Starting phenix.real_space_refine on Tue Aug 26 01:34:47 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/3j7h_5995/08_2025/3j7h_5995.cif Found real_map, /net/cci-nas-00/data/ceres_data/3j7h_5995/08_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 { model { file = "/net/cci-nas-00/data/ceres_data/3j7h_5995/08_2025/3j7h_5995.cif" } default_model = "/net/cci-nas-00/data/ceres_data/3j7h_5995/08_2025/3j7h_5995.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/3j7h_5995/08_2025/3j7h_5995.map" default_real_map = "/net/cci-nas-00/data/ceres_data/3j7h_5995/08_2025/3j7h_5995.map" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.006 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 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: B, C, D Time building chain proxies: 7.45, per 1000 atoms: 0.23 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: 2.46 Conformation dependent library (CDL) restraints added in 1.2 seconds Enol-peptide restraints added in 476.8 nanoseconds 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: 1.29 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: 7.26 Time building geometry restraints manager: 3.26 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: 0.09 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' 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: 2.330 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.560 Check model and map are aligned: 0.100 Set scattering table: 0.060 Process input model: 28.380 Find NCS groups from input model: 0.300 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:0.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.760 ------------------------------------------------------------------------------- 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 : 132.75 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 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 ARG 0.002 0.000 ARG D 800 TYR 0.008 0.001 TYR B 105 PHE 0.009 0.001 PHE A 957 TRP 0.013 0.001 TRP B 553 HIS 0.003 0.001 HIS B 815 Details of bonding type rmsd covalent geometry : bond 0.00465 (33792) covalent geometry : angle 1.16805 (46104) hydrogen bonds : bond 0.28446 ( 1144) hydrogen bonds : angle 10.44541 ( 3288) 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 : 1.273 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: 0.7181 (mmt180) REVERT: A 170 GLU cc_start: 0.6393 (OUTLIER) cc_final: 0.6086 (mp0) REVERT: A 210 ARG cc_start: 0.7533 (OUTLIER) cc_final: 0.6807 (mtt180) REVERT: A 246 MET cc_start: 0.7261 (OUTLIER) cc_final: 0.6939 (ptp) REVERT: A 542 MET cc_start: 0.6418 (OUTLIER) cc_final: 0.6159 (ttm) REVERT: A 881 ARG cc_start: 0.7781 (OUTLIER) cc_final: 0.6796 (ptp-170) REVERT: A 993 ILE cc_start: 0.7986 (pt) cc_final: 0.7786 (pt) REVERT: A 1013 ARG cc_start: 0.7788 (ttm-80) cc_final: 0.7392 (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: 0.7196 (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: 0.6788 (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: 0.6165 (ttm) REVERT: B 881 ARG cc_start: 0.7810 (OUTLIER) cc_final: 0.6832 (ptp-170) REVERT: B 1013 ARG cc_start: 0.7769 (ttm-80) cc_final: 0.7379 (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: 0.7212 (mmt180) REVERT: C 170 GLU cc_start: 0.6429 (OUTLIER) cc_final: 0.6127 (mp0) REVERT: C 210 ARG cc_start: 0.7542 (OUTLIER) cc_final: 0.6778 (mtt180) REVERT: C 246 MET cc_start: 0.7263 (OUTLIER) cc_final: 0.6932 (ptp) REVERT: C 542 MET cc_start: 0.6460 (OUTLIER) cc_final: 0.6187 (ttm) REVERT: C 881 ARG cc_start: 0.7734 (OUTLIER) cc_final: 0.6714 (ptp-170) REVERT: C 1013 ARG cc_start: 0.7776 (ttm-80) cc_final: 0.7362 (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: 0.7198 (mmt180) REVERT: D 170 GLU cc_start: 0.6412 (OUTLIER) cc_final: 0.6115 (mp0) REVERT: D 210 ARG cc_start: 0.7556 (OUTLIER) cc_final: 0.6795 (mtt180) REVERT: D 246 MET cc_start: 0.7258 (OUTLIER) cc_final: 0.6922 (ptp) REVERT: D 542 MET cc_start: 0.6465 (OUTLIER) cc_final: 0.6214 (ttm) REVERT: D 881 ARG cc_start: 0.7754 (OUTLIER) cc_final: 0.6741 (ptp-170) REVERT: D 993 ILE cc_start: 0.7964 (pt) cc_final: 0.7757 (pt) REVERT: D 1013 ARG cc_start: 0.7774 (ttm-80) cc_final: 0.7364 (mtm-85) outliers start: 428 outliers final: 206 residues processed: 1150 average time/residue: 0.2258 time to fit residues: 397.0598 Evaluate side-chains 646 residues out of total 3496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 234 poor density : 412 time to evaluate : 1.332 ------------------------------------------------------------------------------- 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 197 optimal weight: 0.9990 chunk 388 optimal weight: 6.9990 chunk 215 optimal weight: 4.9990 chunk 20 optimal weight: 9.9990 chunk 132 optimal weight: 7.9990 chunk 261 optimal weight: 10.0000 chunk 248 optimal weight: 0.0970 chunk 207 optimal weight: 5.9990 chunk 401 optimal weight: 0.9990 chunk 155 optimal weight: 10.0000 chunk 244 optimal weight: 2.9990 overall best weight: 2.0186 ------------------------------------------------------------------------------- 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 604 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 604 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 604 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 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 604 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 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: 67 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.098227 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.082296 restraints weight = 66776.369| |-----------------------------------------------------------------------------| r_work (start): 0.3222 rms_B_bonded: 2.79 r_work: 0.3105 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3105 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8322 moved from start: 0.4009 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= 0.187 Angle : 0.764 12.126 46104 Z= 0.407 Chirality : 0.049 0.170 4820 Planarity : 0.007 0.060 6088 Dihedral : 11.243 80.140 5056 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 17.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer: Outliers : 7.49 % Allowed : 19.57 % Favored : 72.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.06 % Cis-general : 1.15 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.30 (0.13), residues: 4080 helix: 0.81 (0.21), residues: 556 sheet: 2.25 (0.14), residues: 1368 loop : -0.03 (0.13), residues: 2156 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 442 TYR 0.018 0.002 TYR A 405 PHE 0.023 0.003 PHE C1007 TRP 0.037 0.002 TRP B 769 HIS 0.018 0.002 HIS B 30 Details of bonding type rmsd covalent geometry : bond 0.00418 (33792) covalent geometry : angle 0.76375 (46104) hydrogen bonds : bond 0.04747 ( 1144) hydrogen bonds : angle 6.77998 ( 3288) Misc. bond : bond 0.00214 ( 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 752 residues out of total 3496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 262 poor density : 490 time to evaluate : 0.939 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: 0.9080 (pp30) cc_final: 0.8604 (pp30) REVERT: A 144 ASP cc_start: 0.7877 (m-30) cc_final: 0.7611 (m-30) REVERT: A 412 GLU cc_start: 0.8457 (tt0) cc_final: 0.8105 (tt0) REVERT: A 416 GLU cc_start: 0.8092 (OUTLIER) cc_final: 0.7650 (tt0) REVERT: A 428 ASP cc_start: 0.8303 (t70) cc_final: 0.8068 (t0) REVERT: A 476 LYS cc_start: 0.8907 (OUTLIER) cc_final: 0.8690 (mmtp) REVERT: A 515 VAL cc_start: 0.8258 (t) cc_final: 0.7763 (m) REVERT: A 702 GLN cc_start: 0.8944 (OUTLIER) cc_final: 0.8484 (mp-120) REVERT: A 864 MET cc_start: 0.7715 (ttm) cc_final: 0.7422 (ttm) REVERT: A 898 LEU cc_start: 0.8979 (OUTLIER) cc_final: 0.8778 (tt) REVERT: A 1013 ARG cc_start: 0.8423 (ttm-80) cc_final: 0.7991 (mtm-85) REVERT: B 23 GLN cc_start: 0.9075 (pp30) cc_final: 0.8601 (pp30) REVERT: B 144 ASP cc_start: 0.7878 (m-30) cc_final: 0.7609 (m-30) REVERT: B 412 GLU cc_start: 0.8445 (tt0) cc_final: 0.8087 (tt0) REVERT: B 416 GLU cc_start: 0.8101 (OUTLIER) cc_final: 0.7658 (tt0) REVERT: B 428 ASP cc_start: 0.8311 (t70) cc_final: 0.8068 (t0) REVERT: B 476 LYS cc_start: 0.8910 (OUTLIER) cc_final: 0.8697 (mmtp) REVERT: B 515 VAL cc_start: 0.8253 (t) cc_final: 0.7763 (m) REVERT: B 702 GLN cc_start: 0.8945 (OUTLIER) cc_final: 0.8486 (mp-120) REVERT: B 776 LEU cc_start: 0.9037 (OUTLIER) cc_final: 0.8829 (pp) REVERT: B 801 ILE cc_start: 0.8243 (mm) cc_final: 0.8006 (tt) REVERT: B 808 GLU cc_start: 0.8246 (mm-30) cc_final: 0.7928 (tm-30) REVERT: B 823 LEU cc_start: 0.8487 (mt) cc_final: 0.8206 (mt) REVERT: B 864 MET cc_start: 0.7709 (ttm) cc_final: 0.7391 (ttm) REVERT: B 898 LEU cc_start: 0.8973 (OUTLIER) cc_final: 0.8773 (tt) REVERT: B 1013 ARG cc_start: 0.8412 (ttm-80) cc_final: 0.7987 (mtm-85) REVERT: C 23 GLN cc_start: 0.9049 (pp30) cc_final: 0.8463 (pp30) REVERT: C 412 GLU cc_start: 0.8450 (tt0) cc_final: 0.8090 (tt0) REVERT: C 416 GLU cc_start: 0.8097 (OUTLIER) cc_final: 0.7666 (tt0) REVERT: C 428 ASP cc_start: 0.8300 (t70) cc_final: 0.8077 (t0) REVERT: C 702 GLN cc_start: 0.8935 (OUTLIER) cc_final: 0.8489 (mp-120) REVERT: C 719 GLN cc_start: 0.8476 (OUTLIER) cc_final: 0.8268 (tm-30) REVERT: C 801 ILE cc_start: 0.8274 (mm) cc_final: 0.8031 (tt) REVERT: C 804 ASN cc_start: 0.8576 (m-40) cc_final: 0.8353 (m-40) REVERT: C 808 GLU cc_start: 0.8258 (mm-30) cc_final: 0.7932 (tm-30) REVERT: C 864 MET cc_start: 0.7705 (ttm) cc_final: 0.7402 (ttm) REVERT: C 1013 ARG cc_start: 0.8406 (ttm-80) cc_final: 0.7951 (mtm-85) REVERT: D 23 GLN cc_start: 0.9057 (pp30) cc_final: 0.8595 (pp30) REVERT: D 412 GLU cc_start: 0.8466 (tt0) cc_final: 0.8109 (tt0) REVERT: D 416 GLU cc_start: 0.8104 (OUTLIER) cc_final: 0.7679 (tt0) REVERT: D 428 ASP cc_start: 0.8297 (t70) cc_final: 0.8072 (t0) REVERT: D 702 GLN cc_start: 0.8939 (OUTLIER) cc_final: 0.8494 (mp-120) REVERT: D 719 GLN cc_start: 0.8469 (OUTLIER) cc_final: 0.8268 (tm-30) REVERT: D 768 MET cc_start: 0.8013 (ttm) cc_final: 0.7716 (ttt) REVERT: D 808 GLU cc_start: 0.8266 (mm-30) cc_final: 0.7921 (tm-30) REVERT: D 864 MET cc_start: 0.7707 (ttm) cc_final: 0.7382 (ttm) REVERT: D 884 LEU cc_start: 0.8980 (OUTLIER) cc_final: 0.8739 (pp) REVERT: D 898 LEU cc_start: 0.8985 (OUTLIER) cc_final: 0.8782 (tt) REVERT: D 1013 ARG cc_start: 0.8398 (ttm-80) cc_final: 0.7954 (mtm-85) outliers start: 262 outliers final: 138 residues processed: 694 average time/residue: 0.1954 time to fit residues: 216.9997 Evaluate side-chains 520 residues out of total 3496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 155 poor density : 365 time to evaluate : 0.932 ------------------------------------------------------------------------------- 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 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 469 ASP Chi-restraints excluded: chain A residue 476 LYS Chi-restraints excluded: chain A residue 502 MET Chi-restraints excluded: chain A residue 517 LYS 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 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 898 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 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 469 ASP Chi-restraints excluded: chain B residue 476 LYS Chi-restraints excluded: chain B residue 502 MET Chi-restraints excluded: chain B residue 517 LYS 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 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 898 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 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 517 LYS 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 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 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 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 469 ASP Chi-restraints excluded: chain D residue 517 LYS 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 739 HIS 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 898 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 100 optimal weight: 0.0770 chunk 377 optimal weight: 6.9990 chunk 362 optimal weight: 1.9990 chunk 18 optimal weight: 10.0000 chunk 268 optimal weight: 20.0000 chunk 113 optimal weight: 6.9990 chunk 47 optimal weight: 1.9990 chunk 251 optimal weight: 7.9990 chunk 163 optimal weight: 0.9990 chunk 301 optimal weight: 5.9990 chunk 77 optimal weight: 7.9990 overall best weight: 2.2146 ------------------------------------------------------------------------------- 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 653 HIS ** 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 653 HIS ** 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 381 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 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.095852 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.079908 restraints weight = 66138.025| |-----------------------------------------------------------------------------| r_work (start): 0.3187 rms_B_bonded: 2.76 r_work: 0.3066 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3066 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8380 moved from start: 0.4541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 33812 Z= 0.158 Angle : 0.641 8.176 46104 Z= 0.342 Chirality : 0.045 0.170 4820 Planarity : 0.005 0.049 6088 Dihedral : 8.299 78.043 4600 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 14.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 6.15 % Allowed : 19.25 % Favored : 74.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.06 % Cis-general : 1.15 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.93 (0.13), residues: 4080 helix: 0.72 (0.22), residues: 556 sheet: 1.76 (0.14), residues: 1424 loop : -0.21 (0.13), residues: 2100 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 442 TYR 0.012 0.002 TYR D 105 PHE 0.019 0.002 PHE D 747 TRP 0.019 0.002 TRP B 769 HIS 0.006 0.001 HIS A 653 Details of bonding type rmsd covalent geometry : bond 0.00352 (33792) covalent geometry : angle 0.64133 (46104) hydrogen bonds : bond 0.03856 ( 1144) hydrogen bonds : angle 6.00176 ( 3288) Misc. bond : bond 0.00220 ( 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 612 residues out of total 3496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 215 poor density : 397 time to evaluate : 1.341 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 23 GLN cc_start: 0.9123 (pp30) cc_final: 0.8557 (pp30) REVERT: A 144 ASP cc_start: 0.7948 (m-30) cc_final: 0.7616 (m-30) REVERT: A 202 MET cc_start: 0.8166 (OUTLIER) cc_final: 0.7924 (ptp) REVERT: A 471 LEU cc_start: 0.9249 (OUTLIER) cc_final: 0.8869 (mm) REVERT: A 521 LYS cc_start: 0.8437 (OUTLIER) cc_final: 0.8132 (mttt) REVERT: A 540 HIS cc_start: 0.8190 (OUTLIER) cc_final: 0.7890 (t-170) REVERT: A 572 ASP cc_start: 0.8374 (OUTLIER) cc_final: 0.7728 (m-30) REVERT: A 617 LEU cc_start: 0.8712 (OUTLIER) cc_final: 0.8504 (tp) REVERT: A 702 GLN cc_start: 0.8957 (OUTLIER) cc_final: 0.8569 (mp-120) REVERT: A 726 LEU cc_start: 0.8416 (OUTLIER) cc_final: 0.8199 (mm) REVERT: A 776 LEU cc_start: 0.9070 (OUTLIER) cc_final: 0.8673 (pp) REVERT: A 864 MET cc_start: 0.7722 (ttm) cc_final: 0.7431 (ttm) REVERT: A 1013 ARG cc_start: 0.8444 (ttm-80) cc_final: 0.7860 (mtm-85) REVERT: B 23 GLN cc_start: 0.9123 (pp30) cc_final: 0.8596 (pp30) REVERT: B 144 ASP cc_start: 0.7975 (m-30) cc_final: 0.7637 (m-30) REVERT: B 202 MET cc_start: 0.8178 (OUTLIER) cc_final: 0.7934 (ptp) REVERT: B 372 MET cc_start: 0.8616 (mtm) cc_final: 0.8372 (mtm) REVERT: B 471 LEU cc_start: 0.9250 (OUTLIER) cc_final: 0.8867 (mm) REVERT: B 540 HIS cc_start: 0.8173 (OUTLIER) cc_final: 0.7899 (t-170) REVERT: B 572 ASP cc_start: 0.8373 (OUTLIER) cc_final: 0.7797 (m-30) REVERT: B 617 LEU cc_start: 0.8703 (OUTLIER) cc_final: 0.8498 (tp) REVERT: B 702 GLN cc_start: 0.8950 (OUTLIER) cc_final: 0.8559 (mp-120) REVERT: B 726 LEU cc_start: 0.8428 (OUTLIER) cc_final: 0.8226 (mm) REVERT: B 776 LEU cc_start: 0.9058 (OUTLIER) cc_final: 0.8855 (pp) REVERT: B 801 ILE cc_start: 0.8337 (mm) cc_final: 0.8134 (mp) REVERT: B 864 MET cc_start: 0.7711 (ttm) cc_final: 0.7408 (ttm) REVERT: B 894 ARG cc_start: 0.7744 (mtp85) cc_final: 0.7511 (mtp85) REVERT: B 1013 ARG cc_start: 0.8435 (ttm-80) cc_final: 0.7853 (mtm-85) REVERT: C 202 MET cc_start: 0.8170 (OUTLIER) cc_final: 0.7924 (ptp) REVERT: C 471 LEU cc_start: 0.9259 (OUTLIER) cc_final: 0.8859 (mm) REVERT: C 521 LYS cc_start: 0.8404 (OUTLIER) cc_final: 0.8104 (mttt) REVERT: C 572 ASP cc_start: 0.8402 (OUTLIER) cc_final: 0.7574 (m-30) REVERT: C 702 GLN cc_start: 0.8939 (OUTLIER) cc_final: 0.8544 (mp-120) REVERT: C 719 GLN cc_start: 0.8634 (OUTLIER) cc_final: 0.8159 (tm-30) REVERT: C 726 LEU cc_start: 0.8400 (OUTLIER) cc_final: 0.8177 (mm) REVERT: C 776 LEU cc_start: 0.9058 (OUTLIER) cc_final: 0.8667 (pp) REVERT: C 801 ILE cc_start: 0.8311 (mm) cc_final: 0.8109 (mp) REVERT: C 804 ASN cc_start: 0.8532 (m-40) cc_final: 0.8296 (m-40) REVERT: C 864 MET cc_start: 0.7769 (ttm) cc_final: 0.7475 (ttm) REVERT: C 1013 ARG cc_start: 0.8434 (ttm-80) cc_final: 0.7979 (mtm-85) REVERT: D 202 MET cc_start: 0.8175 (OUTLIER) cc_final: 0.7919 (ptp) REVERT: D 471 LEU cc_start: 0.9258 (OUTLIER) cc_final: 0.8876 (mm) REVERT: D 521 LYS cc_start: 0.8411 (OUTLIER) cc_final: 0.8113 (mttt) REVERT: D 572 ASP cc_start: 0.8397 (OUTLIER) cc_final: 0.7731 (m-30) REVERT: D 702 GLN cc_start: 0.8938 (OUTLIER) cc_final: 0.8546 (mp-120) REVERT: D 719 GLN cc_start: 0.8623 (OUTLIER) cc_final: 0.8157 (tm-30) REVERT: D 726 LEU cc_start: 0.8407 (OUTLIER) cc_final: 0.8179 (mm) REVERT: D 776 LEU cc_start: 0.9067 (OUTLIER) cc_final: 0.8657 (pp) REVERT: D 801 ILE cc_start: 0.8403 (mt) cc_final: 0.8191 (mp) REVERT: D 804 ASN cc_start: 0.8537 (m-40) cc_final: 0.8257 (m-40) REVERT: D 864 MET cc_start: 0.7735 (ttm) cc_final: 0.7438 (ttm) REVERT: D 1013 ARG cc_start: 0.8437 (ttm-80) cc_final: 0.7979 (mtm-85) outliers start: 215 outliers final: 103 residues processed: 566 average time/residue: 0.1990 time to fit residues: 180.0589 Evaluate side-chains 481 residues out of total 3496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 136 poor density : 345 time to evaluate : 1.232 ------------------------------------------------------------------------------- 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 69 VAL Chi-restraints excluded: chain A residue 74 LEU Chi-restraints excluded: chain A residue 200 GLN Chi-restraints excluded: chain A residue 202 MET Chi-restraints excluded: chain A residue 209 PHE 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 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 540 HIS 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 624 GLN Chi-restraints excluded: chain A residue 702 GLN Chi-restraints excluded: chain A residue 726 LEU Chi-restraints excluded: chain A residue 776 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 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 69 VAL Chi-restraints excluded: chain B residue 74 LEU Chi-restraints excluded: chain B residue 200 GLN Chi-restraints excluded: chain B residue 202 MET Chi-restraints excluded: chain B residue 209 PHE Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain B residue 305 ILE Chi-restraints excluded: chain B residue 377 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 540 HIS Chi-restraints excluded: chain B residue 572 ASP Chi-restraints excluded: chain B residue 599 ARG Chi-restraints excluded: chain B residue 600 GLN Chi-restraints excluded: chain B residue 611 ARG Chi-restraints excluded: chain B residue 617 LEU Chi-restraints excluded: chain B residue 624 GLN Chi-restraints excluded: chain B residue 702 GLN Chi-restraints excluded: chain B residue 726 LEU Chi-restraints excluded: chain B residue 776 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 941 THR Chi-restraints excluded: chain B residue 963 SER Chi-restraints excluded: chain B residue 987 ASP 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 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 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 572 ASP 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 719 GLN Chi-restraints excluded: chain C residue 726 LEU Chi-restraints excluded: chain C residue 739 HIS Chi-restraints excluded: chain C residue 776 LEU 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 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 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 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 572 ASP 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 719 GLN Chi-restraints excluded: chain D residue 726 LEU Chi-restraints excluded: chain D residue 776 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 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 199 optimal weight: 9.9990 chunk 227 optimal weight: 5.9990 chunk 298 optimal weight: 10.0000 chunk 349 optimal weight: 4.9990 chunk 81 optimal weight: 9.9990 chunk 352 optimal weight: 4.9990 chunk 10 optimal weight: 9.9990 chunk 232 optimal weight: 10.0000 chunk 195 optimal weight: 10.0000 chunk 287 optimal weight: 9.9990 chunk 14 optimal weight: 10.0000 overall best weight: 7.1990 ------------------------------------------------------------------------------- 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 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 394 ASN ** A 604 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 824 GLN ** A 840 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 890 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1008 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 182 ASN ** B 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 360 HIS B 394 ASN B 563 GLN ** B 604 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 761 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 824 GLN ** B 840 HIS ** 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 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 182 ASN ** C 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 382 ASN C 394 ASN C 563 GLN ** C 604 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 761 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 840 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 863 GLN ** C 890 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 182 ASN ** D 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 382 ASN D 394 ASN ** D 604 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 761 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 840 HIS ** 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: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.089347 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.073417 restraints weight = 67144.104| |-----------------------------------------------------------------------------| r_work (start): 0.3057 rms_B_bonded: 2.70 r_work: 0.2936 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.2936 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8504 moved from start: 0.4920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.049 33812 Z= 0.335 Angle : 0.752 10.389 46104 Z= 0.402 Chirality : 0.050 0.265 4820 Planarity : 0.006 0.108 6088 Dihedral : 7.822 72.094 4568 Min Nonbonded Distance : 1.873 Molprobity Statistics. All-atom Clashscore : 15.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 8.35 % Allowed : 18.68 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.17 (0.13), residues: 4080 helix: -0.22 (0.21), residues: 580 sheet: 1.11 (0.13), residues: 1432 loop : -0.47 (0.13), residues: 2068 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 37 TYR 0.017 0.002 TYR A 906 PHE 0.020 0.003 PHE A 209 TRP 0.025 0.002 TRP A 90 HIS 0.010 0.002 HIS B 653 Details of bonding type rmsd covalent geometry : bond 0.00766 (33792) covalent geometry : angle 0.75243 (46104) hydrogen bonds : bond 0.04777 ( 1144) hydrogen bonds : angle 6.18540 ( 3288) Misc. bond : bond 0.00258 ( 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 632 residues out of total 3496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 292 poor density : 340 time to evaluate : 1.006 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 471 LEU cc_start: 0.9329 (OUTLIER) cc_final: 0.8872 (mm) REVERT: A 521 LYS cc_start: 0.8831 (OUTLIER) cc_final: 0.8566 (mttt) REVERT: A 540 HIS cc_start: 0.8497 (OUTLIER) cc_final: 0.8288 (t-170) REVERT: A 572 ASP cc_start: 0.8331 (OUTLIER) cc_final: 0.7846 (m-30) REVERT: A 719 GLN cc_start: 0.8685 (OUTLIER) cc_final: 0.8156 (tm-30) REVERT: A 776 LEU cc_start: 0.9130 (OUTLIER) cc_final: 0.8808 (pp) REVERT: A 887 GLN cc_start: 0.8568 (OUTLIER) cc_final: 0.7912 (tt0) REVERT: A 911 THR cc_start: 0.9217 (OUTLIER) cc_final: 0.8997 (p) REVERT: B 202 MET cc_start: 0.8205 (OUTLIER) cc_final: 0.8003 (ptt) REVERT: B 416 GLU cc_start: 0.8267 (OUTLIER) cc_final: 0.8034 (tt0) REVERT: B 471 LEU cc_start: 0.9324 (OUTLIER) cc_final: 0.8869 (mm) REVERT: B 572 ASP cc_start: 0.8363 (OUTLIER) cc_final: 0.7892 (m-30) REVERT: B 601 PHE cc_start: 0.8207 (m-80) cc_final: 0.7954 (m-80) REVERT: B 719 GLN cc_start: 0.8687 (OUTLIER) cc_final: 0.8155 (tm-30) REVERT: B 776 LEU cc_start: 0.9110 (OUTLIER) cc_final: 0.8866 (pp) REVERT: B 804 ASN cc_start: 0.8623 (m-40) cc_final: 0.8368 (m-40) REVERT: B 887 GLN cc_start: 0.8554 (OUTLIER) cc_final: 0.7893 (tt0) REVERT: B 911 THR cc_start: 0.9219 (OUTLIER) cc_final: 0.9007 (p) REVERT: C 144 ASP cc_start: 0.8287 (m-30) cc_final: 0.8073 (m-30) REVERT: C 202 MET cc_start: 0.8197 (OUTLIER) cc_final: 0.7993 (ptt) REVERT: C 471 LEU cc_start: 0.9331 (OUTLIER) cc_final: 0.8848 (mm) REVERT: C 521 LYS cc_start: 0.8812 (OUTLIER) cc_final: 0.8549 (mttt) REVERT: C 540 HIS cc_start: 0.8504 (OUTLIER) cc_final: 0.8286 (t-170) REVERT: C 572 ASP cc_start: 0.8496 (OUTLIER) cc_final: 0.8127 (m-30) REVERT: C 601 PHE cc_start: 0.8198 (m-80) cc_final: 0.7987 (m-80) REVERT: C 719 GLN cc_start: 0.8748 (OUTLIER) cc_final: 0.8089 (tm-30) REVERT: C 776 LEU cc_start: 0.9107 (OUTLIER) cc_final: 0.8783 (pp) REVERT: C 804 ASN cc_start: 0.8603 (m-40) cc_final: 0.8340 (m-40) REVERT: C 887 GLN cc_start: 0.8576 (OUTLIER) cc_final: 0.7912 (tt0) REVERT: C 911 THR cc_start: 0.9225 (OUTLIER) cc_final: 0.9010 (p) REVERT: D 471 LEU cc_start: 0.9330 (OUTLIER) cc_final: 0.8874 (mm) REVERT: D 521 LYS cc_start: 0.8823 (OUTLIER) cc_final: 0.8559 (mttt) REVERT: D 540 HIS cc_start: 0.8491 (OUTLIER) cc_final: 0.8267 (t-170) REVERT: D 572 ASP cc_start: 0.8362 (OUTLIER) cc_final: 0.7884 (m-30) REVERT: D 719 GLN cc_start: 0.8753 (OUTLIER) cc_final: 0.8100 (tm-30) REVERT: D 776 LEU cc_start: 0.9100 (OUTLIER) cc_final: 0.8769 (pp) REVERT: D 804 ASN cc_start: 0.8647 (m-40) cc_final: 0.8375 (m-40) REVERT: D 887 GLN cc_start: 0.8575 (OUTLIER) cc_final: 0.7907 (tt0) REVERT: D 911 THR cc_start: 0.9224 (OUTLIER) cc_final: 0.9010 (p) outliers start: 292 outliers final: 164 residues processed: 595 average time/residue: 0.2007 time to fit residues: 194.0205 Evaluate side-chains 476 residues out of total 3496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 197 poor density : 279 time to evaluate : 1.242 ------------------------------------------------------------------------------- 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 69 VAL 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 188 VAL 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 277 GLU 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 418 HIS Chi-restraints excluded: chain A residue 471 LEU Chi-restraints excluded: chain A residue 493 THR 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 540 HIS 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 702 GLN Chi-restraints excluded: chain A residue 714 ILE Chi-restraints excluded: chain A residue 719 GLN Chi-restraints excluded: chain A residue 739 HIS Chi-restraints excluded: chain A residue 776 LEU Chi-restraints excluded: chain A residue 780 LEU Chi-restraints excluded: chain A residue 795 VAL Chi-restraints excluded: chain A residue 828 ASP 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 934 GLU 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 1008 GLN 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 69 VAL 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 188 VAL Chi-restraints excluded: chain B residue 200 GLN Chi-restraints excluded: chain B residue 202 MET 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 321 THR Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain B residue 416 GLU Chi-restraints excluded: chain B residue 418 HIS Chi-restraints excluded: chain B residue 471 LEU Chi-restraints excluded: chain B residue 493 THR 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 611 ARG Chi-restraints excluded: chain B residue 702 GLN Chi-restraints excluded: chain B residue 714 ILE Chi-restraints excluded: chain B residue 719 GLN 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 828 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 934 GLU 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 987 ASP Chi-restraints excluded: chain B residue 997 ASP Chi-restraints excluded: chain B residue 999 TRP Chi-restraints excluded: chain B residue 1008 GLN 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 74 LEU Chi-restraints excluded: chain C residue 124 SER Chi-restraints excluded: chain C residue 181 GLU 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 244 VAL Chi-restraints excluded: chain C residue 321 THR Chi-restraints excluded: chain C residue 322 LEU Chi-restraints excluded: chain C residue 418 HIS Chi-restraints excluded: chain C residue 471 LEU Chi-restraints excluded: chain C residue 493 THR 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 540 HIS 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 702 GLN Chi-restraints excluded: chain C residue 714 ILE Chi-restraints excluded: chain C residue 719 GLN Chi-restraints excluded: chain C residue 739 HIS 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 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 863 GLN 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 934 GLU 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 74 LEU Chi-restraints excluded: chain D residue 124 SER Chi-restraints excluded: chain D residue 181 GLU Chi-restraints excluded: chain D residue 188 VAL Chi-restraints excluded: chain D residue 200 GLN Chi-restraints excluded: chain D residue 209 PHE Chi-restraints excluded: chain D residue 240 LEU Chi-restraints excluded: chain D residue 244 VAL Chi-restraints excluded: chain D residue 321 THR Chi-restraints excluded: chain D residue 322 LEU Chi-restraints excluded: chain D residue 418 HIS Chi-restraints excluded: chain D residue 471 LEU Chi-restraints excluded: chain D residue 493 THR 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 540 HIS 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 702 GLN Chi-restraints excluded: chain D residue 714 ILE Chi-restraints excluded: chain D residue 719 GLN 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 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 934 GLU Chi-restraints excluded: chain D residue 941 THR 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 334 optimal weight: 9.9990 chunk 105 optimal weight: 3.9990 chunk 371 optimal weight: 6.9990 chunk 375 optimal weight: 6.9990 chunk 88 optimal weight: 5.9990 chunk 188 optimal weight: 6.9990 chunk 225 optimal weight: 3.9990 chunk 170 optimal weight: 20.0000 chunk 297 optimal weight: 0.9980 chunk 257 optimal weight: 0.9980 chunk 6 optimal weight: 5.9990 overall best weight: 3.1986 ------------------------------------------------------------------------------- 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 360 HIS A 382 ASN A 394 ASN ** A 604 ASN ** 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 182 ASN ** B 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 382 ASN B 394 ASN ** B 604 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 761 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 791 ASN B 863 GLN ** B 890 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1008 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 182 ASN ** C 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 360 HIS C 394 ASN ** C 604 ASN ** 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 791 ASN C 863 GLN ** C 890 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 182 ASN ** D 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 360 HIS D 394 ASN ** D 604 ASN ** 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 791 ASN 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: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.090970 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.075118 restraints weight = 66769.055| |-----------------------------------------------------------------------------| r_work (start): 0.3086 rms_B_bonded: 2.73 r_work: 0.2966 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.2966 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8464 moved from start: 0.5170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 33812 Z= 0.183 Angle : 0.658 17.237 46104 Z= 0.346 Chirality : 0.045 0.194 4820 Planarity : 0.006 0.149 6088 Dihedral : 7.044 62.564 4550 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 12.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 7.27 % Allowed : 19.51 % Favored : 73.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.06 % Cis-general : 1.15 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.08 (0.13), residues: 4080 helix: -0.05 (0.22), residues: 580 sheet: 0.98 (0.14), residues: 1408 loop : -0.53 (0.13), residues: 2092 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 894 TYR 0.013 0.002 TYR A 906 PHE 0.017 0.002 PHE A 209 TRP 0.020 0.001 TRP C 553 HIS 0.005 0.001 HIS D 653 Details of bonding type rmsd covalent geometry : bond 0.00413 (33792) covalent geometry : angle 0.65776 (46104) hydrogen bonds : bond 0.03871 ( 1144) hydrogen bonds : angle 5.86741 ( 3288) Misc. bond : bond 0.00422 ( 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 587 residues out of total 3496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 254 poor density : 333 time to evaluate : 1.150 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 241 GLU cc_start: 0.8174 (pp20) cc_final: 0.7901 (pp20) REVERT: A 471 LEU cc_start: 0.9291 (OUTLIER) cc_final: 0.8861 (mm) REVERT: A 521 LYS cc_start: 0.8590 (OUTLIER) cc_final: 0.8365 (mttp) REVERT: A 572 ASP cc_start: 0.8295 (OUTLIER) cc_final: 0.7854 (m-30) REVERT: A 744 GLU cc_start: 0.7215 (pm20) cc_final: 0.6711 (tp30) REVERT: A 776 LEU cc_start: 0.9094 (OUTLIER) cc_final: 0.8741 (pp) REVERT: A 887 GLN cc_start: 0.8535 (OUTLIER) cc_final: 0.7870 (tt0) REVERT: B 416 GLU cc_start: 0.8411 (OUTLIER) cc_final: 0.8115 (tt0) REVERT: B 471 LEU cc_start: 0.9287 (OUTLIER) cc_final: 0.8857 (mm) REVERT: B 572 ASP cc_start: 0.8294 (OUTLIER) cc_final: 0.7928 (m-30) REVERT: B 601 PHE cc_start: 0.8290 (m-80) cc_final: 0.8070 (m-80) REVERT: B 744 GLU cc_start: 0.7225 (pm20) cc_final: 0.6601 (tp30) REVERT: B 804 ASN cc_start: 0.8582 (m-40) cc_final: 0.8290 (m-40) REVERT: B 887 GLN cc_start: 0.8543 (OUTLIER) cc_final: 0.7895 (tt0) REVERT: C 241 GLU cc_start: 0.8198 (pp20) cc_final: 0.7926 (pp20) REVERT: C 471 LEU cc_start: 0.9291 (OUTLIER) cc_final: 0.8861 (mm) REVERT: C 521 LYS cc_start: 0.8568 (OUTLIER) cc_final: 0.8346 (mttp) REVERT: C 572 ASP cc_start: 0.8311 (OUTLIER) cc_final: 0.7890 (m-30) REVERT: C 601 PHE cc_start: 0.8248 (m-80) cc_final: 0.8031 (m-80) REVERT: C 719 GLN cc_start: 0.8683 (OUTLIER) cc_final: 0.8100 (tm-30) REVERT: C 744 GLU cc_start: 0.7239 (pm20) cc_final: 0.6548 (tp30) REVERT: C 776 LEU cc_start: 0.9105 (OUTLIER) cc_final: 0.8776 (pp) REVERT: C 804 ASN cc_start: 0.8566 (m-40) cc_final: 0.8298 (m-40) REVERT: C 887 GLN cc_start: 0.8554 (OUTLIER) cc_final: 0.7896 (tt0) REVERT: D 241 GLU cc_start: 0.8178 (pp20) cc_final: 0.7908 (pp20) REVERT: D 471 LEU cc_start: 0.9297 (OUTLIER) cc_final: 0.8869 (mm) REVERT: D 521 LYS cc_start: 0.8581 (OUTLIER) cc_final: 0.8358 (mttp) REVERT: D 572 ASP cc_start: 0.8303 (OUTLIER) cc_final: 0.7863 (m-30) REVERT: D 719 GLN cc_start: 0.8681 (OUTLIER) cc_final: 0.8109 (tm-30) REVERT: D 776 LEU cc_start: 0.9097 (OUTLIER) cc_final: 0.8744 (pp) REVERT: D 804 ASN cc_start: 0.8586 (m-40) cc_final: 0.8290 (m-40) REVERT: D 887 GLN cc_start: 0.8548 (OUTLIER) cc_final: 0.7885 (tt0) outliers start: 254 outliers final: 150 residues processed: 551 average time/residue: 0.1869 time to fit residues: 170.0127 Evaluate side-chains 474 residues out of total 3496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 171 poor density : 303 time to evaluate : 1.059 ------------------------------------------------------------------------------- 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 69 VAL Chi-restraints excluded: chain A residue 74 LEU Chi-restraints excluded: chain A residue 107 ILE Chi-restraints excluded: chain A residue 124 SER Chi-restraints excluded: chain A residue 200 GLN 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 250 LEU Chi-restraints excluded: chain A residue 265 THR Chi-restraints excluded: chain A residue 302 SER Chi-restraints excluded: chain A residue 321 THR Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 394 ASN 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 776 LEU Chi-restraints excluded: chain A residue 780 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 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 941 THR 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 A residue 1022 GLN 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 69 VAL Chi-restraints excluded: chain B residue 74 LEU Chi-restraints excluded: chain B residue 107 ILE Chi-restraints excluded: chain B residue 124 SER Chi-restraints excluded: chain B residue 200 GLN Chi-restraints excluded: chain B residue 209 PHE Chi-restraints excluded: chain B residue 222 ILE Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain B residue 277 GLU Chi-restraints excluded: chain B residue 302 SER Chi-restraints excluded: chain B residue 321 THR 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 394 ASN Chi-restraints excluded: chain B residue 416 GLU 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 530 THR Chi-restraints excluded: chain B residue 572 ASP Chi-restraints excluded: chain B residue 599 ARG 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 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 997 ASP Chi-restraints excluded: chain B residue 999 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 74 LEU Chi-restraints excluded: chain C residue 107 ILE Chi-restraints excluded: chain C residue 124 SER Chi-restraints excluded: chain C residue 200 GLN 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 302 SER Chi-restraints excluded: chain C residue 321 THR Chi-restraints excluded: chain C residue 374 GLN Chi-restraints excluded: chain C residue 377 LEU Chi-restraints excluded: chain C residue 394 ASN 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 776 LEU 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 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 914 CYS Chi-restraints excluded: chain C residue 941 THR 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 C residue 1022 GLN 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 74 LEU Chi-restraints excluded: chain D residue 107 ILE Chi-restraints excluded: chain D residue 124 SER 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 302 SER Chi-restraints excluded: chain D residue 321 THR Chi-restraints excluded: chain D residue 374 GLN Chi-restraints excluded: chain D residue 377 LEU Chi-restraints excluded: chain D residue 394 ASN 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 776 LEU 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 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 361 optimal weight: 1.9990 chunk 382 optimal weight: 5.9990 chunk 90 optimal weight: 6.9990 chunk 331 optimal weight: 0.0370 chunk 176 optimal weight: 0.6980 chunk 259 optimal weight: 0.8980 chunk 115 optimal weight: 10.0000 chunk 325 optimal weight: 4.9990 chunk 210 optimal weight: 0.4980 chunk 300 optimal weight: 1.9990 chunk 263 optimal weight: 8.9990 overall best weight: 0.8260 ------------------------------------------------------------------------------- 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 394 ASN A 604 ASN A 761 GLN 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 394 ASN B 604 ASN B 761 GLN ** B 890 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 394 ASN C 604 ASN ** C 719 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 761 GLN C 890 GLN ** D 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 394 ASN D 604 ASN ** 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: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.094203 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.078223 restraints weight = 65768.862| |-----------------------------------------------------------------------------| r_work (start): 0.3144 rms_B_bonded: 2.75 r_work: 0.3025 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3025 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8409 moved from start: 0.5411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 33812 Z= 0.117 Angle : 0.630 18.966 46104 Z= 0.325 Chirality : 0.043 0.187 4820 Planarity : 0.004 0.073 6088 Dihedral : 5.817 57.624 4528 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 10.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 4.86 % Allowed : 21.91 % Favored : 73.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.06 % Cis-general : 1.15 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.22 (0.13), residues: 4080 helix: 0.33 (0.22), residues: 556 sheet: 1.04 (0.14), residues: 1380 loop : -0.47 (0.13), residues: 2144 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 894 TYR 0.010 0.001 TYR A 906 PHE 0.014 0.001 PHE A 747 TRP 0.021 0.001 TRP D 553 HIS 0.005 0.001 HIS D 395 Details of bonding type rmsd covalent geometry : bond 0.00250 (33792) covalent geometry : angle 0.62991 (46104) hydrogen bonds : bond 0.03258 ( 1144) hydrogen bonds : angle 5.54885 ( 3288) Misc. bond : bond 0.00364 ( 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 528 residues out of total 3496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 170 poor density : 358 time to evaluate : 1.261 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 PHE cc_start: 0.5670 (OUTLIER) cc_final: 0.5259 (p90) REVERT: A 279 ILE cc_start: 0.8214 (tt) cc_final: 0.8005 (tt) REVERT: A 471 LEU cc_start: 0.9221 (OUTLIER) cc_final: 0.8865 (mm) REVERT: A 572 ASP cc_start: 0.8182 (OUTLIER) cc_final: 0.7750 (m-30) REVERT: A 719 GLN cc_start: 0.8583 (OUTLIER) cc_final: 0.8048 (tm-30) REVERT: A 744 GLU cc_start: 0.7214 (pm20) cc_final: 0.6808 (tp30) REVERT: A 776 LEU cc_start: 0.9098 (OUTLIER) cc_final: 0.8748 (pp) REVERT: A 887 GLN cc_start: 0.8536 (OUTLIER) cc_final: 0.7912 (tp40) REVERT: A 894 ARG cc_start: 0.8068 (mmm-85) cc_final: 0.7685 (mmm-85) REVERT: A 908 ASP cc_start: 0.7870 (t0) cc_final: 0.7427 (t0) REVERT: B 33 PHE cc_start: 0.5605 (OUTLIER) cc_final: 0.5192 (p90) REVERT: B 416 GLU cc_start: 0.8484 (OUTLIER) cc_final: 0.8160 (tp30) REVERT: B 471 LEU cc_start: 0.9223 (OUTLIER) cc_final: 0.8865 (mm) REVERT: B 572 ASP cc_start: 0.8159 (OUTLIER) cc_final: 0.7650 (m-30) REVERT: B 719 GLN cc_start: 0.8572 (OUTLIER) cc_final: 0.8032 (tm-30) REVERT: B 887 GLN cc_start: 0.8565 (OUTLIER) cc_final: 0.7981 (tp40) REVERT: C 33 PHE cc_start: 0.5599 (OUTLIER) cc_final: 0.5143 (p90) REVERT: C 471 LEU cc_start: 0.9230 (OUTLIER) cc_final: 0.8868 (mm) REVERT: C 572 ASP cc_start: 0.8193 (OUTLIER) cc_final: 0.7755 (m-30) REVERT: C 719 GLN cc_start: 0.8632 (OUTLIER) cc_final: 0.8123 (tm-30) REVERT: C 744 GLU cc_start: 0.7207 (pm20) cc_final: 0.6943 (tp30) REVERT: C 776 LEU cc_start: 0.9099 (OUTLIER) cc_final: 0.8772 (pp) REVERT: C 887 GLN cc_start: 0.8537 (OUTLIER) cc_final: 0.7905 (tp40) REVERT: D 33 PHE cc_start: 0.5619 (OUTLIER) cc_final: 0.5157 (p90) REVERT: D 471 LEU cc_start: 0.9235 (OUTLIER) cc_final: 0.8879 (mm) REVERT: D 572 ASP cc_start: 0.8198 (OUTLIER) cc_final: 0.7771 (m-30) REVERT: D 719 GLN cc_start: 0.8635 (OUTLIER) cc_final: 0.8132 (tm-30) REVERT: D 744 GLU cc_start: 0.7166 (pm20) cc_final: 0.6738 (tp30) REVERT: D 776 LEU cc_start: 0.9088 (OUTLIER) cc_final: 0.8715 (pp) REVERT: D 887 GLN cc_start: 0.8535 (OUTLIER) cc_final: 0.7912 (tp40) outliers start: 170 outliers final: 95 residues processed: 504 average time/residue: 0.1806 time to fit residues: 151.2696 Evaluate side-chains 439 residues out of total 3496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 320 time to evaluate : 0.910 ------------------------------------------------------------------------------- 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 69 VAL Chi-restraints excluded: chain A residue 200 GLN 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 265 THR Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 471 LEU Chi-restraints excluded: chain A residue 520 ILE 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 776 LEU Chi-restraints excluded: chain A residue 782 ASP 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 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 1022 GLN 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 69 VAL Chi-restraints excluded: chain B residue 209 PHE Chi-restraints excluded: chain B residue 222 ILE Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain B residue 244 VAL Chi-restraints excluded: chain B residue 265 THR Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain B residue 416 GLU 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 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 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 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 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 74 LEU Chi-restraints excluded: chain C residue 200 GLN 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 265 THR Chi-restraints excluded: chain C residue 322 LEU Chi-restraints excluded: chain C residue 374 GLN 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 719 GLN Chi-restraints excluded: chain C residue 776 LEU 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 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 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 1022 GLN 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 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 265 THR Chi-restraints excluded: chain D residue 322 LEU Chi-restraints excluded: chain D residue 374 GLN Chi-restraints excluded: chain D residue 426 LEU Chi-restraints excluded: chain D residue 471 LEU Chi-restraints excluded: chain D residue 520 ILE Chi-restraints excluded: chain D residue 530 THR Chi-restraints excluded: chain D residue 572 ASP Chi-restraints excluded: chain D residue 719 GLN Chi-restraints excluded: chain D residue 776 LEU 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 162 optimal weight: 0.9990 chunk 98 optimal weight: 10.0000 chunk 30 optimal weight: 0.0570 chunk 143 optimal weight: 10.0000 chunk 280 optimal weight: 8.9990 chunk 171 optimal weight: 0.9990 chunk 159 optimal weight: 10.0000 chunk 374 optimal weight: 6.9990 chunk 279 optimal weight: 6.9990 chunk 211 optimal weight: 7.9990 chunk 173 optimal weight: 6.9990 overall best weight: 3.2106 ------------------------------------------------------------------------------- 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 394 ASN A 791 ASN A 863 GLN ** A1008 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 394 ASN ** C 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 394 ASN ** C 719 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 840 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 182 ASN ** D 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 363 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 394 ASN ** 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: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.091769 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.075807 restraints weight = 66355.957| |-----------------------------------------------------------------------------| r_work (start): 0.3103 rms_B_bonded: 2.73 r_work: 0.2983 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.2983 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8456 moved from start: 0.5443 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= 0.178 Angle : 0.649 23.631 46104 Z= 0.337 Chirality : 0.044 0.201 4820 Planarity : 0.004 0.078 6088 Dihedral : 5.648 57.106 4516 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 11.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 4.95 % Allowed : 21.88 % Favored : 73.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.06 % Cis-general : 1.15 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.14 (0.13), residues: 4080 helix: 0.30 (0.23), residues: 556 sheet: 0.86 (0.14), residues: 1384 loop : -0.44 (0.13), residues: 2140 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 442 TYR 0.015 0.002 TYR A 906 PHE 0.018 0.002 PHE D 747 TRP 0.021 0.001 TRP A1020 HIS 0.004 0.001 HIS D 990 Details of bonding type rmsd covalent geometry : bond 0.00404 (33792) covalent geometry : angle 0.64855 (46104) hydrogen bonds : bond 0.03641 ( 1144) hydrogen bonds : angle 5.60111 ( 3288) Misc. bond : bond 0.00338 ( 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 498 residues out of total 3496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 173 poor density : 325 time to evaluate : 0.874 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 471 LEU cc_start: 0.9278 (OUTLIER) cc_final: 0.8851 (mm) REVERT: A 521 LYS cc_start: 0.8760 (OUTLIER) cc_final: 0.8291 (mttt) REVERT: A 572 ASP cc_start: 0.8174 (OUTLIER) cc_final: 0.7659 (m-30) REVERT: A 719 GLN cc_start: 0.8645 (OUTLIER) cc_final: 0.8177 (tm-30) REVERT: A 754 LYS cc_start: 0.6358 (mmtm) cc_final: 0.6025 (mmmm) REVERT: A 776 LEU cc_start: 0.9101 (OUTLIER) cc_final: 0.8760 (pp) REVERT: A 887 GLN cc_start: 0.8587 (OUTLIER) cc_final: 0.7893 (tt0) REVERT: A 908 ASP cc_start: 0.7800 (t0) cc_final: 0.7506 (t0) REVERT: B 416 GLU cc_start: 0.8444 (OUTLIER) cc_final: 0.8195 (tt0) REVERT: B 471 LEU cc_start: 0.9282 (OUTLIER) cc_final: 0.8863 (mm) REVERT: B 515 VAL cc_start: 0.8321 (t) cc_final: 0.7834 (m) REVERT: B 572 ASP cc_start: 0.8206 (OUTLIER) cc_final: 0.7730 (m-30) REVERT: B 719 GLN cc_start: 0.8655 (OUTLIER) cc_final: 0.8187 (tm-30) REVERT: B 823 LEU cc_start: 0.8543 (mt) cc_final: 0.8255 (mt) REVERT: C 471 LEU cc_start: 0.9273 (OUTLIER) cc_final: 0.8843 (mm) REVERT: C 521 LYS cc_start: 0.8738 (OUTLIER) cc_final: 0.8256 (mttt) REVERT: C 572 ASP cc_start: 0.8199 (OUTLIER) cc_final: 0.7805 (m-30) REVERT: C 776 LEU cc_start: 0.9121 (OUTLIER) cc_final: 0.8788 (pp) REVERT: C 823 LEU cc_start: 0.8535 (mt) cc_final: 0.8260 (mt) REVERT: C 887 GLN cc_start: 0.8609 (OUTLIER) cc_final: 0.7915 (tt0) REVERT: D 471 LEU cc_start: 0.9279 (OUTLIER) cc_final: 0.8850 (mm) REVERT: D 521 LYS cc_start: 0.8758 (OUTLIER) cc_final: 0.8275 (mttt) REVERT: D 572 ASP cc_start: 0.8177 (OUTLIER) cc_final: 0.7686 (m-30) REVERT: D 776 LEU cc_start: 0.9124 (OUTLIER) cc_final: 0.8748 (pp) REVERT: D 887 GLN cc_start: 0.8608 (OUTLIER) cc_final: 0.7922 (tt0) outliers start: 173 outliers final: 121 residues processed: 472 average time/residue: 0.1752 time to fit residues: 138.7202 Evaluate side-chains 442 residues out of total 3496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 141 poor density : 301 time to evaluate : 0.847 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 69 VAL 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 209 PHE Chi-restraints excluded: chain A residue 265 THR Chi-restraints excluded: chain A residue 302 SER Chi-restraints excluded: chain A residue 322 LEU 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 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 776 LEU 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 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 A residue 1022 GLN 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 69 VAL 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 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 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 719 GLN 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 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 997 ASP Chi-restraints excluded: chain B residue 999 TRP Chi-restraints excluded: chain C residue 7 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 124 SER Chi-restraints excluded: chain C residue 209 PHE 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 433 LEU Chi-restraints excluded: chain C residue 471 LEU Chi-restraints excluded: chain C residue 494 THR 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 739 HIS Chi-restraints excluded: chain C residue 776 LEU 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 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 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 1022 GLN Chi-restraints excluded: chain D residue 7 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 124 SER Chi-restraints excluded: chain D residue 200 GLN Chi-restraints excluded: chain D residue 209 PHE Chi-restraints excluded: chain D residue 244 VAL Chi-restraints excluded: chain D residue 277 GLU 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 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 521 LYS Chi-restraints excluded: chain D residue 530 THR Chi-restraints excluded: chain D residue 572 ASP Chi-restraints excluded: chain D residue 776 LEU 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 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 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 310 optimal weight: 1.9990 chunk 230 optimal weight: 10.0000 chunk 236 optimal weight: 7.9990 chunk 350 optimal weight: 10.0000 chunk 375 optimal weight: 6.9990 chunk 301 optimal weight: 10.0000 chunk 23 optimal weight: 9.9990 chunk 6 optimal weight: 7.9990 chunk 181 optimal weight: 20.0000 chunk 215 optimal weight: 3.9990 chunk 201 optimal weight: 1.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 182 ASN ** A 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 840 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 863 GLN ** A1008 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 182 ASN ** B 840 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 182 ASN ** C 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 363 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 840 HIS ** 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 840 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 863 GLN ** D1008 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.090355 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.074443 restraints weight = 66815.038| |-----------------------------------------------------------------------------| r_work (start): 0.3075 rms_B_bonded: 2.72 r_work: 0.2955 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.2955 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8482 moved from start: 0.5494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 33812 Z= 0.226 Angle : 0.678 22.555 46104 Z= 0.350 Chirality : 0.045 0.218 4820 Planarity : 0.005 0.088 6088 Dihedral : 5.675 51.645 4508 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 12.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 5.29 % Allowed : 21.97 % Favored : 72.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.06 % Cis-general : 1.15 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.01 (0.13), residues: 4080 helix: 0.14 (0.23), residues: 556 sheet: 0.70 (0.14), residues: 1404 loop : -0.45 (0.13), residues: 2120 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 760 TYR 0.015 0.002 TYR D 906 PHE 0.016 0.002 PHE D 209 TRP 0.022 0.001 TRP A1020 HIS 0.006 0.001 HIS D 990 Details of bonding type rmsd covalent geometry : bond 0.00516 (33792) covalent geometry : angle 0.67803 (46104) hydrogen bonds : bond 0.03876 ( 1144) hydrogen bonds : angle 5.70040 ( 3288) Misc. bond : bond 0.00381 ( 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 482 residues out of total 3496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 185 poor density : 297 time to evaluate : 0.867 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 471 LEU cc_start: 0.9296 (OUTLIER) cc_final: 0.8850 (mm) REVERT: A 515 VAL cc_start: 0.8291 (t) cc_final: 0.7813 (m) REVERT: A 521 LYS cc_start: 0.8822 (OUTLIER) cc_final: 0.8337 (mttt) REVERT: A 572 ASP cc_start: 0.8223 (OUTLIER) cc_final: 0.7763 (m-30) REVERT: A 719 GLN cc_start: 0.8673 (OUTLIER) cc_final: 0.8189 (tm-30) REVERT: A 776 LEU cc_start: 0.9102 (OUTLIER) cc_final: 0.8780 (pp) REVERT: A 808 GLU cc_start: 0.7650 (tm-30) cc_final: 0.7110 (tm-30) REVERT: A 887 GLN cc_start: 0.8605 (OUTLIER) cc_final: 0.7916 (tt0) REVERT: B 416 GLU cc_start: 0.8446 (OUTLIER) cc_final: 0.8188 (tp30) REVERT: B 471 LEU cc_start: 0.9289 (OUTLIER) cc_final: 0.8836 (mm) REVERT: B 515 VAL cc_start: 0.8291 (t) cc_final: 0.7803 (m) REVERT: B 572 ASP cc_start: 0.8213 (OUTLIER) cc_final: 0.7761 (m-30) REVERT: B 719 GLN cc_start: 0.8678 (OUTLIER) cc_final: 0.8196 (tm-30) REVERT: B 887 GLN cc_start: 0.8599 (OUTLIER) cc_final: 0.7999 (tt0) REVERT: C 471 LEU cc_start: 0.9281 (OUTLIER) cc_final: 0.8828 (mm) REVERT: C 515 VAL cc_start: 0.8314 (t) cc_final: 0.7824 (m) REVERT: C 521 LYS cc_start: 0.8817 (OUTLIER) cc_final: 0.8322 (mttt) REVERT: C 572 ASP cc_start: 0.8175 (OUTLIER) cc_final: 0.7807 (m-30) REVERT: C 719 GLN cc_start: 0.8701 (OUTLIER) cc_final: 0.8118 (tm-30) REVERT: C 776 LEU cc_start: 0.9098 (OUTLIER) cc_final: 0.8787 (pp) REVERT: C 887 GLN cc_start: 0.8615 (OUTLIER) cc_final: 0.7915 (tt0) REVERT: D 471 LEU cc_start: 0.9292 (OUTLIER) cc_final: 0.8844 (mm) REVERT: D 515 VAL cc_start: 0.8308 (t) cc_final: 0.7818 (m) REVERT: D 521 LYS cc_start: 0.8836 (OUTLIER) cc_final: 0.8347 (mttt) REVERT: D 572 ASP cc_start: 0.8232 (OUTLIER) cc_final: 0.7777 (m-30) REVERT: D 719 GLN cc_start: 0.8693 (OUTLIER) cc_final: 0.8107 (tm-30) REVERT: D 776 LEU cc_start: 0.9104 (OUTLIER) cc_final: 0.8769 (pp) REVERT: D 887 GLN cc_start: 0.8623 (OUTLIER) cc_final: 0.7934 (tt0) outliers start: 185 outliers final: 135 residues processed: 458 average time/residue: 0.1877 time to fit residues: 142.2886 Evaluate side-chains 443 residues out of total 3496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 158 poor density : 285 time to evaluate : 0.985 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 69 VAL 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 244 VAL Chi-restraints excluded: chain A residue 265 THR 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 376 ILE 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 521 LYS Chi-restraints excluded: chain A residue 530 THR Chi-restraints excluded: chain A residue 572 ASP Chi-restraints excluded: chain A residue 719 GLN 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 828 ASP 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 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 A residue 1022 GLN 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 69 VAL 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 265 THR 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 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 719 GLN Chi-restraints excluded: chain B residue 739 HIS 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 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 997 ASP Chi-restraints excluded: chain B residue 999 TRP Chi-restraints excluded: chain C residue 7 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 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 265 THR Chi-restraints excluded: chain C residue 302 SER Chi-restraints excluded: chain C residue 321 THR 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 433 LEU Chi-restraints excluded: chain C residue 471 LEU Chi-restraints excluded: chain C residue 494 THR 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 719 GLN Chi-restraints excluded: chain C residue 739 HIS Chi-restraints excluded: chain C residue 776 LEU 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 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 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 C residue 1022 GLN Chi-restraints excluded: chain D residue 7 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 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 244 VAL Chi-restraints excluded: chain D residue 265 THR 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 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 521 LYS Chi-restraints excluded: chain D residue 530 THR Chi-restraints excluded: chain D residue 572 ASP Chi-restraints excluded: chain D residue 719 GLN Chi-restraints excluded: chain D residue 739 HIS Chi-restraints excluded: chain D residue 776 LEU Chi-restraints excluded: chain D residue 780 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 887 GLN Chi-restraints excluded: chain D residue 904 GLU 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 225 optimal weight: 8.9990 chunk 106 optimal weight: 3.9990 chunk 177 optimal weight: 0.7980 chunk 79 optimal weight: 8.9990 chunk 187 optimal weight: 9.9990 chunk 335 optimal weight: 2.9990 chunk 169 optimal weight: 0.8980 chunk 369 optimal weight: 9.9990 chunk 258 optimal weight: 0.9980 chunk 119 optimal weight: 3.9990 chunk 277 optimal weight: 0.4980 overall best weight: 1.2382 ------------------------------------------------------------------------------- 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** ** A1008 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 182 ASN ** B 363 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 394 ASN C 182 ASN ** 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** D 182 ASN ** D 363 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 394 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: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.093521 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.077541 restraints weight = 65638.210| |-----------------------------------------------------------------------------| r_work (start): 0.3134 rms_B_bonded: 2.75 r_work: 0.3015 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3015 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8423 moved from start: 0.5671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 33812 Z= 0.121 Angle : 0.629 26.867 46104 Z= 0.320 Chirality : 0.043 0.188 4820 Planarity : 0.007 0.463 6088 Dihedral : 5.439 95.657 4500 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 10.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 4.03 % Allowed : 23.46 % Favored : 72.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.06 % Cis-general : 1.15 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.09 (0.13), residues: 4080 helix: 0.33 (0.23), residues: 556 sheet: 0.79 (0.14), residues: 1380 loop : -0.46 (0.13), residues: 2144 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG B 760 TYR 0.012 0.001 TYR D 906 PHE 0.025 0.001 PHE B 747 TRP 0.022 0.001 TRP D 553 HIS 0.004 0.001 HIS C 990 Details of bonding type rmsd covalent geometry : bond 0.00265 (33792) covalent geometry : angle 0.62920 (46104) hydrogen bonds : bond 0.03183 ( 1144) hydrogen bonds : angle 5.36189 ( 3288) Misc. bond : bond 0.00370 ( 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 475 residues out of total 3496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 141 poor density : 334 time to evaluate : 0.961 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 PHE cc_start: 0.5715 (OUTLIER) cc_final: 0.5252 (p90) REVERT: A 102 ASN cc_start: 0.8427 (t0) cc_final: 0.8222 (t0) REVERT: A 416 GLU cc_start: 0.8285 (tt0) cc_final: 0.7853 (tp30) REVERT: A 471 LEU cc_start: 0.9249 (OUTLIER) cc_final: 0.8870 (mm) REVERT: A 515 VAL cc_start: 0.8259 (t) cc_final: 0.7773 (m) REVERT: A 521 LYS cc_start: 0.8680 (OUTLIER) cc_final: 0.8380 (mttt) REVERT: A 572 ASP cc_start: 0.8146 (OUTLIER) cc_final: 0.7674 (m-30) REVERT: A 719 GLN cc_start: 0.8610 (OUTLIER) cc_final: 0.8125 (tm-30) REVERT: A 776 LEU cc_start: 0.9095 (OUTLIER) cc_final: 0.8784 (pp) REVERT: A 808 GLU cc_start: 0.7635 (tm-30) cc_final: 0.7044 (tm-30) REVERT: A 887 GLN cc_start: 0.8572 (OUTLIER) cc_final: 0.7909 (tp40) REVERT: B 33 PHE cc_start: 0.5645 (OUTLIER) cc_final: 0.5236 (p90) REVERT: B 416 GLU cc_start: 0.8469 (OUTLIER) cc_final: 0.8063 (tp30) REVERT: B 471 LEU cc_start: 0.9245 (OUTLIER) cc_final: 0.8869 (mm) REVERT: B 515 VAL cc_start: 0.8264 (t) cc_final: 0.7774 (m) REVERT: B 572 ASP cc_start: 0.8179 (OUTLIER) cc_final: 0.7730 (m-30) REVERT: B 719 GLN cc_start: 0.8616 (OUTLIER) cc_final: 0.8112 (tm-30) REVERT: B 864 MET cc_start: 0.7740 (ttm) cc_final: 0.7469 (ttm) REVERT: B 887 GLN cc_start: 0.8557 (OUTLIER) cc_final: 0.8127 (tp40) REVERT: C 33 PHE cc_start: 0.5634 (OUTLIER) cc_final: 0.5184 (p90) REVERT: C 471 LEU cc_start: 0.9240 (OUTLIER) cc_final: 0.8867 (mm) REVERT: C 515 VAL cc_start: 0.8280 (t) cc_final: 0.7774 (m) REVERT: C 521 LYS cc_start: 0.8669 (OUTLIER) cc_final: 0.8355 (mttt) REVERT: C 572 ASP cc_start: 0.8133 (OUTLIER) cc_final: 0.7686 (m-30) REVERT: C 719 GLN cc_start: 0.8632 (OUTLIER) cc_final: 0.8110 (tm-30) REVERT: C 776 LEU cc_start: 0.9097 (OUTLIER) cc_final: 0.8812 (pp) REVERT: C 887 GLN cc_start: 0.8597 (OUTLIER) cc_final: 0.7921 (tp40) REVERT: D 33 PHE cc_start: 0.5700 (OUTLIER) cc_final: 0.5237 (p90) REVERT: D 102 ASN cc_start: 0.8452 (t0) cc_final: 0.8238 (t0) REVERT: D 471 LEU cc_start: 0.9251 (OUTLIER) cc_final: 0.8873 (mm) REVERT: D 515 VAL cc_start: 0.8266 (t) cc_final: 0.7770 (m) REVERT: D 521 LYS cc_start: 0.8689 (OUTLIER) cc_final: 0.8363 (mttt) REVERT: D 572 ASP cc_start: 0.8166 (OUTLIER) cc_final: 0.7702 (m-30) REVERT: D 719 GLN cc_start: 0.8637 (OUTLIER) cc_final: 0.8103 (tm-30) REVERT: D 776 LEU cc_start: 0.9096 (OUTLIER) cc_final: 0.8754 (pp) REVERT: D 864 MET cc_start: 0.7721 (ttm) cc_final: 0.7447 (ttm) REVERT: D 887 GLN cc_start: 0.8582 (OUTLIER) cc_final: 0.7910 (tp40) outliers start: 141 outliers final: 99 residues processed: 452 average time/residue: 0.1846 time to fit residues: 138.2113 Evaluate side-chains 432 residues out of total 3496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 126 poor density : 306 time to evaluate : 1.298 ------------------------------------------------------------------------------- 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 69 VAL Chi-restraints excluded: chain A residue 74 LEU 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 265 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 433 LEU Chi-restraints excluded: chain A residue 471 LEU 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 719 GLN Chi-restraints excluded: chain A residue 776 LEU Chi-restraints excluded: chain A residue 795 VAL 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 941 THR 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 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 69 VAL Chi-restraints excluded: chain B residue 74 LEU 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 433 LEU Chi-restraints excluded: chain B residue 471 LEU 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 719 GLN 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 910 LEU Chi-restraints excluded: chain B residue 941 THR Chi-restraints excluded: chain B residue 980 GLU Chi-restraints excluded: chain B residue 987 ASP Chi-restraints excluded: chain B residue 997 ASP Chi-restraints excluded: chain B residue 999 TRP Chi-restraints excluded: chain C residue 7 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 124 SER 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 322 LEU Chi-restraints excluded: chain C residue 374 GLN 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 521 LYS Chi-restraints excluded: chain C residue 530 THR Chi-restraints excluded: chain C residue 572 ASP Chi-restraints excluded: chain C residue 719 GLN Chi-restraints excluded: chain C residue 776 LEU Chi-restraints excluded: chain C residue 780 LEU Chi-restraints excluded: chain C residue 782 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 941 THR 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 1022 GLN 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 124 SER 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 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 521 LYS Chi-restraints excluded: chain D residue 530 THR Chi-restraints excluded: chain D residue 545 SER Chi-restraints excluded: chain D residue 572 ASP Chi-restraints excluded: chain D residue 719 GLN Chi-restraints excluded: chain D residue 776 LEU Chi-restraints excluded: chain D residue 780 LEU 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 914 CYS Chi-restraints excluded: chain D residue 941 THR 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 64 optimal weight: 8.9990 chunk 357 optimal weight: 2.9990 chunk 305 optimal weight: 8.9990 chunk 235 optimal weight: 0.7980 chunk 127 optimal weight: 0.0170 chunk 263 optimal weight: 0.0060 chunk 97 optimal weight: 20.0000 chunk 257 optimal weight: 8.9990 chunk 129 optimal weight: 10.0000 chunk 2 optimal weight: 20.0000 chunk 59 optimal weight: 0.9980 overall best weight: 0.9636 ------------------------------------------------------------------------------- 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 563 GLN A 604 ASN ** B 363 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 394 ASN ** B 840 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 719 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 753 ASN ** D 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 363 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 394 ASN ** 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: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.095225 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.079065 restraints weight = 65777.733| |-----------------------------------------------------------------------------| r_work (start): 0.3156 rms_B_bonded: 2.77 r_work: 0.3038 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3038 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8404 moved from start: 0.5774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 33812 Z= 0.114 Angle : 0.623 31.028 46104 Z= 0.316 Chirality : 0.042 0.192 4820 Planarity : 0.004 0.066 6088 Dihedral : 5.739 179.779 4500 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 9.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 3.63 % Allowed : 24.14 % Favored : 72.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.06 % Cis-general : 1.15 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.17 (0.13), residues: 4080 helix: 0.63 (0.23), residues: 532 sheet: 0.82 (0.14), residues: 1384 loop : -0.46 (0.13), residues: 2164 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG B 760 TYR 0.012 0.001 TYR D 906 PHE 0.017 0.001 PHE B 747 TRP 0.021 0.001 TRP D 553 HIS 0.003 0.000 HIS C 990 Details of bonding type rmsd covalent geometry : bond 0.00251 (33792) covalent geometry : angle 0.62338 (46104) hydrogen bonds : bond 0.03036 ( 1144) hydrogen bonds : angle 5.21936 ( 3288) Misc. bond : bond 0.00416 ( 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 456 residues out of total 3496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 127 poor density : 329 time to evaluate : 0.834 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 13 ARG cc_start: 0.7573 (OUTLIER) cc_final: 0.6689 (pmt-80) REVERT: A 23 GLN cc_start: 0.9064 (pp30) cc_final: 0.8749 (pp30) REVERT: A 33 PHE cc_start: 0.5613 (OUTLIER) cc_final: 0.5284 (p90) REVERT: A 471 LEU cc_start: 0.9224 (OUTLIER) cc_final: 0.8862 (mm) REVERT: A 515 VAL cc_start: 0.8277 (t) cc_final: 0.7784 (m) REVERT: A 572 ASP cc_start: 0.8143 (OUTLIER) cc_final: 0.7593 (m-30) REVERT: A 719 GLN cc_start: 0.8592 (OUTLIER) cc_final: 0.8092 (tm-30) REVERT: A 776 LEU cc_start: 0.9097 (OUTLIER) cc_final: 0.8790 (pp) REVERT: A 808 GLU cc_start: 0.7577 (tm-30) cc_final: 0.7047 (tm-30) REVERT: A 864 MET cc_start: 0.7583 (ttm) cc_final: 0.7365 (ttm) REVERT: A 887 GLN cc_start: 0.8535 (OUTLIER) cc_final: 0.7900 (tp40) REVERT: A 894 ARG cc_start: 0.8225 (mmm-85) cc_final: 0.7675 (mmm-85) REVERT: A 908 ASP cc_start: 0.7897 (t0) cc_final: 0.7363 (m-30) REVERT: B 13 ARG cc_start: 0.7568 (OUTLIER) cc_final: 0.6703 (pmt-80) REVERT: B 23 GLN cc_start: 0.9079 (pp30) cc_final: 0.8754 (pp30) REVERT: B 33 PHE cc_start: 0.5604 (OUTLIER) cc_final: 0.5308 (p90) REVERT: B 416 GLU cc_start: 0.8494 (OUTLIER) cc_final: 0.8041 (tp30) REVERT: B 471 LEU cc_start: 0.9223 (OUTLIER) cc_final: 0.8859 (mm) REVERT: B 572 ASP cc_start: 0.8136 (OUTLIER) cc_final: 0.7595 (m-30) REVERT: B 719 GLN cc_start: 0.8587 (OUTLIER) cc_final: 0.8094 (tm-30) REVERT: B 864 MET cc_start: 0.7630 (ttm) cc_final: 0.7393 (ttm) REVERT: B 887 GLN cc_start: 0.8506 (OUTLIER) cc_final: 0.8146 (tp40) REVERT: C 13 ARG cc_start: 0.7524 (OUTLIER) cc_final: 0.6643 (pmt-80) REVERT: C 23 GLN cc_start: 0.9063 (pp30) cc_final: 0.8741 (pp30) REVERT: C 33 PHE cc_start: 0.5577 (OUTLIER) cc_final: 0.5260 (p90) REVERT: C 471 LEU cc_start: 0.9222 (OUTLIER) cc_final: 0.8869 (mm) REVERT: C 515 VAL cc_start: 0.8287 (t) cc_final: 0.7782 (m) REVERT: C 719 GLN cc_start: 0.8631 (OUTLIER) cc_final: 0.8106 (tm-30) REVERT: C 776 LEU cc_start: 0.9084 (OUTLIER) cc_final: 0.8811 (pp) REVERT: C 887 GLN cc_start: 0.8565 (OUTLIER) cc_final: 0.7913 (tp40) REVERT: D 13 ARG cc_start: 0.7528 (OUTLIER) cc_final: 0.6639 (pmt-80) REVERT: D 33 PHE cc_start: 0.5601 (OUTLIER) cc_final: 0.5277 (p90) REVERT: D 102 ASN cc_start: 0.8428 (t0) cc_final: 0.8219 (t0) REVERT: D 471 LEU cc_start: 0.9222 (OUTLIER) cc_final: 0.8862 (mm) REVERT: D 515 VAL cc_start: 0.8281 (t) cc_final: 0.7784 (m) REVERT: D 572 ASP cc_start: 0.8140 (OUTLIER) cc_final: 0.7634 (m-30) REVERT: D 719 GLN cc_start: 0.8620 (OUTLIER) cc_final: 0.8097 (tm-30) REVERT: D 776 LEU cc_start: 0.9094 (OUTLIER) cc_final: 0.8763 (pp) REVERT: D 864 MET cc_start: 0.7543 (ttm) cc_final: 0.7332 (ttm) REVERT: D 887 GLN cc_start: 0.8546 (OUTLIER) cc_final: 0.7900 (tp40) outliers start: 127 outliers final: 88 residues processed: 437 average time/residue: 0.1831 time to fit residues: 133.8716 Evaluate side-chains 417 residues out of total 3496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 302 time to evaluate : 1.333 ------------------------------------------------------------------------------- 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 69 VAL Chi-restraints excluded: chain A residue 74 LEU 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 265 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 433 LEU Chi-restraints excluded: chain A residue 471 LEU Chi-restraints excluded: chain A residue 530 THR Chi-restraints excluded: chain A residue 572 ASP Chi-restraints excluded: chain A residue 719 GLN Chi-restraints excluded: chain A residue 776 LEU 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 941 THR 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 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 69 VAL Chi-restraints excluded: chain B residue 74 LEU 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 433 LEU Chi-restraints excluded: chain B residue 471 LEU 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 719 GLN Chi-restraints excluded: chain B residue 795 VAL 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 910 LEU Chi-restraints excluded: chain B residue 941 THR Chi-restraints excluded: chain B residue 980 GLU Chi-restraints excluded: chain B residue 987 ASP Chi-restraints excluded: chain B residue 997 ASP Chi-restraints excluded: chain B residue 999 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 124 SER 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 322 LEU Chi-restraints excluded: chain C residue 374 GLN Chi-restraints excluded: chain C residue 433 LEU Chi-restraints excluded: chain C residue 471 LEU Chi-restraints excluded: chain C residue 530 THR Chi-restraints excluded: chain C residue 572 ASP Chi-restraints excluded: chain C residue 719 GLN Chi-restraints excluded: chain C residue 776 LEU Chi-restraints excluded: chain C residue 780 LEU Chi-restraints excluded: chain C residue 782 ASP 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 910 LEU Chi-restraints excluded: chain C residue 914 CYS Chi-restraints excluded: chain C residue 941 THR Chi-restraints excluded: chain C residue 980 GLU Chi-restraints excluded: chain C residue 987 ASP Chi-restraints excluded: chain C residue 1022 GLN 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 124 SER Chi-restraints excluded: chain D residue 209 PHE Chi-restraints excluded: chain D residue 222 ILE Chi-restraints excluded: chain D residue 322 LEU Chi-restraints excluded: chain D residue 374 GLN 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 530 THR Chi-restraints excluded: chain D residue 572 ASP Chi-restraints excluded: chain D residue 719 GLN Chi-restraints excluded: chain D residue 776 LEU Chi-restraints excluded: chain D residue 782 ASP 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 914 CYS Chi-restraints excluded: chain D residue 941 THR Chi-restraints excluded: chain D residue 980 GLU Chi-restraints excluded: chain D residue 987 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 362 optimal weight: 9.9990 chunk 124 optimal weight: 9.9990 chunk 235 optimal weight: 5.9990 chunk 284 optimal weight: 0.0470 chunk 46 optimal weight: 20.0000 chunk 4 optimal weight: 0.1980 chunk 18 optimal weight: 4.9990 chunk 256 optimal weight: 4.9990 chunk 109 optimal weight: 7.9990 chunk 131 optimal weight: 0.0040 chunk 281 optimal weight: 4.9990 overall best weight: 2.0494 ------------------------------------------------------------------------------- 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 863 GLN ** B 363 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 840 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1022 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** ** D 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 719 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 824 GLN D 863 GLN ** 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 = 0.3416 r_free = 0.3416 target = 0.094173 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.077908 restraints weight = 65999.604| |-----------------------------------------------------------------------------| r_work (start): 0.3136 rms_B_bonded: 2.77 r_work: 0.3017 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3017 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8425 moved from start: 0.5778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 33812 Z= 0.135 Angle : 0.623 28.131 46104 Z= 0.316 Chirality : 0.043 0.190 4820 Planarity : 0.004 0.068 6088 Dihedral : 5.666 175.173 4496 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 9.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 3.89 % Allowed : 24.20 % Favored : 71.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.06 % Cis-general : 1.15 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.11 (0.13), residues: 4080 helix: 0.37 (0.23), residues: 556 sheet: 0.79 (0.14), residues: 1384 loop : -0.45 (0.13), residues: 2140 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 894 TYR 0.013 0.001 TYR D 906 PHE 0.016 0.001 PHE B 747 TRP 0.018 0.001 TRP A 553 HIS 0.004 0.001 HIS C 990 Details of bonding type rmsd covalent geometry : bond 0.00305 (33792) covalent geometry : angle 0.62318 (46104) hydrogen bonds : bond 0.03198 ( 1144) hydrogen bonds : angle 5.23583 ( 3288) Misc. bond : bond 0.00351 ( 20) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5956.04 seconds wall clock time: 103 minutes 26.82 seconds (6206.82 seconds total)