Starting phenix.real_space_refine on Mon Aug 25 15:46:25 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8w12_43714/08_2025/8w12_43714.cif Found real_map, /net/cci-nas-00/data/ceres_data/8w12_43714/08_2025/8w12_43714.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/8w12_43714/08_2025/8w12_43714.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8w12_43714/08_2025/8w12_43714.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8w12_43714/08_2025/8w12_43714.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8w12_43714/08_2025/8w12_43714.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= 0.008 sd= 0.071 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: 4 Type Number sf(0) Gaussians S 166 5.16 5 C 18652 2.51 5 N 5070 2.21 5 O 5360 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 53 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 29248 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 6889 Number of conformers: 1 Conformer: "" Number of residues, atoms: 852, 6889 Classifications: {'peptide': 852} Link IDs: {'PTRANS': 44, 'TRANS': 807} Chain breaks: 3 Chain: "B" Number of atoms: 6956 Number of conformers: 1 Conformer: "" Number of residues, atoms: 862, 6956 Classifications: {'peptide': 862} Link IDs: {'PTRANS': 43, 'TRANS': 818} Chain breaks: 2 Chain: "C" Number of atoms: 779 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 779 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 4, 'TRANS': 95} Chain breaks: 1 Chain: "D" Number of atoms: 6889 Number of conformers: 1 Conformer: "" Number of residues, atoms: 852, 6889 Classifications: {'peptide': 852} Link IDs: {'PTRANS': 44, 'TRANS': 807} Chain breaks: 3 Chain: "E" Number of atoms: 6956 Number of conformers: 1 Conformer: "" Number of residues, atoms: 862, 6956 Classifications: {'peptide': 862} Link IDs: {'PTRANS': 43, 'TRANS': 818} Chain breaks: 2 Chain: "F" Number of atoms: 779 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 779 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 4, 'TRANS': 95} Chain breaks: 1 Time building chain proxies: 5.70, per 1000 atoms: 0.19 Number of scatterers: 29248 At special positions: 0 Unit cell: (204.6, 168.3, 143, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 166 16.00 O 5360 8.00 N 5070 7.00 C 18652 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.77 Conformation dependent library (CDL) restraints added in 998.9 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 7184 Ramachandran restraints generated. 3592 Oldfield, 0 Emsley, 3592 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6908 Finding SS restraints... Secondary structure from input PDB file: 142 helices and 51 sheets defined 48.9% alpha, 11.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.91 Creating SS restraints... Processing helix chain 'A' and resid 27 through 48 Processing helix chain 'A' and resid 63 through 77 removed outlier: 3.580A pdb=" N ILE A 67 " --> pdb=" O ASP A 63 " (cutoff:3.500A) Processing helix chain 'A' and resid 106 through 113 removed outlier: 4.005A pdb=" N GLN A 113 " --> pdb=" O GLU A 109 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 141 removed outlier: 3.656A pdb=" N GLY A 141 " --> pdb=" O ILE A 137 " (cutoff:3.500A) Processing helix chain 'A' and resid 176 through 189 Processing helix chain 'A' and resid 210 through 228 removed outlier: 3.820A pdb=" N GLN A 228 " --> pdb=" O ILE A 224 " (cutoff:3.500A) Processing helix chain 'A' and resid 230 through 246 removed outlier: 3.608A pdb=" N ASN A 234 " --> pdb=" O GLN A 230 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 257 removed outlier: 3.911A pdb=" N LEU A 255 " --> pdb=" O SER A 251 " (cutoff:3.500A) Processing helix chain 'A' and resid 284 through 297 Processing helix chain 'A' and resid 306 through 317 removed outlier: 3.761A pdb=" N SER A 310 " --> pdb=" O ASN A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 322 through 327 removed outlier: 3.626A pdb=" N ALA A 325 " --> pdb=" O GLY A 322 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ILE A 326 " --> pdb=" O PRO A 323 " (cutoff:3.500A) Processing helix chain 'A' and resid 333 through 349 Processing helix chain 'A' and resid 366 through 381 removed outlier: 3.789A pdb=" N ARG A 370 " --> pdb=" O ASP A 366 " (cutoff:3.500A) Processing helix chain 'A' and resid 391 through 408 removed outlier: 3.612A pdb=" N ALA A 395 " --> pdb=" O THR A 391 " (cutoff:3.500A) Processing helix chain 'A' and resid 436 through 440 Processing helix chain 'A' and resid 494 through 507 Processing helix chain 'A' and resid 509 through 537 Proline residue: A 521 - end of helix Processing helix chain 'A' and resid 545 through 559 removed outlier: 4.735A pdb=" N LEU A 553 " --> pdb=" O PHE A 549 " (cutoff:3.500A) Proline residue: A 554 - end of helix Processing helix chain 'A' and resid 572 through 582 removed outlier: 3.744A pdb=" N LEU A 576 " --> pdb=" O SER A 572 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N TRP A 577 " --> pdb=" O TRP A 573 " (cutoff:3.500A) Processing helix chain 'A' and resid 595 through 624 removed outlier: 3.759A pdb=" N PHE A 624 " --> pdb=" O MET A 620 " (cutoff:3.500A) Processing helix chain 'A' and resid 632 through 643 removed outlier: 3.900A pdb=" N PHE A 636 " --> pdb=" O ARG A 632 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ASP A 643 " --> pdb=" O ALA A 639 " (cutoff:3.500A) Processing helix chain 'A' and resid 645 through 653 removed outlier: 3.659A pdb=" N LYS A 649 " --> pdb=" O PRO A 645 " (cutoff:3.500A) Processing helix chain 'A' and resid 663 through 672 removed outlier: 3.677A pdb=" N LEU A 672 " --> pdb=" O ARG A 668 " (cutoff:3.500A) Processing helix chain 'A' and resid 678 through 691 Processing helix chain 'A' and resid 692 through 693 No H-bonds generated for 'chain 'A' and resid 692 through 693' Processing helix chain 'A' and resid 694 through 697 Processing helix chain 'A' and resid 717 through 724 removed outlier: 3.501A pdb=" N PHE A 721 " --> pdb=" O ASP A 717 " (cutoff:3.500A) Processing helix chain 'A' and resid 745 through 756 Processing helix chain 'A' and resid 757 through 768 removed outlier: 3.598A pdb=" N ASP A 768 " --> pdb=" O ARG A 764 " (cutoff:3.500A) Processing helix chain 'A' and resid 791 through 796 removed outlier: 3.540A pdb=" N LEU A 795 " --> pdb=" O PRO A 791 " (cutoff:3.500A) Processing helix chain 'A' and resid 829 through 835 removed outlier: 3.905A pdb=" N ASN A 834 " --> pdb=" O GLU A 831 " (cutoff:3.500A) Processing helix chain 'A' and resid 864 through 868 removed outlier: 4.303A pdb=" N LEU A 867 " --> pdb=" O GLY A 864 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ALA A 868 " --> pdb=" O GLN A 865 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 864 through 868' Processing helix chain 'A' and resid 885 through 890 Processing helix chain 'B' and resid 30 through 49 removed outlier: 4.508A pdb=" N ASP B 49 " --> pdb=" O GLN B 45 " (cutoff:3.500A) Processing helix chain 'B' and resid 64 through 76 removed outlier: 3.740A pdb=" N ALA B 76 " --> pdb=" O LYS B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 106 through 115 removed outlier: 4.099A pdb=" N GLY B 115 " --> pdb=" O MET B 111 " (cutoff:3.500A) Processing helix chain 'B' and resid 122 through 142 removed outlier: 3.667A pdb=" N PHE B 126 " --> pdb=" O GLU B 122 " (cutoff:3.500A) Processing helix chain 'B' and resid 161 through 164 Processing helix chain 'B' and resid 171 through 175 Processing helix chain 'B' and resid 176 through 189 Processing helix chain 'B' and resid 210 through 226 removed outlier: 3.742A pdb=" N ALA B 226 " --> pdb=" O GLY B 222 " (cutoff:3.500A) Processing helix chain 'B' and resid 228 through 246 removed outlier: 3.520A pdb=" N LEU B 232 " --> pdb=" O GLN B 228 " (cutoff:3.500A) Processing helix chain 'B' and resid 254 through 260 Processing helix chain 'B' and resid 275 through 280 removed outlier: 3.507A pdb=" N TRP B 279 " --> pdb=" O PRO B 275 " (cutoff:3.500A) Processing helix chain 'B' and resid 284 through 297 Processing helix chain 'B' and resid 313 through 318 Processing helix chain 'B' and resid 322 through 328 Processing helix chain 'B' and resid 333 through 349 removed outlier: 3.792A pdb=" N PHE B 349 " --> pdb=" O LEU B 345 " (cutoff:3.500A) Processing helix chain 'B' and resid 366 through 381 removed outlier: 3.997A pdb=" N ARG B 370 " --> pdb=" O ASP B 366 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N LEU B 379 " --> pdb=" O VAL B 375 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N PHE B 381 " --> pdb=" O GLY B 377 " (cutoff:3.500A) Processing helix chain 'B' and resid 391 through 407 Processing helix chain 'B' and resid 437 through 440 Processing helix chain 'B' and resid 494 through 508 Processing helix chain 'B' and resid 509 through 537 Proline residue: B 521 - end of helix Processing helix chain 'B' and resid 545 through 559 removed outlier: 4.528A pdb=" N LEU B 553 " --> pdb=" O PHE B 549 " (cutoff:3.500A) Proline residue: B 554 - end of helix Processing helix chain 'B' and resid 573 through 581 removed outlier: 4.297A pdb=" N TRP B 577 " --> pdb=" O TRP B 573 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ASN B 581 " --> pdb=" O TRP B 577 " (cutoff:3.500A) Processing helix chain 'B' and resid 595 through 624 removed outlier: 3.597A pdb=" N PHE B 624 " --> pdb=" O MET B 620 " (cutoff:3.500A) Processing helix chain 'B' and resid 632 through 643 removed outlier: 3.662A pdb=" N ASP B 643 " --> pdb=" O ALA B 639 " (cutoff:3.500A) Processing helix chain 'B' and resid 645 through 659 removed outlier: 3.523A pdb=" N LYS B 649 " --> pdb=" O PRO B 645 " (cutoff:3.500A) Processing helix chain 'B' and resid 662 through 672 Processing helix chain 'B' and resid 678 through 691 Processing helix chain 'B' and resid 694 through 697 Processing helix chain 'B' and resid 717 through 725 Processing helix chain 'B' and resid 745 through 756 Processing helix chain 'B' and resid 757 through 768 removed outlier: 3.839A pdb=" N ASP B 768 " --> pdb=" O ARG B 764 " (cutoff:3.500A) Processing helix chain 'B' and resid 791 through 796 removed outlier: 3.595A pdb=" N LEU B 795 " --> pdb=" O PRO B 791 " (cutoff:3.500A) Processing helix chain 'B' and resid 830 through 839 Proline residue: B 836 - end of helix Processing helix chain 'B' and resid 864 through 866 No H-bonds generated for 'chain 'B' and resid 864 through 866' Processing helix chain 'B' and resid 885 through 893 removed outlier: 3.596A pdb=" N GLY B 893 " --> pdb=" O SER B 889 " (cutoff:3.500A) Processing helix chain 'C' and resid 9 through 16 Processing helix chain 'C' and resid 16 through 23 removed outlier: 3.556A pdb=" N LEU C 20 " --> pdb=" O SER C 16 " (cutoff:3.500A) Processing helix chain 'C' and resid 276 through 281 removed outlier: 3.601A pdb=" N VAL C 279 " --> pdb=" O ILE C 276 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N VAL C 280 " --> pdb=" O LYS C 277 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ARG C 281 " --> pdb=" O ASP C 278 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 276 through 281' Processing helix chain 'C' and resid 294 through 305 removed outlier: 3.789A pdb=" N VAL C 298 " --> pdb=" O HIS C 294 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N LYS C 305 " --> pdb=" O GLU C 301 " (cutoff:3.500A) Processing helix chain 'C' and resid 317 through 328 removed outlier: 4.351A pdb=" N GLU C 321 " --> pdb=" O ASP C 317 " (cutoff:3.500A) Processing helix chain 'D' and resid 27 through 48 Processing helix chain 'D' and resid 63 through 77 removed outlier: 3.542A pdb=" N ILE D 67 " --> pdb=" O ASP D 63 " (cutoff:3.500A) Processing helix chain 'D' and resid 106 through 112 removed outlier: 3.592A pdb=" N SER D 112 " --> pdb=" O TYR D 108 " (cutoff:3.500A) Processing helix chain 'D' and resid 122 through 141 removed outlier: 3.502A pdb=" N GLY D 141 " --> pdb=" O ILE D 137 " (cutoff:3.500A) Processing helix chain 'D' and resid 176 through 188 Processing helix chain 'D' and resid 210 through 228 removed outlier: 3.709A pdb=" N GLN D 228 " --> pdb=" O ILE D 224 " (cutoff:3.500A) Processing helix chain 'D' and resid 230 through 246 removed outlier: 3.509A pdb=" N ASN D 234 " --> pdb=" O GLN D 230 " (cutoff:3.500A) Processing helix chain 'D' and resid 252 through 257 Processing helix chain 'D' and resid 274 through 280 removed outlier: 4.478A pdb=" N VAL D 278 " --> pdb=" O ASN D 274 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N TRP D 279 " --> pdb=" O PRO D 275 " (cutoff:3.500A) Processing helix chain 'D' and resid 284 through 297 Processing helix chain 'D' and resid 306 through 317 removed outlier: 3.815A pdb=" N SER D 310 " --> pdb=" O ASN D 306 " (cutoff:3.500A) Processing helix chain 'D' and resid 322 through 326 removed outlier: 3.621A pdb=" N ALA D 325 " --> pdb=" O GLY D 322 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N ILE D 326 " --> pdb=" O PRO D 323 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 322 through 326' Processing helix chain 'D' and resid 333 through 349 removed outlier: 3.774A pdb=" N PHE D 349 " --> pdb=" O LEU D 345 " (cutoff:3.500A) Processing helix chain 'D' and resid 366 through 381 removed outlier: 3.790A pdb=" N ARG D 370 " --> pdb=" O ASP D 366 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N VAL D 375 " --> pdb=" O MET D 371 " (cutoff:3.500A) Processing helix chain 'D' and resid 391 through 409 removed outlier: 3.571A pdb=" N ALA D 395 " --> pdb=" O THR D 391 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N MET D 409 " --> pdb=" O TYR D 405 " (cutoff:3.500A) Processing helix chain 'D' and resid 436 through 440 Processing helix chain 'D' and resid 494 through 507 Processing helix chain 'D' and resid 509 through 537 Proline residue: D 521 - end of helix Processing helix chain 'D' and resid 545 through 559 removed outlier: 4.564A pdb=" N LEU D 553 " --> pdb=" O PHE D 549 " (cutoff:3.500A) Proline residue: D 554 - end of helix Processing helix chain 'D' and resid 573 through 582 removed outlier: 3.987A pdb=" N TRP D 577 " --> pdb=" O TRP D 573 " (cutoff:3.500A) Processing helix chain 'D' and resid 595 through 624 removed outlier: 3.779A pdb=" N ILE D 599 " --> pdb=" O VAL D 595 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N PHE D 624 " --> pdb=" O MET D 620 " (cutoff:3.500A) Processing helix chain 'D' and resid 632 through 643 removed outlier: 3.920A pdb=" N PHE D 636 " --> pdb=" O ARG D 632 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ASP D 643 " --> pdb=" O ALA D 639 " (cutoff:3.500A) Processing helix chain 'D' and resid 645 through 653 Processing helix chain 'D' and resid 663 through 672 removed outlier: 4.177A pdb=" N MET D 667 " --> pdb=" O ILE D 663 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LEU D 672 " --> pdb=" O ARG D 668 " (cutoff:3.500A) Processing helix chain 'D' and resid 678 through 691 Processing helix chain 'D' and resid 717 through 724 Processing helix chain 'D' and resid 745 through 756 Processing helix chain 'D' and resid 757 through 767 Processing helix chain 'D' and resid 791 through 796 Processing helix chain 'D' and resid 830 through 839 removed outlier: 4.115A pdb=" N ASN D 834 " --> pdb=" O GLU D 831 " (cutoff:3.500A) Proline residue: D 836 - end of helix Processing helix chain 'D' and resid 885 through 890 Processing helix chain 'E' and resid 30 through 49 removed outlier: 4.407A pdb=" N ASP E 49 " --> pdb=" O GLN E 45 " (cutoff:3.500A) Processing helix chain 'E' and resid 64 through 76 removed outlier: 3.773A pdb=" N ALA E 76 " --> pdb=" O LYS E 72 " (cutoff:3.500A) Processing helix chain 'E' and resid 106 through 113 removed outlier: 4.117A pdb=" N GLN E 113 " --> pdb=" O GLU E 109 " (cutoff:3.500A) Processing helix chain 'E' and resid 122 through 141 removed outlier: 3.690A pdb=" N PHE E 126 " --> pdb=" O GLU E 122 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N GLY E 141 " --> pdb=" O ILE E 137 " (cutoff:3.500A) Processing helix chain 'E' and resid 161 through 164 Processing helix chain 'E' and resid 171 through 175 Processing helix chain 'E' and resid 176 through 188 Processing helix chain 'E' and resid 210 through 226 removed outlier: 3.518A pdb=" N TYR E 214 " --> pdb=" O SER E 210 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N ALA E 226 " --> pdb=" O GLY E 222 " (cutoff:3.500A) Processing helix chain 'E' and resid 228 through 246 Processing helix chain 'E' and resid 254 through 259 removed outlier: 3.924A pdb=" N PHE E 258 " --> pdb=" O VAL E 254 " (cutoff:3.500A) Processing helix chain 'E' and resid 275 through 280 Processing helix chain 'E' and resid 284 through 297 removed outlier: 3.506A pdb=" N LEU E 297 " --> pdb=" O ILE E 293 " (cutoff:3.500A) Processing helix chain 'E' and resid 313 through 318 removed outlier: 3.895A pdb=" N ARG E 317 " --> pdb=" O THR E 313 " (cutoff:3.500A) Processing helix chain 'E' and resid 322 through 328 Processing helix chain 'E' and resid 333 through 349 removed outlier: 3.611A pdb=" N PHE E 349 " --> pdb=" O LEU E 345 " (cutoff:3.500A) Processing helix chain 'E' and resid 366 through 381 removed outlier: 4.059A pdb=" N ARG E 370 " --> pdb=" O ASP E 366 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N LEU E 379 " --> pdb=" O VAL E 375 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N PHE E 381 " --> pdb=" O GLY E 377 " (cutoff:3.500A) Processing helix chain 'E' and resid 391 through 407 removed outlier: 3.525A pdb=" N LEU E 407 " --> pdb=" O ASN E 403 " (cutoff:3.500A) Processing helix chain 'E' and resid 435 through 440 removed outlier: 3.754A pdb=" N VAL E 438 " --> pdb=" O ASP E 435 " (cutoff:3.500A) Processing helix chain 'E' and resid 494 through 508 Processing helix chain 'E' and resid 510 through 538 Proline residue: E 521 - end of helix removed outlier: 3.730A pdb=" N LEU E 538 " --> pdb=" O ILE E 534 " (cutoff:3.500A) Processing helix chain 'E' and resid 545 through 559 removed outlier: 4.556A pdb=" N LEU E 553 " --> pdb=" O PHE E 549 " (cutoff:3.500A) Proline residue: E 554 - end of helix Processing helix chain 'E' and resid 574 through 582 Processing helix chain 'E' and resid 595 through 624 Processing helix chain 'E' and resid 632 through 643 removed outlier: 3.628A pdb=" N ASP E 643 " --> pdb=" O ALA E 639 " (cutoff:3.500A) Processing helix chain 'E' and resid 645 through 659 Processing helix chain 'E' and resid 662 through 671 Processing helix chain 'E' and resid 678 through 691 Processing helix chain 'E' and resid 717 through 724 Processing helix chain 'E' and resid 745 through 756 Processing helix chain 'E' and resid 757 through 768 removed outlier: 3.761A pdb=" N ASP E 768 " --> pdb=" O ARG E 764 " (cutoff:3.500A) Processing helix chain 'E' and resid 791 through 796 removed outlier: 3.747A pdb=" N LEU E 795 " --> pdb=" O PRO E 791 " (cutoff:3.500A) Processing helix chain 'E' and resid 830 through 839 Proline residue: E 836 - end of helix Processing helix chain 'E' and resid 864 through 870 removed outlier: 5.418A pdb=" N LEU E 867 " --> pdb=" O GLY E 864 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N VAL E 869 " --> pdb=" O ILE E 866 " (cutoff:3.500A) Processing helix chain 'E' and resid 886 through 892 Processing helix chain 'F' and resid 9 through 23 removed outlier: 3.629A pdb=" N ILE F 13 " --> pdb=" O PRO F 9 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ARG F 15 " --> pdb=" O ASP F 11 " (cutoff:3.500A) removed outlier: 5.612A pdb=" N GLU F 18 " --> pdb=" O LYS F 14 " (cutoff:3.500A) removed outlier: 5.635A pdb=" N GLU F 19 " --> pdb=" O ARG F 15 " (cutoff:3.500A) Processing helix chain 'F' and resid 275 through 279 removed outlier: 3.547A pdb=" N VAL F 279 " --> pdb=" O ILE F 276 " (cutoff:3.500A) Processing helix chain 'F' and resid 294 through 305 removed outlier: 3.755A pdb=" N VAL F 298 " --> pdb=" O HIS F 294 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N LYS F 305 " --> pdb=" O GLU F 301 " (cutoff:3.500A) Processing helix chain 'F' and resid 317 through 329 Processing sheet with id=AA1, first strand: chain 'A' and resid 25 through 26 removed outlier: 7.082A pdb=" N THR A 299 " --> pdb=" O THR A 587 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 82 through 83 Processing sheet with id=AA3, first strand: chain 'A' and resid 90 through 94 Processing sheet with id=AA4, first strand: chain 'A' and resid 150 through 153 Processing sheet with id=AA5, first strand: chain 'A' and resid 193 through 196 Processing sheet with id=AA6, first strand: chain 'A' and resid 263 through 265 Processing sheet with id=AA7, first strand: chain 'A' and resid 353 through 357 Processing sheet with id=AA8, first strand: chain 'A' and resid 416 through 418 Processing sheet with id=AA9, first strand: chain 'A' and resid 699 through 700 removed outlier: 7.209A pdb=" N THR A 780 " --> pdb=" O THR A 821 " (cutoff:3.500A) removed outlier: 8.240A pdb=" N ILE A 823 " --> pdb=" O THR A 780 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N ARG A 782 " --> pdb=" O ILE A 823 " (cutoff:3.500A) removed outlier: 8.217A pdb=" N TYR A 825 " --> pdb=" O ARG A 782 " (cutoff:3.500A) removed outlier: 7.180A pdb=" N LYS A 784 " --> pdb=" O TYR A 825 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 741 through 744 removed outlier: 6.680A pdb=" N VAL A 742 " --> pdb=" O ARG A 773 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N VAL A 772 " --> pdb=" O MET A 705 " (cutoff:3.500A) removed outlier: 5.097A pdb=" N VAL A 703 " --> pdb=" O PHE A 774 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N MET A 848 " --> pdb=" O HIS A 706 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N ASP A 708 " --> pdb=" O TYR A 846 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N TYR A 846 " --> pdb=" O ASP A 708 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 800 through 804 Processing sheet with id=AB3, first strand: chain 'B' and resid 17 through 19 removed outlier: 3.542A pdb=" N VAL B 22 " --> pdb=" O GLU B 19 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 82 through 83 Processing sheet with id=AB5, first strand: chain 'B' and resid 90 through 93 Processing sheet with id=AB6, first strand: chain 'B' and resid 150 through 153 Processing sheet with id=AB7, first strand: chain 'B' and resid 203 through 207 Processing sheet with id=AB8, first strand: chain 'B' and resid 299 through 303 removed outlier: 5.852A pdb=" N GLU B 301 " --> pdb=" O PRO B 586 " (cutoff:3.500A) removed outlier: 7.917A pdb=" N ILE B 303 " --> pdb=" O PHE B 584 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N PHE B 584 " --> pdb=" O ILE B 303 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 353 through 357 Processing sheet with id=AC1, first strand: chain 'B' and resid 416 through 418 Processing sheet with id=AC2, first strand: chain 'B' and resid 457 through 458 Processing sheet with id=AC3, first strand: chain 'B' and resid 699 through 700 removed outlier: 3.638A pdb=" N THR B 700 " --> pdb=" O ARG B 779 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N THR B 780 " --> pdb=" O THR B 821 " (cutoff:3.500A) removed outlier: 7.821A pdb=" N ILE B 823 " --> pdb=" O THR B 780 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N ARG B 782 " --> pdb=" O ILE B 823 " (cutoff:3.500A) removed outlier: 8.102A pdb=" N TYR B 825 " --> pdb=" O ARG B 782 " (cutoff:3.500A) removed outlier: 7.146A pdb=" N LYS B 784 " --> pdb=" O TYR B 825 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 741 through 744 removed outlier: 3.616A pdb=" N VAL B 772 " --> pdb=" O MET B 705 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N VAL B 703 " --> pdb=" O PHE B 774 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N MET B 848 " --> pdb=" O HIS B 706 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N ASP B 708 " --> pdb=" O TYR B 846 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N TYR B 846 " --> pdb=" O ASP B 708 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 801 through 804 Processing sheet with id=AC6, first strand: chain 'C' and resid 26 through 28 removed outlier: 6.627A pdb=" N GLN C 26 " --> pdb=" O VAL C 272 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N MET C 5 " --> pdb=" O ALA C 284 " (cutoff:3.500A) removed outlier: 7.971A pdb=" N PHE C 286 " --> pdb=" O MET C 5 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N LEU C 7 " --> pdb=" O PHE C 286 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'D' and resid 25 through 26 Processing sheet with id=AC8, first strand: chain 'D' and resid 82 through 83 Processing sheet with id=AC9, first strand: chain 'D' and resid 90 through 94 Processing sheet with id=AD1, first strand: chain 'D' and resid 150 through 153 Processing sheet with id=AD2, first strand: chain 'D' and resid 193 through 197 Processing sheet with id=AD3, first strand: chain 'D' and resid 263 through 265 removed outlier: 3.565A pdb=" N MET D 884 " --> pdb=" O ILE D 264 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'D' and resid 353 through 357 Processing sheet with id=AD5, first strand: chain 'D' and resid 416 through 417 Processing sheet with id=AD6, first strand: chain 'D' and resid 457 through 458 Processing sheet with id=AD7, first strand: chain 'D' and resid 699 through 700 removed outlier: 3.550A pdb=" N THR D 700 " --> pdb=" O ARG D 779 " (cutoff:3.500A) removed outlier: 7.097A pdb=" N THR D 780 " --> pdb=" O THR D 821 " (cutoff:3.500A) removed outlier: 8.020A pdb=" N ILE D 823 " --> pdb=" O THR D 780 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N ARG D 782 " --> pdb=" O ILE D 823 " (cutoff:3.500A) removed outlier: 8.222A pdb=" N TYR D 825 " --> pdb=" O ARG D 782 " (cutoff:3.500A) removed outlier: 7.246A pdb=" N LYS D 784 " --> pdb=" O TYR D 825 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N TYR D 728 " --> pdb=" O LEU D 826 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'D' and resid 741 through 744 removed outlier: 6.643A pdb=" N VAL D 742 " --> pdb=" O ARG D 773 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N VAL D 772 " --> pdb=" O MET D 705 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N PHE D 774 " --> pdb=" O VAL D 703 " (cutoff:3.500A) removed outlier: 5.228A pdb=" N VAL D 703 " --> pdb=" O PHE D 774 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N MET D 848 " --> pdb=" O HIS D 706 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N ASP D 708 " --> pdb=" O TYR D 846 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N TYR D 846 " --> pdb=" O ASP D 708 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'D' and resid 801 through 803 Processing sheet with id=AE1, first strand: chain 'E' and resid 17 through 19 Processing sheet with id=AE2, first strand: chain 'E' and resid 82 through 83 Processing sheet with id=AE3, first strand: chain 'E' and resid 166 through 167 removed outlier: 6.983A pdb=" N PHE E 90 " --> pdb=" O GLU E 167 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'E' and resid 150 through 152 Processing sheet with id=AE5, first strand: chain 'E' and resid 203 through 207 Processing sheet with id=AE6, first strand: chain 'E' and resid 264 through 266 removed outlier: 6.413A pdb=" N ILE E 264 " --> pdb=" O MET E 884 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE6 Processing sheet with id=AE7, first strand: chain 'E' and resid 299 through 303 removed outlier: 7.108A pdb=" N THR E 299 " --> pdb=" O THR E 587 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ILE E 303 " --> pdb=" O SER E 583 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N SER E 583 " --> pdb=" O ILE E 303 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'E' and resid 353 through 357 removed outlier: 6.325A pdb=" N ILE E 354 " --> pdb=" O LEU E 569 " (cutoff:3.500A) removed outlier: 7.616A pdb=" N VAL E 571 " --> pdb=" O ILE E 354 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N ASP E 356 " --> pdb=" O VAL E 571 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE8 Processing sheet with id=AE9, first strand: chain 'E' and resid 416 through 418 Processing sheet with id=AF1, first strand: chain 'E' and resid 457 through 459 Processing sheet with id=AF2, first strand: chain 'E' and resid 699 through 700 removed outlier: 3.545A pdb=" N THR E 700 " --> pdb=" O ARG E 779 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N THR E 780 " --> pdb=" O THR E 821 " (cutoff:3.500A) removed outlier: 7.872A pdb=" N ILE E 823 " --> pdb=" O THR E 780 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N ARG E 782 " --> pdb=" O ILE E 823 " (cutoff:3.500A) removed outlier: 8.183A pdb=" N TYR E 825 " --> pdb=" O ARG E 782 " (cutoff:3.500A) removed outlier: 6.959A pdb=" N LYS E 784 " --> pdb=" O TYR E 825 " (cutoff:3.500A) removed outlier: 7.934A pdb=" N ILE E 827 " --> pdb=" O LYS E 784 " (cutoff:3.500A) removed outlier: 5.977A pdb=" N TYR E 786 " --> pdb=" O ILE E 827 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'E' and resid 741 through 744 removed outlier: 3.576A pdb=" N VAL E 772 " --> pdb=" O MET E 705 " (cutoff:3.500A) removed outlier: 5.057A pdb=" N VAL E 703 " --> pdb=" O PHE E 774 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N MET E 848 " --> pdb=" O HIS E 706 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N ASP E 708 " --> pdb=" O TYR E 846 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N TYR E 846 " --> pdb=" O ASP E 708 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'E' and resid 801 through 804 Processing sheet with id=AF5, first strand: chain 'F' and resid 5 through 7 removed outlier: 6.203A pdb=" N LEU F 6 " --> pdb=" O SER F 273 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N GLN F 26 " --> pdb=" O VAL F 272 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF5 Processing sheet with id=AF6, first strand: chain 'F' and resid 284 through 287 1288 hydrogen bonds defined for protein. 3657 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: 4.76 Time building geometry restraints manager: 2.43 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 9127 1.34 - 1.46: 5316 1.46 - 1.58: 15125 1.58 - 1.70: 0 1.70 - 1.82: 312 Bond restraints: 29880 Sorted by residual: bond pdb=" N THR E 421 " pdb=" CA THR E 421 " ideal model delta sigma weight residual 1.453 1.491 -0.038 1.37e-02 5.33e+03 7.73e+00 bond pdb=" C ALA F 260 " pdb=" N PRO F 261 " ideal model delta sigma weight residual 1.334 1.361 -0.027 1.11e-02 8.12e+03 6.09e+00 bond pdb=" N GLU A 160 " pdb=" CA GLU A 160 " ideal model delta sigma weight residual 1.456 1.487 -0.031 1.53e-02 4.27e+03 4.17e+00 bond pdb=" N GLY E 422 " pdb=" CA GLY E 422 " ideal model delta sigma weight residual 1.449 1.479 -0.029 1.45e-02 4.76e+03 4.11e+00 bond pdb=" CB PRO D 275 " pdb=" CG PRO D 275 " ideal model delta sigma weight residual 1.492 1.572 -0.080 5.00e-02 4.00e+02 2.59e+00 ... (remaining 29875 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.68: 40041 2.68 - 5.35: 434 5.35 - 8.03: 59 8.03 - 10.70: 14 10.70 - 13.38: 2 Bond angle restraints: 40550 Sorted by residual: angle pdb=" N PRO A 161 " pdb=" CA PRO A 161 " pdb=" C PRO A 161 " ideal model delta sigma weight residual 112.47 121.49 -9.02 2.06e+00 2.36e-01 1.92e+01 angle pdb=" CB LYS F 296 " pdb=" CG LYS F 296 " pdb=" CD LYS F 296 " ideal model delta sigma weight residual 111.30 120.93 -9.63 2.30e+00 1.89e-01 1.75e+01 angle pdb=" CA LEU E 239 " pdb=" CB LEU E 239 " pdb=" CG LEU E 239 " ideal model delta sigma weight residual 116.30 129.68 -13.38 3.50e+00 8.16e-02 1.46e+01 angle pdb=" CB LYS C 296 " pdb=" CG LYS C 296 " pdb=" CD LYS C 296 " ideal model delta sigma weight residual 111.30 119.88 -8.58 2.30e+00 1.89e-01 1.39e+01 angle pdb=" CA THR E 421 " pdb=" C THR E 421 " pdb=" O THR E 421 " ideal model delta sigma weight residual 121.99 117.84 4.15 1.14e+00 7.69e-01 1.32e+01 ... (remaining 40545 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 16191 17.94 - 35.89: 1592 35.89 - 53.83: 236 53.83 - 71.77: 46 71.77 - 89.72: 37 Dihedral angle restraints: 18102 sinusoidal: 7426 harmonic: 10676 Sorted by residual: dihedral pdb=" CA LEU A 379 " pdb=" C LEU A 379 " pdb=" N LEU A 380 " pdb=" CA LEU A 380 " ideal model delta harmonic sigma weight residual -180.00 -160.08 -19.92 0 5.00e+00 4.00e-02 1.59e+01 dihedral pdb=" CA GLN A 230 " pdb=" C GLN A 230 " pdb=" N GLU A 231 " pdb=" CA GLU A 231 " ideal model delta harmonic sigma weight residual -180.00 -161.19 -18.81 0 5.00e+00 4.00e-02 1.42e+01 dihedral pdb=" CA PRO B 645 " pdb=" C PRO B 645 " pdb=" N GLU B 646 " pdb=" CA GLU B 646 " ideal model delta harmonic sigma weight residual -180.00 -162.16 -17.84 0 5.00e+00 4.00e-02 1.27e+01 ... (remaining 18099 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.071: 3978 0.071 - 0.143: 543 0.143 - 0.214: 17 0.214 - 0.286: 3 0.286 - 0.357: 1 Chirality restraints: 4542 Sorted by residual: chirality pdb=" CB ILE D 326 " pdb=" CA ILE D 326 " pdb=" CG1 ILE D 326 " pdb=" CG2 ILE D 326 " both_signs ideal model delta sigma weight residual False 2.64 2.29 0.36 2.00e-01 2.50e+01 3.18e+00 chirality pdb=" CB THR A 835 " pdb=" CA THR A 835 " pdb=" OG1 THR A 835 " pdb=" CG2 THR A 835 " both_signs ideal model delta sigma weight residual False 2.55 2.30 0.25 2.00e-01 2.50e+01 1.54e+00 chirality pdb=" CG LEU E 239 " pdb=" CB LEU E 239 " pdb=" CD1 LEU E 239 " pdb=" CD2 LEU E 239 " both_signs ideal model delta sigma weight residual False -2.59 -2.35 -0.24 2.00e-01 2.50e+01 1.43e+00 ... (remaining 4539 not shown) Planarity restraints: 5250 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR D 331 " -0.065 5.00e-02 4.00e+02 9.80e-02 1.54e+01 pdb=" N PRO D 332 " 0.170 5.00e-02 4.00e+02 pdb=" CA PRO D 332 " -0.051 5.00e-02 4.00e+02 pdb=" CD PRO D 332 " -0.053 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 637 " 0.014 2.00e-02 2.50e+03 1.33e-02 4.44e+00 pdb=" CG TRP A 637 " -0.035 2.00e-02 2.50e+03 pdb=" CD1 TRP A 637 " 0.018 2.00e-02 2.50e+03 pdb=" CD2 TRP A 637 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP A 637 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP A 637 " -0.005 2.00e-02 2.50e+03 pdb=" CE3 TRP A 637 " 0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 637 " 0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 637 " 0.004 2.00e-02 2.50e+03 pdb=" CH2 TRP A 637 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG E 502 " -0.164 9.50e-02 1.11e+02 7.38e-02 4.12e+00 pdb=" NE ARG E 502 " 0.015 2.00e-02 2.50e+03 pdb=" CZ ARG E 502 " -0.014 2.00e-02 2.50e+03 pdb=" NH1 ARG E 502 " 0.007 2.00e-02 2.50e+03 pdb=" NH2 ARG E 502 " -0.001 2.00e-02 2.50e+03 ... (remaining 5247 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 3427 2.76 - 3.29: 29022 3.29 - 3.83: 46718 3.83 - 4.36: 50314 4.36 - 4.90: 88616 Nonbonded interactions: 218097 Sorted by model distance: nonbonded pdb=" O PHE B 324 " pdb=" OG1 THR B 328 " model vdw 2.219 3.040 nonbonded pdb=" OG SER D 251 " pdb=" OE1 GLU D 253 " model vdw 2.219 3.040 nonbonded pdb=" OD2 ASP B 885 " pdb=" OG1 THR B 887 " model vdw 2.220 3.040 nonbonded pdb=" OH TYR A 812 " pdb=" OG SER E 838 " model vdw 2.226 3.040 nonbonded pdb=" OG SER B 838 " pdb=" OH TYR D 812 " model vdw 2.244 3.040 ... (remaining 218092 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: 0.03 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 24 through 49 or resid 63 through 480 or resid 489 through \ 892)) selection = (chain 'B' and (resid 24 through 655 or resid 662 through 806 or resid 811 throu \ gh 892)) selection = (chain 'D' and (resid 24 through 49 or resid 63 through 480 or resid 489 through \ 892)) selection = (chain 'E' and (resid 24 through 655 or resid 662 through 806 or resid 811 throu \ gh 892)) } ncs_group { reference = chain 'C' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.920 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: 0.010 Extract box with map and model: 0.300 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 21.970 Find NCS groups from input model: 0.700 Set up NCS constraints: 0.060 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:1.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.360 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8006 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 : 0.003 0.080 29880 Z= 0.140 Angle : 0.701 13.380 40550 Z= 0.351 Chirality : 0.046 0.357 4542 Planarity : 0.005 0.098 5250 Dihedral : 14.489 89.716 11194 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.98 % Favored : 96.99 % Rotamer: Outliers : 0.00 % Allowed : 0.41 % Favored : 99.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.33 (0.14), residues: 3592 helix: 0.76 (0.13), residues: 1568 sheet: -0.33 (0.27), residues: 370 loop : -1.13 (0.15), residues: 1654 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG E 502 TYR 0.024 0.001 TYR E 746 PHE 0.029 0.001 PHE A 527 TRP 0.035 0.001 TRP A 637 HIS 0.011 0.001 HIS B 244 Details of bonding type rmsd covalent geometry : bond 0.00292 (29880) covalent geometry : angle 0.70079 (40550) hydrogen bonds : bond 0.14829 ( 1288) hydrogen bonds : angle 5.28216 ( 3657) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7184 Ramachandran restraints generated. 3592 Oldfield, 0 Emsley, 3592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7184 Ramachandran restraints generated. 3592 Oldfield, 0 Emsley, 3592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 859 residues out of total 3188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 859 time to evaluate : 0.738 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 110 GLU cc_start: 0.7490 (pp20) cc_final: 0.7242 (pp20) REVERT: A 111 MET cc_start: 0.8786 (tmm) cc_final: 0.8282 (tmm) REVERT: A 248 ILE cc_start: 0.8781 (tp) cc_final: 0.8567 (pt) REVERT: A 257 ASP cc_start: 0.7886 (m-30) cc_final: 0.7650 (m-30) REVERT: A 371 MET cc_start: 0.6593 (mtm) cc_final: 0.6368 (mtt) REVERT: A 381 PHE cc_start: 0.8731 (m-10) cc_final: 0.8487 (m-10) REVERT: A 439 PHE cc_start: 0.7656 (t80) cc_final: 0.7339 (t80) REVERT: A 501 LEU cc_start: 0.8556 (tp) cc_final: 0.8277 (tp) REVERT: A 552 LEU cc_start: 0.8581 (tt) cc_final: 0.8300 (tp) REVERT: A 636 PHE cc_start: 0.7689 (p90) cc_final: 0.7445 (p90) REVERT: A 685 GLU cc_start: 0.8095 (tm-30) cc_final: 0.7862 (tm-30) REVERT: A 709 MET cc_start: 0.8548 (pmm) cc_final: 0.8315 (pmm) REVERT: B 18 LEU cc_start: 0.8771 (tt) cc_final: 0.8453 (tt) REVERT: B 44 ARG cc_start: 0.7944 (ttp-170) cc_final: 0.7708 (ttm170) REVERT: B 113 GLN cc_start: 0.8447 (mm110) cc_final: 0.8244 (mp10) REVERT: B 339 ASP cc_start: 0.8097 (m-30) cc_final: 0.7785 (m-30) REVERT: B 433 GLN cc_start: 0.8252 (mp10) cc_final: 0.7993 (mp10) REVERT: B 503 MET cc_start: 0.8020 (tmm) cc_final: 0.7777 (tmm) REVERT: B 519 MET cc_start: 0.8743 (mmm) cc_final: 0.8424 (mmm) REVERT: B 643 ASP cc_start: 0.8168 (t0) cc_final: 0.7945 (t0) REVERT: B 652 MET cc_start: 0.9120 (tpp) cc_final: 0.8912 (mmp) REVERT: B 667 MET cc_start: 0.8010 (mmm) cc_final: 0.7159 (mmm) REVERT: B 731 MET cc_start: 0.8354 (tpp) cc_final: 0.8110 (tpp) REVERT: D 99 ASP cc_start: 0.8240 (p0) cc_final: 0.7850 (p0) REVERT: D 111 MET cc_start: 0.8557 (tpp) cc_final: 0.8222 (tpp) REVERT: D 161 PRO cc_start: 0.9144 (Cg_exo) cc_final: 0.8939 (Cg_endo) REVERT: D 169 LYS cc_start: 0.8401 (mmmm) cc_final: 0.7947 (mmmt) REVERT: D 209 CYS cc_start: 0.8078 (t) cc_final: 0.7842 (t) REVERT: D 253 GLU cc_start: 0.7722 (mp0) cc_final: 0.7473 (mp0) REVERT: D 257 ASP cc_start: 0.7850 (m-30) cc_final: 0.7501 (m-30) REVERT: D 536 GLU cc_start: 0.7876 (tp30) cc_final: 0.7646 (tp30) REVERT: D 620 MET cc_start: 0.8237 (tpp) cc_final: 0.7993 (tpp) REVERT: D 642 ASN cc_start: 0.8586 (m110) cc_final: 0.8311 (m110) REVERT: D 684 GLU cc_start: 0.8027 (mm-30) cc_final: 0.7790 (tp30) REVERT: D 708 ASP cc_start: 0.8413 (p0) cc_final: 0.8196 (p0) REVERT: E 44 ARG cc_start: 0.8047 (ttp-170) cc_final: 0.7840 (ptm160) REVERT: E 70 ASP cc_start: 0.7691 (t70) cc_final: 0.7319 (t0) REVERT: E 111 MET cc_start: 0.9027 (tmm) cc_final: 0.8413 (tmm) REVERT: E 113 GLN cc_start: 0.8447 (mp10) cc_final: 0.8153 (mp10) REVERT: E 339 ASP cc_start: 0.8248 (m-30) cc_final: 0.7820 (m-30) REVERT: E 411 ASN cc_start: 0.8440 (t0) cc_final: 0.8189 (t0) REVERT: E 498 ASN cc_start: 0.8375 (t0) cc_final: 0.8150 (t0) REVERT: E 600 GLU cc_start: 0.7779 (pt0) cc_final: 0.7530 (pt0) REVERT: E 642 ASN cc_start: 0.8471 (t0) cc_final: 0.8242 (t0) REVERT: E 667 MET cc_start: 0.8056 (mmm) cc_final: 0.7092 (mmm) outliers start: 0 outliers final: 0 residues processed: 859 average time/residue: 0.1752 time to fit residues: 236.4549 Evaluate side-chains 770 residues out of total 3188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 770 time to evaluate : 1.118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 362 random chunks: chunk 197 optimal weight: 8.9990 chunk 215 optimal weight: 4.9990 chunk 20 optimal weight: 0.8980 chunk 132 optimal weight: 5.9990 chunk 261 optimal weight: 0.1980 chunk 248 optimal weight: 9.9990 chunk 207 optimal weight: 0.8980 chunk 155 optimal weight: 8.9990 chunk 244 optimal weight: 0.7980 chunk 183 optimal weight: 0.2980 chunk 298 optimal weight: 3.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 467 HIS ** E 523 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 = 0.3466 r_free = 0.3466 target = 0.095727 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.081393 restraints weight = 70245.562| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.084147 restraints weight = 32197.621| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.085910 restraints weight = 18570.623| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.087079 restraints weight = 12472.828| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.087854 restraints weight = 9404.622| |-----------------------------------------------------------------------------| r_work (final): 0.3330 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8001 moved from start: 0.1327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 29880 Z= 0.113 Angle : 0.599 12.375 40550 Z= 0.298 Chirality : 0.043 0.182 4542 Planarity : 0.004 0.063 5250 Dihedral : 3.951 17.989 4040 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 1.44 % Allowed : 10.98 % Favored : 87.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.12 (0.14), residues: 3592 helix: 1.23 (0.13), residues: 1572 sheet: -0.20 (0.27), residues: 362 loop : -0.98 (0.15), residues: 1658 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 668 TYR 0.021 0.001 TYR B 410 PHE 0.025 0.001 PHE E 694 TRP 0.026 0.001 TRP A 637 HIS 0.011 0.001 HIS D 378 Details of bonding type rmsd covalent geometry : bond 0.00252 (29880) covalent geometry : angle 0.59899 (40550) hydrogen bonds : bond 0.04047 ( 1288) hydrogen bonds : angle 4.06675 ( 3657) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7184 Ramachandran restraints generated. 3592 Oldfield, 0 Emsley, 3592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7184 Ramachandran restraints generated. 3592 Oldfield, 0 Emsley, 3592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 832 residues out of total 3188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 786 time to evaluate : 1.128 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: A 66 LYS cc_start: 0.7919 (tptm) cc_final: 0.7596 (tptm) REVERT: A 110 GLU cc_start: 0.7504 (pp20) cc_final: 0.7133 (tm-30) REVERT: A 111 MET cc_start: 0.8878 (tmm) cc_final: 0.8301 (tmm) REVERT: A 160 GLU cc_start: 0.8344 (mm-30) cc_final: 0.8064 (mm-30) REVERT: A 248 ILE cc_start: 0.8838 (tp) cc_final: 0.8569 (pt) REVERT: A 257 ASP cc_start: 0.8052 (m-30) cc_final: 0.7776 (m-30) REVERT: A 344 TYR cc_start: 0.8827 (OUTLIER) cc_final: 0.8079 (t80) REVERT: A 381 PHE cc_start: 0.8435 (m-10) cc_final: 0.8002 (m-80) REVERT: A 641 LEU cc_start: 0.8424 (OUTLIER) cc_final: 0.7789 (mt) REVERT: A 664 ARG cc_start: 0.7071 (ptt-90) cc_final: 0.6382 (ttp-110) REVERT: A 668 ARG cc_start: 0.8351 (mtm-85) cc_final: 0.7946 (mtm-85) REVERT: A 685 GLU cc_start: 0.8123 (tm-30) cc_final: 0.7889 (tm-30) REVERT: A 766 MET cc_start: 0.7873 (mmm) cc_final: 0.7630 (tpp) REVERT: A 831 GLU cc_start: 0.8136 (tm-30) cc_final: 0.7933 (tm-30) REVERT: B 339 ASP cc_start: 0.8179 (m-30) cc_final: 0.7865 (m-30) REVERT: B 345 LEU cc_start: 0.9139 (tp) cc_final: 0.8901 (tt) REVERT: B 371 MET cc_start: 0.8470 (mtp) cc_final: 0.8266 (mtp) REVERT: B 433 GLN cc_start: 0.8135 (mp10) cc_final: 0.7880 (mp10) REVERT: B 643 ASP cc_start: 0.8138 (t0) cc_final: 0.7891 (t0) REVERT: B 666 MET cc_start: 0.8323 (tpp) cc_final: 0.8032 (tpt) REVERT: B 667 MET cc_start: 0.7999 (mmm) cc_final: 0.7497 (mmm) REVERT: B 685 GLU cc_start: 0.8219 (tm-30) cc_final: 0.7955 (tm-30) REVERT: B 686 GLU cc_start: 0.7887 (tp30) cc_final: 0.7645 (tp30) REVERT: B 724 GLU cc_start: 0.8286 (mm-30) cc_final: 0.7886 (mm-30) REVERT: D 44 ARG cc_start: 0.7857 (mtt180) cc_final: 0.7302 (mtt180) REVERT: D 66 LYS cc_start: 0.8299 (tptm) cc_final: 0.8048 (tptm) REVERT: D 99 ASP cc_start: 0.8262 (p0) cc_final: 0.7851 (p0) REVERT: D 111 MET cc_start: 0.8706 (tpp) cc_final: 0.8318 (tpp) REVERT: D 169 LYS cc_start: 0.8447 (mmmm) cc_final: 0.7845 (mmtt) REVERT: D 201 ASP cc_start: 0.7500 (p0) cc_final: 0.7047 (p0) REVERT: D 209 CYS cc_start: 0.7962 (t) cc_final: 0.7680 (t) REVERT: D 253 GLU cc_start: 0.7983 (mp0) cc_final: 0.7634 (mp0) REVERT: D 257 ASP cc_start: 0.7813 (m-30) cc_final: 0.7436 (m-30) REVERT: D 342 LYS cc_start: 0.8491 (ptpp) cc_final: 0.8163 (ptpp) REVERT: D 344 TYR cc_start: 0.8633 (OUTLIER) cc_final: 0.7772 (t80) REVERT: D 348 MET cc_start: 0.8085 (tpp) cc_final: 0.7608 (tpp) REVERT: D 536 GLU cc_start: 0.7772 (tp30) cc_final: 0.7507 (tp30) REVERT: D 610 MET cc_start: 0.8234 (mmm) cc_final: 0.7806 (mtt) REVERT: D 620 MET cc_start: 0.8194 (tpp) cc_final: 0.7895 (tpp) REVERT: D 642 ASN cc_start: 0.8677 (m110) cc_final: 0.8273 (m110) REVERT: D 684 GLU cc_start: 0.8232 (mm-30) cc_final: 0.7996 (tp30) REVERT: D 773 ARG cc_start: 0.8415 (ttp80) cc_final: 0.8206 (ttp80) REVERT: D 792 ASP cc_start: 0.7497 (p0) cc_final: 0.7223 (p0) REVERT: E 44 ARG cc_start: 0.8108 (ttp-170) cc_final: 0.7823 (ptm160) REVERT: E 81 LYS cc_start: 0.7962 (ptmm) cc_final: 0.7721 (ptmm) REVERT: E 111 MET cc_start: 0.9097 (tmm) cc_final: 0.8646 (tmm) REVERT: E 339 ASP cc_start: 0.8240 (m-30) cc_final: 0.7748 (m-30) REVERT: E 423 GLU cc_start: 0.7560 (mp0) cc_final: 0.7335 (mp0) REVERT: E 498 ASN cc_start: 0.8452 (t0) cc_final: 0.8209 (t0) REVERT: E 503 MET cc_start: 0.8351 (tpp) cc_final: 0.7985 (tpp) REVERT: E 600 GLU cc_start: 0.7890 (pt0) cc_final: 0.7683 (pt0) REVERT: E 642 ASN cc_start: 0.8586 (t0) cc_final: 0.8309 (t0) REVERT: E 667 MET cc_start: 0.8052 (mmm) cc_final: 0.7727 (mmm) REVERT: E 671 MET cc_start: 0.7888 (mpp) cc_final: 0.7674 (mpp) REVERT: F 26 GLN cc_start: 0.7230 (mm-40) cc_final: 0.6774 (mm-40) outliers start: 46 outliers final: 28 residues processed: 799 average time/residue: 0.1741 time to fit residues: 218.6550 Evaluate side-chains 794 residues out of total 3188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 763 time to evaluate : 0.959 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 ILE Chi-restraints excluded: chain A residue 61 VAL Chi-restraints excluded: chain A residue 277 VAL Chi-restraints excluded: chain A residue 340 VAL Chi-restraints excluded: chain A residue 344 TYR Chi-restraints excluded: chain A residue 379 LEU Chi-restraints excluded: chain A residue 477 ILE Chi-restraints excluded: chain A residue 527 PHE Chi-restraints excluded: chain A residue 641 LEU Chi-restraints excluded: chain A residue 674 SER Chi-restraints excluded: chain A residue 732 LEU Chi-restraints excluded: chain B residue 94 VAL Chi-restraints excluded: chain B residue 187 LEU Chi-restraints excluded: chain B residue 435 ASP Chi-restraints excluded: chain B residue 655 SER Chi-restraints excluded: chain B residue 815 ILE Chi-restraints excluded: chain B residue 887 THR Chi-restraints excluded: chain D residue 94 VAL Chi-restraints excluded: chain D residue 97 SER Chi-restraints excluded: chain D residue 344 TYR Chi-restraints excluded: chain D residue 357 LEU Chi-restraints excluded: chain D residue 617 LEU Chi-restraints excluded: chain D residue 795 LEU Chi-restraints excluded: chain E residue 265 TRP Chi-restraints excluded: chain E residue 477 ILE Chi-restraints excluded: chain E residue 575 SER Chi-restraints excluded: chain E residue 655 SER Chi-restraints excluded: chain E residue 886 ILE Chi-restraints excluded: chain F residue 17 SER Chi-restraints excluded: chain F residue 276 ILE Chi-restraints excluded: chain F residue 318 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 362 random chunks: chunk 197 optimal weight: 0.9980 chunk 160 optimal weight: 8.9990 chunk 55 optimal weight: 5.9990 chunk 346 optimal weight: 6.9990 chunk 168 optimal weight: 1.9990 chunk 224 optimal weight: 3.9990 chunk 359 optimal weight: 4.9990 chunk 207 optimal weight: 1.9990 chunk 331 optimal weight: 2.9990 chunk 298 optimal weight: 1.9990 chunk 361 optimal weight: 8.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 113 GLN A 417 ASN D 531 ASN D 642 ASN E 467 HIS E 523 HIS E 539 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.091122 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.076916 restraints weight = 70196.440| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.079564 restraints weight = 32688.206| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.081250 restraints weight = 19053.372| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.082377 restraints weight = 12933.760| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.083129 restraints weight = 9825.327| |-----------------------------------------------------------------------------| r_work (final): 0.3240 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8098 moved from start: 0.1848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 29880 Z= 0.175 Angle : 0.627 10.923 40550 Z= 0.317 Chirality : 0.044 0.184 4542 Planarity : 0.005 0.058 5250 Dihedral : 4.124 21.210 4040 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 2.57 % Allowed : 14.84 % Favored : 82.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.24 (0.14), residues: 3592 helix: 1.38 (0.13), residues: 1582 sheet: -0.31 (0.27), residues: 382 loop : -0.94 (0.15), residues: 1628 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 308 TYR 0.021 0.002 TYR E 17 PHE 0.029 0.002 PHE D 324 TRP 0.025 0.002 TRP A 637 HIS 0.009 0.001 HIS A 378 Details of bonding type rmsd covalent geometry : bond 0.00405 (29880) covalent geometry : angle 0.62697 (40550) hydrogen bonds : bond 0.04777 ( 1288) hydrogen bonds : angle 3.96712 ( 3657) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7184 Ramachandran restraints generated. 3592 Oldfield, 0 Emsley, 3592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7184 Ramachandran restraints generated. 3592 Oldfield, 0 Emsley, 3592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 859 residues out of total 3188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 777 time to evaluate : 0.938 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 LYS cc_start: 0.8059 (tptm) cc_final: 0.7762 (tptm) REVERT: A 110 GLU cc_start: 0.7562 (pp20) cc_final: 0.7311 (tm-30) REVERT: A 111 MET cc_start: 0.8916 (tmm) cc_final: 0.8207 (tmm) REVERT: A 253 GLU cc_start: 0.8340 (mp0) cc_final: 0.7835 (mp0) REVERT: A 257 ASP cc_start: 0.8175 (m-30) cc_final: 0.7896 (m-30) REVERT: A 381 PHE cc_start: 0.8298 (m-10) cc_final: 0.7763 (m-10) REVERT: A 501 LEU cc_start: 0.8652 (tp) cc_final: 0.8391 (tp) REVERT: A 526 ARG cc_start: 0.7899 (ttp80) cc_final: 0.7605 (ttp80) REVERT: A 578 PHE cc_start: 0.8085 (m-80) cc_final: 0.7329 (m-80) REVERT: A 582 ARG cc_start: 0.8324 (mmp80) cc_final: 0.7861 (mmp-170) REVERT: A 591 GLU cc_start: 0.7640 (pp20) cc_final: 0.7433 (tm-30) REVERT: A 641 LEU cc_start: 0.8662 (OUTLIER) cc_final: 0.8404 (mm) REVERT: A 664 ARG cc_start: 0.7095 (ptt-90) cc_final: 0.6394 (ttp-110) REVERT: A 668 ARG cc_start: 0.8372 (mtm-85) cc_final: 0.8065 (mtm-85) REVERT: A 685 GLU cc_start: 0.8193 (tm-30) cc_final: 0.7984 (tm-30) REVERT: B 36 LEU cc_start: 0.8943 (OUTLIER) cc_final: 0.8704 (mm) REVERT: B 339 ASP cc_start: 0.8178 (m-30) cc_final: 0.7853 (m-30) REVERT: B 355 LEU cc_start: 0.8014 (mm) cc_final: 0.7777 (mm) REVERT: B 454 THR cc_start: 0.8891 (p) cc_final: 0.8629 (p) REVERT: B 643 ASP cc_start: 0.8310 (t0) cc_final: 0.7980 (t0) REVERT: B 666 MET cc_start: 0.8375 (tpp) cc_final: 0.8143 (tpt) REVERT: B 667 MET cc_start: 0.8116 (mmm) cc_final: 0.7711 (mmm) REVERT: B 685 GLU cc_start: 0.8171 (tm-30) cc_final: 0.7887 (tm-30) REVERT: B 724 GLU cc_start: 0.8230 (mm-30) cc_final: 0.7910 (mm-30) REVERT: C 266 GLU cc_start: 0.6841 (tt0) cc_final: 0.6220 (mt-10) REVERT: C 301 GLU cc_start: 0.8078 (mt-10) cc_final: 0.7841 (mt-10) REVERT: C 314 THR cc_start: 0.6732 (t) cc_final: 0.6491 (t) REVERT: D 44 ARG cc_start: 0.7856 (mtt180) cc_final: 0.7331 (mtt180) REVERT: D 66 LYS cc_start: 0.8394 (tptm) cc_final: 0.8070 (tptm) REVERT: D 99 ASP cc_start: 0.8290 (p0) cc_final: 0.7907 (p0) REVERT: D 109 GLU cc_start: 0.8185 (tp30) cc_final: 0.7757 (mm-30) REVERT: D 111 MET cc_start: 0.8736 (tpp) cc_final: 0.8385 (tpp) REVERT: D 201 ASP cc_start: 0.7484 (p0) cc_final: 0.7011 (p0) REVERT: D 209 CYS cc_start: 0.8034 (t) cc_final: 0.7762 (t) REVERT: D 253 GLU cc_start: 0.7968 (mp0) cc_final: 0.7675 (mp0) REVERT: D 257 ASP cc_start: 0.7957 (m-30) cc_final: 0.7631 (m-30) REVERT: D 342 LYS cc_start: 0.8537 (ptpp) cc_final: 0.8174 (ptpp) REVERT: D 344 TYR cc_start: 0.8652 (OUTLIER) cc_final: 0.7539 (t80) REVERT: D 348 MET cc_start: 0.8151 (tpp) cc_final: 0.7663 (tpp) REVERT: D 519 MET cc_start: 0.7252 (mmp) cc_final: 0.5978 (mmt) REVERT: D 610 MET cc_start: 0.8195 (mmm) cc_final: 0.7973 (mtp) REVERT: D 620 MET cc_start: 0.8277 (tpp) cc_final: 0.7963 (tpp) REVERT: D 642 ASN cc_start: 0.8781 (m-40) cc_final: 0.8313 (m110) REVERT: D 684 GLU cc_start: 0.8247 (mm-30) cc_final: 0.7988 (tp30) REVERT: D 773 ARG cc_start: 0.8481 (ttp80) cc_final: 0.8191 (ttp80) REVERT: E 36 LEU cc_start: 0.8835 (OUTLIER) cc_final: 0.8564 (mm) REVERT: E 44 ARG cc_start: 0.8133 (ttp-170) cc_final: 0.7805 (ptm160) REVERT: E 111 MET cc_start: 0.9059 (tmm) cc_final: 0.8255 (tmm) REVERT: E 202 VAL cc_start: 0.8331 (t) cc_final: 0.8083 (m) REVERT: E 339 ASP cc_start: 0.8325 (m-30) cc_final: 0.7838 (m-30) REVERT: E 423 GLU cc_start: 0.7633 (mp0) cc_final: 0.7379 (pm20) REVERT: E 498 ASN cc_start: 0.8474 (t0) cc_final: 0.8202 (t0) REVERT: E 529 ARG cc_start: 0.7206 (ttt90) cc_final: 0.6689 (ttt-90) REVERT: E 642 ASN cc_start: 0.8675 (t0) cc_final: 0.8441 (t0) REVERT: E 667 MET cc_start: 0.7974 (mmm) cc_final: 0.7101 (mmm) REVERT: E 686 GLU cc_start: 0.7917 (tp30) cc_final: 0.7697 (tp30) REVERT: E 698 MET cc_start: 0.9044 (mmt) cc_final: 0.8676 (mmm) REVERT: E 709 MET cc_start: 0.7526 (mmm) cc_final: 0.7305 (tpt) REVERT: F 26 GLN cc_start: 0.7167 (mm-40) cc_final: 0.6761 (mm-40) outliers start: 82 outliers final: 59 residues processed: 813 average time/residue: 0.1767 time to fit residues: 225.2912 Evaluate side-chains 825 residues out of total 3188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 762 time to evaluate : 1.056 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 VAL Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 97 SER Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 277 VAL Chi-restraints excluded: chain A residue 340 VAL Chi-restraints excluded: chain A residue 344 TYR Chi-restraints excluded: chain A residue 379 LEU Chi-restraints excluded: chain A residue 500 MET Chi-restraints excluded: chain A residue 527 PHE Chi-restraints excluded: chain A residue 567 VAL Chi-restraints excluded: chain A residue 608 SER Chi-restraints excluded: chain A residue 629 ILE Chi-restraints excluded: chain A residue 641 LEU Chi-restraints excluded: chain A residue 652 MET Chi-restraints excluded: chain A residue 674 SER Chi-restraints excluded: chain A residue 697 LEU Chi-restraints excluded: chain A residue 732 LEU Chi-restraints excluded: chain A residue 777 VAL Chi-restraints excluded: chain B residue 36 LEU Chi-restraints excluded: chain B residue 94 VAL Chi-restraints excluded: chain B residue 104 VAL Chi-restraints excluded: chain B residue 113 GLN Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 265 TRP Chi-restraints excluded: chain B residue 276 GLN Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 391 THR Chi-restraints excluded: chain B residue 435 ASP Chi-restraints excluded: chain B residue 471 TYR Chi-restraints excluded: chain B residue 472 ILE Chi-restraints excluded: chain B residue 655 SER Chi-restraints excluded: chain B residue 772 VAL Chi-restraints excluded: chain B residue 815 ILE Chi-restraints excluded: chain B residue 887 THR Chi-restraints excluded: chain C residue 273 SER Chi-restraints excluded: chain C residue 320 THR Chi-restraints excluded: chain D residue 40 MET Chi-restraints excluded: chain D residue 94 VAL Chi-restraints excluded: chain D residue 97 SER Chi-restraints excluded: chain D residue 264 ILE Chi-restraints excluded: chain D residue 301 GLU Chi-restraints excluded: chain D residue 344 TYR Chi-restraints excluded: chain D residue 357 LEU Chi-restraints excluded: chain D residue 487 THR Chi-restraints excluded: chain D residue 525 VAL Chi-restraints excluded: chain D residue 617 LEU Chi-restraints excluded: chain D residue 629 ILE Chi-restraints excluded: chain D residue 666 MET Chi-restraints excluded: chain D residue 715 LEU Chi-restraints excluded: chain D residue 772 VAL Chi-restraints excluded: chain D residue 795 LEU Chi-restraints excluded: chain E residue 36 LEU Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 236 ILE Chi-restraints excluded: chain E residue 265 TRP Chi-restraints excluded: chain E residue 331 THR Chi-restraints excluded: chain E residue 525 VAL Chi-restraints excluded: chain E residue 527 PHE Chi-restraints excluded: chain E residue 533 ILE Chi-restraints excluded: chain E residue 575 SER Chi-restraints excluded: chain E residue 886 ILE Chi-restraints excluded: chain F residue 318 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 362 random chunks: chunk 21 optimal weight: 0.9980 chunk 184 optimal weight: 8.9990 chunk 183 optimal weight: 10.0000 chunk 141 optimal weight: 2.9990 chunk 361 optimal weight: 0.6980 chunk 250 optimal weight: 2.9990 chunk 62 optimal weight: 1.9990 chunk 313 optimal weight: 1.9990 chunk 148 optimal weight: 0.7980 chunk 61 optimal weight: 2.9990 chunk 55 optimal weight: 5.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 352 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 252 GLN E 539 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.091681 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.077493 restraints weight = 69877.348| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.080149 restraints weight = 32398.166| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.081854 restraints weight = 18842.105| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.082985 restraints weight = 12758.769| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.083731 restraints weight = 9681.863| |-----------------------------------------------------------------------------| r_work (final): 0.3251 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8085 moved from start: 0.2052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 29880 Z= 0.134 Angle : 0.616 12.732 40550 Z= 0.308 Chirality : 0.043 0.207 4542 Planarity : 0.004 0.050 5250 Dihedral : 4.077 20.525 4040 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 2.95 % Allowed : 17.28 % Favored : 79.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.29 (0.14), residues: 3592 helix: 1.42 (0.13), residues: 1596 sheet: -0.32 (0.27), residues: 382 loop : -0.93 (0.15), residues: 1614 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 300 TYR 0.020 0.001 TYR E 17 PHE 0.025 0.001 PHE D 636 TRP 0.019 0.001 TRP B 238 HIS 0.010 0.001 HIS D 378 Details of bonding type rmsd covalent geometry : bond 0.00310 (29880) covalent geometry : angle 0.61550 (40550) hydrogen bonds : bond 0.04207 ( 1288) hydrogen bonds : angle 3.89202 ( 3657) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7184 Ramachandran restraints generated. 3592 Oldfield, 0 Emsley, 3592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7184 Ramachandran restraints generated. 3592 Oldfield, 0 Emsley, 3592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 872 residues out of total 3188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 778 time to evaluate : 0.781 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 LYS cc_start: 0.8055 (tptm) cc_final: 0.7645 (tptm) REVERT: A 111 MET cc_start: 0.8910 (tmm) cc_final: 0.8182 (tmm) REVERT: A 253 GLU cc_start: 0.8326 (mp0) cc_final: 0.7861 (mp0) REVERT: A 257 ASP cc_start: 0.8179 (m-30) cc_final: 0.7890 (m-30) REVERT: A 344 TYR cc_start: 0.8890 (OUTLIER) cc_final: 0.8100 (t80) REVERT: A 381 PHE cc_start: 0.8200 (m-10) cc_final: 0.7778 (m-10) REVERT: A 481 GLU cc_start: 0.8141 (mp0) cc_final: 0.7738 (mp0) REVERT: A 552 LEU cc_start: 0.8720 (OUTLIER) cc_final: 0.8509 (tp) REVERT: A 582 ARG cc_start: 0.8245 (mmp80) cc_final: 0.7793 (mmp80) REVERT: A 637 TRP cc_start: 0.8565 (t60) cc_final: 0.7955 (t60) REVERT: A 671 MET cc_start: 0.7951 (mmm) cc_final: 0.7615 (mmm) REVERT: A 685 GLU cc_start: 0.8185 (tm-30) cc_final: 0.7949 (tm-30) REVERT: A 701 ASP cc_start: 0.8916 (p0) cc_final: 0.8712 (p0) REVERT: A 831 GLU cc_start: 0.8167 (tm-30) cc_final: 0.7955 (tm-30) REVERT: B 291 MET cc_start: 0.7992 (tmm) cc_final: 0.7583 (tmm) REVERT: B 339 ASP cc_start: 0.8182 (m-30) cc_final: 0.7832 (m-30) REVERT: B 355 LEU cc_start: 0.7960 (mm) cc_final: 0.7726 (mm) REVERT: B 386 ARG cc_start: 0.7793 (mpp-170) cc_final: 0.7519 (mpp-170) REVERT: B 399 ASP cc_start: 0.8438 (m-30) cc_final: 0.8172 (m-30) REVERT: B 406 LEU cc_start: 0.9067 (OUTLIER) cc_final: 0.8823 (mp) REVERT: B 512 GLU cc_start: 0.8159 (mp0) cc_final: 0.7840 (mp0) REVERT: B 643 ASP cc_start: 0.8306 (t0) cc_final: 0.8023 (t0) REVERT: B 667 MET cc_start: 0.8032 (mmm) cc_final: 0.7828 (mmm) REVERT: B 685 GLU cc_start: 0.8156 (tm-30) cc_final: 0.7937 (tm-30) REVERT: B 724 GLU cc_start: 0.8232 (mm-30) cc_final: 0.7812 (mm-30) REVERT: B 803 ASP cc_start: 0.7349 (t0) cc_final: 0.6999 (t0) REVERT: C 301 GLU cc_start: 0.8058 (mt-10) cc_final: 0.7840 (mt-10) REVERT: D 44 ARG cc_start: 0.7838 (mtt180) cc_final: 0.7480 (mtt180) REVERT: D 66 LYS cc_start: 0.8344 (tptm) cc_final: 0.7970 (tptm) REVERT: D 99 ASP cc_start: 0.8245 (p0) cc_final: 0.7856 (p0) REVERT: D 109 GLU cc_start: 0.8145 (tp30) cc_final: 0.7908 (mm-30) REVERT: D 111 MET cc_start: 0.8794 (tpp) cc_final: 0.8370 (tpp) REVERT: D 169 LYS cc_start: 0.8419 (mmmm) cc_final: 0.7893 (mmmt) REVERT: D 201 ASP cc_start: 0.7401 (p0) cc_final: 0.6909 (p0) REVERT: D 209 CYS cc_start: 0.7933 (t) cc_final: 0.7647 (t) REVERT: D 253 GLU cc_start: 0.7965 (mp0) cc_final: 0.7422 (mp0) REVERT: D 257 ASP cc_start: 0.8080 (m-30) cc_final: 0.7709 (m-30) REVERT: D 342 LYS cc_start: 0.8542 (ptpp) cc_final: 0.8177 (ptpp) REVERT: D 344 TYR cc_start: 0.8703 (OUTLIER) cc_final: 0.7691 (t80) REVERT: D 348 MET cc_start: 0.8058 (tpp) cc_final: 0.7539 (tpp) REVERT: D 409 MET cc_start: 0.7372 (tpp) cc_final: 0.5673 (tpt) REVERT: D 519 MET cc_start: 0.7272 (mmp) cc_final: 0.6124 (mmt) REVERT: D 552 LEU cc_start: 0.8728 (tt) cc_final: 0.8427 (tp) REVERT: D 573 TRP cc_start: 0.8191 (m100) cc_final: 0.7882 (m100) REVERT: D 610 MET cc_start: 0.8188 (mmm) cc_final: 0.7985 (mtp) REVERT: D 620 MET cc_start: 0.8270 (tpp) cc_final: 0.7932 (tpp) REVERT: D 642 ASN cc_start: 0.8830 (m-40) cc_final: 0.8211 (m110) REVERT: D 769 ASP cc_start: 0.8076 (t0) cc_final: 0.7842 (t0) REVERT: E 36 LEU cc_start: 0.8805 (OUTLIER) cc_final: 0.8517 (mm) REVERT: E 44 ARG cc_start: 0.8131 (ttp-170) cc_final: 0.7813 (ptm160) REVERT: E 111 MET cc_start: 0.9010 (tmm) cc_final: 0.8160 (tmm) REVERT: E 202 VAL cc_start: 0.8322 (t) cc_final: 0.8086 (m) REVERT: E 339 ASP cc_start: 0.8301 (m-30) cc_final: 0.7825 (m-30) REVERT: E 423 GLU cc_start: 0.7646 (mp0) cc_final: 0.7352 (pm20) REVERT: E 498 ASN cc_start: 0.8456 (t0) cc_final: 0.8187 (t0) REVERT: E 529 ARG cc_start: 0.7300 (ttt90) cc_final: 0.6960 (ttt90) REVERT: E 638 LYS cc_start: 0.8793 (tppt) cc_final: 0.8577 (tppt) REVERT: E 642 ASN cc_start: 0.8679 (t0) cc_final: 0.8418 (t0) REVERT: E 698 MET cc_start: 0.8961 (mmt) cc_final: 0.8611 (mmm) REVERT: E 765 ILE cc_start: 0.9080 (tt) cc_final: 0.8869 (tt) REVERT: E 848 MET cc_start: 0.8025 (mmt) cc_final: 0.7753 (mmt) REVERT: F 26 GLN cc_start: 0.7146 (mm-40) cc_final: 0.6738 (mm-40) REVERT: F 290 THR cc_start: 0.7805 (p) cc_final: 0.7582 (t) outliers start: 94 outliers final: 69 residues processed: 818 average time/residue: 0.1804 time to fit residues: 231.3385 Evaluate side-chains 835 residues out of total 3188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 761 time to evaluate : 0.950 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 ILE Chi-restraints excluded: chain A residue 61 VAL Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 97 SER Chi-restraints excluded: chain A residue 191 ILE Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 340 VAL Chi-restraints excluded: chain A residue 344 TYR Chi-restraints excluded: chain A residue 379 LEU Chi-restraints excluded: chain A residue 406 LEU Chi-restraints excluded: chain A residue 410 TYR Chi-restraints excluded: chain A residue 477 ILE Chi-restraints excluded: chain A residue 500 MET Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain A residue 567 VAL Chi-restraints excluded: chain A residue 629 ILE Chi-restraints excluded: chain A residue 641 LEU Chi-restraints excluded: chain A residue 652 MET Chi-restraints excluded: chain A residue 674 SER Chi-restraints excluded: chain A residue 732 LEU Chi-restraints excluded: chain A residue 772 VAL Chi-restraints excluded: chain B residue 104 VAL Chi-restraints excluded: chain B residue 113 GLN Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 174 VAL Chi-restraints excluded: chain B residue 185 ASN Chi-restraints excluded: chain B residue 262 ASP Chi-restraints excluded: chain B residue 265 TRP Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 391 THR Chi-restraints excluded: chain B residue 406 LEU Chi-restraints excluded: chain B residue 435 ASP Chi-restraints excluded: chain B residue 471 TYR Chi-restraints excluded: chain B residue 472 ILE Chi-restraints excluded: chain B residue 541 VAL Chi-restraints excluded: chain B residue 574 ILE Chi-restraints excluded: chain B residue 772 VAL Chi-restraints excluded: chain B residue 815 ILE Chi-restraints excluded: chain B residue 887 THR Chi-restraints excluded: chain C residue 273 SER Chi-restraints excluded: chain C residue 276 ILE Chi-restraints excluded: chain C residue 280 VAL Chi-restraints excluded: chain C residue 320 THR Chi-restraints excluded: chain D residue 31 LEU Chi-restraints excluded: chain D residue 40 MET Chi-restraints excluded: chain D residue 94 VAL Chi-restraints excluded: chain D residue 117 VAL Chi-restraints excluded: chain D residue 264 ILE Chi-restraints excluded: chain D residue 266 VAL Chi-restraints excluded: chain D residue 301 GLU Chi-restraints excluded: chain D residue 344 TYR Chi-restraints excluded: chain D residue 357 LEU Chi-restraints excluded: chain D residue 504 LEU Chi-restraints excluded: chain D residue 617 LEU Chi-restraints excluded: chain D residue 629 ILE Chi-restraints excluded: chain D residue 715 LEU Chi-restraints excluded: chain D residue 772 VAL Chi-restraints excluded: chain D residue 784 LYS Chi-restraints excluded: chain D residue 795 LEU Chi-restraints excluded: chain E residue 36 LEU Chi-restraints excluded: chain E residue 187 LEU Chi-restraints excluded: chain E residue 216 ILE Chi-restraints excluded: chain E residue 236 ILE Chi-restraints excluded: chain E residue 239 LEU Chi-restraints excluded: chain E residue 265 TRP Chi-restraints excluded: chain E residue 273 VAL Chi-restraints excluded: chain E residue 369 VAL Chi-restraints excluded: chain E residue 472 ILE Chi-restraints excluded: chain E residue 527 PHE Chi-restraints excluded: chain E residue 533 ILE Chi-restraints excluded: chain E residue 575 SER Chi-restraints excluded: chain E residue 772 VAL Chi-restraints excluded: chain E residue 867 LEU Chi-restraints excluded: chain F residue 328 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 362 random chunks: chunk 164 optimal weight: 4.9990 chunk 303 optimal weight: 0.9990 chunk 2 optimal weight: 0.8980 chunk 158 optimal weight: 1.9990 chunk 295 optimal weight: 4.9990 chunk 267 optimal weight: 0.9990 chunk 165 optimal weight: 0.8980 chunk 119 optimal weight: 0.6980 chunk 185 optimal weight: 0.9980 chunk 262 optimal weight: 3.9990 chunk 159 optimal weight: 3.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 352 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 252 GLN E 403 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.092506 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.078233 restraints weight = 69876.862| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.080950 restraints weight = 32056.703| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.082688 restraints weight = 18524.429| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.083849 restraints weight = 12468.112| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.084626 restraints weight = 9399.577| |-----------------------------------------------------------------------------| r_work (final): 0.3268 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8070 moved from start: 0.2119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 29880 Z= 0.120 Angle : 0.613 13.419 40550 Z= 0.305 Chirality : 0.043 0.200 4542 Planarity : 0.004 0.051 5250 Dihedral : 3.980 20.123 4040 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 3.17 % Allowed : 18.91 % Favored : 77.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.34 (0.14), residues: 3592 helix: 1.47 (0.13), residues: 1594 sheet: -0.21 (0.28), residues: 362 loop : -0.92 (0.15), residues: 1636 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 623 TYR 0.021 0.001 TYR E 17 PHE 0.035 0.001 PHE D 324 TRP 0.023 0.001 TRP B 238 HIS 0.010 0.001 HIS D 378 Details of bonding type rmsd covalent geometry : bond 0.00276 (29880) covalent geometry : angle 0.61292 (40550) hydrogen bonds : bond 0.03856 ( 1288) hydrogen bonds : angle 3.79066 ( 3657) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7184 Ramachandran restraints generated. 3592 Oldfield, 0 Emsley, 3592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7184 Ramachandran restraints generated. 3592 Oldfield, 0 Emsley, 3592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 876 residues out of total 3188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 775 time to evaluate : 1.191 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 LYS cc_start: 0.8079 (tptm) cc_final: 0.7646 (tptm) REVERT: A 110 GLU cc_start: 0.7856 (tp30) cc_final: 0.7647 (tp30) REVERT: A 111 MET cc_start: 0.8853 (tmm) cc_final: 0.8224 (tmm) REVERT: A 257 ASP cc_start: 0.8180 (m-30) cc_final: 0.7864 (m-30) REVERT: A 344 TYR cc_start: 0.8864 (OUTLIER) cc_final: 0.8099 (t80) REVERT: A 381 PHE cc_start: 0.8086 (m-10) cc_final: 0.7700 (m-10) REVERT: A 481 GLU cc_start: 0.8156 (mp0) cc_final: 0.7757 (mp0) REVERT: A 578 PHE cc_start: 0.7997 (m-80) cc_final: 0.7369 (m-80) REVERT: A 582 ARG cc_start: 0.8212 (mmp80) cc_final: 0.7815 (mmp80) REVERT: A 637 TRP cc_start: 0.8453 (t60) cc_final: 0.8062 (t60) REVERT: A 641 LEU cc_start: 0.8584 (OUTLIER) cc_final: 0.7821 (mt) REVERT: A 664 ARG cc_start: 0.7243 (ptt-90) cc_final: 0.6388 (ttp-110) REVERT: A 668 ARG cc_start: 0.8614 (mtm180) cc_final: 0.8299 (mtm-85) REVERT: A 685 GLU cc_start: 0.8197 (tm-30) cc_final: 0.7929 (tm-30) REVERT: B 36 LEU cc_start: 0.8888 (mm) cc_final: 0.8632 (mm) REVERT: B 291 MET cc_start: 0.7986 (tmm) cc_final: 0.7699 (tmm) REVERT: B 339 ASP cc_start: 0.8156 (m-30) cc_final: 0.7807 (m-30) REVERT: B 355 LEU cc_start: 0.7915 (mm) cc_final: 0.7679 (mm) REVERT: B 386 ARG cc_start: 0.7801 (mpp-170) cc_final: 0.7468 (mpp-170) REVERT: B 406 LEU cc_start: 0.8941 (OUTLIER) cc_final: 0.8656 (mp) REVERT: B 600 GLU cc_start: 0.7920 (mt-10) cc_final: 0.7713 (mt-10) REVERT: B 643 ASP cc_start: 0.8293 (t0) cc_final: 0.8002 (t0) REVERT: B 724 GLU cc_start: 0.8210 (mm-30) cc_final: 0.7749 (mm-30) REVERT: B 747 GLU cc_start: 0.7694 (pp20) cc_final: 0.7454 (pp20) REVERT: B 869 VAL cc_start: 0.8845 (OUTLIER) cc_final: 0.8632 (t) REVERT: C 272 VAL cc_start: 0.9035 (p) cc_final: 0.8751 (t) REVERT: C 314 THR cc_start: 0.6719 (OUTLIER) cc_final: 0.6426 (t) REVERT: D 44 ARG cc_start: 0.7822 (mtt180) cc_final: 0.7392 (mtt180) REVERT: D 66 LYS cc_start: 0.8336 (tptm) cc_final: 0.7969 (tptm) REVERT: D 99 ASP cc_start: 0.8222 (p0) cc_final: 0.7822 (p0) REVERT: D 111 MET cc_start: 0.8805 (tpp) cc_final: 0.8468 (tpp) REVERT: D 169 LYS cc_start: 0.8402 (mmmm) cc_final: 0.7977 (mmmt) REVERT: D 209 CYS cc_start: 0.7842 (t) cc_final: 0.7529 (t) REVERT: D 252 GLN cc_start: 0.8208 (OUTLIER) cc_final: 0.7718 (tm130) REVERT: D 253 GLU cc_start: 0.7966 (mp0) cc_final: 0.7652 (mp0) REVERT: D 257 ASP cc_start: 0.8101 (m-30) cc_final: 0.7809 (m-30) REVERT: D 342 LYS cc_start: 0.8533 (ptpp) cc_final: 0.8166 (ptpp) REVERT: D 344 TYR cc_start: 0.8699 (OUTLIER) cc_final: 0.7747 (t80) REVERT: D 348 MET cc_start: 0.7927 (tpp) cc_final: 0.7387 (tpp) REVERT: D 409 MET cc_start: 0.7307 (tpp) cc_final: 0.5880 (tpt) REVERT: D 519 MET cc_start: 0.7227 (mmp) cc_final: 0.6285 (mmp) REVERT: D 552 LEU cc_start: 0.8707 (tt) cc_final: 0.8430 (tp) REVERT: D 573 TRP cc_start: 0.8175 (m100) cc_final: 0.7857 (m100) REVERT: D 620 MET cc_start: 0.8286 (tpp) cc_final: 0.7950 (tpp) REVERT: D 642 ASN cc_start: 0.8841 (m-40) cc_final: 0.8032 (m-40) REVERT: D 769 ASP cc_start: 0.8064 (t0) cc_final: 0.7854 (t0) REVERT: E 36 LEU cc_start: 0.8723 (OUTLIER) cc_final: 0.8426 (mm) REVERT: E 44 ARG cc_start: 0.8142 (ttp-170) cc_final: 0.7789 (ptm160) REVERT: E 111 MET cc_start: 0.9018 (tmm) cc_final: 0.8144 (tmm) REVERT: E 202 VAL cc_start: 0.8314 (t) cc_final: 0.8080 (m) REVERT: E 339 ASP cc_start: 0.8293 (m-30) cc_final: 0.7798 (m-30) REVERT: E 363 GLU cc_start: 0.6715 (OUTLIER) cc_final: 0.6285 (pm20) REVERT: E 423 GLU cc_start: 0.7631 (mp0) cc_final: 0.7233 (pm20) REVERT: E 498 ASN cc_start: 0.8408 (t0) cc_final: 0.8130 (t0) REVERT: E 529 ARG cc_start: 0.7262 (ttt90) cc_final: 0.7002 (ttt90) REVERT: E 536 GLU cc_start: 0.7544 (tp30) cc_final: 0.7335 (tm-30) REVERT: E 638 LYS cc_start: 0.8758 (tppt) cc_final: 0.8538 (tppt) REVERT: E 642 ASN cc_start: 0.8687 (t0) cc_final: 0.8408 (t0) REVERT: E 667 MET cc_start: 0.8134 (mmm) cc_final: 0.7652 (mmm) REVERT: E 765 ILE cc_start: 0.9086 (tt) cc_final: 0.8867 (tt) REVERT: E 848 MET cc_start: 0.7983 (mmt) cc_final: 0.7662 (mmt) REVERT: F 26 GLN cc_start: 0.7086 (mm-40) cc_final: 0.6606 (mm-40) REVERT: F 290 THR cc_start: 0.7723 (p) cc_final: 0.7516 (t) outliers start: 101 outliers final: 75 residues processed: 824 average time/residue: 0.1743 time to fit residues: 226.3673 Evaluate side-chains 843 residues out of total 3188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 759 time to evaluate : 1.104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 VAL Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 97 SER Chi-restraints excluded: chain A residue 191 ILE Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 340 VAL Chi-restraints excluded: chain A residue 344 TYR Chi-restraints excluded: chain A residue 379 LEU Chi-restraints excluded: chain A residue 406 LEU Chi-restraints excluded: chain A residue 410 TYR Chi-restraints excluded: chain A residue 477 ILE Chi-restraints excluded: chain A residue 500 MET Chi-restraints excluded: chain A residue 567 VAL Chi-restraints excluded: chain A residue 641 LEU Chi-restraints excluded: chain A residue 652 MET Chi-restraints excluded: chain A residue 674 SER Chi-restraints excluded: chain A residue 732 LEU Chi-restraints excluded: chain A residue 772 VAL Chi-restraints excluded: chain A residue 777 VAL Chi-restraints excluded: chain A residue 863 VAL Chi-restraints excluded: chain B residue 104 VAL Chi-restraints excluded: chain B residue 113 GLN Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 174 VAL Chi-restraints excluded: chain B residue 262 ASP Chi-restraints excluded: chain B residue 265 TRP Chi-restraints excluded: chain B residue 276 GLN Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 345 LEU Chi-restraints excluded: chain B residue 369 VAL Chi-restraints excluded: chain B residue 406 LEU Chi-restraints excluded: chain B residue 435 ASP Chi-restraints excluded: chain B residue 471 TYR Chi-restraints excluded: chain B residue 472 ILE Chi-restraints excluded: chain B residue 574 ILE Chi-restraints excluded: chain B residue 815 ILE Chi-restraints excluded: chain B residue 869 VAL Chi-restraints excluded: chain B residue 887 THR Chi-restraints excluded: chain C residue 276 ILE Chi-restraints excluded: chain C residue 314 THR Chi-restraints excluded: chain C residue 320 THR Chi-restraints excluded: chain D residue 31 LEU Chi-restraints excluded: chain D residue 68 LEU Chi-restraints excluded: chain D residue 94 VAL Chi-restraints excluded: chain D residue 95 MET Chi-restraints excluded: chain D residue 117 VAL Chi-restraints excluded: chain D residue 224 ILE Chi-restraints excluded: chain D residue 252 GLN Chi-restraints excluded: chain D residue 264 ILE Chi-restraints excluded: chain D residue 266 VAL Chi-restraints excluded: chain D residue 301 GLU Chi-restraints excluded: chain D residue 344 TYR Chi-restraints excluded: chain D residue 357 LEU Chi-restraints excluded: chain D residue 416 VAL Chi-restraints excluded: chain D residue 487 THR Chi-restraints excluded: chain D residue 617 LEU Chi-restraints excluded: chain D residue 629 ILE Chi-restraints excluded: chain D residue 715 LEU Chi-restraints excluded: chain D residue 784 LYS Chi-restraints excluded: chain D residue 795 LEU Chi-restraints excluded: chain D residue 869 VAL Chi-restraints excluded: chain E residue 36 LEU Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 174 VAL Chi-restraints excluded: chain E residue 227 VAL Chi-restraints excluded: chain E residue 236 ILE Chi-restraints excluded: chain E residue 239 LEU Chi-restraints excluded: chain E residue 265 TRP Chi-restraints excluded: chain E residue 273 VAL Chi-restraints excluded: chain E residue 331 THR Chi-restraints excluded: chain E residue 363 GLU Chi-restraints excluded: chain E residue 369 VAL Chi-restraints excluded: chain E residue 403 ASN Chi-restraints excluded: chain E residue 411 ASN Chi-restraints excluded: chain E residue 421 THR Chi-restraints excluded: chain E residue 472 ILE Chi-restraints excluded: chain E residue 527 PHE Chi-restraints excluded: chain E residue 575 SER Chi-restraints excluded: chain E residue 772 VAL Chi-restraints excluded: chain E residue 867 LEU Chi-restraints excluded: chain E residue 886 ILE Chi-restraints excluded: chain F residue 318 VAL Chi-restraints excluded: chain F residue 328 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 362 random chunks: chunk 335 optimal weight: 1.9990 chunk 282 optimal weight: 0.1980 chunk 220 optimal weight: 0.0050 chunk 54 optimal weight: 0.9990 chunk 256 optimal weight: 4.9990 chunk 43 optimal weight: 0.0370 chunk 180 optimal weight: 7.9990 chunk 116 optimal weight: 0.9980 chunk 40 optimal weight: 0.4980 chunk 105 optimal weight: 7.9990 chunk 70 optimal weight: 2.9990 overall best weight: 0.3472 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 352 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.094043 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.079927 restraints weight = 69730.107| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.082623 restraints weight = 32265.560| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.084341 restraints weight = 18673.921| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.085482 restraints weight = 12614.465| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.086250 restraints weight = 9551.194| |-----------------------------------------------------------------------------| r_work (final): 0.3298 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8035 moved from start: 0.2211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 29880 Z= 0.113 Angle : 0.629 14.230 40550 Z= 0.308 Chirality : 0.042 0.207 4542 Planarity : 0.004 0.050 5250 Dihedral : 3.875 19.115 4040 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 2.92 % Allowed : 19.64 % Favored : 77.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.39 (0.14), residues: 3592 helix: 1.55 (0.13), residues: 1578 sheet: -0.23 (0.28), residues: 364 loop : -0.90 (0.15), residues: 1650 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 623 TYR 0.020 0.001 TYR E 17 PHE 0.026 0.001 PHE D 636 TRP 0.026 0.001 TRP B 238 HIS 0.013 0.001 HIS D 378 Details of bonding type rmsd covalent geometry : bond 0.00255 (29880) covalent geometry : angle 0.62924 (40550) hydrogen bonds : bond 0.03389 ( 1288) hydrogen bonds : angle 3.72029 ( 3657) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7184 Ramachandran restraints generated. 3592 Oldfield, 0 Emsley, 3592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7184 Ramachandran restraints generated. 3592 Oldfield, 0 Emsley, 3592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 885 residues out of total 3188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 792 time to evaluate : 1.049 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 LYS cc_start: 0.8063 (tptm) cc_final: 0.7620 (tptm) REVERT: A 110 GLU cc_start: 0.7876 (tp30) cc_final: 0.7654 (tp30) REVERT: A 111 MET cc_start: 0.8756 (tmm) cc_final: 0.8183 (tmm) REVERT: A 147 ASP cc_start: 0.8456 (t0) cc_final: 0.8151 (t0) REVERT: A 167 GLU cc_start: 0.7765 (tm-30) cc_final: 0.7494 (tm-30) REVERT: A 257 ASP cc_start: 0.8158 (m-30) cc_final: 0.7821 (m-30) REVERT: A 381 PHE cc_start: 0.7958 (m-10) cc_final: 0.7605 (m-10) REVERT: A 481 GLU cc_start: 0.8136 (mp0) cc_final: 0.7719 (mp0) REVERT: A 578 PHE cc_start: 0.7922 (m-80) cc_final: 0.7252 (m-80) REVERT: A 641 LEU cc_start: 0.8527 (OUTLIER) cc_final: 0.8326 (mt) REVERT: A 668 ARG cc_start: 0.8636 (mtm180) cc_final: 0.8407 (mtm180) REVERT: A 685 GLU cc_start: 0.8196 (tm-30) cc_final: 0.7876 (tm-30) REVERT: A 769 ASP cc_start: 0.8161 (t0) cc_final: 0.7905 (t0) REVERT: A 812 TYR cc_start: 0.8068 (t80) cc_final: 0.7847 (t80) REVERT: A 831 GLU cc_start: 0.8188 (tm-30) cc_final: 0.7958 (tm-30) REVERT: B 36 LEU cc_start: 0.8784 (mm) cc_final: 0.8532 (mm) REVERT: B 291 MET cc_start: 0.8001 (tmm) cc_final: 0.7649 (tmm) REVERT: B 339 ASP cc_start: 0.8142 (m-30) cc_final: 0.7788 (m-30) REVERT: B 386 ARG cc_start: 0.7875 (mpp-170) cc_final: 0.7500 (mpp-170) REVERT: B 399 ASP cc_start: 0.8404 (m-30) cc_final: 0.8155 (m-30) REVERT: B 406 LEU cc_start: 0.8854 (OUTLIER) cc_final: 0.8605 (mp) REVERT: B 600 GLU cc_start: 0.7900 (mt-10) cc_final: 0.7684 (mt-10) REVERT: B 643 ASP cc_start: 0.8262 (t0) cc_final: 0.7962 (t0) REVERT: B 724 GLU cc_start: 0.8228 (mm-30) cc_final: 0.7754 (mm-30) REVERT: B 747 GLU cc_start: 0.7664 (pp20) cc_final: 0.7459 (pp20) REVERT: B 803 ASP cc_start: 0.7338 (t0) cc_final: 0.6903 (t0) REVERT: B 869 VAL cc_start: 0.8803 (OUTLIER) cc_final: 0.8594 (t) REVERT: C 314 THR cc_start: 0.6761 (OUTLIER) cc_final: 0.6471 (t) REVERT: D 40 MET cc_start: 0.8308 (mmm) cc_final: 0.7977 (mmp) REVERT: D 44 ARG cc_start: 0.7808 (mtt180) cc_final: 0.7458 (mtt180) REVERT: D 66 LYS cc_start: 0.8303 (tptm) cc_final: 0.7931 (tptm) REVERT: D 99 ASP cc_start: 0.8217 (p0) cc_final: 0.7797 (p0) REVERT: D 109 GLU cc_start: 0.8145 (mm-30) cc_final: 0.7882 (mm-30) REVERT: D 111 MET cc_start: 0.8807 (tpp) cc_final: 0.8516 (tpp) REVERT: D 157 GLU cc_start: 0.7869 (mp0) cc_final: 0.7437 (mp0) REVERT: D 169 LYS cc_start: 0.8433 (mmmm) cc_final: 0.8163 (mmtt) REVERT: D 209 CYS cc_start: 0.7761 (t) cc_final: 0.7421 (t) REVERT: D 253 GLU cc_start: 0.7824 (mp0) cc_final: 0.7229 (mp0) REVERT: D 257 ASP cc_start: 0.8185 (m-30) cc_final: 0.7703 (m-30) REVERT: D 342 LYS cc_start: 0.8517 (ptpp) cc_final: 0.8156 (ptpp) REVERT: D 344 TYR cc_start: 0.8653 (OUTLIER) cc_final: 0.7748 (t80) REVERT: D 348 MET cc_start: 0.7886 (tpp) cc_final: 0.7343 (tpp) REVERT: D 409 MET cc_start: 0.7231 (tpp) cc_final: 0.5825 (tpt) REVERT: D 503 MET cc_start: 0.8634 (tmm) cc_final: 0.8414 (tmm) REVERT: D 519 MET cc_start: 0.7204 (mmp) cc_final: 0.6338 (mmp) REVERT: D 536 GLU cc_start: 0.7797 (tp30) cc_final: 0.7577 (tp30) REVERT: D 573 TRP cc_start: 0.8128 (m100) cc_final: 0.7708 (m100) REVERT: D 620 MET cc_start: 0.8236 (tpp) cc_final: 0.7905 (tpp) REVERT: D 642 ASN cc_start: 0.8815 (m-40) cc_final: 0.8117 (m-40) REVERT: D 769 ASP cc_start: 0.8047 (t0) cc_final: 0.7844 (t0) REVERT: D 792 ASP cc_start: 0.7493 (p0) cc_final: 0.7217 (p0) REVERT: E 36 LEU cc_start: 0.8675 (OUTLIER) cc_final: 0.8383 (mm) REVERT: E 44 ARG cc_start: 0.8142 (ttp-170) cc_final: 0.7812 (ptm160) REVERT: E 81 LYS cc_start: 0.7896 (ptmm) cc_final: 0.7663 (ptmm) REVERT: E 111 MET cc_start: 0.9028 (tmm) cc_final: 0.8146 (tmm) REVERT: E 339 ASP cc_start: 0.8276 (m-30) cc_final: 0.7796 (m-30) REVERT: E 363 GLU cc_start: 0.6650 (OUTLIER) cc_final: 0.6317 (pm20) REVERT: E 407 LEU cc_start: 0.8689 (mm) cc_final: 0.8463 (mm) REVERT: E 423 GLU cc_start: 0.7645 (mp0) cc_final: 0.7229 (pm20) REVERT: E 498 ASN cc_start: 0.8403 (t0) cc_final: 0.8116 (t0) REVERT: E 529 ARG cc_start: 0.7292 (ttt90) cc_final: 0.6996 (ttt90) REVERT: E 638 LYS cc_start: 0.8731 (tppt) cc_final: 0.8508 (tppt) REVERT: E 642 ASN cc_start: 0.8674 (t0) cc_final: 0.8353 (t0) REVERT: E 686 GLU cc_start: 0.8015 (tp30) cc_final: 0.7659 (tp30) REVERT: E 708 ASP cc_start: 0.7218 (m-30) cc_final: 0.7005 (m-30) REVERT: E 765 ILE cc_start: 0.9070 (tt) cc_final: 0.8854 (tt) REVERT: E 848 MET cc_start: 0.7916 (mmt) cc_final: 0.7588 (mmt) REVERT: F 26 GLN cc_start: 0.6970 (mm-40) cc_final: 0.6520 (mm-40) REVERT: F 290 THR cc_start: 0.7652 (p) cc_final: 0.7444 (t) outliers start: 93 outliers final: 64 residues processed: 844 average time/residue: 0.1748 time to fit residues: 233.4668 Evaluate side-chains 839 residues out of total 3188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 768 time to evaluate : 0.992 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 ILE Chi-restraints excluded: chain A residue 61 VAL Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 97 SER Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 340 VAL Chi-restraints excluded: chain A residue 344 TYR Chi-restraints excluded: chain A residue 379 LEU Chi-restraints excluded: chain A residue 477 ILE Chi-restraints excluded: chain A residue 500 MET Chi-restraints excluded: chain A residue 567 VAL Chi-restraints excluded: chain A residue 641 LEU Chi-restraints excluded: chain A residue 732 LEU Chi-restraints excluded: chain A residue 772 VAL Chi-restraints excluded: chain A residue 884 MET Chi-restraints excluded: chain B residue 79 VAL Chi-restraints excluded: chain B residue 104 VAL Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 174 VAL Chi-restraints excluded: chain B residue 262 ASP Chi-restraints excluded: chain B residue 265 TRP Chi-restraints excluded: chain B residue 345 LEU Chi-restraints excluded: chain B residue 406 LEU Chi-restraints excluded: chain B residue 471 TYR Chi-restraints excluded: chain B residue 472 ILE Chi-restraints excluded: chain B residue 493 THR Chi-restraints excluded: chain B residue 574 ILE Chi-restraints excluded: chain B residue 772 VAL Chi-restraints excluded: chain B residue 815 ILE Chi-restraints excluded: chain B residue 869 VAL Chi-restraints excluded: chain B residue 887 THR Chi-restraints excluded: chain C residue 276 ILE Chi-restraints excluded: chain C residue 314 THR Chi-restraints excluded: chain C residue 320 THR Chi-restraints excluded: chain D residue 94 VAL Chi-restraints excluded: chain D residue 264 ILE Chi-restraints excluded: chain D residue 266 VAL Chi-restraints excluded: chain D residue 273 VAL Chi-restraints excluded: chain D residue 301 GLU Chi-restraints excluded: chain D residue 344 TYR Chi-restraints excluded: chain D residue 357 LEU Chi-restraints excluded: chain D residue 487 THR Chi-restraints excluded: chain D residue 504 LEU Chi-restraints excluded: chain D residue 571 VAL Chi-restraints excluded: chain D residue 617 LEU Chi-restraints excluded: chain D residue 629 ILE Chi-restraints excluded: chain D residue 715 LEU Chi-restraints excluded: chain D residue 772 VAL Chi-restraints excluded: chain D residue 795 LEU Chi-restraints excluded: chain E residue 36 LEU Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 104 VAL Chi-restraints excluded: chain E residue 174 VAL Chi-restraints excluded: chain E residue 187 LEU Chi-restraints excluded: chain E residue 227 VAL Chi-restraints excluded: chain E residue 236 ILE Chi-restraints excluded: chain E residue 239 LEU Chi-restraints excluded: chain E residue 273 VAL Chi-restraints excluded: chain E residue 278 VAL Chi-restraints excluded: chain E residue 331 THR Chi-restraints excluded: chain E residue 363 GLU Chi-restraints excluded: chain E residue 369 VAL Chi-restraints excluded: chain E residue 421 THR Chi-restraints excluded: chain E residue 472 ILE Chi-restraints excluded: chain E residue 527 PHE Chi-restraints excluded: chain E residue 575 SER Chi-restraints excluded: chain E residue 772 VAL Chi-restraints excluded: chain E residue 867 LEU Chi-restraints excluded: chain F residue 5 MET Chi-restraints excluded: chain F residue 328 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 362 random chunks: chunk 211 optimal weight: 2.9990 chunk 96 optimal weight: 0.8980 chunk 310 optimal weight: 1.9990 chunk 151 optimal weight: 6.9990 chunk 227 optimal weight: 0.5980 chunk 259 optimal weight: 0.4980 chunk 243 optimal weight: 0.8980 chunk 207 optimal weight: 2.9990 chunk 349 optimal weight: 6.9990 chunk 164 optimal weight: 2.9990 chunk 111 optimal weight: 0.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 352 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 252 GLN D 653 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.093488 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.079361 restraints weight = 70058.725| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.082043 restraints weight = 32489.422| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.083765 restraints weight = 18856.737| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.084910 restraints weight = 12726.005| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.085672 restraints weight = 9634.591| |-----------------------------------------------------------------------------| r_work (final): 0.3287 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8045 moved from start: 0.2298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 29880 Z= 0.119 Angle : 0.648 14.181 40550 Z= 0.318 Chirality : 0.043 0.211 4542 Planarity : 0.004 0.050 5250 Dihedral : 3.851 18.707 4040 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 3.23 % Allowed : 20.92 % Favored : 75.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.38 (0.14), residues: 3592 helix: 1.51 (0.13), residues: 1582 sheet: -0.20 (0.27), residues: 362 loop : -0.89 (0.15), residues: 1648 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 582 TYR 0.021 0.001 TYR E 17 PHE 0.036 0.001 PHE D 324 TRP 0.027 0.001 TRP B 238 HIS 0.011 0.001 HIS D 378 Details of bonding type rmsd covalent geometry : bond 0.00280 (29880) covalent geometry : angle 0.64784 (40550) hydrogen bonds : bond 0.03520 ( 1288) hydrogen bonds : angle 3.72043 ( 3657) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7184 Ramachandran restraints generated. 3592 Oldfield, 0 Emsley, 3592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7184 Ramachandran restraints generated. 3592 Oldfield, 0 Emsley, 3592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 876 residues out of total 3188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 773 time to evaluate : 1.073 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: A 31 LEU cc_start: 0.8725 (OUTLIER) cc_final: 0.8387 (mp) REVERT: A 44 ARG cc_start: 0.8123 (tmm160) cc_final: 0.7917 (ttp80) REVERT: A 66 LYS cc_start: 0.8089 (tptm) cc_final: 0.7687 (tptm) REVERT: A 110 GLU cc_start: 0.7928 (tp30) cc_final: 0.7685 (tp30) REVERT: A 111 MET cc_start: 0.8699 (tmm) cc_final: 0.8211 (tmm) REVERT: A 157 GLU cc_start: 0.7570 (mp0) cc_final: 0.7363 (mp0) REVERT: A 167 GLU cc_start: 0.7777 (tm-30) cc_final: 0.7459 (tm-30) REVERT: A 257 ASP cc_start: 0.8150 (m-30) cc_final: 0.7813 (m-30) REVERT: A 344 TYR cc_start: 0.8827 (OUTLIER) cc_final: 0.8094 (t80) REVERT: A 371 MET cc_start: 0.7041 (mtt) cc_final: 0.6779 (mtm) REVERT: A 381 PHE cc_start: 0.7962 (m-10) cc_final: 0.7597 (m-10) REVERT: A 404 ASP cc_start: 0.8464 (m-30) cc_final: 0.8202 (m-30) REVERT: A 481 GLU cc_start: 0.8169 (mp0) cc_final: 0.7765 (mp0) REVERT: A 582 ARG cc_start: 0.8321 (mmp80) cc_final: 0.8025 (mmp-170) REVERT: A 636 PHE cc_start: 0.7828 (p90) cc_final: 0.7447 (p90) REVERT: A 668 ARG cc_start: 0.8633 (mtm180) cc_final: 0.8282 (mtm-85) REVERT: A 685 GLU cc_start: 0.8215 (tm-30) cc_final: 0.7918 (tm-30) REVERT: A 712 GLU cc_start: 0.7714 (pm20) cc_final: 0.7337 (pm20) REVERT: A 769 ASP cc_start: 0.8162 (t0) cc_final: 0.7930 (t0) REVERT: A 831 GLU cc_start: 0.8193 (tm-30) cc_final: 0.7963 (tm-30) REVERT: B 36 LEU cc_start: 0.8826 (mm) cc_final: 0.8586 (mm) REVERT: B 70 ASP cc_start: 0.7833 (t0) cc_final: 0.7228 (t0) REVERT: B 291 MET cc_start: 0.8134 (tmm) cc_final: 0.7745 (tmm) REVERT: B 339 ASP cc_start: 0.8154 (m-30) cc_final: 0.7788 (m-30) REVERT: B 355 LEU cc_start: 0.7869 (mm) cc_final: 0.7651 (mm) REVERT: B 600 GLU cc_start: 0.7894 (mt-10) cc_final: 0.7677 (mt-10) REVERT: B 643 ASP cc_start: 0.8282 (t0) cc_final: 0.7992 (t0) REVERT: B 724 GLU cc_start: 0.8229 (mm-30) cc_final: 0.7752 (mm-30) REVERT: B 803 ASP cc_start: 0.7350 (t0) cc_final: 0.6892 (t0) REVERT: B 859 GLU cc_start: 0.7293 (tm-30) cc_final: 0.7048 (tm-30) REVERT: B 869 VAL cc_start: 0.8826 (OUTLIER) cc_final: 0.8622 (t) REVERT: C 314 THR cc_start: 0.6801 (OUTLIER) cc_final: 0.6500 (t) REVERT: D 40 MET cc_start: 0.8297 (mmm) cc_final: 0.7988 (mmp) REVERT: D 44 ARG cc_start: 0.7796 (mtt180) cc_final: 0.7415 (mtt180) REVERT: D 66 LYS cc_start: 0.8320 (tptm) cc_final: 0.7950 (tptm) REVERT: D 99 ASP cc_start: 0.8182 (p0) cc_final: 0.7807 (p0) REVERT: D 109 GLU cc_start: 0.8162 (mm-30) cc_final: 0.7841 (mm-30) REVERT: D 111 MET cc_start: 0.8804 (tpp) cc_final: 0.8475 (tpp) REVERT: D 169 LYS cc_start: 0.8403 (mmmm) cc_final: 0.8094 (mmmt) REVERT: D 209 CYS cc_start: 0.7825 (t) cc_final: 0.7502 (t) REVERT: D 253 GLU cc_start: 0.7885 (mp0) cc_final: 0.7216 (mp0) REVERT: D 257 ASP cc_start: 0.8106 (m-30) cc_final: 0.7697 (m-30) REVERT: D 342 LYS cc_start: 0.8558 (ptpp) cc_final: 0.8224 (ptpp) REVERT: D 344 TYR cc_start: 0.8685 (OUTLIER) cc_final: 0.7735 (t80) REVERT: D 503 MET cc_start: 0.8608 (tmm) cc_final: 0.8392 (tmm) REVERT: D 519 MET cc_start: 0.7337 (mmp) cc_final: 0.6448 (mmp) REVERT: D 536 GLU cc_start: 0.7777 (tp30) cc_final: 0.7562 (tp30) REVERT: D 552 LEU cc_start: 0.8693 (tt) cc_final: 0.8383 (tp) REVERT: D 573 TRP cc_start: 0.8140 (m100) cc_final: 0.7736 (m100) REVERT: D 620 MET cc_start: 0.8250 (tpp) cc_final: 0.7973 (tpp) REVERT: D 642 ASN cc_start: 0.8818 (m-40) cc_final: 0.8114 (m-40) REVERT: D 667 MET cc_start: 0.7813 (tpp) cc_final: 0.7504 (mmp) REVERT: D 769 ASP cc_start: 0.8045 (t0) cc_final: 0.7840 (t0) REVERT: E 36 LEU cc_start: 0.8699 (OUTLIER) cc_final: 0.8411 (mm) REVERT: E 44 ARG cc_start: 0.8158 (ttp-170) cc_final: 0.7889 (ptm160) REVERT: E 81 LYS cc_start: 0.7890 (ptmm) cc_final: 0.7639 (ptmm) REVERT: E 111 MET cc_start: 0.9004 (tmm) cc_final: 0.8217 (tmm) REVERT: E 124 GLU cc_start: 0.7819 (pp20) cc_final: 0.7615 (pp20) REVERT: E 339 ASP cc_start: 0.8313 (m-30) cc_final: 0.7842 (m-30) REVERT: E 363 GLU cc_start: 0.6761 (OUTLIER) cc_final: 0.6499 (pt0) REVERT: E 498 ASN cc_start: 0.8435 (t0) cc_final: 0.8137 (t0) REVERT: E 642 ASN cc_start: 0.8679 (t0) cc_final: 0.8377 (t0) REVERT: E 686 GLU cc_start: 0.8024 (tp30) cc_final: 0.7766 (tp30) REVERT: E 708 ASP cc_start: 0.7226 (m-30) cc_final: 0.7005 (m-30) REVERT: E 848 MET cc_start: 0.7929 (mmt) cc_final: 0.7602 (mmt) REVERT: E 884 MET cc_start: 0.6533 (tpt) cc_final: 0.6179 (tpt) REVERT: F 26 GLN cc_start: 0.7029 (mm-40) cc_final: 0.6569 (mm-40) REVERT: F 290 THR cc_start: 0.7636 (p) cc_final: 0.7426 (t) outliers start: 103 outliers final: 77 residues processed: 832 average time/residue: 0.1813 time to fit residues: 236.9805 Evaluate side-chains 841 residues out of total 3188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 757 time to evaluate : 0.707 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 61 VAL Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 97 SER Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 340 VAL Chi-restraints excluded: chain A residue 344 TYR Chi-restraints excluded: chain A residue 379 LEU Chi-restraints excluded: chain A residue 477 ILE Chi-restraints excluded: chain A residue 500 MET Chi-restraints excluded: chain A residue 567 VAL Chi-restraints excluded: chain A residue 652 MET Chi-restraints excluded: chain A residue 674 SER Chi-restraints excluded: chain A residue 697 LEU Chi-restraints excluded: chain A residue 732 LEU Chi-restraints excluded: chain A residue 772 VAL Chi-restraints excluded: chain A residue 869 VAL Chi-restraints excluded: chain A residue 884 MET Chi-restraints excluded: chain B residue 79 VAL Chi-restraints excluded: chain B residue 94 VAL Chi-restraints excluded: chain B residue 104 VAL Chi-restraints excluded: chain B residue 113 GLN Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 174 VAL Chi-restraints excluded: chain B residue 185 ASN Chi-restraints excluded: chain B residue 262 ASP Chi-restraints excluded: chain B residue 265 TRP Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 345 LEU Chi-restraints excluded: chain B residue 369 VAL Chi-restraints excluded: chain B residue 471 TYR Chi-restraints excluded: chain B residue 472 ILE Chi-restraints excluded: chain B residue 493 THR Chi-restraints excluded: chain B residue 527 PHE Chi-restraints excluded: chain B residue 541 VAL Chi-restraints excluded: chain B residue 574 ILE Chi-restraints excluded: chain B residue 772 VAL Chi-restraints excluded: chain B residue 815 ILE Chi-restraints excluded: chain B residue 869 VAL Chi-restraints excluded: chain B residue 887 THR Chi-restraints excluded: chain C residue 266 GLU Chi-restraints excluded: chain C residue 276 ILE Chi-restraints excluded: chain C residue 314 THR Chi-restraints excluded: chain C residue 320 THR Chi-restraints excluded: chain D residue 31 LEU Chi-restraints excluded: chain D residue 94 VAL Chi-restraints excluded: chain D residue 95 MET Chi-restraints excluded: chain D residue 264 ILE Chi-restraints excluded: chain D residue 266 VAL Chi-restraints excluded: chain D residue 273 VAL Chi-restraints excluded: chain D residue 301 GLU Chi-restraints excluded: chain D residue 344 TYR Chi-restraints excluded: chain D residue 357 LEU Chi-restraints excluded: chain D residue 416 VAL Chi-restraints excluded: chain D residue 474 TYR Chi-restraints excluded: chain D residue 487 THR Chi-restraints excluded: chain D residue 617 LEU Chi-restraints excluded: chain D residue 629 ILE Chi-restraints excluded: chain D residue 715 LEU Chi-restraints excluded: chain D residue 772 VAL Chi-restraints excluded: chain D residue 795 LEU Chi-restraints excluded: chain D residue 866 ILE Chi-restraints excluded: chain E residue 36 LEU Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 104 VAL Chi-restraints excluded: chain E residue 174 VAL Chi-restraints excluded: chain E residue 187 LEU Chi-restraints excluded: chain E residue 227 VAL Chi-restraints excluded: chain E residue 236 ILE Chi-restraints excluded: chain E residue 239 LEU Chi-restraints excluded: chain E residue 273 VAL Chi-restraints excluded: chain E residue 363 GLU Chi-restraints excluded: chain E residue 369 VAL Chi-restraints excluded: chain E residue 421 THR Chi-restraints excluded: chain E residue 472 ILE Chi-restraints excluded: chain E residue 527 PHE Chi-restraints excluded: chain E residue 575 SER Chi-restraints excluded: chain E residue 772 VAL Chi-restraints excluded: chain E residue 886 ILE Chi-restraints excluded: chain F residue 5 MET Chi-restraints excluded: chain F residue 298 VAL Chi-restraints excluded: chain F residue 318 VAL Chi-restraints excluded: chain F residue 328 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 362 random chunks: chunk 181 optimal weight: 10.0000 chunk 254 optimal weight: 0.5980 chunk 168 optimal weight: 0.0980 chunk 117 optimal weight: 0.7980 chunk 44 optimal weight: 0.6980 chunk 14 optimal weight: 0.7980 chunk 73 optimal weight: 0.8980 chunk 264 optimal weight: 0.9990 chunk 131 optimal weight: 0.8980 chunk 143 optimal weight: 1.9990 chunk 1 optimal weight: 3.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 352 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 92 HIS B 403 ASN D 252 GLN D 653 ASN D 692 ASN E 539 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.094169 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.080074 restraints weight = 69514.184| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.082752 restraints weight = 32267.064| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.084469 restraints weight = 18749.931| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.085604 restraints weight = 12692.357| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.086365 restraints weight = 9624.147| |-----------------------------------------------------------------------------| r_work (final): 0.3299 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8040 moved from start: 0.2400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 29880 Z= 0.117 Angle : 0.664 14.655 40550 Z= 0.322 Chirality : 0.043 0.222 4542 Planarity : 0.004 0.044 5250 Dihedral : 3.822 18.766 4040 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 2.85 % Allowed : 21.49 % Favored : 75.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.39 (0.14), residues: 3592 helix: 1.51 (0.13), residues: 1584 sheet: -0.24 (0.27), residues: 364 loop : -0.86 (0.15), residues: 1644 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 807 TYR 0.022 0.001 TYR E 17 PHE 0.024 0.001 PHE D 636 TRP 0.030 0.001 TRP B 238 HIS 0.010 0.001 HIS B 378 Details of bonding type rmsd covalent geometry : bond 0.00274 (29880) covalent geometry : angle 0.66409 (40550) hydrogen bonds : bond 0.03350 ( 1288) hydrogen bonds : angle 3.70295 ( 3657) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7184 Ramachandran restraints generated. 3592 Oldfield, 0 Emsley, 3592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7184 Ramachandran restraints generated. 3592 Oldfield, 0 Emsley, 3592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 869 residues out of total 3188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 778 time to evaluate : 0.817 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 LEU cc_start: 0.8755 (OUTLIER) cc_final: 0.8461 (mm) REVERT: A 44 ARG cc_start: 0.8091 (tmm160) cc_final: 0.7890 (ttp80) REVERT: A 66 LYS cc_start: 0.8087 (tptm) cc_final: 0.7679 (tptm) REVERT: A 110 GLU cc_start: 0.7877 (tp30) cc_final: 0.7624 (tp30) REVERT: A 111 MET cc_start: 0.8667 (tmm) cc_final: 0.8179 (tmm) REVERT: A 157 GLU cc_start: 0.7566 (mp0) cc_final: 0.7296 (mp0) REVERT: A 167 GLU cc_start: 0.7701 (tm-30) cc_final: 0.7444 (tm-30) REVERT: A 257 ASP cc_start: 0.8057 (m-30) cc_final: 0.7755 (m-30) REVERT: A 344 TYR cc_start: 0.8834 (OUTLIER) cc_final: 0.8101 (t80) REVERT: A 381 PHE cc_start: 0.7916 (m-10) cc_final: 0.7582 (m-10) REVERT: A 481 GLU cc_start: 0.8154 (mp0) cc_final: 0.7742 (mp0) REVERT: A 582 ARG cc_start: 0.8302 (mmp80) cc_final: 0.7966 (mmp-170) REVERT: A 636 PHE cc_start: 0.7801 (p90) cc_final: 0.7429 (p90) REVERT: A 668 ARG cc_start: 0.8597 (mtm180) cc_final: 0.8276 (mtm-85) REVERT: A 685 GLU cc_start: 0.8220 (tm-30) cc_final: 0.7919 (tm-30) REVERT: A 712 GLU cc_start: 0.7676 (pm20) cc_final: 0.7318 (pm20) REVERT: A 831 GLU cc_start: 0.8177 (tm-30) cc_final: 0.7954 (tm-30) REVERT: B 36 LEU cc_start: 0.8841 (mm) cc_final: 0.8600 (mm) REVERT: B 291 MET cc_start: 0.8125 (tmm) cc_final: 0.7754 (tmm) REVERT: B 339 ASP cc_start: 0.8140 (m-30) cc_final: 0.7761 (m-30) REVERT: B 365 MET cc_start: 0.7591 (ptp) cc_final: 0.7375 (ptp) REVERT: B 399 ASP cc_start: 0.8419 (m-30) cc_final: 0.8145 (m-30) REVERT: B 600 GLU cc_start: 0.7848 (mt-10) cc_final: 0.7608 (mt-10) REVERT: B 643 ASP cc_start: 0.8195 (t0) cc_final: 0.7923 (t0) REVERT: B 652 MET cc_start: 0.9245 (tpp) cc_final: 0.8502 (mmt) REVERT: B 674 SER cc_start: 0.8283 (m) cc_final: 0.7918 (p) REVERT: B 724 GLU cc_start: 0.8227 (mm-30) cc_final: 0.7732 (mm-30) REVERT: B 803 ASP cc_start: 0.7360 (t0) cc_final: 0.6884 (t0) REVERT: B 859 GLU cc_start: 0.7256 (tm-30) cc_final: 0.6995 (tm-30) REVERT: B 869 VAL cc_start: 0.8831 (OUTLIER) cc_final: 0.8623 (t) REVERT: C 314 THR cc_start: 0.6794 (OUTLIER) cc_final: 0.6503 (t) REVERT: D 40 MET cc_start: 0.8261 (mmm) cc_final: 0.7972 (mmp) REVERT: D 44 ARG cc_start: 0.7778 (mtt180) cc_final: 0.7414 (mtt180) REVERT: D 66 LYS cc_start: 0.8318 (tptm) cc_final: 0.7940 (tptm) REVERT: D 99 ASP cc_start: 0.8170 (p0) cc_final: 0.7786 (p0) REVERT: D 109 GLU cc_start: 0.8148 (mm-30) cc_final: 0.7867 (mm-30) REVERT: D 111 MET cc_start: 0.8798 (tpp) cc_final: 0.8525 (tpp) REVERT: D 169 LYS cc_start: 0.8391 (mmmm) cc_final: 0.8098 (mmmt) REVERT: D 209 CYS cc_start: 0.7790 (t) cc_final: 0.7473 (t) REVERT: D 253 GLU cc_start: 0.7876 (mp0) cc_final: 0.7421 (mp0) REVERT: D 257 ASP cc_start: 0.8108 (m-30) cc_final: 0.7811 (m-30) REVERT: D 324 PHE cc_start: 0.6438 (p90) cc_final: 0.6028 (p90) REVERT: D 342 LYS cc_start: 0.8553 (ptpp) cc_final: 0.8214 (ptpp) REVERT: D 344 TYR cc_start: 0.8681 (OUTLIER) cc_final: 0.7786 (t80) REVERT: D 409 MET cc_start: 0.7469 (tpp) cc_final: 0.6145 (tpt) REVERT: D 519 MET cc_start: 0.7254 (mmp) cc_final: 0.6512 (mmp) REVERT: D 552 LEU cc_start: 0.8705 (tt) cc_final: 0.8392 (tp) REVERT: D 573 TRP cc_start: 0.8136 (m100) cc_final: 0.7747 (m100) REVERT: D 610 MET cc_start: 0.8171 (mtp) cc_final: 0.7930 (mtt) REVERT: D 620 MET cc_start: 0.8249 (tpp) cc_final: 0.7961 (tpp) REVERT: D 642 ASN cc_start: 0.8817 (m-40) cc_final: 0.8090 (m-40) REVERT: D 769 ASP cc_start: 0.8043 (t0) cc_final: 0.7822 (t0) REVERT: D 839 LEU cc_start: 0.8883 (mp) cc_final: 0.8678 (mt) REVERT: E 36 LEU cc_start: 0.8696 (OUTLIER) cc_final: 0.8414 (mm) REVERT: E 44 ARG cc_start: 0.8130 (ttp-170) cc_final: 0.7859 (ptm160) REVERT: E 81 LYS cc_start: 0.7859 (ptmm) cc_final: 0.7595 (ptmm) REVERT: E 111 MET cc_start: 0.8988 (tmm) cc_final: 0.8198 (tmm) REVERT: E 339 ASP cc_start: 0.8285 (m-30) cc_final: 0.7834 (m-30) REVERT: E 363 GLU cc_start: 0.6704 (OUTLIER) cc_final: 0.6419 (pt0) REVERT: E 423 GLU cc_start: 0.7667 (mp0) cc_final: 0.7453 (mp0) REVERT: E 498 ASN cc_start: 0.8424 (t0) cc_final: 0.8133 (t0) REVERT: E 642 ASN cc_start: 0.8669 (t0) cc_final: 0.8363 (t0) REVERT: E 686 GLU cc_start: 0.8008 (tp30) cc_final: 0.7760 (tp30) REVERT: E 708 ASP cc_start: 0.7206 (m-30) cc_final: 0.6983 (m-30) REVERT: E 848 MET cc_start: 0.7868 (mmt) cc_final: 0.7547 (mmt) REVERT: E 884 MET cc_start: 0.6443 (tpt) cc_final: 0.6116 (tpt) REVERT: F 26 GLN cc_start: 0.7005 (mm-40) cc_final: 0.6549 (mm-40) REVERT: F 290 THR cc_start: 0.7594 (p) cc_final: 0.7389 (t) REVERT: F 301 GLU cc_start: 0.8149 (mm-30) cc_final: 0.7888 (mm-30) outliers start: 91 outliers final: 81 residues processed: 826 average time/residue: 0.1797 time to fit residues: 233.1596 Evaluate side-chains 852 residues out of total 3188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 764 time to evaluate : 0.969 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 61 VAL Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 97 SER Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 191 ILE Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 340 VAL Chi-restraints excluded: chain A residue 344 TYR Chi-restraints excluded: chain A residue 379 LEU Chi-restraints excluded: chain A residue 477 ILE Chi-restraints excluded: chain A residue 500 MET Chi-restraints excluded: chain A residue 567 VAL Chi-restraints excluded: chain A residue 629 ILE Chi-restraints excluded: chain A residue 641 LEU Chi-restraints excluded: chain A residue 652 MET Chi-restraints excluded: chain A residue 732 LEU Chi-restraints excluded: chain A residue 772 VAL Chi-restraints excluded: chain A residue 869 VAL Chi-restraints excluded: chain A residue 884 MET Chi-restraints excluded: chain B residue 79 VAL Chi-restraints excluded: chain B residue 104 VAL Chi-restraints excluded: chain B residue 113 GLN Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 174 VAL Chi-restraints excluded: chain B residue 185 ASN Chi-restraints excluded: chain B residue 262 ASP Chi-restraints excluded: chain B residue 265 TRP Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 345 LEU Chi-restraints excluded: chain B residue 369 VAL Chi-restraints excluded: chain B residue 471 TYR Chi-restraints excluded: chain B residue 472 ILE Chi-restraints excluded: chain B residue 493 THR Chi-restraints excluded: chain B residue 527 PHE Chi-restraints excluded: chain B residue 574 ILE Chi-restraints excluded: chain B residue 772 VAL Chi-restraints excluded: chain B residue 815 ILE Chi-restraints excluded: chain B residue 869 VAL Chi-restraints excluded: chain B residue 887 THR Chi-restraints excluded: chain C residue 266 GLU Chi-restraints excluded: chain C residue 272 VAL Chi-restraints excluded: chain C residue 276 ILE Chi-restraints excluded: chain C residue 314 THR Chi-restraints excluded: chain C residue 320 THR Chi-restraints excluded: chain D residue 31 LEU Chi-restraints excluded: chain D residue 94 VAL Chi-restraints excluded: chain D residue 95 MET Chi-restraints excluded: chain D residue 117 VAL Chi-restraints excluded: chain D residue 264 ILE Chi-restraints excluded: chain D residue 266 VAL Chi-restraints excluded: chain D residue 273 VAL Chi-restraints excluded: chain D residue 301 GLU Chi-restraints excluded: chain D residue 344 TYR Chi-restraints excluded: chain D residue 357 LEU Chi-restraints excluded: chain D residue 416 VAL Chi-restraints excluded: chain D residue 474 TYR Chi-restraints excluded: chain D residue 487 THR Chi-restraints excluded: chain D residue 571 VAL Chi-restraints excluded: chain D residue 617 LEU Chi-restraints excluded: chain D residue 629 ILE Chi-restraints excluded: chain D residue 692 ASN Chi-restraints excluded: chain D residue 715 LEU Chi-restraints excluded: chain D residue 772 VAL Chi-restraints excluded: chain D residue 795 LEU Chi-restraints excluded: chain D residue 866 ILE Chi-restraints excluded: chain D residue 890 LEU Chi-restraints excluded: chain E residue 36 LEU Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 104 VAL Chi-restraints excluded: chain E residue 174 VAL Chi-restraints excluded: chain E residue 187 LEU Chi-restraints excluded: chain E residue 227 VAL Chi-restraints excluded: chain E residue 236 ILE Chi-restraints excluded: chain E residue 239 LEU Chi-restraints excluded: chain E residue 273 VAL Chi-restraints excluded: chain E residue 331 THR Chi-restraints excluded: chain E residue 363 GLU Chi-restraints excluded: chain E residue 369 VAL Chi-restraints excluded: chain E residue 472 ILE Chi-restraints excluded: chain E residue 527 PHE Chi-restraints excluded: chain E residue 574 ILE Chi-restraints excluded: chain E residue 575 SER Chi-restraints excluded: chain E residue 772 VAL Chi-restraints excluded: chain E residue 867 LEU Chi-restraints excluded: chain F residue 5 MET Chi-restraints excluded: chain F residue 318 VAL Chi-restraints excluded: chain F residue 328 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 362 random chunks: chunk 16 optimal weight: 0.8980 chunk 287 optimal weight: 6.9990 chunk 74 optimal weight: 6.9990 chunk 332 optimal weight: 3.9990 chunk 39 optimal weight: 0.7980 chunk 111 optimal weight: 0.8980 chunk 304 optimal weight: 0.9980 chunk 285 optimal weight: 2.9990 chunk 181 optimal weight: 10.0000 chunk 50 optimal weight: 0.8980 chunk 247 optimal weight: 8.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 352 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 274 ASN D 676 GLN D 692 ASN E 523 HIS E 539 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.093522 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.079424 restraints weight = 69954.355| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.082091 restraints weight = 32388.250| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.083809 restraints weight = 18797.632| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.084948 restraints weight = 12703.074| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.085718 restraints weight = 9619.589| |-----------------------------------------------------------------------------| r_work (final): 0.3287 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8052 moved from start: 0.2434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 29880 Z= 0.127 Angle : 0.686 14.444 40550 Z= 0.333 Chirality : 0.043 0.224 4542 Planarity : 0.004 0.044 5250 Dihedral : 3.849 18.625 4040 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 3.07 % Allowed : 21.64 % Favored : 75.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.39 (0.14), residues: 3592 helix: 1.52 (0.13), residues: 1582 sheet: -0.22 (0.27), residues: 362 loop : -0.87 (0.15), residues: 1648 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 98 TYR 0.022 0.001 TYR E 17 PHE 0.024 0.001 PHE D 636 TRP 0.033 0.001 TRP B 238 HIS 0.011 0.001 HIS D 378 Details of bonding type rmsd covalent geometry : bond 0.00300 (29880) covalent geometry : angle 0.68578 (40550) hydrogen bonds : bond 0.03541 ( 1288) hydrogen bonds : angle 3.73382 ( 3657) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7184 Ramachandran restraints generated. 3592 Oldfield, 0 Emsley, 3592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7184 Ramachandran restraints generated. 3592 Oldfield, 0 Emsley, 3592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 869 residues out of total 3188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 771 time to evaluate : 1.131 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: A 31 LEU cc_start: 0.8766 (OUTLIER) cc_final: 0.8473 (mm) REVERT: A 66 LYS cc_start: 0.8095 (tptm) cc_final: 0.7678 (tptm) REVERT: A 110 GLU cc_start: 0.7910 (tp30) cc_final: 0.7648 (tp30) REVERT: A 111 MET cc_start: 0.8660 (tmm) cc_final: 0.8170 (tmm) REVERT: A 167 GLU cc_start: 0.7716 (tm-30) cc_final: 0.7452 (tm-30) REVERT: A 257 ASP cc_start: 0.8062 (m-30) cc_final: 0.7750 (m-30) REVERT: A 344 TYR cc_start: 0.8848 (OUTLIER) cc_final: 0.8102 (t80) REVERT: A 358 LYS cc_start: 0.8345 (tppt) cc_final: 0.8099 (tptm) REVERT: A 371 MET cc_start: 0.7001 (mtp) cc_final: 0.6620 (mtp) REVERT: A 381 PHE cc_start: 0.7951 (m-10) cc_final: 0.7607 (m-10) REVERT: A 481 GLU cc_start: 0.8163 (mp0) cc_final: 0.7754 (mp0) REVERT: A 582 ARG cc_start: 0.8274 (mmp80) cc_final: 0.7917 (mmp80) REVERT: A 636 PHE cc_start: 0.7791 (p90) cc_final: 0.7411 (p90) REVERT: A 668 ARG cc_start: 0.8629 (mtm180) cc_final: 0.8414 (mtm180) REVERT: A 671 MET cc_start: 0.7639 (mmm) cc_final: 0.7400 (mmp) REVERT: A 685 GLU cc_start: 0.8238 (tm-30) cc_final: 0.7930 (tm-30) REVERT: A 712 GLU cc_start: 0.7686 (pm20) cc_final: 0.7335 (pm20) REVERT: A 766 MET cc_start: 0.7823 (mmm) cc_final: 0.7549 (mmp) REVERT: A 831 GLU cc_start: 0.8188 (tm-30) cc_final: 0.7964 (tm-30) REVERT: B 36 LEU cc_start: 0.8849 (mm) cc_final: 0.8611 (mm) REVERT: B 339 ASP cc_start: 0.8153 (m-30) cc_final: 0.7779 (m-30) REVERT: B 355 LEU cc_start: 0.7869 (mm) cc_final: 0.7647 (mm) REVERT: B 365 MET cc_start: 0.7625 (ptp) cc_final: 0.7407 (ptp) REVERT: B 643 ASP cc_start: 0.8254 (t0) cc_final: 0.7965 (t0) REVERT: B 674 SER cc_start: 0.8304 (m) cc_final: 0.7919 (p) REVERT: B 724 GLU cc_start: 0.8232 (mm-30) cc_final: 0.7728 (mm-30) REVERT: B 803 ASP cc_start: 0.7411 (t0) cc_final: 0.6964 (t0) REVERT: B 859 GLU cc_start: 0.7279 (tm-30) cc_final: 0.7000 (tm-30) REVERT: C 314 THR cc_start: 0.6781 (OUTLIER) cc_final: 0.6503 (t) REVERT: D 40 MET cc_start: 0.8217 (mmm) cc_final: 0.7951 (mmp) REVERT: D 44 ARG cc_start: 0.7790 (mtt180) cc_final: 0.7339 (mtt180) REVERT: D 66 LYS cc_start: 0.8322 (tptm) cc_final: 0.7951 (tptm) REVERT: D 99 ASP cc_start: 0.8169 (p0) cc_final: 0.7824 (p0) REVERT: D 109 GLU cc_start: 0.8157 (mm-30) cc_final: 0.7733 (mm-30) REVERT: D 111 MET cc_start: 0.8800 (tpp) cc_final: 0.8519 (tpp) REVERT: D 209 CYS cc_start: 0.7824 (t) cc_final: 0.7507 (t) REVERT: D 253 GLU cc_start: 0.7881 (mp0) cc_final: 0.7440 (mp0) REVERT: D 324 PHE cc_start: 0.6404 (p90) cc_final: 0.6003 (p90) REVERT: D 342 LYS cc_start: 0.8562 (ptpp) cc_final: 0.8226 (ptpp) REVERT: D 344 TYR cc_start: 0.8709 (OUTLIER) cc_final: 0.7812 (t80) REVERT: D 409 MET cc_start: 0.7490 (tpp) cc_final: 0.6162 (tpt) REVERT: D 519 MET cc_start: 0.7387 (mmp) cc_final: 0.6533 (mmp) REVERT: D 552 LEU cc_start: 0.8703 (tt) cc_final: 0.8390 (tp) REVERT: D 573 TRP cc_start: 0.8145 (m100) cc_final: 0.7773 (m100) REVERT: D 610 MET cc_start: 0.8213 (mtp) cc_final: 0.8002 (mtt) REVERT: D 620 MET cc_start: 0.8272 (tpp) cc_final: 0.7984 (tpp) REVERT: D 642 ASN cc_start: 0.8837 (m-40) cc_final: 0.8101 (m-40) REVERT: D 676 GLN cc_start: 0.8884 (OUTLIER) cc_final: 0.8681 (tm-30) REVERT: D 839 LEU cc_start: 0.8877 (mp) cc_final: 0.8676 (mt) REVERT: E 36 LEU cc_start: 0.8713 (OUTLIER) cc_final: 0.8429 (mm) REVERT: E 44 ARG cc_start: 0.8095 (ttp-170) cc_final: 0.7836 (ptm160) REVERT: E 81 LYS cc_start: 0.7958 (ptmm) cc_final: 0.7694 (ptmm) REVERT: E 111 MET cc_start: 0.8964 (tmm) cc_final: 0.8178 (tmm) REVERT: E 339 ASP cc_start: 0.8298 (m-30) cc_final: 0.7839 (m-30) REVERT: E 363 GLU cc_start: 0.6769 (OUTLIER) cc_final: 0.6460 (pt0) REVERT: E 423 GLU cc_start: 0.7663 (mp0) cc_final: 0.7425 (pm20) REVERT: E 498 ASN cc_start: 0.8427 (t0) cc_final: 0.8137 (t0) REVERT: E 642 ASN cc_start: 0.8667 (t0) cc_final: 0.8366 (t0) REVERT: E 686 GLU cc_start: 0.8016 (tp30) cc_final: 0.7801 (tp30) REVERT: E 695 GLU cc_start: 0.8249 (tp30) cc_final: 0.7974 (tp30) REVERT: E 708 ASP cc_start: 0.7244 (m-30) cc_final: 0.7007 (m-30) REVERT: E 848 MET cc_start: 0.7842 (mmt) cc_final: 0.7523 (mmt) REVERT: E 884 MET cc_start: 0.6460 (tpt) cc_final: 0.6116 (tpt) REVERT: F 26 GLN cc_start: 0.7026 (mm-40) cc_final: 0.6543 (mm-40) REVERT: F 301 GLU cc_start: 0.8144 (mm-30) cc_final: 0.7886 (mm-30) outliers start: 98 outliers final: 82 residues processed: 823 average time/residue: 0.1810 time to fit residues: 233.4863 Evaluate side-chains 846 residues out of total 3188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 757 time to evaluate : 1.108 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 61 VAL Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 97 SER Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 191 ILE Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 340 VAL Chi-restraints excluded: chain A residue 344 TYR Chi-restraints excluded: chain A residue 477 ILE Chi-restraints excluded: chain A residue 500 MET Chi-restraints excluded: chain A residue 567 VAL Chi-restraints excluded: chain A residue 629 ILE Chi-restraints excluded: chain A residue 652 MET Chi-restraints excluded: chain A residue 732 LEU Chi-restraints excluded: chain A residue 772 VAL Chi-restraints excluded: chain A residue 777 VAL Chi-restraints excluded: chain A residue 820 GLU Chi-restraints excluded: chain A residue 869 VAL Chi-restraints excluded: chain A residue 884 MET Chi-restraints excluded: chain B residue 79 VAL Chi-restraints excluded: chain B residue 94 VAL Chi-restraints excluded: chain B residue 104 VAL Chi-restraints excluded: chain B residue 113 GLN Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 174 VAL Chi-restraints excluded: chain B residue 185 ASN Chi-restraints excluded: chain B residue 262 ASP Chi-restraints excluded: chain B residue 265 TRP Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 345 LEU Chi-restraints excluded: chain B residue 369 VAL Chi-restraints excluded: chain B residue 471 TYR Chi-restraints excluded: chain B residue 472 ILE Chi-restraints excluded: chain B residue 493 THR Chi-restraints excluded: chain B residue 527 PHE Chi-restraints excluded: chain B residue 541 VAL Chi-restraints excluded: chain B residue 574 ILE Chi-restraints excluded: chain B residue 772 VAL Chi-restraints excluded: chain B residue 815 ILE Chi-restraints excluded: chain B residue 887 THR Chi-restraints excluded: chain C residue 266 GLU Chi-restraints excluded: chain C residue 272 VAL Chi-restraints excluded: chain C residue 314 THR Chi-restraints excluded: chain C residue 320 THR Chi-restraints excluded: chain D residue 31 LEU Chi-restraints excluded: chain D residue 94 VAL Chi-restraints excluded: chain D residue 95 MET Chi-restraints excluded: chain D residue 117 VAL Chi-restraints excluded: chain D residue 264 ILE Chi-restraints excluded: chain D residue 266 VAL Chi-restraints excluded: chain D residue 273 VAL Chi-restraints excluded: chain D residue 301 GLU Chi-restraints excluded: chain D residue 344 TYR Chi-restraints excluded: chain D residue 357 LEU Chi-restraints excluded: chain D residue 416 VAL Chi-restraints excluded: chain D residue 425 LEU Chi-restraints excluded: chain D residue 474 TYR Chi-restraints excluded: chain D residue 487 THR Chi-restraints excluded: chain D residue 571 VAL Chi-restraints excluded: chain D residue 617 LEU Chi-restraints excluded: chain D residue 629 ILE Chi-restraints excluded: chain D residue 640 VAL Chi-restraints excluded: chain D residue 676 GLN Chi-restraints excluded: chain D residue 692 ASN Chi-restraints excluded: chain D residue 715 LEU Chi-restraints excluded: chain D residue 772 VAL Chi-restraints excluded: chain D residue 795 LEU Chi-restraints excluded: chain D residue 866 ILE Chi-restraints excluded: chain E residue 36 LEU Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 104 VAL Chi-restraints excluded: chain E residue 174 VAL Chi-restraints excluded: chain E residue 187 LEU Chi-restraints excluded: chain E residue 227 VAL Chi-restraints excluded: chain E residue 236 ILE Chi-restraints excluded: chain E residue 239 LEU Chi-restraints excluded: chain E residue 273 VAL Chi-restraints excluded: chain E residue 331 THR Chi-restraints excluded: chain E residue 363 GLU Chi-restraints excluded: chain E residue 369 VAL Chi-restraints excluded: chain E residue 472 ILE Chi-restraints excluded: chain E residue 527 PHE Chi-restraints excluded: chain E residue 574 ILE Chi-restraints excluded: chain E residue 575 SER Chi-restraints excluded: chain E residue 772 VAL Chi-restraints excluded: chain E residue 867 LEU Chi-restraints excluded: chain F residue 318 VAL Chi-restraints excluded: chain F residue 328 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 362 random chunks: chunk 14 optimal weight: 0.5980 chunk 348 optimal weight: 0.9980 chunk 292 optimal weight: 2.9990 chunk 107 optimal weight: 20.0000 chunk 10 optimal weight: 1.9990 chunk 25 optimal weight: 0.9990 chunk 167 optimal weight: 6.9990 chunk 160 optimal weight: 0.9990 chunk 233 optimal weight: 1.9990 chunk 46 optimal weight: 7.9990 chunk 210 optimal weight: 10.0000 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 352 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 274 ASN D 653 ASN E 523 HIS E 539 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.092930 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.078793 restraints weight = 69819.697| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.081445 restraints weight = 32435.432| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.083166 restraints weight = 18893.407| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.084300 restraints weight = 12780.833| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.085065 restraints weight = 9693.005| |-----------------------------------------------------------------------------| r_work (final): 0.3272 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8062 moved from start: 0.2531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 29880 Z= 0.136 Angle : 0.705 14.098 40550 Z= 0.342 Chirality : 0.043 0.236 4542 Planarity : 0.004 0.045 5250 Dihedral : 3.889 19.059 4040 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 2.95 % Allowed : 22.33 % Favored : 74.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.39 (0.14), residues: 3592 helix: 1.50 (0.13), residues: 1586 sheet: -0.16 (0.28), residues: 352 loop : -0.87 (0.15), residues: 1654 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 526 TYR 0.023 0.001 TYR E 17 PHE 0.023 0.001 PHE D 636 TRP 0.034 0.001 TRP B 238 HIS 0.011 0.001 HIS B 378 Details of bonding type rmsd covalent geometry : bond 0.00325 (29880) covalent geometry : angle 0.70544 (40550) hydrogen bonds : bond 0.03705 ( 1288) hydrogen bonds : angle 3.74938 ( 3657) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7184 Ramachandran restraints generated. 3592 Oldfield, 0 Emsley, 3592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7184 Ramachandran restraints generated. 3592 Oldfield, 0 Emsley, 3592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 857 residues out of total 3188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 763 time to evaluate : 0.973 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 LEU cc_start: 0.8790 (OUTLIER) cc_final: 0.8513 (mm) REVERT: A 66 LYS cc_start: 0.8099 (tptm) cc_final: 0.7680 (tptm) REVERT: A 110 GLU cc_start: 0.7960 (tp30) cc_final: 0.7703 (tp30) REVERT: A 111 MET cc_start: 0.8675 (tmm) cc_final: 0.8173 (tmm) REVERT: A 167 GLU cc_start: 0.7754 (tm-30) cc_final: 0.7477 (tm-30) REVERT: A 257 ASP cc_start: 0.8082 (m-30) cc_final: 0.7769 (m-30) REVERT: A 344 TYR cc_start: 0.8872 (OUTLIER) cc_final: 0.7987 (t80) REVERT: A 358 LYS cc_start: 0.8350 (tppt) cc_final: 0.8105 (tptm) REVERT: A 381 PHE cc_start: 0.7990 (m-10) cc_final: 0.7618 (m-10) REVERT: A 481 GLU cc_start: 0.8156 (mp0) cc_final: 0.7739 (mp0) REVERT: A 582 ARG cc_start: 0.8170 (mmp80) cc_final: 0.7766 (mmp80) REVERT: A 636 PHE cc_start: 0.7779 (p90) cc_final: 0.7344 (p90) REVERT: A 668 ARG cc_start: 0.8613 (mtm180) cc_final: 0.8396 (mtm180) REVERT: A 671 MET cc_start: 0.7673 (mmm) cc_final: 0.7432 (mmp) REVERT: A 685 GLU cc_start: 0.8239 (tm-30) cc_final: 0.7959 (tm-30) REVERT: A 712 GLU cc_start: 0.7700 (pm20) cc_final: 0.7337 (pm20) REVERT: B 36 LEU cc_start: 0.8854 (mm) cc_final: 0.8614 (mm) REVERT: B 339 ASP cc_start: 0.8149 (m-30) cc_final: 0.7772 (m-30) REVERT: B 355 LEU cc_start: 0.7852 (mm) cc_final: 0.7620 (mm) REVERT: B 399 ASP cc_start: 0.8418 (m-30) cc_final: 0.8143 (m-30) REVERT: B 433 GLN cc_start: 0.8327 (mp10) cc_final: 0.8072 (mp10) REVERT: B 643 ASP cc_start: 0.8247 (t0) cc_final: 0.7977 (t0) REVERT: B 674 SER cc_start: 0.8320 (m) cc_final: 0.7933 (p) REVERT: B 724 GLU cc_start: 0.8239 (mm-30) cc_final: 0.7733 (mm-30) REVERT: B 803 ASP cc_start: 0.7396 (t0) cc_final: 0.6952 (t0) REVERT: B 859 GLU cc_start: 0.7284 (tm-30) cc_final: 0.6991 (tm-30) REVERT: C 314 THR cc_start: 0.6819 (OUTLIER) cc_final: 0.6536 (t) REVERT: D 40 MET cc_start: 0.8219 (mmm) cc_final: 0.7946 (mmp) REVERT: D 44 ARG cc_start: 0.7803 (mtt180) cc_final: 0.7439 (mtt180) REVERT: D 66 LYS cc_start: 0.8332 (tptm) cc_final: 0.7952 (tptm) REVERT: D 99 ASP cc_start: 0.8174 (p0) cc_final: 0.7834 (p0) REVERT: D 109 GLU cc_start: 0.8173 (mm-30) cc_final: 0.7740 (mm-30) REVERT: D 111 MET cc_start: 0.8820 (tpp) cc_final: 0.8518 (tpp) REVERT: D 209 CYS cc_start: 0.7858 (t) cc_final: 0.7550 (t) REVERT: D 253 GLU cc_start: 0.7877 (mp0) cc_final: 0.7459 (mp0) REVERT: D 257 ASP cc_start: 0.8191 (m-30) cc_final: 0.7937 (m-30) REVERT: D 324 PHE cc_start: 0.6438 (p90) cc_final: 0.6035 (p90) REVERT: D 342 LYS cc_start: 0.8560 (ptpp) cc_final: 0.8226 (ptpp) REVERT: D 344 TYR cc_start: 0.8727 (OUTLIER) cc_final: 0.7745 (t80) REVERT: D 552 LEU cc_start: 0.8756 (tt) cc_final: 0.8458 (tp) REVERT: D 573 TRP cc_start: 0.8157 (m100) cc_final: 0.7791 (m100) REVERT: D 620 MET cc_start: 0.8266 (tpp) cc_final: 0.7968 (tpp) REVERT: D 642 ASN cc_start: 0.8847 (m-40) cc_final: 0.8111 (m-40) REVERT: E 36 LEU cc_start: 0.8726 (OUTLIER) cc_final: 0.8428 (mm) REVERT: E 44 ARG cc_start: 0.8093 (ttp-170) cc_final: 0.7838 (ptm160) REVERT: E 81 LYS cc_start: 0.7988 (ptmm) cc_final: 0.7719 (ptmm) REVERT: E 111 MET cc_start: 0.8919 (tmm) cc_final: 0.8166 (tmm) REVERT: E 276 GLN cc_start: 0.8689 (mm-40) cc_final: 0.8248 (mm-40) REVERT: E 280 ASP cc_start: 0.8543 (m-30) cc_final: 0.8272 (m-30) REVERT: E 339 ASP cc_start: 0.8322 (m-30) cc_final: 0.7874 (m-30) REVERT: E 348 MET cc_start: 0.8149 (mmt) cc_final: 0.7890 (mtp) REVERT: E 363 GLU cc_start: 0.6826 (OUTLIER) cc_final: 0.6489 (pt0) REVERT: E 394 MET cc_start: 0.7768 (mtt) cc_final: 0.7496 (mtm) REVERT: E 498 ASN cc_start: 0.8402 (t0) cc_final: 0.8117 (t0) REVERT: E 522 PHE cc_start: 0.8422 (t80) cc_final: 0.8088 (t80) REVERT: E 642 ASN cc_start: 0.8679 (t0) cc_final: 0.8379 (t0) REVERT: E 686 GLU cc_start: 0.8030 (tp30) cc_final: 0.7807 (tp30) REVERT: E 708 ASP cc_start: 0.7278 (m-30) cc_final: 0.7028 (m-30) REVERT: E 848 MET cc_start: 0.7839 (mmt) cc_final: 0.7533 (mmt) REVERT: E 884 MET cc_start: 0.6547 (tpt) cc_final: 0.6201 (tpt) REVERT: F 26 GLN cc_start: 0.6993 (mm-40) cc_final: 0.6526 (mm-40) REVERT: F 301 GLU cc_start: 0.8144 (mm-30) cc_final: 0.7881 (mm-30) outliers start: 94 outliers final: 84 residues processed: 815 average time/residue: 0.1746 time to fit residues: 223.2770 Evaluate side-chains 845 residues out of total 3188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 755 time to evaluate : 1.155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 61 VAL Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 97 SER Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 160 GLU Chi-restraints excluded: chain A residue 191 ILE Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 340 VAL Chi-restraints excluded: chain A residue 344 TYR Chi-restraints excluded: chain A residue 406 LEU Chi-restraints excluded: chain A residue 477 ILE Chi-restraints excluded: chain A residue 500 MET Chi-restraints excluded: chain A residue 567 VAL Chi-restraints excluded: chain A residue 629 ILE Chi-restraints excluded: chain A residue 641 LEU Chi-restraints excluded: chain A residue 652 MET Chi-restraints excluded: chain A residue 674 SER Chi-restraints excluded: chain A residue 732 LEU Chi-restraints excluded: chain A residue 772 VAL Chi-restraints excluded: chain A residue 777 VAL Chi-restraints excluded: chain A residue 820 GLU Chi-restraints excluded: chain A residue 869 VAL Chi-restraints excluded: chain A residue 884 MET Chi-restraints excluded: chain B residue 79 VAL Chi-restraints excluded: chain B residue 94 VAL Chi-restraints excluded: chain B residue 104 VAL Chi-restraints excluded: chain B residue 113 GLN Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 174 VAL Chi-restraints excluded: chain B residue 185 ASN Chi-restraints excluded: chain B residue 262 ASP Chi-restraints excluded: chain B residue 265 TRP Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 345 LEU Chi-restraints excluded: chain B residue 369 VAL Chi-restraints excluded: chain B residue 472 ILE Chi-restraints excluded: chain B residue 527 PHE Chi-restraints excluded: chain B residue 541 VAL Chi-restraints excluded: chain B residue 574 ILE Chi-restraints excluded: chain B residue 772 VAL Chi-restraints excluded: chain B residue 815 ILE Chi-restraints excluded: chain B residue 887 THR Chi-restraints excluded: chain C residue 266 GLU Chi-restraints excluded: chain C residue 272 VAL Chi-restraints excluded: chain C residue 314 THR Chi-restraints excluded: chain C residue 320 THR Chi-restraints excluded: chain D residue 31 LEU Chi-restraints excluded: chain D residue 94 VAL Chi-restraints excluded: chain D residue 95 MET Chi-restraints excluded: chain D residue 117 VAL Chi-restraints excluded: chain D residue 264 ILE Chi-restraints excluded: chain D residue 266 VAL Chi-restraints excluded: chain D residue 273 VAL Chi-restraints excluded: chain D residue 301 GLU Chi-restraints excluded: chain D residue 344 TYR Chi-restraints excluded: chain D residue 357 LEU Chi-restraints excluded: chain D residue 416 VAL Chi-restraints excluded: chain D residue 425 LEU Chi-restraints excluded: chain D residue 474 TYR Chi-restraints excluded: chain D residue 487 THR Chi-restraints excluded: chain D residue 571 VAL Chi-restraints excluded: chain D residue 617 LEU Chi-restraints excluded: chain D residue 629 ILE Chi-restraints excluded: chain D residue 640 VAL Chi-restraints excluded: chain D residue 715 LEU Chi-restraints excluded: chain D residue 772 VAL Chi-restraints excluded: chain D residue 795 LEU Chi-restraints excluded: chain D residue 866 ILE Chi-restraints excluded: chain E residue 36 LEU Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 104 VAL Chi-restraints excluded: chain E residue 174 VAL Chi-restraints excluded: chain E residue 187 LEU Chi-restraints excluded: chain E residue 227 VAL Chi-restraints excluded: chain E residue 236 ILE Chi-restraints excluded: chain E residue 239 LEU Chi-restraints excluded: chain E residue 273 VAL Chi-restraints excluded: chain E residue 331 THR Chi-restraints excluded: chain E residue 363 GLU Chi-restraints excluded: chain E residue 369 VAL Chi-restraints excluded: chain E residue 472 ILE Chi-restraints excluded: chain E residue 527 PHE Chi-restraints excluded: chain E residue 574 ILE Chi-restraints excluded: chain E residue 575 SER Chi-restraints excluded: chain E residue 772 VAL Chi-restraints excluded: chain E residue 867 LEU Chi-restraints excluded: chain F residue 318 VAL Chi-restraints excluded: chain F residue 328 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 362 random chunks: chunk 285 optimal weight: 0.9980 chunk 137 optimal weight: 0.3980 chunk 324 optimal weight: 4.9990 chunk 111 optimal weight: 0.9990 chunk 68 optimal weight: 1.9990 chunk 166 optimal weight: 5.9990 chunk 309 optimal weight: 0.8980 chunk 152 optimal weight: 3.9990 chunk 359 optimal weight: 1.9990 chunk 71 optimal weight: 0.0980 chunk 316 optimal weight: 1.9990 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 352 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 274 ASN D 692 ASN E 539 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.093834 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.079681 restraints weight = 70462.204| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.082375 restraints weight = 32620.035| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.084102 restraints weight = 18904.470| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.085251 restraints weight = 12769.749| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.086013 restraints weight = 9653.722| |-----------------------------------------------------------------------------| r_work (final): 0.3293 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8043 moved from start: 0.2532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 29880 Z= 0.125 Angle : 0.706 14.415 40550 Z= 0.342 Chirality : 0.043 0.240 4542 Planarity : 0.004 0.044 5250 Dihedral : 3.838 18.963 4040 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 2.73 % Allowed : 22.62 % Favored : 74.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.40 (0.14), residues: 3592 helix: 1.46 (0.13), residues: 1588 sheet: -0.08 (0.28), residues: 350 loop : -0.82 (0.15), residues: 1654 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 98 TYR 0.022 0.001 TYR E 17 PHE 0.025 0.001 PHE D 636 TRP 0.035 0.001 TRP B 238 HIS 0.011 0.001 HIS B 378 Details of bonding type rmsd covalent geometry : bond 0.00295 (29880) covalent geometry : angle 0.70562 (40550) hydrogen bonds : bond 0.03475 ( 1288) hydrogen bonds : angle 3.72779 ( 3657) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5404.77 seconds wall clock time: 93 minutes 23.58 seconds (5603.58 seconds total)