Starting phenix.real_space_refine on Tue May 27 05:06:34 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8w12_43714/05_2025/8w12_43714.cif Found real_map, /net/cci-nas-00/data/ceres_data/8w12_43714/05_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8w12_43714/05_2025/8w12_43714.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8w12_43714/05_2025/8w12_43714.map" model { file = "/net/cci-nas-00/data/ceres_data/8w12_43714/05_2025/8w12_43714.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8w12_43714/05_2025/8w12_43714.cif" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 16.15, per 1000 atoms: 0.55 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: 6.10 Conformation dependent library (CDL) restraints added in 3.3 seconds 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: 3.49 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: 10.52 Time building geometry restraints manager: 7.77 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: 0.06 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: 1.750 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: 0.030 Extract box with map and model: 0.980 Check model and map are aligned: 0.200 Set scattering table: 0.250 Process input model: 59.610 Find NCS groups from input model: 1.490 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.560 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 66.980 ------------------------------------------------------------------------------- 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 : 5.77 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.035 0.001 TRP A 637 HIS 0.011 0.001 HIS B 244 PHE 0.029 0.001 PHE A 527 TYR 0.024 0.001 TYR E 746 ARG 0.016 0.001 ARG E 502 Details of bonding type rmsd hydrogen bonds : bond 0.14829 ( 1288) hydrogen bonds : angle 5.28216 ( 3657) covalent geometry : bond 0.00292 (29880) covalent geometry : angle 0.70079 (40550) *********************** 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 : 3.033 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: 0.4362 time to fit residues: 583.5369 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 : 3.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 362 random chunks: chunk 305 optimal weight: 0.9980 chunk 274 optimal weight: 2.9990 chunk 152 optimal weight: 5.9990 chunk 93 optimal weight: 4.9990 chunk 185 optimal weight: 7.9990 chunk 146 optimal weight: 1.9990 chunk 283 optimal weight: 20.0000 chunk 109 optimal weight: 6.9990 chunk 172 optimal weight: 1.9990 chunk 211 optimal weight: 1.9990 chunk 328 optimal weight: 4.9990 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 D 531 ASN E 467 HIS ** E 523 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 539 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.091966 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.077624 restraints weight = 69948.151| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.080326 restraints weight = 32253.546| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.082033 restraints weight = 18696.130| |-----------------------------------------------------------------------------| r_work (final): 0.3223 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8115 moved from start: 0.1553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 29880 Z= 0.180 Angle : 0.635 12.542 40550 Z= 0.324 Chirality : 0.044 0.203 4542 Planarity : 0.005 0.061 5250 Dihedral : 4.163 20.228 4040 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 1.91 % Allowed : 11.92 % Favored : 86.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.12 (0.14), residues: 3592 helix: 1.27 (0.13), residues: 1564 sheet: -0.33 (0.27), residues: 380 loop : -0.96 (0.15), residues: 1648 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A 637 HIS 0.013 0.001 HIS D 378 PHE 0.024 0.002 PHE E 694 TYR 0.023 0.002 TYR B 410 ARG 0.008 0.001 ARG E 502 Details of bonding type rmsd hydrogen bonds : bond 0.04738 ( 1288) hydrogen bonds : angle 4.15140 ( 3657) covalent geometry : bond 0.00414 (29880) covalent geometry : angle 0.63501 (40550) *********************** 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 839 residues out of total 3188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 778 time to evaluate : 3.170 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 66 LYS cc_start: 0.7968 (tptm) cc_final: 0.7608 (tptm) REVERT: A 110 GLU cc_start: 0.7586 (pp20) cc_final: 0.7292 (tm-30) REVERT: A 111 MET cc_start: 0.8955 (tmm) cc_final: 0.8314 (tmm) REVERT: A 160 GLU cc_start: 0.8414 (mm-30) cc_final: 0.8162 (mm-30) REVERT: A 257 ASP cc_start: 0.8155 (m-30) cc_final: 0.7871 (m-30) REVERT: A 381 PHE cc_start: 0.8566 (m-10) cc_final: 0.8106 (m-80) REVERT: A 664 ARG cc_start: 0.7230 (ptt-90) cc_final: 0.6907 (ptt-90) REVERT: A 668 ARG cc_start: 0.8507 (mtm-85) cc_final: 0.8175 (mtm-85) REVERT: A 709 MET cc_start: 0.8582 (pmm) cc_final: 0.8354 (pmm) REVERT: A 831 GLU cc_start: 0.8200 (tm-30) cc_final: 0.7951 (tm-30) REVERT: B 36 LEU cc_start: 0.8939 (mm) cc_final: 0.8701 (mm) REVERT: B 44 ARG cc_start: 0.7875 (ttp-170) cc_final: 0.7651 (ttm170) REVERT: B 167 GLU cc_start: 0.8260 (pp20) cc_final: 0.7883 (pp20) REVERT: B 339 ASP cc_start: 0.8225 (m-30) cc_final: 0.7897 (m-30) REVERT: B 433 GLN cc_start: 0.8321 (mp10) cc_final: 0.8105 (mp-120) REVERT: B 512 GLU cc_start: 0.8142 (mp0) cc_final: 0.7937 (mp0) REVERT: B 643 ASP cc_start: 0.8296 (t0) cc_final: 0.8029 (t0) REVERT: B 666 MET cc_start: 0.8439 (tpp) cc_final: 0.8148 (tpt) REVERT: B 667 MET cc_start: 0.8100 (mmm) cc_final: 0.7561 (mmm) REVERT: B 685 GLU cc_start: 0.8235 (tm-30) cc_final: 0.7974 (tm-30) REVERT: B 686 GLU cc_start: 0.7863 (tp30) cc_final: 0.7595 (tp30) REVERT: B 724 GLU cc_start: 0.8288 (mm-30) cc_final: 0.7868 (mm-30) REVERT: B 731 MET cc_start: 0.8514 (tpp) cc_final: 0.8209 (tpp) REVERT: D 44 ARG cc_start: 0.7946 (mtt180) cc_final: 0.7483 (mtt180) REVERT: D 66 LYS cc_start: 0.8413 (tptm) cc_final: 0.8188 (tptm) REVERT: D 99 ASP cc_start: 0.8331 (p0) cc_final: 0.7919 (p0) REVERT: D 111 MET cc_start: 0.8708 (tpp) cc_final: 0.8316 (tpp) REVERT: D 201 ASP cc_start: 0.7609 (p0) cc_final: 0.7157 (p0) REVERT: D 209 CYS cc_start: 0.8057 (t) cc_final: 0.7808 (t) REVERT: D 253 GLU cc_start: 0.7990 (mp0) cc_final: 0.7655 (mp0) REVERT: D 257 ASP cc_start: 0.7940 (m-30) cc_final: 0.7599 (m-30) REVERT: D 342 LYS cc_start: 0.8565 (ptpp) cc_final: 0.8243 (ptpp) REVERT: D 344 TYR cc_start: 0.8740 (OUTLIER) cc_final: 0.7730 (t80) REVERT: D 348 MET cc_start: 0.8160 (tpp) cc_final: 0.7676 (tpp) REVERT: D 610 MET cc_start: 0.8216 (mmm) cc_final: 0.7874 (mtt) REVERT: D 620 MET cc_start: 0.8349 (tpp) cc_final: 0.8027 (tpp) REVERT: D 684 GLU cc_start: 0.8236 (mm-30) cc_final: 0.7986 (tp30) REVERT: D 712 GLU cc_start: 0.7501 (pm20) cc_final: 0.7043 (pm20) REVERT: E 36 LEU cc_start: 0.8798 (OUTLIER) cc_final: 0.8526 (mm) REVERT: E 44 ARG cc_start: 0.8169 (ttp-170) cc_final: 0.7852 (ptm160) REVERT: E 81 LYS cc_start: 0.8068 (ptmm) cc_final: 0.7823 (ptmm) REVERT: E 111 MET cc_start: 0.9060 (tmm) cc_final: 0.8542 (tmm) REVERT: E 202 VAL cc_start: 0.8310 (t) cc_final: 0.8021 (m) REVERT: E 339 ASP cc_start: 0.8323 (m-30) cc_final: 0.7826 (m-30) REVERT: E 409 MET cc_start: 0.7865 (mmt) cc_final: 0.7439 (mmt) REVERT: E 467 HIS cc_start: 0.6631 (p90) cc_final: 0.6413 (p-80) REVERT: E 498 ASN cc_start: 0.8464 (t0) cc_final: 0.8227 (t0) REVERT: E 503 MET cc_start: 0.8412 (tpp) cc_final: 0.8181 (tpp) REVERT: E 524 MET cc_start: 0.8607 (mmm) cc_final: 0.8313 (mmm) REVERT: E 600 GLU cc_start: 0.7962 (pt0) cc_final: 0.7757 (pt0) REVERT: E 638 LYS cc_start: 0.8780 (tppt) cc_final: 0.8572 (tppt) REVERT: E 642 ASN cc_start: 0.8625 (t0) cc_final: 0.8396 (t0) REVERT: E 667 MET cc_start: 0.8020 (mmm) cc_final: 0.7598 (mmm) REVERT: E 698 MET cc_start: 0.9029 (mmt) cc_final: 0.8778 (mmt) REVERT: F 26 GLN cc_start: 0.7202 (mm-40) cc_final: 0.6736 (mm-40) outliers start: 61 outliers final: 40 residues processed: 797 average time/residue: 0.4151 time to fit residues: 511.9483 Evaluate side-chains 800 residues out of total 3188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 758 time to evaluate : 3.036 ------------------------------------------------------------------------------- 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 97 SER Chi-restraints excluded: chain A residue 109 GLU 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 527 PHE 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 B residue 94 VAL Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 435 ASP Chi-restraints excluded: chain B residue 472 ILE 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 C residue 273 SER Chi-restraints excluded: chain C residue 320 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 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 795 LEU Chi-restraints excluded: chain E residue 36 LEU Chi-restraints excluded: chain E residue 236 ILE Chi-restraints excluded: chain E residue 265 TRP Chi-restraints excluded: chain E residue 525 VAL Chi-restraints excluded: chain E residue 575 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 196 optimal weight: 0.9990 chunk 310 optimal weight: 3.9990 chunk 90 optimal weight: 6.9990 chunk 53 optimal weight: 10.0000 chunk 250 optimal weight: 3.9990 chunk 356 optimal weight: 2.9990 chunk 23 optimal weight: 2.9990 chunk 209 optimal weight: 20.0000 chunk 345 optimal weight: 1.9990 chunk 225 optimal weight: 3.9990 chunk 98 optimal weight: 5.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 417 ASN ** A 723 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 252 GLN D 642 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 = 0.3340 r_free = 0.3340 target = 0.088691 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.074408 restraints weight = 70321.272| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.077062 restraints weight = 32355.285| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.078756 restraints weight = 18745.031| |-----------------------------------------------------------------------------| r_work (final): 0.3157 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8185 moved from start: 0.2202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 29880 Z= 0.215 Angle : 0.667 10.344 40550 Z= 0.343 Chirality : 0.045 0.223 4542 Planarity : 0.005 0.059 5250 Dihedral : 4.443 23.510 4040 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 3.42 % Allowed : 15.43 % Favored : 81.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.02 (0.14), residues: 3592 helix: 1.19 (0.13), residues: 1598 sheet: -0.45 (0.26), residues: 382 loop : -1.07 (0.15), residues: 1612 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP A 637 HIS 0.011 0.001 HIS A 378 PHE 0.031 0.002 PHE D 324 TYR 0.025 0.002 TYR B 744 ARG 0.009 0.001 ARG A 308 Details of bonding type rmsd hydrogen bonds : bond 0.05424 ( 1288) hydrogen bonds : angle 4.17174 ( 3657) covalent geometry : bond 0.00498 (29880) covalent geometry : angle 0.66676 (40550) *********************** 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 897 residues out of total 3188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 788 time to evaluate : 3.511 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: 0.8164 (tptm) cc_final: 0.7412 (tptm) REVERT: A 70 ASP cc_start: 0.7916 (m-30) cc_final: 0.7378 (m-30) REVERT: A 111 MET cc_start: 0.8946 (tmm) cc_final: 0.8208 (tmm) REVERT: A 169 LYS cc_start: 0.8881 (mppt) cc_final: 0.8636 (mppt) REVERT: A 253 GLU cc_start: 0.8351 (mp0) cc_final: 0.7900 (mp0) REVERT: A 257 ASP cc_start: 0.8242 (m-30) cc_final: 0.7991 (m-30) REVERT: A 381 PHE cc_start: 0.8507 (m-10) cc_final: 0.8297 (m-80) REVERT: A 501 LEU cc_start: 0.8643 (tp) cc_final: 0.8350 (tp) REVERT: A 526 ARG cc_start: 0.8010 (ttp80) cc_final: 0.7754 (ttp80) REVERT: A 578 PHE cc_start: 0.8243 (m-80) cc_final: 0.7516 (m-80) REVERT: A 637 TRP cc_start: 0.8364 (t60) cc_final: 0.7972 (t60) REVERT: A 641 LEU cc_start: 0.8763 (OUTLIER) cc_final: 0.8235 (mt) REVERT: A 664 ARG cc_start: 0.7242 (ptt-90) cc_final: 0.6585 (ttp-110) REVERT: A 668 ARG cc_start: 0.8438 (mtm-85) cc_final: 0.8147 (mtm-85) REVERT: A 709 MET cc_start: 0.8593 (pmm) cc_final: 0.8340 (pmm) REVERT: B 36 LEU cc_start: 0.9001 (OUTLIER) cc_final: 0.8766 (mm) REVERT: B 44 ARG cc_start: 0.7971 (ttp-170) cc_final: 0.7738 (ttm170) REVERT: B 293 ILE cc_start: 0.9186 (tt) cc_final: 0.8937 (pt) REVERT: B 339 ASP cc_start: 0.8235 (m-30) cc_final: 0.7864 (m-30) REVERT: B 355 LEU cc_start: 0.8079 (mm) cc_final: 0.7828 (mm) REVERT: B 454 THR cc_start: 0.8820 (p) cc_final: 0.8504 (p) REVERT: B 512 GLU cc_start: 0.8269 (mp0) cc_final: 0.7933 (mp0) REVERT: B 643 ASP cc_start: 0.8392 (t0) cc_final: 0.8150 (t0) REVERT: B 667 MET cc_start: 0.8155 (mmm) cc_final: 0.7742 (mmm) REVERT: B 685 GLU cc_start: 0.8170 (tm-30) cc_final: 0.7886 (tm-30) REVERT: B 724 GLU cc_start: 0.8275 (mm-30) cc_final: 0.7961 (mm-30) REVERT: C 266 GLU cc_start: 0.6908 (tt0) cc_final: 0.6135 (mt-10) REVERT: C 314 THR cc_start: 0.6841 (t) cc_final: 0.6610 (t) REVERT: D 44 ARG cc_start: 0.7950 (mtt180) cc_final: 0.7518 (mtt180) REVERT: D 66 LYS cc_start: 0.8403 (tptm) cc_final: 0.8020 (tptm) REVERT: D 99 ASP cc_start: 0.8268 (p0) cc_final: 0.7898 (p0) REVERT: D 111 MET cc_start: 0.8765 (tpp) cc_final: 0.8291 (tpp) REVERT: D 201 ASP cc_start: 0.7601 (p0) cc_final: 0.7146 (p0) REVERT: D 209 CYS cc_start: 0.8075 (t) cc_final: 0.7839 (t) REVERT: D 253 GLU cc_start: 0.7982 (mp0) cc_final: 0.7654 (mp0) REVERT: D 257 ASP cc_start: 0.8124 (m-30) cc_final: 0.7723 (m-30) REVERT: D 342 LYS cc_start: 0.8582 (ptpp) cc_final: 0.8240 (ptpp) REVERT: D 344 TYR cc_start: 0.8752 (OUTLIER) cc_final: 0.7554 (t80) REVERT: D 348 MET cc_start: 0.8220 (tpp) cc_final: 0.7759 (tpp) REVERT: D 519 MET cc_start: 0.7450 (mmp) cc_final: 0.6186 (mmt) REVERT: D 573 TRP cc_start: 0.8259 (m100) cc_final: 0.7992 (m100) REVERT: D 620 MET cc_start: 0.8403 (tpp) cc_final: 0.8069 (tpp) REVERT: D 642 ASN cc_start: 0.8805 (m-40) cc_final: 0.8211 (m110) REVERT: E 36 LEU cc_start: 0.8933 (OUTLIER) cc_final: 0.8624 (mm) REVERT: E 44 ARG cc_start: 0.8180 (ttp-170) cc_final: 0.7879 (ptm160) REVERT: E 70 ASP cc_start: 0.7984 (t0) cc_final: 0.7442 (t0) REVERT: E 111 MET cc_start: 0.8931 (tmm) cc_final: 0.8128 (tmm) REVERT: E 202 VAL cc_start: 0.8302 (t) cc_final: 0.8063 (m) REVERT: E 339 ASP cc_start: 0.8332 (m-30) cc_final: 0.7844 (m-30) REVERT: E 409 MET cc_start: 0.7897 (mmt) cc_final: 0.7240 (mmt) REVERT: E 411 ASN cc_start: 0.8513 (t0) cc_final: 0.8307 (t0) REVERT: E 467 HIS cc_start: 0.7044 (p90) cc_final: 0.6782 (p-80) REVERT: E 498 ASN cc_start: 0.8449 (t0) cc_final: 0.8196 (t0) REVERT: E 529 ARG cc_start: 0.7095 (ttt90) cc_final: 0.6736 (ttt90) REVERT: E 600 GLU cc_start: 0.7994 (pt0) cc_final: 0.7731 (pt0) REVERT: E 622 ARG cc_start: 0.7822 (tpp80) cc_final: 0.7503 (tpp80) REVERT: E 638 LYS cc_start: 0.8834 (tppt) cc_final: 0.8613 (tppt) REVERT: E 642 ASN cc_start: 0.8715 (t0) cc_final: 0.8507 (t0) REVERT: E 848 MET cc_start: 0.8147 (mmt) cc_final: 0.7943 (mmt) REVERT: F 26 GLN cc_start: 0.7138 (mm-40) cc_final: 0.6732 (mm-40) outliers start: 109 outliers final: 79 residues processed: 840 average time/residue: 0.4277 time to fit residues: 560.7115 Evaluate side-chains 851 residues out of total 3188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 768 time to evaluate : 3.147 ------------------------------------------------------------------------------- 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 109 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 277 VAL Chi-restraints excluded: chain A residue 286 ILE 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 410 TYR Chi-restraints excluded: chain A residue 500 MET Chi-restraints excluded: chain A residue 527 PHE 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 692 ASN 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 B residue 36 LEU 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 369 VAL Chi-restraints excluded: chain B residue 391 THR Chi-restraints excluded: chain B residue 435 ASP Chi-restraints excluded: chain B residue 472 ILE Chi-restraints excluded: chain B residue 574 ILE Chi-restraints excluded: chain B residue 655 SER Chi-restraints excluded: chain B residue 672 LEU 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 270 MET Chi-restraints excluded: chain C residue 273 SER 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 68 LEU Chi-restraints excluded: chain D residue 224 ILE 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 380 LEU Chi-restraints excluded: chain D residue 410 TYR Chi-restraints excluded: chain D residue 416 VAL Chi-restraints excluded: chain D residue 487 THR Chi-restraints excluded: chain D residue 525 VAL 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 666 MET Chi-restraints excluded: chain D residue 697 LEU 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 134 VAL Chi-restraints excluded: chain E residue 236 ILE Chi-restraints excluded: chain E residue 265 TRP Chi-restraints excluded: chain E residue 403 ASN Chi-restraints excluded: chain E residue 472 ILE 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 772 VAL Chi-restraints excluded: chain E residue 886 ILE Chi-restraints excluded: chain F residue 285 TYR Chi-restraints excluded: chain F residue 318 VAL Chi-restraints excluded: chain F residue 328 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 362 random chunks: chunk 123 optimal weight: 0.9990 chunk 304 optimal weight: 0.6980 chunk 34 optimal weight: 0.8980 chunk 323 optimal weight: 0.9990 chunk 267 optimal weight: 2.9990 chunk 151 optimal weight: 6.9990 chunk 251 optimal weight: 2.9990 chunk 99 optimal weight: 3.9990 chunk 134 optimal weight: 3.9990 chunk 161 optimal weight: 0.7980 chunk 56 optimal weight: 6.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- 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 550 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.091292 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.077080 restraints weight = 70073.426| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.079764 restraints weight = 32473.674| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.081474 restraints weight = 18823.012| |-----------------------------------------------------------------------------| r_work (final): 0.3206 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8129 moved from start: 0.2241 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= 0.121 Angle : 0.618 12.963 40550 Z= 0.309 Chirality : 0.043 0.215 4542 Planarity : 0.004 0.051 5250 Dihedral : 4.193 21.325 4040 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 2.92 % Allowed : 18.63 % Favored : 78.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.20 (0.14), residues: 3592 helix: 1.38 (0.13), residues: 1594 sheet: -0.37 (0.26), residues: 382 loop : -1.01 (0.15), residues: 1616 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 238 HIS 0.010 0.001 HIS B 378 PHE 0.025 0.001 PHE D 636 TYR 0.020 0.001 TYR E 17 ARG 0.007 0.000 ARG D 526 Details of bonding type rmsd hydrogen bonds : bond 0.04161 ( 1288) hydrogen bonds : angle 3.91187 ( 3657) covalent geometry : bond 0.00275 (29880) covalent geometry : angle 0.61782 (40550) *********************** 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 882 residues out of total 3188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 789 time to evaluate : 3.266 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 70 ASP cc_start: 0.7896 (m-30) cc_final: 0.7588 (m-30) REVERT: A 110 GLU cc_start: 0.7928 (tp30) cc_final: 0.7707 (tp30) REVERT: A 111 MET cc_start: 0.8912 (tmm) cc_final: 0.8227 (tmm) REVERT: A 157 GLU cc_start: 0.7654 (mp0) cc_final: 0.7383 (mp0) REVERT: A 257 ASP cc_start: 0.8228 (m-30) cc_final: 0.7934 (m-30) REVERT: A 344 TYR cc_start: 0.8882 (OUTLIER) cc_final: 0.7963 (t80) REVERT: A 614 MET cc_start: 0.7753 (tpt) cc_final: 0.7540 (tpt) REVERT: A 671 MET cc_start: 0.8022 (mmm) cc_final: 0.7685 (mmm) REVERT: A 701 ASP cc_start: 0.8924 (p0) cc_final: 0.8722 (p0) REVERT: A 709 MET cc_start: 0.8542 (pmm) cc_final: 0.8328 (pmm) REVERT: A 831 GLU cc_start: 0.8195 (tm-30) cc_final: 0.7965 (tm-30) REVERT: B 18 LEU cc_start: 0.8704 (tt) cc_final: 0.8495 (tp) REVERT: B 111 MET cc_start: 0.8611 (tpp) cc_final: 0.8369 (tpp) REVERT: B 339 ASP cc_start: 0.8158 (m-30) cc_final: 0.7804 (m-30) REVERT: B 355 LEU cc_start: 0.7935 (mm) cc_final: 0.7655 (mm) REVERT: B 512 GLU cc_start: 0.8229 (mp0) cc_final: 0.7898 (mp0) REVERT: B 643 ASP cc_start: 0.8374 (t0) cc_final: 0.8103 (t0) REVERT: B 667 MET cc_start: 0.8027 (mmm) cc_final: 0.7729 (mmm) REVERT: B 685 GLU cc_start: 0.8131 (tm-30) cc_final: 0.7917 (tm-30) REVERT: B 724 GLU cc_start: 0.8255 (mm-30) cc_final: 0.7852 (mm-30) REVERT: B 796 GLN cc_start: 0.8427 (mt0) cc_final: 0.8184 (mt0) REVERT: B 869 VAL cc_start: 0.8840 (OUTLIER) cc_final: 0.8638 (t) REVERT: C 314 THR cc_start: 0.6915 (t) cc_final: 0.6626 (t) REVERT: D 44 ARG cc_start: 0.7928 (mtt180) cc_final: 0.7607 (mtt180) REVERT: D 66 LYS cc_start: 0.8388 (tptm) cc_final: 0.8041 (tptm) REVERT: D 99 ASP cc_start: 0.8204 (p0) cc_final: 0.7839 (p0) REVERT: D 109 GLU cc_start: 0.8113 (mm-30) cc_final: 0.7908 (mm-30) REVERT: D 111 MET cc_start: 0.8813 (tpp) cc_final: 0.8478 (tpp) REVERT: D 169 LYS cc_start: 0.8405 (mmmm) cc_final: 0.7910 (mmmt) REVERT: D 209 CYS cc_start: 0.7873 (t) cc_final: 0.7581 (t) REVERT: D 253 GLU cc_start: 0.7977 (mp0) cc_final: 0.7599 (mp0) REVERT: D 257 ASP cc_start: 0.8059 (m-30) cc_final: 0.7656 (m-30) REVERT: D 324 PHE cc_start: 0.6586 (p90) cc_final: 0.6331 (p90) REVERT: D 342 LYS cc_start: 0.8543 (ptpp) cc_final: 0.8176 (ptpp) REVERT: D 344 TYR cc_start: 0.8656 (OUTLIER) cc_final: 0.7536 (t80) REVERT: D 348 MET cc_start: 0.8099 (tpp) cc_final: 0.7599 (tpp) REVERT: D 409 MET cc_start: 0.6956 (tpt) cc_final: 0.6671 (tpp) REVERT: D 519 MET cc_start: 0.7274 (mmp) cc_final: 0.6270 (mmp) REVERT: D 552 LEU cc_start: 0.8716 (tt) cc_final: 0.8409 (tp) REVERT: D 573 TRP cc_start: 0.8225 (m100) cc_final: 0.7934 (m100) REVERT: D 620 MET cc_start: 0.8382 (tpp) cc_final: 0.8078 (tpp) REVERT: D 642 ASN cc_start: 0.8841 (m-40) cc_final: 0.8037 (m-40) REVERT: D 684 GLU cc_start: 0.8314 (tp30) cc_final: 0.8109 (tp30) REVERT: E 36 LEU cc_start: 0.8824 (OUTLIER) cc_final: 0.8503 (mm) REVERT: E 44 ARG cc_start: 0.8160 (ttp-170) cc_final: 0.7858 (ptm160) REVERT: E 111 MET cc_start: 0.8976 (tmm) cc_final: 0.8177 (tmm) REVERT: E 202 VAL cc_start: 0.8266 (t) cc_final: 0.8022 (m) REVERT: E 339 ASP cc_start: 0.8277 (m-30) cc_final: 0.7795 (m-30) REVERT: E 409 MET cc_start: 0.7984 (mmt) cc_final: 0.7252 (mmt) REVERT: E 411 ASN cc_start: 0.8444 (t0) cc_final: 0.8172 (t0) REVERT: E 423 GLU cc_start: 0.7716 (mp0) cc_final: 0.7434 (pm20) REVERT: E 467 HIS cc_start: 0.7147 (p90) cc_final: 0.6928 (p-80) REVERT: E 498 ASN cc_start: 0.8411 (t0) cc_final: 0.8162 (t0) REVERT: E 622 ARG cc_start: 0.7624 (tpp80) cc_final: 0.7315 (tpp80) REVERT: E 642 ASN cc_start: 0.8702 (t0) cc_final: 0.8449 (t0) REVERT: E 667 MET cc_start: 0.8169 (mmm) cc_final: 0.7388 (mmm) REVERT: E 686 GLU cc_start: 0.7829 (tp30) cc_final: 0.7609 (tp30) REVERT: E 848 MET cc_start: 0.8060 (mmt) cc_final: 0.7777 (mmt) REVERT: F 26 GLN cc_start: 0.7156 (mm-40) cc_final: 0.6683 (mm-40) outliers start: 93 outliers final: 63 residues processed: 837 average time/residue: 0.4068 time to fit residues: 530.3771 Evaluate side-chains 824 residues out of total 3188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 757 time to evaluate : 3.323 ------------------------------------------------------------------------------- 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 224 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 567 VAL Chi-restraints excluded: chain A residue 629 ILE Chi-restraints excluded: chain A residue 674 SER Chi-restraints excluded: chain A residue 732 LEU 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 187 LEU 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 435 ASP 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 655 SER 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 881 MET 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 D residue 31 LEU 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 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 474 TYR 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 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 79 VAL 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 472 ILE Chi-restraints excluded: chain E residue 512 GLU Chi-restraints excluded: chain E residue 527 PHE Chi-restraints excluded: chain E residue 575 SER Chi-restraints excluded: chain E residue 867 LEU Chi-restraints excluded: chain F residue 18 GLU Chi-restraints excluded: chain F residue 326 ILE 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 342 optimal weight: 0.6980 chunk 231 optimal weight: 1.9990 chunk 309 optimal weight: 4.9990 chunk 170 optimal weight: 7.9990 chunk 141 optimal weight: 3.9990 chunk 247 optimal weight: 0.7980 chunk 293 optimal weight: 0.9990 chunk 110 optimal weight: 2.9990 chunk 106 optimal weight: 7.9990 chunk 358 optimal weight: 0.7980 chunk 230 optimal weight: 1.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- 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** B 550 ASN C 274 ASN D 397 GLN D 692 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.091322 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.077207 restraints weight = 69504.444| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.079875 restraints weight = 32252.316| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.081574 restraints weight = 18729.138| |-----------------------------------------------------------------------------| r_work (final): 0.3209 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8129 moved from start: 0.2316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 29880 Z= 0.125 Angle : 0.623 13.229 40550 Z= 0.309 Chirality : 0.043 0.206 4542 Planarity : 0.004 0.052 5250 Dihedral : 4.118 20.881 4040 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 3.26 % Allowed : 20.23 % Favored : 76.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.27 (0.14), residues: 3592 helix: 1.43 (0.13), residues: 1596 sheet: -0.18 (0.28), residues: 352 loop : -1.00 (0.15), residues: 1644 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP B 238 HIS 0.009 0.001 HIS B 378 PHE 0.025 0.001 PHE D 636 TYR 0.021 0.001 TYR E 17 ARG 0.007 0.000 ARG D 623 Details of bonding type rmsd hydrogen bonds : bond 0.04026 ( 1288) hydrogen bonds : angle 3.85894 ( 3657) covalent geometry : bond 0.00290 (29880) covalent geometry : angle 0.62341 (40550) *********************** 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 884 residues out of total 3188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 780 time to evaluate : 3.105 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: 0.8097 (tptm) cc_final: 0.7143 (tptm) REVERT: A 70 ASP cc_start: 0.7903 (m-30) cc_final: 0.7291 (m-30) REVERT: A 110 GLU cc_start: 0.7991 (tp30) cc_final: 0.7747 (tp30) REVERT: A 111 MET cc_start: 0.8841 (tmm) cc_final: 0.8229 (tmm) REVERT: A 167 GLU cc_start: 0.7897 (tm-30) cc_final: 0.7581 (tm-30) REVERT: A 178 GLU cc_start: 0.7483 (tm-30) cc_final: 0.7203 (tp30) REVERT: A 257 ASP cc_start: 0.8230 (m-30) cc_final: 0.7916 (m-30) REVERT: A 501 LEU cc_start: 0.8645 (tp) cc_final: 0.8352 (tp) REVERT: A 578 PHE cc_start: 0.8091 (m-80) cc_final: 0.7451 (m-80) REVERT: A 667 MET cc_start: 0.8515 (tpp) cc_final: 0.8225 (tpp) REVERT: A 668 ARG cc_start: 0.8630 (mtp85) cc_final: 0.8329 (mtm-85) REVERT: A 709 MET cc_start: 0.8519 (pmm) cc_final: 0.8306 (pmm) REVERT: A 831 GLU cc_start: 0.8227 (tm-30) cc_final: 0.7974 (tm-30) REVERT: B 36 LEU cc_start: 0.8939 (mm) cc_final: 0.8659 (mm) REVERT: B 47 GLN cc_start: 0.8026 (pp30) cc_final: 0.7807 (tm-30) REVERT: B 291 MET cc_start: 0.7980 (tmm) cc_final: 0.7562 (tmm) REVERT: B 339 ASP cc_start: 0.8150 (m-30) cc_final: 0.7799 (m-30) REVERT: B 355 LEU cc_start: 0.7933 (mm) cc_final: 0.7692 (mm) REVERT: B 406 LEU cc_start: 0.9048 (OUTLIER) cc_final: 0.8782 (mp) REVERT: B 515 TYR cc_start: 0.8981 (t80) cc_final: 0.8535 (t80) REVERT: B 643 ASP cc_start: 0.8378 (t0) cc_final: 0.8132 (t0) REVERT: B 724 GLU cc_start: 0.8237 (mm-30) cc_final: 0.7802 (mm-30) REVERT: C 314 THR cc_start: 0.6981 (OUTLIER) cc_final: 0.6675 (t) REVERT: D 40 MET cc_start: 0.8296 (mmm) cc_final: 0.8017 (mmp) REVERT: D 44 ARG cc_start: 0.7930 (mtt180) cc_final: 0.7592 (mtt180) REVERT: D 66 LYS cc_start: 0.8391 (tptm) cc_final: 0.8040 (tptm) REVERT: D 99 ASP cc_start: 0.8209 (p0) cc_final: 0.7844 (p0) REVERT: D 111 MET cc_start: 0.8819 (tpp) cc_final: 0.8465 (tpp) REVERT: D 169 LYS cc_start: 0.8333 (mmmm) cc_final: 0.7926 (mmmt) REVERT: D 209 CYS cc_start: 0.7865 (t) cc_final: 0.7575 (t) REVERT: D 253 GLU cc_start: 0.7970 (mp0) cc_final: 0.7406 (mp0) REVERT: D 257 ASP cc_start: 0.8089 (m-30) cc_final: 0.7842 (m-30) REVERT: D 342 LYS cc_start: 0.8553 (ptpp) cc_final: 0.8174 (ptpp) REVERT: D 344 TYR cc_start: 0.8513 (OUTLIER) cc_final: 0.7506 (t80) REVERT: D 348 MET cc_start: 0.8073 (tpp) cc_final: 0.7534 (tpp) REVERT: D 409 MET cc_start: 0.7003 (tpt) cc_final: 0.6746 (tpp) REVERT: D 519 MET cc_start: 0.7312 (mmp) cc_final: 0.6348 (mmp) REVERT: D 552 LEU cc_start: 0.8714 (tt) cc_final: 0.8441 (tp) REVERT: D 573 TRP cc_start: 0.8226 (m100) cc_final: 0.7874 (m100) REVERT: D 620 MET cc_start: 0.8417 (tpp) cc_final: 0.8087 (tpp) REVERT: D 642 ASN cc_start: 0.8857 (m-40) cc_final: 0.8153 (m-40) REVERT: D 684 GLU cc_start: 0.8313 (tp30) cc_final: 0.8103 (tp30) REVERT: E 36 LEU cc_start: 0.8827 (OUTLIER) cc_final: 0.8515 (mm) REVERT: E 44 ARG cc_start: 0.8192 (ttp-170) cc_final: 0.7892 (ptm160) REVERT: E 111 MET cc_start: 0.8975 (tmm) cc_final: 0.8201 (tmm) REVERT: E 202 VAL cc_start: 0.8289 (t) cc_final: 0.8045 (m) REVERT: E 339 ASP cc_start: 0.8263 (m-30) cc_final: 0.7781 (m-30) REVERT: E 363 GLU cc_start: 0.6919 (OUTLIER) cc_final: 0.6461 (pm20) REVERT: E 409 MET cc_start: 0.7946 (mmt) cc_final: 0.7223 (mmt) REVERT: E 411 ASN cc_start: 0.8462 (t0) cc_final: 0.8232 (t0) REVERT: E 423 GLU cc_start: 0.7702 (mp0) cc_final: 0.7482 (mp0) REVERT: E 467 HIS cc_start: 0.7226 (p90) cc_final: 0.6993 (p-80) REVERT: E 498 ASN cc_start: 0.8408 (t0) cc_final: 0.8139 (t0) REVERT: E 529 ARG cc_start: 0.7273 (ttt90) cc_final: 0.6636 (ttt90) REVERT: E 642 ASN cc_start: 0.8709 (t0) cc_final: 0.8446 (t0) REVERT: E 848 MET cc_start: 0.7941 (mmt) cc_final: 0.7661 (mmt) REVERT: F 26 GLN cc_start: 0.7093 (mm-40) cc_final: 0.6638 (mm-40) outliers start: 104 outliers final: 80 residues processed: 838 average time/residue: 0.4110 time to fit residues: 535.7804 Evaluate side-chains 853 residues out of total 3188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 768 time to evaluate : 3.020 ------------------------------------------------------------------------------- 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 101 VAL Chi-restraints excluded: chain A residue 191 ILE Chi-restraints excluded: chain A residue 224 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 375 VAL Chi-restraints excluded: chain A residue 379 LEU Chi-restraints excluded: chain A residue 406 LEU 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 697 LEU Chi-restraints excluded: chain A residue 732 LEU 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 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 391 THR Chi-restraints excluded: chain B residue 406 LEU Chi-restraints excluded: chain B residue 435 ASP 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 614 MET 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 881 MET Chi-restraints excluded: chain B residue 887 THR 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 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 301 GLU Chi-restraints excluded: chain D residue 344 TYR Chi-restraints excluded: chain D residue 357 LEU Chi-restraints excluded: chain D residue 474 TYR 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 692 ASN 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 D residue 866 ILE 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 104 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 278 VAL Chi-restraints excluded: chain E residue 331 THR Chi-restraints excluded: chain E residue 363 GLU Chi-restraints excluded: chain E residue 472 ILE Chi-restraints excluded: chain E residue 512 GLU 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 362 random chunks: chunk 228 optimal weight: 7.9990 chunk 178 optimal weight: 6.9990 chunk 10 optimal weight: 4.9990 chunk 31 optimal weight: 0.9980 chunk 357 optimal weight: 8.9990 chunk 127 optimal weight: 0.5980 chunk 73 optimal weight: 4.9990 chunk 6 optimal weight: 4.9990 chunk 180 optimal weight: 4.9990 chunk 38 optimal weight: 3.9990 chunk 110 optimal weight: 1.9990 overall best weight: 2.5186 ------------------------------------------------------------------------------- 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** B 179 HIS B 550 ASN C 274 ASN D 692 ASN E 539 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.088123 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.074068 restraints weight = 70391.466| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.076695 restraints weight = 32679.669| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.078383 restraints weight = 18978.019| |-----------------------------------------------------------------------------| r_work (final): 0.3147 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8191 moved from start: 0.2676 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 29880 Z= 0.210 Angle : 0.686 12.482 40550 Z= 0.346 Chirality : 0.045 0.211 4542 Planarity : 0.005 0.055 5250 Dihedral : 4.376 23.138 4040 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 4.45 % Allowed : 21.02 % Favored : 74.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.09 (0.14), residues: 3592 helix: 1.31 (0.13), residues: 1596 sheet: -0.42 (0.26), residues: 392 loop : -1.10 (0.15), residues: 1604 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.002 TRP A 637 HIS 0.011 0.001 HIS A 378 PHE 0.035 0.002 PHE D 324 TYR 0.024 0.002 TYR E 17 ARG 0.006 0.001 ARG D 623 Details of bonding type rmsd hydrogen bonds : bond 0.05100 ( 1288) hydrogen bonds : angle 4.04539 ( 3657) covalent geometry : bond 0.00490 (29880) covalent geometry : angle 0.68555 (40550) *********************** 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 911 residues out of total 3188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 142 poor density : 769 time to evaluate : 3.158 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 LYS cc_start: 0.8201 (tptm) cc_final: 0.7333 (tptm) REVERT: A 70 ASP cc_start: 0.7928 (m-30) cc_final: 0.7322 (m-30) REVERT: A 111 MET cc_start: 0.8820 (tmm) cc_final: 0.8207 (tmm) REVERT: A 257 ASP cc_start: 0.8290 (m-30) cc_final: 0.8019 (m-30) REVERT: A 449 TYR cc_start: 0.7668 (m-80) cc_final: 0.7316 (m-80) REVERT: A 481 GLU cc_start: 0.8235 (mp0) cc_final: 0.7812 (mp0) REVERT: A 501 LEU cc_start: 0.8653 (tp) cc_final: 0.8375 (tp) REVERT: A 578 PHE cc_start: 0.8170 (m-80) cc_final: 0.7505 (m-80) REVERT: A 667 MET cc_start: 0.8531 (tpp) cc_final: 0.8020 (mmm) REVERT: A 668 ARG cc_start: 0.8656 (mtp85) cc_final: 0.8331 (mtm-85) REVERT: A 671 MET cc_start: 0.8088 (mmm) cc_final: 0.7864 (mmp) REVERT: A 709 MET cc_start: 0.8573 (pmm) cc_final: 0.8321 (pmm) REVERT: B 17 TYR cc_start: 0.7748 (p90) cc_final: 0.7191 (p90) REVERT: B 36 LEU cc_start: 0.9013 (OUTLIER) cc_final: 0.8763 (mm) REVERT: B 47 GLN cc_start: 0.7964 (pp30) cc_final: 0.7734 (tm-30) REVERT: B 291 MET cc_start: 0.8198 (tmm) cc_final: 0.7961 (tmm) REVERT: B 293 ILE cc_start: 0.9168 (tt) cc_final: 0.8943 (pt) REVERT: B 339 ASP cc_start: 0.8185 (m-30) cc_final: 0.7805 (m-30) REVERT: B 355 LEU cc_start: 0.8006 (mm) cc_final: 0.7761 (mm) REVERT: B 515 TYR cc_start: 0.9010 (t80) cc_final: 0.8563 (t80) REVERT: B 724 GLU cc_start: 0.8219 (mm-30) cc_final: 0.7793 (mm-30) REVERT: B 869 VAL cc_start: 0.8874 (OUTLIER) cc_final: 0.8665 (t) REVERT: C 314 THR cc_start: 0.7197 (t) cc_final: 0.6992 (t) REVERT: D 44 ARG cc_start: 0.7944 (mtt180) cc_final: 0.7586 (mtt180) REVERT: D 66 LYS cc_start: 0.8392 (tptm) cc_final: 0.8000 (tptm) REVERT: D 99 ASP cc_start: 0.8241 (p0) cc_final: 0.7928 (p0) REVERT: D 111 MET cc_start: 0.8837 (tpp) cc_final: 0.8412 (tpp) REVERT: D 209 CYS cc_start: 0.8022 (t) cc_final: 0.7765 (t) REVERT: D 253 GLU cc_start: 0.7978 (mp0) cc_final: 0.7392 (mp0) REVERT: D 257 ASP cc_start: 0.8170 (m-30) cc_final: 0.7766 (m-30) REVERT: D 342 LYS cc_start: 0.8591 (ptpp) cc_final: 0.8238 (ptpp) REVERT: D 344 TYR cc_start: 0.8790 (OUTLIER) cc_final: 0.7553 (t80) REVERT: D 348 MET cc_start: 0.8109 (tpp) cc_final: 0.7881 (tpp) REVERT: D 381 PHE cc_start: 0.8267 (m-80) cc_final: 0.8035 (m-80) REVERT: D 573 TRP cc_start: 0.8282 (m100) cc_final: 0.8001 (m100) REVERT: D 620 MET cc_start: 0.8445 (tpp) cc_final: 0.7927 (tpp) REVERT: D 695 GLU cc_start: 0.7730 (OUTLIER) cc_final: 0.7327 (mt-10) REVERT: D 744 TYR cc_start: 0.8730 (OUTLIER) cc_final: 0.8206 (m-80) REVERT: D 856 ARG cc_start: 0.7830 (mtp85) cc_final: 0.7599 (mtp85) REVERT: E 36 LEU cc_start: 0.8915 (OUTLIER) cc_final: 0.8571 (mm) REVERT: E 44 ARG cc_start: 0.8204 (ttp-170) cc_final: 0.7908 (ptm160) REVERT: E 81 LYS cc_start: 0.8174 (ptmm) cc_final: 0.7967 (ptmm) REVERT: E 111 MET cc_start: 0.8848 (tmm) cc_final: 0.8172 (tmm) REVERT: E 202 VAL cc_start: 0.8302 (t) cc_final: 0.8060 (m) REVERT: E 339 ASP cc_start: 0.8338 (m-30) cc_final: 0.7900 (m-30) REVERT: E 363 GLU cc_start: 0.7036 (OUTLIER) cc_final: 0.6639 (pt0) REVERT: E 409 MET cc_start: 0.7861 (mmt) cc_final: 0.7165 (mmt) REVERT: E 467 HIS cc_start: 0.7457 (p90) cc_final: 0.7230 (p-80) REVERT: E 498 ASN cc_start: 0.8398 (t0) cc_final: 0.8137 (t0) REVERT: E 524 MET cc_start: 0.8604 (mmm) cc_final: 0.8362 (mmm) REVERT: E 529 ARG cc_start: 0.7186 (ttt90) cc_final: 0.6785 (ttt90) REVERT: E 536 GLU cc_start: 0.7892 (tp30) cc_final: 0.7483 (tt0) REVERT: E 622 ARG cc_start: 0.7752 (tpp80) cc_final: 0.7372 (tpp80) REVERT: E 642 ASN cc_start: 0.8731 (t0) cc_final: 0.8482 (t0) REVERT: E 709 MET cc_start: 0.7535 (mmm) cc_final: 0.7221 (tpt) REVERT: E 848 MET cc_start: 0.8041 (mmt) cc_final: 0.7808 (mmt) REVERT: F 26 GLN cc_start: 0.7160 (mm-40) cc_final: 0.6717 (mm-40) outliers start: 142 outliers final: 103 residues processed: 853 average time/residue: 0.4106 time to fit residues: 546.8526 Evaluate side-chains 872 residues out of total 3188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 762 time to evaluate : 3.265 ------------------------------------------------------------------------------- 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 191 ILE Chi-restraints excluded: chain A residue 224 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 410 TYR 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 652 MET Chi-restraints excluded: chain A residue 692 ASN 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 777 VAL Chi-restraints excluded: chain A residue 835 THR Chi-restraints excluded: chain A residue 875 VAL Chi-restraints excluded: chain A residue 880 LYS Chi-restraints excluded: chain B residue 36 LEU Chi-restraints excluded: chain B residue 67 ILE 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 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 391 THR Chi-restraints excluded: chain B residue 435 ASP 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 614 MET Chi-restraints excluded: chain B residue 772 VAL Chi-restraints excluded: chain B residue 815 ILE Chi-restraints excluded: chain B residue 867 LEU Chi-restraints excluded: chain B residue 869 VAL Chi-restraints excluded: chain B residue 881 MET Chi-restraints excluded: chain B residue 887 THR Chi-restraints excluded: chain C residue 270 MET Chi-restraints excluded: chain C residue 273 SER Chi-restraints excluded: chain C residue 275 SER Chi-restraints excluded: chain C residue 320 THR Chi-restraints excluded: chain D residue 31 LEU Chi-restraints excluded: chain D residue 95 MET Chi-restraints excluded: chain D residue 114 VAL Chi-restraints excluded: chain D residue 117 VAL Chi-restraints excluded: chain D residue 182 MET Chi-restraints excluded: chain D residue 224 ILE 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 376 VAL Chi-restraints excluded: chain D residue 410 TYR 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 527 PHE 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 672 LEU Chi-restraints excluded: chain D residue 692 ASN Chi-restraints excluded: chain D residue 695 GLU Chi-restraints excluded: chain D residue 715 LEU Chi-restraints excluded: chain D residue 744 TYR 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 D residue 866 ILE Chi-restraints excluded: chain D residue 869 VAL Chi-restraints excluded: chain D residue 881 MET 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 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 278 VAL Chi-restraints excluded: chain E residue 363 GLU Chi-restraints excluded: chain E residue 369 VAL Chi-restraints excluded: chain E residue 390 LEU Chi-restraints excluded: chain E residue 472 ILE Chi-restraints excluded: chain E residue 512 GLU Chi-restraints excluded: chain E residue 527 PHE Chi-restraints excluded: chain E residue 533 ILE 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 362 random chunks: chunk 62 optimal weight: 3.9990 chunk 292 optimal weight: 0.9980 chunk 360 optimal weight: 4.9990 chunk 148 optimal weight: 3.9990 chunk 117 optimal weight: 0.8980 chunk 139 optimal weight: 4.9990 chunk 166 optimal weight: 0.1980 chunk 310 optimal weight: 0.8980 chunk 351 optimal weight: 0.9980 chunk 90 optimal weight: 0.9990 chunk 295 optimal weight: 6.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 352 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 550 ASN C 274 ASN D 397 GLN D 692 ASN E 539 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.090762 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.076705 restraints weight = 69721.744| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.079367 restraints weight = 32271.960| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.081081 restraints weight = 18705.809| |-----------------------------------------------------------------------------| r_work (final): 0.3200 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8134 moved from start: 0.2600 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= 0.125 Angle : 0.678 14.327 40550 Z= 0.332 Chirality : 0.043 0.242 4542 Planarity : 0.004 0.050 5250 Dihedral : 4.177 20.803 4040 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 3.32 % Allowed : 22.90 % Favored : 73.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.20 (0.14), residues: 3592 helix: 1.38 (0.13), residues: 1598 sheet: -0.26 (0.27), residues: 372 loop : -1.04 (0.15), residues: 1622 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.057 0.001 TRP A 637 HIS 0.010 0.001 HIS B 378 PHE 0.032 0.001 PHE E 522 TYR 0.025 0.001 TYR E 17 ARG 0.008 0.000 ARG D 526 Details of bonding type rmsd hydrogen bonds : bond 0.04052 ( 1288) hydrogen bonds : angle 3.85642 ( 3657) covalent geometry : bond 0.00289 (29880) covalent geometry : angle 0.67798 (40550) *********************** 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 884 residues out of total 3188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 778 time to evaluate : 3.150 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: symmetry clash REVERT: A 66 LYS cc_start: 0.8071 (tptm) cc_final: 0.7086 (tptm) REVERT: A 70 ASP cc_start: 0.7903 (m-30) cc_final: 0.7279 (m-30) REVERT: A 111 MET cc_start: 0.8737 (tmm) cc_final: 0.8131 (tmm) REVERT: A 257 ASP cc_start: 0.8262 (m-30) cc_final: 0.7968 (m-30) REVERT: A 501 LEU cc_start: 0.8620 (tp) cc_final: 0.8349 (tp) REVERT: A 552 LEU cc_start: 0.8771 (OUTLIER) cc_final: 0.8540 (tp) REVERT: A 667 MET cc_start: 0.8493 (tpp) cc_final: 0.7943 (mmm) REVERT: A 671 MET cc_start: 0.8017 (mmm) cc_final: 0.7805 (mmp) REVERT: A 709 MET cc_start: 0.8543 (pmm) cc_final: 0.8307 (pmm) REVERT: A 831 GLU cc_start: 0.8238 (tm-30) cc_final: 0.7996 (tm-30) REVERT: B 17 TYR cc_start: 0.7728 (p90) cc_final: 0.7141 (p90) REVERT: B 36 LEU cc_start: 0.8939 (mm) cc_final: 0.8660 (mm) REVERT: B 47 GLN cc_start: 0.7981 (pp30) cc_final: 0.7737 (tm-30) REVERT: B 291 MET cc_start: 0.8161 (tmm) cc_final: 0.7847 (tmm) REVERT: B 339 ASP cc_start: 0.8157 (m-30) cc_final: 0.7778 (m-30) REVERT: B 355 LEU cc_start: 0.7917 (mm) cc_final: 0.7662 (mm) REVERT: B 515 TYR cc_start: 0.8983 (t80) cc_final: 0.8536 (t80) REVERT: B 724 GLU cc_start: 0.8246 (mm-30) cc_final: 0.7791 (mm-30) REVERT: B 742 VAL cc_start: 0.8073 (OUTLIER) cc_final: 0.7167 (t) REVERT: B 747 GLU cc_start: 0.7777 (pp20) cc_final: 0.7429 (pp20) REVERT: B 869 VAL cc_start: 0.8839 (OUTLIER) cc_final: 0.8624 (t) REVERT: C 314 THR cc_start: 0.7065 (OUTLIER) cc_final: 0.6855 (t) REVERT: D 40 MET cc_start: 0.8284 (mmm) cc_final: 0.8035 (mmp) REVERT: D 44 ARG cc_start: 0.7953 (mtt180) cc_final: 0.7633 (mtt180) REVERT: D 66 LYS cc_start: 0.8380 (tptm) cc_final: 0.8022 (tptm) REVERT: D 99 ASP cc_start: 0.8218 (p0) cc_final: 0.7881 (p0) REVERT: D 111 MET cc_start: 0.8834 (tpp) cc_final: 0.8475 (tpp) REVERT: D 209 CYS cc_start: 0.7847 (t) cc_final: 0.7553 (t) REVERT: D 253 GLU cc_start: 0.7973 (mp0) cc_final: 0.7492 (mp0) REVERT: D 257 ASP cc_start: 0.8135 (m-30) cc_final: 0.7925 (m-30) REVERT: D 324 PHE cc_start: 0.6781 (p90) cc_final: 0.6360 (p90) REVERT: D 342 LYS cc_start: 0.8550 (ptpp) cc_final: 0.8179 (ptpp) REVERT: D 344 TYR cc_start: 0.8679 (OUTLIER) cc_final: 0.7560 (t80) REVERT: D 348 MET cc_start: 0.7988 (tpp) cc_final: 0.7769 (tpp) REVERT: D 552 LEU cc_start: 0.8705 (tt) cc_final: 0.8389 (tp) REVERT: D 573 TRP cc_start: 0.8231 (m100) cc_final: 0.7935 (m100) REVERT: D 620 MET cc_start: 0.8391 (tpp) cc_final: 0.7885 (tpp) REVERT: D 856 ARG cc_start: 0.7812 (mtp85) cc_final: 0.7543 (mtp85) REVERT: E 44 ARG cc_start: 0.8198 (ttp-170) cc_final: 0.7909 (ptm160) REVERT: E 111 MET cc_start: 0.8905 (tmm) cc_final: 0.8191 (tmm) REVERT: E 202 VAL cc_start: 0.8267 (t) cc_final: 0.8026 (m) REVERT: E 339 ASP cc_start: 0.8256 (m-30) cc_final: 0.7787 (m-30) REVERT: E 363 GLU cc_start: 0.7056 (OUTLIER) cc_final: 0.6786 (pt0) REVERT: E 409 MET cc_start: 0.7962 (mmt) cc_final: 0.7201 (mmt) REVERT: E 411 ASN cc_start: 0.8590 (t0) cc_final: 0.8256 (t0) REVERT: E 423 GLU cc_start: 0.7757 (mp0) cc_final: 0.7467 (pm20) REVERT: E 467 HIS cc_start: 0.7429 (p90) cc_final: 0.7203 (p-80) REVERT: E 498 ASN cc_start: 0.8384 (t0) cc_final: 0.8119 (t0) REVERT: E 524 MET cc_start: 0.8580 (mmm) cc_final: 0.8362 (mmm) REVERT: E 536 GLU cc_start: 0.7867 (tp30) cc_final: 0.7472 (tt0) REVERT: E 622 ARG cc_start: 0.7631 (tpp80) cc_final: 0.7294 (tpp80) REVERT: E 642 ASN cc_start: 0.8715 (t0) cc_final: 0.8461 (t0) REVERT: E 709 MET cc_start: 0.7614 (mmm) cc_final: 0.7375 (tpt) REVERT: F 26 GLN cc_start: 0.7123 (mm-40) cc_final: 0.6687 (mm-40) outliers start: 106 outliers final: 85 residues processed: 838 average time/residue: 0.4232 time to fit residues: 552.7882 Evaluate side-chains 849 residues out of total 3188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 758 time to evaluate : 3.178 ------------------------------------------------------------------------------- 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 191 ILE Chi-restraints excluded: chain A residue 224 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 416 VAL Chi-restraints excluded: chain A residue 500 MET Chi-restraints excluded: chain A residue 527 PHE Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain A residue 567 VAL 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 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 265 TRP Chi-restraints excluded: chain B residue 273 VAL 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 391 THR Chi-restraints excluded: chain B residue 435 ASP 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 614 MET Chi-restraints excluded: chain B residue 655 SER Chi-restraints excluded: chain B residue 742 VAL 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 881 MET Chi-restraints excluded: chain B residue 887 THR Chi-restraints excluded: chain C residue 270 MET Chi-restraints excluded: chain C residue 272 VAL Chi-restraints excluded: chain C residue 275 SER 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 114 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 474 TYR Chi-restraints excluded: chain D residue 527 PHE 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 869 VAL Chi-restraints excluded: chain D residue 890 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 265 TRP Chi-restraints excluded: chain E residue 273 VAL Chi-restraints excluded: chain E residue 278 VAL Chi-restraints excluded: chain E residue 363 GLU Chi-restraints excluded: chain E residue 435 ASP Chi-restraints excluded: chain E residue 472 ILE Chi-restraints excluded: chain E residue 512 GLU Chi-restraints excluded: chain E residue 527 PHE Chi-restraints excluded: chain E residue 533 ILE 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 328 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 362 random chunks: chunk 230 optimal weight: 0.9980 chunk 30 optimal weight: 0.7980 chunk 15 optimal weight: 2.9990 chunk 116 optimal weight: 1.9990 chunk 162 optimal weight: 0.8980 chunk 216 optimal weight: 7.9990 chunk 219 optimal weight: 9.9990 chunk 196 optimal weight: 5.9990 chunk 346 optimal weight: 2.9990 chunk 331 optimal weight: 1.9990 chunk 269 optimal weight: 1.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- 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** B 550 ASN C 274 ASN D 692 ASN E 539 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.090122 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.076059 restraints weight = 70247.898| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.078719 restraints weight = 32538.012| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.080413 restraints weight = 18862.286| |-----------------------------------------------------------------------------| r_work (final): 0.3186 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8150 moved from start: 0.2694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 29880 Z= 0.144 Angle : 0.690 14.208 40550 Z= 0.338 Chirality : 0.044 0.238 4542 Planarity : 0.004 0.052 5250 Dihedral : 4.161 21.311 4040 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 3.54 % Allowed : 23.15 % Favored : 73.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.19 (0.14), residues: 3592 helix: 1.39 (0.13), residues: 1590 sheet: -0.24 (0.28), residues: 372 loop : -1.06 (0.15), residues: 1630 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.069 0.001 TRP A 637 HIS 0.009 0.001 HIS B 378 PHE 0.029 0.001 PHE E 522 TYR 0.026 0.001 TYR E 17 ARG 0.008 0.000 ARG D 526 Details of bonding type rmsd hydrogen bonds : bond 0.04212 ( 1288) hydrogen bonds : angle 3.86492 ( 3657) covalent geometry : bond 0.00340 (29880) covalent geometry : angle 0.68976 (40550) *********************** 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 883 residues out of total 3188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 770 time to evaluate : 3.257 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 66 LYS cc_start: 0.8168 (tptm) cc_final: 0.7254 (tptm) REVERT: A 70 ASP cc_start: 0.7905 (m-30) cc_final: 0.7275 (m-30) REVERT: A 111 MET cc_start: 0.8717 (tmm) cc_final: 0.8094 (tmm) REVERT: A 257 ASP cc_start: 0.8277 (m-30) cc_final: 0.7975 (m-30) REVERT: A 449 TYR cc_start: 0.7578 (m-80) cc_final: 0.7232 (m-80) REVERT: A 481 GLU cc_start: 0.8223 (mp0) cc_final: 0.7790 (mp0) REVERT: A 552 LEU cc_start: 0.8780 (OUTLIER) cc_final: 0.8557 (tp) REVERT: A 591 GLU cc_start: 0.7553 (tm-30) cc_final: 0.7349 (tm-30) REVERT: A 641 LEU cc_start: 0.8904 (mt) cc_final: 0.8668 (mt) REVERT: A 667 MET cc_start: 0.8494 (tpp) cc_final: 0.7876 (mmm) REVERT: A 671 MET cc_start: 0.8022 (mmm) cc_final: 0.7740 (mmp) REVERT: A 709 MET cc_start: 0.8540 (pmm) cc_final: 0.8286 (pmm) REVERT: A 831 GLU cc_start: 0.8244 (tm-30) cc_final: 0.7984 (tm-30) REVERT: B 17 TYR cc_start: 0.7860 (p90) cc_final: 0.7253 (p90) REVERT: B 36 LEU cc_start: 0.8952 (mm) cc_final: 0.8676 (mm) REVERT: B 47 GLN cc_start: 0.7977 (pp30) cc_final: 0.7740 (tm-30) REVERT: B 98 ARG cc_start: 0.7828 (tpt90) cc_final: 0.7590 (tpt90) REVERT: B 99 ASP cc_start: 0.8301 (p0) cc_final: 0.8032 (t0) REVERT: B 193 GLU cc_start: 0.7765 (tm-30) cc_final: 0.7548 (mm-30) REVERT: B 291 MET cc_start: 0.8129 (tmm) cc_final: 0.7795 (tmm) REVERT: B 339 ASP cc_start: 0.8156 (m-30) cc_final: 0.7770 (m-30) REVERT: B 355 LEU cc_start: 0.7905 (mm) cc_final: 0.7682 (mm) REVERT: B 515 TYR cc_start: 0.8980 (t80) cc_final: 0.8527 (t80) REVERT: B 686 GLU cc_start: 0.8003 (tp30) cc_final: 0.7579 (tp30) REVERT: B 724 GLU cc_start: 0.8251 (mm-30) cc_final: 0.7797 (mm-30) REVERT: B 747 GLU cc_start: 0.7765 (pp20) cc_final: 0.7478 (pp20) REVERT: C 314 THR cc_start: 0.7118 (OUTLIER) cc_final: 0.6906 (t) REVERT: D 40 MET cc_start: 0.8271 (mmm) cc_final: 0.8034 (mmp) REVERT: D 44 ARG cc_start: 0.7908 (mtt180) cc_final: 0.7573 (mtt180) REVERT: D 66 LYS cc_start: 0.8397 (tptm) cc_final: 0.8037 (tptm) REVERT: D 99 ASP cc_start: 0.8206 (p0) cc_final: 0.7897 (p0) REVERT: D 111 MET cc_start: 0.8836 (tpp) cc_final: 0.8458 (tpp) REVERT: D 209 CYS cc_start: 0.7895 (t) cc_final: 0.7606 (t) REVERT: D 253 GLU cc_start: 0.7957 (mp0) cc_final: 0.7504 (mp0) REVERT: D 257 ASP cc_start: 0.8101 (m-30) cc_final: 0.7802 (m-30) REVERT: D 324 PHE cc_start: 0.6744 (p90) cc_final: 0.6335 (p90) REVERT: D 342 LYS cc_start: 0.8601 (ptpp) cc_final: 0.8243 (ptpp) REVERT: D 344 TYR cc_start: 0.8739 (OUTLIER) cc_final: 0.7669 (t80) REVERT: D 348 MET cc_start: 0.8010 (tpp) cc_final: 0.7774 (tpp) REVERT: D 573 TRP cc_start: 0.8287 (m100) cc_final: 0.8012 (m100) REVERT: D 620 MET cc_start: 0.8416 (tpp) cc_final: 0.7888 (tpp) REVERT: D 744 TYR cc_start: 0.8718 (OUTLIER) cc_final: 0.8373 (m-80) REVERT: E 44 ARG cc_start: 0.8206 (ttp-170) cc_final: 0.7952 (ptm160) REVERT: E 81 LYS cc_start: 0.8129 (ptmm) cc_final: 0.7890 (ptmm) REVERT: E 111 MET cc_start: 0.8894 (tmm) cc_final: 0.8160 (tmm) REVERT: E 202 VAL cc_start: 0.8305 (t) cc_final: 0.8070 (m) REVERT: E 339 ASP cc_start: 0.8264 (m-30) cc_final: 0.7796 (m-30) REVERT: E 363 GLU cc_start: 0.7110 (OUTLIER) cc_final: 0.6707 (pt0) REVERT: E 409 MET cc_start: 0.7951 (mmt) cc_final: 0.7241 (mmt) REVERT: E 411 ASN cc_start: 0.8591 (t0) cc_final: 0.8277 (t0) REVERT: E 423 GLU cc_start: 0.7728 (mp0) cc_final: 0.7360 (pm20) REVERT: E 467 HIS cc_start: 0.7463 (p90) cc_final: 0.7246 (p-80) REVERT: E 498 ASN cc_start: 0.8386 (t0) cc_final: 0.8122 (t0) REVERT: E 529 ARG cc_start: 0.7305 (ttt90) cc_final: 0.6875 (ttt90) REVERT: E 536 GLU cc_start: 0.7867 (tp30) cc_final: 0.7491 (tt0) REVERT: E 642 ASN cc_start: 0.8717 (t0) cc_final: 0.8457 (t0) REVERT: F 26 GLN cc_start: 0.7143 (mm-40) cc_final: 0.6706 (mm-40) outliers start: 113 outliers final: 97 residues processed: 836 average time/residue: 0.4069 time to fit residues: 529.7606 Evaluate side-chains 861 residues out of total 3188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 759 time to evaluate : 3.066 ------------------------------------------------------------------------------- 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 191 ILE Chi-restraints excluded: chain A residue 224 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 410 TYR Chi-restraints excluded: chain A residue 416 VAL 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 652 MET Chi-restraints excluded: chain A residue 692 ASN 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 880 LYS 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 265 TRP Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 276 GLN Chi-restraints excluded: chain B residue 327 LEU Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 345 LEU Chi-restraints excluded: chain B residue 435 ASP 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 614 MET 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 881 MET Chi-restraints excluded: chain B residue 887 THR Chi-restraints excluded: chain C residue 272 VAL Chi-restraints excluded: chain C residue 275 SER 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 95 MET Chi-restraints excluded: chain D residue 114 VAL Chi-restraints excluded: chain D residue 117 VAL Chi-restraints excluded: chain D residue 224 ILE 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 376 VAL 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 527 PHE 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 672 LEU Chi-restraints excluded: chain D residue 692 ASN Chi-restraints excluded: chain D residue 715 LEU Chi-restraints excluded: chain D residue 744 TYR 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 869 VAL Chi-restraints excluded: chain D residue 890 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 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 278 VAL Chi-restraints excluded: chain E residue 363 GLU Chi-restraints excluded: chain E residue 369 VAL Chi-restraints excluded: chain E residue 435 ASP Chi-restraints excluded: chain E residue 472 ILE Chi-restraints excluded: chain E residue 512 GLU Chi-restraints excluded: chain E residue 527 PHE Chi-restraints excluded: chain E residue 533 ILE 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 E residue 892 MET Chi-restraints excluded: chain F residue 5 MET 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 40 optimal weight: 3.9990 chunk 172 optimal weight: 5.9990 chunk 70 optimal weight: 0.7980 chunk 23 optimal weight: 1.9990 chunk 0 optimal weight: 9.9990 chunk 281 optimal weight: 5.9990 chunk 290 optimal weight: 3.9990 chunk 183 optimal weight: 9.9990 chunk 273 optimal weight: 1.9990 chunk 360 optimal weight: 7.9990 chunk 351 optimal weight: 1.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- 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** B 550 ASN C 274 ASN D 146 HIS D 692 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.088685 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.074677 restraints weight = 70022.374| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.077295 restraints weight = 32511.146| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.078972 restraints weight = 18906.053| |-----------------------------------------------------------------------------| r_work (final): 0.3158 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8181 moved from start: 0.2822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 29880 Z= 0.190 Angle : 0.731 13.617 40550 Z= 0.361 Chirality : 0.045 0.244 4542 Planarity : 0.004 0.053 5250 Dihedral : 4.316 22.364 4040 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 3.83 % Allowed : 23.31 % Favored : 72.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.08 (0.14), residues: 3592 helix: 1.31 (0.13), residues: 1588 sheet: -0.40 (0.27), residues: 392 loop : -1.10 (0.15), residues: 1612 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.057 0.002 TRP A 637 HIS 0.012 0.001 HIS D 378 PHE 0.028 0.002 PHE E 522 TYR 0.028 0.002 TYR E 17 ARG 0.007 0.000 ARG D 623 Details of bonding type rmsd hydrogen bonds : bond 0.04763 ( 1288) hydrogen bonds : angle 3.99429 ( 3657) covalent geometry : bond 0.00449 (29880) covalent geometry : angle 0.73079 (40550) *********************** 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 891 residues out of total 3188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 769 time to evaluate : 3.393 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 66 LYS cc_start: 0.8189 (tptm) cc_final: 0.7316 (tptm) REVERT: A 70 ASP cc_start: 0.7934 (m-30) cc_final: 0.7319 (m-30) REVERT: A 111 MET cc_start: 0.8704 (tmm) cc_final: 0.8092 (tmm) REVERT: A 257 ASP cc_start: 0.8288 (m-30) cc_final: 0.8005 (m-30) REVERT: A 371 MET cc_start: 0.6803 (mtm) cc_final: 0.6558 (mtt) REVERT: A 449 TYR cc_start: 0.7637 (m-80) cc_final: 0.7284 (m-80) REVERT: A 501 LEU cc_start: 0.8673 (tp) cc_final: 0.8408 (tp) REVERT: A 552 LEU cc_start: 0.8778 (OUTLIER) cc_final: 0.8552 (tp) REVERT: A 641 LEU cc_start: 0.8903 (mt) cc_final: 0.8579 (mt) REVERT: A 667 MET cc_start: 0.8504 (tpp) cc_final: 0.8125 (mmm) REVERT: A 709 MET cc_start: 0.8562 (pmm) cc_final: 0.8297 (pmm) REVERT: B 17 TYR cc_start: 0.7922 (p90) cc_final: 0.7266 (p90) REVERT: B 36 LEU cc_start: 0.8982 (mm) cc_final: 0.8703 (mm) REVERT: B 47 GLN cc_start: 0.7989 (pp30) cc_final: 0.7739 (tm-30) REVERT: B 99 ASP cc_start: 0.8290 (p0) cc_final: 0.8046 (t0) REVERT: B 339 ASP cc_start: 0.8123 (m-30) cc_final: 0.7777 (m-30) REVERT: B 515 TYR cc_start: 0.9000 (t80) cc_final: 0.8540 (t80) REVERT: B 686 GLU cc_start: 0.7989 (tp30) cc_final: 0.7592 (tp30) REVERT: B 724 GLU cc_start: 0.8248 (mm-30) cc_final: 0.7796 (mm-30) REVERT: B 747 GLU cc_start: 0.7771 (pp20) cc_final: 0.7531 (pp20) REVERT: B 803 ASP cc_start: 0.7459 (t0) cc_final: 0.7040 (t0) REVERT: C 314 THR cc_start: 0.7306 (OUTLIER) cc_final: 0.7079 (t) REVERT: D 40 MET cc_start: 0.8238 (OUTLIER) cc_final: 0.8018 (mmp) REVERT: D 44 ARG cc_start: 0.7911 (mtt180) cc_final: 0.7577 (mtt180) REVERT: D 66 LYS cc_start: 0.8391 (tptm) cc_final: 0.7990 (tptm) REVERT: D 111 MET cc_start: 0.8812 (tpp) cc_final: 0.8443 (tpp) REVERT: D 209 CYS cc_start: 0.7975 (t) cc_final: 0.7705 (t) REVERT: D 253 GLU cc_start: 0.7958 (mp0) cc_final: 0.7538 (mp0) REVERT: D 257 ASP cc_start: 0.8161 (m-30) cc_final: 0.7873 (m-30) REVERT: D 324 PHE cc_start: 0.6802 (p90) cc_final: 0.6411 (p90) REVERT: D 344 TYR cc_start: 0.8832 (OUTLIER) cc_final: 0.7494 (t80) REVERT: D 348 MET cc_start: 0.8023 (tpp) cc_final: 0.7493 (tpp) REVERT: D 449 TYR cc_start: 0.8017 (m-80) cc_final: 0.7666 (m-80) REVERT: D 620 MET cc_start: 0.8430 (tpp) cc_final: 0.7851 (tpp) REVERT: D 744 TYR cc_start: 0.8745 (OUTLIER) cc_final: 0.8417 (m-80) REVERT: D 769 ASP cc_start: 0.8122 (t0) cc_final: 0.7911 (t0) REVERT: E 36 LEU cc_start: 0.8769 (mm) cc_final: 0.8526 (mm) REVERT: E 44 ARG cc_start: 0.8211 (ttp-170) cc_final: 0.7955 (ptm160) REVERT: E 81 LYS cc_start: 0.8116 (ptmm) cc_final: 0.7848 (ptmm) REVERT: E 111 MET cc_start: 0.8831 (tmm) cc_final: 0.8140 (tmm) REVERT: E 339 ASP cc_start: 0.8275 (m-30) cc_final: 0.7841 (m-30) REVERT: E 348 MET cc_start: 0.8250 (mmt) cc_final: 0.7946 (mtp) REVERT: E 363 GLU cc_start: 0.7024 (OUTLIER) cc_final: 0.6631 (pt0) REVERT: E 409 MET cc_start: 0.7945 (mmt) cc_final: 0.7193 (mmt) REVERT: E 411 ASN cc_start: 0.8594 (t0) cc_final: 0.8258 (t0) REVERT: E 467 HIS cc_start: 0.7544 (p90) cc_final: 0.7277 (p-80) REVERT: E 498 ASN cc_start: 0.8392 (t0) cc_final: 0.8126 (t0) REVERT: E 529 ARG cc_start: 0.7264 (ttt90) cc_final: 0.6911 (ttt90) REVERT: E 536 GLU cc_start: 0.7883 (tp30) cc_final: 0.7659 (tt0) REVERT: E 622 ARG cc_start: 0.7753 (tpp80) cc_final: 0.7368 (tpp80) REVERT: E 642 ASN cc_start: 0.8729 (t0) cc_final: 0.8468 (t0) REVERT: F 26 GLN cc_start: 0.7146 (mm-40) cc_final: 0.6697 (mm-40) outliers start: 122 outliers final: 109 residues processed: 839 average time/residue: 0.4230 time to fit residues: 554.5498 Evaluate side-chains 880 residues out of total 3188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 765 time to evaluate : 3.238 ------------------------------------------------------------------------------- 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 160 GLU Chi-restraints excluded: chain A residue 191 ILE Chi-restraints excluded: chain A residue 224 ILE Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 340 VAL Chi-restraints excluded: chain A residue 344 TYR Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain A residue 379 LEU Chi-restraints excluded: chain A residue 410 TYR Chi-restraints excluded: chain A residue 416 VAL Chi-restraints excluded: chain A residue 500 MET Chi-restraints excluded: chain A residue 527 PHE 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 652 MET Chi-restraints excluded: chain A residue 692 ASN 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 777 VAL Chi-restraints excluded: chain A residue 835 THR Chi-restraints excluded: chain A residue 875 VAL Chi-restraints excluded: chain A residue 880 LYS 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 265 TRP Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 327 LEU 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 472 ILE Chi-restraints excluded: chain B residue 541 VAL Chi-restraints excluded: chain B residue 574 ILE Chi-restraints excluded: chain B residue 614 MET 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 881 MET Chi-restraints excluded: chain B residue 887 THR Chi-restraints excluded: chain C residue 270 MET Chi-restraints excluded: chain C residue 272 VAL Chi-restraints excluded: chain C residue 275 SER 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 40 MET Chi-restraints excluded: chain D residue 95 MET Chi-restraints excluded: chain D residue 114 VAL Chi-restraints excluded: chain D residue 117 VAL Chi-restraints excluded: chain D residue 224 ILE 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 376 VAL Chi-restraints excluded: chain D residue 410 TYR 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 527 PHE 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 672 LEU Chi-restraints excluded: chain D residue 692 ASN Chi-restraints excluded: chain D residue 715 LEU Chi-restraints excluded: chain D residue 744 TYR 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 D residue 866 ILE Chi-restraints excluded: chain D residue 869 VAL Chi-restraints excluded: chain D residue 890 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 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 363 GLU Chi-restraints excluded: chain E residue 369 VAL Chi-restraints excluded: chain E residue 435 ASP Chi-restraints excluded: chain E residue 472 ILE Chi-restraints excluded: chain E residue 512 GLU Chi-restraints excluded: chain E residue 527 PHE Chi-restraints excluded: chain E residue 533 ILE 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 E residue 886 ILE Chi-restraints excluded: chain E residue 892 MET Chi-restraints excluded: chain F residue 5 MET Chi-restraints excluded: chain F residue 326 ILE 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 24 optimal weight: 0.3980 chunk 231 optimal weight: 3.9990 chunk 95 optimal weight: 0.7980 chunk 63 optimal weight: 0.3980 chunk 135 optimal weight: 0.3980 chunk 344 optimal weight: 3.9990 chunk 252 optimal weight: 0.8980 chunk 227 optimal weight: 4.9990 chunk 171 optimal weight: 5.9990 chunk 112 optimal weight: 5.9990 chunk 115 optimal weight: 0.8980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 352 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 550 ASN C 274 ASN D 692 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.091692 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.077670 restraints weight = 70060.707| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.080339 restraints weight = 32343.449| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.082054 restraints weight = 18729.401| |-----------------------------------------------------------------------------| r_work (final): 0.3215 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8117 moved from start: 0.2765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 29880 Z= 0.128 Angle : 0.723 14.726 40550 Z= 0.351 Chirality : 0.044 0.259 4542 Planarity : 0.004 0.056 5250 Dihedral : 4.127 20.520 4040 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 3.04 % Allowed : 24.62 % Favored : 72.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.19 (0.14), residues: 3592 helix: 1.41 (0.13), residues: 1582 sheet: -0.19 (0.28), residues: 370 loop : -1.09 (0.15), residues: 1640 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.001 TRP A 637 HIS 0.011 0.001 HIS D 378 PHE 0.032 0.001 PHE C 286 TYR 0.026 0.001 TYR E 17 ARG 0.008 0.000 ARG D 623 Details of bonding type rmsd hydrogen bonds : bond 0.03764 ( 1288) hydrogen bonds : angle 3.86029 ( 3657) covalent geometry : bond 0.00299 (29880) covalent geometry : angle 0.72319 (40550) ********************** 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 878 residues out of total 3188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 781 time to evaluate : 3.456 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 66 LYS cc_start: 0.8066 (tptm) cc_final: 0.7140 (tptm) REVERT: A 70 ASP cc_start: 0.7907 (m-30) cc_final: 0.7280 (m-30) REVERT: A 111 MET cc_start: 0.8704 (tmm) cc_final: 0.8095 (tmm) REVERT: A 147 ASP cc_start: 0.8540 (t0) cc_final: 0.8295 (t0) REVERT: A 257 ASP cc_start: 0.8261 (m-30) cc_final: 0.7955 (m-30) REVERT: A 501 LEU cc_start: 0.8613 (tp) cc_final: 0.8338 (tp) REVERT: A 526 ARG cc_start: 0.7960 (ttp80) cc_final: 0.7621 (ttp80) REVERT: A 552 LEU cc_start: 0.8786 (OUTLIER) cc_final: 0.8562 (tp) REVERT: A 636 PHE cc_start: 0.7789 (p90) cc_final: 0.7321 (p90) REVERT: A 671 MET cc_start: 0.7874 (mmm) cc_final: 0.7406 (mmp) REVERT: A 709 MET cc_start: 0.8533 (pmm) cc_final: 0.8279 (pmm) REVERT: A 831 GLU cc_start: 0.8230 (tm-30) cc_final: 0.7988 (tm-30) REVERT: B 17 TYR cc_start: 0.7902 (p90) cc_final: 0.7220 (p90) REVERT: B 36 LEU cc_start: 0.8901 (mm) cc_final: 0.8607 (mm) REVERT: B 291 MET cc_start: 0.8121 (tmm) cc_final: 0.7602 (tmm) REVERT: B 339 ASP cc_start: 0.8128 (m-30) cc_final: 0.7741 (m-30) REVERT: B 355 LEU cc_start: 0.7806 (mm) cc_final: 0.7585 (mm) REVERT: B 409 MET cc_start: 0.6425 (tpt) cc_final: 0.6196 (tpt) REVERT: B 515 TYR cc_start: 0.8955 (t80) cc_final: 0.8517 (t80) REVERT: B 666 MET cc_start: 0.8327 (tpp) cc_final: 0.8067 (tpt) REVERT: B 674 SER cc_start: 0.8490 (m) cc_final: 0.8105 (p) REVERT: B 686 GLU cc_start: 0.7976 (tp30) cc_final: 0.7701 (tp30) REVERT: B 724 GLU cc_start: 0.8268 (mm-30) cc_final: 0.7804 (mm-30) REVERT: B 747 GLU cc_start: 0.7694 (pp20) cc_final: 0.7438 (pp20) REVERT: C 314 THR cc_start: 0.7173 (OUTLIER) cc_final: 0.6952 (t) REVERT: D 40 MET cc_start: 0.8199 (OUTLIER) cc_final: 0.7970 (mmp) REVERT: D 44 ARG cc_start: 0.7942 (mtt180) cc_final: 0.7618 (mtt180) REVERT: D 66 LYS cc_start: 0.8352 (tptm) cc_final: 0.7982 (tptm) REVERT: D 99 ASP cc_start: 0.8204 (p0) cc_final: 0.7854 (p0) REVERT: D 111 MET cc_start: 0.8856 (tpp) cc_final: 0.8482 (tpp) REVERT: D 209 CYS cc_start: 0.7805 (t) cc_final: 0.7503 (t) REVERT: D 253 GLU cc_start: 0.7931 (mp0) cc_final: 0.7534 (mp0) REVERT: D 324 PHE cc_start: 0.6703 (p90) cc_final: 0.6335 (p90) REVERT: D 344 TYR cc_start: 0.8745 (OUTLIER) cc_final: 0.7784 (t80) REVERT: D 503 MET cc_start: 0.8617 (tmm) cc_final: 0.8379 (tmm) REVERT: D 620 MET cc_start: 0.8401 (tpp) cc_final: 0.7845 (tpp) REVERT: D 692 ASN cc_start: 0.7898 (OUTLIER) cc_final: 0.7566 (t0) REVERT: D 769 ASP cc_start: 0.8091 (t0) cc_final: 0.7891 (t0) REVERT: D 840 VAL cc_start: 0.9034 (p) cc_final: 0.8796 (m) REVERT: E 44 ARG cc_start: 0.8186 (ttp-170) cc_final: 0.7916 (ptm160) REVERT: E 81 LYS cc_start: 0.8139 (ptmm) cc_final: 0.7847 (ptmm) REVERT: E 111 MET cc_start: 0.8904 (tmm) cc_final: 0.8197 (tmm) REVERT: E 339 ASP cc_start: 0.8239 (m-30) cc_final: 0.7776 (m-30) REVERT: E 348 MET cc_start: 0.8158 (mmt) cc_final: 0.7861 (mtp) REVERT: E 363 GLU cc_start: 0.7066 (OUTLIER) cc_final: 0.6838 (pt0) REVERT: E 409 MET cc_start: 0.7995 (mmt) cc_final: 0.7315 (mmt) REVERT: E 411 ASN cc_start: 0.8549 (t0) cc_final: 0.8066 (t0) REVERT: E 467 HIS cc_start: 0.7504 (p90) cc_final: 0.7262 (p-80) REVERT: E 498 ASN cc_start: 0.8378 (t0) cc_final: 0.8112 (t0) REVERT: E 529 ARG cc_start: 0.7276 (ttt90) cc_final: 0.6969 (ttt90) REVERT: E 536 GLU cc_start: 0.7868 (tp30) cc_final: 0.7637 (tt0) REVERT: E 642 ASN cc_start: 0.8707 (t0) cc_final: 0.8419 (t0) REVERT: F 26 GLN cc_start: 0.7075 (mm-40) cc_final: 0.6643 (mm-40) outliers start: 97 outliers final: 82 residues processed: 836 average time/residue: 0.4105 time to fit residues: 534.6488 Evaluate side-chains 853 residues out of total 3188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 765 time to evaluate : 3.088 ------------------------------------------------------------------------------- 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 160 GLU Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 340 VAL Chi-restraints excluded: chain A residue 344 TYR Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain A residue 379 LEU Chi-restraints excluded: chain A residue 416 VAL 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 732 LEU Chi-restraints excluded: chain A residue 772 VAL Chi-restraints excluded: chain A residue 835 THR Chi-restraints excluded: chain A residue 880 LYS 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 265 TRP Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 276 GLN Chi-restraints excluded: chain B residue 327 LEU Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 345 LEU Chi-restraints excluded: chain B residue 391 THR Chi-restraints excluded: chain B residue 435 ASP 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 655 SER Chi-restraints excluded: chain B residue 772 VAL Chi-restraints excluded: chain B residue 815 ILE Chi-restraints excluded: chain B residue 881 MET Chi-restraints excluded: chain B residue 887 THR Chi-restraints excluded: chain C residue 270 MET Chi-restraints excluded: chain C residue 274 ASN Chi-restraints excluded: chain C residue 275 SER 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 40 MET Chi-restraints excluded: chain D residue 114 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 376 VAL Chi-restraints excluded: chain D residue 416 VAL 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 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 79 VAL Chi-restraints excluded: chain E residue 104 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 244 HIS Chi-restraints excluded: chain E residue 265 TRP 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 435 ASP Chi-restraints excluded: chain E residue 472 ILE Chi-restraints excluded: chain E residue 512 GLU Chi-restraints excluded: chain E residue 527 PHE Chi-restraints excluded: chain E residue 533 ILE 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 F residue 5 MET 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 55 optimal weight: 5.9990 chunk 258 optimal weight: 6.9990 chunk 22 optimal weight: 0.6980 chunk 127 optimal weight: 6.9990 chunk 208 optimal weight: 6.9990 chunk 250 optimal weight: 3.9990 chunk 113 optimal weight: 2.9990 chunk 5 optimal weight: 0.7980 chunk 210 optimal weight: 5.9990 chunk 54 optimal weight: 0.7980 chunk 138 optimal weight: 1.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 352 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 550 ASN C 274 ASN ** E 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.091543 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.077512 restraints weight = 69867.319| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.080182 restraints weight = 32293.343| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.081897 restraints weight = 18730.051| |-----------------------------------------------------------------------------| r_work (final): 0.3212 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8121 moved from start: 0.2770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.149 29880 Z= 0.169 Angle : 0.818 58.791 40550 Z= 0.430 Chirality : 0.046 0.845 4542 Planarity : 0.005 0.112 5250 Dihedral : 4.164 36.389 4040 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 10.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 2.85 % Allowed : 25.19 % Favored : 71.96 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.18 (0.14), residues: 3592 helix: 1.40 (0.13), residues: 1582 sheet: -0.18 (0.28), residues: 370 loop : -1.09 (0.15), residues: 1640 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.002 TRP A 637 HIS 0.015 0.001 HIS D 378 PHE 0.027 0.001 PHE C 286 TYR 0.024 0.001 TYR E 17 ARG 0.011 0.000 ARG E 98 Details of bonding type rmsd hydrogen bonds : bond 0.03804 ( 1288) hydrogen bonds : angle 3.86202 ( 3657) covalent geometry : bond 0.00376 (29880) covalent geometry : angle 0.81821 (40550) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11448.29 seconds wall clock time: 199 minutes 12.97 seconds (11952.97 seconds total)