Starting phenix.real_space_refine on Fri Jun 27 23:43:01 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/3j7h_5995/06_2025/3j7h_5995.cif Found real_map, /net/cci-nas-00/data/ceres_data/3j7h_5995/06_2025/3j7h_5995.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/3j7h_5995/06_2025/3j7h_5995.map" default_real_map = "/net/cci-nas-00/data/ceres_data/3j7h_5995/06_2025/3j7h_5995.map" model { file = "/net/cci-nas-00/data/ceres_data/3j7h_5995/06_2025/3j7h_5995.cif" } default_model = "/net/cci-nas-00/data/ceres_data/3j7h_5995/06_2025/3j7h_5995.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.006 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 Mg 4 5.21 5 S 156 5.16 5 C 20760 2.51 5 N 5808 2.21 5 O 6100 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 232 residue(s): 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 32828 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 8206 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1022, 8206 Classifications: {'peptide': 1022} Link IDs: {'CIS': 11, 'PCIS': 5, 'PTRANS': 57, 'TRANS': 948} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Restraints were copied for chains: C, B, D Time building chain proxies: 21.98, per 1000 atoms: 0.67 Number of scatterers: 32828 At special positions: 0 Unit cell: (191.887, 147.262, 100.088, 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 156 16.00 Mg 4 11.99 O 6100 8.00 N 5808 7.00 C 20760 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=20, symmetry=0 Number of additional bonds: simple=20, symmetry=0 Coordination: Other bonds: Time building additional restraints: 8.43 Conformation dependent library (CDL) restraints added in 4.1 seconds 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7608 Finding SS restraints... Secondary structure from input PDB file: 76 helices and 52 sheets defined 16.8% alpha, 33.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.52 Creating SS restraints... Processing helix chain 'A' and resid 6 through 12 Processing helix chain 'A' and resid 38 through 45 removed outlier: 3.728A pdb=" N ALA A 42 " --> pdb=" O ASN A 38 " (cutoff:3.500A) Processing helix chain 'A' and resid 70 through 75 removed outlier: 3.545A pdb=" N LEU A 74 " --> pdb=" O GLU A 71 " (cutoff:3.500A) Processing helix chain 'A' and resid 89 through 94 Processing helix chain 'A' and resid 130 through 136 removed outlier: 3.732A pdb=" N LEU A 134 " --> pdb=" O ASP A 130 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N GLU A 136 " --> pdb=" O SER A 132 " (cutoff:3.500A) Processing helix chain 'A' and resid 192 through 197 Processing helix chain 'A' and resid 368 through 382 removed outlier: 3.556A pdb=" N MET A 372 " --> pdb=" O ASP A 368 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N VAL A 373 " --> pdb=" O GLU A 369 " (cutoff:3.500A) Processing helix chain 'A' and resid 395 through 406 removed outlier: 3.812A pdb=" N TYR A 399 " --> pdb=" O HIS A 395 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N THR A 400 " --> pdb=" O PRO A 396 " (cutoff:3.500A) Processing helix chain 'A' and resid 424 through 429 Processing helix chain 'A' and resid 432 through 448 removed outlier: 3.513A pdb=" N GLU A 438 " --> pdb=" O PRO A 434 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N ARG A 439 " --> pdb=" O ALA A 435 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N VAL A 440 " --> pdb=" O MET A 436 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N GLN A 445 " --> pdb=" O THR A 441 " (cutoff:3.500A) Processing helix chain 'A' and resid 465 through 479 removed outlier: 3.574A pdb=" N ASP A 469 " --> pdb=" O GLY A 465 " (cutoff:3.500A) Processing helix chain 'A' and resid 519 through 526 removed outlier: 3.693A pdb=" N SER A 525 " --> pdb=" O LYS A 521 " (cutoff:3.500A) Processing helix chain 'A' and resid 548 through 559 removed outlier: 3.576A pdb=" N TYR A 552 " --> pdb=" O GLY A 548 " (cutoff:3.500A) Processing helix chain 'A' and resid 598 through 603 removed outlier: 3.819A pdb=" N PHE A 601 " --> pdb=" O ASP A 598 " (cutoff:3.500A) Processing helix chain 'A' and resid 614 through 625 removed outlier: 4.014A pdb=" N THR A 618 " --> pdb=" O HIS A 614 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N GLU A 619 " --> pdb=" O PRO A 615 " (cutoff:3.500A) Processing helix chain 'A' and resid 789 through 794 Processing helix chain 'A' and resid 805 through 814 Processing helix chain 'A' and resid 922 through 926 removed outlier: 4.107A pdb=" N TYR A 926 " --> pdb=" O LEU A 922 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 922 through 926' Processing helix chain 'A' and resid 963 through 970 Processing helix chain 'B' and resid 6 through 12 Processing helix chain 'B' and resid 38 through 45 removed outlier: 3.728A pdb=" N ALA B 42 " --> pdb=" O ASN B 38 " (cutoff:3.500A) Processing helix chain 'B' and resid 70 through 75 removed outlier: 3.544A pdb=" N LEU B 74 " --> pdb=" O GLU B 71 " (cutoff:3.500A) Processing helix chain 'B' and resid 89 through 94 Processing helix chain 'B' and resid 130 through 136 removed outlier: 3.732A pdb=" N LEU B 134 " --> pdb=" O ASP B 130 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N GLU B 136 " --> pdb=" O SER B 132 " (cutoff:3.500A) Processing helix chain 'B' and resid 192 through 197 Processing helix chain 'B' and resid 368 through 382 removed outlier: 3.557A pdb=" N MET B 372 " --> pdb=" O ASP B 368 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N VAL B 373 " --> pdb=" O GLU B 369 " (cutoff:3.500A) Processing helix chain 'B' and resid 395 through 406 removed outlier: 3.812A pdb=" N TYR B 399 " --> pdb=" O HIS B 395 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N THR B 400 " --> pdb=" O PRO B 396 " (cutoff:3.500A) Processing helix chain 'B' and resid 424 through 429 Processing helix chain 'B' and resid 432 through 448 removed outlier: 3.513A pdb=" N GLU B 438 " --> pdb=" O PRO B 434 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N ARG B 439 " --> pdb=" O ALA B 435 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N VAL B 440 " --> pdb=" O MET B 436 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N GLN B 445 " --> pdb=" O THR B 441 " (cutoff:3.500A) Processing helix chain 'B' and resid 465 through 479 removed outlier: 3.574A pdb=" N ASP B 469 " --> pdb=" O GLY B 465 " (cutoff:3.500A) Processing helix chain 'B' and resid 519 through 526 removed outlier: 3.693A pdb=" N SER B 525 " --> pdb=" O LYS B 521 " (cutoff:3.500A) Processing helix chain 'B' and resid 548 through 559 removed outlier: 3.576A pdb=" N TYR B 552 " --> pdb=" O GLY B 548 " (cutoff:3.500A) Processing helix chain 'B' and resid 598 through 603 removed outlier: 3.819A pdb=" N PHE B 601 " --> pdb=" O ASP B 598 " (cutoff:3.500A) Processing helix chain 'B' and resid 614 through 625 removed outlier: 4.013A pdb=" N THR B 618 " --> pdb=" O HIS B 614 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N GLU B 619 " --> pdb=" O PRO B 615 " (cutoff:3.500A) Processing helix chain 'B' and resid 789 through 794 Processing helix chain 'B' and resid 805 through 814 Processing helix chain 'B' and resid 922 through 926 removed outlier: 4.107A pdb=" N TYR B 926 " --> pdb=" O LEU B 922 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 922 through 926' Processing helix chain 'B' and resid 963 through 970 Processing helix chain 'C' and resid 6 through 12 Processing helix chain 'C' and resid 38 through 45 removed outlier: 3.729A pdb=" N ALA C 42 " --> pdb=" O ASN C 38 " (cutoff:3.500A) Processing helix chain 'C' and resid 70 through 75 removed outlier: 3.545A pdb=" N LEU C 74 " --> pdb=" O GLU C 71 " (cutoff:3.500A) Processing helix chain 'C' and resid 89 through 94 Processing helix chain 'C' and resid 130 through 136 removed outlier: 3.732A pdb=" N LEU C 134 " --> pdb=" O ASP C 130 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N GLU C 136 " --> pdb=" O SER C 132 " (cutoff:3.500A) Processing helix chain 'C' and resid 192 through 197 Processing helix chain 'C' and resid 368 through 382 removed outlier: 3.556A pdb=" N MET C 372 " --> pdb=" O ASP C 368 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N VAL C 373 " --> pdb=" O GLU C 369 " (cutoff:3.500A) Processing helix chain 'C' and resid 395 through 406 removed outlier: 3.813A pdb=" N TYR C 399 " --> pdb=" O HIS C 395 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N THR C 400 " --> pdb=" O PRO C 396 " (cutoff:3.500A) Processing helix chain 'C' and resid 424 through 429 Processing helix chain 'C' and resid 432 through 448 removed outlier: 3.512A pdb=" N GLU C 438 " --> pdb=" O PRO C 434 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N ARG C 439 " --> pdb=" O ALA C 435 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N VAL C 440 " --> pdb=" O MET C 436 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N GLN C 445 " --> pdb=" O THR C 441 " (cutoff:3.500A) Processing helix chain 'C' and resid 465 through 479 removed outlier: 3.574A pdb=" N ASP C 469 " --> pdb=" O GLY C 465 " (cutoff:3.500A) Processing helix chain 'C' and resid 519 through 526 removed outlier: 3.693A pdb=" N SER C 525 " --> pdb=" O LYS C 521 " (cutoff:3.500A) Processing helix chain 'C' and resid 548 through 559 removed outlier: 3.575A pdb=" N TYR C 552 " --> pdb=" O GLY C 548 " (cutoff:3.500A) Processing helix chain 'C' and resid 598 through 603 removed outlier: 3.819A pdb=" N PHE C 601 " --> pdb=" O ASP C 598 " (cutoff:3.500A) Processing helix chain 'C' and resid 614 through 625 removed outlier: 4.014A pdb=" N THR C 618 " --> pdb=" O HIS C 614 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N GLU C 619 " --> pdb=" O PRO C 615 " (cutoff:3.500A) Processing helix chain 'C' and resid 789 through 794 Processing helix chain 'C' and resid 805 through 814 Processing helix chain 'C' and resid 922 through 926 removed outlier: 4.108A pdb=" N TYR C 926 " --> pdb=" O LEU C 922 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 922 through 926' Processing helix chain 'C' and resid 963 through 970 Processing helix chain 'D' and resid 6 through 12 Processing helix chain 'D' and resid 38 through 45 removed outlier: 3.729A pdb=" N ALA D 42 " --> pdb=" O ASN D 38 " (cutoff:3.500A) Processing helix chain 'D' and resid 70 through 75 removed outlier: 3.545A pdb=" N LEU D 74 " --> pdb=" O GLU D 71 " (cutoff:3.500A) Processing helix chain 'D' and resid 89 through 94 Processing helix chain 'D' and resid 130 through 136 removed outlier: 3.732A pdb=" N LEU D 134 " --> pdb=" O ASP D 130 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N GLU D 136 " --> pdb=" O SER D 132 " (cutoff:3.500A) Processing helix chain 'D' and resid 192 through 197 Processing helix chain 'D' and resid 368 through 382 removed outlier: 3.556A pdb=" N MET D 372 " --> pdb=" O ASP D 368 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N VAL D 373 " --> pdb=" O GLU D 369 " (cutoff:3.500A) Processing helix chain 'D' and resid 395 through 406 removed outlier: 3.812A pdb=" N TYR D 399 " --> pdb=" O HIS D 395 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N THR D 400 " --> pdb=" O PRO D 396 " (cutoff:3.500A) Processing helix chain 'D' and resid 424 through 429 Processing helix chain 'D' and resid 432 through 448 removed outlier: 3.512A pdb=" N GLU D 438 " --> pdb=" O PRO D 434 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N ARG D 439 " --> pdb=" O ALA D 435 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N VAL D 440 " --> pdb=" O MET D 436 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N GLN D 445 " --> pdb=" O THR D 441 " (cutoff:3.500A) Processing helix chain 'D' and resid 465 through 479 removed outlier: 3.574A pdb=" N ASP D 469 " --> pdb=" O GLY D 465 " (cutoff:3.500A) Processing helix chain 'D' and resid 519 through 526 removed outlier: 3.694A pdb=" N SER D 525 " --> pdb=" O LYS D 521 " (cutoff:3.500A) Processing helix chain 'D' and resid 548 through 559 removed outlier: 3.576A pdb=" N TYR D 552 " --> pdb=" O GLY D 548 " (cutoff:3.500A) Processing helix chain 'D' and resid 598 through 603 removed outlier: 3.819A pdb=" N PHE D 601 " --> pdb=" O ASP D 598 " (cutoff:3.500A) Processing helix chain 'D' and resid 614 through 625 removed outlier: 4.014A pdb=" N THR D 618 " --> pdb=" O HIS D 614 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N GLU D 619 " --> pdb=" O PRO D 615 " (cutoff:3.500A) Processing helix chain 'D' and resid 789 through 794 Processing helix chain 'D' and resid 805 through 814 Processing helix chain 'D' and resid 922 through 926 removed outlier: 4.106A pdb=" N TYR D 926 " --> pdb=" O LEU D 922 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 922 through 926' Processing helix chain 'D' and resid 963 through 970 Processing sheet with id=A, first strand: chain 'A' and resid 52 through 53 Processing sheet with id=B, first strand: chain 'A' and resid 83 through 86 removed outlier: 3.604A pdb=" N GLY A 56 " --> pdb=" O VAL A 86 " (cutoff:3.500A) removed outlier: 8.863A pdb=" N GLU A 57 " --> pdb=" O THR A 126 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N THR A 126 " --> pdb=" O GLU A 57 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N VAL A 129 " --> pdb=" O GLY A 180 " (cutoff:3.500A) removed outlier: 4.698A pdb=" N GLY A 180 " --> pdb=" O VAL A 129 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ALA A 149 " --> pdb=" O LEU A 189 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N PHE A 150 " --> pdb=" O TYR A 161 " (cutoff:3.500A) removed outlier: 4.688A pdb=" N TYR A 161 " --> pdb=" O PHE A 150 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N LEU A 152 " --> pdb=" O VAL A 159 " (cutoff:3.500A) Processing sheet with id=C, first strand: chain 'A' and resid 222 through 231 Processing sheet with id=D, first strand: chain 'A' and resid 265 through 273 removed outlier: 4.645A pdb=" N GLN A 266 " --> pdb=" O GLN A 262 " (cutoff:3.500A) removed outlier: 5.835A pdb=" N GLN A 262 " --> pdb=" O GLN A 266 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ALA A 268 " --> pdb=" O LEU A 260 " (cutoff:3.500A) Processing sheet with id=E, first strand: chain 'A' and resid 335 through 338 Processing sheet with id=F, first strand: chain 'A' and resid 453 through 457 removed outlier: 7.795A pdb=" N VAL A 409 " --> pdb=" O ILE A 454 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N TRP A 456 " --> pdb=" O VAL A 409 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N ASP A 411 " --> pdb=" O TRP A 456 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N CYS A 389 " --> pdb=" O VAL A 410 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N GLU A 412 " --> pdb=" O CYS A 389 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N GLY A 353 " --> pdb=" O VAL A 567 " (cutoff:3.500A) Processing sheet with id=G, first strand: chain 'A' and resid 511 through 512 Processing sheet with id=H, first strand: chain 'A' and resid 575 through 578 Processing sheet with id=I, first strand: chain 'A' and resid 628 through 632 Processing sheet with id=J, first strand: chain 'A' and resid 661 through 670 removed outlier: 5.864A pdb=" N LEU A 658 " --> pdb=" O PRO A 662 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N GLU A 650 " --> pdb=" O LEU A 670 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N GLY A 692 " --> pdb=" O GLU A 724 " (cutoff:3.500A) removed outlier: 5.599A pdb=" N GLU A 724 " --> pdb=" O GLY A 692 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N LEU A 694 " --> pdb=" O LEU A 722 " (cutoff:3.500A) Processing sheet with id=K, first strand: chain 'A' and resid 739 through 742 removed outlier: 3.545A pdb=" N GLN A 767 " --> pdb=" O GLN A 757 " (cutoff:3.500A) Processing sheet with id=L, first strand: chain 'A' and resid 776 through 783 removed outlier: 5.749A pdb=" N GLN A 887 " --> pdb=" O PRO A 779 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ARG A 781 " --> pdb=" O ASN A 885 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N ILE A 882 " --> pdb=" O GLY A 988 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N PHE A 989 " --> pdb=" O ASP A 954 " (cutoff:3.500A) removed outlier: 12.188A pdb=" N ASP A 954 " --> pdb=" O PHE A 989 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N ASP A 954 " --> pdb=" O GLN A1017 " (cutoff:3.500A) removed outlier: 5.782A pdb=" N GLN A1017 " --> pdb=" O ASP A 954 " (cutoff:3.500A) removed outlier: 10.590A pdb=" N GLN A 956 " --> pdb=" O HIS A1015 " (cutoff:3.500A) removed outlier: 13.701A pdb=" N HIS A1015 " --> pdb=" O GLN A 956 " (cutoff:3.500A) removed outlier: 20.254A pdb=" N ASN A 958 " --> pdb=" O ARG A1013 " (cutoff:3.500A) removed outlier: 23.560A pdb=" N ARG A1013 " --> pdb=" O ASN A 958 " (cutoff:3.500A) removed outlier: 4.929A pdb=" N THR A 848 " --> pdb=" O HIS A 844 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N HIS A 844 " --> pdb=" O THR A 848 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N PHE A 850 " --> pdb=" O TRP A 842 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N ALA A 841 " --> pdb=" O LEU A 822 " (cutoff:3.500A) removed outlier: 5.593A pdb=" N LEU A 822 " --> pdb=" O ALA A 841 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N GLN A 843 " --> pdb=" O ALA A 820 " (cutoff:3.500A) removed outlier: 6.174A pdb=" N ALA A 820 " --> pdb=" O GLN A 843 " (cutoff:3.500A) Processing sheet with id=M, first strand: chain 'A' and resid 776 through 783 removed outlier: 5.749A pdb=" N GLN A 887 " --> pdb=" O PRO A 779 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ARG A 781 " --> pdb=" O ASN A 885 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N ILE A 882 " --> pdb=" O GLY A 988 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N PHE A 989 " --> pdb=" O ASP A 954 " (cutoff:3.500A) removed outlier: 12.188A pdb=" N ASP A 954 " --> pdb=" O PHE A 989 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N ARG A 942 " --> pdb=" O GLY A 953 " (cutoff:3.500A) removed outlier: 6.206A pdb=" N PHE A 955 " --> pdb=" O GLY A 940 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N GLY A 940 " --> pdb=" O PHE A 955 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N THR A 941 " --> pdb=" O LEU A 900 " (cutoff:3.500A) removed outlier: 7.291A pdb=" N LEU A 900 " --> pdb=" O THR A 941 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N GLY A 899 " --> pdb=" O ASP A 916 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N CYS A 914 " --> pdb=" O GLY A 901 " (cutoff:3.500A) Processing sheet with id=N, first strand: chain 'B' and resid 52 through 53 Processing sheet with id=O, first strand: chain 'B' and resid 83 through 86 removed outlier: 3.604A pdb=" N GLY B 56 " --> pdb=" O VAL B 86 " (cutoff:3.500A) removed outlier: 8.863A pdb=" N GLU B 57 " --> pdb=" O THR B 126 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N THR B 126 " --> pdb=" O GLU B 57 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N VAL B 129 " --> pdb=" O GLY B 180 " (cutoff:3.500A) removed outlier: 4.698A pdb=" N GLY B 180 " --> pdb=" O VAL B 129 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ALA B 149 " --> pdb=" O LEU B 189 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N PHE B 150 " --> pdb=" O TYR B 161 " (cutoff:3.500A) removed outlier: 4.688A pdb=" N TYR B 161 " --> pdb=" O PHE B 150 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N LEU B 152 " --> pdb=" O VAL B 159 " (cutoff:3.500A) Processing sheet with id=P, first strand: chain 'B' and resid 222 through 231 Processing sheet with id=Q, first strand: chain 'B' and resid 265 through 273 removed outlier: 4.645A pdb=" N GLN B 266 " --> pdb=" O GLN B 262 " (cutoff:3.500A) removed outlier: 5.835A pdb=" N GLN B 262 " --> pdb=" O GLN B 266 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ALA B 268 " --> pdb=" O LEU B 260 " (cutoff:3.500A) Processing sheet with id=R, first strand: chain 'B' and resid 335 through 338 Processing sheet with id=S, first strand: chain 'B' and resid 453 through 457 removed outlier: 7.795A pdb=" N VAL B 409 " --> pdb=" O ILE B 454 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N TRP B 456 " --> pdb=" O VAL B 409 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N ASP B 411 " --> pdb=" O TRP B 456 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N CYS B 389 " --> pdb=" O VAL B 410 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N GLU B 412 " --> pdb=" O CYS B 389 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N GLY B 353 " --> pdb=" O VAL B 567 " (cutoff:3.500A) Processing sheet with id=T, first strand: chain 'B' and resid 511 through 512 Processing sheet with id=U, first strand: chain 'B' and resid 575 through 578 Processing sheet with id=V, first strand: chain 'B' and resid 628 through 632 Processing sheet with id=W, first strand: chain 'B' and resid 661 through 670 removed outlier: 5.864A pdb=" N LEU B 658 " --> pdb=" O PRO B 662 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N GLU B 650 " --> pdb=" O LEU B 670 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N GLY B 692 " --> pdb=" O GLU B 724 " (cutoff:3.500A) removed outlier: 5.599A pdb=" N GLU B 724 " --> pdb=" O GLY B 692 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N LEU B 694 " --> pdb=" O LEU B 722 " (cutoff:3.500A) Processing sheet with id=X, first strand: chain 'B' and resid 739 through 742 removed outlier: 3.545A pdb=" N GLN B 767 " --> pdb=" O GLN B 757 " (cutoff:3.500A) Processing sheet with id=Y, first strand: chain 'B' and resid 776 through 783 removed outlier: 5.748A pdb=" N GLN B 887 " --> pdb=" O PRO B 779 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ARG B 781 " --> pdb=" O ASN B 885 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N ILE B 882 " --> pdb=" O GLY B 988 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N PHE B 989 " --> pdb=" O ASP B 954 " (cutoff:3.500A) removed outlier: 12.187A pdb=" N ASP B 954 " --> pdb=" O PHE B 989 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N ASP B 954 " --> pdb=" O GLN B1017 " (cutoff:3.500A) removed outlier: 5.782A pdb=" N GLN B1017 " --> pdb=" O ASP B 954 " (cutoff:3.500A) removed outlier: 10.590A pdb=" N GLN B 956 " --> pdb=" O HIS B1015 " (cutoff:3.500A) removed outlier: 13.701A pdb=" N HIS B1015 " --> pdb=" O GLN B 956 " (cutoff:3.500A) removed outlier: 20.254A pdb=" N ASN B 958 " --> pdb=" O ARG B1013 " (cutoff:3.500A) removed outlier: 23.560A pdb=" N ARG B1013 " --> pdb=" O ASN B 958 " (cutoff:3.500A) removed outlier: 4.929A pdb=" N THR B 848 " --> pdb=" O HIS B 844 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N HIS B 844 " --> pdb=" O THR B 848 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N PHE B 850 " --> pdb=" O TRP B 842 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N ALA B 841 " --> pdb=" O LEU B 822 " (cutoff:3.500A) removed outlier: 5.594A pdb=" N LEU B 822 " --> pdb=" O ALA B 841 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N GLN B 843 " --> pdb=" O ALA B 820 " (cutoff:3.500A) removed outlier: 6.173A pdb=" N ALA B 820 " --> pdb=" O GLN B 843 " (cutoff:3.500A) Processing sheet with id=Z, first strand: chain 'B' and resid 776 through 783 removed outlier: 5.748A pdb=" N GLN B 887 " --> pdb=" O PRO B 779 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ARG B 781 " --> pdb=" O ASN B 885 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N ILE B 882 " --> pdb=" O GLY B 988 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N PHE B 989 " --> pdb=" O ASP B 954 " (cutoff:3.500A) removed outlier: 12.187A pdb=" N ASP B 954 " --> pdb=" O PHE B 989 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ARG B 942 " --> pdb=" O GLY B 953 " (cutoff:3.500A) removed outlier: 6.206A pdb=" N PHE B 955 " --> pdb=" O GLY B 940 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N GLY B 940 " --> pdb=" O PHE B 955 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N THR B 941 " --> pdb=" O LEU B 900 " (cutoff:3.500A) removed outlier: 7.291A pdb=" N LEU B 900 " --> pdb=" O THR B 941 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N GLY B 899 " --> pdb=" O ASP B 916 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N CYS B 914 " --> pdb=" O GLY B 901 " (cutoff:3.500A) Processing sheet with id=AA, first strand: chain 'C' and resid 52 through 53 Processing sheet with id=AB, first strand: chain 'C' and resid 83 through 86 removed outlier: 3.604A pdb=" N GLY C 56 " --> pdb=" O VAL C 86 " (cutoff:3.500A) removed outlier: 8.862A pdb=" N GLU C 57 " --> pdb=" O THR C 126 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N THR C 126 " --> pdb=" O GLU C 57 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N VAL C 129 " --> pdb=" O GLY C 180 " (cutoff:3.500A) removed outlier: 4.698A pdb=" N GLY C 180 " --> pdb=" O VAL C 129 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ALA C 149 " --> pdb=" O LEU C 189 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N PHE C 150 " --> pdb=" O TYR C 161 " (cutoff:3.500A) removed outlier: 4.689A pdb=" N TYR C 161 " --> pdb=" O PHE C 150 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N LEU C 152 " --> pdb=" O VAL C 159 " (cutoff:3.500A) Processing sheet with id=AC, first strand: chain 'C' and resid 222 through 231 Processing sheet with id=AD, first strand: chain 'C' and resid 265 through 273 removed outlier: 4.645A pdb=" N GLN C 266 " --> pdb=" O GLN C 262 " (cutoff:3.500A) removed outlier: 5.833A pdb=" N GLN C 262 " --> pdb=" O GLN C 266 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ALA C 268 " --> pdb=" O LEU C 260 " (cutoff:3.500A) Processing sheet with id=AE, first strand: chain 'C' and resid 335 through 338 Processing sheet with id=AF, first strand: chain 'C' and resid 453 through 457 removed outlier: 7.795A pdb=" N VAL C 409 " --> pdb=" O ILE C 454 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N TRP C 456 " --> pdb=" O VAL C 409 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N ASP C 411 " --> pdb=" O TRP C 456 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N CYS C 389 " --> pdb=" O VAL C 410 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N GLU C 412 " --> pdb=" O CYS C 389 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N GLY C 353 " --> pdb=" O VAL C 567 " (cutoff:3.500A) Processing sheet with id=AG, first strand: chain 'C' and resid 511 through 512 Processing sheet with id=AH, first strand: chain 'C' and resid 575 through 578 Processing sheet with id=AI, first strand: chain 'C' and resid 628 through 632 Processing sheet with id=AJ, first strand: chain 'C' and resid 661 through 670 removed outlier: 5.864A pdb=" N LEU C 658 " --> pdb=" O PRO C 662 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N GLU C 650 " --> pdb=" O LEU C 670 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N GLY C 692 " --> pdb=" O GLU C 724 " (cutoff:3.500A) removed outlier: 5.599A pdb=" N GLU C 724 " --> pdb=" O GLY C 692 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N LEU C 694 " --> pdb=" O LEU C 722 " (cutoff:3.500A) Processing sheet with id=AK, first strand: chain 'C' and resid 739 through 742 removed outlier: 3.545A pdb=" N GLN C 767 " --> pdb=" O GLN C 757 " (cutoff:3.500A) Processing sheet with id=AL, first strand: chain 'C' and resid 776 through 783 removed outlier: 5.749A pdb=" N GLN C 887 " --> pdb=" O PRO C 779 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ARG C 781 " --> pdb=" O ASN C 885 " (cutoff:3.500A) removed outlier: 7.014A pdb=" N ILE C 882 " --> pdb=" O GLY C 988 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N PHE C 989 " --> pdb=" O ASP C 954 " (cutoff:3.500A) removed outlier: 12.188A pdb=" N ASP C 954 " --> pdb=" O PHE C 989 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N ASP C 954 " --> pdb=" O GLN C1017 " (cutoff:3.500A) removed outlier: 5.782A pdb=" N GLN C1017 " --> pdb=" O ASP C 954 " (cutoff:3.500A) removed outlier: 10.591A pdb=" N GLN C 956 " --> pdb=" O HIS C1015 " (cutoff:3.500A) removed outlier: 13.701A pdb=" N HIS C1015 " --> pdb=" O GLN C 956 " (cutoff:3.500A) removed outlier: 20.254A pdb=" N ASN C 958 " --> pdb=" O ARG C1013 " (cutoff:3.500A) removed outlier: 23.560A pdb=" N ARG C1013 " --> pdb=" O ASN C 958 " (cutoff:3.500A) removed outlier: 4.929A pdb=" N THR C 848 " --> pdb=" O HIS C 844 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N HIS C 844 " --> pdb=" O THR C 848 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N PHE C 850 " --> pdb=" O TRP C 842 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N ALA C 841 " --> pdb=" O LEU C 822 " (cutoff:3.500A) removed outlier: 5.593A pdb=" N LEU C 822 " --> pdb=" O ALA C 841 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N GLN C 843 " --> pdb=" O ALA C 820 " (cutoff:3.500A) removed outlier: 6.174A pdb=" N ALA C 820 " --> pdb=" O GLN C 843 " (cutoff:3.500A) Processing sheet with id=AM, first strand: chain 'C' and resid 776 through 783 removed outlier: 5.749A pdb=" N GLN C 887 " --> pdb=" O PRO C 779 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ARG C 781 " --> pdb=" O ASN C 885 " (cutoff:3.500A) removed outlier: 7.014A pdb=" N ILE C 882 " --> pdb=" O GLY C 988 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N PHE C 989 " --> pdb=" O ASP C 954 " (cutoff:3.500A) removed outlier: 12.188A pdb=" N ASP C 954 " --> pdb=" O PHE C 989 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N ARG C 942 " --> pdb=" O GLY C 953 " (cutoff:3.500A) removed outlier: 6.206A pdb=" N PHE C 955 " --> pdb=" O GLY C 940 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N GLY C 940 " --> pdb=" O PHE C 955 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N THR C 941 " --> pdb=" O LEU C 900 " (cutoff:3.500A) removed outlier: 7.292A pdb=" N LEU C 900 " --> pdb=" O THR C 941 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N GLY C 899 " --> pdb=" O ASP C 916 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N CYS C 914 " --> pdb=" O GLY C 901 " (cutoff:3.500A) Processing sheet with id=AN, first strand: chain 'D' and resid 52 through 53 Processing sheet with id=AO, first strand: chain 'D' and resid 83 through 86 removed outlier: 3.604A pdb=" N GLY D 56 " --> pdb=" O VAL D 86 " (cutoff:3.500A) removed outlier: 8.863A pdb=" N GLU D 57 " --> pdb=" O THR D 126 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N THR D 126 " --> pdb=" O GLU D 57 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N VAL D 129 " --> pdb=" O GLY D 180 " (cutoff:3.500A) removed outlier: 4.697A pdb=" N GLY D 180 " --> pdb=" O VAL D 129 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ALA D 149 " --> pdb=" O LEU D 189 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N PHE D 150 " --> pdb=" O TYR D 161 " (cutoff:3.500A) removed outlier: 4.688A pdb=" N TYR D 161 " --> pdb=" O PHE D 150 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N LEU D 152 " --> pdb=" O VAL D 159 " (cutoff:3.500A) Processing sheet with id=AP, first strand: chain 'D' and resid 222 through 231 Processing sheet with id=AQ, first strand: chain 'D' and resid 265 through 273 removed outlier: 4.644A pdb=" N GLN D 266 " --> pdb=" O GLN D 262 " (cutoff:3.500A) removed outlier: 5.834A pdb=" N GLN D 262 " --> pdb=" O GLN D 266 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ALA D 268 " --> pdb=" O LEU D 260 " (cutoff:3.500A) Processing sheet with id=AR, first strand: chain 'D' and resid 335 through 338 Processing sheet with id=AS, first strand: chain 'D' and resid 453 through 457 removed outlier: 7.795A pdb=" N VAL D 409 " --> pdb=" O ILE D 454 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N TRP D 456 " --> pdb=" O VAL D 409 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N ASP D 411 " --> pdb=" O TRP D 456 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N CYS D 389 " --> pdb=" O VAL D 410 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N GLU D 412 " --> pdb=" O CYS D 389 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N GLY D 353 " --> pdb=" O VAL D 567 " (cutoff:3.500A) Processing sheet with id=AT, first strand: chain 'D' and resid 511 through 512 Processing sheet with id=AU, first strand: chain 'D' and resid 575 through 578 Processing sheet with id=AV, first strand: chain 'D' and resid 628 through 632 Processing sheet with id=AW, first strand: chain 'D' and resid 661 through 670 removed outlier: 5.864A pdb=" N LEU D 658 " --> pdb=" O PRO D 662 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N GLU D 650 " --> pdb=" O LEU D 670 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N GLY D 692 " --> pdb=" O GLU D 724 " (cutoff:3.500A) removed outlier: 5.600A pdb=" N GLU D 724 " --> pdb=" O GLY D 692 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N LEU D 694 " --> pdb=" O LEU D 722 " (cutoff:3.500A) Processing sheet with id=AX, first strand: chain 'D' and resid 739 through 742 removed outlier: 3.545A pdb=" N GLN D 767 " --> pdb=" O GLN D 757 " (cutoff:3.500A) Processing sheet with id=AY, first strand: chain 'D' and resid 776 through 783 removed outlier: 5.748A pdb=" N GLN D 887 " --> pdb=" O PRO D 779 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ARG D 781 " --> pdb=" O ASN D 885 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N ILE D 882 " --> pdb=" O GLY D 988 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N PHE D 989 " --> pdb=" O ASP D 954 " (cutoff:3.500A) removed outlier: 12.188A pdb=" N ASP D 954 " --> pdb=" O PHE D 989 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N ASP D 954 " --> pdb=" O GLN D1017 " (cutoff:3.500A) removed outlier: 5.782A pdb=" N GLN D1017 " --> pdb=" O ASP D 954 " (cutoff:3.500A) removed outlier: 10.591A pdb=" N GLN D 956 " --> pdb=" O HIS D1015 " (cutoff:3.500A) removed outlier: 13.701A pdb=" N HIS D1015 " --> pdb=" O GLN D 956 " (cutoff:3.500A) removed outlier: 20.255A pdb=" N ASN D 958 " --> pdb=" O ARG D1013 " (cutoff:3.500A) removed outlier: 23.561A pdb=" N ARG D1013 " --> pdb=" O ASN D 958 " (cutoff:3.500A) removed outlier: 4.929A pdb=" N THR D 848 " --> pdb=" O HIS D 844 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N HIS D 844 " --> pdb=" O THR D 848 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N PHE D 850 " --> pdb=" O TRP D 842 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N ALA D 841 " --> pdb=" O LEU D 822 " (cutoff:3.500A) removed outlier: 5.594A pdb=" N LEU D 822 " --> pdb=" O ALA D 841 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N GLN D 843 " --> pdb=" O ALA D 820 " (cutoff:3.500A) removed outlier: 6.174A pdb=" N ALA D 820 " --> pdb=" O GLN D 843 " (cutoff:3.500A) Processing sheet with id=AZ, first strand: chain 'D' and resid 776 through 783 removed outlier: 5.748A pdb=" N GLN D 887 " --> pdb=" O PRO D 779 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ARG D 781 " --> pdb=" O ASN D 885 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N ILE D 882 " --> pdb=" O GLY D 988 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N PHE D 989 " --> pdb=" O ASP D 954 " (cutoff:3.500A) removed outlier: 12.188A pdb=" N ASP D 954 " --> pdb=" O PHE D 989 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N ARG D 942 " --> pdb=" O GLY D 953 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N PHE D 955 " --> pdb=" O GLY D 940 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N GLY D 940 " --> pdb=" O PHE D 955 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N THR D 941 " --> pdb=" O LEU D 900 " (cutoff:3.500A) removed outlier: 7.292A pdb=" N LEU D 900 " --> pdb=" O THR D 941 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N GLY D 899 " --> pdb=" O ASP D 916 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N CYS D 914 " --> pdb=" O GLY D 901 " (cutoff:3.500A) 1208 hydrogen bonds defined for protein. 3288 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: 15.32 Time building geometry restraints manager: 9.97 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 11076 1.34 - 1.46: 7356 1.46 - 1.58: 15112 1.58 - 1.69: 0 1.69 - 1.81: 248 Bond restraints: 33792 Sorted by residual: bond pdb=" C ASN B 110 " pdb=" N PRO B 111 " ideal model delta sigma weight residual 1.329 1.407 -0.078 1.18e-02 7.18e+03 4.33e+01 bond pdb=" C ASN D 110 " pdb=" N PRO D 111 " ideal model delta sigma weight residual 1.329 1.407 -0.078 1.18e-02 7.18e+03 4.33e+01 bond pdb=" C ASN C 110 " pdb=" N PRO C 111 " ideal model delta sigma weight residual 1.329 1.407 -0.078 1.18e-02 7.18e+03 4.33e+01 bond pdb=" C ASN A 110 " pdb=" N PRO A 111 " ideal model delta sigma weight residual 1.329 1.407 -0.078 1.18e-02 7.18e+03 4.33e+01 bond pdb=" C ILE A 305 " pdb=" N PRO A 306 " ideal model delta sigma weight residual 1.335 1.408 -0.073 1.36e-02 5.41e+03 2.85e+01 ... (remaining 33787 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.08: 44739 3.08 - 6.16: 1297 6.16 - 9.25: 44 9.25 - 12.33: 12 12.33 - 15.41: 12 Bond angle restraints: 46104 Sorted by residual: angle pdb=" N ASP D 610 " pdb=" CA ASP D 610 " pdb=" C ASP D 610 " ideal model delta sigma weight residual 111.71 120.08 -8.37 1.15e+00 7.56e-01 5.29e+01 angle pdb=" N ASP B 610 " pdb=" CA ASP B 610 " pdb=" C ASP B 610 " ideal model delta sigma weight residual 111.71 120.06 -8.35 1.15e+00 7.56e-01 5.28e+01 angle pdb=" N ASP C 610 " pdb=" CA ASP C 610 " pdb=" C ASP C 610 " ideal model delta sigma weight residual 111.71 120.06 -8.35 1.15e+00 7.56e-01 5.28e+01 angle pdb=" N ASP A 610 " pdb=" CA ASP A 610 " pdb=" C ASP A 610 " ideal model delta sigma weight residual 111.71 120.06 -8.35 1.15e+00 7.56e-01 5.28e+01 angle pdb=" N TYR D 405 " pdb=" CA TYR D 405 " pdb=" C TYR D 405 " ideal model delta sigma weight residual 111.14 118.93 -7.79 1.08e+00 8.57e-01 5.20e+01 ... (remaining 46099 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.81: 16973 17.81 - 35.61: 1923 35.61 - 53.42: 662 53.42 - 71.23: 194 71.23 - 89.03: 48 Dihedral angle restraints: 19800 sinusoidal: 7984 harmonic: 11816 Sorted by residual: dihedral pdb=" CA ASN C 147 " pdb=" C ASN C 147 " pdb=" N SER C 148 " pdb=" CA SER C 148 " ideal model delta harmonic sigma weight residual 0.00 -24.35 24.35 0 5.00e+00 4.00e-02 2.37e+01 dihedral pdb=" CA ASN D 147 " pdb=" C ASN D 147 " pdb=" N SER D 148 " pdb=" CA SER D 148 " ideal model delta harmonic sigma weight residual 0.00 -24.31 24.31 0 5.00e+00 4.00e-02 2.36e+01 dihedral pdb=" CA ASN A 147 " pdb=" C ASN A 147 " pdb=" N SER A 148 " pdb=" CA SER A 148 " ideal model delta harmonic sigma weight residual 0.00 -24.31 24.31 0 5.00e+00 4.00e-02 2.36e+01 ... (remaining 19797 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 3374 0.058 - 0.117: 1033 0.117 - 0.175: 342 0.175 - 0.234: 55 0.234 - 0.292: 16 Chirality restraints: 4820 Sorted by residual: chirality pdb=" CA ASP B 610 " pdb=" N ASP B 610 " pdb=" C ASP B 610 " pdb=" CB ASP B 610 " both_signs ideal model delta sigma weight residual False 2.51 2.22 0.29 2.00e-01 2.50e+01 2.14e+00 chirality pdb=" CA ASP A 610 " pdb=" N ASP A 610 " pdb=" C ASP A 610 " pdb=" CB ASP A 610 " both_signs ideal model delta sigma weight residual False 2.51 2.22 0.29 2.00e-01 2.50e+01 2.14e+00 chirality pdb=" CA ASP C 610 " pdb=" N ASP C 610 " pdb=" C ASP C 610 " pdb=" CB ASP C 610 " both_signs ideal model delta sigma weight residual False 2.51 2.22 0.29 2.00e-01 2.50e+01 2.14e+00 ... (remaining 4817 not shown) Planarity restraints: 6088 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN A 510 " -0.092 5.00e-02 4.00e+02 1.44e-01 3.31e+01 pdb=" N PRO A 511 " 0.249 5.00e-02 4.00e+02 pdb=" CA PRO A 511 " -0.084 5.00e-02 4.00e+02 pdb=" CD PRO A 511 " -0.073 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN B 510 " 0.092 5.00e-02 4.00e+02 1.44e-01 3.30e+01 pdb=" N PRO B 511 " -0.249 5.00e-02 4.00e+02 pdb=" CA PRO B 511 " 0.084 5.00e-02 4.00e+02 pdb=" CD PRO B 511 " 0.073 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN D 510 " -0.092 5.00e-02 4.00e+02 1.44e-01 3.30e+01 pdb=" N PRO D 511 " 0.249 5.00e-02 4.00e+02 pdb=" CA PRO D 511 " -0.084 5.00e-02 4.00e+02 pdb=" CD PRO D 511 " -0.073 5.00e-02 4.00e+02 ... (remaining 6085 not shown) Histogram of nonbonded interaction distances: 1.09 - 1.85: 158 1.85 - 2.61: 2009 2.61 - 3.37: 46311 3.37 - 4.14: 85478 4.14 - 4.90: 154792 Nonbonded interactions: 288748 Sorted by model distance: nonbonded pdb=" CD2 HIS A 391 " pdb=" OD1 ASN A 460 " model vdw 1.085 3.260 nonbonded pdb=" CD2 HIS C 391 " pdb=" OD1 ASN C 460 " model vdw 1.085 3.260 nonbonded pdb=" CD2 HIS D 391 " pdb=" OD1 ASN D 460 " model vdw 1.085 3.260 nonbonded pdb=" CD2 HIS B 391 " pdb=" OD1 ASN B 460 " model vdw 1.086 3.260 nonbonded pdb=" ND1 HIS C1015 " pdb=" ND1 HIS D1015 " model vdw 1.110 3.200 ... (remaining 288743 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: 0.23 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 3.200 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: 1.660 Check model and map are aligned: 0.240 Set scattering table: 0.290 Process input model: 79.160 Find NCS groups from input model: 0.660 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 88.330 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7608 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 : 0.009 0.446 33812 Z= 0.798 Angle : 1.168 15.411 46104 Z= 0.820 Chirality : 0.064 0.292 4820 Planarity : 0.012 0.144 6088 Dihedral : 17.984 89.033 12192 Min Nonbonded Distance : 1.085 Molprobity Statistics. All-atom Clashscore : 132.80 Ramachandran Plot: Outliers : 0.20 % Allowed : 2.45 % Favored : 97.35 % Rotamer: Outliers : 12.24 % Allowed : 20.68 % Favored : 67.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.06 % Cis-general : 1.15 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.39 (0.13), residues: 4080 helix: 2.48 (0.20), residues: 516 sheet: 3.21 (0.14), residues: 1272 loop : 0.43 (0.12), residues: 2292 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 553 HIS 0.003 0.001 HIS B 815 PHE 0.009 0.001 PHE A 957 TYR 0.008 0.001 TYR B 105 ARG 0.002 0.000 ARG D 800 Details of bonding type rmsd hydrogen bonds : bond 0.28446 ( 1144) hydrogen bonds : angle 10.44541 ( 3288) covalent geometry : bond 0.00465 (33792) covalent geometry : angle 1.16805 (46104) Misc. bond : bond 0.29618 ( 20) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1210 residues out of total 3496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 428 poor density : 782 time to evaluate : 3.788 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 90 TRP cc_start: 0.8175 (OUTLIER) cc_final: 0.7777 (p90) REVERT: A 166 ARG cc_start: 0.7541 (OUTLIER) cc_final: 0.7179 (mmt180) REVERT: A 170 GLU cc_start: 0.6393 (OUTLIER) cc_final: 0.6085 (mp0) REVERT: A 210 ARG cc_start: 0.7533 (OUTLIER) cc_final: 0.6808 (mtt180) REVERT: A 246 MET cc_start: 0.7261 (OUTLIER) cc_final: 0.6940 (ptp) REVERT: A 542 MET cc_start: 0.6418 (OUTLIER) cc_final: 0.6162 (ttm) REVERT: A 881 ARG cc_start: 0.7781 (OUTLIER) cc_final: 0.6797 (ptp-170) REVERT: A 1013 ARG cc_start: 0.7788 (ttm-80) cc_final: 0.7393 (mtm-85) REVERT: B 90 TRP cc_start: 0.8164 (OUTLIER) cc_final: 0.7694 (p90) REVERT: B 166 ARG cc_start: 0.7555 (OUTLIER) cc_final: 0.7194 (mmt180) REVERT: B 170 GLU cc_start: 0.6373 (OUTLIER) cc_final: 0.6064 (mp0) REVERT: B 210 ARG cc_start: 0.7502 (OUTLIER) cc_final: 0.6790 (mtt180) REVERT: B 246 MET cc_start: 0.7265 (OUTLIER) cc_final: 0.6923 (ptp) REVERT: B 542 MET cc_start: 0.6417 (OUTLIER) cc_final: 0.6168 (ttm) REVERT: B 881 ARG cc_start: 0.7810 (OUTLIER) cc_final: 0.6836 (ptp-170) REVERT: B 1013 ARG cc_start: 0.7769 (ttm-80) cc_final: 0.7378 (mtm-85) REVERT: C 90 TRP cc_start: 0.8193 (OUTLIER) cc_final: 0.7767 (p90) REVERT: C 166 ARG cc_start: 0.7584 (OUTLIER) cc_final: 0.7209 (mmt180) REVERT: C 170 GLU cc_start: 0.6429 (OUTLIER) cc_final: 0.6126 (mp0) REVERT: C 210 ARG cc_start: 0.7542 (OUTLIER) cc_final: 0.6779 (mtt180) REVERT: C 246 MET cc_start: 0.7263 (OUTLIER) cc_final: 0.6933 (ptp) REVERT: C 542 MET cc_start: 0.6460 (OUTLIER) cc_final: 0.6190 (ttm) REVERT: C 881 ARG cc_start: 0.7734 (OUTLIER) cc_final: 0.6715 (ptp-170) REVERT: C 1013 ARG cc_start: 0.7776 (ttm-80) cc_final: 0.7361 (mtm-85) REVERT: D 90 TRP cc_start: 0.8175 (OUTLIER) cc_final: 0.7753 (p90) REVERT: D 166 ARG cc_start: 0.7573 (OUTLIER) cc_final: 0.7196 (mmt180) REVERT: D 170 GLU cc_start: 0.6412 (OUTLIER) cc_final: 0.6114 (mp0) REVERT: D 210 ARG cc_start: 0.7556 (OUTLIER) cc_final: 0.6796 (mtt180) REVERT: D 246 MET cc_start: 0.7258 (OUTLIER) cc_final: 0.6923 (ptp) REVERT: D 542 MET cc_start: 0.6465 (OUTLIER) cc_final: 0.6217 (ttm) REVERT: D 881 ARG cc_start: 0.7754 (OUTLIER) cc_final: 0.6742 (ptp-170) REVERT: D 1013 ARG cc_start: 0.7774 (ttm-80) cc_final: 0.7363 (mtm-85) outliers start: 428 outliers final: 206 residues processed: 1150 average time/residue: 0.5343 time to fit residues: 938.6964 Evaluate side-chains 654 residues out of total 3496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 234 poor density : 420 time to evaluate : 3.536 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 ILE Chi-restraints excluded: chain A residue 13 ARG Chi-restraints excluded: chain A residue 23 GLN Chi-restraints excluded: chain A residue 33 PHE Chi-restraints excluded: chain A residue 50 GLN Chi-restraints excluded: chain A residue 90 TRP Chi-restraints excluded: chain A residue 141 ILE Chi-restraints excluded: chain A residue 166 ARG Chi-restraints excluded: chain A residue 169 SER Chi-restraints excluded: chain A residue 170 GLU Chi-restraints excluded: chain A residue 188 VAL Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 202 MET Chi-restraints excluded: chain A residue 209 PHE Chi-restraints excluded: chain A residue 210 ARG Chi-restraints excluded: chain A residue 221 GLN Chi-restraints excluded: chain A residue 232 ASN Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 246 MET Chi-restraints excluded: chain A residue 251 ARG Chi-restraints excluded: chain A residue 255 ARG Chi-restraints excluded: chain A residue 259 SER Chi-restraints excluded: chain A residue 266 GLN Chi-restraints excluded: chain A residue 274 PHE Chi-restraints excluded: chain A residue 333 ARG Chi-restraints excluded: chain A residue 344 LEU Chi-restraints excluded: chain A residue 375 ASP Chi-restraints excluded: chain A residue 380 LYS Chi-restraints excluded: chain A residue 391 HIS Chi-restraints excluded: chain A residue 418 HIS Chi-restraints excluded: chain A residue 420 MET Chi-restraints excluded: chain A residue 439 ARG Chi-restraints excluded: chain A residue 462 SER Chi-restraints excluded: chain A residue 469 ASP Chi-restraints excluded: chain A residue 471 LEU Chi-restraints excluded: chain A residue 542 MET Chi-restraints excluded: chain A residue 567 VAL Chi-restraints excluded: chain A residue 592 PHE Chi-restraints excluded: chain A residue 599 ARG Chi-restraints excluded: chain A residue 601 PHE Chi-restraints excluded: chain A residue 603 MET Chi-restraints excluded: chain A residue 604 ASN Chi-restraints excluded: chain A residue 606 LEU Chi-restraints excluded: chain A residue 624 GLN Chi-restraints excluded: chain A residue 647 SER Chi-restraints excluded: chain A residue 694 LEU Chi-restraints excluded: chain A residue 702 GLN Chi-restraints excluded: chain A residue 749 ILE Chi-restraints excluded: chain A residue 767 GLN Chi-restraints excluded: chain A residue 786 ARG Chi-restraints excluded: chain A residue 815 HIS Chi-restraints excluded: chain A residue 850 PHE Chi-restraints excluded: chain A residue 876 THR Chi-restraints excluded: chain A residue 881 ARG Chi-restraints excluded: chain A residue 898 LEU Chi-restraints excluded: chain A residue 962 TYR Chi-restraints excluded: chain A residue 999 TRP Chi-restraints excluded: chain A residue 1009 LEU Chi-restraints excluded: chain A residue 1020 TRP Chi-restraints excluded: chain B residue 3 ILE Chi-restraints excluded: chain B residue 13 ARG Chi-restraints excluded: chain B residue 23 GLN Chi-restraints excluded: chain B residue 33 PHE Chi-restraints excluded: chain B residue 50 GLN Chi-restraints excluded: chain B residue 90 TRP Chi-restraints excluded: chain B residue 141 ILE Chi-restraints excluded: chain B residue 166 ARG Chi-restraints excluded: chain B residue 169 SER Chi-restraints excluded: chain B residue 170 GLU Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 202 MET Chi-restraints excluded: chain B residue 209 PHE Chi-restraints excluded: chain B residue 210 ARG Chi-restraints excluded: chain B residue 221 GLN Chi-restraints excluded: chain B residue 232 ASN Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain B residue 246 MET Chi-restraints excluded: chain B residue 251 ARG Chi-restraints excluded: chain B residue 255 ARG Chi-restraints excluded: chain B residue 259 SER Chi-restraints excluded: chain B residue 266 GLN Chi-restraints excluded: chain B residue 274 PHE Chi-restraints excluded: chain B residue 333 ARG Chi-restraints excluded: chain B residue 344 LEU Chi-restraints excluded: chain B residue 375 ASP Chi-restraints excluded: chain B residue 380 LYS Chi-restraints excluded: chain B residue 391 HIS Chi-restraints excluded: chain B residue 418 HIS Chi-restraints excluded: chain B residue 420 MET Chi-restraints excluded: chain B residue 439 ARG Chi-restraints excluded: chain B residue 462 SER Chi-restraints excluded: chain B residue 469 ASP Chi-restraints excluded: chain B residue 471 LEU Chi-restraints excluded: chain B residue 542 MET Chi-restraints excluded: chain B residue 592 PHE Chi-restraints excluded: chain B residue 599 ARG Chi-restraints excluded: chain B residue 601 PHE Chi-restraints excluded: chain B residue 603 MET Chi-restraints excluded: chain B residue 604 ASN Chi-restraints excluded: chain B residue 606 LEU Chi-restraints excluded: chain B residue 624 GLN Chi-restraints excluded: chain B residue 647 SER Chi-restraints excluded: chain B residue 694 LEU Chi-restraints excluded: chain B residue 702 GLN Chi-restraints excluded: chain B residue 749 ILE Chi-restraints excluded: chain B residue 767 GLN Chi-restraints excluded: chain B residue 786 ARG Chi-restraints excluded: chain B residue 815 HIS Chi-restraints excluded: chain B residue 850 PHE Chi-restraints excluded: chain B residue 876 THR Chi-restraints excluded: chain B residue 881 ARG Chi-restraints excluded: chain B residue 898 LEU Chi-restraints excluded: chain B residue 962 TYR Chi-restraints excluded: chain B residue 999 TRP Chi-restraints excluded: chain B residue 1009 LEU Chi-restraints excluded: chain B residue 1020 TRP Chi-restraints excluded: chain C residue 3 ILE Chi-restraints excluded: chain C residue 13 ARG Chi-restraints excluded: chain C residue 23 GLN Chi-restraints excluded: chain C residue 33 PHE Chi-restraints excluded: chain C residue 50 GLN Chi-restraints excluded: chain C residue 90 TRP Chi-restraints excluded: chain C residue 141 ILE Chi-restraints excluded: chain C residue 166 ARG Chi-restraints excluded: chain C residue 169 SER Chi-restraints excluded: chain C residue 170 GLU Chi-restraints excluded: chain C residue 188 VAL Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 202 MET Chi-restraints excluded: chain C residue 209 PHE Chi-restraints excluded: chain C residue 210 ARG Chi-restraints excluded: chain C residue 221 GLN Chi-restraints excluded: chain C residue 232 ASN Chi-restraints excluded: chain C residue 240 LEU Chi-restraints excluded: chain C residue 246 MET Chi-restraints excluded: chain C residue 251 ARG Chi-restraints excluded: chain C residue 255 ARG Chi-restraints excluded: chain C residue 259 SER Chi-restraints excluded: chain C residue 266 GLN Chi-restraints excluded: chain C residue 274 PHE Chi-restraints excluded: chain C residue 333 ARG Chi-restraints excluded: chain C residue 344 LEU Chi-restraints excluded: chain C residue 375 ASP Chi-restraints excluded: chain C residue 380 LYS Chi-restraints excluded: chain C residue 391 HIS Chi-restraints excluded: chain C residue 418 HIS Chi-restraints excluded: chain C residue 420 MET Chi-restraints excluded: chain C residue 439 ARG Chi-restraints excluded: chain C residue 462 SER Chi-restraints excluded: chain C residue 469 ASP Chi-restraints excluded: chain C residue 471 LEU Chi-restraints excluded: chain C residue 542 MET Chi-restraints excluded: chain C residue 592 PHE Chi-restraints excluded: chain C residue 599 ARG Chi-restraints excluded: chain C residue 601 PHE Chi-restraints excluded: chain C residue 603 MET Chi-restraints excluded: chain C residue 604 ASN Chi-restraints excluded: chain C residue 606 LEU Chi-restraints excluded: chain C residue 624 GLN Chi-restraints excluded: chain C residue 647 SER Chi-restraints excluded: chain C residue 694 LEU Chi-restraints excluded: chain C residue 702 GLN Chi-restraints excluded: chain C residue 749 ILE Chi-restraints excluded: chain C residue 767 GLN Chi-restraints excluded: chain C residue 786 ARG Chi-restraints excluded: chain C residue 815 HIS Chi-restraints excluded: chain C residue 850 PHE Chi-restraints excluded: chain C residue 876 THR Chi-restraints excluded: chain C residue 881 ARG Chi-restraints excluded: chain C residue 898 LEU Chi-restraints excluded: chain C residue 962 TYR Chi-restraints excluded: chain C residue 999 TRP Chi-restraints excluded: chain C residue 1009 LEU Chi-restraints excluded: chain C residue 1020 TRP Chi-restraints excluded: chain D residue 3 ILE Chi-restraints excluded: chain D residue 13 ARG Chi-restraints excluded: chain D residue 23 GLN Chi-restraints excluded: chain D residue 33 PHE Chi-restraints excluded: chain D residue 50 GLN Chi-restraints excluded: chain D residue 90 TRP Chi-restraints excluded: chain D residue 141 ILE Chi-restraints excluded: chain D residue 166 ARG Chi-restraints excluded: chain D residue 169 SER Chi-restraints excluded: chain D residue 170 GLU Chi-restraints excluded: chain D residue 188 VAL Chi-restraints excluded: chain D residue 189 LEU Chi-restraints excluded: chain D residue 202 MET Chi-restraints excluded: chain D residue 209 PHE Chi-restraints excluded: chain D residue 210 ARG Chi-restraints excluded: chain D residue 221 GLN Chi-restraints excluded: chain D residue 232 ASN Chi-restraints excluded: chain D residue 240 LEU Chi-restraints excluded: chain D residue 246 MET Chi-restraints excluded: chain D residue 251 ARG Chi-restraints excluded: chain D residue 255 ARG Chi-restraints excluded: chain D residue 259 SER Chi-restraints excluded: chain D residue 266 GLN Chi-restraints excluded: chain D residue 274 PHE Chi-restraints excluded: chain D residue 333 ARG Chi-restraints excluded: chain D residue 344 LEU Chi-restraints excluded: chain D residue 375 ASP Chi-restraints excluded: chain D residue 380 LYS Chi-restraints excluded: chain D residue 391 HIS Chi-restraints excluded: chain D residue 418 HIS Chi-restraints excluded: chain D residue 420 MET Chi-restraints excluded: chain D residue 439 ARG Chi-restraints excluded: chain D residue 462 SER Chi-restraints excluded: chain D residue 469 ASP Chi-restraints excluded: chain D residue 471 LEU Chi-restraints excluded: chain D residue 542 MET Chi-restraints excluded: chain D residue 592 PHE Chi-restraints excluded: chain D residue 599 ARG Chi-restraints excluded: chain D residue 601 PHE Chi-restraints excluded: chain D residue 603 MET Chi-restraints excluded: chain D residue 604 ASN Chi-restraints excluded: chain D residue 606 LEU Chi-restraints excluded: chain D residue 624 GLN Chi-restraints excluded: chain D residue 647 SER Chi-restraints excluded: chain D residue 694 LEU Chi-restraints excluded: chain D residue 702 GLN Chi-restraints excluded: chain D residue 749 ILE Chi-restraints excluded: chain D residue 767 GLN Chi-restraints excluded: chain D residue 786 ARG Chi-restraints excluded: chain D residue 815 HIS Chi-restraints excluded: chain D residue 850 PHE Chi-restraints excluded: chain D residue 876 THR Chi-restraints excluded: chain D residue 881 ARG Chi-restraints excluded: chain D residue 898 LEU Chi-restraints excluded: chain D residue 962 TYR Chi-restraints excluded: chain D residue 999 TRP Chi-restraints excluded: chain D residue 1008 GLN Chi-restraints excluded: chain D residue 1009 LEU Chi-restraints excluded: chain D residue 1020 TRP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 344 optimal weight: 2.9990 chunk 309 optimal weight: 7.9990 chunk 171 optimal weight: 3.9990 chunk 105 optimal weight: 0.5980 chunk 208 optimal weight: 10.0000 chunk 165 optimal weight: 7.9990 chunk 319 optimal weight: 10.0000 chunk 123 optimal weight: 9.9990 chunk 194 optimal weight: 9.9990 chunk 238 optimal weight: 0.7980 chunk 370 optimal weight: 7.9990 overall best weight: 3.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 18 ASN A 30 HIS A 50 GLN ** A 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 93 HIS A 163 GLN A 221 GLN A 226 HIS A 245 GLN A 266 GLN ** A 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 391 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 394 ASN ** A 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 468 HIS A 573 GLN A 624 GLN ** A 653 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 713 HIS ** A 719 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 725 ASN ** A 761 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 824 GLN A 878 HIS ** A 890 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1008 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1022 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 18 ASN B 30 HIS B 50 GLN ** B 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 93 HIS B 163 GLN B 221 GLN B 226 HIS B 245 GLN B 266 GLN ** B 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 391 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 394 ASN ** B 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 468 HIS B 573 GLN B 624 GLN ** B 653 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 713 HIS ** B 719 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 725 ASN ** B 761 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 824 GLN B 878 HIS ** B 890 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1008 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1022 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 18 ASN C 30 HIS C 50 GLN ** C 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 93 HIS C 163 GLN C 221 GLN C 226 HIS C 245 GLN C 266 GLN ** C 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 391 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 394 ASN ** C 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 468 HIS C 573 GLN C 624 GLN ** C 653 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 713 HIS ** C 719 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 725 ASN C 739 HIS ** C 761 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 824 GLN C 878 HIS ** C 890 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1008 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1022 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 18 ASN D 30 HIS D 50 GLN ** D 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 93 HIS D 163 GLN D 221 GLN D 226 HIS D 245 GLN D 266 GLN ** D 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 391 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 394 ASN ** D 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 468 HIS D 573 GLN D 624 GLN ** D 653 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 713 HIS ** D 719 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 725 ASN ** D 761 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 824 GLN D 878 HIS ** D 890 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1008 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1022 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 69 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.096348 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.080860 restraints weight = 66545.033| |-----------------------------------------------------------------------------| r_work (start): 0.3192 rms_B_bonded: 2.72 r_work: 0.3074 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3074 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8360 moved from start: 0.4098 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 33812 Z= 0.217 Angle : 0.777 12.828 46104 Z= 0.415 Chirality : 0.050 0.169 4820 Planarity : 0.007 0.064 6088 Dihedral : 11.341 85.429 5056 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 17.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.27 % Favored : 98.73 % Rotamer: Outliers : 7.81 % Allowed : 19.59 % Favored : 72.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.06 % Cis-general : 1.15 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.23 (0.13), residues: 4080 helix: 0.81 (0.21), residues: 556 sheet: 2.28 (0.14), residues: 1340 loop : -0.12 (0.13), residues: 2184 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP B 769 HIS 0.018 0.002 HIS B 30 PHE 0.024 0.003 PHE C1007 TYR 0.017 0.002 TYR D 405 ARG 0.009 0.001 ARG C 442 Details of bonding type rmsd hydrogen bonds : bond 0.04735 ( 1144) hydrogen bonds : angle 6.72886 ( 3288) covalent geometry : bond 0.00490 (33792) covalent geometry : angle 0.77698 (46104) Misc. bond : bond 0.00187 ( 20) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 750 residues out of total 3496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 273 poor density : 477 time to evaluate : 3.718 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 23 GLN cc_start: 0.9070 (pp30) cc_final: 0.8514 (pp30) REVERT: A 43 ARG cc_start: 0.8237 (OUTLIER) cc_final: 0.7801 (tmt170) REVERT: A 144 ASP cc_start: 0.7898 (m-30) cc_final: 0.7623 (m-30) REVERT: A 237 ARG cc_start: 0.8437 (mtp-110) cc_final: 0.8131 (mtp-110) REVERT: A 280 ASP cc_start: 0.7264 (p0) cc_final: 0.7048 (p0) REVERT: A 416 GLU cc_start: 0.8191 (OUTLIER) cc_final: 0.7721 (tt0) REVERT: A 428 ASP cc_start: 0.8303 (t70) cc_final: 0.8083 (t0) REVERT: A 476 LYS cc_start: 0.8941 (OUTLIER) cc_final: 0.8500 (mmtt) REVERT: A 515 VAL cc_start: 0.8312 (t) cc_final: 0.7847 (m) REVERT: A 648 ASP cc_start: 0.7758 (p0) cc_final: 0.7325 (t0) REVERT: A 702 GLN cc_start: 0.8969 (OUTLIER) cc_final: 0.8465 (mp-120) REVERT: A 719 GLN cc_start: 0.8495 (OUTLIER) cc_final: 0.8227 (tm-30) REVERT: A 776 LEU cc_start: 0.9032 (OUTLIER) cc_final: 0.8786 (pp) REVERT: A 804 ASN cc_start: 0.8566 (m-40) cc_final: 0.8339 (m-40) REVERT: A 864 MET cc_start: 0.7840 (ttm) cc_final: 0.7503 (ttm) REVERT: A 1013 ARG cc_start: 0.8478 (ttm-80) cc_final: 0.7871 (mtm-85) REVERT: B 23 GLN cc_start: 0.9067 (pp30) cc_final: 0.8510 (pp30) REVERT: B 43 ARG cc_start: 0.8252 (OUTLIER) cc_final: 0.7824 (tmm-80) REVERT: B 144 ASP cc_start: 0.7898 (m-30) cc_final: 0.7624 (m-30) REVERT: B 237 ARG cc_start: 0.8457 (mtp-110) cc_final: 0.8150 (mtp-110) REVERT: B 280 ASP cc_start: 0.7299 (p0) cc_final: 0.7073 (p0) REVERT: B 416 GLU cc_start: 0.8209 (OUTLIER) cc_final: 0.7765 (tt0) REVERT: B 428 ASP cc_start: 0.8320 (t70) cc_final: 0.8089 (t0) REVERT: B 476 LYS cc_start: 0.8949 (OUTLIER) cc_final: 0.8514 (mmtt) REVERT: B 515 VAL cc_start: 0.8307 (t) cc_final: 0.7845 (m) REVERT: B 702 GLN cc_start: 0.8962 (OUTLIER) cc_final: 0.8453 (mp-120) REVERT: B 719 GLN cc_start: 0.8485 (OUTLIER) cc_final: 0.8229 (tm-30) REVERT: B 776 LEU cc_start: 0.9039 (OUTLIER) cc_final: 0.8800 (pp) REVERT: B 808 GLU cc_start: 0.8241 (mm-30) cc_final: 0.7925 (tm-30) REVERT: B 864 MET cc_start: 0.7806 (ttm) cc_final: 0.7477 (ttm) REVERT: B 1013 ARG cc_start: 0.8457 (ttm-80) cc_final: 0.7862 (mtm-85) REVERT: C 43 ARG cc_start: 0.8240 (OUTLIER) cc_final: 0.7787 (tmt170) REVERT: C 237 ARG cc_start: 0.8438 (mtp-110) cc_final: 0.8068 (mtp-110) REVERT: C 280 ASP cc_start: 0.7266 (p0) cc_final: 0.7064 (p0) REVERT: C 416 GLU cc_start: 0.8165 (OUTLIER) cc_final: 0.7702 (tt0) REVERT: C 428 ASP cc_start: 0.8305 (t70) cc_final: 0.8081 (t0) REVERT: C 476 LYS cc_start: 0.8940 (OUTLIER) cc_final: 0.8512 (mmtt) REVERT: C 515 VAL cc_start: 0.8304 (t) cc_final: 0.7841 (m) REVERT: C 702 GLN cc_start: 0.8961 (OUTLIER) cc_final: 0.8465 (mp-120) REVERT: C 719 GLN cc_start: 0.8484 (OUTLIER) cc_final: 0.8214 (tm-30) REVERT: C 776 LEU cc_start: 0.9004 (OUTLIER) cc_final: 0.8740 (pp) REVERT: C 801 ILE cc_start: 0.8263 (mm) cc_final: 0.7923 (mt) REVERT: C 804 ASN cc_start: 0.8592 (m-40) cc_final: 0.8367 (m-40) REVERT: C 864 MET cc_start: 0.7827 (ttm) cc_final: 0.7486 (ttm) REVERT: C 898 LEU cc_start: 0.9005 (OUTLIER) cc_final: 0.8748 (tt) REVERT: C 1013 ARG cc_start: 0.8472 (ttm-80) cc_final: 0.7851 (mtm-85) REVERT: D 23 GLN cc_start: 0.9041 (pp30) cc_final: 0.8607 (pp30) REVERT: D 43 ARG cc_start: 0.8235 (OUTLIER) cc_final: 0.7797 (tmt170) REVERT: D 237 ARG cc_start: 0.8435 (mtp-110) cc_final: 0.8071 (mtp-110) REVERT: D 280 ASP cc_start: 0.7280 (p0) cc_final: 0.7059 (p0) REVERT: D 416 GLU cc_start: 0.8181 (OUTLIER) cc_final: 0.7738 (tt0) REVERT: D 428 ASP cc_start: 0.8286 (t70) cc_final: 0.8055 (t0) REVERT: D 476 LYS cc_start: 0.8941 (OUTLIER) cc_final: 0.8511 (mmtt) REVERT: D 515 VAL cc_start: 0.8315 (t) cc_final: 0.7871 (m) REVERT: D 702 GLN cc_start: 0.8966 (OUTLIER) cc_final: 0.8474 (mp-120) REVERT: D 719 GLN cc_start: 0.8484 (OUTLIER) cc_final: 0.8219 (tm-30) REVERT: D 776 LEU cc_start: 0.9014 (OUTLIER) cc_final: 0.8766 (pp) REVERT: D 801 ILE cc_start: 0.8260 (mm) cc_final: 0.7926 (mt) REVERT: D 864 MET cc_start: 0.7824 (ttm) cc_final: 0.7474 (ttm) REVERT: D 884 LEU cc_start: 0.9008 (OUTLIER) cc_final: 0.8757 (pp) REVERT: D 1013 ARG cc_start: 0.8468 (ttm-80) cc_final: 0.7862 (mtm-85) outliers start: 273 outliers final: 143 residues processed: 686 average time/residue: 0.4830 time to fit residues: 527.8095 Evaluate side-chains 523 residues out of total 3496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 169 poor density : 354 time to evaluate : 3.671 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 ARG Chi-restraints excluded: chain A residue 33 PHE Chi-restraints excluded: chain A residue 43 ARG Chi-restraints excluded: chain A residue 74 LEU Chi-restraints excluded: chain A residue 124 SER Chi-restraints excluded: chain A residue 200 GLN Chi-restraints excluded: chain A residue 202 MET Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 259 SER Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 416 GLU Chi-restraints excluded: chain A residue 418 HIS Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain A residue 462 SER Chi-restraints excluded: chain A residue 476 LYS Chi-restraints excluded: chain A residue 494 THR Chi-restraints excluded: chain A residue 520 ILE Chi-restraints excluded: chain A residue 530 THR Chi-restraints excluded: chain A residue 599 ARG Chi-restraints excluded: chain A residue 611 ARG Chi-restraints excluded: chain A residue 624 GLN Chi-restraints excluded: chain A residue 702 GLN Chi-restraints excluded: chain A residue 706 THR Chi-restraints excluded: chain A residue 708 TRP Chi-restraints excluded: chain A residue 719 GLN Chi-restraints excluded: chain A residue 722 LEU Chi-restraints excluded: chain A residue 739 HIS Chi-restraints excluded: chain A residue 776 LEU Chi-restraints excluded: chain A residue 795 VAL Chi-restraints excluded: chain A residue 837 THR Chi-restraints excluded: chain A residue 838 THR Chi-restraints excluded: chain A residue 855 THR Chi-restraints excluded: chain A residue 869 ASP Chi-restraints excluded: chain A residue 884 LEU Chi-restraints excluded: chain A residue 914 CYS Chi-restraints excluded: chain A residue 920 LEU Chi-restraints excluded: chain A residue 963 SER Chi-restraints excluded: chain A residue 965 GLN Chi-restraints excluded: chain A residue 980 GLU Chi-restraints excluded: chain A residue 987 ASP Chi-restraints excluded: chain A residue 999 TRP Chi-restraints excluded: chain A residue 1020 TRP Chi-restraints excluded: chain B residue 13 ARG Chi-restraints excluded: chain B residue 33 PHE Chi-restraints excluded: chain B residue 43 ARG Chi-restraints excluded: chain B residue 74 LEU Chi-restraints excluded: chain B residue 124 SER Chi-restraints excluded: chain B residue 200 GLN Chi-restraints excluded: chain B residue 202 MET Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain B residue 259 SER Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain B residue 416 GLU Chi-restraints excluded: chain B residue 418 HIS Chi-restraints excluded: chain B residue 426 LEU Chi-restraints excluded: chain B residue 462 SER Chi-restraints excluded: chain B residue 476 LYS Chi-restraints excluded: chain B residue 494 THR Chi-restraints excluded: chain B residue 520 ILE Chi-restraints excluded: chain B residue 530 THR Chi-restraints excluded: chain B residue 599 ARG Chi-restraints excluded: chain B residue 611 ARG Chi-restraints excluded: chain B residue 624 GLN Chi-restraints excluded: chain B residue 702 GLN Chi-restraints excluded: chain B residue 706 THR Chi-restraints excluded: chain B residue 708 TRP Chi-restraints excluded: chain B residue 719 GLN Chi-restraints excluded: chain B residue 722 LEU Chi-restraints excluded: chain B residue 739 HIS Chi-restraints excluded: chain B residue 776 LEU Chi-restraints excluded: chain B residue 795 VAL Chi-restraints excluded: chain B residue 837 THR Chi-restraints excluded: chain B residue 838 THR Chi-restraints excluded: chain B residue 855 THR Chi-restraints excluded: chain B residue 869 ASP Chi-restraints excluded: chain B residue 884 LEU Chi-restraints excluded: chain B residue 904 GLU Chi-restraints excluded: chain B residue 914 CYS Chi-restraints excluded: chain B residue 963 SER Chi-restraints excluded: chain B residue 965 GLN Chi-restraints excluded: chain B residue 980 GLU Chi-restraints excluded: chain B residue 987 ASP Chi-restraints excluded: chain B residue 999 TRP Chi-restraints excluded: chain B residue 1020 TRP Chi-restraints excluded: chain C residue 13 ARG Chi-restraints excluded: chain C residue 33 PHE Chi-restraints excluded: chain C residue 43 ARG Chi-restraints excluded: chain C residue 74 LEU Chi-restraints excluded: chain C residue 124 SER Chi-restraints excluded: chain C residue 200 GLN Chi-restraints excluded: chain C residue 202 MET Chi-restraints excluded: chain C residue 240 LEU Chi-restraints excluded: chain C residue 259 SER Chi-restraints excluded: chain C residue 377 LEU Chi-restraints excluded: chain C residue 416 GLU Chi-restraints excluded: chain C residue 418 HIS Chi-restraints excluded: chain C residue 426 LEU Chi-restraints excluded: chain C residue 462 SER Chi-restraints excluded: chain C residue 476 LYS Chi-restraints excluded: chain C residue 494 THR Chi-restraints excluded: chain C residue 520 ILE Chi-restraints excluded: chain C residue 530 THR Chi-restraints excluded: chain C residue 599 ARG Chi-restraints excluded: chain C residue 611 ARG Chi-restraints excluded: chain C residue 624 GLN Chi-restraints excluded: chain C residue 702 GLN Chi-restraints excluded: chain C residue 706 THR Chi-restraints excluded: chain C residue 708 TRP Chi-restraints excluded: chain C residue 719 GLN Chi-restraints excluded: chain C residue 722 LEU Chi-restraints excluded: chain C residue 776 LEU Chi-restraints excluded: chain C residue 793 ILE Chi-restraints excluded: chain C residue 795 VAL Chi-restraints excluded: chain C residue 837 THR Chi-restraints excluded: chain C residue 838 THR Chi-restraints excluded: chain C residue 855 THR Chi-restraints excluded: chain C residue 869 ASP Chi-restraints excluded: chain C residue 884 LEU Chi-restraints excluded: chain C residue 898 LEU Chi-restraints excluded: chain C residue 914 CYS Chi-restraints excluded: chain C residue 920 LEU Chi-restraints excluded: chain C residue 963 SER Chi-restraints excluded: chain C residue 965 GLN Chi-restraints excluded: chain C residue 980 GLU Chi-restraints excluded: chain C residue 987 ASP Chi-restraints excluded: chain C residue 999 TRP Chi-restraints excluded: chain C residue 1020 TRP Chi-restraints excluded: chain D residue 13 ARG Chi-restraints excluded: chain D residue 33 PHE Chi-restraints excluded: chain D residue 43 ARG Chi-restraints excluded: chain D residue 74 LEU Chi-restraints excluded: chain D residue 124 SER Chi-restraints excluded: chain D residue 200 GLN Chi-restraints excluded: chain D residue 202 MET Chi-restraints excluded: chain D residue 240 LEU Chi-restraints excluded: chain D residue 259 SER Chi-restraints excluded: chain D residue 377 LEU Chi-restraints excluded: chain D residue 416 GLU Chi-restraints excluded: chain D residue 418 HIS Chi-restraints excluded: chain D residue 426 LEU Chi-restraints excluded: chain D residue 462 SER Chi-restraints excluded: chain D residue 476 LYS Chi-restraints excluded: chain D residue 494 THR Chi-restraints excluded: chain D residue 520 ILE Chi-restraints excluded: chain D residue 530 THR Chi-restraints excluded: chain D residue 599 ARG Chi-restraints excluded: chain D residue 611 ARG Chi-restraints excluded: chain D residue 624 GLN Chi-restraints excluded: chain D residue 702 GLN Chi-restraints excluded: chain D residue 706 THR Chi-restraints excluded: chain D residue 708 TRP Chi-restraints excluded: chain D residue 719 GLN Chi-restraints excluded: chain D residue 722 LEU Chi-restraints excluded: chain D residue 739 HIS Chi-restraints excluded: chain D residue 776 LEU Chi-restraints excluded: chain D residue 793 ILE Chi-restraints excluded: chain D residue 795 VAL Chi-restraints excluded: chain D residue 837 THR Chi-restraints excluded: chain D residue 838 THR Chi-restraints excluded: chain D residue 855 THR Chi-restraints excluded: chain D residue 869 ASP Chi-restraints excluded: chain D residue 884 LEU Chi-restraints excluded: chain D residue 914 CYS Chi-restraints excluded: chain D residue 963 SER Chi-restraints excluded: chain D residue 965 GLN Chi-restraints excluded: chain D residue 980 GLU Chi-restraints excluded: chain D residue 987 ASP Chi-restraints excluded: chain D residue 999 TRP Chi-restraints excluded: chain D residue 1020 TRP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 336 optimal weight: 8.9990 chunk 383 optimal weight: 8.9990 chunk 128 optimal weight: 3.9990 chunk 263 optimal weight: 0.3980 chunk 154 optimal weight: 0.7980 chunk 397 optimal weight: 10.0000 chunk 318 optimal weight: 3.9990 chunk 262 optimal weight: 9.9990 chunk 223 optimal weight: 9.9990 chunk 219 optimal weight: 8.9990 chunk 1 optimal weight: 5.9990 overall best weight: 3.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 563 GLN ** A 653 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 719 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 761 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 863 GLN ** A 890 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1008 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 563 GLN ** B 653 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 719 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 761 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 863 GLN ** B 890 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1008 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 563 GLN ** C 653 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 719 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 761 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 890 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1008 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 563 GLN ** D 604 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 653 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 719 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 761 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 890 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1008 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.093805 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.077963 restraints weight = 66833.983| |-----------------------------------------------------------------------------| r_work (start): 0.3146 rms_B_bonded: 2.75 r_work: 0.3024 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3024 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8417 moved from start: 0.4620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 33812 Z= 0.182 Angle : 0.662 10.720 46104 Z= 0.350 Chirality : 0.046 0.180 4820 Planarity : 0.005 0.050 6088 Dihedral : 7.997 73.311 4590 Min Nonbonded Distance : 1.910 Molprobity Statistics. All-atom Clashscore : 14.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 7.24 % Allowed : 19.34 % Favored : 73.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.06 % Cis-general : 1.15 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.81 (0.13), residues: 4080 helix: 0.37 (0.21), residues: 580 sheet: 1.69 (0.13), residues: 1424 loop : -0.21 (0.13), residues: 2076 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 769 HIS 0.006 0.001 HIS C 653 PHE 0.020 0.002 PHE C1007 TYR 0.014 0.002 TYR C 105 ARG 0.007 0.001 ARG D 442 Details of bonding type rmsd hydrogen bonds : bond 0.04030 ( 1144) hydrogen bonds : angle 5.98739 ( 3288) covalent geometry : bond 0.00411 (33792) covalent geometry : angle 0.66160 (46104) Misc. bond : bond 0.00151 ( 20) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 670 residues out of total 3496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 253 poor density : 417 time to evaluate : 3.788 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 144 ASP cc_start: 0.8059 (m-30) cc_final: 0.7788 (m-30) REVERT: A 202 MET cc_start: 0.8168 (OUTLIER) cc_final: 0.7959 (ptp) REVERT: A 237 ARG cc_start: 0.8375 (mtp-110) cc_final: 0.7983 (mtp-110) REVERT: A 262 GLN cc_start: 0.8058 (tm130) cc_final: 0.7772 (tp40) REVERT: A 358 GLU cc_start: 0.7469 (tt0) cc_final: 0.7230 (tt0) REVERT: A 394 ASN cc_start: 0.9131 (m-40) cc_final: 0.8684 (m-40) REVERT: A 471 LEU cc_start: 0.9289 (OUTLIER) cc_final: 0.8822 (mm) REVERT: A 521 LYS cc_start: 0.8556 (OUTLIER) cc_final: 0.8267 (mttt) REVERT: A 544 ASN cc_start: 0.8376 (OUTLIER) cc_final: 0.8173 (m-40) REVERT: A 572 ASP cc_start: 0.8457 (OUTLIER) cc_final: 0.7927 (m-30) REVERT: A 601 PHE cc_start: 0.7896 (m-80) cc_final: 0.7655 (m-80) REVERT: A 648 ASP cc_start: 0.7574 (p0) cc_final: 0.7343 (t0) REVERT: A 667 GLU cc_start: 0.8253 (OUTLIER) cc_final: 0.8032 (mm-30) REVERT: A 702 GLN cc_start: 0.9019 (OUTLIER) cc_final: 0.8579 (mp-120) REVERT: A 719 GLN cc_start: 0.8628 (OUTLIER) cc_final: 0.8097 (tm-30) REVERT: A 726 LEU cc_start: 0.8455 (OUTLIER) cc_final: 0.8218 (mm) REVERT: A 804 ASN cc_start: 0.8543 (m-40) cc_final: 0.8287 (m-40) REVERT: A 808 GLU cc_start: 0.7497 (tm-30) cc_final: 0.6880 (tm-30) REVERT: A 864 MET cc_start: 0.7902 (ttm) cc_final: 0.7591 (ttm) REVERT: A 894 ARG cc_start: 0.7733 (mtp85) cc_final: 0.7528 (mtp85) REVERT: B 144 ASP cc_start: 0.8052 (m-30) cc_final: 0.7780 (m-30) REVERT: B 202 MET cc_start: 0.8189 (OUTLIER) cc_final: 0.7974 (ptp) REVERT: B 237 ARG cc_start: 0.8391 (mtp-110) cc_final: 0.8098 (mtp-110) REVERT: B 262 GLN cc_start: 0.8052 (tm130) cc_final: 0.7777 (tp40) REVERT: B 358 GLU cc_start: 0.7486 (tt0) cc_final: 0.7205 (tt0) REVERT: B 394 ASN cc_start: 0.9117 (m-40) cc_final: 0.8662 (m-40) REVERT: B 471 LEU cc_start: 0.9283 (OUTLIER) cc_final: 0.8815 (mm) REVERT: B 521 LYS cc_start: 0.8555 (OUTLIER) cc_final: 0.8253 (mttt) REVERT: B 572 ASP cc_start: 0.8465 (OUTLIER) cc_final: 0.8072 (m-30) REVERT: B 601 PHE cc_start: 0.7931 (m-80) cc_final: 0.7671 (m-80) REVERT: B 648 ASP cc_start: 0.7579 (p0) cc_final: 0.7341 (t0) REVERT: B 667 GLU cc_start: 0.8247 (OUTLIER) cc_final: 0.8031 (mm-30) REVERT: B 702 GLN cc_start: 0.9021 (OUTLIER) cc_final: 0.8584 (mp-120) REVERT: B 719 GLN cc_start: 0.8619 (OUTLIER) cc_final: 0.8057 (tm-30) REVERT: B 726 LEU cc_start: 0.8422 (OUTLIER) cc_final: 0.8201 (mm) REVERT: B 801 ILE cc_start: 0.8397 (mt) cc_final: 0.8187 (mp) REVERT: B 804 ASN cc_start: 0.8574 (m-40) cc_final: 0.8320 (m-40) REVERT: B 864 MET cc_start: 0.7860 (ttm) cc_final: 0.7546 (ttm) REVERT: C 202 MET cc_start: 0.8196 (OUTLIER) cc_final: 0.7975 (ptp) REVERT: C 237 ARG cc_start: 0.8397 (mtp-110) cc_final: 0.8116 (mtp-110) REVERT: C 262 GLN cc_start: 0.8062 (tm130) cc_final: 0.7770 (tp40) REVERT: C 394 ASN cc_start: 0.9139 (m-40) cc_final: 0.8698 (m-40) REVERT: C 471 LEU cc_start: 0.9285 (OUTLIER) cc_final: 0.8833 (mm) REVERT: C 521 LYS cc_start: 0.8548 (OUTLIER) cc_final: 0.8259 (mttt) REVERT: C 572 ASP cc_start: 0.8476 (OUTLIER) cc_final: 0.7957 (m-30) REVERT: C 601 PHE cc_start: 0.7930 (m-80) cc_final: 0.7671 (m-80) REVERT: C 648 ASP cc_start: 0.7566 (p0) cc_final: 0.7324 (t0) REVERT: C 702 GLN cc_start: 0.9013 (OUTLIER) cc_final: 0.8572 (mp-120) REVERT: C 719 GLN cc_start: 0.8639 (OUTLIER) cc_final: 0.8102 (tm-30) REVERT: C 726 LEU cc_start: 0.8445 (OUTLIER) cc_final: 0.8218 (mm) REVERT: C 804 ASN cc_start: 0.8543 (m-40) cc_final: 0.8312 (m-40) REVERT: C 864 MET cc_start: 0.7927 (ttm) cc_final: 0.7617 (ttm) REVERT: C 917 ARG cc_start: 0.8999 (OUTLIER) cc_final: 0.7334 (tpp-160) REVERT: D 202 MET cc_start: 0.8186 (OUTLIER) cc_final: 0.7972 (ptp) REVERT: D 237 ARG cc_start: 0.8387 (mtp-110) cc_final: 0.7979 (mtp-110) REVERT: D 262 GLN cc_start: 0.8052 (tm130) cc_final: 0.7769 (tp40) REVERT: D 394 ASN cc_start: 0.9128 (m-40) cc_final: 0.8681 (m-40) REVERT: D 471 LEU cc_start: 0.9292 (OUTLIER) cc_final: 0.8843 (mm) REVERT: D 521 LYS cc_start: 0.8552 (OUTLIER) cc_final: 0.8260 (mttt) REVERT: D 572 ASP cc_start: 0.8459 (OUTLIER) cc_final: 0.7937 (m-30) REVERT: D 601 PHE cc_start: 0.7892 (m-80) cc_final: 0.7655 (m-80) REVERT: D 648 ASP cc_start: 0.7633 (p0) cc_final: 0.7332 (t0) REVERT: D 667 GLU cc_start: 0.8248 (OUTLIER) cc_final: 0.8042 (mm-30) REVERT: D 702 GLN cc_start: 0.9013 (OUTLIER) cc_final: 0.8574 (mp-120) REVERT: D 719 GLN cc_start: 0.8626 (OUTLIER) cc_final: 0.8089 (tm-30) REVERT: D 726 LEU cc_start: 0.8449 (OUTLIER) cc_final: 0.8205 (mm) REVERT: D 804 ASN cc_start: 0.8573 (m-40) cc_final: 0.8299 (m-40) REVERT: D 864 MET cc_start: 0.7907 (ttm) cc_final: 0.7610 (ttm) outliers start: 253 outliers final: 121 residues processed: 615 average time/residue: 0.5066 time to fit residues: 492.9582 Evaluate side-chains 501 residues out of total 3496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 154 poor density : 347 time to evaluate : 3.936 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 ARG Chi-restraints excluded: chain A residue 33 PHE Chi-restraints excluded: chain A residue 36 TRP Chi-restraints excluded: chain A residue 43 ARG Chi-restraints excluded: chain A residue 74 LEU Chi-restraints excluded: chain A residue 188 VAL Chi-restraints excluded: chain A residue 200 GLN Chi-restraints excluded: chain A residue 202 MET Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 305 ILE Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 389 CYS Chi-restraints excluded: chain A residue 390 SER Chi-restraints excluded: chain A residue 471 LEU Chi-restraints excluded: chain A residue 494 THR Chi-restraints excluded: chain A residue 502 MET Chi-restraints excluded: chain A residue 520 ILE Chi-restraints excluded: chain A residue 521 LYS Chi-restraints excluded: chain A residue 544 ASN Chi-restraints excluded: chain A residue 572 ASP Chi-restraints excluded: chain A residue 599 ARG Chi-restraints excluded: chain A residue 611 ARG Chi-restraints excluded: chain A residue 617 LEU Chi-restraints excluded: chain A residue 667 GLU Chi-restraints excluded: chain A residue 702 GLN Chi-restraints excluded: chain A residue 719 GLN Chi-restraints excluded: chain A residue 726 LEU Chi-restraints excluded: chain A residue 837 THR Chi-restraints excluded: chain A residue 838 THR Chi-restraints excluded: chain A residue 855 THR Chi-restraints excluded: chain A residue 869 ASP Chi-restraints excluded: chain A residue 904 GLU Chi-restraints excluded: chain A residue 941 THR Chi-restraints excluded: chain A residue 963 SER Chi-restraints excluded: chain A residue 987 ASP Chi-restraints excluded: chain A residue 999 TRP Chi-restraints excluded: chain A residue 1020 TRP Chi-restraints excluded: chain B residue 13 ARG Chi-restraints excluded: chain B residue 33 PHE Chi-restraints excluded: chain B residue 36 TRP Chi-restraints excluded: chain B residue 43 ARG Chi-restraints excluded: chain B residue 74 LEU Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain B residue 200 GLN Chi-restraints excluded: chain B residue 202 MET Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain B residue 305 ILE Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain B residue 389 CYS Chi-restraints excluded: chain B residue 390 SER Chi-restraints excluded: chain B residue 471 LEU Chi-restraints excluded: chain B residue 494 THR Chi-restraints excluded: chain B residue 502 MET Chi-restraints excluded: chain B residue 520 ILE Chi-restraints excluded: chain B residue 521 LYS Chi-restraints excluded: chain B residue 572 ASP Chi-restraints excluded: chain B residue 599 ARG Chi-restraints excluded: chain B residue 611 ARG Chi-restraints excluded: chain B residue 617 LEU Chi-restraints excluded: chain B residue 667 GLU Chi-restraints excluded: chain B residue 702 GLN Chi-restraints excluded: chain B residue 719 GLN Chi-restraints excluded: chain B residue 726 LEU Chi-restraints excluded: chain B residue 837 THR Chi-restraints excluded: chain B residue 838 THR Chi-restraints excluded: chain B residue 855 THR Chi-restraints excluded: chain B residue 869 ASP Chi-restraints excluded: chain B residue 911 THR Chi-restraints excluded: chain B residue 941 THR Chi-restraints excluded: chain B residue 963 SER Chi-restraints excluded: chain B residue 987 ASP Chi-restraints excluded: chain B residue 999 TRP Chi-restraints excluded: chain B residue 1020 TRP Chi-restraints excluded: chain C residue 13 ARG Chi-restraints excluded: chain C residue 33 PHE Chi-restraints excluded: chain C residue 36 TRP Chi-restraints excluded: chain C residue 43 ARG Chi-restraints excluded: chain C residue 74 LEU Chi-restraints excluded: chain C residue 188 VAL Chi-restraints excluded: chain C residue 200 GLN Chi-restraints excluded: chain C residue 202 MET Chi-restraints excluded: chain C residue 209 PHE Chi-restraints excluded: chain C residue 240 LEU Chi-restraints excluded: chain C residue 305 ILE Chi-restraints excluded: chain C residue 377 LEU Chi-restraints excluded: chain C residue 389 CYS Chi-restraints excluded: chain C residue 390 SER Chi-restraints excluded: chain C residue 426 LEU Chi-restraints excluded: chain C residue 471 LEU Chi-restraints excluded: chain C residue 494 THR Chi-restraints excluded: chain C residue 502 MET Chi-restraints excluded: chain C residue 520 ILE Chi-restraints excluded: chain C residue 521 LYS Chi-restraints excluded: chain C residue 572 ASP Chi-restraints excluded: chain C residue 599 ARG Chi-restraints excluded: chain C residue 611 ARG Chi-restraints excluded: chain C residue 617 LEU Chi-restraints excluded: chain C residue 702 GLN Chi-restraints excluded: chain C residue 719 GLN Chi-restraints excluded: chain C residue 726 LEU Chi-restraints excluded: chain C residue 739 HIS Chi-restraints excluded: chain C residue 793 ILE Chi-restraints excluded: chain C residue 837 THR Chi-restraints excluded: chain C residue 838 THR Chi-restraints excluded: chain C residue 855 THR Chi-restraints excluded: chain C residue 869 ASP Chi-restraints excluded: chain C residue 904 GLU Chi-restraints excluded: chain C residue 917 ARG Chi-restraints excluded: chain C residue 941 THR Chi-restraints excluded: chain C residue 963 SER Chi-restraints excluded: chain C residue 987 ASP Chi-restraints excluded: chain C residue 999 TRP Chi-restraints excluded: chain C residue 1020 TRP Chi-restraints excluded: chain D residue 13 ARG Chi-restraints excluded: chain D residue 33 PHE Chi-restraints excluded: chain D residue 36 TRP Chi-restraints excluded: chain D residue 43 ARG Chi-restraints excluded: chain D residue 74 LEU Chi-restraints excluded: chain D residue 188 VAL Chi-restraints excluded: chain D residue 200 GLN Chi-restraints excluded: chain D residue 202 MET Chi-restraints excluded: chain D residue 209 PHE Chi-restraints excluded: chain D residue 240 LEU Chi-restraints excluded: chain D residue 305 ILE Chi-restraints excluded: chain D residue 377 LEU Chi-restraints excluded: chain D residue 389 CYS Chi-restraints excluded: chain D residue 390 SER Chi-restraints excluded: chain D residue 426 LEU Chi-restraints excluded: chain D residue 471 LEU Chi-restraints excluded: chain D residue 494 THR Chi-restraints excluded: chain D residue 502 MET Chi-restraints excluded: chain D residue 520 ILE Chi-restraints excluded: chain D residue 521 LYS Chi-restraints excluded: chain D residue 572 ASP Chi-restraints excluded: chain D residue 599 ARG Chi-restraints excluded: chain D residue 611 ARG Chi-restraints excluded: chain D residue 617 LEU Chi-restraints excluded: chain D residue 667 GLU Chi-restraints excluded: chain D residue 702 GLN Chi-restraints excluded: chain D residue 719 GLN Chi-restraints excluded: chain D residue 726 LEU Chi-restraints excluded: chain D residue 793 ILE Chi-restraints excluded: chain D residue 837 THR Chi-restraints excluded: chain D residue 838 THR Chi-restraints excluded: chain D residue 855 THR Chi-restraints excluded: chain D residue 869 ASP Chi-restraints excluded: chain D residue 904 GLU Chi-restraints excluded: chain D residue 911 THR Chi-restraints excluded: chain D residue 941 THR Chi-restraints excluded: chain D residue 963 SER Chi-restraints excluded: chain D residue 987 ASP Chi-restraints excluded: chain D residue 999 TRP Chi-restraints excluded: chain D residue 1020 TRP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 165 optimal weight: 10.0000 chunk 236 optimal weight: 10.0000 chunk 118 optimal weight: 0.0870 chunk 97 optimal weight: 20.0000 chunk 328 optimal weight: 5.9990 chunk 193 optimal weight: 9.9990 chunk 86 optimal weight: 20.0000 chunk 246 optimal weight: 8.9990 chunk 54 optimal weight: 0.0980 chunk 304 optimal weight: 9.9990 chunk 182 optimal weight: 0.9990 overall best weight: 3.2364 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 360 HIS ** A 604 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 653 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 719 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 761 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 890 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 360 HIS ** B 604 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 653 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 719 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 761 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 863 GLN ** B 890 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 360 HIS ** C 604 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 653 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 719 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 761 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 863 GLN ** C 890 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 360 HIS ** D 604 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 653 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 719 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 761 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 863 GLN ** D 890 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1008 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.092789 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.077044 restraints weight = 66613.624| |-----------------------------------------------------------------------------| r_work (start): 0.3124 rms_B_bonded: 2.74 r_work: 0.3003 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3003 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8436 moved from start: 0.4954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 33812 Z= 0.181 Angle : 0.641 8.795 46104 Z= 0.340 Chirality : 0.045 0.190 4820 Planarity : 0.005 0.096 6088 Dihedral : 7.196 66.606 4560 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 13.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 7.07 % Allowed : 19.97 % Favored : 72.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.06 % Cis-general : 1.15 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.47 (0.13), residues: 4080 helix: 0.17 (0.22), residues: 580 sheet: 1.38 (0.13), residues: 1416 loop : -0.38 (0.13), residues: 2084 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP D1020 HIS 0.006 0.001 HIS D 653 PHE 0.016 0.002 PHE A 209 TYR 0.012 0.002 TYR D1014 ARG 0.004 0.001 ARG A 853 Details of bonding type rmsd hydrogen bonds : bond 0.03825 ( 1144) hydrogen bonds : angle 5.75336 ( 3288) covalent geometry : bond 0.00409 (33792) covalent geometry : angle 0.64092 (46104) Misc. bond : bond 0.00234 ( 20) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 583 residues out of total 3496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 247 poor density : 336 time to evaluate : 3.503 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 144 ASP cc_start: 0.8113 (m-30) cc_final: 0.7841 (m-30) REVERT: A 372 MET cc_start: 0.8612 (mtm) cc_final: 0.8303 (mtm) REVERT: A 416 GLU cc_start: 0.8345 (OUTLIER) cc_final: 0.8049 (tt0) REVERT: A 433 LEU cc_start: 0.9354 (OUTLIER) cc_final: 0.9119 (tp) REVERT: A 471 LEU cc_start: 0.9290 (OUTLIER) cc_final: 0.8845 (mm) REVERT: A 521 LYS cc_start: 0.8572 (OUTLIER) cc_final: 0.8352 (mttp) REVERT: A 572 ASP cc_start: 0.8362 (OUTLIER) cc_final: 0.7701 (m-30) REVERT: A 601 PHE cc_start: 0.8200 (m-80) cc_final: 0.7982 (m-80) REVERT: A 702 GLN cc_start: 0.9042 (OUTLIER) cc_final: 0.8573 (mp-120) REVERT: A 719 GLN cc_start: 0.8661 (OUTLIER) cc_final: 0.8094 (tm-30) REVERT: A 804 ASN cc_start: 0.8545 (m-40) cc_final: 0.8300 (m-40) REVERT: A 887 GLN cc_start: 0.8555 (OUTLIER) cc_final: 0.8189 (tp40) REVERT: A 911 THR cc_start: 0.9150 (OUTLIER) cc_final: 0.8832 (p) REVERT: B 144 ASP cc_start: 0.8111 (m-30) cc_final: 0.7838 (m-30) REVERT: B 237 ARG cc_start: 0.8384 (mtp-110) cc_final: 0.8126 (mtp-110) REVERT: B 416 GLU cc_start: 0.8353 (OUTLIER) cc_final: 0.8060 (tt0) REVERT: B 433 LEU cc_start: 0.9358 (OUTLIER) cc_final: 0.9124 (tp) REVERT: B 471 LEU cc_start: 0.9288 (OUTLIER) cc_final: 0.8835 (mm) REVERT: B 521 LYS cc_start: 0.8579 (OUTLIER) cc_final: 0.8296 (mttt) REVERT: B 572 ASP cc_start: 0.8374 (OUTLIER) cc_final: 0.7854 (m-30) REVERT: B 601 PHE cc_start: 0.8187 (m-80) cc_final: 0.7968 (m-80) REVERT: B 702 GLN cc_start: 0.9044 (OUTLIER) cc_final: 0.8584 (mp-120) REVERT: B 719 GLN cc_start: 0.8662 (OUTLIER) cc_final: 0.8098 (tm-30) REVERT: B 804 ASN cc_start: 0.8545 (m-40) cc_final: 0.8277 (m-40) REVERT: B 911 THR cc_start: 0.9172 (OUTLIER) cc_final: 0.8851 (p) REVERT: C 237 ARG cc_start: 0.8397 (mtp-110) cc_final: 0.8144 (mtp-110) REVERT: C 372 MET cc_start: 0.8598 (mtm) cc_final: 0.8340 (mtm) REVERT: C 394 ASN cc_start: 0.9115 (m-40) cc_final: 0.8766 (m-40) REVERT: C 416 GLU cc_start: 0.8337 (OUTLIER) cc_final: 0.8050 (tt0) REVERT: C 471 LEU cc_start: 0.9286 (OUTLIER) cc_final: 0.8840 (mm) REVERT: C 521 LYS cc_start: 0.8555 (OUTLIER) cc_final: 0.8280 (mttt) REVERT: C 572 ASP cc_start: 0.8348 (OUTLIER) cc_final: 0.7719 (m-30) REVERT: C 601 PHE cc_start: 0.8094 (m-80) cc_final: 0.7834 (m-80) REVERT: C 702 GLN cc_start: 0.9035 (OUTLIER) cc_final: 0.8572 (mp-120) REVERT: C 719 GLN cc_start: 0.8638 (OUTLIER) cc_final: 0.8091 (tm-30) REVERT: C 804 ASN cc_start: 0.8526 (m-40) cc_final: 0.8280 (m-40) REVERT: C 887 GLN cc_start: 0.8589 (OUTLIER) cc_final: 0.8225 (tp40) REVERT: C 911 THR cc_start: 0.9139 (OUTLIER) cc_final: 0.8814 (p) REVERT: C 917 ARG cc_start: 0.9050 (OUTLIER) cc_final: 0.7388 (tpp-160) REVERT: D 372 MET cc_start: 0.8589 (mtm) cc_final: 0.8332 (mtm) REVERT: D 394 ASN cc_start: 0.9113 (m-40) cc_final: 0.8764 (m-40) REVERT: D 416 GLU cc_start: 0.8355 (OUTLIER) cc_final: 0.8076 (tt0) REVERT: D 471 LEU cc_start: 0.9299 (OUTLIER) cc_final: 0.8851 (mm) REVERT: D 521 LYS cc_start: 0.8566 (OUTLIER) cc_final: 0.8292 (mttt) REVERT: D 572 ASP cc_start: 0.8367 (OUTLIER) cc_final: 0.7734 (m-30) REVERT: D 702 GLN cc_start: 0.9035 (OUTLIER) cc_final: 0.8576 (mp-120) REVERT: D 719 GLN cc_start: 0.8658 (OUTLIER) cc_final: 0.8097 (tm-30) REVERT: D 804 ASN cc_start: 0.8578 (m-40) cc_final: 0.8296 (m-40) REVERT: D 887 GLN cc_start: 0.8579 (OUTLIER) cc_final: 0.8215 (tp40) REVERT: D 911 THR cc_start: 0.9168 (OUTLIER) cc_final: 0.8846 (p) outliers start: 247 outliers final: 151 residues processed: 543 average time/residue: 0.4697 time to fit residues: 410.0972 Evaluate side-chains 494 residues out of total 3496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 185 poor density : 309 time to evaluate : 3.529 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 MET Chi-restraints excluded: chain A residue 13 ARG Chi-restraints excluded: chain A residue 33 PHE Chi-restraints excluded: chain A residue 36 TRP Chi-restraints excluded: chain A residue 43 ARG Chi-restraints excluded: chain A residue 74 LEU Chi-restraints excluded: chain A residue 124 SER Chi-restraints excluded: chain A residue 181 GLU Chi-restraints excluded: chain A residue 200 GLN Chi-restraints excluded: chain A residue 209 PHE Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 244 VAL Chi-restraints excluded: chain A residue 305 ILE Chi-restraints excluded: chain A residue 321 THR Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 374 GLN Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 416 GLU Chi-restraints excluded: chain A residue 418 HIS Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain A residue 433 LEU Chi-restraints excluded: chain A residue 471 LEU Chi-restraints excluded: chain A residue 494 THR Chi-restraints excluded: chain A residue 502 MET Chi-restraints excluded: chain A residue 520 ILE Chi-restraints excluded: chain A residue 521 LYS Chi-restraints excluded: chain A residue 530 THR Chi-restraints excluded: chain A residue 572 ASP Chi-restraints excluded: chain A residue 599 ARG Chi-restraints excluded: chain A residue 617 LEU Chi-restraints excluded: chain A residue 702 GLN Chi-restraints excluded: chain A residue 719 GLN Chi-restraints excluded: chain A residue 837 THR Chi-restraints excluded: chain A residue 838 THR Chi-restraints excluded: chain A residue 855 THR Chi-restraints excluded: chain A residue 869 ASP Chi-restraints excluded: chain A residue 887 GLN Chi-restraints excluded: chain A residue 904 GLU Chi-restraints excluded: chain A residue 911 THR Chi-restraints excluded: chain A residue 914 CYS Chi-restraints excluded: chain A residue 941 THR Chi-restraints excluded: chain A residue 963 SER Chi-restraints excluded: chain A residue 980 GLU Chi-restraints excluded: chain A residue 987 ASP Chi-restraints excluded: chain A residue 999 TRP Chi-restraints excluded: chain A residue 1020 TRP Chi-restraints excluded: chain B residue 2 MET Chi-restraints excluded: chain B residue 13 ARG Chi-restraints excluded: chain B residue 33 PHE Chi-restraints excluded: chain B residue 36 TRP Chi-restraints excluded: chain B residue 43 ARG Chi-restraints excluded: chain B residue 74 LEU Chi-restraints excluded: chain B residue 124 SER Chi-restraints excluded: chain B residue 181 GLU Chi-restraints excluded: chain B residue 200 GLN Chi-restraints excluded: chain B residue 209 PHE Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain B residue 244 VAL Chi-restraints excluded: chain B residue 305 ILE Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain B residue 343 LEU Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain B residue 416 GLU Chi-restraints excluded: chain B residue 418 HIS Chi-restraints excluded: chain B residue 426 LEU Chi-restraints excluded: chain B residue 433 LEU Chi-restraints excluded: chain B residue 471 LEU Chi-restraints excluded: chain B residue 494 THR Chi-restraints excluded: chain B residue 502 MET Chi-restraints excluded: chain B residue 520 ILE Chi-restraints excluded: chain B residue 521 LYS Chi-restraints excluded: chain B residue 530 THR Chi-restraints excluded: chain B residue 572 ASP Chi-restraints excluded: chain B residue 599 ARG Chi-restraints excluded: chain B residue 617 LEU Chi-restraints excluded: chain B residue 702 GLN Chi-restraints excluded: chain B residue 719 GLN Chi-restraints excluded: chain B residue 780 LEU Chi-restraints excluded: chain B residue 795 VAL Chi-restraints excluded: chain B residue 837 THR Chi-restraints excluded: chain B residue 838 THR Chi-restraints excluded: chain B residue 855 THR Chi-restraints excluded: chain B residue 869 ASP Chi-restraints excluded: chain B residue 904 GLU Chi-restraints excluded: chain B residue 911 THR Chi-restraints excluded: chain B residue 914 CYS Chi-restraints excluded: chain B residue 941 THR Chi-restraints excluded: chain B residue 963 SER Chi-restraints excluded: chain B residue 980 GLU Chi-restraints excluded: chain B residue 987 ASP Chi-restraints excluded: chain B residue 999 TRP Chi-restraints excluded: chain B residue 1020 TRP Chi-restraints excluded: chain C residue 13 ARG Chi-restraints excluded: chain C residue 33 PHE Chi-restraints excluded: chain C residue 36 TRP Chi-restraints excluded: chain C residue 43 ARG Chi-restraints excluded: chain C residue 74 LEU Chi-restraints excluded: chain C residue 124 SER Chi-restraints excluded: chain C residue 181 GLU Chi-restraints excluded: chain C residue 200 GLN Chi-restraints excluded: chain C residue 209 PHE Chi-restraints excluded: chain C residue 240 LEU Chi-restraints excluded: chain C residue 244 VAL Chi-restraints excluded: chain C residue 305 ILE Chi-restraints excluded: chain C residue 321 THR Chi-restraints excluded: chain C residue 322 LEU Chi-restraints excluded: chain C residue 377 LEU Chi-restraints excluded: chain C residue 416 GLU Chi-restraints excluded: chain C residue 418 HIS Chi-restraints excluded: chain C residue 426 LEU Chi-restraints excluded: chain C residue 471 LEU Chi-restraints excluded: chain C residue 494 THR Chi-restraints excluded: chain C residue 502 MET Chi-restraints excluded: chain C residue 520 ILE Chi-restraints excluded: chain C residue 521 LYS Chi-restraints excluded: chain C residue 530 THR Chi-restraints excluded: chain C residue 572 ASP Chi-restraints excluded: chain C residue 599 ARG Chi-restraints excluded: chain C residue 617 LEU Chi-restraints excluded: chain C residue 702 GLN Chi-restraints excluded: chain C residue 719 GLN Chi-restraints excluded: chain C residue 780 LEU Chi-restraints excluded: chain C residue 793 ILE Chi-restraints excluded: chain C residue 795 VAL Chi-restraints excluded: chain C residue 828 ASP Chi-restraints excluded: chain C residue 837 THR Chi-restraints excluded: chain C residue 838 THR Chi-restraints excluded: chain C residue 855 THR Chi-restraints excluded: chain C residue 869 ASP Chi-restraints excluded: chain C residue 887 GLN Chi-restraints excluded: chain C residue 904 GLU Chi-restraints excluded: chain C residue 911 THR Chi-restraints excluded: chain C residue 917 ARG Chi-restraints excluded: chain C residue 941 THR Chi-restraints excluded: chain C residue 963 SER Chi-restraints excluded: chain C residue 980 GLU Chi-restraints excluded: chain C residue 987 ASP Chi-restraints excluded: chain C residue 999 TRP Chi-restraints excluded: chain C residue 1020 TRP Chi-restraints excluded: chain D residue 13 ARG Chi-restraints excluded: chain D residue 33 PHE Chi-restraints excluded: chain D residue 36 TRP Chi-restraints excluded: chain D residue 43 ARG Chi-restraints excluded: chain D residue 74 LEU Chi-restraints excluded: chain D residue 124 SER Chi-restraints excluded: chain D residue 181 GLU Chi-restraints excluded: chain D residue 200 GLN Chi-restraints excluded: chain D residue 209 PHE Chi-restraints excluded: chain D residue 222 ILE Chi-restraints excluded: chain D residue 240 LEU Chi-restraints excluded: chain D residue 244 VAL Chi-restraints excluded: chain D residue 305 ILE Chi-restraints excluded: chain D residue 322 LEU Chi-restraints excluded: chain D residue 377 LEU Chi-restraints excluded: chain D residue 416 GLU Chi-restraints excluded: chain D residue 418 HIS Chi-restraints excluded: chain D residue 426 LEU Chi-restraints excluded: chain D residue 471 LEU Chi-restraints excluded: chain D residue 494 THR Chi-restraints excluded: chain D residue 502 MET Chi-restraints excluded: chain D residue 520 ILE Chi-restraints excluded: chain D residue 521 LYS Chi-restraints excluded: chain D residue 530 THR Chi-restraints excluded: chain D residue 572 ASP Chi-restraints excluded: chain D residue 599 ARG Chi-restraints excluded: chain D residue 617 LEU Chi-restraints excluded: chain D residue 702 GLN Chi-restraints excluded: chain D residue 719 GLN Chi-restraints excluded: chain D residue 780 LEU Chi-restraints excluded: chain D residue 793 ILE Chi-restraints excluded: chain D residue 795 VAL Chi-restraints excluded: chain D residue 837 THR Chi-restraints excluded: chain D residue 838 THR Chi-restraints excluded: chain D residue 855 THR Chi-restraints excluded: chain D residue 869 ASP Chi-restraints excluded: chain D residue 887 GLN Chi-restraints excluded: chain D residue 904 GLU Chi-restraints excluded: chain D residue 911 THR Chi-restraints excluded: chain D residue 914 CYS Chi-restraints excluded: chain D residue 941 THR Chi-restraints excluded: chain D residue 963 SER Chi-restraints excluded: chain D residue 980 GLU Chi-restraints excluded: chain D residue 987 ASP Chi-restraints excluded: chain D residue 999 TRP Chi-restraints excluded: chain D residue 1020 TRP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 337 optimal weight: 6.9990 chunk 115 optimal weight: 5.9990 chunk 242 optimal weight: 2.9990 chunk 239 optimal weight: 10.0000 chunk 262 optimal weight: 0.9980 chunk 294 optimal weight: 2.9990 chunk 1 optimal weight: 9.9990 chunk 39 optimal weight: 5.9990 chunk 152 optimal weight: 8.9990 chunk 264 optimal weight: 0.9980 chunk 403 optimal weight: 0.8980 overall best weight: 1.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 363 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 604 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 624 GLN ** A 719 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 761 GLN A 863 GLN ** A 890 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 363 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 604 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 719 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 761 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 863 GLN ** B 890 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 604 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 624 GLN ** C 719 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 761 GLN C 863 GLN ** C 890 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 604 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 719 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 761 GLN D 863 GLN ** D 890 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1008 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 = 0.3420 r_free = 0.3420 target = 0.094735 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.078997 restraints weight = 66336.360| |-----------------------------------------------------------------------------| r_work (start): 0.3148 rms_B_bonded: 2.75 r_work: 0.3027 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3027 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8404 moved from start: 0.5171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 33812 Z= 0.132 Angle : 0.614 16.328 46104 Z= 0.318 Chirality : 0.043 0.184 4820 Planarity : 0.004 0.057 6088 Dihedral : 6.296 51.853 4548 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 11.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 6.06 % Allowed : 20.62 % Favored : 73.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.06 % Cis-general : 1.15 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.42 (0.13), residues: 4080 helix: 0.39 (0.22), residues: 556 sheet: 1.22 (0.13), residues: 1416 loop : -0.38 (0.13), residues: 2108 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP D 553 HIS 0.006 0.001 HIS A 653 PHE 0.016 0.001 PHE A 747 TYR 0.011 0.001 TYR B 906 ARG 0.005 0.000 ARG D 630 Details of bonding type rmsd hydrogen bonds : bond 0.03403 ( 1144) hydrogen bonds : angle 5.55687 ( 3288) covalent geometry : bond 0.00293 (33792) covalent geometry : angle 0.61397 (46104) Misc. bond : bond 0.00316 ( 20) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 577 residues out of total 3496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 212 poor density : 365 time to evaluate : 3.667 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 394 ASN cc_start: 0.9124 (m-40) cc_final: 0.8766 (m-40) REVERT: A 416 GLU cc_start: 0.8436 (OUTLIER) cc_final: 0.8057 (tp30) REVERT: A 461 GLU cc_start: 0.8078 (mt-10) cc_final: 0.7849 (mt-10) REVERT: A 471 LEU cc_start: 0.9251 (OUTLIER) cc_final: 0.8835 (mm) REVERT: A 521 LYS cc_start: 0.8475 (OUTLIER) cc_final: 0.8260 (mttp) REVERT: A 572 ASP cc_start: 0.8268 (OUTLIER) cc_final: 0.7732 (m-30) REVERT: A 601 PHE cc_start: 0.8267 (m-80) cc_final: 0.8044 (m-80) REVERT: A 702 GLN cc_start: 0.8974 (OUTLIER) cc_final: 0.8487 (mt0) REVERT: A 719 GLN cc_start: 0.8608 (OUTLIER) cc_final: 0.8113 (tm-30) REVERT: A 744 GLU cc_start: 0.7238 (pm20) cc_final: 0.6698 (tp30) REVERT: A 887 GLN cc_start: 0.8518 (OUTLIER) cc_final: 0.8084 (tp40) REVERT: A 911 THR cc_start: 0.9120 (OUTLIER) cc_final: 0.8818 (p) REVERT: B 237 ARG cc_start: 0.8371 (mtp-110) cc_final: 0.8121 (mtp-110) REVERT: B 394 ASN cc_start: 0.9062 (m-40) cc_final: 0.8413 (t0) REVERT: B 416 GLU cc_start: 0.8433 (OUTLIER) cc_final: 0.8063 (tp30) REVERT: B 461 GLU cc_start: 0.8070 (mt-10) cc_final: 0.7827 (mt-10) REVERT: B 471 LEU cc_start: 0.9248 (OUTLIER) cc_final: 0.8827 (mm) REVERT: B 521 LYS cc_start: 0.8468 (OUTLIER) cc_final: 0.8252 (mttp) REVERT: B 572 ASP cc_start: 0.8214 (OUTLIER) cc_final: 0.7690 (m-30) REVERT: B 601 PHE cc_start: 0.8268 (m-80) cc_final: 0.8068 (m-80) REVERT: B 702 GLN cc_start: 0.8968 (OUTLIER) cc_final: 0.8476 (mt0) REVERT: B 719 GLN cc_start: 0.8605 (OUTLIER) cc_final: 0.8093 (tm-30) REVERT: B 744 GLU cc_start: 0.7206 (pm20) cc_final: 0.6690 (tp30) REVERT: B 769 TRP cc_start: 0.7823 (m100) cc_final: 0.7616 (m100) REVERT: B 887 GLN cc_start: 0.8549 (OUTLIER) cc_final: 0.8111 (tp40) REVERT: C 237 ARG cc_start: 0.8408 (mtp-110) cc_final: 0.8169 (mtp-110) REVERT: C 372 MET cc_start: 0.8579 (mtm) cc_final: 0.8369 (mtm) REVERT: C 416 GLU cc_start: 0.8423 (OUTLIER) cc_final: 0.8115 (tp30) REVERT: C 471 LEU cc_start: 0.9244 (OUTLIER) cc_final: 0.8805 (mm) REVERT: C 521 LYS cc_start: 0.8463 (OUTLIER) cc_final: 0.8247 (mttp) REVERT: C 572 ASP cc_start: 0.8243 (OUTLIER) cc_final: 0.7733 (m-30) REVERT: C 702 GLN cc_start: 0.8983 (OUTLIER) cc_final: 0.8527 (mt0) REVERT: C 719 GLN cc_start: 0.8629 (OUTLIER) cc_final: 0.8128 (tm-30) REVERT: C 744 GLU cc_start: 0.7201 (pm20) cc_final: 0.6655 (tp30) REVERT: C 887 GLN cc_start: 0.8544 (OUTLIER) cc_final: 0.8175 (tp40) REVERT: C 911 THR cc_start: 0.9127 (OUTLIER) cc_final: 0.8811 (p) REVERT: D 372 MET cc_start: 0.8580 (mtm) cc_final: 0.8374 (mtm) REVERT: D 416 GLU cc_start: 0.8432 (OUTLIER) cc_final: 0.8128 (tp30) REVERT: D 471 LEU cc_start: 0.9261 (OUTLIER) cc_final: 0.8822 (mm) REVERT: D 521 LYS cc_start: 0.8462 (OUTLIER) cc_final: 0.8246 (mttp) REVERT: D 572 ASP cc_start: 0.8250 (OUTLIER) cc_final: 0.7727 (m-30) REVERT: D 702 GLN cc_start: 0.8972 (OUTLIER) cc_final: 0.8490 (mt0) REVERT: D 719 GLN cc_start: 0.8616 (OUTLIER) cc_final: 0.8118 (tm-30) REVERT: D 744 GLU cc_start: 0.7221 (pm20) cc_final: 0.6640 (tp30) REVERT: D 804 ASN cc_start: 0.8548 (m-40) cc_final: 0.8246 (m-40) REVERT: D 887 GLN cc_start: 0.8547 (OUTLIER) cc_final: 0.8183 (tp40) outliers start: 212 outliers final: 136 residues processed: 540 average time/residue: 0.6404 time to fit residues: 573.6969 Evaluate side-chains 481 residues out of total 3496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 166 poor density : 315 time to evaluate : 4.457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 MET Chi-restraints excluded: chain A residue 11 LEU Chi-restraints excluded: chain A residue 13 ARG Chi-restraints excluded: chain A residue 33 PHE Chi-restraints excluded: chain A residue 36 TRP Chi-restraints excluded: chain A residue 43 ARG Chi-restraints excluded: chain A residue 74 LEU Chi-restraints excluded: chain A residue 124 SER Chi-restraints excluded: chain A residue 209 PHE Chi-restraints excluded: chain A residue 222 ILE Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 244 VAL Chi-restraints excluded: chain A residue 305 ILE Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 416 GLU Chi-restraints excluded: chain A residue 471 LEU Chi-restraints excluded: chain A residue 520 ILE Chi-restraints excluded: chain A residue 521 LYS Chi-restraints excluded: chain A residue 530 THR Chi-restraints excluded: chain A residue 572 ASP Chi-restraints excluded: chain A residue 599 ARG Chi-restraints excluded: chain A residue 702 GLN Chi-restraints excluded: chain A residue 719 GLN Chi-restraints excluded: chain A residue 760 ARG Chi-restraints excluded: chain A residue 782 ASP Chi-restraints excluded: chain A residue 795 VAL Chi-restraints excluded: chain A residue 837 THR Chi-restraints excluded: chain A residue 838 THR Chi-restraints excluded: chain A residue 855 THR Chi-restraints excluded: chain A residue 864 MET Chi-restraints excluded: chain A residue 869 ASP Chi-restraints excluded: chain A residue 887 GLN Chi-restraints excluded: chain A residue 904 GLU Chi-restraints excluded: chain A residue 911 THR Chi-restraints excluded: chain A residue 941 THR Chi-restraints excluded: chain A residue 963 SER Chi-restraints excluded: chain A residue 980 GLU Chi-restraints excluded: chain A residue 987 ASP Chi-restraints excluded: chain A residue 999 TRP Chi-restraints excluded: chain B residue 2 MET Chi-restraints excluded: chain B residue 11 LEU Chi-restraints excluded: chain B residue 13 ARG Chi-restraints excluded: chain B residue 33 PHE Chi-restraints excluded: chain B residue 36 TRP Chi-restraints excluded: chain B residue 43 ARG Chi-restraints excluded: chain B residue 74 LEU Chi-restraints excluded: chain B residue 124 SER Chi-restraints excluded: chain B residue 209 PHE Chi-restraints excluded: chain B residue 241 GLU Chi-restraints excluded: chain B residue 305 ILE Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain B residue 374 GLN Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain B residue 416 GLU Chi-restraints excluded: chain B residue 426 LEU Chi-restraints excluded: chain B residue 471 LEU Chi-restraints excluded: chain B residue 520 ILE Chi-restraints excluded: chain B residue 521 LYS Chi-restraints excluded: chain B residue 530 THR Chi-restraints excluded: chain B residue 572 ASP Chi-restraints excluded: chain B residue 599 ARG Chi-restraints excluded: chain B residue 702 GLN Chi-restraints excluded: chain B residue 719 GLN Chi-restraints excluded: chain B residue 780 LEU Chi-restraints excluded: chain B residue 782 ASP Chi-restraints excluded: chain B residue 837 THR Chi-restraints excluded: chain B residue 838 THR Chi-restraints excluded: chain B residue 855 THR Chi-restraints excluded: chain B residue 864 MET Chi-restraints excluded: chain B residue 869 ASP Chi-restraints excluded: chain B residue 887 GLN Chi-restraints excluded: chain B residue 904 GLU Chi-restraints excluded: chain B residue 941 THR Chi-restraints excluded: chain B residue 963 SER Chi-restraints excluded: chain B residue 980 GLU Chi-restraints excluded: chain B residue 987 ASP Chi-restraints excluded: chain B residue 999 TRP Chi-restraints excluded: chain C residue 2 MET Chi-restraints excluded: chain C residue 13 ARG Chi-restraints excluded: chain C residue 33 PHE Chi-restraints excluded: chain C residue 36 TRP Chi-restraints excluded: chain C residue 43 ARG Chi-restraints excluded: chain C residue 74 LEU Chi-restraints excluded: chain C residue 124 SER Chi-restraints excluded: chain C residue 209 PHE Chi-restraints excluded: chain C residue 222 ILE Chi-restraints excluded: chain C residue 241 GLU Chi-restraints excluded: chain C residue 244 VAL Chi-restraints excluded: chain C residue 305 ILE Chi-restraints excluded: chain C residue 322 LEU Chi-restraints excluded: chain C residue 343 LEU Chi-restraints excluded: chain C residue 374 GLN Chi-restraints excluded: chain C residue 377 LEU Chi-restraints excluded: chain C residue 416 GLU Chi-restraints excluded: chain C residue 426 LEU Chi-restraints excluded: chain C residue 433 LEU Chi-restraints excluded: chain C residue 471 LEU Chi-restraints excluded: chain C residue 520 ILE Chi-restraints excluded: chain C residue 521 LYS Chi-restraints excluded: chain C residue 530 THR Chi-restraints excluded: chain C residue 572 ASP Chi-restraints excluded: chain C residue 599 ARG Chi-restraints excluded: chain C residue 702 GLN Chi-restraints excluded: chain C residue 719 GLN Chi-restraints excluded: chain C residue 739 HIS Chi-restraints excluded: chain C residue 780 LEU Chi-restraints excluded: chain C residue 782 ASP Chi-restraints excluded: chain C residue 793 ILE Chi-restraints excluded: chain C residue 837 THR Chi-restraints excluded: chain C residue 838 THR Chi-restraints excluded: chain C residue 855 THR Chi-restraints excluded: chain C residue 864 MET Chi-restraints excluded: chain C residue 869 ASP Chi-restraints excluded: chain C residue 887 GLN Chi-restraints excluded: chain C residue 904 GLU Chi-restraints excluded: chain C residue 911 THR Chi-restraints excluded: chain C residue 914 CYS Chi-restraints excluded: chain C residue 941 THR Chi-restraints excluded: chain C residue 963 SER Chi-restraints excluded: chain C residue 980 GLU Chi-restraints excluded: chain C residue 987 ASP Chi-restraints excluded: chain C residue 999 TRP Chi-restraints excluded: chain D residue 2 MET Chi-restraints excluded: chain D residue 13 ARG Chi-restraints excluded: chain D residue 33 PHE Chi-restraints excluded: chain D residue 36 TRP Chi-restraints excluded: chain D residue 43 ARG Chi-restraints excluded: chain D residue 74 LEU Chi-restraints excluded: chain D residue 124 SER Chi-restraints excluded: chain D residue 209 PHE Chi-restraints excluded: chain D residue 222 ILE Chi-restraints excluded: chain D residue 241 GLU Chi-restraints excluded: chain D residue 244 VAL Chi-restraints excluded: chain D residue 250 LEU Chi-restraints excluded: chain D residue 305 ILE Chi-restraints excluded: chain D residue 322 LEU Chi-restraints excluded: chain D residue 343 LEU Chi-restraints excluded: chain D residue 374 GLN Chi-restraints excluded: chain D residue 377 LEU Chi-restraints excluded: chain D residue 416 GLU Chi-restraints excluded: chain D residue 426 LEU Chi-restraints excluded: chain D residue 433 LEU Chi-restraints excluded: chain D residue 471 LEU Chi-restraints excluded: chain D residue 520 ILE Chi-restraints excluded: chain D residue 521 LYS Chi-restraints excluded: chain D residue 530 THR Chi-restraints excluded: chain D residue 572 ASP Chi-restraints excluded: chain D residue 599 ARG Chi-restraints excluded: chain D residue 702 GLN Chi-restraints excluded: chain D residue 719 GLN Chi-restraints excluded: chain D residue 780 LEU Chi-restraints excluded: chain D residue 782 ASP Chi-restraints excluded: chain D residue 793 ILE Chi-restraints excluded: chain D residue 837 THR Chi-restraints excluded: chain D residue 838 THR Chi-restraints excluded: chain D residue 855 THR Chi-restraints excluded: chain D residue 869 ASP Chi-restraints excluded: chain D residue 887 GLN Chi-restraints excluded: chain D residue 904 GLU Chi-restraints excluded: chain D residue 941 THR Chi-restraints excluded: chain D residue 963 SER Chi-restraints excluded: chain D residue 980 GLU Chi-restraints excluded: chain D residue 987 ASP Chi-restraints excluded: chain D residue 999 TRP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 401 optimal weight: 9.9990 chunk 74 optimal weight: 3.9990 chunk 289 optimal weight: 10.0000 chunk 32 optimal weight: 10.0000 chunk 35 optimal weight: 9.9990 chunk 37 optimal weight: 2.9990 chunk 395 optimal weight: 5.9990 chunk 49 optimal weight: 4.9990 chunk 147 optimal weight: 6.9990 chunk 143 optimal weight: 6.9990 chunk 138 optimal weight: 0.9980 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 182 ASN ** A 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 363 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 382 ASN ** A 604 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 624 GLN ** A 719 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 791 ASN A 863 GLN ** B 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 363 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 382 ASN ** B 604 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 719 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 761 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 791 ASN ** B 863 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 182 ASN ** C 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 382 ASN ** C 604 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 624 GLN ** C 719 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 863 GLN D 182 ASN ** D 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 382 ASN ** D 604 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 719 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 791 ASN ** D 863 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1008 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.091649 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.075781 restraints weight = 66648.403| |-----------------------------------------------------------------------------| r_work (start): 0.3106 rms_B_bonded: 2.74 r_work: 0.2986 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.2986 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8455 moved from start: 0.5269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 33812 Z= 0.197 Angle : 0.658 19.516 46104 Z= 0.342 Chirality : 0.045 0.204 4820 Planarity : 0.005 0.084 6088 Dihedral : 6.014 53.800 4534 Min Nonbonded Distance : 1.910 Molprobity Statistics. All-atom Clashscore : 12.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 5.95 % Allowed : 20.85 % Favored : 73.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.06 % Cis-general : 1.15 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.27 (0.13), residues: 4080 helix: 0.32 (0.22), residues: 556 sheet: 1.02 (0.14), residues: 1416 loop : -0.41 (0.13), residues: 2108 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP C1020 HIS 0.005 0.001 HIS C 653 PHE 0.015 0.002 PHE A 209 TYR 0.013 0.002 TYR B 906 ARG 0.005 0.001 ARG D 760 Details of bonding type rmsd hydrogen bonds : bond 0.03804 ( 1144) hydrogen bonds : angle 5.66815 ( 3288) covalent geometry : bond 0.00448 (33792) covalent geometry : angle 0.65834 (46104) Misc. bond : bond 0.00467 ( 20) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 530 residues out of total 3496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 208 poor density : 322 time to evaluate : 3.356 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 416 GLU cc_start: 0.8436 (OUTLIER) cc_final: 0.8153 (tp30) REVERT: A 471 LEU cc_start: 0.9288 (OUTLIER) cc_final: 0.8828 (mm) REVERT: A 521 LYS cc_start: 0.8658 (OUTLIER) cc_final: 0.8449 (mttp) REVERT: A 572 ASP cc_start: 0.8255 (OUTLIER) cc_final: 0.7821 (m-30) REVERT: A 601 PHE cc_start: 0.8336 (m-80) cc_final: 0.8105 (m-80) REVERT: A 887 GLN cc_start: 0.8589 (OUTLIER) cc_final: 0.7884 (tt0) REVERT: A 911 THR cc_start: 0.9122 (OUTLIER) cc_final: 0.8816 (p) REVERT: B 237 ARG cc_start: 0.8360 (mtp-110) cc_final: 0.8143 (mtp-110) REVERT: B 394 ASN cc_start: 0.9147 (m-40) cc_final: 0.8624 (t0) REVERT: B 416 GLU cc_start: 0.8420 (OUTLIER) cc_final: 0.8162 (tt0) REVERT: B 471 LEU cc_start: 0.9286 (OUTLIER) cc_final: 0.8822 (mm) REVERT: B 521 LYS cc_start: 0.8645 (OUTLIER) cc_final: 0.8439 (mttp) REVERT: B 572 ASP cc_start: 0.8221 (OUTLIER) cc_final: 0.7756 (m-30) REVERT: B 601 PHE cc_start: 0.8374 (m-80) cc_final: 0.8148 (m-80) REVERT: B 887 GLN cc_start: 0.8599 (OUTLIER) cc_final: 0.7903 (tt0) REVERT: B 908 ASP cc_start: 0.7844 (t0) cc_final: 0.7401 (t0) REVERT: B 911 THR cc_start: 0.9126 (OUTLIER) cc_final: 0.8820 (p) REVERT: C 237 ARG cc_start: 0.8358 (mtp-110) cc_final: 0.8137 (mtp-110) REVERT: C 416 GLU cc_start: 0.8426 (OUTLIER) cc_final: 0.8166 (tp30) REVERT: C 471 LEU cc_start: 0.9285 (OUTLIER) cc_final: 0.8825 (mm) REVERT: C 521 LYS cc_start: 0.8654 (OUTLIER) cc_final: 0.8447 (mttp) REVERT: C 572 ASP cc_start: 0.8219 (OUTLIER) cc_final: 0.7769 (m-30) REVERT: C 719 GLN cc_start: 0.8680 (OUTLIER) cc_final: 0.8124 (tm-30) REVERT: C 911 THR cc_start: 0.9121 (OUTLIER) cc_final: 0.8818 (p) REVERT: D 416 GLU cc_start: 0.8441 (OUTLIER) cc_final: 0.8177 (tp30) REVERT: D 471 LEU cc_start: 0.9299 (OUTLIER) cc_final: 0.8843 (mm) REVERT: D 521 LYS cc_start: 0.8652 (OUTLIER) cc_final: 0.8441 (mttp) REVERT: D 542 MET cc_start: 0.8061 (ttm) cc_final: 0.7788 (ttm) REVERT: D 572 ASP cc_start: 0.8219 (OUTLIER) cc_final: 0.7779 (m-30) REVERT: D 719 GLN cc_start: 0.8692 (OUTLIER) cc_final: 0.8126 (tm-30) REVERT: D 804 ASN cc_start: 0.8554 (m-40) cc_final: 0.8268 (m-40) REVERT: D 908 ASP cc_start: 0.7821 (t0) cc_final: 0.7394 (t0) REVERT: D 911 THR cc_start: 0.9125 (OUTLIER) cc_final: 0.8824 (p) outliers start: 208 outliers final: 147 residues processed: 498 average time/residue: 0.4367 time to fit residues: 356.2232 Evaluate side-chains 470 residues out of total 3496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 171 poor density : 299 time to evaluate : 3.677 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 MET Chi-restraints excluded: chain A residue 11 LEU Chi-restraints excluded: chain A residue 13 ARG Chi-restraints excluded: chain A residue 33 PHE Chi-restraints excluded: chain A residue 36 TRP Chi-restraints excluded: chain A residue 43 ARG Chi-restraints excluded: chain A residue 74 LEU Chi-restraints excluded: chain A residue 124 SER Chi-restraints excluded: chain A residue 181 GLU Chi-restraints excluded: chain A residue 209 PHE Chi-restraints excluded: chain A residue 244 VAL Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 374 GLN Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 416 GLU Chi-restraints excluded: chain A residue 433 LEU Chi-restraints excluded: chain A residue 471 LEU Chi-restraints excluded: chain A residue 494 THR Chi-restraints excluded: chain A residue 520 ILE Chi-restraints excluded: chain A residue 521 LYS Chi-restraints excluded: chain A residue 530 THR Chi-restraints excluded: chain A residue 572 ASP Chi-restraints excluded: chain A residue 599 ARG Chi-restraints excluded: chain A residue 739 HIS Chi-restraints excluded: chain A residue 782 ASP Chi-restraints excluded: chain A residue 795 VAL Chi-restraints excluded: chain A residue 837 THR Chi-restraints excluded: chain A residue 838 THR Chi-restraints excluded: chain A residue 855 THR Chi-restraints excluded: chain A residue 864 MET Chi-restraints excluded: chain A residue 869 ASP Chi-restraints excluded: chain A residue 887 GLN Chi-restraints excluded: chain A residue 904 GLU Chi-restraints excluded: chain A residue 911 THR Chi-restraints excluded: chain A residue 914 CYS Chi-restraints excluded: chain A residue 941 THR Chi-restraints excluded: chain A residue 963 SER Chi-restraints excluded: chain A residue 980 GLU Chi-restraints excluded: chain A residue 982 THR Chi-restraints excluded: chain A residue 987 ASP Chi-restraints excluded: chain A residue 997 ASP Chi-restraints excluded: chain A residue 999 TRP Chi-restraints excluded: chain A residue 1022 GLN Chi-restraints excluded: chain B residue 2 MET Chi-restraints excluded: chain B residue 11 LEU Chi-restraints excluded: chain B residue 13 ARG Chi-restraints excluded: chain B residue 33 PHE Chi-restraints excluded: chain B residue 36 TRP Chi-restraints excluded: chain B residue 43 ARG Chi-restraints excluded: chain B residue 74 LEU Chi-restraints excluded: chain B residue 124 SER Chi-restraints excluded: chain B residue 181 GLU Chi-restraints excluded: chain B residue 209 PHE Chi-restraints excluded: chain B residue 244 VAL Chi-restraints excluded: chain B residue 250 LEU Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain B residue 374 GLN Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain B residue 416 GLU Chi-restraints excluded: chain B residue 426 LEU Chi-restraints excluded: chain B residue 433 LEU Chi-restraints excluded: chain B residue 471 LEU Chi-restraints excluded: chain B residue 494 THR Chi-restraints excluded: chain B residue 521 LYS Chi-restraints excluded: chain B residue 530 THR Chi-restraints excluded: chain B residue 572 ASP Chi-restraints excluded: chain B residue 599 ARG Chi-restraints excluded: chain B residue 780 LEU Chi-restraints excluded: chain B residue 782 ASP Chi-restraints excluded: chain B residue 837 THR Chi-restraints excluded: chain B residue 838 THR Chi-restraints excluded: chain B residue 855 THR Chi-restraints excluded: chain B residue 864 MET Chi-restraints excluded: chain B residue 869 ASP Chi-restraints excluded: chain B residue 887 GLN Chi-restraints excluded: chain B residue 904 GLU Chi-restraints excluded: chain B residue 911 THR Chi-restraints excluded: chain B residue 914 CYS Chi-restraints excluded: chain B residue 941 THR Chi-restraints excluded: chain B residue 963 SER Chi-restraints excluded: chain B residue 980 GLU Chi-restraints excluded: chain B residue 987 ASP Chi-restraints excluded: chain B residue 999 TRP Chi-restraints excluded: chain C residue 11 LEU Chi-restraints excluded: chain C residue 13 ARG Chi-restraints excluded: chain C residue 33 PHE Chi-restraints excluded: chain C residue 36 TRP Chi-restraints excluded: chain C residue 43 ARG Chi-restraints excluded: chain C residue 74 LEU Chi-restraints excluded: chain C residue 124 SER Chi-restraints excluded: chain C residue 181 GLU Chi-restraints excluded: chain C residue 209 PHE Chi-restraints excluded: chain C residue 244 VAL Chi-restraints excluded: chain C residue 250 LEU Chi-restraints excluded: chain C residue 322 LEU Chi-restraints excluded: chain C residue 374 GLN Chi-restraints excluded: chain C residue 377 LEU Chi-restraints excluded: chain C residue 416 GLU Chi-restraints excluded: chain C residue 426 LEU Chi-restraints excluded: chain C residue 433 LEU Chi-restraints excluded: chain C residue 471 LEU Chi-restraints excluded: chain C residue 494 THR Chi-restraints excluded: chain C residue 520 ILE Chi-restraints excluded: chain C residue 521 LYS Chi-restraints excluded: chain C residue 530 THR Chi-restraints excluded: chain C residue 572 ASP Chi-restraints excluded: chain C residue 599 ARG Chi-restraints excluded: chain C residue 719 GLN Chi-restraints excluded: chain C residue 739 HIS Chi-restraints excluded: chain C residue 780 LEU Chi-restraints excluded: chain C residue 782 ASP Chi-restraints excluded: chain C residue 793 ILE Chi-restraints excluded: chain C residue 795 VAL Chi-restraints excluded: chain C residue 828 ASP Chi-restraints excluded: chain C residue 837 THR Chi-restraints excluded: chain C residue 838 THR Chi-restraints excluded: chain C residue 855 THR Chi-restraints excluded: chain C residue 864 MET Chi-restraints excluded: chain C residue 869 ASP Chi-restraints excluded: chain C residue 904 GLU Chi-restraints excluded: chain C residue 911 THR Chi-restraints excluded: chain C residue 914 CYS Chi-restraints excluded: chain C residue 941 THR Chi-restraints excluded: chain C residue 963 SER Chi-restraints excluded: chain C residue 980 GLU Chi-restraints excluded: chain C residue 982 THR Chi-restraints excluded: chain C residue 987 ASP Chi-restraints excluded: chain C residue 997 ASP Chi-restraints excluded: chain C residue 999 TRP Chi-restraints excluded: chain D residue 2 MET Chi-restraints excluded: chain D residue 11 LEU Chi-restraints excluded: chain D residue 13 ARG Chi-restraints excluded: chain D residue 33 PHE Chi-restraints excluded: chain D residue 36 TRP Chi-restraints excluded: chain D residue 43 ARG Chi-restraints excluded: chain D residue 74 LEU Chi-restraints excluded: chain D residue 124 SER Chi-restraints excluded: chain D residue 181 GLU Chi-restraints excluded: chain D residue 209 PHE Chi-restraints excluded: chain D residue 244 VAL Chi-restraints excluded: chain D residue 250 LEU Chi-restraints excluded: chain D residue 322 LEU Chi-restraints excluded: chain D residue 374 GLN Chi-restraints excluded: chain D residue 377 LEU Chi-restraints excluded: chain D residue 416 GLU Chi-restraints excluded: chain D residue 426 LEU Chi-restraints excluded: chain D residue 433 LEU Chi-restraints excluded: chain D residue 471 LEU Chi-restraints excluded: chain D residue 494 THR Chi-restraints excluded: chain D residue 520 ILE Chi-restraints excluded: chain D residue 521 LYS Chi-restraints excluded: chain D residue 530 THR Chi-restraints excluded: chain D residue 572 ASP Chi-restraints excluded: chain D residue 599 ARG Chi-restraints excluded: chain D residue 719 GLN Chi-restraints excluded: chain D residue 780 LEU Chi-restraints excluded: chain D residue 782 ASP Chi-restraints excluded: chain D residue 793 ILE Chi-restraints excluded: chain D residue 837 THR Chi-restraints excluded: chain D residue 838 THR Chi-restraints excluded: chain D residue 855 THR Chi-restraints excluded: chain D residue 869 ASP Chi-restraints excluded: chain D residue 904 GLU Chi-restraints excluded: chain D residue 911 THR Chi-restraints excluded: chain D residue 914 CYS Chi-restraints excluded: chain D residue 941 THR Chi-restraints excluded: chain D residue 963 SER Chi-restraints excluded: chain D residue 980 GLU Chi-restraints excluded: chain D residue 987 ASP Chi-restraints excluded: chain D residue 997 ASP Chi-restraints excluded: chain D residue 999 TRP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 369 optimal weight: 4.9990 chunk 182 optimal weight: 0.9990 chunk 217 optimal weight: 9.9990 chunk 330 optimal weight: 20.0000 chunk 278 optimal weight: 5.9990 chunk 258 optimal weight: 0.9980 chunk 29 optimal weight: 5.9990 chunk 166 optimal weight: 4.9990 chunk 346 optimal weight: 2.9990 chunk 130 optimal weight: 10.0000 chunk 398 optimal weight: 10.0000 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 182 ASN ** A 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 363 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 604 ASN A 624 GLN ** A 719 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 863 GLN ** B 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 363 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 604 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 719 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 761 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 863 GLN C 182 ASN ** C 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 604 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 624 GLN ** C 719 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 863 GLN D 182 ASN ** D 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 363 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 604 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 719 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 863 GLN ** D1008 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.092154 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.076264 restraints weight = 66560.612| |-----------------------------------------------------------------------------| r_work (start): 0.3115 rms_B_bonded: 2.75 r_work: 0.2996 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.2996 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8445 moved from start: 0.5410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 33812 Z= 0.167 Angle : 0.636 25.299 46104 Z= 0.330 Chirality : 0.044 0.195 4820 Planarity : 0.004 0.072 6088 Dihedral : 5.707 54.257 4520 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 11.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 5.84 % Allowed : 21.37 % Favored : 72.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.06 % Cis-general : 1.15 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.18 (0.13), residues: 4080 helix: 0.11 (0.22), residues: 580 sheet: 0.93 (0.14), residues: 1416 loop : -0.39 (0.13), residues: 2084 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP D1020 HIS 0.004 0.001 HIS D 653 PHE 0.014 0.002 PHE A 209 TYR 0.012 0.001 TYR A 906 ARG 0.006 0.001 ARG C 630 Details of bonding type rmsd hydrogen bonds : bond 0.03560 ( 1144) hydrogen bonds : angle 5.59541 ( 3288) covalent geometry : bond 0.00379 (33792) covalent geometry : angle 0.63594 (46104) Misc. bond : bond 0.00387 ( 20) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 539 residues out of total 3496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 204 poor density : 335 time to evaluate : 3.814 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 416 GLU cc_start: 0.8496 (OUTLIER) cc_final: 0.8170 (tp30) REVERT: A 471 LEU cc_start: 0.9287 (OUTLIER) cc_final: 0.8857 (mm) REVERT: A 521 LYS cc_start: 0.8613 (OUTLIER) cc_final: 0.8403 (mttp) REVERT: A 572 ASP cc_start: 0.8162 (OUTLIER) cc_final: 0.7732 (m-30) REVERT: A 601 PHE cc_start: 0.8398 (m-80) cc_final: 0.8181 (m-80) REVERT: A 719 GLN cc_start: 0.8632 (OUTLIER) cc_final: 0.8047 (tm-30) REVERT: A 887 GLN cc_start: 0.8603 (OUTLIER) cc_final: 0.8195 (tp40) REVERT: A 908 ASP cc_start: 0.7808 (t0) cc_final: 0.6934 (t0) REVERT: A 911 THR cc_start: 0.9095 (OUTLIER) cc_final: 0.8822 (p) REVERT: B 237 ARG cc_start: 0.8322 (mtp-110) cc_final: 0.8117 (mtp-110) REVERT: B 394 ASN cc_start: 0.9152 (m-40) cc_final: 0.8703 (t0) REVERT: B 416 GLU cc_start: 0.8501 (OUTLIER) cc_final: 0.8166 (tp30) REVERT: B 471 LEU cc_start: 0.9288 (OUTLIER) cc_final: 0.8861 (mm) REVERT: B 515 VAL cc_start: 0.8328 (t) cc_final: 0.7829 (m) REVERT: B 521 LYS cc_start: 0.8618 (OUTLIER) cc_final: 0.8415 (mttp) REVERT: B 542 MET cc_start: 0.8108 (ttm) cc_final: 0.7775 (ttm) REVERT: B 572 ASP cc_start: 0.8175 (OUTLIER) cc_final: 0.7793 (m-30) REVERT: B 601 PHE cc_start: 0.8340 (m-80) cc_final: 0.8132 (m-80) REVERT: B 719 GLN cc_start: 0.8638 (OUTLIER) cc_final: 0.8084 (tm-30) REVERT: B 726 LEU cc_start: 0.8418 (OUTLIER) cc_final: 0.8207 (mm) REVERT: B 887 GLN cc_start: 0.8588 (OUTLIER) cc_final: 0.8156 (tp40) REVERT: B 911 THR cc_start: 0.9099 (OUTLIER) cc_final: 0.8804 (p) REVERT: C 237 ARG cc_start: 0.8321 (mtp-110) cc_final: 0.8115 (mtp-110) REVERT: C 416 GLU cc_start: 0.8507 (OUTLIER) cc_final: 0.8176 (tp30) REVERT: C 471 LEU cc_start: 0.9274 (OUTLIER) cc_final: 0.8847 (mm) REVERT: C 521 LYS cc_start: 0.8619 (OUTLIER) cc_final: 0.8407 (mttp) REVERT: C 572 ASP cc_start: 0.8190 (OUTLIER) cc_final: 0.7808 (m-30) REVERT: C 719 GLN cc_start: 0.8687 (OUTLIER) cc_final: 0.8149 (tm-30) REVERT: C 911 THR cc_start: 0.9091 (OUTLIER) cc_final: 0.8807 (p) REVERT: D 416 GLU cc_start: 0.8493 (OUTLIER) cc_final: 0.8177 (tp30) REVERT: D 471 LEU cc_start: 0.9284 (OUTLIER) cc_final: 0.8862 (mm) REVERT: D 515 VAL cc_start: 0.8341 (t) cc_final: 0.7843 (m) REVERT: D 521 LYS cc_start: 0.8619 (OUTLIER) cc_final: 0.8405 (mttp) REVERT: D 542 MET cc_start: 0.8074 (ttm) cc_final: 0.7803 (ttm) REVERT: D 572 ASP cc_start: 0.8174 (OUTLIER) cc_final: 0.7767 (m-30) REVERT: D 719 GLN cc_start: 0.8682 (OUTLIER) cc_final: 0.8153 (tm-30) REVERT: D 804 ASN cc_start: 0.8514 (m-40) cc_final: 0.8213 (m-40) REVERT: D 911 THR cc_start: 0.9098 (OUTLIER) cc_final: 0.8804 (p) outliers start: 204 outliers final: 149 residues processed: 511 average time/residue: 0.4566 time to fit residues: 388.0089 Evaluate side-chains 490 residues out of total 3496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 176 poor density : 314 time to evaluate : 3.867 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 MET Chi-restraints excluded: chain A residue 11 LEU Chi-restraints excluded: chain A residue 13 ARG Chi-restraints excluded: chain A residue 33 PHE Chi-restraints excluded: chain A residue 36 TRP Chi-restraints excluded: chain A residue 43 ARG Chi-restraints excluded: chain A residue 74 LEU Chi-restraints excluded: chain A residue 124 SER Chi-restraints excluded: chain A residue 181 GLU Chi-restraints excluded: chain A residue 209 PHE Chi-restraints excluded: chain A residue 222 ILE Chi-restraints excluded: chain A residue 244 VAL Chi-restraints excluded: chain A residue 302 SER Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 374 GLN Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 416 GLU Chi-restraints excluded: chain A residue 433 LEU Chi-restraints excluded: chain A residue 471 LEU Chi-restraints excluded: chain A residue 494 THR Chi-restraints excluded: chain A residue 520 ILE Chi-restraints excluded: chain A residue 521 LYS Chi-restraints excluded: chain A residue 530 THR Chi-restraints excluded: chain A residue 572 ASP Chi-restraints excluded: chain A residue 599 ARG Chi-restraints excluded: chain A residue 719 GLN Chi-restraints excluded: chain A residue 780 LEU Chi-restraints excluded: chain A residue 782 ASP Chi-restraints excluded: chain A residue 795 VAL Chi-restraints excluded: chain A residue 837 THR Chi-restraints excluded: chain A residue 838 THR Chi-restraints excluded: chain A residue 855 THR Chi-restraints excluded: chain A residue 869 ASP Chi-restraints excluded: chain A residue 887 GLN Chi-restraints excluded: chain A residue 904 GLU Chi-restraints excluded: chain A residue 911 THR Chi-restraints excluded: chain A residue 914 CYS Chi-restraints excluded: chain A residue 941 THR Chi-restraints excluded: chain A residue 963 SER Chi-restraints excluded: chain A residue 980 GLU Chi-restraints excluded: chain A residue 982 THR Chi-restraints excluded: chain A residue 987 ASP Chi-restraints excluded: chain A residue 997 ASP Chi-restraints excluded: chain A residue 999 TRP Chi-restraints excluded: chain A residue 1022 GLN Chi-restraints excluded: chain B residue 2 MET Chi-restraints excluded: chain B residue 11 LEU Chi-restraints excluded: chain B residue 13 ARG Chi-restraints excluded: chain B residue 33 PHE Chi-restraints excluded: chain B residue 36 TRP Chi-restraints excluded: chain B residue 43 ARG Chi-restraints excluded: chain B residue 74 LEU Chi-restraints excluded: chain B residue 124 SER Chi-restraints excluded: chain B residue 181 GLU Chi-restraints excluded: chain B residue 209 PHE Chi-restraints excluded: chain B residue 222 ILE Chi-restraints excluded: chain B residue 244 VAL Chi-restraints excluded: chain B residue 302 SER Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain B residue 374 GLN Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain B residue 416 GLU Chi-restraints excluded: chain B residue 426 LEU Chi-restraints excluded: chain B residue 433 LEU Chi-restraints excluded: chain B residue 471 LEU Chi-restraints excluded: chain B residue 520 ILE Chi-restraints excluded: chain B residue 521 LYS Chi-restraints excluded: chain B residue 530 THR Chi-restraints excluded: chain B residue 572 ASP Chi-restraints excluded: chain B residue 599 ARG Chi-restraints excluded: chain B residue 719 GLN Chi-restraints excluded: chain B residue 726 LEU Chi-restraints excluded: chain B residue 782 ASP Chi-restraints excluded: chain B residue 837 THR Chi-restraints excluded: chain B residue 838 THR Chi-restraints excluded: chain B residue 855 THR Chi-restraints excluded: chain B residue 869 ASP Chi-restraints excluded: chain B residue 887 GLN Chi-restraints excluded: chain B residue 904 GLU Chi-restraints excluded: chain B residue 911 THR Chi-restraints excluded: chain B residue 914 CYS Chi-restraints excluded: chain B residue 941 THR Chi-restraints excluded: chain B residue 963 SER Chi-restraints excluded: chain B residue 980 GLU Chi-restraints excluded: chain B residue 982 THR Chi-restraints excluded: chain B residue 987 ASP Chi-restraints excluded: chain B residue 999 TRP Chi-restraints excluded: chain C residue 11 LEU Chi-restraints excluded: chain C residue 13 ARG Chi-restraints excluded: chain C residue 33 PHE Chi-restraints excluded: chain C residue 36 TRP Chi-restraints excluded: chain C residue 43 ARG Chi-restraints excluded: chain C residue 74 LEU Chi-restraints excluded: chain C residue 124 SER Chi-restraints excluded: chain C residue 181 GLU Chi-restraints excluded: chain C residue 209 PHE Chi-restraints excluded: chain C residue 222 ILE Chi-restraints excluded: chain C residue 244 VAL Chi-restraints excluded: chain C residue 302 SER Chi-restraints excluded: chain C residue 322 LEU Chi-restraints excluded: chain C residue 374 GLN Chi-restraints excluded: chain C residue 376 ILE Chi-restraints excluded: chain C residue 377 LEU Chi-restraints excluded: chain C residue 416 GLU Chi-restraints excluded: chain C residue 426 LEU Chi-restraints excluded: chain C residue 433 LEU Chi-restraints excluded: chain C residue 471 LEU Chi-restraints excluded: chain C residue 494 THR Chi-restraints excluded: chain C residue 520 ILE Chi-restraints excluded: chain C residue 521 LYS Chi-restraints excluded: chain C residue 530 THR Chi-restraints excluded: chain C residue 572 ASP Chi-restraints excluded: chain C residue 599 ARG Chi-restraints excluded: chain C residue 719 GLN Chi-restraints excluded: chain C residue 739 HIS Chi-restraints excluded: chain C residue 780 LEU Chi-restraints excluded: chain C residue 782 ASP Chi-restraints excluded: chain C residue 793 ILE Chi-restraints excluded: chain C residue 837 THR Chi-restraints excluded: chain C residue 838 THR Chi-restraints excluded: chain C residue 855 THR Chi-restraints excluded: chain C residue 869 ASP Chi-restraints excluded: chain C residue 904 GLU Chi-restraints excluded: chain C residue 911 THR Chi-restraints excluded: chain C residue 914 CYS Chi-restraints excluded: chain C residue 941 THR Chi-restraints excluded: chain C residue 963 SER Chi-restraints excluded: chain C residue 980 GLU Chi-restraints excluded: chain C residue 982 THR Chi-restraints excluded: chain C residue 987 ASP Chi-restraints excluded: chain C residue 997 ASP Chi-restraints excluded: chain C residue 999 TRP Chi-restraints excluded: chain D residue 11 LEU Chi-restraints excluded: chain D residue 13 ARG Chi-restraints excluded: chain D residue 33 PHE Chi-restraints excluded: chain D residue 36 TRP Chi-restraints excluded: chain D residue 43 ARG Chi-restraints excluded: chain D residue 74 LEU Chi-restraints excluded: chain D residue 124 SER Chi-restraints excluded: chain D residue 181 GLU Chi-restraints excluded: chain D residue 209 PHE Chi-restraints excluded: chain D residue 222 ILE Chi-restraints excluded: chain D residue 244 VAL Chi-restraints excluded: chain D residue 302 SER Chi-restraints excluded: chain D residue 322 LEU Chi-restraints excluded: chain D residue 374 GLN Chi-restraints excluded: chain D residue 376 ILE Chi-restraints excluded: chain D residue 377 LEU Chi-restraints excluded: chain D residue 416 GLU Chi-restraints excluded: chain D residue 426 LEU Chi-restraints excluded: chain D residue 433 LEU Chi-restraints excluded: chain D residue 471 LEU Chi-restraints excluded: chain D residue 494 THR Chi-restraints excluded: chain D residue 520 ILE Chi-restraints excluded: chain D residue 521 LYS Chi-restraints excluded: chain D residue 530 THR Chi-restraints excluded: chain D residue 572 ASP Chi-restraints excluded: chain D residue 599 ARG Chi-restraints excluded: chain D residue 632 SER Chi-restraints excluded: chain D residue 719 GLN Chi-restraints excluded: chain D residue 782 ASP Chi-restraints excluded: chain D residue 793 ILE Chi-restraints excluded: chain D residue 837 THR Chi-restraints excluded: chain D residue 838 THR Chi-restraints excluded: chain D residue 855 THR Chi-restraints excluded: chain D residue 869 ASP Chi-restraints excluded: chain D residue 904 GLU Chi-restraints excluded: chain D residue 911 THR Chi-restraints excluded: chain D residue 914 CYS Chi-restraints excluded: chain D residue 941 THR Chi-restraints excluded: chain D residue 963 SER Chi-restraints excluded: chain D residue 980 GLU Chi-restraints excluded: chain D residue 982 THR Chi-restraints excluded: chain D residue 987 ASP Chi-restraints excluded: chain D residue 997 ASP Chi-restraints excluded: chain D residue 999 TRP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 31 optimal weight: 7.9990 chunk 342 optimal weight: 9.9990 chunk 401 optimal weight: 0.9990 chunk 78 optimal weight: 3.9990 chunk 21 optimal weight: 0.0170 chunk 5 optimal weight: 10.0000 chunk 290 optimal weight: 8.9990 chunk 374 optimal weight: 6.9990 chunk 373 optimal weight: 0.0010 chunk 82 optimal weight: 5.9990 chunk 339 optimal weight: 7.9990 overall best weight: 2.2030 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 363 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 719 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 863 GLN B 604 ASN ** B 719 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 761 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 863 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 363 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 719 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 863 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 363 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 604 ASN ** D 719 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 863 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1008 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.093061 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.077127 restraints weight = 66202.852| |-----------------------------------------------------------------------------| r_work (start): 0.3130 rms_B_bonded: 2.75 r_work: 0.3010 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3010 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8432 moved from start: 0.5525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 33812 Z= 0.140 Angle : 0.606 9.346 46104 Z= 0.314 Chirality : 0.043 0.189 4820 Planarity : 0.004 0.070 6088 Dihedral : 5.550 53.297 4520 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 11.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 5.32 % Allowed : 21.77 % Favored : 72.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.06 % Cis-general : 1.15 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.29 (0.13), residues: 4080 helix: 0.57 (0.23), residues: 532 sheet: 0.91 (0.14), residues: 1388 loop : -0.34 (0.13), residues: 2160 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 553 HIS 0.004 0.001 HIS C 653 PHE 0.021 0.001 PHE B1007 TYR 0.013 0.001 TYR A 906 ARG 0.006 0.001 ARG A 760 Details of bonding type rmsd hydrogen bonds : bond 0.03343 ( 1144) hydrogen bonds : angle 5.46176 ( 3288) covalent geometry : bond 0.00314 (33792) covalent geometry : angle 0.60576 (46104) Misc. bond : bond 0.00207 ( 20) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 534 residues out of total 3496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 186 poor density : 348 time to evaluate : 12.615 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 23 GLN cc_start: 0.9104 (pp30) cc_final: 0.8766 (pp30) REVERT: A 416 GLU cc_start: 0.8482 (OUTLIER) cc_final: 0.8140 (tp30) REVERT: A 471 LEU cc_start: 0.9269 (OUTLIER) cc_final: 0.8846 (mm) REVERT: A 521 LYS cc_start: 0.8587 (OUTLIER) cc_final: 0.8383 (mttp) REVERT: A 572 ASP cc_start: 0.8162 (OUTLIER) cc_final: 0.7788 (m-30) REVERT: A 601 PHE cc_start: 0.8391 (m-80) cc_final: 0.8183 (m-80) REVERT: A 719 GLN cc_start: 0.8632 (OUTLIER) cc_final: 0.8074 (tm-30) REVERT: A 823 LEU cc_start: 0.8511 (mt) cc_final: 0.8257 (mt) REVERT: A 887 GLN cc_start: 0.8608 (OUTLIER) cc_final: 0.8208 (tp40) REVERT: A 908 ASP cc_start: 0.7735 (t0) cc_final: 0.6917 (t0) REVERT: A 911 THR cc_start: 0.9078 (OUTLIER) cc_final: 0.8821 (p) REVERT: B 237 ARG cc_start: 0.8338 (mtp-110) cc_final: 0.8119 (mtp-110) REVERT: B 394 ASN cc_start: 0.9129 (m-40) cc_final: 0.8717 (m-40) REVERT: B 416 GLU cc_start: 0.8496 (OUTLIER) cc_final: 0.8145 (tp30) REVERT: B 471 LEU cc_start: 0.9266 (OUTLIER) cc_final: 0.8849 (mm) REVERT: B 515 VAL cc_start: 0.8315 (t) cc_final: 0.7813 (m) REVERT: B 572 ASP cc_start: 0.8092 (OUTLIER) cc_final: 0.7707 (m-30) REVERT: B 601 PHE cc_start: 0.8366 (m-80) cc_final: 0.8147 (m-80) REVERT: B 719 GLN cc_start: 0.8641 (OUTLIER) cc_final: 0.8077 (tm-30) REVERT: B 726 LEU cc_start: 0.8368 (OUTLIER) cc_final: 0.8154 (mm) REVERT: B 887 GLN cc_start: 0.8588 (OUTLIER) cc_final: 0.8161 (tp40) REVERT: B 911 THR cc_start: 0.9089 (OUTLIER) cc_final: 0.8793 (p) REVERT: C 237 ARG cc_start: 0.8321 (mtp-110) cc_final: 0.8110 (mtp-110) REVERT: C 416 GLU cc_start: 0.8466 (OUTLIER) cc_final: 0.8106 (tp30) REVERT: C 439 ARG cc_start: 0.8194 (OUTLIER) cc_final: 0.6702 (mpt90) REVERT: C 471 LEU cc_start: 0.9259 (OUTLIER) cc_final: 0.8848 (mm) REVERT: C 572 ASP cc_start: 0.8095 (OUTLIER) cc_final: 0.7741 (m-30) REVERT: C 719 GLN cc_start: 0.8645 (OUTLIER) cc_final: 0.8113 (tm-30) REVERT: C 823 LEU cc_start: 0.8513 (mt) cc_final: 0.8246 (mt) REVERT: C 887 GLN cc_start: 0.8555 (OUTLIER) cc_final: 0.8016 (tp40) REVERT: C 908 ASP cc_start: 0.7836 (t0) cc_final: 0.7332 (t0) REVERT: C 911 THR cc_start: 0.9081 (OUTLIER) cc_final: 0.8790 (p) REVERT: D 416 GLU cc_start: 0.8485 (OUTLIER) cc_final: 0.8133 (tp30) REVERT: D 471 LEU cc_start: 0.9263 (OUTLIER) cc_final: 0.8852 (mm) REVERT: D 515 VAL cc_start: 0.8309 (t) cc_final: 0.7810 (m) REVERT: D 521 LYS cc_start: 0.8589 (OUTLIER) cc_final: 0.8384 (mttp) REVERT: D 542 MET cc_start: 0.8079 (ttm) cc_final: 0.7823 (ttm) REVERT: D 572 ASP cc_start: 0.8169 (OUTLIER) cc_final: 0.7792 (m-30) REVERT: D 719 GLN cc_start: 0.8653 (OUTLIER) cc_final: 0.8139 (tm-30) REVERT: D 823 LEU cc_start: 0.8513 (mt) cc_final: 0.8265 (mt) REVERT: D 887 GLN cc_start: 0.8568 (OUTLIER) cc_final: 0.8030 (tp40) REVERT: D 911 THR cc_start: 0.9086 (OUTLIER) cc_final: 0.8791 (p) outliers start: 186 outliers final: 140 residues processed: 509 average time/residue: 0.6688 time to fit residues: 568.1282 Evaluate side-chains 485 residues out of total 3496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 168 poor density : 317 time to evaluate : 4.113 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 MET Chi-restraints excluded: chain A residue 11 LEU Chi-restraints excluded: chain A residue 13 ARG Chi-restraints excluded: chain A residue 33 PHE Chi-restraints excluded: chain A residue 36 TRP Chi-restraints excluded: chain A residue 43 ARG Chi-restraints excluded: chain A residue 74 LEU Chi-restraints excluded: chain A residue 124 SER Chi-restraints excluded: chain A residue 181 GLU Chi-restraints excluded: chain A residue 209 PHE Chi-restraints excluded: chain A residue 222 ILE Chi-restraints excluded: chain A residue 244 VAL Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 416 GLU Chi-restraints excluded: chain A residue 433 LEU Chi-restraints excluded: chain A residue 471 LEU Chi-restraints excluded: chain A residue 520 ILE Chi-restraints excluded: chain A residue 521 LYS Chi-restraints excluded: chain A residue 530 THR Chi-restraints excluded: chain A residue 572 ASP Chi-restraints excluded: chain A residue 599 ARG Chi-restraints excluded: chain A residue 632 SER Chi-restraints excluded: chain A residue 719 GLN Chi-restraints excluded: chain A residue 782 ASP Chi-restraints excluded: chain A residue 795 VAL Chi-restraints excluded: chain A residue 837 THR Chi-restraints excluded: chain A residue 838 THR Chi-restraints excluded: chain A residue 855 THR Chi-restraints excluded: chain A residue 869 ASP Chi-restraints excluded: chain A residue 887 GLN Chi-restraints excluded: chain A residue 904 GLU Chi-restraints excluded: chain A residue 911 THR Chi-restraints excluded: chain A residue 914 CYS Chi-restraints excluded: chain A residue 941 THR Chi-restraints excluded: chain A residue 963 SER Chi-restraints excluded: chain A residue 980 GLU Chi-restraints excluded: chain A residue 982 THR Chi-restraints excluded: chain A residue 987 ASP Chi-restraints excluded: chain A residue 997 ASP Chi-restraints excluded: chain A residue 999 TRP Chi-restraints excluded: chain B residue 2 MET Chi-restraints excluded: chain B residue 11 LEU Chi-restraints excluded: chain B residue 13 ARG Chi-restraints excluded: chain B residue 33 PHE Chi-restraints excluded: chain B residue 36 TRP Chi-restraints excluded: chain B residue 43 ARG Chi-restraints excluded: chain B residue 74 LEU Chi-restraints excluded: chain B residue 124 SER Chi-restraints excluded: chain B residue 181 GLU Chi-restraints excluded: chain B residue 209 PHE Chi-restraints excluded: chain B residue 222 ILE Chi-restraints excluded: chain B residue 244 VAL Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain B residue 374 GLN Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain B residue 416 GLU Chi-restraints excluded: chain B residue 426 LEU Chi-restraints excluded: chain B residue 433 LEU Chi-restraints excluded: chain B residue 471 LEU Chi-restraints excluded: chain B residue 494 THR Chi-restraints excluded: chain B residue 520 ILE Chi-restraints excluded: chain B residue 530 THR Chi-restraints excluded: chain B residue 572 ASP Chi-restraints excluded: chain B residue 599 ARG Chi-restraints excluded: chain B residue 632 SER Chi-restraints excluded: chain B residue 719 GLN Chi-restraints excluded: chain B residue 726 LEU Chi-restraints excluded: chain B residue 782 ASP Chi-restraints excluded: chain B residue 837 THR Chi-restraints excluded: chain B residue 838 THR Chi-restraints excluded: chain B residue 855 THR Chi-restraints excluded: chain B residue 869 ASP Chi-restraints excluded: chain B residue 887 GLN Chi-restraints excluded: chain B residue 904 GLU Chi-restraints excluded: chain B residue 911 THR Chi-restraints excluded: chain B residue 914 CYS Chi-restraints excluded: chain B residue 941 THR Chi-restraints excluded: chain B residue 963 SER Chi-restraints excluded: chain B residue 980 GLU Chi-restraints excluded: chain B residue 982 THR Chi-restraints excluded: chain B residue 987 ASP Chi-restraints excluded: chain B residue 999 TRP Chi-restraints excluded: chain C residue 2 MET Chi-restraints excluded: chain C residue 11 LEU Chi-restraints excluded: chain C residue 13 ARG Chi-restraints excluded: chain C residue 33 PHE Chi-restraints excluded: chain C residue 36 TRP Chi-restraints excluded: chain C residue 43 ARG Chi-restraints excluded: chain C residue 74 LEU Chi-restraints excluded: chain C residue 124 SER Chi-restraints excluded: chain C residue 181 GLU Chi-restraints excluded: chain C residue 209 PHE Chi-restraints excluded: chain C residue 222 ILE Chi-restraints excluded: chain C residue 240 LEU Chi-restraints excluded: chain C residue 244 VAL Chi-restraints excluded: chain C residue 322 LEU Chi-restraints excluded: chain C residue 374 GLN Chi-restraints excluded: chain C residue 377 LEU Chi-restraints excluded: chain C residue 416 GLU Chi-restraints excluded: chain C residue 426 LEU Chi-restraints excluded: chain C residue 433 LEU Chi-restraints excluded: chain C residue 439 ARG Chi-restraints excluded: chain C residue 471 LEU Chi-restraints excluded: chain C residue 520 ILE Chi-restraints excluded: chain C residue 530 THR Chi-restraints excluded: chain C residue 572 ASP Chi-restraints excluded: chain C residue 599 ARG Chi-restraints excluded: chain C residue 719 GLN Chi-restraints excluded: chain C residue 739 HIS Chi-restraints excluded: chain C residue 782 ASP Chi-restraints excluded: chain C residue 793 ILE Chi-restraints excluded: chain C residue 837 THR Chi-restraints excluded: chain C residue 838 THR Chi-restraints excluded: chain C residue 855 THR Chi-restraints excluded: chain C residue 869 ASP Chi-restraints excluded: chain C residue 887 GLN Chi-restraints excluded: chain C residue 904 GLU Chi-restraints excluded: chain C residue 911 THR Chi-restraints excluded: chain C residue 914 CYS Chi-restraints excluded: chain C residue 941 THR Chi-restraints excluded: chain C residue 963 SER Chi-restraints excluded: chain C residue 980 GLU Chi-restraints excluded: chain C residue 987 ASP Chi-restraints excluded: chain C residue 997 ASP Chi-restraints excluded: chain C residue 999 TRP Chi-restraints excluded: chain D residue 11 LEU Chi-restraints excluded: chain D residue 13 ARG Chi-restraints excluded: chain D residue 33 PHE Chi-restraints excluded: chain D residue 36 TRP Chi-restraints excluded: chain D residue 43 ARG Chi-restraints excluded: chain D residue 74 LEU Chi-restraints excluded: chain D residue 124 SER Chi-restraints excluded: chain D residue 181 GLU Chi-restraints excluded: chain D residue 209 PHE Chi-restraints excluded: chain D residue 222 ILE Chi-restraints excluded: chain D residue 244 VAL Chi-restraints excluded: chain D residue 322 LEU Chi-restraints excluded: chain D residue 374 GLN Chi-restraints excluded: chain D residue 377 LEU Chi-restraints excluded: chain D residue 416 GLU Chi-restraints excluded: chain D residue 426 LEU Chi-restraints excluded: chain D residue 433 LEU Chi-restraints excluded: chain D residue 471 LEU Chi-restraints excluded: chain D residue 520 ILE Chi-restraints excluded: chain D residue 521 LYS Chi-restraints excluded: chain D residue 530 THR Chi-restraints excluded: chain D residue 572 ASP Chi-restraints excluded: chain D residue 599 ARG Chi-restraints excluded: chain D residue 632 SER Chi-restraints excluded: chain D residue 719 GLN Chi-restraints excluded: chain D residue 782 ASP Chi-restraints excluded: chain D residue 793 ILE Chi-restraints excluded: chain D residue 837 THR Chi-restraints excluded: chain D residue 838 THR Chi-restraints excluded: chain D residue 855 THR Chi-restraints excluded: chain D residue 869 ASP Chi-restraints excluded: chain D residue 887 GLN Chi-restraints excluded: chain D residue 904 GLU Chi-restraints excluded: chain D residue 911 THR Chi-restraints excluded: chain D residue 914 CYS Chi-restraints excluded: chain D residue 941 THR Chi-restraints excluded: chain D residue 963 SER Chi-restraints excluded: chain D residue 980 GLU Chi-restraints excluded: chain D residue 982 THR Chi-restraints excluded: chain D residue 987 ASP Chi-restraints excluded: chain D residue 997 ASP Chi-restraints excluded: chain D residue 999 TRP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 56 optimal weight: 9.9990 chunk 315 optimal weight: 5.9990 chunk 89 optimal weight: 6.9990 chunk 406 optimal weight: 0.9990 chunk 53 optimal weight: 0.0030 chunk 405 optimal weight: 5.9990 chunk 28 optimal weight: 9.9990 chunk 97 optimal weight: 3.9990 chunk 66 optimal weight: 7.9990 chunk 291 optimal weight: 5.9990 chunk 217 optimal weight: 2.9990 overall best weight: 2.7998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 363 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 719 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 863 GLN ** B 719 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 863 GLN C 182 ASN ** C 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 363 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 604 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 719 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 863 GLN ** D 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 363 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 719 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 863 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.092357 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.076440 restraints weight = 66366.667| |-----------------------------------------------------------------------------| r_work (start): 0.3115 rms_B_bonded: 2.74 r_work: 0.2995 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.2995 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8444 moved from start: 0.5570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 33812 Z= 0.162 Angle : 0.646 22.263 46104 Z= 0.327 Chirality : 0.044 0.195 4820 Planarity : 0.004 0.059 6088 Dihedral : 5.613 52.444 4520 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 11.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 5.29 % Allowed : 22.37 % Favored : 72.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.06 % Cis-general : 1.15 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.21 (0.13), residues: 4080 helix: 0.51 (0.23), residues: 532 sheet: 0.82 (0.14), residues: 1388 loop : -0.37 (0.13), residues: 2160 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP C1020 HIS 0.004 0.001 HIS C 653 PHE 0.016 0.001 PHE D1007 TYR 0.013 0.001 TYR A 906 ARG 0.005 0.001 ARG C 699 Details of bonding type rmsd hydrogen bonds : bond 0.03474 ( 1144) hydrogen bonds : angle 5.38802 ( 3288) covalent geometry : bond 0.00369 (33792) covalent geometry : angle 0.64596 (46104) Misc. bond : bond 0.00411 ( 20) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 521 residues out of total 3496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 185 poor density : 336 time to evaluate : 3.858 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 416 GLU cc_start: 0.8505 (OUTLIER) cc_final: 0.8163 (tp30) REVERT: A 471 LEU cc_start: 0.9278 (OUTLIER) cc_final: 0.8849 (mm) REVERT: A 515 VAL cc_start: 0.8312 (t) cc_final: 0.7821 (m) REVERT: A 521 LYS cc_start: 0.8628 (OUTLIER) cc_final: 0.8426 (mttp) REVERT: A 542 MET cc_start: 0.8126 (ttm) cc_final: 0.7855 (ttm) REVERT: A 572 ASP cc_start: 0.8096 (OUTLIER) cc_final: 0.7752 (m-30) REVERT: A 601 PHE cc_start: 0.8336 (m-80) cc_final: 0.8130 (m-80) REVERT: A 719 GLN cc_start: 0.8638 (OUTLIER) cc_final: 0.8072 (tm-30) REVERT: A 823 LEU cc_start: 0.8520 (mt) cc_final: 0.8269 (mt) REVERT: A 887 GLN cc_start: 0.8610 (OUTLIER) cc_final: 0.8218 (tp40) REVERT: A 911 THR cc_start: 0.9087 (OUTLIER) cc_final: 0.8815 (p) REVERT: B 279 ILE cc_start: 0.8257 (tt) cc_final: 0.8053 (tt) REVERT: B 394 ASN cc_start: 0.9135 (m-40) cc_final: 0.8698 (m-40) REVERT: B 416 GLU cc_start: 0.8503 (OUTLIER) cc_final: 0.8152 (tp30) REVERT: B 471 LEU cc_start: 0.9279 (OUTLIER) cc_final: 0.8857 (mm) REVERT: B 515 VAL cc_start: 0.8316 (t) cc_final: 0.7813 (m) REVERT: B 572 ASP cc_start: 0.8127 (OUTLIER) cc_final: 0.7703 (m-30) REVERT: B 719 GLN cc_start: 0.8649 (OUTLIER) cc_final: 0.8081 (tm-30) REVERT: B 726 LEU cc_start: 0.8370 (OUTLIER) cc_final: 0.8151 (mm) REVERT: B 823 LEU cc_start: 0.8544 (mt) cc_final: 0.8284 (mt) REVERT: B 887 GLN cc_start: 0.8602 (OUTLIER) cc_final: 0.8194 (tp40) REVERT: B 908 ASP cc_start: 0.7890 (t0) cc_final: 0.7558 (m-30) REVERT: B 911 THR cc_start: 0.9077 (OUTLIER) cc_final: 0.8789 (p) REVERT: C 416 GLU cc_start: 0.8503 (OUTLIER) cc_final: 0.8159 (tp30) REVERT: C 471 LEU cc_start: 0.9269 (OUTLIER) cc_final: 0.8852 (mm) REVERT: C 515 VAL cc_start: 0.8331 (t) cc_final: 0.7831 (m) REVERT: C 572 ASP cc_start: 0.8095 (OUTLIER) cc_final: 0.7713 (m-30) REVERT: C 719 GLN cc_start: 0.8667 (OUTLIER) cc_final: 0.8118 (tm-30) REVERT: C 823 LEU cc_start: 0.8519 (mt) cc_final: 0.8268 (mt) REVERT: C 908 ASP cc_start: 0.7831 (t0) cc_final: 0.7424 (t0) REVERT: C 911 THR cc_start: 0.9081 (OUTLIER) cc_final: 0.8788 (p) REVERT: D 416 GLU cc_start: 0.8501 (OUTLIER) cc_final: 0.8165 (tp30) REVERT: D 471 LEU cc_start: 0.9283 (OUTLIER) cc_final: 0.8865 (mm) REVERT: D 515 VAL cc_start: 0.8316 (t) cc_final: 0.7819 (m) REVERT: D 521 LYS cc_start: 0.8632 (OUTLIER) cc_final: 0.8421 (mttp) REVERT: D 542 MET cc_start: 0.8075 (ttm) cc_final: 0.7805 (ttm) REVERT: D 572 ASP cc_start: 0.8090 (OUTLIER) cc_final: 0.7790 (m-30) REVERT: D 719 GLN cc_start: 0.8675 (OUTLIER) cc_final: 0.8123 (tm-30) REVERT: D 823 LEU cc_start: 0.8515 (mt) cc_final: 0.8264 (mt) REVERT: D 908 ASP cc_start: 0.7906 (t0) cc_final: 0.7281 (m-30) REVERT: D 911 THR cc_start: 0.9086 (OUTLIER) cc_final: 0.8804 (p) outliers start: 185 outliers final: 148 residues processed: 497 average time/residue: 0.5738 time to fit residues: 467.9884 Evaluate side-chains 491 residues out of total 3496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 173 poor density : 318 time to evaluate : 8.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 MET Chi-restraints excluded: chain A residue 11 LEU Chi-restraints excluded: chain A residue 13 ARG Chi-restraints excluded: chain A residue 33 PHE Chi-restraints excluded: chain A residue 36 TRP Chi-restraints excluded: chain A residue 43 ARG Chi-restraints excluded: chain A residue 74 LEU Chi-restraints excluded: chain A residue 124 SER Chi-restraints excluded: chain A residue 181 GLU Chi-restraints excluded: chain A residue 209 PHE Chi-restraints excluded: chain A residue 222 ILE Chi-restraints excluded: chain A residue 244 VAL Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 374 GLN Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 416 GLU Chi-restraints excluded: chain A residue 433 LEU Chi-restraints excluded: chain A residue 471 LEU Chi-restraints excluded: chain A residue 494 THR Chi-restraints excluded: chain A residue 520 ILE Chi-restraints excluded: chain A residue 521 LYS Chi-restraints excluded: chain A residue 530 THR Chi-restraints excluded: chain A residue 572 ASP Chi-restraints excluded: chain A residue 599 ARG Chi-restraints excluded: chain A residue 632 SER Chi-restraints excluded: chain A residue 719 GLN Chi-restraints excluded: chain A residue 782 ASP Chi-restraints excluded: chain A residue 795 VAL Chi-restraints excluded: chain A residue 837 THR Chi-restraints excluded: chain A residue 838 THR Chi-restraints excluded: chain A residue 855 THR Chi-restraints excluded: chain A residue 869 ASP Chi-restraints excluded: chain A residue 887 GLN Chi-restraints excluded: chain A residue 904 GLU Chi-restraints excluded: chain A residue 910 LEU Chi-restraints excluded: chain A residue 911 THR Chi-restraints excluded: chain A residue 914 CYS Chi-restraints excluded: chain A residue 941 THR Chi-restraints excluded: chain A residue 963 SER Chi-restraints excluded: chain A residue 980 GLU Chi-restraints excluded: chain A residue 982 THR Chi-restraints excluded: chain A residue 987 ASP Chi-restraints excluded: chain A residue 997 ASP Chi-restraints excluded: chain A residue 999 TRP Chi-restraints excluded: chain B residue 2 MET Chi-restraints excluded: chain B residue 11 LEU Chi-restraints excluded: chain B residue 13 ARG Chi-restraints excluded: chain B residue 33 PHE Chi-restraints excluded: chain B residue 36 TRP Chi-restraints excluded: chain B residue 43 ARG Chi-restraints excluded: chain B residue 74 LEU Chi-restraints excluded: chain B residue 124 SER Chi-restraints excluded: chain B residue 181 GLU Chi-restraints excluded: chain B residue 209 PHE Chi-restraints excluded: chain B residue 244 VAL Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain B residue 374 GLN Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain B residue 416 GLU Chi-restraints excluded: chain B residue 426 LEU Chi-restraints excluded: chain B residue 433 LEU Chi-restraints excluded: chain B residue 471 LEU Chi-restraints excluded: chain B residue 494 THR Chi-restraints excluded: chain B residue 520 ILE Chi-restraints excluded: chain B residue 530 THR Chi-restraints excluded: chain B residue 572 ASP Chi-restraints excluded: chain B residue 599 ARG Chi-restraints excluded: chain B residue 632 SER Chi-restraints excluded: chain B residue 719 GLN Chi-restraints excluded: chain B residue 726 LEU Chi-restraints excluded: chain B residue 782 ASP Chi-restraints excluded: chain B residue 795 VAL Chi-restraints excluded: chain B residue 837 THR Chi-restraints excluded: chain B residue 838 THR Chi-restraints excluded: chain B residue 855 THR Chi-restraints excluded: chain B residue 869 ASP Chi-restraints excluded: chain B residue 887 GLN Chi-restraints excluded: chain B residue 904 GLU Chi-restraints excluded: chain B residue 911 THR Chi-restraints excluded: chain B residue 914 CYS Chi-restraints excluded: chain B residue 941 THR Chi-restraints excluded: chain B residue 963 SER Chi-restraints excluded: chain B residue 980 GLU Chi-restraints excluded: chain B residue 982 THR Chi-restraints excluded: chain B residue 987 ASP Chi-restraints excluded: chain B residue 999 TRP Chi-restraints excluded: chain C residue 2 MET Chi-restraints excluded: chain C residue 11 LEU Chi-restraints excluded: chain C residue 13 ARG Chi-restraints excluded: chain C residue 33 PHE Chi-restraints excluded: chain C residue 36 TRP Chi-restraints excluded: chain C residue 43 ARG Chi-restraints excluded: chain C residue 74 LEU Chi-restraints excluded: chain C residue 124 SER Chi-restraints excluded: chain C residue 181 GLU Chi-restraints excluded: chain C residue 209 PHE Chi-restraints excluded: chain C residue 222 ILE Chi-restraints excluded: chain C residue 240 LEU Chi-restraints excluded: chain C residue 244 VAL Chi-restraints excluded: chain C residue 302 SER Chi-restraints excluded: chain C residue 322 LEU Chi-restraints excluded: chain C residue 374 GLN Chi-restraints excluded: chain C residue 377 LEU Chi-restraints excluded: chain C residue 416 GLU Chi-restraints excluded: chain C residue 426 LEU Chi-restraints excluded: chain C residue 433 LEU Chi-restraints excluded: chain C residue 471 LEU Chi-restraints excluded: chain C residue 494 THR Chi-restraints excluded: chain C residue 520 ILE Chi-restraints excluded: chain C residue 530 THR Chi-restraints excluded: chain C residue 572 ASP Chi-restraints excluded: chain C residue 599 ARG Chi-restraints excluded: chain C residue 632 SER Chi-restraints excluded: chain C residue 719 GLN Chi-restraints excluded: chain C residue 739 HIS Chi-restraints excluded: chain C residue 782 ASP Chi-restraints excluded: chain C residue 793 ILE Chi-restraints excluded: chain C residue 837 THR Chi-restraints excluded: chain C residue 838 THR Chi-restraints excluded: chain C residue 855 THR Chi-restraints excluded: chain C residue 869 ASP Chi-restraints excluded: chain C residue 904 GLU Chi-restraints excluded: chain C residue 911 THR Chi-restraints excluded: chain C residue 914 CYS Chi-restraints excluded: chain C residue 941 THR Chi-restraints excluded: chain C residue 963 SER Chi-restraints excluded: chain C residue 980 GLU Chi-restraints excluded: chain C residue 982 THR Chi-restraints excluded: chain C residue 987 ASP Chi-restraints excluded: chain C residue 997 ASP Chi-restraints excluded: chain C residue 999 TRP Chi-restraints excluded: chain D residue 11 LEU Chi-restraints excluded: chain D residue 13 ARG Chi-restraints excluded: chain D residue 33 PHE Chi-restraints excluded: chain D residue 36 TRP Chi-restraints excluded: chain D residue 43 ARG Chi-restraints excluded: chain D residue 74 LEU Chi-restraints excluded: chain D residue 124 SER Chi-restraints excluded: chain D residue 181 GLU Chi-restraints excluded: chain D residue 209 PHE Chi-restraints excluded: chain D residue 222 ILE Chi-restraints excluded: chain D residue 244 VAL Chi-restraints excluded: chain D residue 302 SER Chi-restraints excluded: chain D residue 322 LEU Chi-restraints excluded: chain D residue 374 GLN Chi-restraints excluded: chain D residue 377 LEU Chi-restraints excluded: chain D residue 416 GLU Chi-restraints excluded: chain D residue 426 LEU Chi-restraints excluded: chain D residue 433 LEU Chi-restraints excluded: chain D residue 471 LEU Chi-restraints excluded: chain D residue 520 ILE Chi-restraints excluded: chain D residue 521 LYS Chi-restraints excluded: chain D residue 530 THR Chi-restraints excluded: chain D residue 572 ASP Chi-restraints excluded: chain D residue 599 ARG Chi-restraints excluded: chain D residue 632 SER Chi-restraints excluded: chain D residue 719 GLN Chi-restraints excluded: chain D residue 739 HIS Chi-restraints excluded: chain D residue 782 ASP Chi-restraints excluded: chain D residue 837 THR Chi-restraints excluded: chain D residue 838 THR Chi-restraints excluded: chain D residue 855 THR Chi-restraints excluded: chain D residue 869 ASP Chi-restraints excluded: chain D residue 904 GLU Chi-restraints excluded: chain D residue 911 THR Chi-restraints excluded: chain D residue 914 CYS Chi-restraints excluded: chain D residue 941 THR Chi-restraints excluded: chain D residue 963 SER Chi-restraints excluded: chain D residue 980 GLU Chi-restraints excluded: chain D residue 982 THR Chi-restraints excluded: chain D residue 987 ASP Chi-restraints excluded: chain D residue 997 ASP Chi-restraints excluded: chain D residue 999 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 43 optimal weight: 0.8980 chunk 259 optimal weight: 2.9990 chunk 136 optimal weight: 2.9990 chunk 404 optimal weight: 10.0000 chunk 129 optimal weight: 5.9990 chunk 114 optimal weight: 9.9990 chunk 381 optimal weight: 5.9990 chunk 250 optimal weight: 20.0000 chunk 19 optimal weight: 4.9990 chunk 108 optimal weight: 6.9990 chunk 269 optimal weight: 10.0000 overall best weight: 3.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 182 ASN ** A 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 363 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 719 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 840 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 182 ASN ** B 719 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 840 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 363 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 604 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 719 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 840 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 182 ASN ** D 363 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 719 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 840 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1008 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.091490 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.075570 restraints weight = 66466.158| |-----------------------------------------------------------------------------| r_work (start): 0.3100 rms_B_bonded: 2.72 r_work: 0.2980 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.2980 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8458 moved from start: 0.5611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 33812 Z= 0.189 Angle : 0.659 20.805 46104 Z= 0.336 Chirality : 0.044 0.242 4820 Planarity : 0.004 0.059 6088 Dihedral : 5.695 53.228 4520 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 11.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 5.06 % Allowed : 22.54 % Favored : 72.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.06 % Cis-general : 1.15 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.12 (0.13), residues: 4080 helix: 0.42 (0.23), residues: 532 sheet: 0.75 (0.14), residues: 1384 loop : -0.41 (0.13), residues: 2164 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP C1020 HIS 0.004 0.001 HIS C 653 PHE 0.019 0.002 PHE B1007 TYR 0.014 0.002 TYR C 906 ARG 0.005 0.001 ARG C 699 Details of bonding type rmsd hydrogen bonds : bond 0.03672 ( 1144) hydrogen bonds : angle 5.48056 ( 3288) covalent geometry : bond 0.00433 (33792) covalent geometry : angle 0.65913 (46104) Misc. bond : bond 0.00395 ( 20) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 487 residues out of total 3496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 177 poor density : 310 time to evaluate : 4.080 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 471 LEU cc_start: 0.9279 (OUTLIER) cc_final: 0.8828 (mm) REVERT: A 515 VAL cc_start: 0.8325 (t) cc_final: 0.7836 (m) REVERT: A 521 LYS cc_start: 0.8673 (OUTLIER) cc_final: 0.8464 (mttp) REVERT: A 542 MET cc_start: 0.8102 (ttm) cc_final: 0.7798 (ttm) REVERT: A 601 PHE cc_start: 0.8344 (m-80) cc_final: 0.8122 (m-80) REVERT: A 719 GLN cc_start: 0.8653 (OUTLIER) cc_final: 0.8083 (tm-30) REVERT: A 808 GLU cc_start: 0.7613 (tm-30) cc_final: 0.7142 (tm-30) REVERT: A 823 LEU cc_start: 0.8523 (mt) cc_final: 0.8281 (mt) REVERT: A 887 GLN cc_start: 0.8593 (OUTLIER) cc_final: 0.8210 (tp40) REVERT: A 911 THR cc_start: 0.9082 (OUTLIER) cc_final: 0.8817 (p) REVERT: B 416 GLU cc_start: 0.8493 (OUTLIER) cc_final: 0.8145 (tp30) REVERT: B 471 LEU cc_start: 0.9280 (OUTLIER) cc_final: 0.8825 (mm) REVERT: B 515 VAL cc_start: 0.8295 (t) cc_final: 0.7790 (m) REVERT: B 572 ASP cc_start: 0.8142 (OUTLIER) cc_final: 0.7735 (m-30) REVERT: B 719 GLN cc_start: 0.8661 (OUTLIER) cc_final: 0.8090 (tm-30) REVERT: B 726 LEU cc_start: 0.8403 (OUTLIER) cc_final: 0.8187 (mm) REVERT: B 864 MET cc_start: 0.7898 (ttm) cc_final: 0.7629 (ttm) REVERT: B 887 GLN cc_start: 0.8582 (OUTLIER) cc_final: 0.8173 (tp40) REVERT: B 911 THR cc_start: 0.9087 (OUTLIER) cc_final: 0.8820 (p) REVERT: C 471 LEU cc_start: 0.9267 (OUTLIER) cc_final: 0.8813 (mm) REVERT: C 515 VAL cc_start: 0.8326 (t) cc_final: 0.7828 (m) REVERT: C 719 GLN cc_start: 0.8686 (OUTLIER) cc_final: 0.8121 (tm-30) REVERT: C 823 LEU cc_start: 0.8525 (mt) cc_final: 0.8281 (mt) REVERT: C 864 MET cc_start: 0.7990 (ttm) cc_final: 0.7703 (ttm) REVERT: C 911 THR cc_start: 0.9091 (OUTLIER) cc_final: 0.8798 (p) REVERT: D 416 GLU cc_start: 0.8521 (OUTLIER) cc_final: 0.8195 (tp30) REVERT: D 471 LEU cc_start: 0.9278 (OUTLIER) cc_final: 0.8818 (mm) REVERT: D 515 VAL cc_start: 0.8296 (t) cc_final: 0.7805 (m) REVERT: D 521 LYS cc_start: 0.8685 (OUTLIER) cc_final: 0.8471 (mttp) REVERT: D 719 GLN cc_start: 0.8686 (OUTLIER) cc_final: 0.8120 (tm-30) REVERT: D 823 LEU cc_start: 0.8526 (mt) cc_final: 0.8285 (mt) REVERT: D 864 MET cc_start: 0.7921 (ttm) cc_final: 0.7650 (ttm) REVERT: D 908 ASP cc_start: 0.7937 (t0) cc_final: 0.7424 (m-30) REVERT: D 911 THR cc_start: 0.9096 (OUTLIER) cc_final: 0.8840 (p) outliers start: 177 outliers final: 148 residues processed: 463 average time/residue: 0.5195 time to fit residues: 397.5122 Evaluate side-chains 462 residues out of total 3496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 168 poor density : 294 time to evaluate : 3.702 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 MET Chi-restraints excluded: chain A residue 11 LEU Chi-restraints excluded: chain A residue 13 ARG Chi-restraints excluded: chain A residue 33 PHE Chi-restraints excluded: chain A residue 36 TRP Chi-restraints excluded: chain A residue 43 ARG Chi-restraints excluded: chain A residue 74 LEU Chi-restraints excluded: chain A residue 124 SER Chi-restraints excluded: chain A residue 181 GLU Chi-restraints excluded: chain A residue 209 PHE Chi-restraints excluded: chain A residue 244 VAL Chi-restraints excluded: chain A residue 302 SER Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 374 GLN Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 433 LEU Chi-restraints excluded: chain A residue 471 LEU Chi-restraints excluded: chain A residue 494 THR Chi-restraints excluded: chain A residue 520 ILE Chi-restraints excluded: chain A residue 521 LYS Chi-restraints excluded: chain A residue 530 THR Chi-restraints excluded: chain A residue 572 ASP Chi-restraints excluded: chain A residue 599 ARG Chi-restraints excluded: chain A residue 632 SER Chi-restraints excluded: chain A residue 719 GLN Chi-restraints excluded: chain A residue 782 ASP Chi-restraints excluded: chain A residue 795 VAL Chi-restraints excluded: chain A residue 799 THR Chi-restraints excluded: chain A residue 837 THR Chi-restraints excluded: chain A residue 838 THR Chi-restraints excluded: chain A residue 855 THR Chi-restraints excluded: chain A residue 869 ASP Chi-restraints excluded: chain A residue 887 GLN Chi-restraints excluded: chain A residue 904 GLU Chi-restraints excluded: chain A residue 910 LEU Chi-restraints excluded: chain A residue 911 THR Chi-restraints excluded: chain A residue 914 CYS Chi-restraints excluded: chain A residue 941 THR Chi-restraints excluded: chain A residue 963 SER Chi-restraints excluded: chain A residue 980 GLU Chi-restraints excluded: chain A residue 987 ASP Chi-restraints excluded: chain A residue 997 ASP Chi-restraints excluded: chain A residue 999 TRP Chi-restraints excluded: chain B residue 2 MET Chi-restraints excluded: chain B residue 11 LEU Chi-restraints excluded: chain B residue 13 ARG Chi-restraints excluded: chain B residue 33 PHE Chi-restraints excluded: chain B residue 36 TRP Chi-restraints excluded: chain B residue 43 ARG Chi-restraints excluded: chain B residue 74 LEU Chi-restraints excluded: chain B residue 124 SER Chi-restraints excluded: chain B residue 181 GLU Chi-restraints excluded: chain B residue 209 PHE Chi-restraints excluded: chain B residue 237 ARG Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain B residue 244 VAL Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain B residue 374 GLN Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain B residue 416 GLU Chi-restraints excluded: chain B residue 426 LEU Chi-restraints excluded: chain B residue 433 LEU Chi-restraints excluded: chain B residue 471 LEU Chi-restraints excluded: chain B residue 494 THR Chi-restraints excluded: chain B residue 520 ILE Chi-restraints excluded: chain B residue 530 THR Chi-restraints excluded: chain B residue 572 ASP Chi-restraints excluded: chain B residue 599 ARG Chi-restraints excluded: chain B residue 632 SER Chi-restraints excluded: chain B residue 719 GLN Chi-restraints excluded: chain B residue 726 LEU Chi-restraints excluded: chain B residue 782 ASP Chi-restraints excluded: chain B residue 795 VAL Chi-restraints excluded: chain B residue 837 THR Chi-restraints excluded: chain B residue 838 THR Chi-restraints excluded: chain B residue 855 THR Chi-restraints excluded: chain B residue 869 ASP Chi-restraints excluded: chain B residue 887 GLN Chi-restraints excluded: chain B residue 904 GLU Chi-restraints excluded: chain B residue 911 THR Chi-restraints excluded: chain B residue 914 CYS Chi-restraints excluded: chain B residue 941 THR Chi-restraints excluded: chain B residue 963 SER Chi-restraints excluded: chain B residue 965 GLN Chi-restraints excluded: chain B residue 980 GLU Chi-restraints excluded: chain B residue 982 THR Chi-restraints excluded: chain B residue 987 ASP Chi-restraints excluded: chain B residue 999 TRP Chi-restraints excluded: chain C residue 2 MET Chi-restraints excluded: chain C residue 13 ARG Chi-restraints excluded: chain C residue 33 PHE Chi-restraints excluded: chain C residue 36 TRP Chi-restraints excluded: chain C residue 43 ARG Chi-restraints excluded: chain C residue 124 SER Chi-restraints excluded: chain C residue 181 GLU Chi-restraints excluded: chain C residue 209 PHE Chi-restraints excluded: chain C residue 240 LEU Chi-restraints excluded: chain C residue 244 VAL Chi-restraints excluded: chain C residue 302 SER Chi-restraints excluded: chain C residue 322 LEU Chi-restraints excluded: chain C residue 374 GLN Chi-restraints excluded: chain C residue 377 LEU Chi-restraints excluded: chain C residue 426 LEU Chi-restraints excluded: chain C residue 433 LEU Chi-restraints excluded: chain C residue 471 LEU Chi-restraints excluded: chain C residue 494 THR Chi-restraints excluded: chain C residue 530 THR Chi-restraints excluded: chain C residue 572 ASP Chi-restraints excluded: chain C residue 599 ARG Chi-restraints excluded: chain C residue 632 SER Chi-restraints excluded: chain C residue 719 GLN Chi-restraints excluded: chain C residue 739 HIS Chi-restraints excluded: chain C residue 782 ASP Chi-restraints excluded: chain C residue 793 ILE Chi-restraints excluded: chain C residue 837 THR Chi-restraints excluded: chain C residue 838 THR Chi-restraints excluded: chain C residue 855 THR Chi-restraints excluded: chain C residue 869 ASP Chi-restraints excluded: chain C residue 904 GLU Chi-restraints excluded: chain C residue 911 THR Chi-restraints excluded: chain C residue 914 CYS Chi-restraints excluded: chain C residue 941 THR Chi-restraints excluded: chain C residue 963 SER Chi-restraints excluded: chain C residue 980 GLU Chi-restraints excluded: chain C residue 987 ASP Chi-restraints excluded: chain C residue 997 ASP Chi-restraints excluded: chain C residue 999 TRP Chi-restraints excluded: chain D residue 2 MET Chi-restraints excluded: chain D residue 13 ARG Chi-restraints excluded: chain D residue 33 PHE Chi-restraints excluded: chain D residue 36 TRP Chi-restraints excluded: chain D residue 43 ARG Chi-restraints excluded: chain D residue 124 SER Chi-restraints excluded: chain D residue 181 GLU Chi-restraints excluded: chain D residue 209 PHE Chi-restraints excluded: chain D residue 244 VAL Chi-restraints excluded: chain D residue 302 SER Chi-restraints excluded: chain D residue 322 LEU Chi-restraints excluded: chain D residue 374 GLN Chi-restraints excluded: chain D residue 377 LEU Chi-restraints excluded: chain D residue 416 GLU Chi-restraints excluded: chain D residue 426 LEU Chi-restraints excluded: chain D residue 433 LEU Chi-restraints excluded: chain D residue 471 LEU Chi-restraints excluded: chain D residue 494 THR Chi-restraints excluded: chain D residue 520 ILE Chi-restraints excluded: chain D residue 521 LYS Chi-restraints excluded: chain D residue 530 THR Chi-restraints excluded: chain D residue 572 ASP Chi-restraints excluded: chain D residue 599 ARG Chi-restraints excluded: chain D residue 632 SER Chi-restraints excluded: chain D residue 719 GLN Chi-restraints excluded: chain D residue 739 HIS Chi-restraints excluded: chain D residue 782 ASP Chi-restraints excluded: chain D residue 793 ILE Chi-restraints excluded: chain D residue 837 THR Chi-restraints excluded: chain D residue 838 THR Chi-restraints excluded: chain D residue 855 THR Chi-restraints excluded: chain D residue 869 ASP Chi-restraints excluded: chain D residue 904 GLU Chi-restraints excluded: chain D residue 911 THR Chi-restraints excluded: chain D residue 914 CYS Chi-restraints excluded: chain D residue 941 THR Chi-restraints excluded: chain D residue 963 SER Chi-restraints excluded: chain D residue 980 GLU Chi-restraints excluded: chain D residue 987 ASP Chi-restraints excluded: chain D residue 997 ASP Chi-restraints excluded: chain D residue 999 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 95 optimal weight: 6.9990 chunk 65 optimal weight: 8.9990 chunk 92 optimal weight: 5.9990 chunk 204 optimal weight: 0.0970 chunk 296 optimal weight: 1.9990 chunk 158 optimal weight: 0.5980 chunk 393 optimal weight: 9.9990 chunk 185 optimal weight: 20.0000 chunk 157 optimal weight: 0.9980 chunk 163 optimal weight: 0.9980 chunk 63 optimal weight: 4.9990 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 182 ASN ** A 363 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 719 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 182 ASN ** B 719 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 182 ASN ** C 604 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 719 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 182 ASN ** D 719 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1008 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.095458 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.079496 restraints weight = 66135.204| |-----------------------------------------------------------------------------| r_work (start): 0.3161 rms_B_bonded: 2.75 r_work: 0.3043 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3043 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8394 moved from start: 0.5787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.054 33812 Z= 0.113 Angle : 0.616 16.842 46104 Z= 0.313 Chirality : 0.043 0.185 4820 Planarity : 0.004 0.042 6088 Dihedral : 5.387 49.473 4520 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 10.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 4.00 % Allowed : 23.86 % Favored : 72.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.06 % Cis-general : 1.15 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.17 (0.13), residues: 4080 helix: 0.46 (0.23), residues: 532 sheet: 0.86 (0.14), residues: 1388 loop : -0.44 (0.13), residues: 2160 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 553 HIS 0.004 0.001 HIS C 653 PHE 0.013 0.001 PHE B 747 TYR 0.011 0.001 TYR A 906 ARG 0.007 0.000 ARG B 894 Details of bonding type rmsd hydrogen bonds : bond 0.03054 ( 1144) hydrogen bonds : angle 5.25203 ( 3288) covalent geometry : bond 0.00250 (33792) covalent geometry : angle 0.61634 (46104) Misc. bond : bond 0.00307 ( 20) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 16981.32 seconds wall clock time: 301 minutes 33.87 seconds (18093.87 seconds total)