Starting phenix.real_space_refine on Thu Mar 5 16:44:03 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7kgg_22869/03_2026/7kgg_22869.cif Found real_map, /net/cci-nas-00/data/ceres_data/7kgg_22869/03_2026/7kgg_22869.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.97 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7kgg_22869/03_2026/7kgg_22869.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7kgg_22869/03_2026/7kgg_22869.map" model { file = "/net/cci-nas-00/data/ceres_data/7kgg_22869/03_2026/7kgg_22869.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7kgg_22869/03_2026/7kgg_22869.cif" } resolution = 2.97 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.211 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 6 5.49 5 S 135 5.16 5 C 15374 2.51 5 N 3807 2.21 5 O 4355 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 105 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 23677 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 7785 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1020, 7785 Classifications: {'peptide': 1020} Link IDs: {'PCIS': 1, 'PTRANS': 45, 'TRANS': 973} Chain breaks: 1 Chain: "B" Number of atoms: 7784 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1020, 7784 Classifications: {'peptide': 1020} Link IDs: {'PCIS': 1, 'PTRANS': 45, 'TRANS': 973} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "C" Number of atoms: 7785 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1020, 7785 Classifications: {'peptide': 1020} Link IDs: {'PCIS': 1, 'PTRANS': 45, 'TRANS': 973} Chain breaks: 1 Chain: "A" Number of atoms: 81 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 81 Unusual residues: {'PTY': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 19 Chain: "B" Number of atoms: 89 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 89 Unusual residues: {'PTY': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 11 Chain: "C" Number of atoms: 153 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 153 Unusual residues: {' ET': 3, 'PTY': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 19 Time building chain proxies: 5.77, per 1000 atoms: 0.24 Number of scatterers: 23677 At special positions: 0 Unit cell: (119.88, 114.48, 141.48, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 135 16.00 P 6 15.00 O 4355 8.00 N 3807 7.00 C 15374 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: 2.26 Conformation dependent library (CDL) restraints added in 1.1 seconds 6096 Ramachandran restraints generated. 3048 Oldfield, 0 Emsley, 3048 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5706 Finding SS restraints... Secondary structure from input PDB file: 115 helices and 24 sheets defined 60.8% alpha, 20.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.11 Creating SS restraints... Processing helix chain 'A' and resid 1 through 7 removed outlier: 3.882A pdb=" N PHE A 5 " --> pdb=" O MET A 1 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ARG A 7 " --> pdb=" O GLN A 3 " (cutoff:3.500A) Processing helix chain 'A' and resid 8 through 30 removed outlier: 3.621A pdb=" N ALA A 12 " --> pdb=" O ARG A 8 " (cutoff:3.500A) Proline residue: A 28 - end of helix Processing helix chain 'A' and resid 53 through 61 Processing helix chain 'A' and resid 61 through 68 removed outlier: 3.954A pdb=" N GLU A 68 " --> pdb=" O LEU A 64 " (cutoff:3.500A) Processing helix chain 'A' and resid 69 through 72 removed outlier: 3.823A pdb=" N VAL A 72 " --> pdb=" O LEU A 69 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 69 through 72' Processing helix chain 'A' and resid 99 through 112 Processing helix chain 'A' and resid 113 through 116 removed outlier: 4.425A pdb=" N ALA A 116 " --> pdb=" O ALA A 113 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 113 through 116' Processing helix chain 'A' and resid 119 through 126 Processing helix chain 'A' and resid 150 through 162 Processing helix chain 'A' and resid 162 through 167 Processing helix chain 'A' and resid 189 through 196 removed outlier: 3.537A pdb=" N TYR A 196 " --> pdb=" O LYS A 192 " (cutoff:3.500A) Processing helix chain 'A' and resid 199 through 211 Processing helix chain 'A' and resid 242 through 248 Processing helix chain 'A' and resid 262 through 265 No H-bonds generated for 'chain 'A' and resid 262 through 265' Processing helix chain 'A' and resid 298 through 317 removed outlier: 3.925A pdb=" N ASN A 316 " --> pdb=" O GLU A 312 " (cutoff:3.500A) Processing helix chain 'A' and resid 329 through 360 removed outlier: 3.982A pdb=" N VAL A 333 " --> pdb=" O THR A 329 " (cutoff:3.500A) Processing helix chain 'A' and resid 361 through 387 Proline residue: A 368 - end of helix removed outlier: 4.108A pdb=" N VAL A 371 " --> pdb=" O ILE A 367 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N ALA A 372 " --> pdb=" O PRO A 368 " (cutoff:3.500A) Proline residue: A 373 - end of helix Processing helix chain 'A' and resid 391 through 405 removed outlier: 4.400A pdb=" N GLY A 403 " --> pdb=" O VAL A 399 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N ILE A 404 " --> pdb=" O LEU A 400 " (cutoff:3.500A) Processing helix chain 'A' and resid 406 through 424 Processing helix chain 'A' and resid 426 through 454 removed outlier: 5.428A pdb=" N SER A 440 " --> pdb=" O LYS A 436 " (cutoff:3.500A) Proline residue: A 441 - end of helix removed outlier: 4.061A pdb=" N PHE A 453 " --> pdb=" O LEU A 449 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N LEU A 454 " --> pdb=" O ALA A 450 " (cutoff:3.500A) Processing helix chain 'A' and resid 455 through 459 Processing helix chain 'A' and resid 460 through 486 removed outlier: 3.524A pdb=" N GLY A 464 " --> pdb=" O SER A 460 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N GLN A 469 " --> pdb=" O VAL A 465 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N PHE A 470 " --> pdb=" O ILE A 466 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N SER A 477 " --> pdb=" O THR A 473 " (cutoff:3.500A) Processing helix chain 'A' and resid 487 through 496 removed outlier: 3.972A pdb=" N ALA A 491 " --> pdb=" O ILE A 487 " (cutoff:3.500A) Processing helix chain 'A' and resid 509 through 534 removed outlier: 3.731A pdb=" N HIS A 534 " --> pdb=" O LYS A 530 " (cutoff:3.500A) Processing helix chain 'A' and resid 534 through 556 removed outlier: 4.029A pdb=" N MET A 538 " --> pdb=" O HIS A 534 " (cutoff:3.500A) Processing helix chain 'A' and resid 580 through 596 Processing helix chain 'A' and resid 635 through 651 removed outlier: 4.013A pdb=" N ASN A 649 " --> pdb=" O SER A 645 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N SER A 650 " --> pdb=" O SER A 646 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N THR A 651 " --> pdb=" O MET A 647 " (cutoff:3.500A) Processing helix chain 'A' and resid 683 through 701 removed outlier: 3.800A pdb=" N LYS A 700 " --> pdb=" O ALA A 696 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ASN A 701 " --> pdb=" O MET A 697 " (cutoff:3.500A) Processing helix chain 'A' and resid 723 through 731 Processing helix chain 'A' and resid 733 through 743 Processing helix chain 'A' and resid 768 through 771 Processing helix chain 'A' and resid 773 through 779 removed outlier: 3.506A pdb=" N ILE A 777 " --> pdb=" O GLN A 773 " (cutoff:3.500A) Processing helix chain 'A' and resid 792 through 795 No H-bonds generated for 'chain 'A' and resid 792 through 795' Processing helix chain 'A' and resid 827 through 840 Processing helix chain 'A' and resid 852 through 884 removed outlier: 3.634A pdb=" N GLN A 856 " --> pdb=" O GLY A 852 " (cutoff:3.500A) removed outlier: 4.799A pdb=" N ALA A 865 " --> pdb=" O GLU A 861 " (cutoff:3.500A) removed outlier: 4.906A pdb=" N PHE A 866 " --> pdb=" O SER A 862 " (cutoff:3.500A) Processing helix chain 'A' and resid 887 through 893 Processing helix chain 'A' and resid 895 through 911 removed outlier: 3.544A pdb=" N GLY A 899 " --> pdb=" O VAL A 895 " (cutoff:3.500A) Processing helix chain 'A' and resid 915 through 948 removed outlier: 3.831A pdb=" N ILE A 936 " --> pdb=" O ASN A 932 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N PHE A 939 " --> pdb=" O LEU A 935 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N MET A 948 " --> pdb=" O LYS A 944 " (cutoff:3.500A) Processing helix chain 'A' and resid 949 through 981 removed outlier: 5.006A pdb=" N ARG A 963 " --> pdb=" O LYS A 959 " (cutoff:3.500A) Proline residue: A 964 - end of helix Proline residue: A 978 - end of helix Processing helix chain 'A' and resid 986 through 1027 removed outlier: 3.726A pdb=" N GLN A 990 " --> pdb=" O SER A 986 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N GLY A 996 " --> pdb=" O ALA A 992 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N VAL A 997 " --> pdb=" O LEU A 993 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N PHE A1010 " --> pdb=" O ILE A1006 " (cutoff:3.500A) Proline residue: A1013 - end of helix Processing helix chain 'B' and resid 8 through 27 removed outlier: 3.579A pdb=" N ALA B 12 " --> pdb=" O ARG B 8 " (cutoff:3.500A) WARNING: missing atoms! Processing helix chain 'B' and resid 28 through 30 No H-bonds generated for 'chain 'B' and resid 28 through 30' Processing helix chain 'B' and resid 53 through 61 Processing helix chain 'B' and resid 61 through 70 removed outlier: 4.013A pdb=" N GLU B 68 " --> pdb=" O LEU B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 99 through 112 Processing helix chain 'B' and resid 113 through 115 No H-bonds generated for 'chain 'B' and resid 113 through 115' Processing helix chain 'B' and resid 119 through 126 Processing helix chain 'B' and resid 150 through 162 Processing helix chain 'B' and resid 162 through 168 Processing helix chain 'B' and resid 189 through 196 removed outlier: 3.563A pdb=" N LEU B 193 " --> pdb=" O ASP B 189 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N VAL B 194 " --> pdb=" O PRO B 190 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N SER B 195 " --> pdb=" O ASN B 191 " (cutoff:3.500A) Processing helix chain 'B' and resid 199 through 211 Processing helix chain 'B' and resid 242 through 248 removed outlier: 3.540A pdb=" N PHE B 246 " --> pdb=" O SER B 242 " (cutoff:3.500A) Processing helix chain 'B' and resid 262 through 265 No H-bonds generated for 'chain 'B' and resid 262 through 265' Processing helix chain 'B' and resid 298 through 316 removed outlier: 4.146A pdb=" N LEU B 315 " --> pdb=" O GLU B 311 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N ASN B 316 " --> pdb=" O GLU B 312 " (cutoff:3.500A) Processing helix chain 'B' and resid 329 through 360 removed outlier: 4.008A pdb=" N VAL B 333 " --> pdb=" O THR B 329 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N LYS B 334 " --> pdb=" O ALA B 330 " (cutoff:3.500A) Processing helix chain 'B' and resid 361 through 370 Proline residue: B 368 - end of helix Processing helix chain 'B' and resid 370 through 387 removed outlier: 3.758A pdb=" N ILE B 374 " --> pdb=" O ILE B 370 " (cutoff:3.500A) Processing helix chain 'B' and resid 391 through 405 removed outlier: 4.416A pdb=" N GLY B 403 " --> pdb=" O VAL B 399 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N ILE B 404 " --> pdb=" O LEU B 400 " (cutoff:3.500A) Processing helix chain 'B' and resid 406 through 424 Processing helix chain 'B' and resid 426 through 452 removed outlier: 5.800A pdb=" N SER B 440 " --> pdb=" O LYS B 436 " (cutoff:3.500A) Proline residue: B 441 - end of helix Processing helix chain 'B' and resid 454 through 459 removed outlier: 3.614A pdb=" N ALA B 459 " --> pdb=" O MET B 456 " (cutoff:3.500A) Processing helix chain 'B' and resid 460 through 496 removed outlier: 3.682A pdb=" N GLY B 464 " --> pdb=" O SER B 460 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N GLN B 469 " --> pdb=" O VAL B 465 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N PHE B 470 " --> pdb=" O ILE B 466 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N SER B 477 " --> pdb=" O THR B 473 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N THR B 489 " --> pdb=" O ALA B 485 " (cutoff:3.500A) Proline residue: B 490 - end of helix Processing helix chain 'B' and resid 509 through 534 removed outlier: 3.989A pdb=" N LYS B 533 " --> pdb=" O LEU B 529 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N HIS B 534 " --> pdb=" O LYS B 530 " (cutoff:3.500A) Processing helix chain 'B' and resid 535 through 556 Processing helix chain 'B' and resid 580 through 596 Processing helix chain 'B' and resid 635 through 650 removed outlier: 3.797A pdb=" N ASN B 649 " --> pdb=" O SER B 645 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N SER B 650 " --> pdb=" O SER B 646 " (cutoff:3.500A) Processing helix chain 'B' and resid 683 through 700 removed outlier: 3.761A pdb=" N LYS B 700 " --> pdb=" O ALA B 696 " (cutoff:3.500A) Processing helix chain 'B' and resid 723 through 731 Processing helix chain 'B' and resid 733 through 743 removed outlier: 3.500A pdb=" N VAL B 737 " --> pdb=" O LYS B 733 " (cutoff:3.500A) Processing helix chain 'B' and resid 768 through 771 Processing helix chain 'B' and resid 773 through 780 removed outlier: 3.803A pdb=" N ILE B 777 " --> pdb=" O GLN B 773 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LEU B 780 " --> pdb=" O ASP B 776 " (cutoff:3.500A) Processing helix chain 'B' and resid 792 through 795 No H-bonds generated for 'chain 'B' and resid 792 through 795' Processing helix chain 'B' and resid 827 through 841 removed outlier: 3.676A pdb=" N LYS B 841 " --> pdb=" O GLN B 837 " (cutoff:3.500A) Processing helix chain 'B' and resid 852 through 863 Processing helix chain 'B' and resid 863 through 884 Processing helix chain 'B' and resid 887 through 893 Processing helix chain 'B' and resid 895 through 910 removed outlier: 4.749A pdb=" N GLY B 902 " --> pdb=" O LEU B 898 " (cutoff:3.500A) removed outlier: 6.202A pdb=" N ILE B 905 " --> pdb=" O PHE B 901 " (cutoff:3.500A) Processing helix chain 'B' and resid 915 through 947 removed outlier: 3.835A pdb=" N ILE B 936 " --> pdb=" O ASN B 932 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N PHE B 939 " --> pdb=" O LEU B 935 " (cutoff:3.500A) Processing helix chain 'B' and resid 949 through 981 removed outlier: 5.093A pdb=" N ARG B 963 " --> pdb=" O LYS B 959 " (cutoff:3.500A) Proline residue: B 964 - end of helix Proline residue: B 978 - end of helix Processing helix chain 'B' and resid 986 through 1027 removed outlier: 4.477A pdb=" N GLY B 996 " --> pdb=" O ALA B 992 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N VAL B 997 " --> pdb=" O LEU B 993 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ILE B1009 " --> pdb=" O THR B1005 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N PHE B1010 " --> pdb=" O ILE B1006 " (cutoff:3.500A) Proline residue: B1013 - end of helix Processing helix chain 'C' and resid 2 through 7 Processing helix chain 'C' and resid 8 through 30 removed outlier: 3.547A pdb=" N ALA C 12 " --> pdb=" O ARG C 8 " (cutoff:3.500A) Proline residue: C 28 - end of helix Processing helix chain 'C' and resid 53 through 61 Processing helix chain 'C' and resid 61 through 70 removed outlier: 3.908A pdb=" N GLU C 68 " --> pdb=" O LEU C 64 " (cutoff:3.500A) Processing helix chain 'C' and resid 99 through 115 removed outlier: 3.886A pdb=" N ALA C 113 " --> pdb=" O ASN C 109 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N VAL C 114 " --> pdb=" O LYS C 110 " (cutoff:3.500A) Processing helix chain 'C' and resid 119 through 126 Processing helix chain 'C' and resid 150 through 162 Processing helix chain 'C' and resid 162 through 168 Processing helix chain 'C' and resid 189 through 196 Processing helix chain 'C' and resid 199 through 211 Processing helix chain 'C' and resid 242 through 248 Processing helix chain 'C' and resid 262 through 265 No H-bonds generated for 'chain 'C' and resid 262 through 265' Processing helix chain 'C' and resid 298 through 316 removed outlier: 3.828A pdb=" N LEU C 315 " --> pdb=" O GLU C 311 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N ASN C 316 " --> pdb=" O GLU C 312 " (cutoff:3.500A) Processing helix chain 'C' and resid 329 through 360 removed outlier: 3.773A pdb=" N VAL C 333 " --> pdb=" O THR C 329 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N THR C 343 " --> pdb=" O LYS C 339 " (cutoff:3.500A) Processing helix chain 'C' and resid 362 through 387 removed outlier: 3.734A pdb=" N LEU C 366 " --> pdb=" O VAL C 362 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N ILE C 367 " --> pdb=" O ARG C 363 " (cutoff:3.500A) Proline residue: C 368 - end of helix Proline residue: C 373 - end of helix Processing helix chain 'C' and resid 391 through 424 removed outlier: 4.379A pdb=" N GLY C 403 " --> pdb=" O VAL C 399 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N ILE C 404 " --> pdb=" O LEU C 400 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N VAL C 411 " --> pdb=" O ASP C 407 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N VAL C 412 " --> pdb=" O ASP C 408 " (cutoff:3.500A) Processing helix chain 'C' and resid 426 through 458 removed outlier: 5.619A pdb=" N SER C 440 " --> pdb=" O LYS C 436 " (cutoff:3.500A) Proline residue: C 441 - end of helix Proline residue: C 455 - end of helix Processing helix chain 'C' and resid 461 through 496 removed outlier: 3.657A pdb=" N PHE C 470 " --> pdb=" O ILE C 466 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N THR C 473 " --> pdb=" O GLN C 469 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N THR C 489 " --> pdb=" O ALA C 485 " (cutoff:3.500A) Proline residue: C 490 - end of helix Processing helix chain 'C' and resid 509 through 534 removed outlier: 3.631A pdb=" N HIS C 534 " --> pdb=" O LYS C 530 " (cutoff:3.500A) Processing helix chain 'C' and resid 534 through 556 removed outlier: 3.954A pdb=" N MET C 538 " --> pdb=" O HIS C 534 " (cutoff:3.500A) Processing helix chain 'C' and resid 580 through 597 removed outlier: 4.154A pdb=" N ASP C 597 " --> pdb=" O ASN C 593 " (cutoff:3.500A) Processing helix chain 'C' and resid 635 through 647 Processing helix chain 'C' and resid 683 through 700 removed outlier: 3.858A pdb=" N LYS C 700 " --> pdb=" O ALA C 696 " (cutoff:3.500A) Processing helix chain 'C' and resid 723 through 730 Processing helix chain 'C' and resid 733 through 746 Processing helix chain 'C' and resid 768 through 771 removed outlier: 3.568A pdb=" N ARG C 771 " --> pdb=" O ALA C 768 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 768 through 771' Processing helix chain 'C' and resid 773 through 779 removed outlier: 3.929A pdb=" N ILE C 777 " --> pdb=" O GLN C 773 " (cutoff:3.500A) Processing helix chain 'C' and resid 827 through 841 Processing helix chain 'C' and resid 852 through 860 removed outlier: 3.576A pdb=" N GLN C 856 " --> pdb=" O GLY C 852 " (cutoff:3.500A) Processing helix chain 'C' and resid 862 through 884 Processing helix chain 'C' and resid 888 through 894 removed outlier: 4.148A pdb=" N VAL C 892 " --> pdb=" O ILE C 888 " (cutoff:3.500A) Processing helix chain 'C' and resid 895 through 911 removed outlier: 4.282A pdb=" N GLY C 899 " --> pdb=" O VAL C 895 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ILE C 900 " --> pdb=" O VAL C 896 " (cutoff:3.500A) Processing helix chain 'C' and resid 915 through 946 removed outlier: 3.558A pdb=" N PHE C 939 " --> pdb=" O LEU C 935 " (cutoff:3.500A) Processing helix chain 'C' and resid 949 through 981 removed outlier: 4.731A pdb=" N ARG C 963 " --> pdb=" O LYS C 959 " (cutoff:3.500A) Proline residue: C 964 - end of helix Proline residue: C 978 - end of helix Processing helix chain 'C' and resid 986 through 1027 removed outlier: 4.395A pdb=" N GLY C 996 " --> pdb=" O ALA C 992 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N VAL C 997 " --> pdb=" O LEU C 993 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N ILE C1009 " --> pdb=" O THR C1005 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N PHE C1010 " --> pdb=" O ILE C1006 " (cutoff:3.500A) Proline residue: C1013 - end of helix Processing sheet with id=AA1, first strand: chain 'A' and resid 128 through 131 removed outlier: 7.892A pdb=" N THR A 87 " --> pdb=" O THR A 82 " (cutoff:3.500A) removed outlier: 5.130A pdb=" N THR A 82 " --> pdb=" O THR A 87 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N GLU A 89 " --> pdb=" O ALA A 80 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N ALA A 80 " --> pdb=" O GLU A 89 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N THR A 91 " --> pdb=" O TYR A 78 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N TYR A 78 " --> pdb=" O THR A 91 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N THR A 93 " --> pdb=" O LEU A 76 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N ASN A 808 " --> pdb=" O SER A 815 " (cutoff:3.500A) removed outlier: 7.686A pdb=" N SER A 817 " --> pdb=" O ASN A 709 " (cutoff:3.500A) removed outlier: 5.052A pdb=" N ASN A 709 " --> pdb=" O SER A 817 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N ALA A 819 " --> pdb=" O VAL A 707 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N VAL A 707 " --> pdb=" O ALA A 819 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N ILE A 821 " --> pdb=" O TYR A 705 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 128 through 131 removed outlier: 7.892A pdb=" N THR A 87 " --> pdb=" O THR A 82 " (cutoff:3.500A) removed outlier: 5.130A pdb=" N THR A 82 " --> pdb=" O THR A 87 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N GLU A 89 " --> pdb=" O ALA A 80 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N ALA A 80 " --> pdb=" O GLU A 89 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N THR A 91 " --> pdb=" O TYR A 78 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N TYR A 78 " --> pdb=" O THR A 91 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N THR A 93 " --> pdb=" O LEU A 76 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N ASN A 808 " --> pdb=" O SER A 815 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 172 through 177 removed outlier: 6.955A pdb=" N LEU A 139 " --> pdb=" O PRO A 326 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 172 through 177 removed outlier: 3.505A pdb=" N ALA A 286 " --> pdb=" O ILE A 279 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N ILE A 279 " --> pdb=" O ALA A 286 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N SER A 603 " --> pdb=" O THR A 625 " (cutoff:3.500A) removed outlier: 6.075A pdb=" N VAL A 619 " --> pdb=" O GLY A 609 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 266 through 272 removed outlier: 7.551A pdb=" N LYS A 182 " --> pdb=" O GLN A 761 " (cutoff:3.500A) removed outlier: 8.449A pdb=" N ILE A 763 " --> pdb=" O LYS A 182 " (cutoff:3.500A) removed outlier: 6.050A pdb=" N MET A 184 " --> pdb=" O ILE A 763 " (cutoff:3.500A) removed outlier: 7.348A pdb=" N GLN A 765 " --> pdb=" O MET A 184 " (cutoff:3.500A) removed outlier: 5.719A pdb=" N ILE A 186 " --> pdb=" O GLN A 765 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N ASN A 751 " --> pdb=" O VAL A 762 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N VAL A 764 " --> pdb=" O TYR A 749 " (cutoff:3.500A) removed outlier: 5.349A pdb=" N TYR A 749 " --> pdb=" O VAL A 764 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 218 through 219 removed outlier: 7.712A pdb=" N LEU C 720 " --> pdb=" O PRO A 233 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N SER A 235 " --> pdb=" O LEU C 720 " (cutoff:3.500A) removed outlier: 7.567A pdb=" N ILE C 722 " --> pdb=" O SER A 235 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 250 through 252 Processing sheet with id=AA8, first strand: chain 'A' and resid 796 through 803 removed outlier: 4.766A pdb=" N ILE A 722 " --> pdb=" O GLN B 237 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 781 through 783 Processing sheet with id=AB1, first strand: chain 'B' and resid 128 through 131 removed outlier: 7.693A pdb=" N THR B 87 " --> pdb=" O THR B 82 " (cutoff:3.500A) removed outlier: 5.012A pdb=" N THR B 82 " --> pdb=" O THR B 87 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N GLU B 89 " --> pdb=" O ALA B 80 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N ALA B 80 " --> pdb=" O GLU B 89 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N THR B 91 " --> pdb=" O TYR B 78 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N TYR B 78 " --> pdb=" O THR B 91 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N THR B 93 " --> pdb=" O LEU B 76 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N ASN B 808 " --> pdb=" O SER B 815 " (cutoff:3.500A) removed outlier: 7.785A pdb=" N SER B 817 " --> pdb=" O ASN B 709 " (cutoff:3.500A) removed outlier: 5.078A pdb=" N ASN B 709 " --> pdb=" O SER B 817 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N ALA B 819 " --> pdb=" O VAL B 707 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N VAL B 707 " --> pdb=" O ALA B 819 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N ILE B 821 " --> pdb=" O TYR B 705 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 128 through 131 removed outlier: 7.693A pdb=" N THR B 87 " --> pdb=" O THR B 82 " (cutoff:3.500A) removed outlier: 5.012A pdb=" N THR B 82 " --> pdb=" O THR B 87 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N GLU B 89 " --> pdb=" O ALA B 80 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N ALA B 80 " --> pdb=" O GLU B 89 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N THR B 91 " --> pdb=" O TYR B 78 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N TYR B 78 " --> pdb=" O THR B 91 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N THR B 93 " --> pdb=" O LEU B 76 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N ASN B 808 " --> pdb=" O SER B 815 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 172 through 177 removed outlier: 3.577A pdb=" N MET B 138 " --> pdb=" O ILE B 291 " (cutoff:3.500A) removed outlier: 7.037A pdb=" N LEU B 139 " --> pdb=" O PRO B 326 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 172 through 177 removed outlier: 4.016A pdb=" N ILE B 279 " --> pdb=" O ALA B 286 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N SER B 603 " --> pdb=" O THR B 625 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 266 through 272 removed outlier: 8.084A pdb=" N LYS B 182 " --> pdb=" O MET B 759 " (cutoff:3.500A) removed outlier: 4.670A pdb=" N GLN B 761 " --> pdb=" O LYS B 182 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N ASN B 751 " --> pdb=" O VAL B 762 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N VAL B 764 " --> pdb=" O TYR B 749 " (cutoff:3.500A) removed outlier: 5.465A pdb=" N TYR B 749 " --> pdb=" O VAL B 764 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 250 through 252 Processing sheet with id=AB7, first strand: chain 'B' and resid 796 through 803 removed outlier: 7.414A pdb=" N ASP B 716 " --> pdb=" O PRO C 233 " (cutoff:3.500A) removed outlier: 8.527A pdb=" N SER C 235 " --> pdb=" O ASP B 716 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N ILE B 718 " --> pdb=" O SER C 235 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 781 through 783 Processing sheet with id=AB9, first strand: chain 'C' and resid 128 through 131 removed outlier: 4.564A pdb=" N THR C 87 " --> pdb=" O ASP C 83 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ASP C 83 " --> pdb=" O THR C 87 " (cutoff:3.500A) removed outlier: 12.271A pdb=" N GLN C 806 " --> pdb=" O SER C 817 " (cutoff:3.500A) removed outlier: 9.645A pdb=" N SER C 817 " --> pdb=" O GLN C 806 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N ASN C 808 " --> pdb=" O SER C 815 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N SER C 817 " --> pdb=" O GLU C 710 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 128 through 131 removed outlier: 4.564A pdb=" N THR C 87 " --> pdb=" O ASP C 83 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ASP C 83 " --> pdb=" O THR C 87 " (cutoff:3.500A) removed outlier: 12.271A pdb=" N GLN C 806 " --> pdb=" O SER C 817 " (cutoff:3.500A) removed outlier: 9.645A pdb=" N SER C 817 " --> pdb=" O GLN C 806 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N ASN C 808 " --> pdb=" O SER C 815 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 172 through 178 removed outlier: 3.836A pdb=" N LYS C 174 " --> pdb=" O GLN C 292 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ALA C 288 " --> pdb=" O PHE C 178 " (cutoff:3.500A) removed outlier: 5.015A pdb=" N ASN C 143 " --> pdb=" O PRO C 285 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N THR C 287 " --> pdb=" O GLY C 141 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N GLY C 141 " --> pdb=" O THR C 287 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N ALA C 289 " --> pdb=" O LEU C 139 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N LEU C 139 " --> pdb=" O ALA C 289 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N ILE C 291 " --> pdb=" O LEU C 137 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 172 through 178 removed outlier: 3.836A pdb=" N LYS C 174 " --> pdb=" O GLN C 292 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ALA C 288 " --> pdb=" O PHE C 178 " (cutoff:3.500A) removed outlier: 4.681A pdb=" N ILE C 279 " --> pdb=" O ALA C 286 " (cutoff:3.500A) removed outlier: 5.933A pdb=" N VAL C 619 " --> pdb=" O GLY C 609 " (cutoff:3.500A) removed outlier: 9.243A pdb=" N GLY C 611 " --> pdb=" O GLN C 617 " (cutoff:3.500A) removed outlier: 10.215A pdb=" N GLN C 617 " --> pdb=" O GLY C 611 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 266 through 272 removed outlier: 7.637A pdb=" N LYS C 182 " --> pdb=" O GLN C 761 " (cutoff:3.500A) removed outlier: 8.524A pdb=" N ILE C 763 " --> pdb=" O LYS C 182 " (cutoff:3.500A) removed outlier: 6.149A pdb=" N MET C 184 " --> pdb=" O ILE C 763 " (cutoff:3.500A) removed outlier: 7.634A pdb=" N GLN C 765 " --> pdb=" O MET C 184 " (cutoff:3.500A) removed outlier: 5.925A pdb=" N ILE C 186 " --> pdb=" O GLN C 765 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N ASN C 751 " --> pdb=" O VAL C 762 " (cutoff:3.500A) removed outlier: 7.075A pdb=" N VAL C 764 " --> pdb=" O TYR C 749 " (cutoff:3.500A) removed outlier: 5.495A pdb=" N TYR C 749 " --> pdb=" O VAL C 764 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 250 through 252 Processing sheet with id=AC6, first strand: chain 'C' and resid 781 through 783 1591 hydrogen bonds defined for protein. 4635 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.03 Time building geometry restraints manager: 2.99 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.10 - 1.24: 3221 1.24 - 1.38: 5348 1.38 - 1.53: 11556 1.53 - 1.67: 3717 1.67 - 1.81: 264 Bond restraints: 24106 Sorted by residual: bond pdb=" C PHE B 22 " pdb=" O PHE B 22 " ideal model delta sigma weight residual 1.236 1.097 0.140 1.15e-02 7.56e+03 1.48e+02 bond pdb=" C PHE B 480 " pdb=" O PHE B 480 " ideal model delta sigma weight residual 1.237 1.098 0.138 1.17e-02 7.31e+03 1.40e+02 bond pdb=" C SER B 738 " pdb=" O SER B 738 " ideal model delta sigma weight residual 1.236 1.102 0.135 1.15e-02 7.56e+03 1.37e+02 bond pdb=" C LEU C 674 " pdb=" O LEU C 674 " ideal model delta sigma weight residual 1.234 1.097 0.137 1.26e-02 6.30e+03 1.18e+02 bond pdb=" C MET A 639 " pdb=" O MET A 639 " ideal model delta sigma weight residual 1.237 1.114 0.123 1.19e-02 7.06e+03 1.07e+02 ... (remaining 24101 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.35: 32107 3.35 - 6.71: 462 6.71 - 10.06: 59 10.06 - 13.41: 6 13.41 - 16.77: 6 Bond angle restraints: 32640 Sorted by residual: angle pdb=" CA PHE B 22 " pdb=" C PHE B 22 " pdb=" O PHE B 22 " ideal model delta sigma weight residual 120.82 105.15 15.67 1.05e+00 9.07e-01 2.23e+02 angle pdb=" CA PHE B 22 " pdb=" C PHE B 22 " pdb=" N GLY B 23 " ideal model delta sigma weight residual 117.07 129.37 -12.30 1.14e+00 7.69e-01 1.16e+02 angle pdb=" CA PHE B 480 " pdb=" C PHE B 480 " pdb=" O PHE B 480 " ideal model delta sigma weight residual 120.55 110.25 10.30 1.06e+00 8.90e-01 9.44e+01 angle pdb=" CA SER B 738 " pdb=" C SER B 738 " pdb=" O SER B 738 " ideal model delta sigma weight residual 120.82 110.88 9.94 1.05e+00 9.07e-01 8.97e+01 angle pdb=" CA TYR B 364 " pdb=" C TYR B 364 " pdb=" O TYR B 364 " ideal model delta sigma weight residual 120.90 111.23 9.67 1.07e+00 8.73e-01 8.17e+01 ... (remaining 32635 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.62: 14233 31.62 - 63.23: 357 63.23 - 94.85: 34 94.85 - 126.46: 4 126.46 - 158.08: 2 Dihedral angle restraints: 14630 sinusoidal: 5813 harmonic: 8817 Sorted by residual: dihedral pdb=" C ASN B 751 " pdb=" N ASN B 751 " pdb=" CA ASN B 751 " pdb=" CB ASN B 751 " ideal model delta harmonic sigma weight residual -122.60 -111.25 -11.35 0 2.50e+00 1.60e-01 2.06e+01 dihedral pdb=" C3 PTY C1102 " pdb=" O11 PTY C1102 " pdb=" P1 PTY C1102 " pdb=" O12 PTY C1102 " ideal model delta sinusoidal sigma weight residual -59.77 98.31 -158.08 1 3.00e+01 1.11e-03 2.06e+01 dihedral pdb=" C3 PTY C1101 " pdb=" O11 PTY C1101 " pdb=" P1 PTY C1101 " pdb=" O12 PTY C1101 " ideal model delta sinusoidal sigma weight residual -59.77 72.97 -132.74 1 3.00e+01 1.11e-03 1.79e+01 ... (remaining 14627 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.093: 3660 0.093 - 0.185: 195 0.185 - 0.278: 15 0.278 - 0.371: 4 0.371 - 0.464: 2 Chirality restraints: 3876 Sorted by residual: chirality pdb=" CB ILE C 777 " pdb=" CA ILE C 777 " pdb=" CG1 ILE C 777 " pdb=" CG2 ILE C 777 " both_signs ideal model delta sigma weight residual False 2.64 2.18 0.46 2.00e-01 2.50e+01 5.37e+00 chirality pdb=" CA GLN C 292 " pdb=" N GLN C 292 " pdb=" C GLN C 292 " pdb=" CB GLN C 292 " both_signs ideal model delta sigma weight residual False 2.51 2.88 -0.37 2.00e-01 2.50e+01 3.48e+00 chirality pdb=" CA ARG B 363 " pdb=" N ARG B 363 " pdb=" C ARG B 363 " pdb=" CB ARG B 363 " both_signs ideal model delta sigma weight residual False 2.51 2.85 -0.34 2.00e-01 2.50e+01 2.89e+00 ... (remaining 3873 not shown) Planarity restraints: 4073 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER C 46 " 0.021 2.00e-02 2.50e+03 4.47e-02 2.00e+01 pdb=" C SER C 46 " -0.077 2.00e-02 2.50e+03 pdb=" O SER C 46 " 0.029 2.00e-02 2.50e+03 pdb=" N ALA C 47 " 0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR C 77 " 0.021 2.00e-02 2.50e+03 4.44e-02 1.98e+01 pdb=" C TYR C 77 " -0.077 2.00e-02 2.50e+03 pdb=" O TYR C 77 " 0.028 2.00e-02 2.50e+03 pdb=" N TYR C 78 " 0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN A 590 " 0.021 2.00e-02 2.50e+03 4.36e-02 1.90e+01 pdb=" C GLN A 590 " -0.075 2.00e-02 2.50e+03 pdb=" O GLN A 590 " 0.028 2.00e-02 2.50e+03 pdb=" N PHE A 591 " 0.026 2.00e-02 2.50e+03 ... (remaining 4070 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 268 2.67 - 3.22: 22607 3.22 - 3.78: 36751 3.78 - 4.34: 51178 4.34 - 4.90: 84655 Nonbonded interactions: 195459 Sorted by model distance: nonbonded pdb=" OG SER B 786 " pdb=" OE1 GLN B 788 " model vdw 2.108 3.040 nonbonded pdb=" OE2 GLU B 213 " pdb=" NE2 GLN B 239 " model vdw 2.111 3.120 nonbonded pdb=" O LYS B 941 " pdb=" OE1 GLU B 945 " model vdw 2.174 3.040 nonbonded pdb=" O ALA B 308 " pdb=" OE1 GLU B 312 " model vdw 2.180 3.040 nonbonded pdb=" OD1 ASP B 716 " pdb=" NZ LYS B 802 " model vdw 2.196 3.120 ... (remaining 195454 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 1 through 14 or (resid 15 and (name N or name CA or name C \ or name CB or name CG1 or name CG2 or name CD1)) or resid 16 through 1027 or (r \ esid 1101 and (name C1 or name C11 or name C12 or name C13 or name C14 or name C \ 15 or name C16 or name C17 or name C18 or name C19 or name C2 or name C20 or nam \ e C3 or name C30 or name C31 or name C32 or name C33 or name C34 or name C35 or \ name C36 or name C37 or name C38 or name C39 or name C5 or name C6 or name C8 or \ name N1 or name O10 or name O11 or name O12 or name O13 or name O14 or name O30 \ or name O4 or name O7 or name P1 )) or (resid 1102 and (name C1 or name C11 or \ name C12 or name C13 or name C14 or name C15 or name C16 or name C17 or name C18 \ or name C19 or name C2 or name C20 or name C21 or name C22 or name C3 or name C \ 30 or name C31 or name C32 or name C33 or name C34 or name C35 or name C36 or na \ me C37 or name C38 or name C39 or name C40 or name C41 or name C5 or name C6 or \ name C8 or name N1 or name O10 or name O11 or name O12 or name O13 or name O14 o \ r name O30 or name O4 or name O7 or name P1 )))) selection = (chain 'B' and (resid 1 through 1027 or (resid 1101 and (name C1 or name C11 or \ name C12 or name C13 or name C14 or name C15 or name C16 or name C17 or name C18 \ or name C19 or name C2 or name C20 or name C3 or name C30 or name C31 or name C \ 32 or name C33 or name C34 or name C35 or name C36 or name C37 or name C38 or na \ me C39 or name C5 or name C6 or name C8 or name N1 or name O10 or name O11 or na \ me O12 or name O13 or name O14 or name O30 or name O4 or name O7 or name P1 )) o \ r (resid 1102 and (name C1 or name C11 or name C12 or name C13 or name C14 or na \ me C15 or name C16 or name C17 or name C18 or name C19 or name C2 or name C20 or \ name C21 or name C22 or name C23 or name C24 or name C25 or name C26 or name C3 \ or name C30 or name C31 or name C32 or name C33 or name C34 or name C35 or name \ C36 or name C37 or name C5 or name C6 or name C8 or name N1 or name O10 or name \ O11 or name O12 or name O13 or name O14 or name O30 or name O4 or name O7 or na \ me P1 )))) selection = (chain 'C' and (resid 1 through 14 or (resid 15 and (name N or name CA or name C \ or name CB or name CG1 or name CG2 or name CD1)) or resid 16 through 1027 or (r \ esid 1101 and (name C1 or name C11 or name C12 or name C13 or name C14 or name C \ 15 or name C16 or name C17 or name C18 or name C19 or name C2 or name C20 or nam \ e C3 or name C30 or name C31 or name C32 or name C33 or name C34 or name C35 or \ name C36 or name C37 or name C38 or name C39 or name C5 or name C6 or name C8 or \ name N1 or name O10 or name O11 or name O12 or name O13 or name O14 or name O30 \ or name O4 or name O7 or name P1 )) or resid 1102)) } 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.090 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: 0.390 Check model and map are aligned: 0.070 Set scattering table: 0.070 Process input model: 25.030 Find NCS groups from input model: 0.600 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:8.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.250 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7910 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 : 0.006 0.140 24106 Z= 0.406 Angle : 0.903 16.768 32640 Z= 0.572 Chirality : 0.046 0.464 3876 Planarity : 0.006 0.090 4073 Dihedral : 14.149 158.079 8924 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.95 % Favored : 99.05 % Rotamer: Outliers : 1.09 % Allowed : 1.13 % Favored : 97.78 % Cbeta Deviations : 0.11 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.20 (0.15), residues: 3048 helix: 2.38 (0.13), residues: 1684 sheet: 0.44 (0.21), residues: 529 loop : 0.33 (0.21), residues: 835 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG C 724 TYR 0.047 0.002 TYR C 77 PHE 0.058 0.002 PHE B 569 TRP 0.004 0.001 TRP C 568 HIS 0.002 0.000 HIS C 342 Details of bonding type rmsd covalent geometry : bond 0.00578 (24106) covalent geometry : angle 0.90279 (32640) hydrogen bonds : bond 0.12912 ( 1522) hydrogen bonds : angle 5.70177 ( 4635) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6096 Ramachandran restraints generated. 3048 Oldfield, 0 Emsley, 3048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6096 Ramachandran restraints generated. 3048 Oldfield, 0 Emsley, 3048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 665 residues out of total 2565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 637 time to evaluate : 0.947 Fit side-chains revert: symmetry clash REVERT: A 112 LYS cc_start: 0.7249 (mmmt) cc_final: 0.6934 (mmtt) REVERT: A 321 MET cc_start: 0.8174 (mtt) cc_final: 0.7846 (mtt) REVERT: A 366 LEU cc_start: 0.8200 (mt) cc_final: 0.7945 (mt) REVERT: A 639 MET cc_start: 0.8618 (mtp) cc_final: 0.8116 (mtm) REVERT: A 706 MET cc_start: 0.7509 (mtp) cc_final: 0.7094 (mtp) REVERT: A 884 GLU cc_start: 0.8246 (tp30) cc_final: 0.7763 (tp30) REVERT: A 893 MET cc_start: 0.8513 (mmm) cc_final: 0.8202 (mmm) REVERT: B 68 GLU cc_start: 0.6863 (mm-30) cc_final: 0.6521 (mm-30) REVERT: B 293 LEU cc_start: 0.8106 (mt) cc_final: 0.7892 (tp) REVERT: B 402 ILE cc_start: 0.9103 (OUTLIER) cc_final: 0.8786 (mm) REVERT: B 545 ILE cc_start: 0.9068 (mt) cc_final: 0.8842 (mt) REVERT: B 553 MET cc_start: 0.8472 (mmm) cc_final: 0.8234 (mmm) REVERT: B 697 MET cc_start: 0.8614 (mtm) cc_final: 0.8295 (mtt) REVERT: B 706 MET cc_start: 0.8275 (mtp) cc_final: 0.8036 (mtp) REVERT: B 799 GLN cc_start: 0.7427 (tt0) cc_final: 0.7212 (mt0) REVERT: B 913 MET cc_start: 0.8744 (OUTLIER) cc_final: 0.8418 (mpp) REVERT: B 931 LYS cc_start: 0.8950 (OUTLIER) cc_final: 0.8343 (ttpt) REVERT: C 8 ARG cc_start: 0.8375 (mtt-85) cc_final: 0.8006 (mtp180) REVERT: C 66 GLU cc_start: 0.7631 (tt0) cc_final: 0.7242 (tt0) REVERT: C 292 GLN cc_start: 0.7453 (OUTLIER) cc_final: 0.7243 (mp10) REVERT: C 352 PHE cc_start: 0.7175 (m-10) cc_final: 0.6798 (t80) REVERT: C 407 ASP cc_start: 0.8182 (OUTLIER) cc_final: 0.7873 (t0) REVERT: C 592 GLU cc_start: 0.7201 (OUTLIER) cc_final: 0.6990 (mm-30) REVERT: C 612 PHE cc_start: 0.6603 (m-80) cc_final: 0.5283 (m-80) REVERT: C 745 MET cc_start: 0.7598 (mmt) cc_final: 0.7372 (mmt) REVERT: C 931 LYS cc_start: 0.9055 (OUTLIER) cc_final: 0.8305 (mttt) outliers start: 28 outliers final: 7 residues processed: 655 average time/residue: 0.6506 time to fit residues: 489.9301 Evaluate side-chains 532 residues out of total 2565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 518 time to evaluate : 0.877 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 GLU Chi-restraints excluded: chain A residue 793 SER Chi-restraints excluded: chain B residue 338 GLU Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 449 LEU Chi-restraints excluded: chain B residue 538 MET Chi-restraints excluded: chain B residue 738 SER Chi-restraints excluded: chain B residue 913 MET Chi-restraints excluded: chain B residue 931 LYS Chi-restraints excluded: chain C residue 292 GLN Chi-restraints excluded: chain C residue 407 ASP Chi-restraints excluded: chain C residue 592 GLU Chi-restraints excluded: chain C residue 709 ASN Chi-restraints excluded: chain C residue 931 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 197 optimal weight: 7.9990 chunk 215 optimal weight: 0.0870 chunk 20 optimal weight: 1.9990 chunk 132 optimal weight: 5.9990 chunk 261 optimal weight: 10.0000 chunk 248 optimal weight: 2.9990 chunk 207 optimal weight: 0.0570 chunk 155 optimal weight: 3.9990 chunk 244 optimal weight: 9.9990 chunk 183 optimal weight: 8.9990 chunk 298 optimal weight: 6.9990 overall best weight: 1.8282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 125 GLN A 147 ASN A 914 ASN B 799 GLN C 104 GLN C 124 GLN C 205 ASN C 239 GLN C 298 ASN C 594 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.141933 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.123099 restraints weight = 25603.004| |-----------------------------------------------------------------------------| r_work (start): 0.3176 rms_B_bonded: 1.11 r_work: 0.3039 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.2926 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.2926 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8253 moved from start: 0.1294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 24106 Z= 0.131 Angle : 0.538 7.104 32640 Z= 0.283 Chirality : 0.041 0.182 3876 Planarity : 0.005 0.051 4073 Dihedral : 9.828 176.028 3455 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.21 % Favored : 98.79 % Rotamer: Outliers : 2.50 % Allowed : 11.97 % Favored : 85.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.26 (0.15), residues: 3048 helix: 2.39 (0.13), residues: 1711 sheet: 0.44 (0.21), residues: 547 loop : 0.38 (0.22), residues: 790 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 7 TYR 0.012 0.001 TYR C 77 PHE 0.015 0.001 PHE A 998 TRP 0.008 0.001 TRP B 800 HIS 0.002 0.001 HIS B 991 Details of bonding type rmsd covalent geometry : bond 0.00293 (24106) covalent geometry : angle 0.53765 (32640) hydrogen bonds : bond 0.04498 ( 1522) hydrogen bonds : angle 4.47941 ( 4635) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6096 Ramachandran restraints generated. 3048 Oldfield, 0 Emsley, 3048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6096 Ramachandran restraints generated. 3048 Oldfield, 0 Emsley, 3048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 611 residues out of total 2565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 547 time to evaluate : 0.890 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 67 ARG cc_start: 0.7615 (ttp-170) cc_final: 0.7406 (ptm160) REVERT: A 73 LYS cc_start: 0.7874 (mtmt) cc_final: 0.7449 (pttp) REVERT: A 149 TYR cc_start: 0.8129 (m-80) cc_final: 0.7697 (m-80) REVERT: A 319 GLU cc_start: 0.7936 (tm-30) cc_final: 0.7405 (tm-30) REVERT: A 321 MET cc_start: 0.8444 (mtt) cc_final: 0.8162 (mtt) REVERT: A 346 GLU cc_start: 0.8755 (mt-10) cc_final: 0.8428 (mt-10) REVERT: A 366 LEU cc_start: 0.8442 (mt) cc_final: 0.8148 (mt) REVERT: A 383 MET cc_start: 0.8826 (mtp) cc_final: 0.8404 (mtp) REVERT: A 415 ASN cc_start: 0.8396 (OUTLIER) cc_final: 0.7790 (m110) REVERT: A 590 GLN cc_start: 0.8033 (tp-100) cc_final: 0.7801 (tp40) REVERT: A 639 MET cc_start: 0.8713 (mtp) cc_final: 0.8200 (mtm) REVERT: A 647 MET cc_start: 0.8611 (mmm) cc_final: 0.8358 (tpp) REVERT: A 677 GLN cc_start: 0.8935 (mt0) cc_final: 0.8730 (mt0) REVERT: A 893 MET cc_start: 0.8856 (mmm) cc_final: 0.8545 (mmm) REVERT: B 68 GLU cc_start: 0.7446 (mm-30) cc_final: 0.7115 (mm-30) REVERT: B 111 ILE cc_start: 0.8602 (pt) cc_final: 0.8385 (pt) REVERT: B 248 ASN cc_start: 0.8224 (m-40) cc_final: 0.8006 (m-40) REVERT: B 312 GLU cc_start: 0.6914 (mp0) cc_final: 0.6388 (mp0) REVERT: B 325 ILE cc_start: 0.8409 (OUTLIER) cc_final: 0.7969 (mm) REVERT: B 402 ILE cc_start: 0.9205 (OUTLIER) cc_final: 0.8850 (mm) REVERT: B 439 THR cc_start: 0.8416 (m) cc_final: 0.8167 (m) REVERT: B 541 ILE cc_start: 0.8623 (mt) cc_final: 0.8399 (mt) REVERT: B 545 ILE cc_start: 0.9124 (mt) cc_final: 0.8898 (mt) REVERT: B 561 MET cc_start: 0.8560 (mtp) cc_final: 0.8148 (mtm) REVERT: B 752 ASP cc_start: 0.8175 (m-30) cc_final: 0.7956 (m-30) REVERT: B 799 GLN cc_start: 0.7825 (tt0) cc_final: 0.7215 (mt0) REVERT: B 942 MET cc_start: 0.8256 (tmt) cc_final: 0.7994 (tmm) REVERT: B 945 GLU cc_start: 0.7510 (OUTLIER) cc_final: 0.6630 (mp0) REVERT: C 8 ARG cc_start: 0.8673 (mtt-85) cc_final: 0.8180 (mtt180) REVERT: C 66 GLU cc_start: 0.7798 (tt0) cc_final: 0.7447 (tt0) REVERT: C 176 GLN cc_start: 0.8177 (OUTLIER) cc_final: 0.7520 (tt0) REVERT: C 178 PHE cc_start: 0.8410 (m-80) cc_final: 0.8178 (m-80) REVERT: C 264 ASP cc_start: 0.7512 (m-30) cc_final: 0.7289 (m-30) REVERT: C 292 GLN cc_start: 0.7626 (mt0) cc_final: 0.7365 (mp10) REVERT: C 339 LYS cc_start: 0.7430 (OUTLIER) cc_final: 0.6596 (mmtp) REVERT: C 352 PHE cc_start: 0.7339 (m-10) cc_final: 0.6741 (t80) REVERT: C 356 TYR cc_start: 0.8676 (t80) cc_final: 0.8305 (t80) REVERT: C 408 ASP cc_start: 0.8096 (OUTLIER) cc_final: 0.7879 (t0) REVERT: C 589 ASN cc_start: 0.7882 (m110) cc_final: 0.7453 (m110) REVERT: C 592 GLU cc_start: 0.7078 (OUTLIER) cc_final: 0.6847 (mm-30) REVERT: C 612 PHE cc_start: 0.6786 (m-80) cc_final: 0.5740 (m-80) REVERT: C 692 ASP cc_start: 0.8435 (m-30) cc_final: 0.8139 (m-30) REVERT: C 697 MET cc_start: 0.8966 (mtt) cc_final: 0.8542 (mtt) REVERT: C 735 SER cc_start: 0.8109 (t) cc_final: 0.7660 (p) REVERT: C 736 ASP cc_start: 0.7732 (m-30) cc_final: 0.6858 (m-30) REVERT: C 745 MET cc_start: 0.7678 (mmt) cc_final: 0.7309 (mmt) REVERT: C 799 GLN cc_start: 0.8337 (tt0) cc_final: 0.7844 (tt0) REVERT: C 830 GLU cc_start: 0.7927 (mm-30) cc_final: 0.7604 (mp0) outliers start: 64 outliers final: 20 residues processed: 578 average time/residue: 0.6470 time to fit residues: 431.3282 Evaluate side-chains 540 residues out of total 2565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 512 time to evaluate : 0.953 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 ILE Chi-restraints excluded: chain A residue 100 VAL Chi-restraints excluded: chain A residue 241 SER Chi-restraints excluded: chain A residue 345 LEU Chi-restraints excluded: chain A residue 415 ASN Chi-restraints excluded: chain A residue 717 ASN Chi-restraints excluded: chain A residue 790 VAL Chi-restraints excluded: chain A residue 868 LEU Chi-restraints excluded: chain A residue 1014 VAL Chi-restraints excluded: chain B residue 29 LYS Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 231 THR Chi-restraints excluded: chain B residue 235 SER Chi-restraints excluded: chain B residue 325 ILE Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 862 SER Chi-restraints excluded: chain B residue 895 VAL Chi-restraints excluded: chain B residue 945 GLU Chi-restraints excluded: chain C residue 111 ILE Chi-restraints excluded: chain C residue 137 LEU Chi-restraints excluded: chain C residue 176 GLN Chi-restraints excluded: chain C residue 265 VAL Chi-restraints excluded: chain C residue 339 LYS Chi-restraints excluded: chain C residue 408 ASP Chi-restraints excluded: chain C residue 426 SER Chi-restraints excluded: chain C residue 592 GLU Chi-restraints excluded: chain C residue 709 ASN Chi-restraints excluded: chain C residue 986 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 82 optimal weight: 9.9990 chunk 180 optimal weight: 8.9990 chunk 100 optimal weight: 1.9990 chunk 9 optimal weight: 7.9990 chunk 196 optimal weight: 9.9990 chunk 164 optimal weight: 30.0000 chunk 132 optimal weight: 9.9990 chunk 212 optimal weight: 0.5980 chunk 129 optimal weight: 2.9990 chunk 7 optimal weight: 1.9990 chunk 10 optimal weight: 5.9990 overall best weight: 2.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 125 GLN A 147 ASN A 586 ASN ** A 691 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 859 GLN A 863 GLN B 210 ASN B 342 HIS B 691 GLN B 779 ASN C 124 GLN C 205 ASN C 594 ASN ** C 859 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.139614 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.120612 restraints weight = 25486.672| |-----------------------------------------------------------------------------| r_work (start): 0.3136 rms_B_bonded: 1.12 r_work: 0.3009 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.2894 rms_B_bonded: 3.37 restraints_weight: 0.2500 r_work (final): 0.2894 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8282 moved from start: 0.1723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 24106 Z= 0.134 Angle : 0.523 7.452 32640 Z= 0.274 Chirality : 0.041 0.191 3876 Planarity : 0.005 0.051 4073 Dihedral : 9.272 168.622 3426 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Rotamer: Outliers : 2.77 % Allowed : 12.98 % Favored : 84.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.13 (0.15), residues: 3048 helix: 2.29 (0.13), residues: 1716 sheet: 0.42 (0.21), residues: 544 loop : 0.29 (0.22), residues: 788 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 7 TYR 0.013 0.001 TYR A 49 PHE 0.017 0.001 PHE B 672 TRP 0.010 0.001 TRP B 800 HIS 0.002 0.001 HIS B 342 Details of bonding type rmsd covalent geometry : bond 0.00309 (24106) covalent geometry : angle 0.52285 (32640) hydrogen bonds : bond 0.04509 ( 1522) hydrogen bonds : angle 4.28363 ( 4635) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6096 Ramachandran restraints generated. 3048 Oldfield, 0 Emsley, 3048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6096 Ramachandran restraints generated. 3048 Oldfield, 0 Emsley, 3048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 622 residues out of total 2565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 551 time to evaluate : 0.912 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.6173 (OUTLIER) cc_final: 0.5956 (ttt) REVERT: A 89 GLU cc_start: 0.8330 (OUTLIER) cc_final: 0.7323 (tm-30) REVERT: A 149 TYR cc_start: 0.8104 (m-80) cc_final: 0.7602 (m-10) REVERT: A 319 GLU cc_start: 0.7895 (tm-30) cc_final: 0.7479 (tm-30) REVERT: A 321 MET cc_start: 0.8401 (mtt) cc_final: 0.8176 (mtt) REVERT: A 346 GLU cc_start: 0.8856 (mt-10) cc_final: 0.8438 (mt-10) REVERT: A 383 MET cc_start: 0.8756 (mtp) cc_final: 0.8438 (mtp) REVERT: A 415 ASN cc_start: 0.8385 (OUTLIER) cc_final: 0.7822 (m110) REVERT: A 639 MET cc_start: 0.8708 (mtp) cc_final: 0.8145 (mtm) REVERT: A 647 MET cc_start: 0.8647 (mmm) cc_final: 0.8415 (tpp) REVERT: A 652 GLU cc_start: 0.7730 (pt0) cc_final: 0.7473 (pt0) REVERT: A 665 GLU cc_start: 0.8082 (mt-10) cc_final: 0.7651 (mp0) REVERT: A 802 LYS cc_start: 0.8477 (OUTLIER) cc_final: 0.8028 (mtpp) REVERT: A 893 MET cc_start: 0.8868 (mmm) cc_final: 0.8522 (mmm) REVERT: A 946 GLU cc_start: 0.7283 (OUTLIER) cc_final: 0.5877 (mp0) REVERT: A 1018 PHE cc_start: 0.8239 (t80) cc_final: 0.7967 (t80) REVERT: B 68 GLU cc_start: 0.7454 (mm-30) cc_final: 0.7077 (mm-30) REVERT: B 226 LYS cc_start: 0.8515 (mtpt) cc_final: 0.8293 (mppt) REVERT: B 312 GLU cc_start: 0.6934 (mp0) cc_final: 0.6435 (mp0) REVERT: B 325 ILE cc_start: 0.8453 (OUTLIER) cc_final: 0.7995 (mm) REVERT: B 402 ILE cc_start: 0.9262 (OUTLIER) cc_final: 0.8868 (mm) REVERT: B 518 ASP cc_start: 0.7594 (m-30) cc_final: 0.7007 (m-30) REVERT: B 561 MET cc_start: 0.8584 (mtp) cc_final: 0.8140 (mtm) REVERT: B 631 GLU cc_start: 0.8130 (mt-10) cc_final: 0.7822 (mt-10) REVERT: B 716 ASP cc_start: 0.8239 (OUTLIER) cc_final: 0.8032 (m-30) REVERT: B 779 ASN cc_start: 0.8311 (OUTLIER) cc_final: 0.8001 (t160) REVERT: B 799 GLN cc_start: 0.7831 (tt0) cc_final: 0.7197 (mt0) REVERT: B 942 MET cc_start: 0.8134 (tmt) cc_final: 0.7829 (tmm) REVERT: B 945 GLU cc_start: 0.7420 (OUTLIER) cc_final: 0.6628 (mp0) REVERT: C 66 GLU cc_start: 0.7881 (tt0) cc_final: 0.7588 (tt0) REVERT: C 176 GLN cc_start: 0.8141 (OUTLIER) cc_final: 0.7539 (tt0) REVERT: C 178 PHE cc_start: 0.8442 (m-80) cc_final: 0.8218 (m-80) REVERT: C 200 ILE cc_start: 0.7929 (mm) cc_final: 0.7596 (mm) REVERT: C 292 GLN cc_start: 0.7888 (mt0) cc_final: 0.7562 (mp10) REVERT: C 352 PHE cc_start: 0.7365 (m-10) cc_final: 0.6782 (t80) REVERT: C 356 TYR cc_start: 0.8779 (t80) cc_final: 0.8325 (t80) REVERT: C 589 ASN cc_start: 0.7870 (m110) cc_final: 0.7453 (m110) REVERT: C 592 GLU cc_start: 0.6899 (OUTLIER) cc_final: 0.6571 (mm-30) REVERT: C 612 PHE cc_start: 0.6882 (m-80) cc_final: 0.5706 (m-80) REVERT: C 697 MET cc_start: 0.8912 (mtt) cc_final: 0.8428 (mtt) REVERT: C 736 ASP cc_start: 0.7469 (m-30) cc_final: 0.7044 (m-30) REVERT: C 745 MET cc_start: 0.7903 (mmt) cc_final: 0.6678 (mpp) REVERT: C 748 MET cc_start: 0.8140 (mtm) cc_final: 0.7778 (mpp) REVERT: C 783 MET cc_start: 0.6653 (pmm) cc_final: 0.6321 (tpt) REVERT: C 799 GLN cc_start: 0.8391 (tt0) cc_final: 0.8173 (tt0) REVERT: C 805 GLN cc_start: 0.8164 (mm110) cc_final: 0.7962 (mm-40) REVERT: C 836 GLU cc_start: 0.7729 (mt-10) cc_final: 0.7504 (mt-10) REVERT: C 973 THR cc_start: 0.9075 (m) cc_final: 0.8663 (p) outliers start: 71 outliers final: 27 residues processed: 584 average time/residue: 0.6221 time to fit residues: 419.7159 Evaluate side-chains 560 residues out of total 2565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 521 time to evaluate : 0.936 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 89 GLU Chi-restraints excluded: chain A residue 100 VAL Chi-restraints excluded: chain A residue 241 SER Chi-restraints excluded: chain A residue 415 ASN Chi-restraints excluded: chain A residue 483 LEU Chi-restraints excluded: chain A residue 655 THR Chi-restraints excluded: chain A residue 716 ASP Chi-restraints excluded: chain A residue 717 ASN Chi-restraints excluded: chain A residue 802 LYS Chi-restraints excluded: chain A residue 872 MET Chi-restraints excluded: chain A residue 946 GLU Chi-restraints excluded: chain B residue 29 LYS Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 231 THR Chi-restraints excluded: chain B residue 235 SER Chi-restraints excluded: chain B residue 325 ILE Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 716 ASP Chi-restraints excluded: chain B residue 717 ASN Chi-restraints excluded: chain B residue 732 VAL Chi-restraints excluded: chain B residue 779 ASN Chi-restraints excluded: chain B residue 796 VAL Chi-restraints excluded: chain B residue 862 SER Chi-restraints excluded: chain B residue 895 VAL Chi-restraints excluded: chain B residue 913 MET Chi-restraints excluded: chain B residue 945 GLU Chi-restraints excluded: chain B residue 977 ILE Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 127 LEU Chi-restraints excluded: chain C residue 137 LEU Chi-restraints excluded: chain C residue 176 GLN Chi-restraints excluded: chain C residue 265 VAL Chi-restraints excluded: chain C residue 572 SER Chi-restraints excluded: chain C residue 578 ASP Chi-restraints excluded: chain C residue 592 GLU Chi-restraints excluded: chain C residue 709 ASN Chi-restraints excluded: chain C residue 759 MET Chi-restraints excluded: chain C residue 986 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 60 optimal weight: 10.0000 chunk 180 optimal weight: 0.0980 chunk 106 optimal weight: 10.0000 chunk 141 optimal weight: 9.9990 chunk 110 optimal weight: 10.0000 chunk 116 optimal weight: 9.9990 chunk 118 optimal weight: 0.9990 chunk 5 optimal weight: 1.9990 chunk 63 optimal weight: 10.0000 chunk 190 optimal weight: 5.9990 chunk 28 optimal weight: 6.9990 overall best weight: 3.2188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 125 GLN ** A 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 267 ASN A 593 ASN A 644 ASN A 677 GLN ** A 691 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 805 GLN A 914 ASN B 342 HIS C 124 GLN C 205 ASN C 594 ASN ** C 859 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.137602 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.118262 restraints weight = 25509.103| |-----------------------------------------------------------------------------| r_work (start): 0.3118 rms_B_bonded: 1.12 r_work: 0.2993 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.2876 rms_B_bonded: 3.39 restraints_weight: 0.2500 r_work (final): 0.2876 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8301 moved from start: 0.1943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 24106 Z= 0.142 Angle : 0.529 7.442 32640 Z= 0.277 Chirality : 0.041 0.206 3876 Planarity : 0.005 0.052 4073 Dihedral : 9.208 164.355 3426 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer: Outliers : 3.12 % Allowed : 14.39 % Favored : 82.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.02 (0.15), residues: 3048 helix: 2.23 (0.13), residues: 1718 sheet: 0.31 (0.21), residues: 557 loop : 0.22 (0.22), residues: 773 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 7 TYR 0.016 0.001 TYR A 49 PHE 0.016 0.001 PHE B 672 TRP 0.007 0.001 TRP B 800 HIS 0.002 0.001 HIS B 360 Details of bonding type rmsd covalent geometry : bond 0.00336 (24106) covalent geometry : angle 0.52934 (32640) hydrogen bonds : bond 0.04579 ( 1522) hydrogen bonds : angle 4.26197 ( 4635) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6096 Ramachandran restraints generated. 3048 Oldfield, 0 Emsley, 3048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6096 Ramachandran restraints generated. 3048 Oldfield, 0 Emsley, 3048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 606 residues out of total 2565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 526 time to evaluate : 0.915 Fit side-chains revert: symmetry clash REVERT: A 1 MET cc_start: 0.6178 (OUTLIER) cc_final: 0.5958 (ttt) REVERT: A 73 LYS cc_start: 0.8072 (mtmt) cc_final: 0.7658 (pttp) REVERT: A 89 GLU cc_start: 0.8309 (OUTLIER) cc_final: 0.7266 (tm-30) REVERT: A 102 MET cc_start: 0.6906 (OUTLIER) cc_final: 0.6236 (mmm) REVERT: A 147 ASN cc_start: 0.7651 (m110) cc_final: 0.7340 (t0) REVERT: A 149 TYR cc_start: 0.8124 (m-80) cc_final: 0.7738 (m-10) REVERT: A 209 GLU cc_start: 0.7957 (OUTLIER) cc_final: 0.7743 (pt0) REVERT: A 314 LYS cc_start: 0.7048 (ttpt) cc_final: 0.6839 (ptpt) REVERT: A 319 GLU cc_start: 0.7884 (tm-30) cc_final: 0.7519 (tm-30) REVERT: A 321 MET cc_start: 0.8392 (mtt) cc_final: 0.8184 (mtt) REVERT: A 346 GLU cc_start: 0.8859 (mt-10) cc_final: 0.8475 (mt-10) REVERT: A 366 LEU cc_start: 0.8506 (mt) cc_final: 0.8200 (mt) REVERT: A 383 MET cc_start: 0.8731 (mtp) cc_final: 0.8430 (mtp) REVERT: A 639 MET cc_start: 0.8812 (mtp) cc_final: 0.8231 (mtm) REVERT: A 772 MET cc_start: 0.8960 (mmt) cc_final: 0.8372 (mmt) REVERT: A 893 MET cc_start: 0.8860 (mmm) cc_final: 0.8660 (mmm) REVERT: A 946 GLU cc_start: 0.7276 (OUTLIER) cc_final: 0.5807 (mp0) REVERT: A 1018 PHE cc_start: 0.8232 (t80) cc_final: 0.7967 (t80) REVERT: B 68 GLU cc_start: 0.7405 (mm-30) cc_final: 0.7085 (mm-30) REVERT: B 111 ILE cc_start: 0.8630 (pt) cc_final: 0.8323 (pt) REVERT: B 226 LYS cc_start: 0.8537 (mtpt) cc_final: 0.8278 (mppt) REVERT: B 273 GLN cc_start: 0.8507 (tt0) cc_final: 0.7790 (tt0) REVERT: B 307 ARG cc_start: 0.7533 (ttm110) cc_final: 0.7262 (mtt-85) REVERT: B 312 GLU cc_start: 0.6912 (OUTLIER) cc_final: 0.6377 (mp0) REVERT: B 325 ILE cc_start: 0.8481 (OUTLIER) cc_final: 0.8025 (mm) REVERT: B 357 LEU cc_start: 0.8783 (OUTLIER) cc_final: 0.8453 (tp) REVERT: B 561 MET cc_start: 0.8606 (mtp) cc_final: 0.8135 (mtm) REVERT: B 716 ASP cc_start: 0.8319 (OUTLIER) cc_final: 0.8097 (m-30) REVERT: B 779 ASN cc_start: 0.8256 (t0) cc_final: 0.7926 (t160) REVERT: B 799 GLN cc_start: 0.7855 (tt0) cc_final: 0.7223 (mt0) REVERT: B 942 MET cc_start: 0.8126 (tmt) cc_final: 0.7893 (tmm) REVERT: B 945 GLU cc_start: 0.7516 (OUTLIER) cc_final: 0.6759 (mp0) REVERT: C 8 ARG cc_start: 0.8664 (mtt-85) cc_final: 0.8236 (mtt180) REVERT: C 66 GLU cc_start: 0.7919 (tt0) cc_final: 0.7690 (tt0) REVERT: C 176 GLN cc_start: 0.8179 (OUTLIER) cc_final: 0.7648 (tt0) REVERT: C 200 ILE cc_start: 0.7959 (mm) cc_final: 0.7679 (mm) REVERT: C 221 ASP cc_start: 0.8603 (t70) cc_final: 0.8360 (t0) REVERT: C 292 GLN cc_start: 0.7925 (mt0) cc_final: 0.7674 (mp-120) REVERT: C 352 PHE cc_start: 0.7373 (m-10) cc_final: 0.6788 (t80) REVERT: C 356 TYR cc_start: 0.8806 (t80) cc_final: 0.8267 (t80) REVERT: C 439 THR cc_start: 0.8852 (m) cc_final: 0.8541 (m) REVERT: C 561 MET cc_start: 0.8892 (OUTLIER) cc_final: 0.8447 (ttm) REVERT: C 592 GLU cc_start: 0.6800 (OUTLIER) cc_final: 0.6492 (mm-30) REVERT: C 612 PHE cc_start: 0.6946 (m-80) cc_final: 0.5739 (m-80) REVERT: C 654 GLU cc_start: 0.7630 (mm-30) cc_final: 0.7340 (mm-30) REVERT: C 665 GLU cc_start: 0.7076 (mp0) cc_final: 0.6808 (mp0) REVERT: C 697 MET cc_start: 0.8910 (mtt) cc_final: 0.8410 (mtt) REVERT: C 736 ASP cc_start: 0.7473 (m-30) cc_final: 0.7068 (m-30) REVERT: C 748 MET cc_start: 0.8112 (mtm) cc_final: 0.7759 (mpp) REVERT: C 779 ASN cc_start: 0.7819 (t0) cc_final: 0.7538 (t0) REVERT: C 783 MET cc_start: 0.6724 (pmm) cc_final: 0.6322 (tpt) REVERT: C 799 GLN cc_start: 0.8436 (tt0) cc_final: 0.8200 (tt0) REVERT: C 836 GLU cc_start: 0.7742 (mt-10) cc_final: 0.7519 (mt-10) REVERT: C 973 THR cc_start: 0.9112 (m) cc_final: 0.8714 (p) outliers start: 80 outliers final: 37 residues processed: 561 average time/residue: 0.6464 time to fit residues: 418.1943 Evaluate side-chains 562 residues out of total 2565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 512 time to evaluate : 0.895 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 32 ILE Chi-restraints excluded: chain A residue 89 GLU Chi-restraints excluded: chain A residue 100 VAL Chi-restraints excluded: chain A residue 102 MET Chi-restraints excluded: chain A residue 209 GLU Chi-restraints excluded: chain A residue 241 SER Chi-restraints excluded: chain A residue 477 SER Chi-restraints excluded: chain A residue 483 LEU Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 595 LEU Chi-restraints excluded: chain A residue 799 GLN Chi-restraints excluded: chain A residue 828 SER Chi-restraints excluded: chain A residue 868 LEU Chi-restraints excluded: chain A residue 946 GLU Chi-restraints excluded: chain B residue 64 LEU Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 231 THR Chi-restraints excluded: chain B residue 235 SER Chi-restraints excluded: chain B residue 312 GLU Chi-restraints excluded: chain B residue 325 ILE Chi-restraints excluded: chain B residue 357 LEU Chi-restraints excluded: chain B residue 398 MET Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 449 LEU Chi-restraints excluded: chain B residue 535 THR Chi-restraints excluded: chain B residue 716 ASP Chi-restraints excluded: chain B residue 717 ASN Chi-restraints excluded: chain B residue 732 VAL Chi-restraints excluded: chain B residue 862 SER Chi-restraints excluded: chain B residue 895 VAL Chi-restraints excluded: chain B residue 913 MET Chi-restraints excluded: chain B residue 945 GLU Chi-restraints excluded: chain B residue 960 LEU Chi-restraints excluded: chain B residue 977 ILE Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 108 GLN Chi-restraints excluded: chain C residue 127 LEU Chi-restraints excluded: chain C residue 137 LEU Chi-restraints excluded: chain C residue 176 GLN Chi-restraints excluded: chain C residue 230 ILE Chi-restraints excluded: chain C residue 265 VAL Chi-restraints excluded: chain C residue 561 MET Chi-restraints excluded: chain C residue 572 SER Chi-restraints excluded: chain C residue 592 GLU Chi-restraints excluded: chain C residue 594 ASN Chi-restraints excluded: chain C residue 709 ASN Chi-restraints excluded: chain C residue 759 MET Chi-restraints excluded: chain C residue 986 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 4 optimal weight: 8.9990 chunk 158 optimal weight: 0.0020 chunk 27 optimal weight: 8.9990 chunk 211 optimal weight: 9.9990 chunk 147 optimal weight: 7.9990 chunk 251 optimal weight: 5.9990 chunk 226 optimal weight: 9.9990 chunk 86 optimal weight: 9.9990 chunk 112 optimal weight: 4.9990 chunk 11 optimal weight: 20.0000 chunk 106 optimal weight: 7.9990 overall best weight: 5.3996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 125 GLN A 267 ASN A 593 ASN A 649 ASN ** A 691 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 342 HIS B 691 GLN B 779 ASN C 124 GLN ** C 859 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.134225 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.114427 restraints weight = 25375.560| |-----------------------------------------------------------------------------| r_work (start): 0.3066 rms_B_bonded: 1.14 r_work: 0.2924 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.2806 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.2806 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8372 moved from start: 0.2219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 24106 Z= 0.198 Angle : 0.590 7.372 32640 Z= 0.309 Chirality : 0.043 0.201 3876 Planarity : 0.005 0.055 4073 Dihedral : 9.382 162.555 3426 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 3.51 % Allowed : 14.62 % Favored : 81.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.72 (0.15), residues: 3048 helix: 2.01 (0.13), residues: 1713 sheet: 0.23 (0.21), residues: 544 loop : 0.01 (0.22), residues: 791 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 7 TYR 0.026 0.002 TYR A 49 PHE 0.020 0.002 PHE B 672 TRP 0.009 0.001 TRP A 610 HIS 0.003 0.001 HIS A 991 Details of bonding type rmsd covalent geometry : bond 0.00481 (24106) covalent geometry : angle 0.58998 (32640) hydrogen bonds : bond 0.05360 ( 1522) hydrogen bonds : angle 4.42120 ( 4635) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6096 Ramachandran restraints generated. 3048 Oldfield, 0 Emsley, 3048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6096 Ramachandran restraints generated. 3048 Oldfield, 0 Emsley, 3048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 636 residues out of total 2565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 546 time to evaluate : 1.088 Fit side-chains revert: symmetry clash REVERT: A 1 MET cc_start: 0.6334 (OUTLIER) cc_final: 0.6126 (ttt) REVERT: A 67 ARG cc_start: 0.7941 (ptm160) cc_final: 0.7739 (ptp-170) REVERT: A 89 GLU cc_start: 0.8402 (OUTLIER) cc_final: 0.7344 (tm-30) REVERT: A 102 MET cc_start: 0.7156 (OUTLIER) cc_final: 0.6550 (mmm) REVERT: A 123 ARG cc_start: 0.7892 (mtp180) cc_final: 0.7644 (mtp85) REVERT: A 147 ASN cc_start: 0.7675 (m110) cc_final: 0.7348 (t0) REVERT: A 201 SER cc_start: 0.8874 (p) cc_final: 0.8348 (m) REVERT: A 254 LYS cc_start: 0.6898 (mmpt) cc_final: 0.6575 (mmmm) REVERT: A 314 LYS cc_start: 0.7130 (ttpt) cc_final: 0.6910 (ptmt) REVERT: A 319 GLU cc_start: 0.7947 (tm-30) cc_final: 0.7670 (tm-30) REVERT: A 321 MET cc_start: 0.8346 (mtt) cc_final: 0.8088 (mtt) REVERT: A 346 GLU cc_start: 0.8905 (mt-10) cc_final: 0.8463 (mt-10) REVERT: A 366 LEU cc_start: 0.8564 (mt) cc_final: 0.8238 (mt) REVERT: A 383 MET cc_start: 0.8830 (mtp) cc_final: 0.8506 (mtp) REVERT: A 605 THR cc_start: 0.8950 (m) cc_final: 0.8671 (m) REVERT: A 693 GLU cc_start: 0.8327 (tt0) cc_final: 0.8004 (tt0) REVERT: A 772 MET cc_start: 0.9017 (mmt) cc_final: 0.8490 (mmt) REVERT: A 893 MET cc_start: 0.8909 (mmm) cc_final: 0.8704 (mmm) REVERT: A 946 GLU cc_start: 0.7280 (OUTLIER) cc_final: 0.5832 (mp0) REVERT: A 988 GLU cc_start: 0.7853 (mp0) cc_final: 0.7535 (mp0) REVERT: A 1018 PHE cc_start: 0.8275 (t80) cc_final: 0.8023 (t80) REVERT: B 1 MET cc_start: 0.7084 (ptm) cc_final: 0.6866 (ptp) REVERT: B 68 GLU cc_start: 0.7516 (mm-30) cc_final: 0.7220 (mm-30) REVERT: B 111 ILE cc_start: 0.8718 (pt) cc_final: 0.8406 (pt) REVERT: B 226 LYS cc_start: 0.8559 (mtpt) cc_final: 0.8295 (mppt) REVERT: B 293 LEU cc_start: 0.8223 (mt) cc_final: 0.7910 (tp) REVERT: B 307 ARG cc_start: 0.7694 (ttm110) cc_final: 0.7424 (mtt-85) REVERT: B 312 GLU cc_start: 0.6934 (OUTLIER) cc_final: 0.6282 (mp0) REVERT: B 325 ILE cc_start: 0.8553 (OUTLIER) cc_final: 0.8116 (mm) REVERT: B 716 ASP cc_start: 0.8353 (OUTLIER) cc_final: 0.8130 (m-30) REVERT: B 779 ASN cc_start: 0.8541 (OUTLIER) cc_final: 0.8137 (t160) REVERT: B 799 GLN cc_start: 0.7872 (tt0) cc_final: 0.7232 (mt0) REVERT: B 942 MET cc_start: 0.8167 (tmt) cc_final: 0.7960 (tmm) REVERT: B 945 GLU cc_start: 0.7537 (OUTLIER) cc_final: 0.6772 (mp0) REVERT: C 8 ARG cc_start: 0.8692 (mtt-85) cc_final: 0.8385 (mtp180) REVERT: C 176 GLN cc_start: 0.8304 (OUTLIER) cc_final: 0.7907 (tt0) REVERT: C 200 ILE cc_start: 0.8080 (mm) cc_final: 0.7815 (mm) REVERT: C 221 ASP cc_start: 0.8665 (t70) cc_final: 0.8416 (t0) REVERT: C 292 GLN cc_start: 0.8019 (mt0) cc_final: 0.7624 (mp10) REVERT: C 352 PHE cc_start: 0.7425 (m-10) cc_final: 0.6801 (t80) REVERT: C 356 TYR cc_start: 0.8979 (t80) cc_final: 0.8370 (t80) REVERT: C 439 THR cc_start: 0.8883 (m) cc_final: 0.8578 (m) REVERT: C 592 GLU cc_start: 0.6860 (OUTLIER) cc_final: 0.6592 (tt0) REVERT: C 612 PHE cc_start: 0.7087 (m-80) cc_final: 0.6157 (m-80) REVERT: C 654 GLU cc_start: 0.7696 (mm-30) cc_final: 0.7420 (mm-30) REVERT: C 656 MET cc_start: 0.8489 (ttm) cc_final: 0.8287 (ttm) REVERT: C 665 GLU cc_start: 0.7136 (mp0) cc_final: 0.6897 (mp0) REVERT: C 697 MET cc_start: 0.8967 (mtt) cc_final: 0.8523 (mtt) REVERT: C 736 ASP cc_start: 0.7492 (m-30) cc_final: 0.7144 (m-30) REVERT: C 748 MET cc_start: 0.8191 (mtm) cc_final: 0.7833 (mpp) REVERT: C 779 ASN cc_start: 0.7705 (t0) cc_final: 0.7434 (t0) REVERT: C 783 MET cc_start: 0.6768 (OUTLIER) cc_final: 0.6344 (tpt) REVERT: C 799 GLN cc_start: 0.8507 (tt0) cc_final: 0.8281 (tt0) outliers start: 90 outliers final: 46 residues processed: 587 average time/residue: 0.6215 time to fit residues: 422.1730 Evaluate side-chains 580 residues out of total 2565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 522 time to evaluate : 0.861 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 32 ILE Chi-restraints excluded: chain A residue 89 GLU Chi-restraints excluded: chain A residue 100 VAL Chi-restraints excluded: chain A residue 102 MET Chi-restraints excluded: chain A residue 241 SER Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 477 SER Chi-restraints excluded: chain A residue 483 LEU Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 543 LEU Chi-restraints excluded: chain A residue 578 ASP Chi-restraints excluded: chain A residue 595 LEU Chi-restraints excluded: chain A residue 655 THR Chi-restraints excluded: chain A residue 717 ASN Chi-restraints excluded: chain A residue 732 VAL Chi-restraints excluded: chain A residue 799 GLN Chi-restraints excluded: chain A residue 828 SER Chi-restraints excluded: chain A residue 868 LEU Chi-restraints excluded: chain A residue 872 MET Chi-restraints excluded: chain A residue 946 GLU Chi-restraints excluded: chain A residue 1014 VAL Chi-restraints excluded: chain B residue 64 LEU Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 231 THR Chi-restraints excluded: chain B residue 235 SER Chi-restraints excluded: chain B residue 312 GLU Chi-restraints excluded: chain B residue 325 ILE Chi-restraints excluded: chain B residue 398 MET Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 449 LEU Chi-restraints excluded: chain B residue 535 THR Chi-restraints excluded: chain B residue 716 ASP Chi-restraints excluded: chain B residue 732 VAL Chi-restraints excluded: chain B residue 779 ASN Chi-restraints excluded: chain B residue 862 SER Chi-restraints excluded: chain B residue 893 MET Chi-restraints excluded: chain B residue 895 VAL Chi-restraints excluded: chain B residue 913 MET Chi-restraints excluded: chain B residue 945 GLU Chi-restraints excluded: chain B residue 960 LEU Chi-restraints excluded: chain B residue 977 ILE Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 108 GLN Chi-restraints excluded: chain C residue 127 LEU Chi-restraints excluded: chain C residue 137 LEU Chi-restraints excluded: chain C residue 176 GLN Chi-restraints excluded: chain C residue 230 ILE Chi-restraints excluded: chain C residue 265 VAL Chi-restraints excluded: chain C residue 561 MET Chi-restraints excluded: chain C residue 572 SER Chi-restraints excluded: chain C residue 592 GLU Chi-restraints excluded: chain C residue 709 ASN Chi-restraints excluded: chain C residue 759 MET Chi-restraints excluded: chain C residue 783 MET Chi-restraints excluded: chain C residue 986 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 274 optimal weight: 9.9990 chunk 288 optimal weight: 5.9990 chunk 75 optimal weight: 7.9990 chunk 132 optimal weight: 8.9990 chunk 267 optimal weight: 5.9990 chunk 162 optimal weight: 10.0000 chunk 301 optimal weight: 7.9990 chunk 227 optimal weight: 7.9990 chunk 168 optimal weight: 10.0000 chunk 31 optimal weight: 0.9990 chunk 41 optimal weight: 1.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 125 GLN A 267 ASN A 649 ASN B 109 ASN B 342 HIS B 779 ASN C 124 GLN C 594 ASN ** C 859 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.134267 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.114674 restraints weight = 25450.817| |-----------------------------------------------------------------------------| r_work (start): 0.3073 rms_B_bonded: 1.13 r_work: 0.2935 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.2817 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.2817 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8360 moved from start: 0.2297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 24106 Z= 0.176 Angle : 0.571 7.938 32640 Z= 0.299 Chirality : 0.042 0.202 3876 Planarity : 0.005 0.056 4073 Dihedral : 9.340 165.031 3426 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Rotamer: Outliers : 3.04 % Allowed : 16.06 % Favored : 80.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.68 (0.15), residues: 3048 helix: 1.99 (0.13), residues: 1711 sheet: 0.22 (0.21), residues: 544 loop : -0.05 (0.21), residues: 793 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 7 TYR 0.024 0.002 TYR A 49 PHE 0.020 0.002 PHE B 509 TRP 0.008 0.001 TRP A 610 HIS 0.002 0.001 HIS B 360 Details of bonding type rmsd covalent geometry : bond 0.00426 (24106) covalent geometry : angle 0.57103 (32640) hydrogen bonds : bond 0.05117 ( 1522) hydrogen bonds : angle 4.39420 ( 4635) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6096 Ramachandran restraints generated. 3048 Oldfield, 0 Emsley, 3048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6096 Ramachandran restraints generated. 3048 Oldfield, 0 Emsley, 3048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 612 residues out of total 2565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 534 time to evaluate : 0.905 Fit side-chains revert: symmetry clash REVERT: A 1 MET cc_start: 0.6375 (OUTLIER) cc_final: 0.6164 (ttt) REVERT: A 67 ARG cc_start: 0.7925 (ptm160) cc_final: 0.7699 (ptp-170) REVERT: A 89 GLU cc_start: 0.8410 (OUTLIER) cc_final: 0.7386 (tm-30) REVERT: A 102 MET cc_start: 0.7063 (OUTLIER) cc_final: 0.6392 (mmm) REVERT: A 123 ARG cc_start: 0.7926 (mtp180) cc_final: 0.7654 (mtp85) REVERT: A 147 ASN cc_start: 0.7673 (m110) cc_final: 0.7263 (m-40) REVERT: A 201 SER cc_start: 0.8861 (p) cc_final: 0.8355 (m) REVERT: A 209 GLU cc_start: 0.7716 (pt0) cc_final: 0.7490 (tt0) REVERT: A 276 ASN cc_start: 0.8347 (p0) cc_final: 0.8022 (p0) REVERT: A 314 LYS cc_start: 0.7112 (ttpt) cc_final: 0.6859 (ptmt) REVERT: A 319 GLU cc_start: 0.7859 (tm-30) cc_final: 0.7656 (tm-30) REVERT: A 321 MET cc_start: 0.8333 (mtt) cc_final: 0.8124 (mtt) REVERT: A 346 GLU cc_start: 0.8899 (mt-10) cc_final: 0.8455 (mt-10) REVERT: A 366 LEU cc_start: 0.8552 (mt) cc_final: 0.8221 (mt) REVERT: A 383 MET cc_start: 0.8810 (mtp) cc_final: 0.8316 (mtp) REVERT: A 605 THR cc_start: 0.8920 (m) cc_final: 0.8678 (m) REVERT: A 693 GLU cc_start: 0.8308 (tt0) cc_final: 0.8006 (tt0) REVERT: A 772 MET cc_start: 0.9025 (mmt) cc_final: 0.8497 (mmt) REVERT: A 802 LYS cc_start: 0.8455 (OUTLIER) cc_final: 0.8000 (mtpp) REVERT: A 893 MET cc_start: 0.8903 (mmm) cc_final: 0.8698 (mmm) REVERT: A 988 GLU cc_start: 0.7825 (mp0) cc_final: 0.7507 (mp0) REVERT: A 1018 PHE cc_start: 0.8271 (t80) cc_final: 0.7985 (t80) REVERT: B 68 GLU cc_start: 0.7494 (mm-30) cc_final: 0.7202 (mm-30) REVERT: B 111 ILE cc_start: 0.8687 (pt) cc_final: 0.8389 (pt) REVERT: B 226 LYS cc_start: 0.8561 (mtpt) cc_final: 0.8311 (mppt) REVERT: B 293 LEU cc_start: 0.8210 (mt) cc_final: 0.7871 (tp) REVERT: B 312 GLU cc_start: 0.6943 (OUTLIER) cc_final: 0.6318 (mp0) REVERT: B 325 ILE cc_start: 0.8536 (OUTLIER) cc_final: 0.8101 (mm) REVERT: B 518 ASP cc_start: 0.7791 (OUTLIER) cc_final: 0.7340 (m-30) REVERT: B 716 ASP cc_start: 0.8361 (OUTLIER) cc_final: 0.8135 (m-30) REVERT: B 779 ASN cc_start: 0.8579 (OUTLIER) cc_final: 0.8261 (t0) REVERT: B 799 GLN cc_start: 0.7855 (tt0) cc_final: 0.7216 (mt0) REVERT: B 942 MET cc_start: 0.8166 (tmt) cc_final: 0.7939 (tmm) REVERT: B 945 GLU cc_start: 0.7527 (OUTLIER) cc_final: 0.6723 (mp0) REVERT: C 8 ARG cc_start: 0.8684 (mtt-85) cc_final: 0.8278 (mtp180) REVERT: C 176 GLN cc_start: 0.8280 (OUTLIER) cc_final: 0.7835 (tt0) REVERT: C 205 ASN cc_start: 0.7485 (OUTLIER) cc_final: 0.7174 (m110) REVERT: C 221 ASP cc_start: 0.8657 (t70) cc_final: 0.8388 (t0) REVERT: C 292 GLN cc_start: 0.7995 (mt0) cc_final: 0.7599 (mp10) REVERT: C 352 PHE cc_start: 0.7370 (m-10) cc_final: 0.6774 (t80) REVERT: C 356 TYR cc_start: 0.8955 (t80) cc_final: 0.8346 (t80) REVERT: C 408 ASP cc_start: 0.8305 (OUTLIER) cc_final: 0.8065 (t70) REVERT: C 439 THR cc_start: 0.8856 (m) cc_final: 0.8554 (m) REVERT: C 592 GLU cc_start: 0.6838 (OUTLIER) cc_final: 0.6440 (mm-30) REVERT: C 612 PHE cc_start: 0.6923 (m-80) cc_final: 0.6044 (m-80) REVERT: C 654 GLU cc_start: 0.7673 (mm-30) cc_final: 0.7391 (mm-30) REVERT: C 656 MET cc_start: 0.8439 (ttm) cc_final: 0.8233 (ttm) REVERT: C 665 GLU cc_start: 0.7142 (mp0) cc_final: 0.6847 (mp0) REVERT: C 697 MET cc_start: 0.8941 (mtt) cc_final: 0.8738 (mtt) REVERT: C 736 ASP cc_start: 0.7450 (m-30) cc_final: 0.7075 (m-30) REVERT: C 779 ASN cc_start: 0.7695 (t0) cc_final: 0.7432 (t0) REVERT: C 783 MET cc_start: 0.6761 (pmm) cc_final: 0.6319 (tpt) REVERT: C 862 SER cc_start: 0.8647 (m) cc_final: 0.8351 (p) outliers start: 78 outliers final: 44 residues processed: 567 average time/residue: 0.6143 time to fit residues: 403.3039 Evaluate side-chains 579 residues out of total 2565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 521 time to evaluate : 0.655 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 32 ILE Chi-restraints excluded: chain A residue 70 SER Chi-restraints excluded: chain A residue 89 GLU Chi-restraints excluded: chain A residue 100 VAL Chi-restraints excluded: chain A residue 102 MET Chi-restraints excluded: chain A residue 241 SER Chi-restraints excluded: chain A residue 477 SER Chi-restraints excluded: chain A residue 483 LEU Chi-restraints excluded: chain A residue 543 LEU Chi-restraints excluded: chain A residue 595 LEU Chi-restraints excluded: chain A residue 655 THR Chi-restraints excluded: chain A residue 717 ASN Chi-restraints excluded: chain A residue 732 VAL Chi-restraints excluded: chain A residue 802 LYS Chi-restraints excluded: chain A residue 828 SER Chi-restraints excluded: chain A residue 868 LEU Chi-restraints excluded: chain A residue 872 MET Chi-restraints excluded: chain A residue 946 GLU Chi-restraints excluded: chain B residue 64 LEU Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 231 THR Chi-restraints excluded: chain B residue 235 SER Chi-restraints excluded: chain B residue 312 GLU Chi-restraints excluded: chain B residue 325 ILE Chi-restraints excluded: chain B residue 398 MET Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 449 LEU Chi-restraints excluded: chain B residue 518 ASP Chi-restraints excluded: chain B residue 535 THR Chi-restraints excluded: chain B residue 563 GLU Chi-restraints excluded: chain B residue 716 ASP Chi-restraints excluded: chain B residue 732 VAL Chi-restraints excluded: chain B residue 779 ASN Chi-restraints excluded: chain B residue 862 SER Chi-restraints excluded: chain B residue 893 MET Chi-restraints excluded: chain B residue 895 VAL Chi-restraints excluded: chain B residue 913 MET Chi-restraints excluded: chain B residue 945 GLU Chi-restraints excluded: chain B residue 960 LEU Chi-restraints excluded: chain B residue 977 ILE Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 108 GLN Chi-restraints excluded: chain C residue 127 LEU Chi-restraints excluded: chain C residue 137 LEU Chi-restraints excluded: chain C residue 176 GLN Chi-restraints excluded: chain C residue 205 ASN Chi-restraints excluded: chain C residue 230 ILE Chi-restraints excluded: chain C residue 265 VAL Chi-restraints excluded: chain C residue 408 ASP Chi-restraints excluded: chain C residue 420 MET Chi-restraints excluded: chain C residue 572 SER Chi-restraints excluded: chain C residue 592 GLU Chi-restraints excluded: chain C residue 633 THR Chi-restraints excluded: chain C residue 709 ASN Chi-restraints excluded: chain C residue 759 MET Chi-restraints excluded: chain C residue 986 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 193 optimal weight: 7.9990 chunk 234 optimal weight: 5.9990 chunk 46 optimal weight: 7.9990 chunk 287 optimal weight: 6.9990 chunk 303 optimal weight: 4.9990 chunk 155 optimal weight: 0.9990 chunk 95 optimal weight: 20.0000 chunk 70 optimal weight: 7.9990 chunk 86 optimal weight: 5.9990 chunk 195 optimal weight: 4.9990 chunk 31 optimal weight: 8.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 125 GLN A 267 ASN A 586 ASN A 649 ASN ** B 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 342 HIS B 779 ASN C 124 GLN C 594 ASN C 801 ASN ** C 859 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.133867 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.113776 restraints weight = 25434.638| |-----------------------------------------------------------------------------| r_work (start): 0.3058 rms_B_bonded: 1.17 r_work: 0.2931 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.2809 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.2809 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8356 moved from start: 0.2375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 24106 Z= 0.176 Angle : 0.573 8.267 32640 Z= 0.300 Chirality : 0.042 0.201 3876 Planarity : 0.005 0.056 4073 Dihedral : 9.309 167.247 3426 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 3.47 % Allowed : 16.41 % Favored : 80.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.65 (0.15), residues: 3048 helix: 1.98 (0.13), residues: 1711 sheet: 0.21 (0.21), residues: 542 loop : -0.09 (0.21), residues: 795 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 7 TYR 0.024 0.002 TYR A 49 PHE 0.023 0.002 PHE B 509 TRP 0.008 0.001 TRP A 610 HIS 0.002 0.001 HIS B 360 Details of bonding type rmsd covalent geometry : bond 0.00426 (24106) covalent geometry : angle 0.57322 (32640) hydrogen bonds : bond 0.05103 ( 1522) hydrogen bonds : angle 4.38975 ( 4635) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6096 Ramachandran restraints generated. 3048 Oldfield, 0 Emsley, 3048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6096 Ramachandran restraints generated. 3048 Oldfield, 0 Emsley, 3048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 617 residues out of total 2565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 528 time to evaluate : 0.924 Fit side-chains revert: symmetry clash REVERT: A 67 ARG cc_start: 0.7899 (ptm160) cc_final: 0.7664 (ptp-170) REVERT: A 89 GLU cc_start: 0.8358 (OUTLIER) cc_final: 0.7322 (tm-30) REVERT: A 102 MET cc_start: 0.7078 (OUTLIER) cc_final: 0.6402 (mmm) REVERT: A 147 ASN cc_start: 0.7711 (m110) cc_final: 0.7304 (m-40) REVERT: A 201 SER cc_start: 0.8879 (p) cc_final: 0.8377 (m) REVERT: A 209 GLU cc_start: 0.7711 (pt0) cc_final: 0.7453 (tt0) REVERT: A 254 LYS cc_start: 0.6899 (mmpt) cc_final: 0.6561 (mmmm) REVERT: A 276 ASN cc_start: 0.8431 (OUTLIER) cc_final: 0.8063 (p0) REVERT: A 314 LYS cc_start: 0.7087 (ttpt) cc_final: 0.6837 (ptmt) REVERT: A 319 GLU cc_start: 0.7860 (tm-30) cc_final: 0.7625 (tm-30) REVERT: A 346 GLU cc_start: 0.8828 (mt-10) cc_final: 0.8376 (mt-10) REVERT: A 366 LEU cc_start: 0.8549 (mt) cc_final: 0.8216 (mt) REVERT: A 383 MET cc_start: 0.8786 (mtp) cc_final: 0.8328 (mtp) REVERT: A 411 VAL cc_start: 0.8805 (p) cc_final: 0.8584 (m) REVERT: A 605 THR cc_start: 0.8928 (m) cc_final: 0.8687 (m) REVERT: A 642 ASP cc_start: 0.8405 (m-30) cc_final: 0.8106 (m-30) REVERT: A 693 GLU cc_start: 0.8250 (tt0) cc_final: 0.7943 (tt0) REVERT: A 772 MET cc_start: 0.9044 (mmt) cc_final: 0.8557 (mmt) REVERT: A 802 LYS cc_start: 0.8423 (OUTLIER) cc_final: 0.7973 (mtpp) REVERT: A 864 MET cc_start: 0.8600 (ttp) cc_final: 0.8368 (ttt) REVERT: A 893 MET cc_start: 0.8909 (mmm) cc_final: 0.8702 (mmm) REVERT: A 942 MET cc_start: 0.7905 (tpp) cc_final: 0.7221 (tmm) REVERT: A 988 GLU cc_start: 0.7797 (mp0) cc_final: 0.7465 (mp0) REVERT: A 1018 PHE cc_start: 0.8225 (t80) cc_final: 0.7993 (t80) REVERT: B 1 MET cc_start: 0.7110 (ptm) cc_final: 0.6885 (ptp) REVERT: B 68 GLU cc_start: 0.7547 (mm-30) cc_final: 0.7283 (mm-30) REVERT: B 111 ILE cc_start: 0.8663 (pt) cc_final: 0.8385 (pt) REVERT: B 312 GLU cc_start: 0.6935 (OUTLIER) cc_final: 0.6451 (mp0) REVERT: B 325 ILE cc_start: 0.8527 (OUTLIER) cc_final: 0.8086 (mm) REVERT: B 518 ASP cc_start: 0.7768 (OUTLIER) cc_final: 0.7308 (m-30) REVERT: B 716 ASP cc_start: 0.8332 (OUTLIER) cc_final: 0.8104 (m-30) REVERT: B 779 ASN cc_start: 0.8532 (OUTLIER) cc_final: 0.8244 (t160) REVERT: B 799 GLN cc_start: 0.7859 (tt0) cc_final: 0.7173 (mt0) REVERT: B 942 MET cc_start: 0.8191 (tmt) cc_final: 0.7960 (tmm) REVERT: B 945 GLU cc_start: 0.7544 (OUTLIER) cc_final: 0.6721 (mp0) REVERT: C 8 ARG cc_start: 0.8757 (mtt-85) cc_final: 0.8439 (mtp180) REVERT: C 176 GLN cc_start: 0.8255 (OUTLIER) cc_final: 0.7817 (tt0) REVERT: C 205 ASN cc_start: 0.7499 (OUTLIER) cc_final: 0.7166 (m110) REVERT: C 221 ASP cc_start: 0.8650 (t70) cc_final: 0.8386 (t0) REVERT: C 292 GLN cc_start: 0.8024 (mt0) cc_final: 0.7687 (mp-120) REVERT: C 352 PHE cc_start: 0.7357 (m-10) cc_final: 0.6769 (t80) REVERT: C 356 TYR cc_start: 0.8950 (t80) cc_final: 0.8309 (t80) REVERT: C 408 ASP cc_start: 0.8295 (OUTLIER) cc_final: 0.7993 (t70) REVERT: C 439 THR cc_start: 0.8954 (OUTLIER) cc_final: 0.8664 (m) REVERT: C 592 GLU cc_start: 0.6991 (OUTLIER) cc_final: 0.6622 (mm-30) REVERT: C 612 PHE cc_start: 0.7050 (m-80) cc_final: 0.6161 (m-80) REVERT: C 654 GLU cc_start: 0.7671 (mm-30) cc_final: 0.7386 (mm-30) REVERT: C 656 MET cc_start: 0.8421 (ttm) cc_final: 0.8203 (ttm) REVERT: C 665 GLU cc_start: 0.7138 (mp0) cc_final: 0.6747 (mp0) REVERT: C 697 MET cc_start: 0.8915 (mtt) cc_final: 0.8670 (mtt) REVERT: C 736 ASP cc_start: 0.7457 (m-30) cc_final: 0.7128 (m-30) REVERT: C 779 ASN cc_start: 0.7685 (t0) cc_final: 0.7410 (t0) REVERT: C 783 MET cc_start: 0.6665 (OUTLIER) cc_final: 0.6268 (tpt) REVERT: C 848 TYR cc_start: 0.8597 (p90) cc_final: 0.8248 (p90) REVERT: C 862 SER cc_start: 0.8620 (m) cc_final: 0.8319 (p) outliers start: 89 outliers final: 54 residues processed: 565 average time/residue: 0.6436 time to fit residues: 420.2069 Evaluate side-chains 586 residues out of total 2565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 516 time to evaluate : 0.924 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 ILE Chi-restraints excluded: chain A residue 70 SER Chi-restraints excluded: chain A residue 89 GLU Chi-restraints excluded: chain A residue 100 VAL Chi-restraints excluded: chain A residue 102 MET Chi-restraints excluded: chain A residue 241 SER Chi-restraints excluded: chain A residue 276 ASN Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 477 SER Chi-restraints excluded: chain A residue 483 LEU Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 543 LEU Chi-restraints excluded: chain A residue 595 LEU Chi-restraints excluded: chain A residue 655 THR Chi-restraints excluded: chain A residue 674 LEU Chi-restraints excluded: chain A residue 717 ASN Chi-restraints excluded: chain A residue 732 VAL Chi-restraints excluded: chain A residue 799 GLN Chi-restraints excluded: chain A residue 802 LYS Chi-restraints excluded: chain A residue 828 SER Chi-restraints excluded: chain A residue 868 LEU Chi-restraints excluded: chain A residue 872 MET Chi-restraints excluded: chain A residue 946 GLU Chi-restraints excluded: chain A residue 1014 VAL Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 64 LEU Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 231 THR Chi-restraints excluded: chain B residue 235 SER Chi-restraints excluded: chain B residue 312 GLU Chi-restraints excluded: chain B residue 325 ILE Chi-restraints excluded: chain B residue 398 MET Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 449 LEU Chi-restraints excluded: chain B residue 518 ASP Chi-restraints excluded: chain B residue 535 THR Chi-restraints excluded: chain B residue 536 VAL Chi-restraints excluded: chain B residue 563 GLU Chi-restraints excluded: chain B residue 716 ASP Chi-restraints excluded: chain B residue 732 VAL Chi-restraints excluded: chain B residue 779 ASN Chi-restraints excluded: chain B residue 862 SER Chi-restraints excluded: chain B residue 893 MET Chi-restraints excluded: chain B residue 895 VAL Chi-restraints excluded: chain B residue 913 MET Chi-restraints excluded: chain B residue 945 GLU Chi-restraints excluded: chain B residue 960 LEU Chi-restraints excluded: chain B residue 977 ILE Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 108 GLN Chi-restraints excluded: chain C residue 127 LEU Chi-restraints excluded: chain C residue 137 LEU Chi-restraints excluded: chain C residue 176 GLN Chi-restraints excluded: chain C residue 205 ASN Chi-restraints excluded: chain C residue 265 VAL Chi-restraints excluded: chain C residue 342 HIS Chi-restraints excluded: chain C residue 357 LEU Chi-restraints excluded: chain C residue 408 ASP Chi-restraints excluded: chain C residue 420 MET Chi-restraints excluded: chain C residue 439 THR Chi-restraints excluded: chain C residue 536 VAL Chi-restraints excluded: chain C residue 572 SER Chi-restraints excluded: chain C residue 592 GLU Chi-restraints excluded: chain C residue 633 THR Chi-restraints excluded: chain C residue 709 ASN Chi-restraints excluded: chain C residue 759 MET Chi-restraints excluded: chain C residue 783 MET Chi-restraints excluded: chain C residue 986 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 174 optimal weight: 9.9990 chunk 131 optimal weight: 0.7980 chunk 47 optimal weight: 8.9990 chunk 51 optimal weight: 20.0000 chunk 177 optimal weight: 4.9990 chunk 189 optimal weight: 7.9990 chunk 288 optimal weight: 0.8980 chunk 267 optimal weight: 5.9990 chunk 95 optimal weight: 20.0000 chunk 52 optimal weight: 30.0000 chunk 245 optimal weight: 5.9990 overall best weight: 3.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 125 GLN A 267 ASN A 586 ASN A 593 ASN A 649 ASN B 109 ASN B 342 HIS B 779 ASN C 124 GLN ** C 859 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.134476 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.115505 restraints weight = 25372.861| |-----------------------------------------------------------------------------| r_work (start): 0.3085 rms_B_bonded: 1.11 r_work: 0.2958 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.2842 rms_B_bonded: 3.27 restraints_weight: 0.2500 r_work (final): 0.2842 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8337 moved from start: 0.2412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 24106 Z= 0.156 Angle : 0.561 8.238 32640 Z= 0.293 Chirality : 0.041 0.199 3876 Planarity : 0.005 0.069 4073 Dihedral : 9.204 169.883 3426 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 3.35 % Allowed : 16.96 % Favored : 79.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.71 (0.15), residues: 3048 helix: 2.03 (0.13), residues: 1712 sheet: 0.21 (0.21), residues: 542 loop : -0.07 (0.21), residues: 794 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 123 TYR 0.024 0.002 TYR A 49 PHE 0.024 0.001 PHE B 509 TRP 0.007 0.001 TRP A 610 HIS 0.002 0.001 HIS B 360 Details of bonding type rmsd covalent geometry : bond 0.00372 (24106) covalent geometry : angle 0.56068 (32640) hydrogen bonds : bond 0.04870 ( 1522) hydrogen bonds : angle 4.33915 ( 4635) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6096 Ramachandran restraints generated. 3048 Oldfield, 0 Emsley, 3048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6096 Ramachandran restraints generated. 3048 Oldfield, 0 Emsley, 3048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 613 residues out of total 2565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 527 time to evaluate : 0.913 Fit side-chains revert: symmetry clash REVERT: A 89 GLU cc_start: 0.8315 (OUTLIER) cc_final: 0.7269 (tm-30) REVERT: A 102 MET cc_start: 0.7056 (OUTLIER) cc_final: 0.6373 (mmm) REVERT: A 147 ASN cc_start: 0.7701 (m110) cc_final: 0.7303 (m-40) REVERT: A 201 SER cc_start: 0.8853 (p) cc_final: 0.8342 (m) REVERT: A 254 LYS cc_start: 0.6897 (mmpt) cc_final: 0.6563 (mmmm) REVERT: A 314 LYS cc_start: 0.7039 (ttpt) cc_final: 0.6810 (ptmt) REVERT: A 346 GLU cc_start: 0.8789 (mt-10) cc_final: 0.8327 (mt-10) REVERT: A 366 LEU cc_start: 0.8529 (mt) cc_final: 0.8201 (mt) REVERT: A 605 THR cc_start: 0.8866 (m) cc_final: 0.8609 (m) REVERT: A 642 ASP cc_start: 0.8288 (m-30) cc_final: 0.7949 (m-30) REVERT: A 772 MET cc_start: 0.9049 (mmt) cc_final: 0.8575 (mmt) REVERT: A 802 LYS cc_start: 0.8381 (OUTLIER) cc_final: 0.7953 (mtpp) REVERT: A 864 MET cc_start: 0.8672 (ttp) cc_final: 0.8448 (ttt) REVERT: A 893 MET cc_start: 0.8872 (mmm) cc_final: 0.8569 (mmm) REVERT: A 942 MET cc_start: 0.7938 (tpp) cc_final: 0.7294 (tmm) REVERT: A 988 GLU cc_start: 0.7748 (mp0) cc_final: 0.7440 (mp0) REVERT: A 1018 PHE cc_start: 0.8255 (t80) cc_final: 0.7992 (t80) REVERT: B 1 MET cc_start: 0.7080 (ptm) cc_final: 0.6838 (ptp) REVERT: B 68 GLU cc_start: 0.7473 (mm-30) cc_final: 0.7208 (mm-30) REVERT: B 89 GLU cc_start: 0.7532 (tp30) cc_final: 0.7329 (tp30) REVERT: B 111 ILE cc_start: 0.8625 (pt) cc_final: 0.8337 (pt) REVERT: B 138 MET cc_start: 0.8919 (ptm) cc_final: 0.8427 (ptp) REVERT: B 307 ARG cc_start: 0.7669 (ttm110) cc_final: 0.7384 (mtt-85) REVERT: B 312 GLU cc_start: 0.6902 (OUTLIER) cc_final: 0.6423 (mp0) REVERT: B 325 ILE cc_start: 0.8530 (OUTLIER) cc_final: 0.8105 (mm) REVERT: B 518 ASP cc_start: 0.7739 (OUTLIER) cc_final: 0.7061 (m-30) REVERT: B 716 ASP cc_start: 0.8296 (OUTLIER) cc_final: 0.8067 (m-30) REVERT: B 779 ASN cc_start: 0.8465 (OUTLIER) cc_final: 0.8210 (t160) REVERT: B 799 GLN cc_start: 0.7809 (tt0) cc_final: 0.7176 (mt0) REVERT: B 942 MET cc_start: 0.8159 (tmt) cc_final: 0.7923 (tmm) REVERT: B 945 GLU cc_start: 0.7490 (OUTLIER) cc_final: 0.6647 (mp0) REVERT: C 8 ARG cc_start: 0.8737 (mtt-85) cc_final: 0.8412 (mtp180) REVERT: C 176 GLN cc_start: 0.8219 (OUTLIER) cc_final: 0.7801 (tt0) REVERT: C 205 ASN cc_start: 0.7485 (OUTLIER) cc_final: 0.7150 (m110) REVERT: C 221 ASP cc_start: 0.8616 (t70) cc_final: 0.8358 (t0) REVERT: C 292 GLN cc_start: 0.7979 (mt0) cc_final: 0.7649 (mp-120) REVERT: C 352 PHE cc_start: 0.7302 (m-10) cc_final: 0.6779 (t80) REVERT: C 356 TYR cc_start: 0.8914 (t80) cc_final: 0.8251 (t80) REVERT: C 395 MET cc_start: 0.8563 (mmp) cc_final: 0.8316 (mmm) REVERT: C 408 ASP cc_start: 0.8288 (OUTLIER) cc_final: 0.7922 (t70) REVERT: C 439 THR cc_start: 0.8939 (OUTLIER) cc_final: 0.8659 (m) REVERT: C 592 GLU cc_start: 0.6949 (OUTLIER) cc_final: 0.6607 (mm-30) REVERT: C 612 PHE cc_start: 0.7031 (m-80) cc_final: 0.6131 (m-80) REVERT: C 654 GLU cc_start: 0.7603 (mm-30) cc_final: 0.7347 (mm-30) REVERT: C 656 MET cc_start: 0.8379 (ttm) cc_final: 0.8154 (ttm) REVERT: C 665 GLU cc_start: 0.7087 (mp0) cc_final: 0.6728 (mp0) REVERT: C 697 MET cc_start: 0.8891 (mtt) cc_final: 0.8679 (mtt) REVERT: C 736 ASP cc_start: 0.7387 (m-30) cc_final: 0.7044 (m-30) REVERT: C 779 ASN cc_start: 0.7663 (t0) cc_final: 0.7377 (t0) REVERT: C 783 MET cc_start: 0.6663 (OUTLIER) cc_final: 0.6289 (tpt) REVERT: C 862 SER cc_start: 0.8626 (m) cc_final: 0.8329 (p) outliers start: 86 outliers final: 53 residues processed: 567 average time/residue: 0.6421 time to fit residues: 419.7141 Evaluate side-chains 591 residues out of total 2565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 523 time to evaluate : 0.891 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 ILE Chi-restraints excluded: chain A residue 70 SER Chi-restraints excluded: chain A residue 89 GLU Chi-restraints excluded: chain A residue 100 VAL Chi-restraints excluded: chain A residue 102 MET Chi-restraints excluded: chain A residue 241 SER Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 477 SER Chi-restraints excluded: chain A residue 483 LEU Chi-restraints excluded: chain A residue 543 LEU Chi-restraints excluded: chain A residue 595 LEU Chi-restraints excluded: chain A residue 634 SER Chi-restraints excluded: chain A residue 655 THR Chi-restraints excluded: chain A residue 674 LEU Chi-restraints excluded: chain A residue 717 ASN Chi-restraints excluded: chain A residue 732 VAL Chi-restraints excluded: chain A residue 799 GLN Chi-restraints excluded: chain A residue 802 LYS Chi-restraints excluded: chain A residue 828 SER Chi-restraints excluded: chain A residue 868 LEU Chi-restraints excluded: chain A residue 872 MET Chi-restraints excluded: chain A residue 946 GLU Chi-restraints excluded: chain A residue 1014 VAL Chi-restraints excluded: chain B residue 37 SER Chi-restraints excluded: chain B residue 64 LEU Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 231 THR Chi-restraints excluded: chain B residue 235 SER Chi-restraints excluded: chain B residue 312 GLU Chi-restraints excluded: chain B residue 325 ILE Chi-restraints excluded: chain B residue 398 MET Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 518 ASP Chi-restraints excluded: chain B residue 526 LEU Chi-restraints excluded: chain B residue 535 THR Chi-restraints excluded: chain B residue 716 ASP Chi-restraints excluded: chain B residue 717 ASN Chi-restraints excluded: chain B residue 732 VAL Chi-restraints excluded: chain B residue 779 ASN Chi-restraints excluded: chain B residue 862 SER Chi-restraints excluded: chain B residue 893 MET Chi-restraints excluded: chain B residue 895 VAL Chi-restraints excluded: chain B residue 913 MET Chi-restraints excluded: chain B residue 945 GLU Chi-restraints excluded: chain B residue 960 LEU Chi-restraints excluded: chain B residue 977 ILE Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 108 GLN Chi-restraints excluded: chain C residue 127 LEU Chi-restraints excluded: chain C residue 137 LEU Chi-restraints excluded: chain C residue 176 GLN Chi-restraints excluded: chain C residue 205 ASN Chi-restraints excluded: chain C residue 265 VAL Chi-restraints excluded: chain C residue 342 HIS Chi-restraints excluded: chain C residue 357 LEU Chi-restraints excluded: chain C residue 408 ASP Chi-restraints excluded: chain C residue 420 MET Chi-restraints excluded: chain C residue 439 THR Chi-restraints excluded: chain C residue 536 VAL Chi-restraints excluded: chain C residue 572 SER Chi-restraints excluded: chain C residue 592 GLU Chi-restraints excluded: chain C residue 633 THR Chi-restraints excluded: chain C residue 709 ASN Chi-restraints excluded: chain C residue 759 MET Chi-restraints excluded: chain C residue 783 MET Chi-restraints excluded: chain C residue 986 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 105 optimal weight: 2.9990 chunk 68 optimal weight: 10.0000 chunk 112 optimal weight: 4.9990 chunk 233 optimal weight: 8.9990 chunk 31 optimal weight: 8.9990 chunk 62 optimal weight: 0.6980 chunk 125 optimal weight: 0.8980 chunk 37 optimal weight: 7.9990 chunk 4 optimal weight: 10.0000 chunk 88 optimal weight: 0.9980 chunk 305 optimal weight: 4.9990 overall best weight: 2.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 125 GLN A 267 ASN A 586 ASN A 593 ASN A 649 ASN B 342 HIS B 779 ASN C 124 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.135663 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.117095 restraints weight = 25411.607| |-----------------------------------------------------------------------------| r_work (start): 0.3104 rms_B_bonded: 1.14 r_work: 0.2972 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.2857 rms_B_bonded: 3.32 restraints_weight: 0.2500 r_work (final): 0.2857 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8307 moved from start: 0.2427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 24106 Z= 0.125 Angle : 0.535 8.503 32640 Z= 0.279 Chirality : 0.040 0.197 3876 Planarity : 0.005 0.056 4073 Dihedral : 8.995 173.727 3426 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 3.04 % Allowed : 17.70 % Favored : 79.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.86 (0.15), residues: 3048 helix: 2.15 (0.13), residues: 1713 sheet: 0.26 (0.21), residues: 542 loop : -0.00 (0.22), residues: 793 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 7 TYR 0.019 0.001 TYR A 49 PHE 0.026 0.001 PHE B 509 TRP 0.005 0.001 TRP A 610 HIS 0.002 0.001 HIS C 360 Details of bonding type rmsd covalent geometry : bond 0.00285 (24106) covalent geometry : angle 0.53494 (32640) hydrogen bonds : bond 0.04342 ( 1522) hydrogen bonds : angle 4.23083 ( 4635) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6096 Ramachandran restraints generated. 3048 Oldfield, 0 Emsley, 3048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6096 Ramachandran restraints generated. 3048 Oldfield, 0 Emsley, 3048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 619 residues out of total 2565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 541 time to evaluate : 0.953 Fit side-chains revert: symmetry clash REVERT: A 73 LYS cc_start: 0.8063 (mtmt) cc_final: 0.7657 (pttp) REVERT: A 89 GLU cc_start: 0.8279 (OUTLIER) cc_final: 0.7248 (tm-30) REVERT: A 147 ASN cc_start: 0.7693 (m110) cc_final: 0.7308 (m-40) REVERT: A 161 ASN cc_start: 0.8262 (m-40) cc_final: 0.7886 (m110) REVERT: A 201 SER cc_start: 0.8787 (p) cc_final: 0.8338 (m) REVERT: A 209 GLU cc_start: 0.7591 (pt0) cc_final: 0.7370 (tt0) REVERT: A 254 LYS cc_start: 0.6890 (mmpt) cc_final: 0.6613 (mmmm) REVERT: A 314 LYS cc_start: 0.6971 (ttpt) cc_final: 0.6702 (ptmt) REVERT: A 346 GLU cc_start: 0.8782 (mt-10) cc_final: 0.8297 (mt-10) REVERT: A 366 LEU cc_start: 0.8468 (mt) cc_final: 0.8153 (mt) REVERT: A 383 MET cc_start: 0.8924 (mtp) cc_final: 0.8649 (mtp) REVERT: A 642 ASP cc_start: 0.8272 (m-30) cc_final: 0.7946 (m-30) REVERT: A 772 MET cc_start: 0.9029 (mmt) cc_final: 0.8476 (mmt) REVERT: A 802 LYS cc_start: 0.8351 (OUTLIER) cc_final: 0.7929 (mtpp) REVERT: A 864 MET cc_start: 0.8594 (ttp) cc_final: 0.8388 (ttt) REVERT: A 893 MET cc_start: 0.8875 (mmm) cc_final: 0.8578 (mmm) REVERT: A 942 MET cc_start: 0.7961 (tpp) cc_final: 0.7275 (tmm) REVERT: A 988 GLU cc_start: 0.7679 (mp0) cc_final: 0.7390 (mp0) REVERT: A 1018 PHE cc_start: 0.8206 (t80) cc_final: 0.7967 (t80) REVERT: B 1 MET cc_start: 0.6924 (ptm) cc_final: 0.6693 (ptp) REVERT: B 68 GLU cc_start: 0.7508 (mm-30) cc_final: 0.7224 (mm-30) REVERT: B 111 ILE cc_start: 0.8608 (pt) cc_final: 0.8289 (pt) REVERT: B 138 MET cc_start: 0.8897 (ptm) cc_final: 0.8415 (ptp) REVERT: B 307 ARG cc_start: 0.7548 (ttm110) cc_final: 0.7278 (mtt-85) REVERT: B 312 GLU cc_start: 0.6858 (OUTLIER) cc_final: 0.6367 (mp0) REVERT: B 325 ILE cc_start: 0.8510 (OUTLIER) cc_final: 0.8081 (mm) REVERT: B 518 ASP cc_start: 0.7660 (OUTLIER) cc_final: 0.6975 (m-30) REVERT: B 799 GLN cc_start: 0.7821 (tt0) cc_final: 0.7204 (mt0) REVERT: B 942 MET cc_start: 0.8161 (tmt) cc_final: 0.7918 (tmm) REVERT: B 945 GLU cc_start: 0.7389 (OUTLIER) cc_final: 0.6566 (mp0) REVERT: C 8 ARG cc_start: 0.8629 (mtt-85) cc_final: 0.8221 (mtp180) REVERT: C 68 GLU cc_start: 0.8414 (mm-30) cc_final: 0.8201 (mm-30) REVERT: C 176 GLN cc_start: 0.8248 (OUTLIER) cc_final: 0.7846 (tt0) REVERT: C 205 ASN cc_start: 0.7524 (OUTLIER) cc_final: 0.7184 (m110) REVERT: C 221 ASP cc_start: 0.8533 (t70) cc_final: 0.8300 (t0) REVERT: C 292 GLN cc_start: 0.7931 (mt0) cc_final: 0.7560 (mp10) REVERT: C 352 PHE cc_start: 0.7187 (m-10) cc_final: 0.6736 (t80) REVERT: C 356 TYR cc_start: 0.8927 (t80) cc_final: 0.8299 (t80) REVERT: C 395 MET cc_start: 0.8609 (mmp) cc_final: 0.8358 (mmm) REVERT: C 439 THR cc_start: 0.8926 (OUTLIER) cc_final: 0.8679 (m) REVERT: C 592 GLU cc_start: 0.6969 (OUTLIER) cc_final: 0.6711 (mm-30) REVERT: C 612 PHE cc_start: 0.6990 (m-80) cc_final: 0.6124 (m-80) REVERT: C 654 GLU cc_start: 0.7517 (mm-30) cc_final: 0.7283 (mm-30) REVERT: C 665 GLU cc_start: 0.7059 (mp0) cc_final: 0.6743 (mp0) REVERT: C 697 MET cc_start: 0.8903 (mtt) cc_final: 0.8661 (mtt) REVERT: C 736 ASP cc_start: 0.7388 (m-30) cc_final: 0.7120 (m-30) REVERT: C 779 ASN cc_start: 0.7675 (t0) cc_final: 0.7399 (t0) REVERT: C 783 MET cc_start: 0.6752 (OUTLIER) cc_final: 0.6194 (tpt) REVERT: C 792 LEU cc_start: 0.8171 (mt) cc_final: 0.7901 (mp) REVERT: C 799 GLN cc_start: 0.8261 (tt0) cc_final: 0.7970 (tt0) REVERT: C 836 GLU cc_start: 0.7838 (mt-10) cc_final: 0.7625 (mm-30) REVERT: C 862 SER cc_start: 0.8626 (m) cc_final: 0.8321 (p) REVERT: C 973 THR cc_start: 0.9074 (m) cc_final: 0.8677 (p) outliers start: 78 outliers final: 46 residues processed: 572 average time/residue: 0.6515 time to fit residues: 428.6918 Evaluate side-chains 581 residues out of total 2565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 524 time to evaluate : 0.882 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 SER Chi-restraints excluded: chain A residue 89 GLU Chi-restraints excluded: chain A residue 100 VAL Chi-restraints excluded: chain A residue 241 SER Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 477 SER Chi-restraints excluded: chain A residue 483 LEU Chi-restraints excluded: chain A residue 543 LEU Chi-restraints excluded: chain A residue 595 LEU Chi-restraints excluded: chain A residue 634 SER Chi-restraints excluded: chain A residue 655 THR Chi-restraints excluded: chain A residue 732 VAL Chi-restraints excluded: chain A residue 799 GLN Chi-restraints excluded: chain A residue 802 LYS Chi-restraints excluded: chain A residue 828 SER Chi-restraints excluded: chain A residue 868 LEU Chi-restraints excluded: chain A residue 946 GLU Chi-restraints excluded: chain B residue 37 SER Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 64 LEU Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 231 THR Chi-restraints excluded: chain B residue 235 SER Chi-restraints excluded: chain B residue 312 GLU Chi-restraints excluded: chain B residue 325 ILE Chi-restraints excluded: chain B residue 398 MET Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 449 LEU Chi-restraints excluded: chain B residue 518 ASP Chi-restraints excluded: chain B residue 526 LEU Chi-restraints excluded: chain B residue 535 THR Chi-restraints excluded: chain B residue 717 ASN Chi-restraints excluded: chain B residue 732 VAL Chi-restraints excluded: chain B residue 893 MET Chi-restraints excluded: chain B residue 895 VAL Chi-restraints excluded: chain B residue 913 MET Chi-restraints excluded: chain B residue 945 GLU Chi-restraints excluded: chain B residue 960 LEU Chi-restraints excluded: chain B residue 977 ILE Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 108 GLN Chi-restraints excluded: chain C residue 137 LEU Chi-restraints excluded: chain C residue 176 GLN Chi-restraints excluded: chain C residue 205 ASN Chi-restraints excluded: chain C residue 265 VAL Chi-restraints excluded: chain C residue 342 HIS Chi-restraints excluded: chain C residue 357 LEU Chi-restraints excluded: chain C residue 420 MET Chi-restraints excluded: chain C residue 439 THR Chi-restraints excluded: chain C residue 572 SER Chi-restraints excluded: chain C residue 592 GLU Chi-restraints excluded: chain C residue 633 THR Chi-restraints excluded: chain C residue 709 ASN Chi-restraints excluded: chain C residue 759 MET Chi-restraints excluded: chain C residue 783 MET Chi-restraints excluded: chain C residue 986 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 231 optimal weight: 5.9990 chunk 208 optimal weight: 10.0000 chunk 88 optimal weight: 0.9980 chunk 128 optimal weight: 10.0000 chunk 299 optimal weight: 0.9980 chunk 67 optimal weight: 10.0000 chunk 248 optimal weight: 8.9990 chunk 209 optimal weight: 7.9990 chunk 57 optimal weight: 2.9990 chunk 117 optimal weight: 5.9990 chunk 212 optimal weight: 20.0000 overall best weight: 3.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 125 GLN A 267 ASN A 586 ASN A 593 ASN B 109 ASN B 342 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.134784 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.115735 restraints weight = 25337.425| |-----------------------------------------------------------------------------| r_work (start): 0.3084 rms_B_bonded: 1.07 r_work: 0.2940 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.2821 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.2821 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8353 moved from start: 0.2473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 24106 Z= 0.149 Angle : 0.560 8.871 32640 Z= 0.291 Chirality : 0.041 0.198 3876 Planarity : 0.005 0.056 4073 Dihedral : 8.980 176.133 3426 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Rotamer: Outliers : 2.50 % Allowed : 18.83 % Favored : 78.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.79 (0.15), residues: 3048 helix: 2.10 (0.13), residues: 1713 sheet: 0.24 (0.21), residues: 543 loop : -0.03 (0.22), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 7 TYR 0.023 0.001 TYR A 49 PHE 0.028 0.001 PHE B 509 TRP 0.007 0.001 TRP A 610 HIS 0.002 0.001 HIS C 534 Details of bonding type rmsd covalent geometry : bond 0.00355 (24106) covalent geometry : angle 0.55995 (32640) hydrogen bonds : bond 0.04658 ( 1522) hydrogen bonds : angle 4.27808 ( 4635) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6096 Ramachandran restraints generated. 3048 Oldfield, 0 Emsley, 3048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6096 Ramachandran restraints generated. 3048 Oldfield, 0 Emsley, 3048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 587 residues out of total 2565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 523 time to evaluate : 0.932 Fit side-chains revert: symmetry clash REVERT: A 73 LYS cc_start: 0.8100 (mtmt) cc_final: 0.7707 (pttp) REVERT: A 89 GLU cc_start: 0.8287 (OUTLIER) cc_final: 0.7222 (tm-30) REVERT: A 147 ASN cc_start: 0.7745 (m110) cc_final: 0.7332 (m-40) REVERT: A 201 SER cc_start: 0.8856 (p) cc_final: 0.8384 (m) REVERT: A 209 GLU cc_start: 0.7670 (pt0) cc_final: 0.7424 (tt0) REVERT: A 276 ASN cc_start: 0.8376 (OUTLIER) cc_final: 0.8049 (p0) REVERT: A 314 LYS cc_start: 0.6999 (ttpt) cc_final: 0.6733 (ptmt) REVERT: A 346 GLU cc_start: 0.8825 (mt-10) cc_final: 0.8336 (mt-10) REVERT: A 366 LEU cc_start: 0.8484 (mt) cc_final: 0.8148 (mt) REVERT: A 383 MET cc_start: 0.8922 (mtp) cc_final: 0.8673 (mtp) REVERT: A 605 THR cc_start: 0.8881 (m) cc_final: 0.8615 (m) REVERT: A 642 ASP cc_start: 0.8320 (m-30) cc_final: 0.8046 (m-30) REVERT: A 772 MET cc_start: 0.9036 (mmt) cc_final: 0.8524 (mmt) REVERT: A 802 LYS cc_start: 0.8276 (OUTLIER) cc_final: 0.7855 (mtpp) REVERT: A 864 MET cc_start: 0.8689 (ttp) cc_final: 0.8468 (ttt) REVERT: A 893 MET cc_start: 0.8878 (mmm) cc_final: 0.8590 (mmm) REVERT: A 942 MET cc_start: 0.7994 (tpp) cc_final: 0.7299 (tmm) REVERT: A 988 GLU cc_start: 0.7773 (mp0) cc_final: 0.7465 (mp0) REVERT: A 1018 PHE cc_start: 0.8280 (t80) cc_final: 0.8039 (t80) REVERT: B 68 GLU cc_start: 0.7511 (mm-30) cc_final: 0.7271 (mm-30) REVERT: B 111 ILE cc_start: 0.8646 (pt) cc_final: 0.8342 (pt) REVERT: B 138 MET cc_start: 0.8926 (ptm) cc_final: 0.8489 (ptp) REVERT: B 307 ARG cc_start: 0.7638 (ttm110) cc_final: 0.7361 (mtt-85) REVERT: B 312 GLU cc_start: 0.6927 (OUTLIER) cc_final: 0.6436 (mp0) REVERT: B 325 ILE cc_start: 0.8540 (OUTLIER) cc_final: 0.8116 (mm) REVERT: B 518 ASP cc_start: 0.7729 (OUTLIER) cc_final: 0.7054 (m-30) REVERT: B 799 GLN cc_start: 0.7855 (tt0) cc_final: 0.7254 (mt0) REVERT: B 942 MET cc_start: 0.8224 (tmt) cc_final: 0.7999 (tmm) REVERT: B 945 GLU cc_start: 0.7468 (OUTLIER) cc_final: 0.6656 (mp0) REVERT: C 8 ARG cc_start: 0.8662 (mtt-85) cc_final: 0.8320 (mtp180) REVERT: C 176 GLN cc_start: 0.8265 (OUTLIER) cc_final: 0.7878 (tt0) REVERT: C 205 ASN cc_start: 0.7622 (OUTLIER) cc_final: 0.7318 (m110) REVERT: C 221 ASP cc_start: 0.8572 (t70) cc_final: 0.8339 (t0) REVERT: C 292 GLN cc_start: 0.8010 (mt0) cc_final: 0.7723 (mp-120) REVERT: C 352 PHE cc_start: 0.7179 (m-10) cc_final: 0.6748 (t80) REVERT: C 356 TYR cc_start: 0.8966 (t80) cc_final: 0.8315 (t80) REVERT: C 395 MET cc_start: 0.8661 (mmp) cc_final: 0.8417 (mmm) REVERT: C 439 THR cc_start: 0.8957 (OUTLIER) cc_final: 0.8695 (m) REVERT: C 561 MET cc_start: 0.8845 (mtp) cc_final: 0.8497 (ttm) REVERT: C 592 GLU cc_start: 0.7017 (OUTLIER) cc_final: 0.6750 (mm-30) REVERT: C 612 PHE cc_start: 0.7038 (m-80) cc_final: 0.6168 (m-80) REVERT: C 654 GLU cc_start: 0.7642 (mm-30) cc_final: 0.7376 (mm-30) REVERT: C 665 GLU cc_start: 0.7071 (mp0) cc_final: 0.6826 (mp0) REVERT: C 697 MET cc_start: 0.8955 (mtt) cc_final: 0.8724 (mtt) REVERT: C 736 ASP cc_start: 0.7432 (m-30) cc_final: 0.7151 (m-30) REVERT: C 779 ASN cc_start: 0.7695 (t0) cc_final: 0.7413 (t0) REVERT: C 783 MET cc_start: 0.6664 (OUTLIER) cc_final: 0.6042 (tpt) REVERT: C 799 GLN cc_start: 0.8366 (tt0) cc_final: 0.8127 (tt0) REVERT: C 836 GLU cc_start: 0.7960 (mt-10) cc_final: 0.7681 (mm-30) REVERT: C 862 SER cc_start: 0.8665 (m) cc_final: 0.8369 (p) outliers start: 64 outliers final: 45 residues processed: 552 average time/residue: 0.6532 time to fit residues: 415.4255 Evaluate side-chains 578 residues out of total 2565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 521 time to evaluate : 0.895 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 SER Chi-restraints excluded: chain A residue 89 GLU Chi-restraints excluded: chain A residue 100 VAL Chi-restraints excluded: chain A residue 241 SER Chi-restraints excluded: chain A residue 276 ASN Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 477 SER Chi-restraints excluded: chain A residue 483 LEU Chi-restraints excluded: chain A residue 595 LEU Chi-restraints excluded: chain A residue 634 SER Chi-restraints excluded: chain A residue 655 THR Chi-restraints excluded: chain A residue 732 VAL Chi-restraints excluded: chain A residue 799 GLN Chi-restraints excluded: chain A residue 802 LYS Chi-restraints excluded: chain A residue 828 SER Chi-restraints excluded: chain A residue 868 LEU Chi-restraints excluded: chain A residue 946 GLU Chi-restraints excluded: chain B residue 37 SER Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 64 LEU Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 231 THR Chi-restraints excluded: chain B residue 235 SER Chi-restraints excluded: chain B residue 312 GLU Chi-restraints excluded: chain B residue 325 ILE Chi-restraints excluded: chain B residue 398 MET Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 449 LEU Chi-restraints excluded: chain B residue 518 ASP Chi-restraints excluded: chain B residue 526 LEU Chi-restraints excluded: chain B residue 535 THR Chi-restraints excluded: chain B residue 717 ASN Chi-restraints excluded: chain B residue 732 VAL Chi-restraints excluded: chain B residue 893 MET Chi-restraints excluded: chain B residue 895 VAL Chi-restraints excluded: chain B residue 913 MET Chi-restraints excluded: chain B residue 945 GLU Chi-restraints excluded: chain B residue 960 LEU Chi-restraints excluded: chain B residue 977 ILE Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 108 GLN Chi-restraints excluded: chain C residue 137 LEU Chi-restraints excluded: chain C residue 176 GLN Chi-restraints excluded: chain C residue 205 ASN Chi-restraints excluded: chain C residue 265 VAL Chi-restraints excluded: chain C residue 357 LEU Chi-restraints excluded: chain C residue 420 MET Chi-restraints excluded: chain C residue 439 THR Chi-restraints excluded: chain C residue 572 SER Chi-restraints excluded: chain C residue 592 GLU Chi-restraints excluded: chain C residue 633 THR Chi-restraints excluded: chain C residue 639 MET Chi-restraints excluded: chain C residue 709 ASN Chi-restraints excluded: chain C residue 759 MET Chi-restraints excluded: chain C residue 783 MET Chi-restraints excluded: chain C residue 986 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 274 optimal weight: 5.9990 chunk 59 optimal weight: 2.9990 chunk 163 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 16 optimal weight: 10.0000 chunk 151 optimal weight: 3.9990 chunk 278 optimal weight: 1.9990 chunk 185 optimal weight: 5.9990 chunk 143 optimal weight: 2.9990 chunk 84 optimal weight: 10.0000 chunk 99 optimal weight: 5.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 267 ASN A 586 ASN A 593 ASN B 342 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.134385 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.115521 restraints weight = 25238.885| |-----------------------------------------------------------------------------| r_work (start): 0.3081 rms_B_bonded: 1.09 r_work: 0.2945 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.2827 rms_B_bonded: 3.43 restraints_weight: 0.2500 r_work (final): 0.2827 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8340 moved from start: 0.2511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 24106 Z= 0.153 Angle : 0.566 8.916 32640 Z= 0.294 Chirality : 0.041 0.198 3876 Planarity : 0.005 0.056 4073 Dihedral : 8.959 178.431 3426 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Rotamer: Outliers : 2.65 % Allowed : 18.95 % Favored : 78.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.79 (0.15), residues: 3048 helix: 2.08 (0.13), residues: 1712 sheet: 0.24 (0.22), residues: 539 loop : -0.01 (0.22), residues: 797 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 123 TYR 0.023 0.002 TYR A 49 PHE 0.027 0.001 PHE B 509 TRP 0.007 0.001 TRP A 610 HIS 0.002 0.001 HIS C 360 Details of bonding type rmsd covalent geometry : bond 0.00366 (24106) covalent geometry : angle 0.56577 (32640) hydrogen bonds : bond 0.04704 ( 1522) hydrogen bonds : angle 4.29841 ( 4635) =============================================================================== Job complete usr+sys time: 9237.02 seconds wall clock time: 157 minutes 47.66 seconds (9467.66 seconds total)