Starting phenix.real_space_refine on Mon Jul 6 11:26:37 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9czh_46416/07_2026/9czh_46416.cif Found real_map, /net/cci-nas-00/data/ceres_data/9czh_46416/07_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 { model { file = "/net/cci-nas-00/data/ceres_data/9czh_46416/07_2026/9czh_46416.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9czh_46416/07_2026/9czh_46416.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9czh_46416/07_2026/9czh_46416.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9czh_46416/07_2026/9czh_46416.map" } 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): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 35014 Number of models: 1 Model: "" Number of chains: 12 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: "B" 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: "C" 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: "D" 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: "F" 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: "G" 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: "H" 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, 93 Ad-hoc single atom residues: {' CA': 2, ' K': 4} Unusual residues: {'POV': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain breaks: 6 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, 79 Ad-hoc single atom residues: {' CA': 2} Unusual residues: {'POV': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain breaks: 2 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, 84 Ad-hoc single atom residues: {' CA': 2} Unusual residues: {'POV': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain breaks: 2 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, 94 Ad-hoc single atom residues: {' CA': 2} Unusual residues: {'POV': 3} Classifications: {'undetermined': 3} Link IDs: {None: 1} Chain breaks: 2 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 Time building chain proxies: 6.72, per 1000 atoms: 0.19 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=16, symmetry=0 Simple disulfide: pdb=" SG CYS E 84 " - pdb=" SG CYS E 178 " distance=2.04 Simple disulfide: pdb=" SG CYS E 98 " - pdb=" SG CYS E 149 " distance=2.03 Simple disulfide: pdb=" SG CYS E 102 " - pdb=" SG CYS E 106 " distance=2.03 Simple disulfide: pdb=" SG CYS E 114 " - pdb=" SG CYS E 143 " distance=2.03 Simple disulfide: pdb=" SG CYS F 84 " - pdb=" SG CYS F 178 " distance=2.03 Simple disulfide: pdb=" SG CYS F 98 " - pdb=" SG CYS F 149 " distance=2.03 Simple disulfide: pdb=" SG CYS F 102 " - pdb=" SG CYS F 106 " distance=2.03 Simple disulfide: pdb=" SG CYS F 114 " - pdb=" SG CYS F 143 " distance=2.03 Simple disulfide: pdb=" SG CYS G 84 " - pdb=" SG CYS G 178 " distance=2.04 Simple disulfide: pdb=" SG CYS G 98 " - pdb=" SG CYS G 149 " distance=2.03 Simple disulfide: pdb=" SG CYS G 102 " - pdb=" SG CYS G 106 " distance=2.03 Simple disulfide: pdb=" SG CYS G 114 " - pdb=" SG CYS G 143 " distance=2.03 Simple disulfide: pdb=" SG CYS H 84 " - pdb=" SG CYS H 178 " distance=2.04 Simple disulfide: pdb=" SG CYS H 98 " - pdb=" SG CYS H 149 " distance=2.03 Simple disulfide: pdb=" SG CYS H 102 " - pdb=" SG CYS H 106 " distance=2.03 Simple disulfide: pdb=" SG CYS H 114 " - pdb=" SG CYS H 143 " distance=2.03 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: 3.08 Conformation dependent library (CDL) restraints added in 1.4 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: 1.22 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: 7.43 Time building geometry restraints manager: 3.86 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: 20659 34.68 - 69.37: 525 69.37 - 104.05: 50 104.05 - 138.74: 1 138.74 - 173.42: 1 Dihedral angle restraints: 21236 sinusoidal: 8496 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 21233 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: 2.20 - 2.78: 7066 2.78 - 3.37: 39989 3.37 - 3.96: 66298 3.96 - 4.55: 90969 4.55 - 5.14: 139643 Nonbonded interactions: 343965 Sorted by model distance: nonbonded pdb=" N GLU C 354 " pdb=" OE1 GLU C 354 " model vdw 2.195 3.120 nonbonded pdb=" N GLU B 354 " pdb=" OE1 GLU B 354 " model vdw 2.195 3.120 nonbonded pdb=" N GLU D 354 " pdb=" OE1 GLU D 354 " model vdw 2.195 3.120 nonbonded pdb=" N GLU A 354 " pdb=" OE1 GLU A 354 " model vdw 2.195 3.120 nonbonded pdb=" O GLU B 386 " pdb=" OE1 GLU B 386 " model vdw 2.324 3.040 ... (remaining 343960 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: 4.010 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.590 Check model and map are aligned: 0.110 Set scattering table: 0.090 Process input model: 30.020 Find NCS groups from input model: 1.080 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.570 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.590 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8462 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 35814 Z= 0.301 Angle : 1.010 19.804 48569 Z= 0.543 Chirality : 0.055 0.333 5536 Planarity : 0.007 0.087 6066 Dihedral : 15.412 173.424 12924 Min Nonbonded Distance : 2.195 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/Z covalent geometry : bond 0.00626 / 0.30 (35796) covalent geometry : angle 1.00982 / 0.54 (48537) SS BOND : bond 0.00237 / 0.14 ( 16) SS BOND : angle 1.46345 / 1.03 ( 32) hydrogen bonds : bond 0.13500 / 8.51 ( 1616) hydrogen bonds : angle 7.28073 / 5.24 ( 4428) Misc. bond : bond 0.00499 / 0.25 ( 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 : 1.268 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: 0.8445 (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: 0.7203 time to fit residues: 242.9855 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 : 1.374 ------------------------------------------------------------------------------- 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: 9.9990 chunk 424 optimal weight: 6.9990 chunk 155 optimal weight: 5.9990 overall best weight: 1.2182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 231 ASN A 582 ASN ** A 807 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1054 GLN B 231 ASN B 582 ASN ** B 807 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1054 GLN C 231 ASN C 582 ASN ** C 807 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1054 GLN D 231 ASN 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: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.084072 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.059775 restraints weight = 115966.910| |-----------------------------------------------------------------------------| r_work (start): 0.3178 rms_B_bonded: 2.99 r_work: 0.3039 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3039 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8734 moved from start: 0.1540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 35814 Z= 0.143 Angle : 0.660 14.879 48569 Z= 0.344 Chirality : 0.044 0.165 5536 Planarity : 0.004 0.042 6066 Dihedral : 9.756 148.503 4920 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.49 % Favored : 96.42 % Rotamer: Outliers : 1.33 % Allowed : 10.78 % Favored : 87.89 % 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: 0.06 (0.13), residues: 4304 helix: 0.28 (0.12), residues: 1984 sheet: 0.10 (0.21), residues: 560 loop : -0.05 (0.16), residues: 1760 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG G 151 TYR 0.020 0.001 TYR H 166 PHE 0.024 0.002 PHE C 610 TRP 0.022 0.002 TRP G 167 HIS 0.006 0.001 HIS B 771 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.14 (35796) covalent geometry : angle 0.65996 / 0.34 (48537) SS BOND : bond 0.00167 / 0.10 ( 16) SS BOND : angle 1.15844 / 0.78 ( 32) hydrogen bonds : bond 0.04948 / 3.14 ( 1616) hydrogen bonds : angle 5.49308 / 3.92 ( 4428) Misc. bond : bond 0.00173 / 0.09 ( 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 281 residues out of total 3848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 230 time to evaluate : 1.286 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 94 MET cc_start: 0.7333 (mtm) cc_final: 0.6781 (mpt) REVERT: A 154 MET cc_start: 0.8590 (tpp) cc_final: 0.8376 (tpt) REVERT: A 314 MET cc_start: 0.7097 (ttt) cc_final: 0.6213 (tmt) REVERT: B 94 MET cc_start: 0.7343 (mtm) cc_final: 0.6807 (mpt) REVERT: B 154 MET cc_start: 0.8592 (tpp) cc_final: 0.8382 (tpt) REVERT: B 314 MET cc_start: 0.7138 (ttt) cc_final: 0.6249 (tmt) REVERT: C 94 MET cc_start: 0.7370 (mtm) cc_final: 0.6828 (mpt) REVERT: C 154 MET cc_start: 0.8524 (tpp) cc_final: 0.8279 (tpt) REVERT: C 314 MET cc_start: 0.7073 (ttt) cc_final: 0.6134 (tmt) REVERT: D 94 MET cc_start: 0.7372 (mtm) cc_final: 0.6796 (mpt) REVERT: D 154 MET cc_start: 0.8553 (tpp) cc_final: 0.8321 (tpt) REVERT: D 314 MET cc_start: 0.7061 (ttt) cc_final: 0.6164 (tmt) REVERT: E 105 ASP cc_start: 0.8635 (OUTLIER) cc_final: 0.8376 (p0) REVERT: E 107 ARG cc_start: 0.8317 (tpp-160) cc_final: 0.8042 (tpp-160) REVERT: E 188 ASP cc_start: 0.7070 (m-30) cc_final: 0.6786 (m-30) REVERT: E 230 LYS cc_start: 0.5773 (tmtt) cc_final: 0.5349 (tppp) REVERT: F 230 LYS cc_start: 0.6284 (tmtt) cc_final: 0.5735 (tppp) REVERT: G 230 LYS cc_start: 0.7140 (tmtt) cc_final: 0.6606 (tppp) outliers start: 51 outliers final: 7 residues processed: 267 average time/residue: 0.5877 time to fit residues: 192.9775 Evaluate side-chains 207 residues out of total 3848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 199 time to evaluate : 1.213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 105 ASP 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 198 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 417 optimal weight: 7.9990 chunk 202 optimal weight: 0.9990 chunk 414 optimal weight: 1.9990 chunk 86 optimal weight: 0.9980 chunk 255 optimal weight: 0.9990 chunk 126 optimal weight: 0.1980 chunk 204 optimal weight: 0.0670 chunk 328 optimal weight: 7.9990 chunk 162 optimal weight: 0.0570 chunk 192 optimal weight: 7.9990 chunk 391 optimal weight: 10.0000 overall best weight: 0.4638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 807 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 807 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3785 r_free = 0.3785 target = 0.084923 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.060848 restraints weight = 115299.367| |-----------------------------------------------------------------------------| r_work (start): 0.3204 rms_B_bonded: 3.00 r_work: 0.3069 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3069 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8701 moved from start: 0.1964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 35814 Z= 0.118 Angle : 0.600 12.085 48569 Z= 0.310 Chirality : 0.042 0.162 5536 Planarity : 0.004 0.043 6066 Dihedral : 9.020 138.029 4916 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.28 % Allowed : 3.32 % Favored : 96.40 % Rotamer: Outliers : 1.17 % Allowed : 12.21 % Favored : 86.62 % 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: 0.34 (0.13), residues: 4304 helix: 0.59 (0.12), residues: 1984 sheet: 0.12 (0.21), residues: 580 loop : 0.03 (0.16), residues: 1740 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 151 TYR 0.013 0.001 TYR E 166 PHE 0.014 0.001 PHE G 180 TRP 0.017 0.001 TRP H 167 HIS 0.004 0.001 HIS F 202 Details of bonding type rmsd/Z covalent geometry : bond 0.00240 / 0.12 (35796) covalent geometry : angle 0.59958 / 0.31 (48537) SS BOND : bond 0.00172 / 0.10 ( 16) SS BOND : angle 0.98290 / 0.68 ( 32) hydrogen bonds : bond 0.04279 / 2.71 ( 1616) hydrogen bonds : angle 5.14208 / 3.67 ( 4428) Misc. bond : bond 0.00139 / 0.07 ( 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 273 residues out of total 3848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 228 time to evaluate : 1.352 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 94 MET cc_start: 0.7336 (mtm) cc_final: 0.6774 (mpt) REVERT: A 124 ILE cc_start: 0.8697 (OUTLIER) cc_final: 0.8483 (mm) REVERT: A 314 MET cc_start: 0.6949 (ttt) cc_final: 0.6088 (tmt) REVERT: B 94 MET cc_start: 0.7304 (mtm) cc_final: 0.6768 (mpt) REVERT: B 124 ILE cc_start: 0.8699 (OUTLIER) cc_final: 0.8490 (mm) REVERT: B 314 MET cc_start: 0.6969 (ttt) cc_final: 0.6114 (tmt) REVERT: C 94 MET cc_start: 0.7349 (mtm) cc_final: 0.6806 (mpt) REVERT: C 124 ILE cc_start: 0.8674 (OUTLIER) cc_final: 0.8447 (mm) REVERT: C 314 MET cc_start: 0.6856 (ttt) cc_final: 0.6021 (tmt) REVERT: D 94 MET cc_start: 0.7349 (mtm) cc_final: 0.6786 (mpt) REVERT: D 124 ILE cc_start: 0.8702 (OUTLIER) cc_final: 0.8485 (mm) REVERT: D 314 MET cc_start: 0.6904 (ttt) cc_final: 0.6041 (tmt) REVERT: E 105 ASP cc_start: 0.8538 (OUTLIER) cc_final: 0.8252 (p0) REVERT: E 107 ARG cc_start: 0.8247 (tpp-160) cc_final: 0.8000 (tpp-160) REVERT: E 188 ASP cc_start: 0.6751 (m-30) cc_final: 0.6380 (m-30) REVERT: E 230 LYS cc_start: 0.5739 (tmtt) cc_final: 0.5340 (tppp) REVERT: F 105 ASP cc_start: 0.8844 (OUTLIER) cc_final: 0.8590 (p0) REVERT: F 107 ARG cc_start: 0.8133 (pmm150) cc_final: 0.7612 (pmm150) REVERT: F 188 ASP cc_start: 0.7284 (m-30) cc_final: 0.6953 (m-30) REVERT: F 230 LYS cc_start: 0.6245 (tmtt) cc_final: 0.5775 (tppp) REVERT: G 230 LYS cc_start: 0.7150 (tmtt) cc_final: 0.6607 (tppp) REVERT: H 230 LYS cc_start: 0.5983 (tmtt) cc_final: 0.5326 (ttmp) outliers start: 45 outliers final: 11 residues processed: 265 average time/residue: 0.6569 time to fit residues: 210.6396 Evaluate side-chains 219 residues out of total 3848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 202 time to evaluate : 1.221 ------------------------------------------------------------------------------- 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 105 ASP 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 105 ASP 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 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: 5.9990 chunk 114 optimal weight: 9.9990 chunk 76 optimal weight: 7.9990 chunk 192 optimal weight: 8.9990 chunk 133 optimal weight: 5.9990 chunk 118 optimal weight: 6.9990 chunk 91 optimal weight: 6.9990 chunk 286 optimal weight: 5.9990 chunk 176 optimal weight: 0.9990 chunk 405 optimal weight: 7.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3727 r_free = 0.3727 target = 0.082247 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.057111 restraints weight = 115331.966| |-----------------------------------------------------------------------------| r_work (start): 0.3106 rms_B_bonded: 3.02 r_work: 0.2967 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.2967 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8759 moved from start: 0.2192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.078 35814 Z= 0.247 Angle : 0.655 10.085 48569 Z= 0.335 Chirality : 0.045 0.227 5536 Planarity : 0.004 0.040 6066 Dihedral : 8.792 137.382 4916 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.28 % Allowed : 3.97 % Favored : 95.75 % Rotamer: Outliers : 1.95 % Allowed : 13.05 % Favored : 85.01 % 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: 0.24 (0.13), residues: 4304 helix: 0.52 (0.12), residues: 2000 sheet: 0.24 (0.23), residues: 532 loop : -0.10 (0.16), residues: 1772 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 151 TYR 0.025 0.002 TYR E 166 PHE 0.020 0.002 PHE D1050 TRP 0.017 0.001 TRP E 167 HIS 0.005 0.001 HIS D 365 Details of bonding type rmsd/Z covalent geometry : bond 0.00584 / 0.25 (35796) covalent geometry : angle 0.65480 / 0.34 (48537) SS BOND : bond 0.00071 / 0.04 ( 16) SS BOND : angle 1.02528 / 0.69 ( 32) hydrogen bonds : bond 0.04631 / 2.95 ( 1616) hydrogen bonds : angle 5.21357 / 3.71 ( 4428) Misc. bond : bond 0.00164 / 0.08 ( 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 283 residues out of total 3848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 208 time to evaluate : 1.116 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 94 MET cc_start: 0.7387 (mtm) cc_final: 0.6809 (mpt) REVERT: A 314 MET cc_start: 0.7161 (ttt) cc_final: 0.6074 (tmm) REVERT: B 94 MET cc_start: 0.7373 (mtm) cc_final: 0.6367 (mmt) REVERT: B 314 MET cc_start: 0.7168 (ttt) cc_final: 0.6099 (tmm) REVERT: C 94 MET cc_start: 0.7421 (mtm) cc_final: 0.6769 (mpt) REVERT: C 314 MET cc_start: 0.7146 (ttt) cc_final: 0.6055 (tmm) REVERT: D 94 MET cc_start: 0.7467 (mtm) cc_final: 0.6852 (mpt) REVERT: D 314 MET cc_start: 0.7129 (ttt) cc_final: 0.6054 (tmm) REVERT: E 105 ASP cc_start: 0.8488 (OUTLIER) cc_final: 0.8197 (p0) REVERT: E 107 ARG cc_start: 0.8214 (tpp-160) cc_final: 0.7985 (tpp-160) REVERT: E 230 LYS cc_start: 0.5708 (tmtt) cc_final: 0.5279 (tppp) REVERT: F 45 ASP cc_start: 0.7916 (m-30) cc_final: 0.7713 (m-30) REVERT: F 230 LYS cc_start: 0.6227 (tmtt) cc_final: 0.5752 (tppp) REVERT: G 188 ASP cc_start: 0.7472 (OUTLIER) cc_final: 0.7129 (m-30) REVERT: G 230 LYS cc_start: 0.7075 (tmtt) cc_final: 0.6548 (ttmt) outliers start: 75 outliers final: 27 residues processed: 273 average time/residue: 0.6273 time to fit residues: 211.3262 Evaluate side-chains 211 residues out of total 3848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 182 time to evaluate : 1.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 26 LEU Chi-restraints excluded: chain C residue 406 LEU Chi-restraints excluded: chain C residue 919 VAL Chi-restraints excluded: chain C residue 941 VAL Chi-restraints excluded: chain D residue 26 LEU Chi-restraints excluded: chain D residue 406 LEU Chi-restraints excluded: chain D residue 919 VAL Chi-restraints excluded: chain D residue 941 VAL Chi-restraints excluded: chain E residue 48 ILE Chi-restraints excluded: chain E residue 105 ASP 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 188 ASP 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 1 optimal weight: 8.9990 chunk 111 optimal weight: 3.9990 chunk 331 optimal weight: 2.9990 chunk 269 optimal weight: 0.9990 chunk 86 optimal weight: 0.9980 chunk 103 optimal weight: 9.9990 chunk 84 optimal weight: 0.4980 chunk 388 optimal weight: 2.9990 chunk 59 optimal weight: 0.8980 chunk 325 optimal weight: 10.0000 chunk 216 optimal weight: 1.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 131 HIS E 202 HIS F 131 HIS G 91 GLN G 202 HIS H 202 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.083823 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.058885 restraints weight = 114621.223| |-----------------------------------------------------------------------------| r_work (start): 0.3152 rms_B_bonded: 3.05 r_work: 0.3015 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3015 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8689 moved from start: 0.2440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 35814 Z= 0.120 Angle : 0.587 10.231 48569 Z= 0.300 Chirality : 0.042 0.181 5536 Planarity : 0.004 0.039 6066 Dihedral : 8.379 131.271 4916 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.28 % Allowed : 3.60 % Favored : 96.12 % Rotamer: Outliers : 1.69 % Allowed : 14.58 % Favored : 83.73 % 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: 0.48 (0.13), residues: 4304 helix: 0.74 (0.12), residues: 2000 sheet: 0.24 (0.22), residues: 532 loop : 0.02 (0.16), residues: 1772 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 151 TYR 0.015 0.001 TYR D 290 PHE 0.028 0.001 PHE C 610 TRP 0.014 0.001 TRP E 163 HIS 0.011 0.001 HIS F 131 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.12 (35796) covalent geometry : angle 0.58694 / 0.30 (48537) SS BOND : bond 0.00149 / 0.07 ( 16) SS BOND : angle 0.95563 / 0.66 ( 32) hydrogen bonds : bond 0.03965 / 2.52 ( 1616) hydrogen bonds : angle 4.95454 / 3.53 ( 4428) Misc. bond : bond 0.00152 / 0.07 ( 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 264 residues out of total 3848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 199 time to evaluate : 1.322 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 94 MET cc_start: 0.7363 (mtm) cc_final: 0.6734 (mpt) REVERT: A 314 MET cc_start: 0.6915 (ttt) cc_final: 0.6006 (tmt) REVERT: B 94 MET cc_start: 0.7352 (mtm) cc_final: 0.6309 (mmt) REVERT: B 314 MET cc_start: 0.6963 (ttt) cc_final: 0.6071 (tmt) REVERT: C 94 MET cc_start: 0.7395 (mtm) cc_final: 0.6757 (mpt) REVERT: C 314 MET cc_start: 0.6860 (ttt) cc_final: 0.5958 (tmt) REVERT: D 94 MET cc_start: 0.7398 (mtm) cc_final: 0.6771 (mpt) REVERT: D 314 MET cc_start: 0.6879 (ttt) cc_final: 0.5981 (tmt) REVERT: E 230 LYS cc_start: 0.5570 (tmtt) cc_final: 0.5187 (tppp) REVERT: F 45 ASP cc_start: 0.7834 (m-30) cc_final: 0.7594 (m-30) REVERT: F 230 LYS cc_start: 0.6170 (tmtt) cc_final: 0.5715 (tppp) REVERT: G 230 LYS cc_start: 0.6830 (tmtt) cc_final: 0.6347 (tppp) outliers start: 65 outliers final: 21 residues processed: 253 average time/residue: 0.6485 time to fit residues: 201.4722 Evaluate side-chains 198 residues out of total 3848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 177 time to evaluate : 1.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 229 THR Chi-restraints excluded: chain A residue 919 VAL Chi-restraints excluded: chain B residue 229 THR Chi-restraints excluded: chain B residue 919 VAL Chi-restraints excluded: chain C residue 229 THR Chi-restraints excluded: chain C residue 919 VAL Chi-restraints excluded: chain D residue 229 THR Chi-restraints excluded: chain D residue 919 VAL Chi-restraints excluded: chain E residue 194 THR 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 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 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: 1.9990 chunk 211 optimal weight: 4.9990 chunk 6 optimal weight: 6.9990 chunk 109 optimal weight: 4.9990 chunk 82 optimal weight: 0.8980 chunk 258 optimal weight: 6.9990 chunk 125 optimal weight: 4.9990 chunk 266 optimal weight: 0.9990 chunk 204 optimal weight: 0.7980 chunk 242 optimal weight: 0.9980 chunk 411 optimal weight: 2.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 808 ASN G 91 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.084049 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.059281 restraints weight = 114766.087| |-----------------------------------------------------------------------------| r_work (start): 0.3162 rms_B_bonded: 3.03 r_work: 0.3026 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3026 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8682 moved from start: 0.2618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 35814 Z= 0.117 Angle : 0.586 10.282 48569 Z= 0.297 Chirality : 0.042 0.318 5536 Planarity : 0.004 0.039 6066 Dihedral : 8.105 127.545 4916 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.28 % Allowed : 3.51 % Favored : 96.21 % Rotamer: Outliers : 1.51 % Allowed : 15.20 % Favored : 83.29 % 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: 0.53 (0.13), residues: 4304 helix: 0.85 (0.12), residues: 2004 sheet: 0.13 (0.21), residues: 588 loop : 0.00 (0.16), residues: 1712 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 151 TYR 0.024 0.001 TYR E 166 PHE 0.026 0.001 PHE B 610 TRP 0.015 0.001 TRP H 167 HIS 0.006 0.001 HIS G 131 Details of bonding type rmsd/Z covalent geometry : bond 0.00255 / 0.12 (35796) covalent geometry : angle 0.58594 / 0.30 (48537) SS BOND : bond 0.00154 / 0.09 ( 16) SS BOND : angle 1.04325 / 0.69 ( 32) hydrogen bonds : bond 0.03783 / 2.41 ( 1616) hydrogen bonds : angle 4.81945 / 3.43 ( 4428) Misc. bond : bond 0.00153 / 0.07 ( 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 250 residues out of total 3848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 192 time to evaluate : 1.313 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 94 MET cc_start: 0.7351 (mtm) cc_final: 0.6742 (mpt) REVERT: A 314 MET cc_start: 0.6906 (ttt) cc_final: 0.5853 (tmm) REVERT: B 94 MET cc_start: 0.7282 (mtm) cc_final: 0.6224 (mmt) REVERT: B 154 MET cc_start: 0.8771 (tpp) cc_final: 0.8269 (mpp) REVERT: B 314 MET cc_start: 0.6866 (ttt) cc_final: 0.5800 (tmm) REVERT: C 94 MET cc_start: 0.7376 (mtm) cc_final: 0.6755 (mpt) REVERT: C 314 MET cc_start: 0.6827 (ttt) cc_final: 0.5766 (tmm) REVERT: D 94 MET cc_start: 0.7367 (mtm) cc_final: 0.6273 (mmt) REVERT: D 314 MET cc_start: 0.6873 (ttt) cc_final: 0.5829 (tmm) REVERT: E 45 ASP cc_start: 0.7990 (m-30) cc_final: 0.7790 (m-30) REVERT: E 127 ARG cc_start: 0.7106 (mmp-170) cc_final: 0.6133 (ttt-90) REVERT: E 230 LYS cc_start: 0.5633 (tmtt) cc_final: 0.5220 (tppp) REVERT: F 230 LYS cc_start: 0.6292 (tmtt) cc_final: 0.5846 (tppp) REVERT: G 230 LYS cc_start: 0.6848 (tmtt) cc_final: 0.6381 (tppp) REVERT: H 230 LYS cc_start: 0.6051 (tmtt) cc_final: 0.5391 (ttmp) outliers start: 58 outliers final: 37 residues processed: 237 average time/residue: 0.6230 time to fit residues: 182.3467 Evaluate side-chains 216 residues out of total 3848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 179 time to evaluate : 1.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 229 THR 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 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 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 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 194 THR 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 194 THR 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 103 optimal weight: 10.0000 chunk 291 optimal weight: 8.9990 chunk 200 optimal weight: 3.9990 chunk 280 optimal weight: 3.9990 chunk 357 optimal weight: 2.9990 chunk 314 optimal weight: 2.9990 chunk 217 optimal weight: 1.9990 chunk 180 optimal weight: 3.9990 chunk 244 optimal weight: 3.9990 chunk 330 optimal weight: 10.0000 chunk 119 optimal weight: 0.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C1054 GLN G 91 GLN G 131 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.083130 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.058279 restraints weight = 115211.962| |-----------------------------------------------------------------------------| r_work (start): 0.3137 rms_B_bonded: 3.03 r_work: 0.3000 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3000 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8708 moved from start: 0.2683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 35814 Z= 0.156 Angle : 0.586 9.858 48569 Z= 0.298 Chirality : 0.043 0.260 5536 Planarity : 0.004 0.038 6066 Dihedral : 8.028 126.614 4916 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.28 % Allowed : 3.72 % Favored : 96.00 % Rotamer: Outliers : 1.46 % Allowed : 15.67 % Favored : 82.87 % 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: 0.59 (0.13), residues: 4304 helix: 0.81 (0.12), residues: 2028 sheet: 0.40 (0.23), residues: 516 loop : 0.05 (0.16), residues: 1760 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 151 TYR 0.013 0.001 TYR D 290 PHE 0.029 0.001 PHE C 610 TRP 0.014 0.001 TRP H 167 HIS 0.004 0.001 HIS A 344 Details of bonding type rmsd/Z covalent geometry : bond 0.00362 / 0.16 (35796) covalent geometry : angle 0.58615 / 0.30 (48537) SS BOND : bond 0.00123 / 0.08 ( 16) SS BOND : angle 0.93901 / 0.66 ( 32) hydrogen bonds : bond 0.03883 / 2.47 ( 1616) hydrogen bonds : angle 4.85099 / 3.46 ( 4428) Misc. bond : bond 0.00158 / 0.08 ( 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 241 residues out of total 3848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 185 time to evaluate : 1.447 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 94 MET cc_start: 0.7331 (mtm) cc_final: 0.6233 (mmt) REVERT: A 314 MET cc_start: 0.6942 (ttt) cc_final: 0.5835 (tmm) REVERT: B 94 MET cc_start: 0.7301 (mtm) cc_final: 0.6229 (mmt) REVERT: B 154 MET cc_start: 0.8769 (tpp) cc_final: 0.8224 (mpp) REVERT: B 314 MET cc_start: 0.6919 (ttt) cc_final: 0.5852 (tmm) REVERT: C 94 MET cc_start: 0.7385 (mtm) cc_final: 0.6253 (mmt) REVERT: C 314 MET cc_start: 0.6875 (ttt) cc_final: 0.5777 (tmm) REVERT: D 314 MET cc_start: 0.6874 (ttt) cc_final: 0.5800 (tmm) REVERT: E 230 LYS cc_start: 0.5824 (tmtt) cc_final: 0.5359 (tppp) REVERT: F 230 LYS cc_start: 0.6329 (tmtt) cc_final: 0.5882 (tppp) REVERT: G 127 ARG cc_start: 0.6784 (mmp-170) cc_final: 0.5574 (tpt-90) REVERT: G 161 MET cc_start: 0.8840 (mmm) cc_final: 0.8597 (mmt) REVERT: G 230 LYS cc_start: 0.6883 (tmtt) cc_final: 0.6256 (tppp) REVERT: H 45 ASP cc_start: 0.7890 (m-30) cc_final: 0.7684 (m-30) REVERT: H 230 LYS cc_start: 0.6059 (tmtt) cc_final: 0.5451 (tppp) outliers start: 56 outliers final: 42 residues processed: 232 average time/residue: 0.6228 time to fit residues: 178.5842 Evaluate side-chains 215 residues out of total 3848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 173 time to evaluate : 1.307 ------------------------------------------------------------------------------- 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 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 64 ILE Chi-restraints excluded: chain E residue 194 THR 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 194 THR 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 Chi-restraints excluded: chain H residue 234 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 137 optimal weight: 10.0000 chunk 271 optimal weight: 0.0870 chunk 359 optimal weight: 0.9980 chunk 411 optimal weight: 2.9990 chunk 12 optimal weight: 6.9990 chunk 189 optimal weight: 5.9990 chunk 392 optimal weight: 2.9990 chunk 51 optimal weight: 0.9990 chunk 138 optimal weight: 3.9990 chunk 237 optimal weight: 5.9990 chunk 420 optimal weight: 9.9990 overall best weight: 1.6164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1054 GLN B1054 GLN C 808 ASN D1054 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.083691 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.058904 restraints weight = 114645.226| |-----------------------------------------------------------------------------| r_work (start): 0.3156 rms_B_bonded: 3.03 r_work: 0.3019 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3019 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8701 moved from start: 0.2802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 35814 Z= 0.122 Angle : 0.570 10.580 48569 Z= 0.288 Chirality : 0.042 0.258 5536 Planarity : 0.004 0.039 6066 Dihedral : 7.855 123.477 4916 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.28 % Allowed : 3.69 % Favored : 96.03 % Rotamer: Outliers : 1.51 % Allowed : 16.01 % Favored : 82.48 % 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: 0.63 (0.13), residues: 4304 helix: 0.87 (0.12), residues: 2032 sheet: 0.46 (0.23), residues: 524 loop : 0.04 (0.16), residues: 1748 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 107 TYR 0.013 0.001 TYR D 290 PHE 0.029 0.001 PHE D 610 TRP 0.015 0.001 TRP E 167 HIS 0.004 0.001 HIS A 344 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.12 (35796) covalent geometry : angle 0.56951 / 0.29 (48537) SS BOND : bond 0.00139 / 0.07 ( 16) SS BOND : angle 0.97814 / 0.70 ( 32) hydrogen bonds : bond 0.03667 / 2.33 ( 1616) hydrogen bonds : angle 4.77193 / 3.39 ( 4428) Misc. bond : bond 0.00161 / 0.08 ( 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 240 residues out of total 3848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 182 time to evaluate : 1.443 Fit side-chains revert: symmetry clash REVERT: A 314 MET cc_start: 0.6835 (ttt) cc_final: 0.5735 (tmm) REVERT: B 21 MET cc_start: 0.6945 (ttm) cc_final: 0.6697 (tmm) REVERT: B 314 MET cc_start: 0.6822 (ttt) cc_final: 0.5742 (tmm) REVERT: B 1009 MET cc_start: 0.8553 (mmp) cc_final: 0.8267 (tpt) REVERT: C 314 MET cc_start: 0.6778 (ttt) cc_final: 0.5685 (tmm) REVERT: D 314 MET cc_start: 0.6796 (ttt) cc_final: 0.5708 (tmm) REVERT: E 127 ARG cc_start: 0.7197 (mmp-170) cc_final: 0.6261 (tpt-90) REVERT: E 230 LYS cc_start: 0.5860 (tmtt) cc_final: 0.5342 (tppp) REVERT: F 41 LYS cc_start: 0.8452 (tptp) cc_final: 0.8111 (tmmm) REVERT: F 225 LYS cc_start: 0.7405 (OUTLIER) cc_final: 0.7178 (mmmm) REVERT: F 230 LYS cc_start: 0.6365 (tmtt) cc_final: 0.5893 (ttmt) REVERT: G 127 ARG cc_start: 0.6862 (mmp-170) cc_final: 0.5696 (tpt-90) REVERT: G 161 MET cc_start: 0.8878 (mmm) cc_final: 0.8625 (mmt) REVERT: G 162 ASN cc_start: 0.9343 (m-40) cc_final: 0.8959 (p0) REVERT: G 230 LYS cc_start: 0.6798 (tmtt) cc_final: 0.6290 (tppp) REVERT: H 45 ASP cc_start: 0.7863 (m-30) cc_final: 0.7644 (m-30) REVERT: H 107 ARG cc_start: 0.8255 (pmm150) cc_final: 0.7770 (pmm150) REVERT: H 230 LYS cc_start: 0.6117 (tmtt) cc_final: 0.5495 (tppp) outliers start: 58 outliers final: 42 residues processed: 230 average time/residue: 0.6361 time to fit residues: 180.4707 Evaluate side-chains 217 residues out of total 3848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 174 time to evaluate : 1.360 ------------------------------------------------------------------------------- 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 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 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 64 ILE Chi-restraints excluded: chain E residue 194 THR 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 225 LYS 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 201 optimal weight: 3.9990 chunk 391 optimal weight: 0.8980 chunk 27 optimal weight: 3.9990 chunk 145 optimal weight: 0.9990 chunk 306 optimal weight: 0.8980 chunk 307 optimal weight: 1.9990 chunk 20 optimal weight: 5.9990 chunk 346 optimal weight: 20.0000 chunk 181 optimal weight: 2.9990 chunk 273 optimal weight: 9.9990 chunk 39 optimal weight: 2.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 808 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.083710 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.058989 restraints weight = 115217.150| |-----------------------------------------------------------------------------| r_work (start): 0.3157 rms_B_bonded: 2.99 r_work: 0.3020 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3020 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8726 moved from start: 0.2890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 35814 Z= 0.123 Angle : 0.579 13.786 48569 Z= 0.290 Chirality : 0.042 0.308 5536 Planarity : 0.004 0.038 6066 Dihedral : 7.692 120.517 4916 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.28 % Allowed : 3.51 % Favored : 96.21 % Rotamer: Outliers : 1.46 % Allowed : 16.14 % Favored : 82.41 % 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: 0.67 (0.13), residues: 4304 helix: 0.91 (0.12), residues: 2032 sheet: 0.48 (0.23), residues: 516 loop : 0.05 (0.16), residues: 1756 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 107 TYR 0.012 0.001 TYR D 290 PHE 0.027 0.001 PHE B 610 TRP 0.016 0.001 TRP H 167 HIS 0.006 0.001 HIS H 131 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.12 (35796) covalent geometry : angle 0.57829 / 0.29 (48537) SS BOND : bond 0.00136 / 0.08 ( 16) SS BOND : angle 0.92794 / 0.68 ( 32) hydrogen bonds : bond 0.03606 / 2.29 ( 1616) hydrogen bonds : angle 4.73665 / 3.37 ( 4428) Misc. bond : bond 0.00169 / 0.08 ( 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 232 residues out of total 3848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 176 time to evaluate : 1.446 Fit side-chains revert: symmetry clash REVERT: A 94 MET cc_start: 0.8006 (mtp) cc_final: 0.6635 (mmt) REVERT: A 314 MET cc_start: 0.6722 (ttt) cc_final: 0.5673 (tmm) REVERT: B 314 MET cc_start: 0.6734 (ttt) cc_final: 0.5704 (tmm) REVERT: C 314 MET cc_start: 0.6664 (ttt) cc_final: 0.5606 (tmm) REVERT: D 21 MET cc_start: 0.7032 (ttm) cc_final: 0.6762 (tmm) REVERT: D 314 MET cc_start: 0.6690 (ttt) cc_final: 0.5645 (tmm) REVERT: E 127 ARG cc_start: 0.7260 (mmp-170) cc_final: 0.6325 (ttt-90) REVERT: E 230 LYS cc_start: 0.5978 (tmtt) cc_final: 0.5478 (tppp) REVERT: F 41 LYS cc_start: 0.8422 (tptp) cc_final: 0.8025 (tmmm) REVERT: F 225 LYS cc_start: 0.7440 (OUTLIER) cc_final: 0.7221 (mmmm) REVERT: F 230 LYS cc_start: 0.6438 (tmtt) cc_final: 0.5956 (ttmt) REVERT: G 127 ARG cc_start: 0.6924 (mmp-170) cc_final: 0.5675 (tpt170) REVERT: G 161 MET cc_start: 0.8893 (mmm) cc_final: 0.8650 (mmt) REVERT: G 230 LYS cc_start: 0.6801 (tmtt) cc_final: 0.6286 (tppp) REVERT: H 230 LYS cc_start: 0.6134 (tmtt) cc_final: 0.5521 (tppp) outliers start: 56 outliers final: 43 residues processed: 228 average time/residue: 0.6380 time to fit residues: 179.5294 Evaluate side-chains 215 residues out of total 3848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 171 time to evaluate : 1.386 ------------------------------------------------------------------------------- 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 197 VAL 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 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 64 ILE Chi-restraints excluded: chain E residue 194 THR 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 225 LYS 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: 0.2980 chunk 90 optimal weight: 5.9990 chunk 104 optimal weight: 0.9990 chunk 272 optimal weight: 7.9990 chunk 226 optimal weight: 10.0000 chunk 49 optimal weight: 0.9990 chunk 111 optimal weight: 3.9990 chunk 100 optimal weight: 8.9990 chunk 327 optimal weight: 6.9990 chunk 62 optimal weight: 7.9990 chunk 345 optimal weight: 7.9990 overall best weight: 2.4588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 449 ASN B 449 ASN C 449 ASN D 449 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.083184 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.058358 restraints weight = 115371.964| |-----------------------------------------------------------------------------| r_work (start): 0.3138 rms_B_bonded: 3.03 r_work: 0.2996 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.2996 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8711 moved from start: 0.2929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 35814 Z= 0.150 Angle : 0.592 12.044 48569 Z= 0.297 Chirality : 0.042 0.272 5536 Planarity : 0.004 0.038 6066 Dihedral : 7.648 118.913 4916 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.28 % Allowed : 3.86 % Favored : 95.86 % Rotamer: Outliers : 1.30 % Allowed : 16.32 % Favored : 82.38 % 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: 0.64 (0.13), residues: 4304 helix: 0.89 (0.12), residues: 2032 sheet: 0.45 (0.23), residues: 512 loop : 0.03 (0.16), residues: 1760 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 107 TYR 0.013 0.001 TYR D 290 PHE 0.030 0.001 PHE H 180 TRP 0.016 0.001 TRP H 163 HIS 0.004 0.001 HIS A 344 Details of bonding type rmsd/Z covalent geometry : bond 0.00346 / 0.15 (35796) covalent geometry : angle 0.59174 / 0.30 (48537) SS BOND : bond 0.00115 / 0.06 ( 16) SS BOND : angle 0.96930 / 0.70 ( 32) hydrogen bonds : bond 0.03739 / 2.37 ( 1616) hydrogen bonds : angle 4.79346 / 3.41 ( 4428) Misc. bond : bond 0.00180 / 0.09 ( 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 228 residues out of total 3848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 178 time to evaluate : 1.412 Fit side-chains revert: symmetry clash REVERT: A 314 MET cc_start: 0.6772 (ttt) cc_final: 0.5674 (tmm) REVERT: B 314 MET cc_start: 0.6819 (ttt) cc_final: 0.5768 (tmm) REVERT: C 314 MET cc_start: 0.6714 (ttt) cc_final: 0.5621 (tmm) REVERT: D 314 MET cc_start: 0.6739 (ttt) cc_final: 0.5649 (tmm) REVERT: E 127 ARG cc_start: 0.7296 (mmp-170) cc_final: 0.6486 (tpt170) REVERT: E 230 LYS cc_start: 0.5879 (tmtt) cc_final: 0.5405 (tppp) REVERT: F 41 LYS cc_start: 0.8301 (tptp) cc_final: 0.7992 (tmmm) REVERT: F 225 LYS cc_start: 0.7378 (OUTLIER) cc_final: 0.7160 (mmmm) REVERT: F 230 LYS cc_start: 0.6425 (tmtt) cc_final: 0.5962 (ttmt) REVERT: G 127 ARG cc_start: 0.6975 (mmp-170) cc_final: 0.5926 (tpt170) REVERT: G 161 MET cc_start: 0.8925 (mmm) cc_final: 0.8667 (mmt) REVERT: G 162 ASN cc_start: 0.9351 (m-40) cc_final: 0.8996 (p0) REVERT: G 230 LYS cc_start: 0.6747 (tmtt) cc_final: 0.6257 (tppp) REVERT: H 107 ARG cc_start: 0.8356 (pmm150) cc_final: 0.7905 (pmm150) REVERT: H 230 LYS cc_start: 0.6108 (tmtt) cc_final: 0.5536 (tppp) outliers start: 50 outliers final: 41 residues processed: 222 average time/residue: 0.6388 time to fit residues: 174.8195 Evaluate side-chains 215 residues out of total 3848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 173 time to evaluate : 1.377 ------------------------------------------------------------------------------- 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 64 ILE Chi-restraints excluded: chain E residue 194 THR 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 225 LYS 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: 1.9990 chunk 102 optimal weight: 1.9990 chunk 216 optimal weight: 0.6980 chunk 24 optimal weight: 0.6980 chunk 264 optimal weight: 0.9980 chunk 299 optimal weight: 5.9990 chunk 190 optimal weight: 5.9990 chunk 150 optimal weight: 0.0670 chunk 317 optimal weight: 2.9990 chunk 286 optimal weight: 2.9990 chunk 257 optimal weight: 10.0000 overall best weight: 0.8920 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 216 GLN B 808 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.084178 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.059471 restraints weight = 114825.915| |-----------------------------------------------------------------------------| r_work (start): 0.3167 rms_B_bonded: 3.05 r_work: 0.3026 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3026 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8682 moved from start: 0.3037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 35814 Z= 0.109 Angle : 0.577 12.287 48569 Z= 0.289 Chirality : 0.042 0.218 5536 Planarity : 0.004 0.039 6066 Dihedral : 7.425 115.792 4916 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.28 % Allowed : 3.55 % Favored : 96.17 % Rotamer: Outliers : 1.09 % Allowed : 16.63 % Favored : 82.28 % 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: 0.67 (0.13), residues: 4304 helix: 0.92 (0.12), residues: 2060 sheet: 0.47 (0.23), residues: 516 loop : 0.02 (0.16), residues: 1728 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 107 TYR 0.012 0.001 TYR D 290 PHE 0.024 0.001 PHE B 159 TRP 0.015 0.001 TRP H 163 HIS 0.004 0.001 HIS A 344 Details of bonding type rmsd/Z covalent geometry : bond 0.00236 / 0.11 (35796) covalent geometry : angle 0.57640 / 0.29 (48537) SS BOND : bond 0.00164 / 0.09 ( 16) SS BOND : angle 0.94025 / 0.68 ( 32) hydrogen bonds : bond 0.03513 / 2.22 ( 1616) hydrogen bonds : angle 4.68207 / 3.33 ( 4428) Misc. bond : bond 0.00185 / 0.09 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10353.53 seconds wall clock time: 177 minutes 54.01 seconds (10674.01 seconds total)