 LEU Chi-restraints excluded: chain B residue 947 LEU Chi-restraints excluded: chain B residue 972 MET Chi-restraints excluded: chain B residue 984 ILE Chi-restraints excluded: chain C residue 17 THR Chi-restraints excluded: chain C residue 117 THR Chi-restraints excluded: chain C residue 126 GLU Chi-restraints excluded: chain C residue 178 THR Chi-restraints excluded: chain C residue 185 ASP Chi-restraints excluded: chain C residue 234 THR Chi-restraints excluded: chain C residue 267 SER Chi-restraints excluded: chain C residue 362 SER Chi-restraints excluded: chain C residue 391 SER Chi-restraints excluded: chain C residue 410 CYS Chi-restraints excluded: chain C residue 594 LEU Chi-restraints excluded: chain C residue 643 LEU Chi-restraints excluded: chain C residue 671 HIS Chi-restraints excluded: chain C residue 678 MET Chi-restraints excluded: chain C residue 690 LEU Chi-restraints excluded: chain C residue 701 MET Chi-restraints excluded: chain C residue 713 ILE Chi-restraints excluded: chain C residue 783 LEU Chi-restraints excluded: chain C residue 803 LEU Chi-restraints excluded: chain C residue 827 THR Chi-restraints excluded: chain C residue 829 ASN Chi-restraints excluded: chain C residue 855 SER Chi-restraints excluded: chain C residue 926 THR Chi-restraints excluded: chain C residue 927 PHE Chi-restraints excluded: chain C residue 933 PHE Chi-restraints excluded: chain C residue 951 HIS Chi-restraints excluded: chain D residue 17 THR Chi-restraints excluded: chain D residue 30 SER Chi-restraints excluded: chain D residue 41 ILE Chi-restraints excluded: chain D residue 63 ILE Chi-restraints excluded: chain D residue 71 VAL Chi-restraints excluded: chain D residue 89 GLU Chi-restraints excluded: chain D residue 96 TYR Chi-restraints excluded: chain D residue 102 MET Chi-restraints excluded: chain D residue 117 THR Chi-restraints excluded: chain D residue 172 SER Chi-restraints excluded: chain D residue 182 ASP Chi-restraints excluded: chain D residue 187 VAL Chi-restraints excluded: chain D residue 368 MET Chi-restraints excluded: chain D residue 369 ASP Chi-restraints excluded: chain D residue 396 SER Chi-restraints excluded: chain D residue 404 LEU Chi-restraints excluded: chain D residue 437 THR Chi-restraints excluded: chain D residue 469 ARG Chi-restraints excluded: chain D residue 493 ILE Chi-restraints excluded: chain D residue 499 GLN Chi-restraints excluded: chain D residue 563 HIS Chi-restraints excluded: chain D residue 579 ARG Chi-restraints excluded: chain D residue 616 LEU Chi-restraints excluded: chain D residue 622 CYS Chi-restraints excluded: chain D residue 627 LYS Chi-restraints excluded: chain D residue 647 THR Chi-restraints excluded: chain D residue 654 VAL Chi-restraints excluded: chain D residue 658 THR Chi-restraints excluded: chain D residue 663 LEU Chi-restraints excluded: chain D residue 666 SER Chi-restraints excluded: chain D residue 697 THR Chi-restraints excluded: chain D residue 717 ILE Chi-restraints excluded: chain D residue 723 THR Chi-restraints excluded: chain D residue 742 THR Chi-restraints excluded: chain D residue 748 SER Chi-restraints excluded: chain D residue 790 CYS Chi-restraints excluded: chain D residue 810 LEU Chi-restraints excluded: chain D residue 813 ASP Chi-restraints excluded: chain D residue 840 LEU Chi-restraints excluded: chain D residue 854 VAL Chi-restraints excluded: chain D residue 897 ASN Chi-restraints excluded: chain D residue 905 VAL Chi-restraints excluded: chain D residue 949 ILE Chi-restraints excluded: chain D residue 954 LEU Chi-restraints excluded: chain D residue 985 LEU Chi-restraints excluded: chain D residue 987 CYS Chi-restraints excluded: chain D residue 989 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 416 random chunks: chunk 146 optimal weight: 0.6980 chunk 42 optimal weight: 7.9990 chunk 106 optimal weight: 3.9990 chunk 328 optimal weight: 6.9990 chunk 139 optimal weight: 10.0000 chunk 316 optimal weight: 40.0000 chunk 335 optimal weight: 1.9990 chunk 65 optimal weight: 0.6980 chunk 237 optimal weight: 0.9980 chunk 115 optimal weight: 20.0000 chunk 175 optimal weight: 4.9990 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Q 41 GLN R 41 GLN ** A 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 928 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 951 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 = 0.3964 r_free = 0.3964 target = 0.142231 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.085999 restraints weight = 56978.062| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.089386 restraints weight = 33640.426| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.090194 restraints weight = 21547.423| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.090785 restraints weight = 16208.437| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.091083 restraints weight = 17048.455| |-----------------------------------------------------------------------------| r_work (final): 0.3169 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8301 moved from start: 0.2104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 33956 Z= 0.168 Angle : 0.597 12.498 45932 Z= 0.300 Chirality : 0.044 0.270 5260 Planarity : 0.004 0.046 5818 Dihedral : 7.764 177.681 4549 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 10.07 Ramachandran Plot: Outliers : 0.14 % Allowed : 6.87 % Favored : 92.99 % Rotamer: Outliers : 5.40 % Allowed : 26.42 % Favored : 68.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.02 % 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: -1.12 (0.13), residues: 4163 helix: 1.15 (0.15), residues: 1316 sheet: -1.66 (0.21), residues: 591 loop : -1.70 (0.12), residues: 2256 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG Q 52 TYR 0.011 0.001 TYR C 833 PHE 0.021 0.001 PHE C 933 TRP 0.020 0.001 TRP D 857 HIS 0.005 0.001 HIS D 946 Details of bonding type rmsd covalent geometry : bond 0.00407 (33953) covalent geometry : angle 0.59651 (45926) SS BOND : bond 0.00396 ( 3) SS BOND : angle 2.27433 ( 6) hydrogen bonds : bond 0.03416 ( 1027) hydrogen bonds : angle 4.75067 ( 2991) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8326 Ramachandran restraints generated. 4163 Oldfield, 0 Emsley, 4163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8326 Ramachandran restraints generated. 4163 Oldfield, 0 Emsley, 4163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 440 residues out of total 3762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 203 poor density : 237 time to evaluate : 1.407 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Q 41 GLN cc_start: 0.5290 (OUTLIER) cc_final: 0.4974 (mm110) REVERT: R 74 PHE cc_start: 0.7920 (m-80) cc_final: 0.7448 (m-80) REVERT: A 23 ASP cc_start: 0.8518 (OUTLIER) cc_final: 0.8296 (t0) REVERT: A 50 GLU cc_start: 0.7097 (OUTLIER) cc_final: 0.4515 (mp0) REVERT: A 97 ILE cc_start: 0.8758 (tt) cc_final: 0.8522 (pt) REVERT: A 362 SER cc_start: 0.8875 (OUTLIER) cc_final: 0.8454 (p) REVERT: A 379 ASP cc_start: 0.8852 (t0) cc_final: 0.8389 (t70) REVERT: A 404 LEU cc_start: 0.8733 (OUTLIER) cc_final: 0.8322 (mp) REVERT: A 521 THR cc_start: 0.8930 (OUTLIER) cc_final: 0.8649 (p) REVERT: A 601 GLU cc_start: 0.7787 (OUTLIER) cc_final: 0.7390 (mm-30) REVERT: A 614 GLN cc_start: 0.8440 (OUTLIER) cc_final: 0.8009 (mt0) REVERT: A 743 ILE cc_start: 0.7122 (OUTLIER) cc_final: 0.6867 (mp) REVERT: A 809 ILE cc_start: 0.7734 (OUTLIER) cc_final: 0.7099 (mp) REVERT: A 932 MET cc_start: 0.5493 (OUTLIER) cc_final: 0.4491 (pp-130) REVERT: B 97 ILE cc_start: 0.8427 (tp) cc_final: 0.8176 (pt) REVERT: B 469 ARG cc_start: 0.8848 (OUTLIER) cc_final: 0.7782 (mtm-85) REVERT: B 486 ARG cc_start: 0.8867 (OUTLIER) cc_final: 0.8505 (ttp80) REVERT: B 599 PHE cc_start: 0.8318 (t80) cc_final: 0.7938 (t80) REVERT: B 712 ASP cc_start: 0.7197 (OUTLIER) cc_final: 0.6876 (p0) REVERT: B 825 LEU cc_start: 0.5260 (OUTLIER) cc_final: 0.4643 (tt) REVERT: B 834 PHE cc_start: 0.6667 (OUTLIER) cc_final: 0.5560 (p90) REVERT: C 126 GLU cc_start: 0.7458 (OUTLIER) cc_final: 0.7005 (mp0) REVERT: C 362 SER cc_start: 0.8854 (OUTLIER) cc_final: 0.8429 (p) REVERT: C 535 GLU cc_start: 0.8164 (mp0) cc_final: 0.7932 (mp0) REVERT: C 713 ILE cc_start: 0.8487 (OUTLIER) cc_final: 0.8172 (pp) REVERT: C 734 LEU cc_start: 0.8408 (tt) cc_final: 0.7980 (pt) REVERT: C 833 TYR cc_start: 0.5781 (m-80) cc_final: 0.5509 (m-80) REVERT: C 927 PHE cc_start: 0.4451 (OUTLIER) cc_final: 0.3751 (m-80) REVERT: D 469 ARG cc_start: 0.8882 (OUTLIER) cc_final: 0.8338 (mtm-85) REVERT: D 579 ARG cc_start: 0.7771 (OUTLIER) cc_final: 0.7483 (mtm-85) REVERT: D 627 LYS cc_start: 0.8020 (OUTLIER) cc_final: 0.7603 (mttp) REVERT: D 787 HIS cc_start: 0.7083 (m-70) cc_final: 0.6700 (m-70) REVERT: D 840 LEU cc_start: 0.3143 (OUTLIER) cc_final: 0.2731 (tt) REVERT: D 932 MET cc_start: 0.4019 (tpt) cc_final: 0.3811 (tpt) REVERT: D 949 ILE cc_start: 0.6055 (OUTLIER) cc_final: 0.5627 (mt) outliers start: 203 outliers final: 139 residues processed: 410 average time/residue: 0.2016 time to fit residues: 138.9342 Evaluate side-chains 392 residues out of total 3762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 164 poor density : 228 time to evaluate : 1.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 28 ILE Chi-restraints excluded: chain P residue 68 THR Chi-restraints excluded: chain P residue 77 LEU Chi-restraints excluded: chain P residue 79 VAL Chi-restraints excluded: chain P residue 84 VAL Chi-restraints excluded: chain Q residue 28 ILE Chi-restraints excluded: chain Q residue 31 THR Chi-restraints excluded: chain Q residue 40 CYS Chi-restraints excluded: chain Q residue 41 GLN Chi-restraints excluded: chain Q residue 43 CYS Chi-restraints excluded: chain Q residue 71 ASP Chi-restraints excluded: chain R residue 23 SER Chi-restraints excluded: chain R residue 28 ILE Chi-restraints excluded: chain R residue 68 THR Chi-restraints excluded: chain S residue 45 LEU Chi-restraints excluded: chain S residue 71 ASP Chi-restraints excluded: chain S residue 73 VAL Chi-restraints excluded: chain S residue 85 ASN Chi-restraints excluded: chain A residue 23 ASP Chi-restraints excluded: chain A residue 50 GLU Chi-restraints excluded: chain A residue 52 SER Chi-restraints excluded: chain A residue 54 ILE Chi-restraints excluded: chain A residue 79 SER Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 178 THR Chi-restraints excluded: chain A residue 207 VAL Chi-restraints excluded: chain A residue 213 SER Chi-restraints excluded: chain A residue 267 SER Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 362 SER Chi-restraints excluded: chain A residue 404 LEU Chi-restraints excluded: chain A residue 410 CYS Chi-restraints excluded: chain A residue 457 LEU Chi-restraints excluded: chain A residue 521 THR Chi-restraints excluded: chain A residue 557 VAL Chi-restraints excluded: chain A residue 563 HIS Chi-restraints excluded: chain A residue 580 THR Chi-restraints excluded: chain A residue 596 SER Chi-restraints excluded: chain A residue 601 GLU Chi-restraints excluded: chain A residue 614 GLN Chi-restraints excluded: chain A residue 647 THR Chi-restraints excluded: chain A residue 656 SER Chi-restraints excluded: chain A residue 690 LEU Chi-restraints excluded: chain A residue 713 ILE Chi-restraints excluded: chain A residue 729 GLU Chi-restraints excluded: chain A residue 733 SER Chi-restraints excluded: chain A residue 743 ILE Chi-restraints excluded: chain A residue 786 LEU Chi-restraints excluded: chain A residue 809 ILE Chi-restraints excluded: chain A residue 819 GLU Chi-restraints excluded: chain A residue 827 THR Chi-restraints excluded: chain A residue 932 MET Chi-restraints excluded: chain A residue 938 VAL Chi-restraints excluded: chain A residue 987 CYS Chi-restraints excluded: chain B residue 17 THR Chi-restraints excluded: chain B residue 41 ILE Chi-restraints excluded: chain B residue 66 SER Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 136 ARG Chi-restraints excluded: chain B residue 182 ASP Chi-restraints excluded: chain B residue 209 MET Chi-restraints excluded: chain B residue 302 LEU Chi-restraints excluded: chain B residue 362 SER Chi-restraints excluded: chain B residue 398 THR Chi-restraints excluded: chain B residue 404 LEU Chi-restraints excluded: chain B residue 410 CYS Chi-restraints excluded: chain B residue 437 THR Chi-restraints excluded: chain B residue 469 ARG Chi-restraints excluded: chain B residue 486 ARG Chi-restraints excluded: chain B residue 493 ILE Chi-restraints excluded: chain B residue 508 VAL Chi-restraints excluded: chain B residue 513 ILE Chi-restraints excluded: chain B residue 519 GLU Chi-restraints excluded: chain B residue 563 HIS Chi-restraints excluded: chain B residue 616 LEU Chi-restraints excluded: chain B residue 647 THR Chi-restraints excluded: chain B residue 652 LEU Chi-restraints excluded: chain B residue 663 LEU Chi-restraints excluded: chain B residue 712 ASP Chi-restraints excluded: chain B residue 757 GLU Chi-restraints excluded: chain B residue 758 LEU Chi-restraints excluded: chain B residue 818 LEU Chi-restraints excluded: chain B residue 825 LEU Chi-restraints excluded: chain B residue 834 PHE Chi-restraints excluded: chain B residue 854 VAL Chi-restraints excluded: chain B residue 916 ILE Chi-restraints excluded: chain B residue 926 THR Chi-restraints excluded: chain B residue 932 MET Chi-restraints excluded: chain B residue 942 LEU Chi-restraints excluded: chain B residue 972 MET Chi-restraints excluded: chain B residue 984 ILE Chi-restraints excluded: chain C residue 17 THR Chi-restraints excluded: chain C residue 117 THR Chi-restraints excluded: chain C residue 126 GLU Chi-restraints excluded: chain C residue 178 THR Chi-restraints excluded: chain C residue 185 ASP Chi-restraints excluded: chain C residue 234 THR Chi-restraints excluded: chain C residue 267 SER Chi-restraints excluded: chain C residue 362 SER Chi-restraints excluded: chain C residue 391 SER Chi-restraints excluded: chain C residue 410 CYS Chi-restraints excluded: chain C residue 594 LEU Chi-restraints excluded: chain C residue 643 LEU Chi-restraints excluded: chain C residue 671 HIS Chi-restraints excluded: chain C residue 678 MET Chi-restraints excluded: chain C residue 690 LEU Chi-restraints excluded: chain C residue 713 ILE Chi-restraints excluded: chain C residue 803 LEU Chi-restraints excluded: chain C residue 827 THR Chi-restraints excluded: chain C residue 829 ASN Chi-restraints excluded: chain C residue 855 SER Chi-restraints excluded: chain C residue 926 THR Chi-restraints excluded: chain C residue 927 PHE Chi-restraints excluded: chain C residue 933 PHE Chi-restraints excluded: chain C residue 951 HIS Chi-restraints excluded: chain D residue 17 THR Chi-restraints excluded: chain D residue 30 SER Chi-restraints excluded: chain D residue 41 ILE Chi-restraints excluded: chain D residue 63 ILE Chi-restraints excluded: chain D residue 71 VAL Chi-restraints excluded: chain D residue 89 GLU Chi-restraints excluded: chain D residue 102 MET Chi-restraints excluded: chain D residue 117 THR Chi-restraints excluded: chain D residue 172 SER Chi-restraints excluded: chain D residue 182 ASP Chi-restraints excluded: chain D residue 187 VAL Chi-restraints excluded: chain D residue 368 MET Chi-restraints excluded: chain D residue 369 ASP Chi-restraints excluded: chain D residue 396 SER Chi-restraints excluded: chain D residue 404 LEU Chi-restraints excluded: chain D residue 414 ILE Chi-restraints excluded: chain D residue 437 THR Chi-restraints excluded: chain D residue 469 ARG Chi-restraints excluded: chain D residue 493 ILE Chi-restraints excluded: chain D residue 499 GLN Chi-restraints excluded: chain D residue 513 ILE Chi-restraints excluded: chain D residue 563 HIS Chi-restraints excluded: chain D residue 579 ARG Chi-restraints excluded: chain D residue 616 LEU Chi-restraints excluded: chain D residue 627 LYS Chi-restraints excluded: chain D residue 647 THR Chi-restraints excluded: chain D residue 654 VAL Chi-restraints excluded: chain D residue 658 THR Chi-restraints excluded: chain D residue 663 LEU Chi-restraints excluded: chain D residue 666 SER Chi-restraints excluded: chain D residue 697 THR Chi-restraints excluded: chain D residue 717 ILE Chi-restraints excluded: chain D residue 723 THR Chi-restraints excluded: chain D residue 742 THR Chi-restraints excluded: chain D residue 748 SER Chi-restraints excluded: chain D residue 784 HIS Chi-restraints excluded: chain D residue 790 CYS Chi-restraints excluded: chain D residue 810 LEU Chi-restraints excluded: chain D residue 813 ASP Chi-restraints excluded: chain D residue 818 LEU Chi-restraints excluded: chain D residue 840 LEU Chi-restraints excluded: chain D residue 854 VAL Chi-restraints excluded: chain D residue 905 VAL Chi-restraints excluded: chain D residue 949 ILE Chi-restraints excluded: chain D residue 951 HIS Chi-restraints excluded: chain D residue 954 LEU Chi-restraints excluded: chain D residue 985 LEU Chi-restraints excluded: chain D residue 987 CYS Chi-restraints excluded: chain D residue 989 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 416 random chunks: chunk 147 optimal weight: 0.4980 chunk 133 optimal weight: 2.9990 chunk 270 optimal weight: 1.9990 chunk 355 optimal weight: 3.9990 chunk 322 optimal weight: 0.9980 chunk 231 optimal weight: 0.8980 chunk 68 optimal weight: 0.0070 chunk 412 optimal weight: 6.9990 chunk 360 optimal weight: 2.9990 chunk 226 optimal weight: 5.9990 chunk 102 optimal weight: 4.9990 overall best weight: 0.8800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Q 41 GLN R 41 GLN ** A 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 850 GLN C 886 ASN ** C 928 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 934 ASN ** 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 = 0.3979 r_free = 0.3979 target = 0.143412 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.087237 restraints weight = 56432.644| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 66)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.089905 restraints weight = 30944.049| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 63)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.091666 restraints weight = 20851.404| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 60)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.092794 restraints weight = 16160.200| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.093319 restraints weight = 13826.732| |-----------------------------------------------------------------------------| r_work (final): 0.3220 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8245 moved from start: 0.2195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 33956 Z= 0.119 Angle : 0.585 12.923 45932 Z= 0.292 Chirality : 0.043 0.224 5260 Planarity : 0.004 0.043 5818 Dihedral : 7.635 177.878 4547 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 9.69 Ramachandran Plot: Outliers : 0.14 % Allowed : 6.41 % Favored : 93.44 % Rotamer: Outliers : 4.87 % Allowed : 27.04 % Favored : 68.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.02 % 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: -1.03 (0.13), residues: 4163 helix: 1.33 (0.15), residues: 1303 sheet: -1.65 (0.21), residues: 578 loop : -1.68 (0.12), residues: 2282 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 136 TYR 0.011 0.001 TYR C 833 PHE 0.022 0.001 PHE C 933 TRP 0.022 0.001 TRP A 617 HIS 0.006 0.001 HIS D 946 Details of bonding type rmsd covalent geometry : bond 0.00279 (33953) covalent geometry : angle 0.58345 (45926) SS BOND : bond 0.00511 ( 3) SS BOND : angle 4.27079 ( 6) hydrogen bonds : bond 0.03115 ( 1027) hydrogen bonds : angle 4.67101 ( 2991) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8326 Ramachandran restraints generated. 4163 Oldfield, 0 Emsley, 4163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8326 Ramachandran restraints generated. 4163 Oldfield, 0 Emsley, 4163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 423 residues out of total 3762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 183 poor density : 240 time to evaluate : 1.340 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 29 LYS cc_start: 0.7275 (tptm) cc_final: 0.7013 (tptp) REVERT: R 74 PHE cc_start: 0.7978 (m-80) cc_final: 0.7536 (m-80) REVERT: A 362 SER cc_start: 0.8829 (OUTLIER) cc_final: 0.8419 (p) REVERT: A 379 ASP cc_start: 0.8827 (t0) cc_final: 0.8431 (t70) REVERT: A 404 LEU cc_start: 0.8729 (OUTLIER) cc_final: 0.8364 (mp) REVERT: A 521 THR cc_start: 0.8934 (OUTLIER) cc_final: 0.8659 (p) REVERT: A 601 GLU cc_start: 0.7731 (OUTLIER) cc_final: 0.7409 (mm-30) REVERT: A 614 GLN cc_start: 0.8436 (OUTLIER) cc_final: 0.7994 (mt0) REVERT: A 743 ILE cc_start: 0.7192 (OUTLIER) cc_final: 0.6932 (mp) REVERT: A 809 ILE cc_start: 0.7759 (OUTLIER) cc_final: 0.7107 (mp) REVERT: A 932 MET cc_start: 0.5259 (OUTLIER) cc_final: 0.4285 (pp-130) REVERT: B 97 ILE cc_start: 0.8476 (tp) cc_final: 0.8191 (pt) REVERT: B 311 MET cc_start: 0.7285 (ptm) cc_final: 0.7056 (ptp) REVERT: B 469 ARG cc_start: 0.8828 (OUTLIER) cc_final: 0.7827 (mtm-85) REVERT: B 486 ARG cc_start: 0.8798 (OUTLIER) cc_final: 0.8457 (ttp80) REVERT: B 712 ASP cc_start: 0.7145 (OUTLIER) cc_final: 0.6766 (p0) REVERT: B 825 LEU cc_start: 0.5159 (OUTLIER) cc_final: 0.4472 (tp) REVERT: B 834 PHE cc_start: 0.6650 (OUTLIER) cc_final: 0.5432 (p90) REVERT: C 126 GLU cc_start: 0.7269 (OUTLIER) cc_final: 0.6849 (mp0) REVERT: C 362 SER cc_start: 0.8811 (OUTLIER) cc_final: 0.8398 (p) REVERT: C 713 ILE cc_start: 0.8475 (OUTLIER) cc_final: 0.8170 (pp) REVERT: C 734 LEU cc_start: 0.8164 (tt) cc_final: 0.7788 (pt) REVERT: C 833 TYR cc_start: 0.5774 (m-80) cc_final: 0.5562 (m-80) REVERT: C 894 MET cc_start: 0.4893 (tpp) cc_final: 0.4483 (tpt) REVERT: C 927 PHE cc_start: 0.4345 (OUTLIER) cc_final: 0.3650 (m-80) REVERT: D 60 LYS cc_start: 0.7872 (OUTLIER) cc_final: 0.7515 (ttmm) REVERT: D 76 ASN cc_start: 0.8420 (m-40) cc_final: 0.8176 (m-40) REVERT: D 469 ARG cc_start: 0.8866 (OUTLIER) cc_final: 0.8071 (mtm-85) REVERT: D 787 HIS cc_start: 0.7159 (m-70) cc_final: 0.6763 (m-70) REVERT: D 840 LEU cc_start: 0.3235 (OUTLIER) cc_final: 0.2783 (tt) REVERT: D 859 LEU cc_start: 0.5144 (OUTLIER) cc_final: 0.4853 (tt) REVERT: D 949 ILE cc_start: 0.6010 (OUTLIER) cc_final: 0.5594 (mt) outliers start: 183 outliers final: 130 residues processed: 400 average time/residue: 0.2014 time to fit residues: 136.3486 Evaluate side-chains 381 residues out of total 3762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 152 poor density : 229 time to evaluate : 1.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 28 ILE Chi-restraints excluded: chain P residue 68 THR Chi-restraints excluded: chain P residue 77 LEU Chi-restraints excluded: chain P residue 79 VAL Chi-restraints excluded: chain P residue 84 VAL Chi-restraints excluded: chain Q residue 28 ILE Chi-restraints excluded: chain Q residue 31 THR Chi-restraints excluded: chain Q residue 43 CYS Chi-restraints excluded: chain Q residue 71 ASP Chi-restraints excluded: chain Q residue 77 LEU Chi-restraints excluded: chain R residue 23 SER Chi-restraints excluded: chain R residue 28 ILE Chi-restraints excluded: chain R residue 32 ASP Chi-restraints excluded: chain R residue 41 GLN Chi-restraints excluded: chain R residue 68 THR Chi-restraints excluded: chain S residue 38 SER Chi-restraints excluded: chain S residue 45 LEU Chi-restraints excluded: chain S residue 73 VAL Chi-restraints excluded: chain S residue 85 ASN Chi-restraints excluded: chain S residue 87 CYS Chi-restraints excluded: chain A residue 52 SER Chi-restraints excluded: chain A residue 54 ILE Chi-restraints excluded: chain A residue 178 THR Chi-restraints excluded: chain A residue 207 VAL Chi-restraints excluded: chain A residue 213 SER Chi-restraints excluded: chain A residue 229 SER Chi-restraints excluded: chain A residue 267 SER Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 362 SER Chi-restraints excluded: chain A residue 404 LEU Chi-restraints excluded: chain A residue 410 CYS Chi-restraints excluded: chain A residue 414 ILE Chi-restraints excluded: chain A residue 521 THR Chi-restraints excluded: chain A residue 557 VAL Chi-restraints excluded: chain A residue 563 HIS Chi-restraints excluded: chain A residue 580 THR Chi-restraints excluded: chain A residue 601 GLU Chi-restraints excluded: chain A residue 614 GLN Chi-restraints excluded: chain A residue 647 THR Chi-restraints excluded: chain A residue 656 SER Chi-restraints excluded: chain A residue 690 LEU Chi-restraints excluded: chain A residue 713 ILE Chi-restraints excluded: chain A residue 729 GLU Chi-restraints excluded: chain A residue 733 SER Chi-restraints excluded: chain A residue 743 ILE Chi-restraints excluded: chain A residue 786 LEU Chi-restraints excluded: chain A residue 809 ILE Chi-restraints excluded: chain A residue 819 GLU Chi-restraints excluded: chain A residue 822 ASN Chi-restraints excluded: chain A residue 827 THR Chi-restraints excluded: chain A residue 932 MET Chi-restraints excluded: chain A residue 938 VAL Chi-restraints excluded: chain A residue 987 CYS Chi-restraints excluded: chain B residue 41 ILE Chi-restraints excluded: chain B residue 54 ILE Chi-restraints excluded: chain B residue 66 SER Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 136 ARG Chi-restraints excluded: chain B residue 182 ASP Chi-restraints excluded: chain B residue 209 MET Chi-restraints excluded: chain B residue 302 LEU Chi-restraints excluded: chain B residue 362 SER Chi-restraints excluded: chain B residue 398 THR Chi-restraints excluded: chain B residue 404 LEU Chi-restraints excluded: chain B residue 410 CYS Chi-restraints excluded: chain B residue 437 THR Chi-restraints excluded: chain B residue 469 ARG Chi-restraints excluded: chain B residue 486 ARG Chi-restraints excluded: chain B residue 513 ILE Chi-restraints excluded: chain B residue 519 GLU Chi-restraints excluded: chain B residue 616 LEU Chi-restraints excluded: chain B residue 647 THR Chi-restraints excluded: chain B residue 652 LEU Chi-restraints excluded: chain B residue 663 LEU Chi-restraints excluded: chain B residue 712 ASP Chi-restraints excluded: chain B residue 758 LEU Chi-restraints excluded: chain B residue 818 LEU Chi-restraints excluded: chain B residue 825 LEU Chi-restraints excluded: chain B residue 834 PHE Chi-restraints excluded: chain B residue 916 ILE Chi-restraints excluded: chain B residue 926 THR Chi-restraints excluded: chain B residue 942 LEU Chi-restraints excluded: chain B residue 984 ILE Chi-restraints excluded: chain C residue 23 ASP Chi-restraints excluded: chain C residue 126 GLU Chi-restraints excluded: chain C residue 178 THR Chi-restraints excluded: chain C residue 185 ASP Chi-restraints excluded: chain C residue 234 THR Chi-restraints excluded: chain C residue 267 SER Chi-restraints excluded: chain C residue 362 SER Chi-restraints excluded: chain C residue 391 SER Chi-restraints excluded: chain C residue 410 CYS Chi-restraints excluded: chain C residue 414 ILE Chi-restraints excluded: chain C residue 557 VAL Chi-restraints excluded: chain C residue 594 LEU Chi-restraints excluded: chain C residue 643 LEU Chi-restraints excluded: chain C residue 671 HIS Chi-restraints excluded: chain C residue 690 LEU Chi-restraints excluded: chain C residue 713 ILE Chi-restraints excluded: chain C residue 803 LEU Chi-restraints excluded: chain C residue 827 THR Chi-restraints excluded: chain C residue 829 ASN Chi-restraints excluded: chain C residue 855 SER Chi-restraints excluded: chain C residue 927 PHE Chi-restraints excluded: chain C residue 933 PHE Chi-restraints excluded: chain C residue 951 HIS Chi-restraints excluded: chain D residue 30 SER Chi-restraints excluded: chain D residue 41 ILE Chi-restraints excluded: chain D residue 60 LYS Chi-restraints excluded: chain D residue 63 ILE Chi-restraints excluded: chain D residue 89 GLU Chi-restraints excluded: chain D residue 102 MET Chi-restraints excluded: chain D residue 117 THR Chi-restraints excluded: chain D residue 172 SER Chi-restraints excluded: chain D residue 182 ASP Chi-restraints excluded: chain D residue 187 VAL Chi-restraints excluded: chain D residue 368 MET Chi-restraints excluded: chain D residue 369 ASP Chi-restraints excluded: chain D residue 396 SER Chi-restraints excluded: chain D residue 404 LEU Chi-restraints excluded: chain D residue 414 ILE Chi-restraints excluded: chain D residue 437 THR Chi-restraints excluded: chain D residue 469 ARG Chi-restraints excluded: chain D residue 493 ILE Chi-restraints excluded: chain D residue 499 GLN Chi-restraints excluded: chain D residue 513 ILE Chi-restraints excluded: chain D residue 563 HIS Chi-restraints excluded: chain D residue 616 LEU Chi-restraints excluded: chain D residue 622 CYS Chi-restraints excluded: chain D residue 647 THR Chi-restraints excluded: chain D residue 654 VAL Chi-restraints excluded: chain D residue 658 THR Chi-restraints excluded: chain D residue 666 SER Chi-restraints excluded: chain D residue 697 THR Chi-restraints excluded: chain D residue 717 ILE Chi-restraints excluded: chain D residue 742 THR Chi-restraints excluded: chain D residue 748 SER Chi-restraints excluded: chain D residue 784 HIS Chi-restraints excluded: chain D residue 790 CYS Chi-restraints excluded: chain D residue 810 LEU Chi-restraints excluded: chain D residue 813 ASP Chi-restraints excluded: chain D residue 818 LEU Chi-restraints excluded: chain D residue 840 LEU Chi-restraints excluded: chain D residue 854 VAL Chi-restraints excluded: chain D residue 859 LEU Chi-restraints excluded: chain D residue 928 HIS Chi-restraints excluded: chain D residue 949 ILE Chi-restraints excluded: chain D residue 951 HIS Chi-restraints excluded: chain D residue 954 LEU Chi-restraints excluded: chain D residue 985 LEU Chi-restraints excluded: chain D residue 987 CYS Chi-restraints excluded: chain D residue 989 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 416 random chunks: chunk 146 optimal weight: 0.8980 chunk 272 optimal weight: 0.6980 chunk 322 optimal weight: 4.9990 chunk 415 optimal weight: 0.4980 chunk 390 optimal weight: 6.9990 chunk 342 optimal weight: 1.9990 chunk 157 optimal weight: 1.9990 chunk 253 optimal weight: 1.9990 chunk 407 optimal weight: 10.0000 chunk 337 optimal weight: 3.9990 chunk 362 optimal weight: 2.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 41 GLN ** A 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 928 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.143402 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.086640 restraints weight = 57072.691| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.090008 restraints weight = 34067.084| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.090969 restraints weight = 21275.380| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.092308 restraints weight = 15663.570| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.092219 restraints weight = 15197.515| |-----------------------------------------------------------------------------| r_work (final): 0.3192 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8279 moved from start: 0.2269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 33956 Z= 0.138 Angle : 0.590 12.294 45932 Z= 0.294 Chirality : 0.043 0.225 5260 Planarity : 0.004 0.043 5818 Dihedral : 7.532 178.527 4544 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 9.86 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.58 % Favored : 93.30 % Rotamer: Outliers : 4.71 % Allowed : 27.33 % Favored : 67.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.02 % 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: -1.03 (0.13), residues: 4163 helix: 1.29 (0.15), residues: 1308 sheet: -1.65 (0.21), residues: 585 loop : -1.67 (0.12), residues: 2270 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 136 TYR 0.014 0.001 TYR R 65 PHE 0.022 0.001 PHE C 933 TRP 0.021 0.001 TRP D 857 HIS 0.006 0.001 HIS D 946 Details of bonding type rmsd covalent geometry : bond 0.00332 (33953) covalent geometry : angle 0.58846 (45926) SS BOND : bond 0.00293 ( 3) SS BOND : angle 4.07233 ( 6) hydrogen bonds : bond 0.03167 ( 1027) hydrogen bonds : angle 4.65255 ( 2991) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8326 Ramachandran restraints generated. 4163 Oldfield, 0 Emsley, 4163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8326 Ramachandran restraints generated. 4163 Oldfield, 0 Emsley, 4163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 409 residues out of total 3762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 177 poor density : 232 time to evaluate : 1.391 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 29 LYS cc_start: 0.7145 (tptm) cc_final: 0.6879 (tptp) REVERT: Q 41 GLN cc_start: 0.5387 (tm130) cc_final: 0.4956 (mm110) REVERT: R 74 PHE cc_start: 0.7968 (m-80) cc_final: 0.7488 (m-80) REVERT: A 50 GLU cc_start: 0.7110 (OUTLIER) cc_final: 0.4470 (mp0) REVERT: A 362 SER cc_start: 0.8819 (OUTLIER) cc_final: 0.8408 (p) REVERT: A 379 ASP cc_start: 0.8815 (t0) cc_final: 0.8390 (t70) REVERT: A 404 LEU cc_start: 0.8774 (OUTLIER) cc_final: 0.8371 (mp) REVERT: A 521 THR cc_start: 0.8935 (OUTLIER) cc_final: 0.8661 (p) REVERT: A 614 GLN cc_start: 0.8436 (OUTLIER) cc_final: 0.7956 (mt0) REVERT: A 743 ILE cc_start: 0.7136 (OUTLIER) cc_final: 0.6880 (mp) REVERT: A 809 ILE cc_start: 0.7720 (OUTLIER) cc_final: 0.7108 (mp) REVERT: A 894 MET cc_start: 0.2945 (mmp) cc_final: 0.2044 (ptp) REVERT: A 932 MET cc_start: 0.5410 (OUTLIER) cc_final: 0.4465 (pp-130) REVERT: B 97 ILE cc_start: 0.8406 (tp) cc_final: 0.8142 (pt) REVERT: B 311 MET cc_start: 0.7318 (ptm) cc_final: 0.7086 (ptp) REVERT: B 469 ARG cc_start: 0.8874 (OUTLIER) cc_final: 0.7816 (mtm-85) REVERT: B 486 ARG cc_start: 0.8813 (OUTLIER) cc_final: 0.8468 (ttp80) REVERT: B 712 ASP cc_start: 0.7080 (OUTLIER) cc_final: 0.6752 (p0) REVERT: B 825 LEU cc_start: 0.5207 (OUTLIER) cc_final: 0.4529 (tp) REVERT: B 834 PHE cc_start: 0.6648 (OUTLIER) cc_final: 0.5435 (p90) REVERT: C 126 GLU cc_start: 0.7407 (OUTLIER) cc_final: 0.6969 (mp0) REVERT: C 362 SER cc_start: 0.8804 (OUTLIER) cc_final: 0.8384 (p) REVERT: C 713 ILE cc_start: 0.8484 (OUTLIER) cc_final: 0.8180 (pp) REVERT: C 734 LEU cc_start: 0.8348 (tt) cc_final: 0.7917 (pt) REVERT: C 833 TYR cc_start: 0.5689 (m-80) cc_final: 0.5395 (m-80) REVERT: C 894 MET cc_start: 0.4864 (tpp) cc_final: 0.4471 (tpt) REVERT: C 927 PHE cc_start: 0.4441 (OUTLIER) cc_final: 0.3732 (m-80) REVERT: D 76 ASN cc_start: 0.8492 (m-40) cc_final: 0.8213 (m-40) REVERT: D 469 ARG cc_start: 0.8869 (OUTLIER) cc_final: 0.8063 (mtm-85) REVERT: D 787 HIS cc_start: 0.7100 (m-70) cc_final: 0.6688 (m-70) REVERT: D 840 LEU cc_start: 0.3249 (OUTLIER) cc_final: 0.2783 (tt) REVERT: D 859 LEU cc_start: 0.5208 (OUTLIER) cc_final: 0.4915 (tt) REVERT: D 949 ILE cc_start: 0.6121 (OUTLIER) cc_final: 0.5689 (mt) outliers start: 177 outliers final: 136 residues processed: 387 average time/residue: 0.2049 time to fit residues: 134.0164 Evaluate side-chains 384 residues out of total 3762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 157 poor density : 227 time to evaluate : 1.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 28 ILE Chi-restraints excluded: chain P residue 68 THR Chi-restraints excluded: chain P residue 77 LEU Chi-restraints excluded: chain P residue 79 VAL Chi-restraints excluded: chain P residue 84 VAL Chi-restraints excluded: chain Q residue 28 ILE Chi-restraints excluded: chain Q residue 31 THR Chi-restraints excluded: chain Q residue 71 ASP Chi-restraints excluded: chain Q residue 77 LEU Chi-restraints excluded: chain R residue 23 SER Chi-restraints excluded: chain R residue 28 ILE Chi-restraints excluded: chain R residue 41 GLN Chi-restraints excluded: chain R residue 68 THR Chi-restraints excluded: chain S residue 45 LEU Chi-restraints excluded: chain S residue 71 ASP Chi-restraints excluded: chain S residue 73 VAL Chi-restraints excluded: chain S residue 85 ASN Chi-restraints excluded: chain S residue 87 CYS Chi-restraints excluded: chain A residue 50 GLU Chi-restraints excluded: chain A residue 52 SER Chi-restraints excluded: chain A residue 54 ILE Chi-restraints excluded: chain A residue 79 SER Chi-restraints excluded: chain A residue 172 SER Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 178 THR Chi-restraints excluded: chain A residue 207 VAL Chi-restraints excluded: chain A residue 213 SER Chi-restraints excluded: chain A residue 229 SER Chi-restraints excluded: chain A residue 267 SER Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 362 SER Chi-restraints excluded: chain A residue 404 LEU Chi-restraints excluded: chain A residue 410 CYS Chi-restraints excluded: chain A residue 414 ILE Chi-restraints excluded: chain A residue 457 LEU Chi-restraints excluded: chain A residue 469 ARG Chi-restraints excluded: chain A residue 521 THR Chi-restraints excluded: chain A residue 557 VAL Chi-restraints excluded: chain A residue 563 HIS Chi-restraints excluded: chain A residue 580 THR Chi-restraints excluded: chain A residue 596 SER Chi-restraints excluded: chain A residue 614 GLN Chi-restraints excluded: chain A residue 647 THR Chi-restraints excluded: chain A residue 656 SER Chi-restraints excluded: chain A residue 690 LEU Chi-restraints excluded: chain A residue 713 ILE Chi-restraints excluded: chain A residue 729 GLU Chi-restraints excluded: chain A residue 733 SER Chi-restraints excluded: chain A residue 743 ILE Chi-restraints excluded: chain A residue 786 LEU Chi-restraints excluded: chain A residue 809 ILE Chi-restraints excluded: chain A residue 819 GLU Chi-restraints excluded: chain A residue 822 ASN Chi-restraints excluded: chain A residue 827 THR Chi-restraints excluded: chain A residue 932 MET Chi-restraints excluded: chain A residue 938 VAL Chi-restraints excluded: chain B residue 41 ILE Chi-restraints excluded: chain B residue 66 SER Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 136 ARG Chi-restraints excluded: chain B residue 182 ASP Chi-restraints excluded: chain B residue 209 MET Chi-restraints excluded: chain B residue 302 LEU Chi-restraints excluded: chain B residue 362 SER Chi-restraints excluded: chain B residue 398 THR Chi-restraints excluded: chain B residue 404 LEU Chi-restraints excluded: chain B residue 410 CYS Chi-restraints excluded: chain B residue 414 ILE Chi-restraints excluded: chain B residue 437 THR Chi-restraints excluded: chain B residue 469 ARG Chi-restraints excluded: chain B residue 486 ARG Chi-restraints excluded: chain B residue 493 ILE Chi-restraints excluded: chain B residue 508 VAL Chi-restraints excluded: chain B residue 513 ILE Chi-restraints excluded: chain B residue 519 GLU Chi-restraints excluded: chain B residue 563 HIS Chi-restraints excluded: chain B residue 616 LEU Chi-restraints excluded: chain B residue 647 THR Chi-restraints excluded: chain B residue 652 LEU Chi-restraints excluded: chain B residue 663 LEU Chi-restraints excluded: chain B residue 712 ASP Chi-restraints excluded: chain B residue 757 GLU Chi-restraints excluded: chain B residue 758 LEU Chi-restraints excluded: chain B residue 818 LEU Chi-restraints excluded: chain B residue 825 LEU Chi-restraints excluded: chain B residue 834 PHE Chi-restraints excluded: chain B residue 916 ILE Chi-restraints excluded: chain B residue 926 THR Chi-restraints excluded: chain B residue 942 LEU Chi-restraints excluded: chain B residue 972 MET Chi-restraints excluded: chain B residue 984 ILE Chi-restraints excluded: chain C residue 23 ASP Chi-restraints excluded: chain C residue 126 GLU Chi-restraints excluded: chain C residue 178 THR Chi-restraints excluded: chain C residue 185 ASP Chi-restraints excluded: chain C residue 234 THR Chi-restraints excluded: chain C residue 267 SER Chi-restraints excluded: chain C residue 362 SER Chi-restraints excluded: chain C residue 391 SER Chi-restraints excluded: chain C residue 410 CYS Chi-restraints excluded: chain C residue 557 VAL Chi-restraints excluded: chain C residue 594 LEU Chi-restraints excluded: chain C residue 643 LEU Chi-restraints excluded: chain C residue 671 HIS Chi-restraints excluded: chain C residue 690 LEU Chi-restraints excluded: chain C residue 713 ILE Chi-restraints excluded: chain C residue 803 LEU Chi-restraints excluded: chain C residue 827 THR Chi-restraints excluded: chain C residue 829 ASN Chi-restraints excluded: chain C residue 926 THR Chi-restraints excluded: chain C residue 927 PHE Chi-restraints excluded: chain C residue 933 PHE Chi-restraints excluded: chain D residue 30 SER Chi-restraints excluded: chain D residue 63 ILE Chi-restraints excluded: chain D residue 71 VAL Chi-restraints excluded: chain D residue 89 GLU Chi-restraints excluded: chain D residue 102 MET Chi-restraints excluded: chain D residue 117 THR Chi-restraints excluded: chain D residue 172 SER Chi-restraints excluded: chain D residue 182 ASP Chi-restraints excluded: chain D residue 187 VAL Chi-restraints excluded: chain D residue 368 MET Chi-restraints excluded: chain D residue 369 ASP Chi-restraints excluded: chain D residue 396 SER Chi-restraints excluded: chain D residue 404 LEU Chi-restraints excluded: chain D residue 414 ILE Chi-restraints excluded: chain D residue 437 THR Chi-restraints excluded: chain D residue 469 ARG Chi-restraints excluded: chain D residue 493 ILE Chi-restraints excluded: chain D residue 499 GLN Chi-restraints excluded: chain D residue 513 ILE Chi-restraints excluded: chain D residue 563 HIS Chi-restraints excluded: chain D residue 616 LEU Chi-restraints excluded: chain D residue 622 CYS Chi-restraints excluded: chain D residue 647 THR Chi-restraints excluded: chain D residue 654 VAL Chi-restraints excluded: chain D residue 658 THR Chi-restraints excluded: chain D residue 666 SER Chi-restraints excluded: chain D residue 697 THR Chi-restraints excluded: chain D residue 717 ILE Chi-restraints excluded: chain D residue 742 THR Chi-restraints excluded: chain D residue 748 SER Chi-restraints excluded: chain D residue 784 HIS Chi-restraints excluded: chain D residue 790 CYS Chi-restraints excluded: chain D residue 810 LEU Chi-restraints excluded: chain D residue 813 ASP Chi-restraints excluded: chain D residue 818 LEU Chi-restraints excluded: chain D residue 840 LEU Chi-restraints excluded: chain D residue 854 VAL Chi-restraints excluded: chain D residue 859 LEU Chi-restraints excluded: chain D residue 905 VAL Chi-restraints excluded: chain D residue 949 ILE Chi-restraints excluded: chain D residue 951 HIS Chi-restraints excluded: chain D residue 954 LEU Chi-restraints excluded: chain D residue 985 LEU Chi-restraints excluded: chain D residue 987 CYS Chi-restraints excluded: chain D residue 989 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 416 random chunks: chunk 138 optimal weight: 2.9990 chunk 1 optimal weight: 0.0020 chunk 128 optimal weight: 0.1980 chunk 157 optimal weight: 1.9990 chunk 216 optimal weight: 9.9990 chunk 224 optimal weight: 3.9990 chunk 125 optimal weight: 2.9990 chunk 80 optimal weight: 6.9990 chunk 158 optimal weight: 0.5980 chunk 334 optimal weight: 3.9990 chunk 103 optimal weight: 6.9990 overall best weight: 1.1592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 41 GLN A 176 ASN ** C 928 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 = 0.3977 r_free = 0.3977 target = 0.143349 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.087196 restraints weight = 57245.069| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.089753 restraints weight = 32651.404| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.091067 restraints weight = 22613.637| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.091376 restraints weight = 17907.979| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.091505 restraints weight = 16986.183| |-----------------------------------------------------------------------------| r_work (final): 0.3177 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8291 moved from start: 0.2328 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 33956 Z= 0.134 Angle : 0.589 12.987 45932 Z= 0.293 Chirality : 0.043 0.235 5260 Planarity : 0.004 0.042 5818 Dihedral : 7.498 178.622 4544 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 9.98 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.29 % Favored : 93.59 % Rotamer: Outliers : 4.55 % Allowed : 27.59 % Favored : 67.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.02 % 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: -1.02 (0.13), residues: 4163 helix: 1.30 (0.15), residues: 1308 sheet: -1.63 (0.21), residues: 581 loop : -1.66 (0.12), residues: 2274 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 136 TYR 0.013 0.001 TYR R 65 PHE 0.023 0.001 PHE C 933 TRP 0.023 0.001 TRP D 857 HIS 0.006 0.001 HIS D 946 Details of bonding type rmsd covalent geometry : bond 0.00322 (33953) covalent geometry : angle 0.58676 (45926) SS BOND : bond 0.00344 ( 3) SS BOND : angle 4.37678 ( 6) hydrogen bonds : bond 0.03120 ( 1027) hydrogen bonds : angle 4.62093 ( 2991) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8326 Ramachandran restraints generated. 4163 Oldfield, 0 Emsley, 4163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8326 Ramachandran restraints generated. 4163 Oldfield, 0 Emsley, 4163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 402 residues out of total 3762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 171 poor density : 231 time to evaluate : 1.269 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 29 LYS cc_start: 0.7165 (tptm) cc_final: 0.6896 (tptp) REVERT: P 41 GLN cc_start: 0.7159 (tp40) cc_final: 0.6881 (tp-100) REVERT: P 68 THR cc_start: 0.7133 (OUTLIER) cc_final: 0.6609 (p) REVERT: R 74 PHE cc_start: 0.7972 (m-80) cc_final: 0.7486 (m-80) REVERT: A 362 SER cc_start: 0.8807 (OUTLIER) cc_final: 0.8394 (p) REVERT: A 379 ASP cc_start: 0.8831 (t0) cc_final: 0.8402 (t70) REVERT: A 404 LEU cc_start: 0.8760 (OUTLIER) cc_final: 0.8393 (mp) REVERT: A 521 THR cc_start: 0.8947 (OUTLIER) cc_final: 0.8673 (p) REVERT: A 614 GLN cc_start: 0.8432 (OUTLIER) cc_final: 0.7921 (mt0) REVERT: A 743 ILE cc_start: 0.7168 (OUTLIER) cc_final: 0.6907 (mp) REVERT: A 809 ILE cc_start: 0.7743 (OUTLIER) cc_final: 0.7139 (mp) REVERT: A 932 MET cc_start: 0.5425 (OUTLIER) cc_final: 0.4480 (pp-130) REVERT: B 97 ILE cc_start: 0.8403 (tp) cc_final: 0.8131 (pt) REVERT: B 469 ARG cc_start: 0.8869 (OUTLIER) cc_final: 0.7818 (mtm-85) REVERT: B 486 ARG cc_start: 0.8816 (OUTLIER) cc_final: 0.8474 (ttp80) REVERT: B 712 ASP cc_start: 0.7037 (OUTLIER) cc_final: 0.6723 (p0) REVERT: B 825 LEU cc_start: 0.5147 (OUTLIER) cc_final: 0.4546 (tt) REVERT: B 834 PHE cc_start: 0.6716 (OUTLIER) cc_final: 0.5495 (p90) REVERT: C 126 GLU cc_start: 0.7469 (OUTLIER) cc_final: 0.7000 (mp0) REVERT: C 362 SER cc_start: 0.8788 (OUTLIER) cc_final: 0.8345 (p) REVERT: C 713 ILE cc_start: 0.8493 (OUTLIER) cc_final: 0.8169 (pp) REVERT: C 734 LEU cc_start: 0.8362 (tt) cc_final: 0.7919 (pt) REVERT: C 833 TYR cc_start: 0.5654 (m-80) cc_final: 0.5397 (m-80) REVERT: C 894 MET cc_start: 0.4926 (tpp) cc_final: 0.4581 (tpt) REVERT: C 927 PHE cc_start: 0.4458 (OUTLIER) cc_final: 0.3738 (m-80) REVERT: D 60 LYS cc_start: 0.7896 (OUTLIER) cc_final: 0.7493 (ttmm) REVERT: D 76 ASN cc_start: 0.8504 (m-40) cc_final: 0.8213 (m-40) REVERT: D 469 ARG cc_start: 0.8873 (OUTLIER) cc_final: 0.8076 (mtm-85) REVERT: D 787 HIS cc_start: 0.7154 (m-70) cc_final: 0.6767 (m-70) REVERT: D 840 LEU cc_start: 0.3242 (OUTLIER) cc_final: 0.2780 (tt) REVERT: D 859 LEU cc_start: 0.5127 (OUTLIER) cc_final: 0.4830 (tt) REVERT: D 949 ILE cc_start: 0.6122 (OUTLIER) cc_final: 0.5680 (mt) outliers start: 171 outliers final: 137 residues processed: 381 average time/residue: 0.1950 time to fit residues: 125.8869 Evaluate side-chains 388 residues out of total 3762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 159 poor density : 229 time to evaluate : 1.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 28 ILE Chi-restraints excluded: chain P residue 68 THR Chi-restraints excluded: chain P residue 77 LEU Chi-restraints excluded: chain P residue 79 VAL Chi-restraints excluded: chain P residue 84 VAL Chi-restraints excluded: chain Q residue 28 ILE Chi-restraints excluded: chain Q residue 31 THR Chi-restraints excluded: chain Q residue 43 CYS Chi-restraints excluded: chain Q residue 71 ASP Chi-restraints excluded: chain Q residue 77 LEU Chi-restraints excluded: chain R residue 23 SER Chi-restraints excluded: chain R residue 28 ILE Chi-restraints excluded: chain R residue 68 THR Chi-restraints excluded: chain S residue 45 LEU Chi-restraints excluded: chain S residue 71 ASP Chi-restraints excluded: chain S residue 73 VAL Chi-restraints excluded: chain S residue 85 ASN Chi-restraints excluded: chain A residue 52 SER Chi-restraints excluded: chain A residue 54 ILE Chi-restraints excluded: chain A residue 79 SER Chi-restraints excluded: chain A residue 172 SER Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 178 THR Chi-restraints excluded: chain A residue 207 VAL Chi-restraints excluded: chain A residue 213 SER Chi-restraints excluded: chain A residue 229 SER Chi-restraints excluded: chain A residue 267 SER Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 362 SER Chi-restraints excluded: chain A residue 404 LEU Chi-restraints excluded: chain A residue 410 CYS Chi-restraints excluded: chain A residue 414 ILE Chi-restraints excluded: chain A residue 457 LEU Chi-restraints excluded: chain A residue 469 ARG Chi-restraints excluded: chain A residue 521 THR Chi-restraints excluded: chain A residue 557 VAL Chi-restraints excluded: chain A residue 563 HIS Chi-restraints excluded: chain A residue 580 THR Chi-restraints excluded: chain A residue 596 SER Chi-restraints excluded: chain A residue 614 GLN Chi-restraints excluded: chain A residue 647 THR Chi-restraints excluded: chain A residue 656 SER Chi-restraints excluded: chain A residue 690 LEU Chi-restraints excluded: chain A residue 713 ILE Chi-restraints excluded: chain A residue 729 GLU Chi-restraints excluded: chain A residue 733 SER Chi-restraints excluded: chain A residue 743 ILE Chi-restraints excluded: chain A residue 786 LEU Chi-restraints excluded: chain A residue 809 ILE Chi-restraints excluded: chain A residue 819 GLU Chi-restraints excluded: chain A residue 822 ASN Chi-restraints excluded: chain A residue 827 THR Chi-restraints excluded: chain A residue 932 MET Chi-restraints excluded: chain A residue 938 VAL Chi-restraints excluded: chain A residue 987 CYS Chi-restraints excluded: chain B residue 41 ILE Chi-restraints excluded: chain B residue 66 SER Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 136 ARG Chi-restraints excluded: chain B residue 182 ASP Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 209 MET Chi-restraints excluded: chain B residue 302 LEU Chi-restraints excluded: chain B residue 362 SER Chi-restraints excluded: chain B residue 398 THR Chi-restraints excluded: chain B residue 404 LEU Chi-restraints excluded: chain B residue 410 CYS Chi-restraints excluded: chain B residue 414 ILE Chi-restraints excluded: chain B residue 437 THR Chi-restraints excluded: chain B residue 469 ARG Chi-restraints excluded: chain B residue 486 ARG Chi-restraints excluded: chain B residue 493 ILE Chi-restraints excluded: chain B residue 508 VAL Chi-restraints excluded: chain B residue 513 ILE Chi-restraints excluded: chain B residue 519 GLU Chi-restraints excluded: chain B residue 616 LEU Chi-restraints excluded: chain B residue 647 THR Chi-restraints excluded: chain B residue 652 LEU Chi-restraints excluded: chain B residue 663 LEU Chi-restraints excluded: chain B residue 712 ASP Chi-restraints excluded: chain B residue 757 GLU Chi-restraints excluded: chain B residue 758 LEU Chi-restraints excluded: chain B residue 818 LEU Chi-restraints excluded: chain B residue 825 LEU Chi-restraints excluded: chain B residue 834 PHE Chi-restraints excluded: chain B residue 916 ILE Chi-restraints excluded: chain B residue 926 THR Chi-restraints excluded: chain B residue 942 LEU Chi-restraints excluded: chain B residue 972 MET Chi-restraints excluded: chain B residue 984 ILE Chi-restraints excluded: chain C residue 17 THR Chi-restraints excluded: chain C residue 23 ASP Chi-restraints excluded: chain C residue 126 GLU Chi-restraints excluded: chain C residue 178 THR Chi-restraints excluded: chain C residue 185 ASP Chi-restraints excluded: chain C residue 234 THR Chi-restraints excluded: chain C residue 267 SER Chi-restraints excluded: chain C residue 362 SER Chi-restraints excluded: chain C residue 391 SER Chi-restraints excluded: chain C residue 410 CYS Chi-restraints excluded: chain C residue 557 VAL Chi-restraints excluded: chain C residue 594 LEU Chi-restraints excluded: chain C residue 643 LEU Chi-restraints excluded: chain C residue 671 HIS Chi-restraints excluded: chain C residue 690 LEU Chi-restraints excluded: chain C residue 713 ILE Chi-restraints excluded: chain C residue 803 LEU Chi-restraints excluded: chain C residue 827 THR Chi-restraints excluded: chain C residue 829 ASN Chi-restraints excluded: chain C residue 926 THR Chi-restraints excluded: chain C residue 927 PHE Chi-restraints excluded: chain C residue 933 PHE Chi-restraints excluded: chain D residue 30 SER Chi-restraints excluded: chain D residue 60 LYS Chi-restraints excluded: chain D residue 63 ILE Chi-restraints excluded: chain D residue 71 VAL Chi-restraints excluded: chain D residue 89 GLU Chi-restraints excluded: chain D residue 102 MET Chi-restraints excluded: chain D residue 117 THR Chi-restraints excluded: chain D residue 172 SER Chi-restraints excluded: chain D residue 182 ASP Chi-restraints excluded: chain D residue 187 VAL Chi-restraints excluded: chain D residue 368 MET Chi-restraints excluded: chain D residue 369 ASP Chi-restraints excluded: chain D residue 396 SER Chi-restraints excluded: chain D residue 404 LEU Chi-restraints excluded: chain D residue 414 ILE Chi-restraints excluded: chain D residue 437 THR Chi-restraints excluded: chain D residue 469 ARG Chi-restraints excluded: chain D residue 493 ILE Chi-restraints excluded: chain D residue 499 GLN Chi-restraints excluded: chain D residue 513 ILE Chi-restraints excluded: chain D residue 616 LEU Chi-restraints excluded: chain D residue 622 CYS Chi-restraints excluded: chain D residue 647 THR Chi-restraints excluded: chain D residue 654 VAL Chi-restraints excluded: chain D residue 658 THR Chi-restraints excluded: chain D residue 666 SER Chi-restraints excluded: chain D residue 697 THR Chi-restraints excluded: chain D residue 717 ILE Chi-restraints excluded: chain D residue 723 THR Chi-restraints excluded: chain D residue 742 THR Chi-restraints excluded: chain D residue 748 SER Chi-restraints excluded: chain D residue 784 HIS Chi-restraints excluded: chain D residue 790 CYS Chi-restraints excluded: chain D residue 810 LEU Chi-restraints excluded: chain D residue 813 ASP Chi-restraints excluded: chain D residue 818 LEU Chi-restraints excluded: chain D residue 840 LEU Chi-restraints excluded: chain D residue 854 VAL Chi-restraints excluded: chain D residue 859 LEU Chi-restraints excluded: chain D residue 905 VAL Chi-restraints excluded: chain D residue 928 HIS Chi-restraints excluded: chain D residue 949 ILE Chi-restraints excluded: chain D residue 951 HIS Chi-restraints excluded: chain D residue 954 LEU Chi-restraints excluded: chain D residue 985 LEU Chi-restraints excluded: chain D residue 987 CYS Chi-restraints excluded: chain D residue 989 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 416 random chunks: chunk 106 optimal weight: 20.0000 chunk 261 optimal weight: 0.8980 chunk 415 optimal weight: 0.0870 chunk 290 optimal weight: 4.9990 chunk 215 optimal weight: 0.9990 chunk 389 optimal weight: 5.9990 chunk 199 optimal weight: 0.7980 chunk 103 optimal weight: 6.9990 chunk 59 optimal weight: 1.9990 chunk 328 optimal weight: 0.5980 chunk 352 optimal weight: 0.2980 overall best weight: 0.5358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 609 GLN A 899 HIS ** C 764 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 928 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 934 ASN D 20 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.144805 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.088325 restraints weight = 56961.836| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.091006 restraints weight = 31274.559| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 62)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.092788 restraints weight = 21085.780| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 52)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.093855 restraints weight = 16348.796| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.094407 restraints weight = 13989.037| |-----------------------------------------------------------------------------| r_work (final): 0.3239 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8215 moved from start: 0.2442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 33956 Z= 0.102 Angle : 0.575 13.013 45932 Z= 0.286 Chirality : 0.042 0.197 5260 Planarity : 0.003 0.043 5818 Dihedral : 7.357 179.789 4544 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 9.86 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.22 % Favored : 93.66 % Rotamer: Outliers : 3.83 % Allowed : 28.42 % Favored : 67.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.02 % 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: -0.92 (0.13), residues: 4163 helix: 1.42 (0.15), residues: 1307 sheet: -1.55 (0.22), residues: 573 loop : -1.63 (0.12), residues: 2283 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG Q 52 TYR 0.011 0.001 TYR C 833 PHE 0.018 0.001 PHE C 933 TRP 0.023 0.001 TRP D 857 HIS 0.006 0.001 HIS D 946 Details of bonding type rmsd covalent geometry : bond 0.00234 (33953) covalent geometry : angle 0.57349 (45926) SS BOND : bond 0.00272 ( 3) SS BOND : angle 4.16405 ( 6) hydrogen bonds : bond 0.02819 ( 1027) hydrogen bonds : angle 4.52293 ( 2991) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6642.74 seconds wall clock time: 115 minutes 46.29 seconds (6946.29 seconds total)