Starting phenix.real_space_refine on Fri Jan 16 08:57:19 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9czh_46416/01_2026/9czh_46416.cif Found real_map, /net/cci-nas-00/data/ceres_data/9czh_46416/01_2026/9czh_46416.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9czh_46416/01_2026/9czh_46416.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9czh_46416/01_2026/9czh_46416.map" model { file = "/net/cci-nas-00/data/ceres_data/9czh_46416/01_2026/9czh_46416.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9czh_46416/01_2026/9czh_46416.cif" } resolution = 2.9 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= 0.002 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: 7 Type Number sf(0) Gaussians Ca 8 9.91 5 K 4 8.98 5 P 9 5.49 5 S 244 5.16 5 C 22718 2.51 5 N 5678 2.21 5 O 6353 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5927/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 35014 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 7105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 891, 7105 Classifications: {'peptide': 891} Link IDs: {'PTRANS': 27, 'TRANS': 863} Chain breaks: 4 Chain: "E" Number of atoms: 1558 Number of conformers: 1 Conformer: "" Number of residues, atoms: 197, 1558 Classifications: {'peptide': 197} Link IDs: {'PTRANS': 8, 'TRANS': 188} Chain: "A" Number of atoms: 99 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 99 Unusual residues: {' K': 4, ' CA': 2, 'POV': 3} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 63 Unresolved non-hydrogen angles: 74 Unresolved non-hydrogen dihedrals: 57 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'POV:plan-1': 2, 'POV:plan-3': 1} Unresolved non-hydrogen planarities: 12 Chain: "B" Number of atoms: 81 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 81 Unusual residues: {' CA': 2, 'POV': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 21 Planarities with less than four sites: {'POV:plan-1': 1} Unresolved non-hydrogen planarities: 3 Chain: "C" Number of atoms: 86 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 86 Unusual residues: {' CA': 2, 'POV': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'POV:plan-1': 1} Unresolved non-hydrogen planarities: 3 Chain: "D" Number of atoms: 96 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 96 Unusual residues: {' CA': 2, 'POV': 3} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 62 Unresolved non-hydrogen angles: 73 Unresolved non-hydrogen dihedrals: 56 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'POV:plan-1': 2, 'POV:plan-3': 1} Unresolved non-hydrogen planarities: 10 Restraints were copied for chains: B, C, D, F, G, H Time building chain proxies: 9.12, per 1000 atoms: 0.26 Number of scatterers: 35014 At special positions: 0 Unit cell: (146.025, 146.025, 168.3, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Ca 8 19.99 K 4 19.00 S 244 16.00 P 9 15.00 O 6353 8.00 N 5678 7.00 C 22718 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.89 Conformation dependent library (CDL) restraints added in 1.5 seconds 8608 Ramachandran restraints generated. 4304 Oldfield, 0 Emsley, 4304 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8264 Finding SS restraints... Secondary structure from input PDB file: 204 helices and 28 sheets defined 54.5% alpha, 13.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.40 Creating SS restraints... Processing helix chain 'A' and resid 21 through 54 removed outlier: 4.147A pdb=" N PHE A 25 " --> pdb=" O MET A 21 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N SER A 28 " --> pdb=" O ALA A 24 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N SER A 29 " --> pdb=" O PHE A 25 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N THR A 51 " --> pdb=" O LYS A 47 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N VAL A 52 " --> pdb=" O TYR A 48 " (cutoff:3.500A) Processing helix chain 'A' and resid 96 through 100 Processing helix chain 'A' and resid 102 through 107 removed outlier: 4.690A pdb=" N ALA A 107 " --> pdb=" O VAL A 103 " (cutoff:3.500A) Processing helix chain 'A' and resid 113 through 134 removed outlier: 5.490A pdb=" N VAL A 119 " --> pdb=" O LEU A 115 " (cutoff:3.500A) Processing helix chain 'A' and resid 148 through 171 removed outlier: 3.829A pdb=" N ALA A 155 " --> pdb=" O GLN A 151 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N PHE A 156 " --> pdb=" O ILE A 152 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N PHE A 159 " --> pdb=" O ALA A 155 " (cutoff:3.500A) Processing helix chain 'A' and resid 173 through 179 Processing helix chain 'A' and resid 180 through 199 Proline residue: A 191 - end of helix removed outlier: 3.750A pdb=" N PHE A 194 " --> pdb=" O VAL A 190 " (cutoff:3.500A) Processing helix chain 'A' and resid 205 through 215 removed outlier: 4.390A pdb=" N PHE A 208 " --> pdb=" O GLY A 205 " (cutoff:3.500A) Processing helix chain 'A' and resid 216 through 224 removed outlier: 3.687A pdb=" N ILE A 220 " --> pdb=" O GLN A 216 " (cutoff:3.500A) Processing helix chain 'A' and resid 229 through 259 Processing helix chain 'A' and resid 261 through 265 Processing helix chain 'A' and resid 273 through 286 Processing helix chain 'A' and resid 297 through 312 Processing helix chain 'A' and resid 319 through 325 Processing helix chain 'A' and resid 326 through 331 removed outlier: 3.870A pdb=" N LYS A 331 " --> pdb=" O GLY A 327 " (cutoff:3.500A) Processing helix chain 'A' and resid 352 through 364 removed outlier: 5.210A pdb=" N ASN A 358 " --> pdb=" O GLU A 354 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N PHE A 359 " --> pdb=" O SER A 355 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ASP A 362 " --> pdb=" O ASN A 358 " (cutoff:3.500A) Processing helix chain 'A' and resid 385 through 394 removed outlier: 3.789A pdb=" N ALA A 389 " --> pdb=" O LEU A 385 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N HIS A 394 " --> pdb=" O LEU A 390 " (cutoff:3.500A) Processing helix chain 'A' and resid 407 through 414 Processing helix chain 'A' and resid 415 through 419 Processing helix chain 'A' and resid 432 through 451 Processing helix chain 'A' and resid 465 through 470 removed outlier: 3.670A pdb=" N LEU A 469 " --> pdb=" O ASN A 465 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N LEU A 470 " --> pdb=" O LYS A 466 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 465 through 470' Processing helix chain 'A' and resid 476 through 480 Processing helix chain 'A' and resid 486 through 500 removed outlier: 3.532A pdb=" N LEU A 499 " --> pdb=" O ALA A 495 " (cutoff:3.500A) Processing helix chain 'A' and resid 502 through 512 removed outlier: 3.767A pdb=" N PHE A 511 " --> pdb=" O LEU A 507 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N SER A 512 " --> pdb=" O ALA A 508 " (cutoff:3.500A) Processing helix chain 'A' and resid 523 through 533 removed outlier: 4.119A pdb=" N TYR A 527 " --> pdb=" O THR A 523 " (cutoff:3.500A) Processing helix chain 'A' and resid 542 through 546 Processing helix chain 'A' and resid 549 through 562 Processing helix chain 'A' and resid 601 through 606 removed outlier: 3.851A pdb=" N VAL A 605 " --> pdb=" O ASP A 601 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N LYS A 606 " --> pdb=" O ALA A 602 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 601 through 606' Processing helix chain 'A' and resid 607 through 609 No H-bonds generated for 'chain 'A' and resid 607 through 609' Processing helix chain 'A' and resid 699 through 703 Processing helix chain 'A' and resid 706 through 713 Processing helix chain 'A' and resid 734 through 739 Processing helix chain 'A' and resid 740 through 743 removed outlier: 3.826A pdb=" N ALA A 743 " --> pdb=" O PRO A 740 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 740 through 743' Processing helix chain 'A' and resid 759 through 768 removed outlier: 4.403A pdb=" N ARG A 765 " --> pdb=" O GLU A 761 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N GLU A 766 " --> pdb=" O TYR A 762 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N GLU A 768 " --> pdb=" O LYS A 764 " (cutoff:3.500A) Processing helix chain 'A' and resid 785 through 792 Processing helix chain 'A' and resid 793 through 797 removed outlier: 3.570A pdb=" N CYS A 797 " --> pdb=" O ILE A 794 " (cutoff:3.500A) Processing helix chain 'A' and resid 817 through 829 Processing helix chain 'A' and resid 872 through 876 removed outlier: 3.981A pdb=" N ASN A 875 " --> pdb=" O THR A 872 " (cutoff:3.500A) Processing helix chain 'A' and resid 884 through 891 Processing helix chain 'A' and resid 902 through 905 Processing helix chain 'A' and resid 906 through 911 Processing helix chain 'A' and resid 918 through 920 No H-bonds generated for 'chain 'A' and resid 918 through 920' Processing helix chain 'A' and resid 921 through 930 removed outlier: 4.337A pdb=" N SER A 925 " --> pdb=" O ASP A 921 " (cutoff:3.500A) Processing helix chain 'A' and resid 931 through 942 removed outlier: 3.934A pdb=" N THR A 935 " --> pdb=" O ASP A 931 " (cutoff:3.500A) Processing helix chain 'A' and resid 946 through 957 Processing helix chain 'A' and resid 965 through 971 Processing helix chain 'A' and resid 996 through 1008 Processing helix chain 'B' and resid 21 through 54 removed outlier: 4.148A pdb=" N PHE B 25 " --> pdb=" O MET B 21 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N SER B 28 " --> pdb=" O ALA B 24 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N SER B 29 " --> pdb=" O PHE B 25 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N THR B 51 " --> pdb=" O LYS B 47 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N VAL B 52 " --> pdb=" O TYR B 48 " (cutoff:3.500A) Processing helix chain 'B' and resid 96 through 100 Processing helix chain 'B' and resid 102 through 107 removed outlier: 4.690A pdb=" N ALA B 107 " --> pdb=" O VAL B 103 " (cutoff:3.500A) Processing helix chain 'B' and resid 113 through 134 removed outlier: 5.490A pdb=" N VAL B 119 " --> pdb=" O LEU B 115 " (cutoff:3.500A) Processing helix chain 'B' and resid 148 through 171 removed outlier: 3.830A pdb=" N ALA B 155 " --> pdb=" O GLN B 151 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N PHE B 156 " --> pdb=" O ILE B 152 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N PHE B 159 " --> pdb=" O ALA B 155 " (cutoff:3.500A) Processing helix chain 'B' and resid 173 through 179 Processing helix chain 'B' and resid 180 through 199 Proline residue: B 191 - end of helix removed outlier: 3.750A pdb=" N PHE B 194 " --> pdb=" O VAL B 190 " (cutoff:3.500A) Processing helix chain 'B' and resid 205 through 215 removed outlier: 4.390A pdb=" N PHE B 208 " --> pdb=" O GLY B 205 " (cutoff:3.500A) Processing helix chain 'B' and resid 216 through 224 removed outlier: 3.687A pdb=" N ILE B 220 " --> pdb=" O GLN B 216 " (cutoff:3.500A) Processing helix chain 'B' and resid 229 through 259 Processing helix chain 'B' and resid 261 through 265 Processing helix chain 'B' and resid 273 through 286 Processing helix chain 'B' and resid 297 through 312 Processing helix chain 'B' and resid 319 through 325 Processing helix chain 'B' and resid 326 through 331 removed outlier: 3.870A pdb=" N LYS B 331 " --> pdb=" O GLY B 327 " (cutoff:3.500A) Processing helix chain 'B' and resid 352 through 364 removed outlier: 5.210A pdb=" N ASN B 358 " --> pdb=" O GLU B 354 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N PHE B 359 " --> pdb=" O SER B 355 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ASP B 362 " --> pdb=" O ASN B 358 " (cutoff:3.500A) Processing helix chain 'B' and resid 385 through 394 removed outlier: 3.789A pdb=" N ALA B 389 " --> pdb=" O LEU B 385 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N HIS B 394 " --> pdb=" O LEU B 390 " (cutoff:3.500A) Processing helix chain 'B' and resid 407 through 414 Processing helix chain 'B' and resid 415 through 419 Processing helix chain 'B' and resid 432 through 451 Processing helix chain 'B' and resid 465 through 470 removed outlier: 3.670A pdb=" N LEU B 469 " --> pdb=" O ASN B 465 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N LEU B 470 " --> pdb=" O LYS B 466 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 465 through 470' Processing helix chain 'B' and resid 476 through 480 Processing helix chain 'B' and resid 486 through 500 removed outlier: 3.533A pdb=" N LEU B 499 " --> pdb=" O ALA B 495 " (cutoff:3.500A) Processing helix chain 'B' and resid 502 through 512 removed outlier: 3.767A pdb=" N PHE B 511 " --> pdb=" O LEU B 507 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N SER B 512 " --> pdb=" O ALA B 508 " (cutoff:3.500A) Processing helix chain 'B' and resid 523 through 533 removed outlier: 4.119A pdb=" N TYR B 527 " --> pdb=" O THR B 523 " (cutoff:3.500A) Processing helix chain 'B' and resid 542 through 546 Processing helix chain 'B' and resid 549 through 562 Processing helix chain 'B' and resid 601 through 606 removed outlier: 3.851A pdb=" N VAL B 605 " --> pdb=" O ASP B 601 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N LYS B 606 " --> pdb=" O ALA B 602 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 601 through 606' Processing helix chain 'B' and resid 607 through 609 No H-bonds generated for 'chain 'B' and resid 607 through 609' Processing helix chain 'B' and resid 699 through 703 Processing helix chain 'B' and resid 706 through 713 Processing helix chain 'B' and resid 734 through 739 Processing helix chain 'B' and resid 740 through 743 removed outlier: 3.827A pdb=" N ALA B 743 " --> pdb=" O PRO B 740 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 740 through 743' Processing helix chain 'B' and resid 759 through 768 removed outlier: 4.403A pdb=" N ARG B 765 " --> pdb=" O GLU B 761 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N GLU B 766 " --> pdb=" O TYR B 762 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N GLU B 768 " --> pdb=" O LYS B 764 " (cutoff:3.500A) Processing helix chain 'B' and resid 785 through 792 Processing helix chain 'B' and resid 793 through 797 removed outlier: 3.570A pdb=" N CYS B 797 " --> pdb=" O ILE B 794 " (cutoff:3.500A) Processing helix chain 'B' and resid 817 through 829 Processing helix chain 'B' and resid 872 through 876 removed outlier: 3.981A pdb=" N ASN B 875 " --> pdb=" O THR B 872 " (cutoff:3.500A) Processing helix chain 'B' and resid 884 through 891 Processing helix chain 'B' and resid 902 through 905 Processing helix chain 'B' and resid 906 through 911 Processing helix chain 'B' and resid 918 through 920 No H-bonds generated for 'chain 'B' and resid 918 through 920' Processing helix chain 'B' and resid 921 through 930 removed outlier: 4.337A pdb=" N SER B 925 " --> pdb=" O ASP B 921 " (cutoff:3.500A) Processing helix chain 'B' and resid 931 through 942 removed outlier: 3.933A pdb=" N THR B 935 " --> pdb=" O ASP B 931 " (cutoff:3.500A) Processing helix chain 'B' and resid 946 through 957 Processing helix chain 'B' and resid 965 through 971 Processing helix chain 'B' and resid 996 through 1008 Processing helix chain 'C' and resid 21 through 54 removed outlier: 4.147A pdb=" N PHE C 25 " --> pdb=" O MET C 21 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N SER C 28 " --> pdb=" O ALA C 24 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N SER C 29 " --> pdb=" O PHE C 25 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N THR C 51 " --> pdb=" O LYS C 47 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N VAL C 52 " --> pdb=" O TYR C 48 " (cutoff:3.500A) Processing helix chain 'C' and resid 96 through 100 Processing helix chain 'C' and resid 102 through 107 removed outlier: 4.690A pdb=" N ALA C 107 " --> pdb=" O VAL C 103 " (cutoff:3.500A) Processing helix chain 'C' and resid 113 through 134 removed outlier: 5.489A pdb=" N VAL C 119 " --> pdb=" O LEU C 115 " (cutoff:3.500A) Processing helix chain 'C' and resid 148 through 171 removed outlier: 3.830A pdb=" N ALA C 155 " --> pdb=" O GLN C 151 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N PHE C 156 " --> pdb=" O ILE C 152 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N PHE C 159 " --> pdb=" O ALA C 155 " (cutoff:3.500A) Processing helix chain 'C' and resid 173 through 179 Processing helix chain 'C' and resid 180 through 199 Proline residue: C 191 - end of helix removed outlier: 3.750A pdb=" N PHE C 194 " --> pdb=" O VAL C 190 " (cutoff:3.500A) Processing helix chain 'C' and resid 205 through 215 removed outlier: 4.390A pdb=" N PHE C 208 " --> pdb=" O GLY C 205 " (cutoff:3.500A) Processing helix chain 'C' and resid 216 through 224 removed outlier: 3.686A pdb=" N ILE C 220 " --> pdb=" O GLN C 216 " (cutoff:3.500A) Processing helix chain 'C' and resid 229 through 259 Processing helix chain 'C' and resid 261 through 265 Processing helix chain 'C' and resid 273 through 286 Processing helix chain 'C' and resid 297 through 312 Processing helix chain 'C' and resid 319 through 325 Processing helix chain 'C' and resid 326 through 331 removed outlier: 3.870A pdb=" N LYS C 331 " --> pdb=" O GLY C 327 " (cutoff:3.500A) Processing helix chain 'C' and resid 352 through 364 removed outlier: 5.210A pdb=" N ASN C 358 " --> pdb=" O GLU C 354 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N PHE C 359 " --> pdb=" O SER C 355 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ASP C 362 " --> pdb=" O ASN C 358 " (cutoff:3.500A) Processing helix chain 'C' and resid 385 through 394 removed outlier: 3.788A pdb=" N ALA C 389 " --> pdb=" O LEU C 385 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N HIS C 394 " --> pdb=" O LEU C 390 " (cutoff:3.500A) Processing helix chain 'C' and resid 407 through 414 Processing helix chain 'C' and resid 415 through 419 Processing helix chain 'C' and resid 432 through 451 Processing helix chain 'C' and resid 465 through 470 removed outlier: 3.669A pdb=" N LEU C 469 " --> pdb=" O ASN C 465 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N LEU C 470 " --> pdb=" O LYS C 466 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 465 through 470' Processing helix chain 'C' and resid 476 through 480 Processing helix chain 'C' and resid 486 through 500 removed outlier: 3.532A pdb=" N LEU C 499 " --> pdb=" O ALA C 495 " (cutoff:3.500A) Processing helix chain 'C' and resid 502 through 512 removed outlier: 3.767A pdb=" N PHE C 511 " --> pdb=" O LEU C 507 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N SER C 512 " --> pdb=" O ALA C 508 " (cutoff:3.500A) Processing helix chain 'C' and resid 523 through 533 removed outlier: 4.119A pdb=" N TYR C 527 " --> pdb=" O THR C 523 " (cutoff:3.500A) Processing helix chain 'C' and resid 542 through 546 Processing helix chain 'C' and resid 549 through 562 Processing helix chain 'C' and resid 601 through 606 removed outlier: 3.851A pdb=" N VAL C 605 " --> pdb=" O ASP C 601 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N LYS C 606 " --> pdb=" O ALA C 602 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 601 through 606' Processing helix chain 'C' and resid 607 through 609 No H-bonds generated for 'chain 'C' and resid 607 through 609' Processing helix chain 'C' and resid 699 through 703 Processing helix chain 'C' and resid 706 through 713 Processing helix chain 'C' and resid 734 through 739 Processing helix chain 'C' and resid 740 through 743 removed outlier: 3.827A pdb=" N ALA C 743 " --> pdb=" O PRO C 740 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 740 through 743' Processing helix chain 'C' and resid 759 through 768 removed outlier: 4.403A pdb=" N ARG C 765 " --> pdb=" O GLU C 761 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N GLU C 766 " --> pdb=" O TYR C 762 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N GLU C 768 " --> pdb=" O LYS C 764 " (cutoff:3.500A) Processing helix chain 'C' and resid 785 through 792 Processing helix chain 'C' and resid 793 through 797 removed outlier: 3.569A pdb=" N CYS C 797 " --> pdb=" O ILE C 794 " (cutoff:3.500A) Processing helix chain 'C' and resid 817 through 829 Processing helix chain 'C' and resid 872 through 876 removed outlier: 3.981A pdb=" N ASN C 875 " --> pdb=" O THR C 872 " (cutoff:3.500A) Processing helix chain 'C' and resid 884 through 891 Processing helix chain 'C' and resid 902 through 905 Processing helix chain 'C' and resid 906 through 911 Processing helix chain 'C' and resid 918 through 920 No H-bonds generated for 'chain 'C' and resid 918 through 920' Processing helix chain 'C' and resid 921 through 930 removed outlier: 4.337A pdb=" N SER C 925 " --> pdb=" O ASP C 921 " (cutoff:3.500A) Processing helix chain 'C' and resid 931 through 942 removed outlier: 3.934A pdb=" N THR C 935 " --> pdb=" O ASP C 931 " (cutoff:3.500A) Processing helix chain 'C' and resid 946 through 957 Processing helix chain 'C' and resid 965 through 971 Processing helix chain 'C' and resid 996 through 1008 Processing helix chain 'D' and resid 21 through 54 removed outlier: 4.147A pdb=" N PHE D 25 " --> pdb=" O MET D 21 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N SER D 28 " --> pdb=" O ALA D 24 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N SER D 29 " --> pdb=" O PHE D 25 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N THR D 51 " --> pdb=" O LYS D 47 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N VAL D 52 " --> pdb=" O TYR D 48 " (cutoff:3.500A) Processing helix chain 'D' and resid 96 through 100 Processing helix chain 'D' and resid 102 through 107 removed outlier: 4.690A pdb=" N ALA D 107 " --> pdb=" O VAL D 103 " (cutoff:3.500A) Processing helix chain 'D' and resid 113 through 134 removed outlier: 5.489A pdb=" N VAL D 119 " --> pdb=" O LEU D 115 " (cutoff:3.500A) Processing helix chain 'D' and resid 148 through 171 removed outlier: 3.829A pdb=" N ALA D 155 " --> pdb=" O GLN D 151 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N PHE D 156 " --> pdb=" O ILE D 152 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N PHE D 159 " --> pdb=" O ALA D 155 " (cutoff:3.500A) Processing helix chain 'D' and resid 173 through 179 Processing helix chain 'D' and resid 180 through 199 Proline residue: D 191 - end of helix removed outlier: 3.750A pdb=" N PHE D 194 " --> pdb=" O VAL D 190 " (cutoff:3.500A) Processing helix chain 'D' and resid 205 through 215 removed outlier: 4.390A pdb=" N PHE D 208 " --> pdb=" O GLY D 205 " (cutoff:3.500A) Processing helix chain 'D' and resid 216 through 224 removed outlier: 3.686A pdb=" N ILE D 220 " --> pdb=" O GLN D 216 " (cutoff:3.500A) Processing helix chain 'D' and resid 229 through 259 Processing helix chain 'D' and resid 261 through 265 Processing helix chain 'D' and resid 273 through 286 Processing helix chain 'D' and resid 297 through 312 Processing helix chain 'D' and resid 319 through 325 Processing helix chain 'D' and resid 326 through 331 removed outlier: 3.870A pdb=" N LYS D 331 " --> pdb=" O GLY D 327 " (cutoff:3.500A) Processing helix chain 'D' and resid 352 through 364 removed outlier: 5.210A pdb=" N ASN D 358 " --> pdb=" O GLU D 354 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N PHE D 359 " --> pdb=" O SER D 355 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ASP D 362 " --> pdb=" O ASN D 358 " (cutoff:3.500A) Processing helix chain 'D' and resid 385 through 394 removed outlier: 3.789A pdb=" N ALA D 389 " --> pdb=" O LEU D 385 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N HIS D 394 " --> pdb=" O LEU D 390 " (cutoff:3.500A) Processing helix chain 'D' and resid 407 through 414 Processing helix chain 'D' and resid 415 through 419 Processing helix chain 'D' and resid 432 through 451 Processing helix chain 'D' and resid 465 through 470 removed outlier: 3.670A pdb=" N LEU D 469 " --> pdb=" O ASN D 465 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LEU D 470 " --> pdb=" O LYS D 466 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 465 through 470' Processing helix chain 'D' and resid 476 through 480 Processing helix chain 'D' and resid 486 through 500 removed outlier: 3.532A pdb=" N LEU D 499 " --> pdb=" O ALA D 495 " (cutoff:3.500A) Processing helix chain 'D' and resid 502 through 512 removed outlier: 3.767A pdb=" N PHE D 511 " --> pdb=" O LEU D 507 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N SER D 512 " --> pdb=" O ALA D 508 " (cutoff:3.500A) Processing helix chain 'D' and resid 523 through 533 removed outlier: 4.118A pdb=" N TYR D 527 " --> pdb=" O THR D 523 " (cutoff:3.500A) Processing helix chain 'D' and resid 542 through 546 Processing helix chain 'D' and resid 549 through 562 Processing helix chain 'D' and resid 601 through 606 removed outlier: 3.851A pdb=" N VAL D 605 " --> pdb=" O ASP D 601 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N LYS D 606 " --> pdb=" O ALA D 602 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 601 through 606' Processing helix chain 'D' and resid 607 through 609 No H-bonds generated for 'chain 'D' and resid 607 through 609' Processing helix chain 'D' and resid 699 through 703 Processing helix chain 'D' and resid 706 through 713 Processing helix chain 'D' and resid 734 through 739 Processing helix chain 'D' and resid 740 through 743 removed outlier: 3.827A pdb=" N ALA D 743 " --> pdb=" O PRO D 740 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 740 through 743' Processing helix chain 'D' and resid 759 through 768 removed outlier: 4.404A pdb=" N ARG D 765 " --> pdb=" O GLU D 761 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N GLU D 766 " --> pdb=" O TYR D 762 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N GLU D 768 " --> pdb=" O LYS D 764 " (cutoff:3.500A) Processing helix chain 'D' and resid 785 through 792 Processing helix chain 'D' and resid 793 through 797 removed outlier: 3.570A pdb=" N CYS D 797 " --> pdb=" O ILE D 794 " (cutoff:3.500A) Processing helix chain 'D' and resid 817 through 829 Processing helix chain 'D' and resid 872 through 876 removed outlier: 3.981A pdb=" N ASN D 875 " --> pdb=" O THR D 872 " (cutoff:3.500A) Processing helix chain 'D' and resid 884 through 891 Processing helix chain 'D' and resid 902 through 905 Processing helix chain 'D' and resid 906 through 911 Processing helix chain 'D' and resid 918 through 920 No H-bonds generated for 'chain 'D' and resid 918 through 920' Processing helix chain 'D' and resid 921 through 930 removed outlier: 4.336A pdb=" N SER D 925 " --> pdb=" O ASP D 921 " (cutoff:3.500A) Processing helix chain 'D' and resid 931 through 942 removed outlier: 3.933A pdb=" N THR D 935 " --> pdb=" O ASP D 931 " (cutoff:3.500A) Processing helix chain 'D' and resid 946 through 957 Processing helix chain 'D' and resid 965 through 971 Processing helix chain 'D' and resid 996 through 1008 Processing helix chain 'E' and resid 40 through 79 removed outlier: 3.752A pdb=" N ASP E 45 " --> pdb=" O LYS E 41 " (cutoff:3.500A) removed outlier: 5.525A pdb=" N LYS E 46 " --> pdb=" O ALA E 42 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N SER E 47 " --> pdb=" O GLY E 43 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N SER E 71 " --> pdb=" O PHE E 67 " (cutoff:3.500A) Proline residue: E 72 - end of helix removed outlier: 3.520A pdb=" N ALA E 79 " --> pdb=" O GLN E 75 " (cutoff:3.500A) Processing helix chain 'E' and resid 133 through 140 Processing helix chain 'E' and resid 152 through 170 removed outlier: 3.509A pdb=" N ASN E 156 " --> pdb=" O GLU E 152 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N TYR E 166 " --> pdb=" O ASN E 162 " (cutoff:3.500A) Processing helix chain 'E' and resid 196 through 233 removed outlier: 3.931A pdb=" N LEU E 200 " --> pdb=" O ASP E 196 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N TRP E 206 " --> pdb=" O HIS E 202 " (cutoff:3.500A) Proline residue: E 207 - end of helix removed outlier: 4.524A pdb=" N ALA E 228 " --> pdb=" O ALA E 224 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N VAL E 229 " --> pdb=" O LYS E 225 " (cutoff:3.500A) Processing helix chain 'F' and resid 40 through 79 removed outlier: 3.752A pdb=" N ASP F 45 " --> pdb=" O LYS F 41 " (cutoff:3.500A) removed outlier: 5.525A pdb=" N LYS F 46 " --> pdb=" O ALA F 42 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N SER F 47 " --> pdb=" O GLY F 43 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N SER F 71 " --> pdb=" O PHE F 67 " (cutoff:3.500A) Proline residue: F 72 - end of helix removed outlier: 3.520A pdb=" N ALA F 79 " --> pdb=" O GLN F 75 " (cutoff:3.500A) Processing helix chain 'F' and resid 133 through 140 Processing helix chain 'F' and resid 152 through 170 removed outlier: 3.508A pdb=" N ASN F 156 " --> pdb=" O GLU F 152 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N TYR F 166 " --> pdb=" O ASN F 162 " (cutoff:3.500A) Processing helix chain 'F' and resid 196 through 233 removed outlier: 3.931A pdb=" N LEU F 200 " --> pdb=" O ASP F 196 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N TRP F 206 " --> pdb=" O HIS F 202 " (cutoff:3.500A) Proline residue: F 207 - end of helix removed outlier: 4.524A pdb=" N ALA F 228 " --> pdb=" O ALA F 224 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N VAL F 229 " --> pdb=" O LYS F 225 " (cutoff:3.500A) Processing helix chain 'G' and resid 40 through 79 removed outlier: 3.752A pdb=" N ASP G 45 " --> pdb=" O LYS G 41 " (cutoff:3.500A) removed outlier: 5.524A pdb=" N LYS G 46 " --> pdb=" O ALA G 42 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N SER G 47 " --> pdb=" O GLY G 43 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N SER G 71 " --> pdb=" O PHE G 67 " (cutoff:3.500A) Proline residue: G 72 - end of helix removed outlier: 3.520A pdb=" N ALA G 79 " --> pdb=" O GLN G 75 " (cutoff:3.500A) Processing helix chain 'G' and resid 133 through 140 Processing helix chain 'G' and resid 152 through 170 removed outlier: 3.509A pdb=" N ASN G 156 " --> pdb=" O GLU G 152 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N TYR G 166 " --> pdb=" O ASN G 162 " (cutoff:3.500A) Processing helix chain 'G' and resid 196 through 233 removed outlier: 3.931A pdb=" N LEU G 200 " --> pdb=" O ASP G 196 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N TRP G 206 " --> pdb=" O HIS G 202 " (cutoff:3.500A) Proline residue: G 207 - end of helix removed outlier: 4.525A pdb=" N ALA G 228 " --> pdb=" O ALA G 224 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N VAL G 229 " --> pdb=" O LYS G 225 " (cutoff:3.500A) Processing helix chain 'H' and resid 40 through 79 removed outlier: 3.751A pdb=" N ASP H 45 " --> pdb=" O LYS H 41 " (cutoff:3.500A) removed outlier: 5.525A pdb=" N LYS H 46 " --> pdb=" O ALA H 42 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N SER H 47 " --> pdb=" O GLY H 43 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N SER H 71 " --> pdb=" O PHE H 67 " (cutoff:3.500A) Proline residue: H 72 - end of helix removed outlier: 3.520A pdb=" N ALA H 79 " --> pdb=" O GLN H 75 " (cutoff:3.500A) Processing helix chain 'H' and resid 133 through 140 Processing helix chain 'H' and resid 152 through 170 removed outlier: 3.508A pdb=" N ASN H 156 " --> pdb=" O GLU H 152 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N TYR H 166 " --> pdb=" O ASN H 162 " (cutoff:3.500A) Processing helix chain 'H' and resid 196 through 233 removed outlier: 3.931A pdb=" N LEU H 200 " --> pdb=" O ASP H 196 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N TRP H 206 " --> pdb=" O HIS H 202 " (cutoff:3.500A) Proline residue: H 207 - end of helix removed outlier: 4.524A pdb=" N ALA H 228 " --> pdb=" O ALA H 224 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N VAL H 229 " --> pdb=" O LYS H 225 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 398 through 402 removed outlier: 3.600A pdb=" N HIS A 379 " --> pdb=" O TYR A 401 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N GLY A 349 " --> pdb=" O LEU A 378 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N VAL A 346 " --> pdb=" O LEU A 423 " (cutoff:3.500A) removed outlier: 7.921A pdb=" N LEU A 425 " --> pdb=" O VAL A 346 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N CYS A 348 " --> pdb=" O LEU A 425 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N ILE A 456 " --> pdb=" O ASP A 482 " (cutoff:3.500A) removed outlier: 7.743A pdb=" N ILE A 484 " --> pdb=" O ILE A 456 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N THR A 458 " --> pdb=" O ILE A 484 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 535 through 540 removed outlier: 6.659A pdb=" N LEU A 594 " --> pdb=" O ILE A 568 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N ILE A 568 " --> pdb=" O LEU A 594 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N PHE A 596 " --> pdb=" O ILE A 566 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N LEU A 564 " --> pdb=" O ILE A 598 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 686 through 687 removed outlier: 4.211A pdb=" N TYR A 686 " --> pdb=" O GLY A 962 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 776 through 780 removed outlier: 6.403A pdb=" N ILE A 754 " --> pdb=" O SER A 777 " (cutoff:3.500A) removed outlier: 7.591A pdb=" N LEU A 779 " --> pdb=" O ILE A 754 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N PHE A 756 " --> pdb=" O LEU A 779 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N VAL A 720 " --> pdb=" O VAL A 801 " (cutoff:3.500A) removed outlier: 7.751A pdb=" N LEU A 803 " --> pdb=" O VAL A 720 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N CYS A 722 " --> pdb=" O LEU A 803 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N CYS A 800 " --> pdb=" O ILE A 879 " (cutoff:3.500A) removed outlier: 7.752A pdb=" N GLU A 881 " --> pdb=" O CYS A 800 " (cutoff:3.500A) removed outlier: 7.054A pdb=" N ILE A 802 " --> pdb=" O GLU A 881 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 976 through 981 removed outlier: 3.746A pdb=" N GLY A1013 " --> pdb=" O PHE A1050 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 994 through 995 removed outlier: 3.744A pdb=" N GLY A 994 " --> pdb=" O LEU A1043 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 398 through 402 removed outlier: 3.600A pdb=" N HIS B 379 " --> pdb=" O TYR B 401 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N GLY B 349 " --> pdb=" O LEU B 378 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N VAL B 346 " --> pdb=" O LEU B 423 " (cutoff:3.500A) removed outlier: 7.921A pdb=" N LEU B 425 " --> pdb=" O VAL B 346 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N CYS B 348 " --> pdb=" O LEU B 425 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N ILE B 456 " --> pdb=" O ASP B 482 " (cutoff:3.500A) removed outlier: 7.743A pdb=" N ILE B 484 " --> pdb=" O ILE B 456 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N THR B 458 " --> pdb=" O ILE B 484 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 535 through 540 removed outlier: 6.659A pdb=" N LEU B 594 " --> pdb=" O ILE B 568 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N ILE B 568 " --> pdb=" O LEU B 594 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N PHE B 596 " --> pdb=" O ILE B 566 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N LEU B 564 " --> pdb=" O ILE B 598 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 686 through 687 removed outlier: 4.212A pdb=" N TYR B 686 " --> pdb=" O GLY B 962 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 776 through 780 removed outlier: 6.404A pdb=" N ILE B 754 " --> pdb=" O SER B 777 " (cutoff:3.500A) removed outlier: 7.590A pdb=" N LEU B 779 " --> pdb=" O ILE B 754 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N PHE B 756 " --> pdb=" O LEU B 779 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N VAL B 720 " --> pdb=" O VAL B 801 " (cutoff:3.500A) removed outlier: 7.750A pdb=" N LEU B 803 " --> pdb=" O VAL B 720 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N CYS B 722 " --> pdb=" O LEU B 803 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N CYS B 800 " --> pdb=" O ILE B 879 " (cutoff:3.500A) removed outlier: 7.752A pdb=" N GLU B 881 " --> pdb=" O CYS B 800 " (cutoff:3.500A) removed outlier: 7.054A pdb=" N ILE B 802 " --> pdb=" O GLU B 881 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 976 through 981 removed outlier: 3.746A pdb=" N GLY B1013 " --> pdb=" O PHE B1050 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 994 through 995 removed outlier: 3.744A pdb=" N GLY B 994 " --> pdb=" O LEU B1043 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 398 through 402 removed outlier: 3.600A pdb=" N HIS C 379 " --> pdb=" O TYR C 401 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N GLY C 349 " --> pdb=" O LEU C 378 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N VAL C 346 " --> pdb=" O LEU C 423 " (cutoff:3.500A) removed outlier: 7.920A pdb=" N LEU C 425 " --> pdb=" O VAL C 346 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N CYS C 348 " --> pdb=" O LEU C 425 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N ILE C 456 " --> pdb=" O ASP C 482 " (cutoff:3.500A) removed outlier: 7.743A pdb=" N ILE C 484 " --> pdb=" O ILE C 456 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N THR C 458 " --> pdb=" O ILE C 484 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 535 through 540 removed outlier: 6.660A pdb=" N LEU C 594 " --> pdb=" O ILE C 568 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N ILE C 568 " --> pdb=" O LEU C 594 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N PHE C 596 " --> pdb=" O ILE C 566 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N LEU C 564 " --> pdb=" O ILE C 598 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 686 through 687 removed outlier: 4.211A pdb=" N TYR C 686 " --> pdb=" O GLY C 962 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 776 through 780 removed outlier: 6.403A pdb=" N ILE C 754 " --> pdb=" O SER C 777 " (cutoff:3.500A) removed outlier: 7.591A pdb=" N LEU C 779 " --> pdb=" O ILE C 754 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N PHE C 756 " --> pdb=" O LEU C 779 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N VAL C 720 " --> pdb=" O VAL C 801 " (cutoff:3.500A) removed outlier: 7.751A pdb=" N LEU C 803 " --> pdb=" O VAL C 720 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N CYS C 722 " --> pdb=" O LEU C 803 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N CYS C 800 " --> pdb=" O ILE C 879 " (cutoff:3.500A) removed outlier: 7.752A pdb=" N GLU C 881 " --> pdb=" O CYS C 800 " (cutoff:3.500A) removed outlier: 7.054A pdb=" N ILE C 802 " --> pdb=" O GLU C 881 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 976 through 981 removed outlier: 3.746A pdb=" N GLY C1013 " --> pdb=" O PHE C1050 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 994 through 995 removed outlier: 3.744A pdb=" N GLY C 994 " --> pdb=" O LEU C1043 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 398 through 402 removed outlier: 3.600A pdb=" N HIS D 379 " --> pdb=" O TYR D 401 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N GLY D 349 " --> pdb=" O LEU D 378 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N VAL D 346 " --> pdb=" O LEU D 423 " (cutoff:3.500A) removed outlier: 7.920A pdb=" N LEU D 425 " --> pdb=" O VAL D 346 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N CYS D 348 " --> pdb=" O LEU D 425 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N ILE D 456 " --> pdb=" O ASP D 482 " (cutoff:3.500A) removed outlier: 7.742A pdb=" N ILE D 484 " --> pdb=" O ILE D 456 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N THR D 458 " --> pdb=" O ILE D 484 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 535 through 540 removed outlier: 6.660A pdb=" N LEU D 594 " --> pdb=" O ILE D 568 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N ILE D 568 " --> pdb=" O LEU D 594 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N PHE D 596 " --> pdb=" O ILE D 566 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N LEU D 564 " --> pdb=" O ILE D 598 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 686 through 687 removed outlier: 4.211A pdb=" N TYR D 686 " --> pdb=" O GLY D 962 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 776 through 780 removed outlier: 6.403A pdb=" N ILE D 754 " --> pdb=" O SER D 777 " (cutoff:3.500A) removed outlier: 7.591A pdb=" N LEU D 779 " --> pdb=" O ILE D 754 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N PHE D 756 " --> pdb=" O LEU D 779 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N VAL D 720 " --> pdb=" O VAL D 801 " (cutoff:3.500A) removed outlier: 7.750A pdb=" N LEU D 803 " --> pdb=" O VAL D 720 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N CYS D 722 " --> pdb=" O LEU D 803 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N CYS D 800 " --> pdb=" O ILE D 879 " (cutoff:3.500A) removed outlier: 7.752A pdb=" N GLU D 881 " --> pdb=" O CYS D 800 " (cutoff:3.500A) removed outlier: 7.054A pdb=" N ILE D 802 " --> pdb=" O GLU D 881 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 976 through 981 removed outlier: 3.746A pdb=" N GLY D1013 " --> pdb=" O PHE D1050 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 994 through 995 removed outlier: 3.743A pdb=" N GLY D 994 " --> pdb=" O LEU D1043 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 80 through 100 removed outlier: 3.590A pdb=" N THR E 85 " --> pdb=" O ASN E 120 " (cutoff:3.500A) removed outlier: 7.024A pdb=" N TYR E 118 " --> pdb=" O LEU E 87 " (cutoff:3.500A) removed outlier: 4.752A pdb=" N VAL E 89 " --> pdb=" O GLN E 116 " (cutoff:3.500A) removed outlier: 6.995A pdb=" N GLN E 116 " --> pdb=" O VAL E 89 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N GLN E 91 " --> pdb=" O CYS E 114 " (cutoff:3.500A) removed outlier: 7.208A pdb=" N CYS E 114 " --> pdb=" O GLN E 91 " (cutoff:3.500A) removed outlier: 8.429A pdb=" N GLY E 93 " --> pdb=" O TYR E 112 " (cutoff:3.500A) removed outlier: 9.170A pdb=" N TYR E 112 " --> pdb=" O GLY E 93 " (cutoff:3.500A) removed outlier: 9.781A pdb=" N VAL E 95 " --> pdb=" O SER E 110 " (cutoff:3.500A) removed outlier: 10.453A pdb=" N SER E 110 " --> pdb=" O VAL E 95 " (cutoff:3.500A) removed outlier: 9.958A pdb=" N GLU E 97 " --> pdb=" O GLY E 108 " (cutoff:3.500A) removed outlier: 11.247A pdb=" N GLY E 108 " --> pdb=" O GLU E 97 " (cutoff:3.500A) removed outlier: 4.855A pdb=" N VAL E 117 " --> pdb=" O LEU E 130 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N ASN E 181 " --> pdb=" O ARG E 185 " (cutoff:3.500A) removed outlier: 9.071A pdb=" N ASP E 187 " --> pdb=" O TYR E 179 " (cutoff:3.500A) removed outlier: 11.194A pdb=" N TYR E 179 " --> pdb=" O ASP E 187 " (cutoff:3.500A) removed outlier: 9.942A pdb=" N VAL E 189 " --> pdb=" O THR E 177 " (cutoff:3.500A) removed outlier: 11.316A pdb=" N THR E 177 " --> pdb=" O VAL E 189 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'F' and resid 80 through 100 removed outlier: 3.590A pdb=" N THR F 85 " --> pdb=" O ASN F 120 " (cutoff:3.500A) removed outlier: 7.023A pdb=" N TYR F 118 " --> pdb=" O LEU F 87 " (cutoff:3.500A) removed outlier: 4.753A pdb=" N VAL F 89 " --> pdb=" O GLN F 116 " (cutoff:3.500A) removed outlier: 6.995A pdb=" N GLN F 116 " --> pdb=" O VAL F 89 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N GLN F 91 " --> pdb=" O CYS F 114 " (cutoff:3.500A) removed outlier: 7.208A pdb=" N CYS F 114 " --> pdb=" O GLN F 91 " (cutoff:3.500A) removed outlier: 8.429A pdb=" N GLY F 93 " --> pdb=" O TYR F 112 " (cutoff:3.500A) removed outlier: 9.169A pdb=" N TYR F 112 " --> pdb=" O GLY F 93 " (cutoff:3.500A) removed outlier: 9.781A pdb=" N VAL F 95 " --> pdb=" O SER F 110 " (cutoff:3.500A) removed outlier: 10.453A pdb=" N SER F 110 " --> pdb=" O VAL F 95 " (cutoff:3.500A) removed outlier: 9.957A pdb=" N GLU F 97 " --> pdb=" O GLY F 108 " (cutoff:3.500A) removed outlier: 11.247A pdb=" N GLY F 108 " --> pdb=" O GLU F 97 " (cutoff:3.500A) removed outlier: 4.854A pdb=" N VAL F 117 " --> pdb=" O LEU F 130 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N ASN F 181 " --> pdb=" O ARG F 185 " (cutoff:3.500A) removed outlier: 9.071A pdb=" N ASP F 187 " --> pdb=" O TYR F 179 " (cutoff:3.500A) removed outlier: 11.194A pdb=" N TYR F 179 " --> pdb=" O ASP F 187 " (cutoff:3.500A) removed outlier: 9.942A pdb=" N VAL F 189 " --> pdb=" O THR F 177 " (cutoff:3.500A) removed outlier: 11.317A pdb=" N THR F 177 " --> pdb=" O VAL F 189 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'G' and resid 80 through 100 removed outlier: 3.590A pdb=" N THR G 85 " --> pdb=" O ASN G 120 " (cutoff:3.500A) removed outlier: 7.023A pdb=" N TYR G 118 " --> pdb=" O LEU G 87 " (cutoff:3.500A) removed outlier: 4.753A pdb=" N VAL G 89 " --> pdb=" O GLN G 116 " (cutoff:3.500A) removed outlier: 6.995A pdb=" N GLN G 116 " --> pdb=" O VAL G 89 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N GLN G 91 " --> pdb=" O CYS G 114 " (cutoff:3.500A) removed outlier: 7.208A pdb=" N CYS G 114 " --> pdb=" O GLN G 91 " (cutoff:3.500A) removed outlier: 8.429A pdb=" N GLY G 93 " --> pdb=" O TYR G 112 " (cutoff:3.500A) removed outlier: 9.170A pdb=" N TYR G 112 " --> pdb=" O GLY G 93 " (cutoff:3.500A) removed outlier: 9.781A pdb=" N VAL G 95 " --> pdb=" O SER G 110 " (cutoff:3.500A) removed outlier: 10.453A pdb=" N SER G 110 " --> pdb=" O VAL G 95 " (cutoff:3.500A) removed outlier: 9.957A pdb=" N GLU G 97 " --> pdb=" O GLY G 108 " (cutoff:3.500A) removed outlier: 11.248A pdb=" N GLY G 108 " --> pdb=" O GLU G 97 " (cutoff:3.500A) removed outlier: 4.855A pdb=" N VAL G 117 " --> pdb=" O LEU G 130 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N ASN G 181 " --> pdb=" O ARG G 185 " (cutoff:3.500A) removed outlier: 9.072A pdb=" N ASP G 187 " --> pdb=" O TYR G 179 " (cutoff:3.500A) removed outlier: 11.194A pdb=" N TYR G 179 " --> pdb=" O ASP G 187 " (cutoff:3.500A) removed outlier: 9.942A pdb=" N VAL G 189 " --> pdb=" O THR G 177 " (cutoff:3.500A) removed outlier: 11.316A pdb=" N THR G 177 " --> pdb=" O VAL G 189 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'H' and resid 80 through 100 removed outlier: 3.590A pdb=" N THR H 85 " --> pdb=" O ASN H 120 " (cutoff:3.500A) removed outlier: 7.024A pdb=" N TYR H 118 " --> pdb=" O LEU H 87 " (cutoff:3.500A) removed outlier: 4.752A pdb=" N VAL H 89 " --> pdb=" O GLN H 116 " (cutoff:3.500A) removed outlier: 6.995A pdb=" N GLN H 116 " --> pdb=" O VAL H 89 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N GLN H 91 " --> pdb=" O CYS H 114 " (cutoff:3.500A) removed outlier: 7.209A pdb=" N CYS H 114 " --> pdb=" O GLN H 91 " (cutoff:3.500A) removed outlier: 8.428A pdb=" N GLY H 93 " --> pdb=" O TYR H 112 " (cutoff:3.500A) removed outlier: 9.170A pdb=" N TYR H 112 " --> pdb=" O GLY H 93 " (cutoff:3.500A) removed outlier: 9.782A pdb=" N VAL H 95 " --> pdb=" O SER H 110 " (cutoff:3.500A) removed outlier: 10.453A pdb=" N SER H 110 " --> pdb=" O VAL H 95 " (cutoff:3.500A) removed outlier: 9.958A pdb=" N GLU H 97 " --> pdb=" O GLY H 108 " (cutoff:3.500A) removed outlier: 11.247A pdb=" N GLY H 108 " --> pdb=" O GLU H 97 " (cutoff:3.500A) removed outlier: 4.854A pdb=" N VAL H 117 " --> pdb=" O LEU H 130 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N ASN H 181 " --> pdb=" O ARG H 185 " (cutoff:3.500A) removed outlier: 9.071A pdb=" N ASP H 187 " --> pdb=" O TYR H 179 " (cutoff:3.500A) removed outlier: 11.194A pdb=" N TYR H 179 " --> pdb=" O ASP H 187 " (cutoff:3.500A) removed outlier: 9.943A pdb=" N VAL H 189 " --> pdb=" O THR H 177 " (cutoff:3.500A) removed outlier: 11.316A pdb=" N THR H 177 " --> pdb=" O VAL H 189 " (cutoff:3.500A) 1616 hydrogen bonds defined for protein. 4428 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: 7.65 Time building geometry restraints manager: 3.84 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.31: 5619 1.31 - 1.44: 9776 1.44 - 1.57: 20039 1.57 - 1.70: 18 1.70 - 1.84: 344 Bond restraints: 35796 Sorted by residual: bond pdb=" CG1 ILE F 48 " pdb=" CD1 ILE F 48 " ideal model delta sigma weight residual 1.513 1.348 0.165 3.90e-02 6.57e+02 1.79e+01 bond pdb=" CG1 ILE G 48 " pdb=" CD1 ILE G 48 " ideal model delta sigma weight residual 1.513 1.348 0.165 3.90e-02 6.57e+02 1.79e+01 bond pdb=" CG1 ILE E 48 " pdb=" CD1 ILE E 48 " ideal model delta sigma weight residual 1.513 1.349 0.164 3.90e-02 6.57e+02 1.78e+01 bond pdb=" CG1 ILE H 48 " pdb=" CD1 ILE H 48 " ideal model delta sigma weight residual 1.513 1.349 0.164 3.90e-02 6.57e+02 1.77e+01 bond pdb=" CG1 ILE C1014 " pdb=" CD1 ILE C1014 " ideal model delta sigma weight residual 1.513 1.361 0.152 3.90e-02 6.57e+02 1.51e+01 ... (remaining 35791 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.96: 48045 3.96 - 7.92: 452 7.92 - 11.88: 28 11.88 - 15.84: 7 15.84 - 19.80: 5 Bond angle restraints: 48537 Sorted by residual: angle pdb=" N VAL B 376 " pdb=" CA VAL B 376 " pdb=" C VAL B 376 " ideal model delta sigma weight residual 107.28 122.52 -15.24 1.59e+00 3.96e-01 9.19e+01 angle pdb=" N VAL A 376 " pdb=" CA VAL A 376 " pdb=" C VAL A 376 " ideal model delta sigma weight residual 107.28 122.51 -15.23 1.59e+00 3.96e-01 9.18e+01 angle pdb=" N VAL C 376 " pdb=" CA VAL C 376 " pdb=" C VAL C 376 " ideal model delta sigma weight residual 107.28 122.50 -15.22 1.59e+00 3.96e-01 9.17e+01 angle pdb=" N VAL D 376 " pdb=" CA VAL D 376 " pdb=" C VAL D 376 " ideal model delta sigma weight residual 107.28 122.48 -15.20 1.59e+00 3.96e-01 9.14e+01 angle pdb=" C3 POV A1108 " pdb=" O31 POV A1108 " pdb=" C31 POV A1108 " ideal model delta sigma weight residual 118.73 138.53 -19.80 3.00e+00 1.11e-01 4.36e+01 ... (remaining 48532 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.68: 20611 34.68 - 69.37: 525 69.37 - 104.05: 50 104.05 - 138.74: 1 138.74 - 173.42: 1 Dihedral angle restraints: 21188 sinusoidal: 8448 harmonic: 12740 Sorted by residual: dihedral pdb=" CA ASP B 147 " pdb=" C ASP B 147 " pdb=" N PHE B 148 " pdb=" CA PHE B 148 " ideal model delta harmonic sigma weight residual 180.00 150.54 29.46 0 5.00e+00 4.00e-02 3.47e+01 dihedral pdb=" CA ASP C 147 " pdb=" C ASP C 147 " pdb=" N PHE C 148 " pdb=" CA PHE C 148 " ideal model delta harmonic sigma weight residual 180.00 150.56 29.44 0 5.00e+00 4.00e-02 3.47e+01 dihedral pdb=" CA ASP A 147 " pdb=" C ASP A 147 " pdb=" N PHE A 148 " pdb=" CA PHE A 148 " ideal model delta harmonic sigma weight residual 180.00 150.58 29.42 0 5.00e+00 4.00e-02 3.46e+01 ... (remaining 21185 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.067: 4523 0.067 - 0.133: 861 0.133 - 0.200: 136 0.200 - 0.267: 8 0.267 - 0.333: 8 Chirality restraints: 5536 Sorted by residual: chirality pdb=" CA LEU D 385 " pdb=" N LEU D 385 " pdb=" C LEU D 385 " pdb=" CB LEU D 385 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.33 2.00e-01 2.50e+01 2.78e+00 chirality pdb=" CA LEU C 385 " pdb=" N LEU C 385 " pdb=" C LEU C 385 " pdb=" CB LEU C 385 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.33 2.00e-01 2.50e+01 2.77e+00 chirality pdb=" CA LEU A 385 " pdb=" N LEU A 385 " pdb=" C LEU A 385 " pdb=" CB LEU A 385 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.33 2.00e-01 2.50e+01 2.76e+00 ... (remaining 5533 not shown) Planarity restraints: 6066 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C31 POV D1105 " -0.057 2.00e-02 2.50e+03 3.27e-02 1.07e+01 pdb=" C32 POV D1105 " 0.017 2.00e-02 2.50e+03 pdb=" O31 POV D1105 " 0.018 2.00e-02 2.50e+03 pdb=" O32 POV D1105 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA CYS F 106 " -0.015 2.00e-02 2.50e+03 3.15e-02 9.95e+00 pdb=" C CYS F 106 " 0.055 2.00e-02 2.50e+03 pdb=" O CYS F 106 " -0.021 2.00e-02 2.50e+03 pdb=" N ARG F 107 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA CYS G 106 " -0.015 2.00e-02 2.50e+03 3.15e-02 9.91e+00 pdb=" C CYS G 106 " 0.054 2.00e-02 2.50e+03 pdb=" O CYS G 106 " -0.021 2.00e-02 2.50e+03 pdb=" N ARG G 107 " -0.018 2.00e-02 2.50e+03 ... (remaining 6063 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.65: 315 2.65 - 3.27: 38705 3.27 - 3.90: 67109 3.90 - 4.52: 91340 4.52 - 5.14: 146544 Nonbonded interactions: 344013 Sorted by model distance: nonbonded pdb=" SG CYS E 114 " pdb=" SG CYS E 143 " model vdw 2.029 3.760 nonbonded pdb=" SG CYS G 114 " pdb=" SG CYS G 143 " model vdw 2.029 3.760 nonbonded pdb=" SG CYS F 114 " pdb=" SG CYS F 143 " model vdw 2.030 3.760 nonbonded pdb=" SG CYS H 114 " pdb=" SG CYS H 143 " model vdw 2.030 3.760 nonbonded pdb=" SG CYS E 98 " pdb=" SG CYS E 149 " model vdw 2.031 3.760 ... (remaining 344008 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 19 through 1056 or resid 1102)) selection = (chain 'B' and (resid 19 through 1056 or resid 1102)) selection = (chain 'C' and (resid 19 through 1056 or resid 1102)) selection = (chain 'D' and (resid 19 through 1056 or resid 1102)) } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.630 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.530 Check model and map are aligned: 0.090 Set scattering table: 0.090 Process input model: 34.030 Find NCS groups from input model: 0.940 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.690 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8382 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.165 35798 Z= 0.301 Angle : 1.010 19.804 48537 Z= 0.543 Chirality : 0.055 0.333 5536 Planarity : 0.007 0.087 6066 Dihedral : 15.412 173.424 12924 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.19 % Allowed : 4.81 % Favored : 95.00 % Rotamer: Outliers : 0.62 % Allowed : 10.29 % Favored : 89.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.93 (0.12), residues: 4304 helix: -0.83 (0.11), residues: 1920 sheet: 0.75 (0.23), residues: 468 loop : -0.56 (0.15), residues: 1916 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG F 127 TYR 0.025 0.003 TYR B 762 PHE 0.033 0.003 PHE D 38 TRP 0.020 0.002 TRP A 50 HIS 0.013 0.002 HIS F 202 Details of bonding type rmsd covalent geometry : bond 0.00626 (35796) covalent geometry : angle 1.00982 (48537) hydrogen bonds : bond 0.13500 ( 1616) hydrogen bonds : angle 7.28073 ( 4428) Misc. bond : bond 0.00499 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8608 Ramachandran restraints generated. 4304 Oldfield, 0 Emsley, 4304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8608 Ramachandran restraints generated. 4304 Oldfield, 0 Emsley, 4304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 3848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 272 time to evaluate : 1.400 Fit side-chains revert: symmetry clash REVERT: A 94 MET cc_start: 0.7504 (mtm) cc_final: 0.6921 (mpt) REVERT: A 154 MET cc_start: 0.8473 (tpp) cc_final: 0.8188 (tpt) REVERT: A 314 MET cc_start: 0.7301 (ttt) cc_final: 0.6415 (tmt) REVERT: A 1053 MET cc_start: 0.8727 (ptp) cc_final: 0.8442 (mtm) REVERT: B 94 MET cc_start: 0.7491 (mtm) cc_final: 0.6971 (mpt) REVERT: B 154 MET cc_start: 0.8502 (tpp) cc_final: 0.8230 (tpt) REVERT: B 314 MET cc_start: 0.7284 (ttt) cc_final: 0.6434 (tmt) REVERT: B 1053 MET cc_start: 0.8718 (ptp) cc_final: 0.8456 (mtm) REVERT: C 94 MET cc_start: 0.7478 (mtm) cc_final: 0.6900 (mpt) REVERT: C 154 MET cc_start: 0.8426 (tpp) cc_final: 0.8141 (tpt) REVERT: C 314 MET cc_start: 0.7244 (ttt) cc_final: 0.6356 (tmt) REVERT: C 1053 MET cc_start: 0.8720 (ptp) cc_final: 0.8414 (mtm) REVERT: D 94 MET cc_start: 0.7452 (mtm) cc_final: 0.6899 (mpt) REVERT: D 154 MET cc_start: 0.8457 (tpp) cc_final: 0.8177 (tpt) REVERT: D 314 MET cc_start: 0.7260 (ttt) cc_final: 0.6356 (tmt) REVERT: D 1053 MET cc_start: 0.8730 (ptp) cc_final: 0.8444 (mtm) REVERT: E 127 ARG cc_start: 0.6687 (mmp-170) cc_final: 0.6370 (mmp-170) REVERT: E 188 ASP cc_start: 0.7936 (m-30) cc_final: 0.7089 (m-30) REVERT: E 230 LYS cc_start: 0.6571 (tmtt) cc_final: 0.5921 (ttmt) REVERT: F 188 ASP cc_start: 0.7986 (m-30) cc_final: 0.7368 (m-30) REVERT: F 230 LYS cc_start: 0.6931 (tmtt) cc_final: 0.6384 (tppp) REVERT: G 167 TRP cc_start: 0.7967 (m100) cc_final: 0.7402 (m-90) REVERT: G 180 PHE cc_start: 0.7497 (t80) cc_final: 0.7278 (t80) REVERT: G 230 LYS cc_start: 0.7550 (tmtt) cc_final: 0.7070 (ttmp) REVERT: H 188 ASP cc_start: 0.7806 (m-30) cc_final: 0.6776 (m-30) outliers start: 24 outliers final: 2 residues processed: 284 average time/residue: 0.7832 time to fit residues: 262.2119 Evaluate side-chains 192 residues out of total 3848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 190 time to evaluate : 1.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 64 ILE Chi-restraints excluded: chain H residue 64 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 197 optimal weight: 8.9990 chunk 388 optimal weight: 20.0000 chunk 215 optimal weight: 0.2980 chunk 20 optimal weight: 0.8980 chunk 132 optimal weight: 0.9980 chunk 261 optimal weight: 5.9990 chunk 248 optimal weight: 0.8980 chunk 207 optimal weight: 2.9990 chunk 401 optimal weight: 8.9990 chunk 424 optimal weight: 20.0000 chunk 155 optimal weight: 5.9990 overall best weight: 1.2182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 582 ASN ** A 807 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 582 ASN ** B 807 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1054 GLN C 582 ASN ** C 807 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1054 GLN D 582 ASN ** D 807 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1054 GLN F 202 HIS ** G 202 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 131 HIS ** H 202 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.083754 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.059513 restraints weight = 116128.035| |-----------------------------------------------------------------------------| r_work (start): 0.3170 rms_B_bonded: 2.98 r_work: 0.3032 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3032 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8640 moved from start: 0.1496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 35798 Z= 0.142 Angle : 0.659 15.465 48537 Z= 0.344 Chirality : 0.044 0.165 5536 Planarity : 0.004 0.042 6066 Dihedral : 9.801 149.804 4920 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.49 % Favored : 96.42 % Rotamer: Outliers : 1.22 % Allowed : 10.71 % Favored : 88.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.02 (0.13), residues: 4304 helix: 0.25 (0.12), residues: 1984 sheet: 0.36 (0.23), residues: 504 loop : -0.18 (0.15), residues: 1816 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 151 TYR 0.019 0.001 TYR E 166 PHE 0.025 0.002 PHE A 610 TRP 0.022 0.001 TRP H 167 HIS 0.005 0.001 HIS A 771 Details of bonding type rmsd covalent geometry : bond 0.00307 (35796) covalent geometry : angle 0.65898 (48537) hydrogen bonds : bond 0.05030 ( 1616) hydrogen bonds : angle 5.51444 ( 4428) Misc. bond : bond 0.00195 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8608 Ramachandran restraints generated. 4304 Oldfield, 0 Emsley, 4304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8608 Ramachandran restraints generated. 4304 Oldfield, 0 Emsley, 4304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 3848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 226 time to evaluate : 1.343 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 94 MET cc_start: 0.7333 (mtm) cc_final: 0.6786 (mpt) REVERT: A 154 MET cc_start: 0.8585 (tpp) cc_final: 0.8369 (tpt) REVERT: A 314 MET cc_start: 0.7093 (ttt) cc_final: 0.6183 (tmt) REVERT: B 94 MET cc_start: 0.7342 (mtm) cc_final: 0.6809 (mpt) REVERT: B 154 MET cc_start: 0.8581 (tpp) cc_final: 0.8364 (tpt) REVERT: B 314 MET cc_start: 0.7122 (ttt) cc_final: 0.6238 (tmt) REVERT: C 94 MET cc_start: 0.7386 (mtm) cc_final: 0.6848 (mpt) REVERT: C 154 MET cc_start: 0.8512 (tpp) cc_final: 0.8264 (tpt) REVERT: C 314 MET cc_start: 0.7054 (ttt) cc_final: 0.6121 (tmt) REVERT: D 94 MET cc_start: 0.7362 (mtm) cc_final: 0.6805 (mpt) REVERT: D 154 MET cc_start: 0.8555 (tpp) cc_final: 0.8319 (tpt) REVERT: D 314 MET cc_start: 0.7055 (ttt) cc_final: 0.6131 (tmt) REVERT: E 188 ASP cc_start: 0.6999 (m-30) cc_final: 0.6720 (m-30) REVERT: E 230 LYS cc_start: 0.5806 (tmtt) cc_final: 0.5379 (tppp) REVERT: F 101 THR cc_start: 0.8947 (p) cc_final: 0.8636 (m) REVERT: F 230 LYS cc_start: 0.6342 (tmtt) cc_final: 0.5763 (tppp) REVERT: G 230 LYS cc_start: 0.7194 (tmtt) cc_final: 0.6652 (tppp) outliers start: 47 outliers final: 8 residues processed: 262 average time/residue: 0.6561 time to fit residues: 208.8751 Evaluate side-chains 198 residues out of total 3848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 190 time to evaluate : 1.117 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 198 ILE Chi-restraints excluded: chain E residue 222 ILE Chi-restraints excluded: chain F residue 198 ILE Chi-restraints excluded: chain F residue 222 ILE Chi-restraints excluded: chain G residue 222 ILE Chi-restraints excluded: chain H residue 45 ASP Chi-restraints excluded: chain H residue 105 ASP Chi-restraints excluded: chain H residue 198 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 417 optimal weight: 40.0000 chunk 202 optimal weight: 2.9990 chunk 414 optimal weight: 5.9990 chunk 86 optimal weight: 0.6980 chunk 255 optimal weight: 1.9990 chunk 126 optimal weight: 0.9990 chunk 204 optimal weight: 0.9990 chunk 328 optimal weight: 7.9990 chunk 162 optimal weight: 6.9990 chunk 192 optimal weight: 2.9990 chunk 391 optimal weight: 10.0000 overall best weight: 1.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 202 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 202 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 202 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.083876 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.059648 restraints weight = 115517.912| |-----------------------------------------------------------------------------| r_work (start): 0.3169 rms_B_bonded: 2.97 r_work: 0.3032 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3032 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8637 moved from start: 0.1908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 35798 Z= 0.131 Angle : 0.606 13.057 48537 Z= 0.312 Chirality : 0.042 0.190 5536 Planarity : 0.004 0.043 6066 Dihedral : 9.038 139.461 4916 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.28 % Allowed : 3.55 % Favored : 96.17 % Rotamer: Outliers : 1.12 % Allowed : 12.14 % Favored : 86.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.28 (0.13), residues: 4304 helix: 0.57 (0.12), residues: 1988 sheet: 0.15 (0.21), residues: 580 loop : -0.07 (0.16), residues: 1736 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 151 TYR 0.014 0.001 TYR E 166 PHE 0.016 0.001 PHE G 180 TRP 0.019 0.001 TRP H 167 HIS 0.004 0.001 HIS F 202 Details of bonding type rmsd covalent geometry : bond 0.00290 (35796) covalent geometry : angle 0.60594 (48537) hydrogen bonds : bond 0.04416 ( 1616) hydrogen bonds : angle 5.18471 ( 4428) Misc. bond : bond 0.00144 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8608 Ramachandran restraints generated. 4304 Oldfield, 0 Emsley, 4304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8608 Ramachandran restraints generated. 4304 Oldfield, 0 Emsley, 4304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 3848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 213 time to evaluate : 1.364 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 94 MET cc_start: 0.7354 (mtm) cc_final: 0.6793 (mpt) REVERT: A 124 ILE cc_start: 0.8708 (OUTLIER) cc_final: 0.8498 (mm) REVERT: A 314 MET cc_start: 0.7024 (ttt) cc_final: 0.6171 (tmt) REVERT: B 94 MET cc_start: 0.7348 (mtm) cc_final: 0.6782 (mpt) REVERT: B 124 ILE cc_start: 0.8714 (OUTLIER) cc_final: 0.8514 (mm) REVERT: B 314 MET cc_start: 0.7004 (ttt) cc_final: 0.6150 (tmt) REVERT: C 94 MET cc_start: 0.7337 (mtm) cc_final: 0.6777 (mpt) REVERT: C 124 ILE cc_start: 0.8688 (OUTLIER) cc_final: 0.8475 (mm) REVERT: C 154 MET cc_start: 0.8562 (tpp) cc_final: 0.8251 (tpp) REVERT: C 314 MET cc_start: 0.6968 (ttt) cc_final: 0.6124 (tmt) REVERT: D 94 MET cc_start: 0.7375 (mtm) cc_final: 0.6811 (mpt) REVERT: D 124 ILE cc_start: 0.8713 (OUTLIER) cc_final: 0.8501 (mm) REVERT: D 314 MET cc_start: 0.6977 (ttt) cc_final: 0.6120 (tmt) REVERT: E 230 LYS cc_start: 0.5755 (tmtt) cc_final: 0.5341 (tppp) REVERT: F 151 ARG cc_start: 0.7851 (tpt90) cc_final: 0.7240 (tpt170) REVERT: F 188 ASP cc_start: 0.7173 (m-30) cc_final: 0.6882 (m-30) REVERT: F 230 LYS cc_start: 0.6225 (tmtt) cc_final: 0.5757 (tppp) REVERT: G 230 LYS cc_start: 0.7177 (tmtt) cc_final: 0.6599 (tppp) outliers start: 43 outliers final: 12 residues processed: 248 average time/residue: 0.7060 time to fit residues: 211.0607 Evaluate side-chains 206 residues out of total 3848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 190 time to evaluate : 1.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain B residue 124 ILE Chi-restraints excluded: chain C residue 124 ILE Chi-restraints excluded: chain D residue 124 ILE Chi-restraints excluded: chain E residue 198 ILE Chi-restraints excluded: chain E residue 218 VAL Chi-restraints excluded: chain E residue 222 ILE Chi-restraints excluded: chain F residue 198 ILE Chi-restraints excluded: chain F residue 218 VAL Chi-restraints excluded: chain F residue 222 ILE Chi-restraints excluded: chain G residue 198 ILE Chi-restraints excluded: chain G residue 218 VAL Chi-restraints excluded: chain G residue 222 ILE Chi-restraints excluded: chain H residue 198 ILE Chi-restraints excluded: chain H residue 218 VAL Chi-restraints excluded: chain H residue 222 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 61 optimal weight: 3.9990 chunk 393 optimal weight: 6.9990 chunk 114 optimal weight: 9.9990 chunk 76 optimal weight: 4.9990 chunk 192 optimal weight: 3.9990 chunk 133 optimal weight: 3.9990 chunk 118 optimal weight: 0.9980 chunk 91 optimal weight: 7.9990 chunk 286 optimal weight: 5.9990 chunk 176 optimal weight: 0.0870 chunk 405 optimal weight: 30.0000 overall best weight: 2.6164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 202 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 202 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 202 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.082918 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.058445 restraints weight = 115953.275| |-----------------------------------------------------------------------------| r_work (start): 0.3140 rms_B_bonded: 2.98 r_work: 0.3004 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3004 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8667 moved from start: 0.2212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.086 35798 Z= 0.159 Angle : 0.589 11.462 48537 Z= 0.303 Chirality : 0.043 0.191 5536 Planarity : 0.004 0.040 6066 Dihedral : 8.600 134.358 4916 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.28 % Allowed : 3.97 % Favored : 95.75 % Rotamer: Outliers : 2.13 % Allowed : 12.66 % Favored : 85.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.40 (0.13), residues: 4304 helix: 0.65 (0.12), residues: 1992 sheet: 0.22 (0.23), residues: 540 loop : 0.02 (0.16), residues: 1772 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 151 TYR 0.024 0.001 TYR E 166 PHE 0.025 0.001 PHE C 159 TRP 0.017 0.001 TRP E 167 HIS 0.004 0.001 HIS F 202 Details of bonding type rmsd covalent geometry : bond 0.00367 (35796) covalent geometry : angle 0.58911 (48537) hydrogen bonds : bond 0.04213 ( 1616) hydrogen bonds : angle 5.04902 ( 4428) Misc. bond : bond 0.00151 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8608 Ramachandran restraints generated. 4304 Oldfield, 0 Emsley, 4304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8608 Ramachandran restraints generated. 4304 Oldfield, 0 Emsley, 4304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 3848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 204 time to evaluate : 1.007 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 94 MET cc_start: 0.7339 (mtm) cc_final: 0.6800 (mpt) REVERT: A 314 MET cc_start: 0.6949 (ttt) cc_final: 0.6077 (tmt) REVERT: B 94 MET cc_start: 0.7318 (mtm) cc_final: 0.6371 (mmt) REVERT: B 314 MET cc_start: 0.6968 (ttt) cc_final: 0.6125 (tmt) REVERT: C 94 MET cc_start: 0.7411 (mtm) cc_final: 0.6813 (mpt) REVERT: C 124 ILE cc_start: 0.8681 (OUTLIER) cc_final: 0.8470 (mm) REVERT: C 154 MET cc_start: 0.8560 (tpp) cc_final: 0.8250 (tpp) REVERT: C 314 MET cc_start: 0.6808 (ttt) cc_final: 0.5964 (tmt) REVERT: D 94 MET cc_start: 0.7407 (mtm) cc_final: 0.6825 (mpt) REVERT: D 124 ILE cc_start: 0.8718 (OUTLIER) cc_final: 0.8505 (mm) REVERT: D 314 MET cc_start: 0.6906 (ttt) cc_final: 0.6034 (tmt) REVERT: E 166 TYR cc_start: 0.8386 (t80) cc_final: 0.8176 (t80) REVERT: E 188 ASP cc_start: 0.7096 (OUTLIER) cc_final: 0.6857 (m-30) REVERT: E 230 LYS cc_start: 0.5716 (tmtt) cc_final: 0.5290 (tppp) REVERT: F 45 ASP cc_start: 0.7944 (m-30) cc_final: 0.7693 (m-30) REVERT: F 188 ASP cc_start: 0.7080 (m-30) cc_final: 0.6835 (m-30) REVERT: F 230 LYS cc_start: 0.6256 (tmtt) cc_final: 0.5783 (tppp) REVERT: G 127 ARG cc_start: 0.6803 (mmp-170) cc_final: 0.5639 (ttt-90) REVERT: G 188 ASP cc_start: 0.7429 (OUTLIER) cc_final: 0.7065 (m-30) REVERT: G 230 LYS cc_start: 0.7081 (tmtt) cc_final: 0.6568 (ttmt) outliers start: 82 outliers final: 32 residues processed: 272 average time/residue: 0.6365 time to fit residues: 211.9799 Evaluate side-chains 215 residues out of total 3848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 179 time to evaluate : 1.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 406 LEU Chi-restraints excluded: chain A residue 919 VAL Chi-restraints excluded: chain A residue 941 VAL Chi-restraints excluded: chain B residue 197 VAL Chi-restraints excluded: chain B residue 406 LEU Chi-restraints excluded: chain B residue 919 VAL Chi-restraints excluded: chain B residue 941 VAL Chi-restraints excluded: chain C residue 124 ILE Chi-restraints excluded: chain C residue 406 LEU Chi-restraints excluded: chain C residue 460 MET Chi-restraints excluded: chain C residue 919 VAL Chi-restraints excluded: chain C residue 941 VAL Chi-restraints excluded: chain D residue 124 ILE Chi-restraints excluded: chain D residue 197 VAL Chi-restraints excluded: chain D residue 406 LEU Chi-restraints excluded: chain D residue 460 MET Chi-restraints excluded: chain D residue 919 VAL Chi-restraints excluded: chain D residue 941 VAL Chi-restraints excluded: chain E residue 188 ASP Chi-restraints excluded: chain E residue 198 ILE Chi-restraints excluded: chain E residue 205 LEU Chi-restraints excluded: chain E residue 218 VAL Chi-restraints excluded: chain E residue 222 ILE Chi-restraints excluded: chain F residue 198 ILE Chi-restraints excluded: chain F residue 205 LEU Chi-restraints excluded: chain F residue 218 VAL Chi-restraints excluded: chain F residue 222 ILE Chi-restraints excluded: chain G residue 64 ILE Chi-restraints excluded: chain G residue 105 ASP Chi-restraints excluded: chain G residue 188 ASP Chi-restraints excluded: chain G residue 198 ILE Chi-restraints excluded: chain G residue 222 ILE Chi-restraints excluded: chain H residue 105 ASP Chi-restraints excluded: chain H residue 198 ILE Chi-restraints excluded: chain H residue 218 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 1 optimal weight: 0.7980 chunk 111 optimal weight: 1.9990 chunk 331 optimal weight: 8.9990 chunk 269 optimal weight: 0.9990 chunk 86 optimal weight: 0.7980 chunk 103 optimal weight: 9.9990 chunk 84 optimal weight: 5.9990 chunk 388 optimal weight: 9.9990 chunk 59 optimal weight: 5.9990 chunk 325 optimal weight: 10.0000 chunk 216 optimal weight: 0.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 131 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 202 HIS ** F 131 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 202 HIS H 202 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.084049 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.059236 restraints weight = 115542.252| |-----------------------------------------------------------------------------| r_work (start): 0.3157 rms_B_bonded: 3.04 r_work: 0.3017 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3017 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8579 moved from start: 0.2457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 35798 Z= 0.116 Angle : 0.572 9.976 48537 Z= 0.294 Chirality : 0.042 0.242 5536 Planarity : 0.004 0.039 6066 Dihedral : 8.250 129.106 4916 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.28 % Allowed : 3.67 % Favored : 96.05 % Rotamer: Outliers : 2.00 % Allowed : 13.72 % Favored : 84.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.51 (0.13), residues: 4304 helix: 0.79 (0.12), residues: 2004 sheet: 0.19 (0.22), residues: 588 loop : 0.02 (0.16), residues: 1712 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 151 TYR 0.018 0.001 TYR E 166 PHE 0.030 0.001 PHE D 610 TRP 0.015 0.001 TRP E 163 HIS 0.004 0.001 HIS B 344 Details of bonding type rmsd covalent geometry : bond 0.00254 (35796) covalent geometry : angle 0.57235 (48537) hydrogen bonds : bond 0.03853 ( 1616) hydrogen bonds : angle 4.86306 ( 4428) Misc. bond : bond 0.00153 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8608 Ramachandran restraints generated. 4304 Oldfield, 0 Emsley, 4304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8608 Ramachandran restraints generated. 4304 Oldfield, 0 Emsley, 4304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 3848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 194 time to evaluate : 1.429 Fit side-chains revert: symmetry clash REVERT: A 94 MET cc_start: 0.7382 (mtm) cc_final: 0.6789 (mpt) REVERT: A 314 MET cc_start: 0.6901 (ttt) cc_final: 0.5997 (tmt) REVERT: B 94 MET cc_start: 0.7355 (mtm) cc_final: 0.6330 (mmt) REVERT: B 314 MET cc_start: 0.6935 (ttt) cc_final: 0.6047 (tmt) REVERT: C 94 MET cc_start: 0.7382 (mtm) cc_final: 0.6759 (mpt) REVERT: C 124 ILE cc_start: 0.8561 (OUTLIER) cc_final: 0.8359 (mm) REVERT: C 314 MET cc_start: 0.6837 (ttt) cc_final: 0.5942 (tmt) REVERT: D 94 MET cc_start: 0.7394 (mtm) cc_final: 0.6773 (mpt) REVERT: D 124 ILE cc_start: 0.8572 (OUTLIER) cc_final: 0.8367 (mm) REVERT: D 314 MET cc_start: 0.6853 (ttt) cc_final: 0.5946 (tmt) REVERT: E 188 ASP cc_start: 0.7226 (OUTLIER) cc_final: 0.6880 (m-30) REVERT: E 230 LYS cc_start: 0.5604 (tmtt) cc_final: 0.5216 (tppp) REVERT: F 45 ASP cc_start: 0.7842 (m-30) cc_final: 0.7581 (m-30) REVERT: F 188 ASP cc_start: 0.7058 (m-30) cc_final: 0.6642 (m-30) REVERT: F 230 LYS cc_start: 0.6134 (tmtt) cc_final: 0.5701 (tppp) REVERT: G 127 ARG cc_start: 0.6892 (mmp-170) cc_final: 0.5817 (ttt-90) REVERT: G 230 LYS cc_start: 0.6881 (tmtt) cc_final: 0.6415 (ttmt) outliers start: 77 outliers final: 29 residues processed: 260 average time/residue: 0.5538 time to fit residues: 180.3895 Evaluate side-chains 206 residues out of total 3848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 174 time to evaluate : 1.492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 229 THR Chi-restraints excluded: chain A residue 919 VAL Chi-restraints excluded: chain A residue 941 VAL Chi-restraints excluded: chain B residue 229 THR Chi-restraints excluded: chain B residue 919 VAL Chi-restraints excluded: chain B residue 941 VAL Chi-restraints excluded: chain C residue 124 ILE Chi-restraints excluded: chain C residue 229 THR Chi-restraints excluded: chain C residue 919 VAL Chi-restraints excluded: chain C residue 941 VAL Chi-restraints excluded: chain D residue 124 ILE Chi-restraints excluded: chain D residue 229 THR Chi-restraints excluded: chain D residue 919 VAL Chi-restraints excluded: chain D residue 941 VAL Chi-restraints excluded: chain E residue 188 ASP Chi-restraints excluded: chain E residue 194 THR Chi-restraints excluded: chain E residue 198 ILE Chi-restraints excluded: chain E residue 205 LEU Chi-restraints excluded: chain E residue 218 VAL Chi-restraints excluded: chain E residue 222 ILE Chi-restraints excluded: chain F residue 194 THR Chi-restraints excluded: chain F residue 198 ILE Chi-restraints excluded: chain F residue 205 LEU Chi-restraints excluded: chain F residue 222 ILE Chi-restraints excluded: chain G residue 198 ILE Chi-restraints excluded: chain G residue 218 VAL Chi-restraints excluded: chain G residue 222 ILE Chi-restraints excluded: chain H residue 105 ASP Chi-restraints excluded: chain H residue 194 THR Chi-restraints excluded: chain H residue 198 ILE Chi-restraints excluded: chain H residue 218 VAL Chi-restraints excluded: chain H residue 222 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 280 optimal weight: 0.9980 chunk 211 optimal weight: 5.9990 chunk 6 optimal weight: 5.9990 chunk 109 optimal weight: 4.9990 chunk 82 optimal weight: 3.9990 chunk 258 optimal weight: 0.6980 chunk 125 optimal weight: 4.9990 chunk 266 optimal weight: 0.2980 chunk 204 optimal weight: 10.0000 chunk 242 optimal weight: 10.0000 chunk 411 optimal weight: 0.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 449 ASN A 808 ASN B 449 ASN D 449 ASN ** E 131 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 131 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 131 HIS ** 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 = 0.3763 r_free = 0.3763 target = 0.083951 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.059136 restraints weight = 115403.497| |-----------------------------------------------------------------------------| r_work (start): 0.3154 rms_B_bonded: 3.04 r_work: 0.3016 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3016 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8579 moved from start: 0.2628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 35798 Z= 0.118 Angle : 0.568 9.842 48537 Z= 0.289 Chirality : 0.042 0.180 5536 Planarity : 0.004 0.039 6066 Dihedral : 8.032 126.066 4916 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.28 % Allowed : 3.65 % Favored : 96.07 % Rotamer: Outliers : 1.51 % Allowed : 14.86 % Favored : 83.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.60 (0.13), residues: 4304 helix: 0.89 (0.12), residues: 1992 sheet: 0.26 (0.22), residues: 572 loop : 0.04 (0.16), residues: 1740 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 107 TYR 0.024 0.001 TYR H 166 PHE 0.021 0.001 PHE H 180 TRP 0.015 0.001 TRP H 167 HIS 0.004 0.001 HIS B 344 Details of bonding type rmsd covalent geometry : bond 0.00263 (35796) covalent geometry : angle 0.56819 (48537) hydrogen bonds : bond 0.03733 ( 1616) hydrogen bonds : angle 4.77653 ( 4428) Misc. bond : bond 0.00150 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8608 Ramachandran restraints generated. 4304 Oldfield, 0 Emsley, 4304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8608 Ramachandran restraints generated. 4304 Oldfield, 0 Emsley, 4304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 3848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 184 time to evaluate : 1.410 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 94 MET cc_start: 0.7348 (mtm) cc_final: 0.6742 (mpt) REVERT: A 314 MET cc_start: 0.6910 (ttt) cc_final: 0.5864 (tmm) REVERT: B 94 MET cc_start: 0.7282 (mtm) cc_final: 0.6230 (mmt) REVERT: B 314 MET cc_start: 0.6882 (ttt) cc_final: 0.5806 (tmm) REVERT: C 94 MET cc_start: 0.7365 (mtm) cc_final: 0.6751 (mpt) REVERT: C 314 MET cc_start: 0.6868 (ttt) cc_final: 0.5780 (tmm) REVERT: D 94 MET cc_start: 0.7387 (mtm) cc_final: 0.6763 (mpt) REVERT: D 154 MET cc_start: 0.8783 (tpp) cc_final: 0.8551 (tpp) REVERT: D 314 MET cc_start: 0.6845 (ttt) cc_final: 0.5767 (tmm) REVERT: E 230 LYS cc_start: 0.5585 (tmtt) cc_final: 0.5190 (tppp) REVERT: F 230 LYS cc_start: 0.6283 (tmtt) cc_final: 0.5856 (tppp) REVERT: G 127 ARG cc_start: 0.6824 (mmp-170) cc_final: 0.5847 (tpt170) REVERT: G 230 LYS cc_start: 0.6810 (tmtt) cc_final: 0.6371 (ttmt) REVERT: H 166 TYR cc_start: 0.8471 (t80) cc_final: 0.8262 (t80) REVERT: H 230 LYS cc_start: 0.5992 (tmtt) cc_final: 0.5365 (ttmp) outliers start: 58 outliers final: 47 residues processed: 231 average time/residue: 0.5730 time to fit residues: 164.9946 Evaluate side-chains 216 residues out of total 3848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 169 time to evaluate : 1.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 229 THR Chi-restraints excluded: chain A residue 406 LEU Chi-restraints excluded: chain A residue 561 LEU Chi-restraints excluded: chain A residue 919 VAL Chi-restraints excluded: chain A residue 941 VAL Chi-restraints excluded: chain A residue 995 CYS Chi-restraints excluded: chain A residue 1015 TYR Chi-restraints excluded: chain A residue 1053 MET Chi-restraints excluded: chain B residue 229 THR Chi-restraints excluded: chain B residue 406 LEU Chi-restraints excluded: chain B residue 561 LEU Chi-restraints excluded: chain B residue 919 VAL Chi-restraints excluded: chain B residue 941 VAL Chi-restraints excluded: chain B residue 995 CYS Chi-restraints excluded: chain B residue 1015 TYR Chi-restraints excluded: chain B residue 1053 MET Chi-restraints excluded: chain C residue 229 THR Chi-restraints excluded: chain C residue 406 LEU Chi-restraints excluded: chain C residue 561 LEU Chi-restraints excluded: chain C residue 919 VAL Chi-restraints excluded: chain C residue 941 VAL Chi-restraints excluded: chain C residue 995 CYS Chi-restraints excluded: chain C residue 1015 TYR Chi-restraints excluded: chain C residue 1053 MET Chi-restraints excluded: chain D residue 229 THR Chi-restraints excluded: chain D residue 406 LEU Chi-restraints excluded: chain D residue 561 LEU Chi-restraints excluded: chain D residue 919 VAL Chi-restraints excluded: chain D residue 941 VAL Chi-restraints excluded: chain D residue 995 CYS Chi-restraints excluded: chain D residue 1015 TYR Chi-restraints excluded: chain D residue 1053 MET Chi-restraints excluded: chain E residue 198 ILE Chi-restraints excluded: chain E residue 205 LEU Chi-restraints excluded: chain E residue 218 VAL Chi-restraints excluded: chain E residue 222 ILE Chi-restraints excluded: chain F residue 198 ILE Chi-restraints excluded: chain F residue 218 VAL Chi-restraints excluded: chain F residue 222 ILE Chi-restraints excluded: chain G residue 64 ILE Chi-restraints excluded: chain G residue 198 ILE Chi-restraints excluded: chain G residue 218 VAL Chi-restraints excluded: chain G residue 222 ILE Chi-restraints excluded: chain H residue 105 ASP Chi-restraints excluded: chain H residue 198 ILE Chi-restraints excluded: chain H residue 218 VAL Chi-restraints excluded: chain H residue 222 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 103 optimal weight: 10.0000 chunk 291 optimal weight: 0.9990 chunk 200 optimal weight: 4.9990 chunk 280 optimal weight: 0.6980 chunk 357 optimal weight: 1.9990 chunk 314 optimal weight: 3.9990 chunk 217 optimal weight: 1.9990 chunk 180 optimal weight: 5.9990 chunk 244 optimal weight: 0.8980 chunk 330 optimal weight: 0.7980 chunk 119 optimal weight: 6.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 808 ASN B1054 GLN C 449 ASN C 808 ASN D 808 ASN D1054 GLN ** E 131 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 131 HIS ** 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 = 0.3769 r_free = 0.3769 target = 0.084284 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.059605 restraints weight = 115847.341| |-----------------------------------------------------------------------------| r_work (start): 0.3171 rms_B_bonded: 3.00 r_work: 0.3035 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3035 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8614 moved from start: 0.2754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 35798 Z= 0.109 Angle : 0.552 10.441 48537 Z= 0.281 Chirality : 0.041 0.199 5536 Planarity : 0.004 0.039 6066 Dihedral : 7.816 122.926 4916 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.28 % Allowed : 3.51 % Favored : 96.21 % Rotamer: Outliers : 1.61 % Allowed : 15.31 % Favored : 83.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.68 (0.13), residues: 4304 helix: 0.96 (0.12), residues: 1996 sheet: 0.35 (0.22), residues: 572 loop : 0.06 (0.16), residues: 1736 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 107 TYR 0.025 0.001 TYR E 166 PHE 0.030 0.001 PHE C 610 TRP 0.014 0.001 TRP E 167 HIS 0.004 0.001 HIS B 344 Details of bonding type rmsd covalent geometry : bond 0.00234 (35796) covalent geometry : angle 0.55198 (48537) hydrogen bonds : bond 0.03561 ( 1616) hydrogen bonds : angle 4.69142 ( 4428) Misc. bond : bond 0.00150 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8608 Ramachandran restraints generated. 4304 Oldfield, 0 Emsley, 4304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8608 Ramachandran restraints generated. 4304 Oldfield, 0 Emsley, 4304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 3848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 183 time to evaluate : 1.258 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 94 MET cc_start: 0.7279 (mtm) cc_final: 0.6203 (mmt) REVERT: A 314 MET cc_start: 0.6724 (ttt) cc_final: 0.5698 (tmm) REVERT: B 94 MET cc_start: 0.7251 (mtm) cc_final: 0.6190 (mmt) REVERT: B 314 MET cc_start: 0.6768 (ttt) cc_final: 0.5778 (tmm) REVERT: C 94 MET cc_start: 0.7285 (mtm) cc_final: 0.6211 (mmt) REVERT: C 314 MET cc_start: 0.6752 (ttt) cc_final: 0.5707 (tmm) REVERT: D 94 MET cc_start: 0.7299 (mtm) cc_final: 0.6233 (mmt) REVERT: D 314 MET cc_start: 0.6708 (ttt) cc_final: 0.5687 (tmm) REVERT: E 230 LYS cc_start: 0.5802 (tmtt) cc_final: 0.5322 (tppp) REVERT: F 230 LYS cc_start: 0.6433 (tmtt) cc_final: 0.5971 (tppp) REVERT: G 127 ARG cc_start: 0.6892 (mmp-170) cc_final: 0.5907 (tpt170) REVERT: G 230 LYS cc_start: 0.6852 (tmtt) cc_final: 0.6384 (ttmt) REVERT: H 230 LYS cc_start: 0.6103 (tmtt) cc_final: 0.5490 (tppp) outliers start: 62 outliers final: 43 residues processed: 236 average time/residue: 0.5811 time to fit residues: 170.4606 Evaluate side-chains 210 residues out of total 3848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 167 time to evaluate : 1.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 229 THR Chi-restraints excluded: chain A residue 406 LEU Chi-restraints excluded: chain A residue 561 LEU Chi-restraints excluded: chain A residue 919 VAL Chi-restraints excluded: chain A residue 941 VAL Chi-restraints excluded: chain A residue 995 CYS Chi-restraints excluded: chain A residue 1015 TYR Chi-restraints excluded: chain B residue 229 THR Chi-restraints excluded: chain B residue 406 LEU Chi-restraints excluded: chain B residue 561 LEU Chi-restraints excluded: chain B residue 919 VAL Chi-restraints excluded: chain B residue 941 VAL Chi-restraints excluded: chain B residue 995 CYS Chi-restraints excluded: chain B residue 1015 TYR Chi-restraints excluded: chain C residue 229 THR Chi-restraints excluded: chain C residue 406 LEU Chi-restraints excluded: chain C residue 561 LEU Chi-restraints excluded: chain C residue 919 VAL Chi-restraints excluded: chain C residue 941 VAL Chi-restraints excluded: chain C residue 995 CYS Chi-restraints excluded: chain C residue 1015 TYR Chi-restraints excluded: chain D residue 229 THR Chi-restraints excluded: chain D residue 406 LEU Chi-restraints excluded: chain D residue 561 LEU Chi-restraints excluded: chain D residue 919 VAL Chi-restraints excluded: chain D residue 941 VAL Chi-restraints excluded: chain D residue 995 CYS Chi-restraints excluded: chain D residue 1015 TYR Chi-restraints excluded: chain D residue 1053 MET Chi-restraints excluded: chain E residue 198 ILE Chi-restraints excluded: chain E residue 218 VAL Chi-restraints excluded: chain E residue 222 ILE Chi-restraints excluded: chain F residue 64 ILE Chi-restraints excluded: chain F residue 198 ILE Chi-restraints excluded: chain F residue 218 VAL Chi-restraints excluded: chain G residue 64 ILE Chi-restraints excluded: chain G residue 198 ILE Chi-restraints excluded: chain G residue 218 VAL Chi-restraints excluded: chain G residue 222 ILE Chi-restraints excluded: chain H residue 105 ASP Chi-restraints excluded: chain H residue 198 ILE Chi-restraints excluded: chain H residue 218 VAL Chi-restraints excluded: chain H residue 222 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 137 optimal weight: 4.9990 chunk 271 optimal weight: 2.9990 chunk 359 optimal weight: 0.9990 chunk 411 optimal weight: 3.9990 chunk 12 optimal weight: 7.9990 chunk 189 optimal weight: 1.9990 chunk 392 optimal weight: 0.9990 chunk 51 optimal weight: 0.0170 chunk 138 optimal weight: 6.9990 chunk 237 optimal weight: 6.9990 chunk 420 optimal weight: 7.9990 overall best weight: 1.4026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C1054 GLN ** E 131 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 131 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.084066 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.059360 restraints weight = 115370.655| |-----------------------------------------------------------------------------| r_work (start): 0.3163 rms_B_bonded: 3.04 r_work: 0.3025 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3025 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8571 moved from start: 0.2827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 35798 Z= 0.115 Angle : 0.563 10.288 48537 Z= 0.285 Chirality : 0.042 0.294 5536 Planarity : 0.004 0.038 6066 Dihedral : 7.715 120.406 4916 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.28 % Allowed : 3.51 % Favored : 96.21 % Rotamer: Outliers : 1.53 % Allowed : 15.85 % Favored : 82.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.76 (0.13), residues: 4304 helix: 0.98 (0.12), residues: 1996 sheet: 0.50 (0.23), residues: 516 loop : 0.13 (0.16), residues: 1792 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG G 107 TYR 0.009 0.001 TYR G 166 PHE 0.032 0.001 PHE B 610 TRP 0.013 0.001 TRP H 167 HIS 0.004 0.001 HIS B 344 Details of bonding type rmsd covalent geometry : bond 0.00257 (35796) covalent geometry : angle 0.56275 (48537) hydrogen bonds : bond 0.03570 ( 1616) hydrogen bonds : angle 4.68214 ( 4428) Misc. bond : bond 0.00154 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8608 Ramachandran restraints generated. 4304 Oldfield, 0 Emsley, 4304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8608 Ramachandran restraints generated. 4304 Oldfield, 0 Emsley, 4304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 3848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 178 time to evaluate : 1.451 Fit side-chains revert: symmetry clash REVERT: A 94 MET cc_start: 0.7317 (mtm) cc_final: 0.6218 (mmt) REVERT: A 314 MET cc_start: 0.6764 (ttt) cc_final: 0.5708 (tmm) REVERT: A 605 VAL cc_start: 0.9387 (OUTLIER) cc_final: 0.9136 (p) REVERT: A 1009 MET cc_start: 0.8463 (mmp) cc_final: 0.8254 (tpt) REVERT: B 94 MET cc_start: 0.7291 (mtm) cc_final: 0.6214 (mmt) REVERT: B 314 MET cc_start: 0.6800 (ttt) cc_final: 0.5759 (tmm) REVERT: B 605 VAL cc_start: 0.9385 (OUTLIER) cc_final: 0.9135 (p) REVERT: C 314 MET cc_start: 0.6718 (ttt) cc_final: 0.5641 (tmm) REVERT: D 21 MET cc_start: 0.7072 (ttm) cc_final: 0.6771 (tmm) REVERT: D 154 MET cc_start: 0.8721 (tpp) cc_final: 0.8294 (mpp) REVERT: D 314 MET cc_start: 0.6719 (ttt) cc_final: 0.5668 (tmm) REVERT: D 605 VAL cc_start: 0.9383 (OUTLIER) cc_final: 0.9136 (p) REVERT: E 230 LYS cc_start: 0.5771 (tmtt) cc_final: 0.5328 (tppp) REVERT: F 41 LYS cc_start: 0.8435 (tptp) cc_final: 0.8055 (tmmm) REVERT: F 230 LYS cc_start: 0.6399 (tmtt) cc_final: 0.5938 (ttmt) REVERT: G 127 ARG cc_start: 0.6934 (mmp-170) cc_final: 0.5946 (tpt170) REVERT: G 230 LYS cc_start: 0.6892 (tmtt) cc_final: 0.6370 (tppp) outliers start: 59 outliers final: 42 residues processed: 232 average time/residue: 0.5960 time to fit residues: 171.5588 Evaluate side-chains 213 residues out of total 3848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 168 time to evaluate : 1.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 229 THR Chi-restraints excluded: chain A residue 406 LEU Chi-restraints excluded: chain A residue 561 LEU Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 919 VAL Chi-restraints excluded: chain A residue 941 VAL Chi-restraints excluded: chain A residue 995 CYS Chi-restraints excluded: chain A residue 1015 TYR Chi-restraints excluded: chain B residue 229 THR Chi-restraints excluded: chain B residue 406 LEU Chi-restraints excluded: chain B residue 561 LEU Chi-restraints excluded: chain B residue 605 VAL Chi-restraints excluded: chain B residue 919 VAL Chi-restraints excluded: chain B residue 941 VAL Chi-restraints excluded: chain B residue 995 CYS Chi-restraints excluded: chain B residue 1015 TYR Chi-restraints excluded: chain C residue 229 THR Chi-restraints excluded: chain C residue 406 LEU Chi-restraints excluded: chain C residue 561 LEU Chi-restraints excluded: chain C residue 919 VAL Chi-restraints excluded: chain C residue 941 VAL Chi-restraints excluded: chain C residue 995 CYS Chi-restraints excluded: chain C residue 1015 TYR Chi-restraints excluded: chain D residue 197 VAL Chi-restraints excluded: chain D residue 229 THR Chi-restraints excluded: chain D residue 406 LEU Chi-restraints excluded: chain D residue 561 LEU Chi-restraints excluded: chain D residue 605 VAL Chi-restraints excluded: chain D residue 919 VAL Chi-restraints excluded: chain D residue 941 VAL Chi-restraints excluded: chain D residue 995 CYS Chi-restraints excluded: chain D residue 1015 TYR Chi-restraints excluded: chain E residue 198 ILE Chi-restraints excluded: chain E residue 218 VAL Chi-restraints excluded: chain E residue 222 ILE Chi-restraints excluded: chain F residue 64 ILE Chi-restraints excluded: chain F residue 198 ILE Chi-restraints excluded: chain F residue 218 VAL Chi-restraints excluded: chain G residue 198 ILE Chi-restraints excluded: chain G residue 218 VAL Chi-restraints excluded: chain G residue 222 ILE Chi-restraints excluded: chain H residue 105 ASP Chi-restraints excluded: chain H residue 198 ILE Chi-restraints excluded: chain H residue 218 VAL Chi-restraints excluded: chain H residue 222 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 201 optimal weight: 5.9990 chunk 391 optimal weight: 5.9990 chunk 27 optimal weight: 9.9990 chunk 145 optimal weight: 0.5980 chunk 306 optimal weight: 3.9990 chunk 307 optimal weight: 7.9990 chunk 20 optimal weight: 3.9990 chunk 346 optimal weight: 20.0000 chunk 181 optimal weight: 0.8980 chunk 273 optimal weight: 9.9990 chunk 39 optimal weight: 0.9990 overall best weight: 2.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 131 HIS ** G 131 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.083513 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.058639 restraints weight = 115887.507| |-----------------------------------------------------------------------------| r_work (start): 0.3147 rms_B_bonded: 3.04 r_work: 0.3010 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3010 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8599 moved from start: 0.2874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 35798 Z= 0.136 Angle : 0.577 14.137 48537 Z= 0.291 Chirality : 0.042 0.292 5536 Planarity : 0.004 0.038 6066 Dihedral : 7.695 118.496 4916 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.28 % Allowed : 3.53 % Favored : 96.19 % Rotamer: Outliers : 1.46 % Allowed : 16.09 % Favored : 82.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.73 (0.13), residues: 4304 helix: 0.94 (0.12), residues: 2036 sheet: 0.50 (0.23), residues: 516 loop : 0.09 (0.16), residues: 1752 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG G 107 TYR 0.035 0.001 TYR F 166 PHE 0.031 0.001 PHE G 180 TRP 0.014 0.001 TRP E 163 HIS 0.008 0.001 HIS E 131 Details of bonding type rmsd covalent geometry : bond 0.00312 (35796) covalent geometry : angle 0.57744 (48537) hydrogen bonds : bond 0.03683 ( 1616) hydrogen bonds : angle 4.73692 ( 4428) Misc. bond : bond 0.00173 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8608 Ramachandran restraints generated. 4304 Oldfield, 0 Emsley, 4304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8608 Ramachandran restraints generated. 4304 Oldfield, 0 Emsley, 4304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 3848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 172 time to evaluate : 1.471 Fit side-chains REVERT: A 314 MET cc_start: 0.6765 (ttt) cc_final: 0.5707 (tmm) REVERT: B 314 MET cc_start: 0.6805 (ttt) cc_final: 0.5770 (tmm) REVERT: C 21 MET cc_start: 0.6957 (ttm) cc_final: 0.6717 (tmm) REVERT: C 94 MET cc_start: 0.8018 (mtp) cc_final: 0.6701 (mmt) REVERT: C 314 MET cc_start: 0.6713 (ttt) cc_final: 0.5653 (tmm) REVERT: D 94 MET cc_start: 0.8045 (mtp) cc_final: 0.6713 (mmt) REVERT: D 314 MET cc_start: 0.6730 (ttt) cc_final: 0.5675 (tmm) REVERT: E 230 LYS cc_start: 0.5965 (tmtt) cc_final: 0.5478 (tppp) REVERT: F 41 LYS cc_start: 0.8420 (tptp) cc_final: 0.7998 (tmmm) REVERT: F 230 LYS cc_start: 0.6428 (tmtt) cc_final: 0.5950 (ttmt) REVERT: G 127 ARG cc_start: 0.6964 (mmp-170) cc_final: 0.6004 (tpt170) REVERT: G 230 LYS cc_start: 0.6887 (tmtt) cc_final: 0.6284 (tppp) REVERT: H 230 LYS cc_start: 0.6071 (tmtt) cc_final: 0.5459 (tppp) outliers start: 56 outliers final: 40 residues processed: 225 average time/residue: 0.5747 time to fit residues: 162.2458 Evaluate side-chains 205 residues out of total 3848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 165 time to evaluate : 1.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 229 THR Chi-restraints excluded: chain A residue 406 LEU Chi-restraints excluded: chain A residue 561 LEU Chi-restraints excluded: chain A residue 919 VAL Chi-restraints excluded: chain A residue 941 VAL Chi-restraints excluded: chain A residue 995 CYS Chi-restraints excluded: chain A residue 1015 TYR Chi-restraints excluded: chain B residue 229 THR Chi-restraints excluded: chain B residue 406 LEU Chi-restraints excluded: chain B residue 561 LEU Chi-restraints excluded: chain B residue 919 VAL Chi-restraints excluded: chain B residue 941 VAL Chi-restraints excluded: chain B residue 995 CYS Chi-restraints excluded: chain B residue 1015 TYR Chi-restraints excluded: chain C residue 229 THR Chi-restraints excluded: chain C residue 406 LEU Chi-restraints excluded: chain C residue 561 LEU Chi-restraints excluded: chain C residue 919 VAL Chi-restraints excluded: chain C residue 941 VAL Chi-restraints excluded: chain C residue 995 CYS Chi-restraints excluded: chain C residue 1015 TYR Chi-restraints excluded: chain D residue 229 THR Chi-restraints excluded: chain D residue 406 LEU Chi-restraints excluded: chain D residue 561 LEU Chi-restraints excluded: chain D residue 919 VAL Chi-restraints excluded: chain D residue 941 VAL Chi-restraints excluded: chain D residue 995 CYS Chi-restraints excluded: chain D residue 1015 TYR Chi-restraints excluded: chain E residue 198 ILE Chi-restraints excluded: chain E residue 218 VAL Chi-restraints excluded: chain E residue 222 ILE Chi-restraints excluded: chain F residue 64 ILE Chi-restraints excluded: chain F residue 198 ILE Chi-restraints excluded: chain F residue 218 VAL Chi-restraints excluded: chain G residue 198 ILE Chi-restraints excluded: chain G residue 218 VAL Chi-restraints excluded: chain G residue 222 ILE Chi-restraints excluded: chain H residue 198 ILE Chi-restraints excluded: chain H residue 218 VAL Chi-restraints excluded: chain H residue 222 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 200 optimal weight: 2.9990 chunk 90 optimal weight: 7.9990 chunk 104 optimal weight: 0.9990 chunk 272 optimal weight: 0.0470 chunk 226 optimal weight: 0.9990 chunk 49 optimal weight: 0.0050 chunk 111 optimal weight: 3.9990 chunk 100 optimal weight: 6.9990 chunk 327 optimal weight: 0.8980 chunk 62 optimal weight: 6.9990 chunk 345 optimal weight: 0.7980 overall best weight: 0.5494 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 131 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.084678 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.060033 restraints weight = 115709.981| |-----------------------------------------------------------------------------| r_work (start): 0.3179 rms_B_bonded: 3.06 r_work: 0.3039 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3039 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8556 moved from start: 0.3029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.081 35798 Z= 0.107 Angle : 0.576 14.200 48537 Z= 0.289 Chirality : 0.042 0.270 5536 Planarity : 0.004 0.038 6066 Dihedral : 7.466 114.996 4916 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.28 % Allowed : 3.62 % Favored : 96.10 % Rotamer: Outliers : 1.07 % Allowed : 16.74 % Favored : 82.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.83 (0.13), residues: 4304 helix: 1.04 (0.12), residues: 2036 sheet: 0.55 (0.23), residues: 516 loop : 0.13 (0.16), residues: 1752 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 107 TYR 0.008 0.001 TYR G 166 PHE 0.033 0.001 PHE C 159 TRP 0.014 0.001 TRP E 163 HIS 0.004 0.001 HIS B 344 Details of bonding type rmsd covalent geometry : bond 0.00231 (35796) covalent geometry : angle 0.57601 (48537) hydrogen bonds : bond 0.03480 ( 1616) hydrogen bonds : angle 4.64545 ( 4428) Misc. bond : bond 0.00154 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8608 Ramachandran restraints generated. 4304 Oldfield, 0 Emsley, 4304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8608 Ramachandran restraints generated. 4304 Oldfield, 0 Emsley, 4304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 3848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 174 time to evaluate : 1.464 Fit side-chains REVERT: A 314 MET cc_start: 0.6605 (ttt) cc_final: 0.5603 (tmm) REVERT: B 94 MET cc_start: 0.7931 (mtp) cc_final: 0.6529 (mmt) REVERT: B 314 MET cc_start: 0.6610 (ttt) cc_final: 0.5608 (tmm) REVERT: C 94 MET cc_start: 0.8003 (mtp) cc_final: 0.6655 (mmt) REVERT: C 314 MET cc_start: 0.6582 (ttt) cc_final: 0.5542 (tmm) REVERT: C 1009 MET cc_start: 0.8498 (mmp) cc_final: 0.8236 (tpt) REVERT: D 314 MET cc_start: 0.6560 (ttt) cc_final: 0.5559 (tmm) REVERT: E 230 LYS cc_start: 0.5920 (tmtt) cc_final: 0.5424 (tppp) REVERT: F 41 LYS cc_start: 0.8325 (tptp) cc_final: 0.7977 (tmmm) REVERT: F 230 LYS cc_start: 0.6407 (tmtt) cc_final: 0.5957 (ttmt) REVERT: G 127 ARG cc_start: 0.6920 (mmp-170) cc_final: 0.6138 (tpt-90) REVERT: G 230 LYS cc_start: 0.6745 (tmtt) cc_final: 0.6266 (tppp) REVERT: H 230 LYS cc_start: 0.6059 (tmtt) cc_final: 0.5515 (tppp) outliers start: 41 outliers final: 36 residues processed: 211 average time/residue: 0.5694 time to fit residues: 149.8821 Evaluate side-chains 203 residues out of total 3848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 167 time to evaluate : 1.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 229 THR Chi-restraints excluded: chain A residue 406 LEU Chi-restraints excluded: chain A residue 561 LEU Chi-restraints excluded: chain A residue 919 VAL Chi-restraints excluded: chain A residue 995 CYS Chi-restraints excluded: chain A residue 1015 TYR Chi-restraints excluded: chain B residue 229 THR Chi-restraints excluded: chain B residue 406 LEU Chi-restraints excluded: chain B residue 561 LEU Chi-restraints excluded: chain B residue 919 VAL Chi-restraints excluded: chain B residue 995 CYS Chi-restraints excluded: chain B residue 1015 TYR Chi-restraints excluded: chain C residue 229 THR Chi-restraints excluded: chain C residue 406 LEU Chi-restraints excluded: chain C residue 561 LEU Chi-restraints excluded: chain C residue 919 VAL Chi-restraints excluded: chain C residue 995 CYS Chi-restraints excluded: chain C residue 1015 TYR Chi-restraints excluded: chain D residue 229 THR Chi-restraints excluded: chain D residue 406 LEU Chi-restraints excluded: chain D residue 561 LEU Chi-restraints excluded: chain D residue 919 VAL Chi-restraints excluded: chain D residue 995 CYS Chi-restraints excluded: chain D residue 1015 TYR Chi-restraints excluded: chain E residue 198 ILE Chi-restraints excluded: chain E residue 218 VAL Chi-restraints excluded: chain F residue 64 ILE Chi-restraints excluded: chain F residue 198 ILE Chi-restraints excluded: chain F residue 205 LEU Chi-restraints excluded: chain F residue 218 VAL Chi-restraints excluded: chain G residue 198 ILE Chi-restraints excluded: chain G residue 218 VAL Chi-restraints excluded: chain G residue 222 ILE Chi-restraints excluded: chain H residue 198 ILE Chi-restraints excluded: chain H residue 218 VAL Chi-restraints excluded: chain H residue 222 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 103 optimal weight: 3.9990 chunk 102 optimal weight: 5.9990 chunk 216 optimal weight: 5.9990 chunk 24 optimal weight: 0.0870 chunk 264 optimal weight: 0.8980 chunk 299 optimal weight: 7.9990 chunk 190 optimal weight: 6.9990 chunk 150 optimal weight: 0.7980 chunk 317 optimal weight: 1.9990 chunk 286 optimal weight: 3.9990 chunk 257 optimal weight: 10.0000 overall best weight: 1.5562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 131 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.084011 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.059313 restraints weight = 115565.405| |-----------------------------------------------------------------------------| r_work (start): 0.3166 rms_B_bonded: 3.00 r_work: 0.3028 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3028 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8622 moved from start: 0.3045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 35798 Z= 0.122 Angle : 0.580 13.715 48537 Z= 0.290 Chirality : 0.042 0.289 5536 Planarity : 0.004 0.039 6066 Dihedral : 7.395 112.731 4916 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.28 % Allowed : 3.55 % Favored : 96.17 % Rotamer: Outliers : 1.01 % Allowed : 17.18 % Favored : 81.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.80 (0.13), residues: 4304 helix: 1.00 (0.12), residues: 2060 sheet: 0.55 (0.23), residues: 516 loop : 0.10 (0.16), residues: 1728 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG G 107 TYR 0.030 0.001 TYR G 166 PHE 0.034 0.001 PHE G 180 TRP 0.014 0.001 TRP E 163 HIS 0.004 0.001 HIS C 344 Details of bonding type rmsd covalent geometry : bond 0.00275 (35796) covalent geometry : angle 0.57956 (48537) hydrogen bonds : bond 0.03569 ( 1616) hydrogen bonds : angle 4.65067 ( 4428) Misc. bond : bond 0.00153 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11245.64 seconds wall clock time: 192 minutes 29.19 seconds (11549.19 seconds total)