Starting phenix.real_space_refine on Tue May 27 01:49:18 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8tqk_41506/05_2025/8tqk_41506.cif Found real_map, /net/cci-nas-00/data/ceres_data/8tqk_41506/05_2025/8tqk_41506.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8tqk_41506/05_2025/8tqk_41506.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8tqk_41506/05_2025/8tqk_41506.map" model { file = "/net/cci-nas-00/data/ceres_data/8tqk_41506/05_2025/8tqk_41506.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8tqk_41506/05_2025/8tqk_41506.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.049 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 76 5.16 5 C 9322 2.51 5 N 2473 2.21 5 O 2854 1.98 5 H 14504 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 27 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 29229 Number of models: 1 Model: "" Number of chains: 9 Chain: "D" Number of atoms: 1757 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 1757 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 2, 'TRANS': 113} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "E" Number of atoms: 1528 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 1528 Classifications: {'peptide': 105} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 99} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'PHE:plan': 1, 'ASP%NH3:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "F" Number of atoms: 1765 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 1765 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 2, 'TRANS': 113} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 1527 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 1527 Classifications: {'peptide': 105} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 99} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "H" Number of atoms: 1740 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 1740 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 2, 'TRANS': 113} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "L" Number of atoms: 1514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 1514 Classifications: {'peptide': 104} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 98} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "A" Number of atoms: 6440 Number of conformers: 1 Conformer: "" Number of residues, atoms: 417, 6440 Classifications: {'peptide': 417} Link IDs: {'PTRANS': 14, 'TRANS': 402} Chain breaks: 5 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'GLN:plan1': 2} Unresolved non-hydrogen planarities: 8 Chain: "B" Number of atoms: 6463 Number of conformers: 1 Conformer: "" Number of residues, atoms: 415, 6463 Classifications: {'peptide': 415} Link IDs: {'CIS': 1, 'PTRANS': 14, 'TRANS': 399} Chain breaks: 4 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLN:plan1': 2} Unresolved non-hydrogen planarities: 8 Chain: "C" Number of atoms: 6495 Number of conformers: 1 Conformer: "" Number of residues, atoms: 418, 6495 Classifications: {'peptide': 418} Link IDs: {'PTRANS': 14, 'TRANS': 403} Chain breaks: 5 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLN:plan1': 2} Unresolved non-hydrogen planarities: 8 Time building chain proxies: 14.10, per 1000 atoms: 0.48 Number of scatterers: 29229 At special positions: 0 Unit cell: (101.48, 103.2, 158.24, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 76 16.00 O 2854 8.00 N 2473 7.00 C 9322 6.00 H 14504 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=26, symmetry=0 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 92 " distance=2.79 Simple disulfide: pdb=" SG CYS E 23 " - pdb=" SG CYS E 88 " distance=2.69 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 92 " distance=2.26 Simple disulfide: pdb=" SG CYS G 23 " - pdb=" SG CYS G 88 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.04 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.80 Simple disulfide: pdb=" SG CYS A 63 " - pdb=" SG CYS A 192 " distance=2.03 Simple disulfide: pdb=" SG CYS A 162 " - pdb=" SG CYS A 168 " distance=2.03 Simple disulfide: pdb=" SG CYS A 213 " - pdb=" SG CYS A 230 " distance=2.53 Simple disulfide: pdb=" SG CYS A 331 " - pdb=" SG CYS A 340 " distance=2.03 Simple disulfide: pdb=" SG CYS A 355 " - pdb=" SG CYS A 363 " distance=2.03 Simple disulfide: pdb=" SG CYS A 387 " - pdb=" SG CYS A 392 " distance=2.03 Simple disulfide: pdb=" SG CYS A 394 " - pdb=" SG CYS A 417 " distance=2.03 Simple disulfide: pdb=" SG CYS B 63 " - pdb=" SG CYS B 192 " distance=2.04 Simple disulfide: pdb=" SG CYS B 213 " - pdb=" SG CYS B 230 " distance=2.05 Simple disulfide: pdb=" SG CYS B 331 " - pdb=" SG CYS B 340 " distance=2.03 Simple disulfide: pdb=" SG CYS B 355 " - pdb=" SG CYS B 363 " distance=2.03 Simple disulfide: pdb=" SG CYS B 387 " - pdb=" SG CYS B 392 " distance=2.03 Simple disulfide: pdb=" SG CYS B 394 " - pdb=" SG CYS B 417 " distance=2.04 Simple disulfide: pdb=" SG CYS C 63 " - pdb=" SG CYS C 192 " distance=2.03 Simple disulfide: pdb=" SG CYS C 162 " - pdb=" SG CYS C 168 " distance=2.03 Simple disulfide: pdb=" SG CYS C 213 " - pdb=" SG CYS C 230 " distance=2.05 Simple disulfide: pdb=" SG CYS C 331 " - pdb=" SG CYS C 340 " distance=2.03 Simple disulfide: pdb=" SG CYS C 355 " - pdb=" SG CYS C 363 " distance=2.03 Simple disulfide: pdb=" SG CYS C 387 " - pdb=" SG CYS C 392 " distance=2.03 Simple disulfide: pdb=" SG CYS C 394 " - pdb=" SG CYS C 417 " 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 6.94 Conformation dependent library (CDL) restraints added in 2.2 seconds 3732 Ramachandran restraints generated. 1866 Oldfield, 0 Emsley, 1866 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3548 Finding SS restraints... Secondary structure from input PDB file: 42 helices and 32 sheets defined 25.7% alpha, 22.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.51 Creating SS restraints... Processing helix chain 'D' and resid 28 through 32 removed outlier: 4.284A pdb=" N LYS D 31 " --> pdb=" O THR D 28 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N TYR D 32 " --> pdb=" O PHE D 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 28 through 32' Processing helix chain 'F' and resid 28 through 32 removed outlier: 3.784A pdb=" N LYS F 31 " --> pdb=" O THR F 28 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N TYR F 32 " --> pdb=" O PHE F 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 28 through 32' Processing helix chain 'F' and resid 61 through 64 Processing helix chain 'G' and resid 79 through 83 removed outlier: 4.116A pdb=" N PHE G 83 " --> pdb=" O PRO G 80 " (cutoff:3.500A) Processing helix chain 'H' and resid 61 through 64 Processing helix chain 'L' and resid 79 through 83 removed outlier: 4.150A pdb=" N PHE L 83 " --> pdb=" O PRO L 80 " (cutoff:3.500A) Processing helix chain 'A' and resid 23 through 28 removed outlier: 3.597A pdb=" N GLN A 26 " --> pdb=" O THR A 23 " (cutoff:3.500A) Processing helix chain 'A' and resid 67 through 89 removed outlier: 3.846A pdb=" N ARG A 77 " --> pdb=" O ARG A 73 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N LEU A 78 " --> pdb=" O LEU A 74 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ILE A 80 " --> pdb=" O ASP A 76 " (cutoff:3.500A) Proline residue: A 81 - end of helix removed outlier: 3.617A pdb=" N LYS A 87 " --> pdb=" O TYR A 83 " (cutoff:3.500A) Processing helix chain 'A' and resid 125 through 139 removed outlier: 4.000A pdb=" N ALA A 130 " --> pdb=" O ALA A 126 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ALA A 133 " --> pdb=" O THR A 129 " (cutoff:3.500A) Processing helix chain 'A' and resid 140 through 151 removed outlier: 3.886A pdb=" N ILE A 144 " --> pdb=" O ALA A 140 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LYS A 146 " --> pdb=" O SER A 142 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ALA A 150 " --> pdb=" O LYS A 146 " (cutoff:3.500A) Processing helix chain 'A' and resid 175 through 191 removed outlier: 4.784A pdb=" N VAL A 184 " --> pdb=" O ASN A 180 " (cutoff:3.500A) Proline residue: A 185 - end of helix removed outlier: 4.494A pdb=" N ALA A 188 " --> pdb=" O VAL A 184 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N ARG A 189 " --> pdb=" O PRO A 185 " (cutoff:3.500A) Processing helix chain 'A' and resid 191 through 210 Processing helix chain 'A' and resid 227 through 234 removed outlier: 4.260A pdb=" N ILE A 231 " --> pdb=" O LYS A 227 " (cutoff:3.500A) Processing helix chain 'A' and resid 238 through 243 removed outlier: 3.618A pdb=" N ILE A 242 " --> pdb=" O ASN A 238 " (cutoff:3.500A) Processing helix chain 'A' and resid 246 through 250 removed outlier: 4.277A pdb=" N ASP A 249 " --> pdb=" O SER A 246 " (cutoff:3.500A) Processing helix chain 'A' and resid 252 through 260 removed outlier: 3.774A pdb=" N LEU A 257 " --> pdb=" O ILE A 253 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N PHE A 258 " --> pdb=" O TYR A 254 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N THR A 259 " --> pdb=" O ASP A 255 " (cutoff:3.500A) Processing helix chain 'A' and resid 349 through 357 Processing helix chain 'A' and resid 358 through 363 removed outlier: 5.500A pdb=" N SER A 361 " --> pdb=" O GLY A 358 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N GLN A 362 " --> pdb=" O ASN A 359 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N CYS A 363 " --> pdb=" O ILE A 360 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 358 through 363' Processing helix chain 'A' and resid 452 through 471 removed outlier: 3.540A pdb=" N LYS A 471 " --> pdb=" O LEU A 467 " (cutoff:3.500A) Processing helix chain 'B' and resid 21 through 26 removed outlier: 3.605A pdb=" N GLN B 26 " --> pdb=" O ILE B 22 " (cutoff:3.500A) Processing helix chain 'B' and resid 64 through 88 removed outlier: 3.815A pdb=" N ARG B 77 " --> pdb=" O ARG B 73 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N LEU B 78 " --> pdb=" O LEU B 74 " (cutoff:3.500A) Proline residue: B 81 - end of helix Processing helix chain 'B' and resid 124 through 152 removed outlier: 3.751A pdb=" N THR B 129 " --> pdb=" O SER B 125 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N ALA B 130 " --> pdb=" O ALA B 126 " (cutoff:3.500A) removed outlier: 4.825A pdb=" N SER B 142 " --> pdb=" O LYS B 138 " (cutoff:3.500A) removed outlier: 5.448A pdb=" N ASP B 143 " --> pdb=" O GLN B 139 " (cutoff:3.500A) Processing helix chain 'B' and resid 176 through 210 removed outlier: 5.449A pdb=" N VAL B 184 " --> pdb=" O ASN B 180 " (cutoff:3.500A) Proline residue: B 185 - end of helix removed outlier: 4.338A pdb=" N ALA B 188 " --> pdb=" O VAL B 184 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N ARG B 189 " --> pdb=" O PRO B 185 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLY B 191 " --> pdb=" O ILE B 187 " (cutoff:3.500A) removed outlier: 8.325A pdb=" N CYS B 192 " --> pdb=" O ALA B 188 " (cutoff:3.500A) removed outlier: 8.909A pdb=" N GLU B 193 " --> pdb=" O ARG B 189 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N ALA B 194 " --> pdb=" O LEU B 190 " (cutoff:3.500A) Processing helix chain 'B' and resid 228 through 235 Processing helix chain 'B' and resid 238 through 243 removed outlier: 3.601A pdb=" N ILE B 242 " --> pdb=" O ASN B 238 " (cutoff:3.500A) Processing helix chain 'B' and resid 246 through 250 removed outlier: 4.083A pdb=" N ASP B 249 " --> pdb=" O SER B 246 " (cutoff:3.500A) Processing helix chain 'B' and resid 252 through 260 removed outlier: 3.502A pdb=" N LEU B 256 " --> pdb=" O ASP B 252 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N LEU B 257 " --> pdb=" O ILE B 253 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N PHE B 258 " --> pdb=" O TYR B 254 " (cutoff:3.500A) Processing helix chain 'B' and resid 349 through 358 Processing helix chain 'B' and resid 359 through 363 removed outlier: 3.605A pdb=" N GLN B 362 " --> pdb=" O ASN B 359 " (cutoff:3.500A) Processing helix chain 'B' and resid 452 through 472 removed outlier: 3.951A pdb=" N GLU B 472 " --> pdb=" O GLU B 468 " (cutoff:3.500A) Processing helix chain 'C' and resid 21 through 26 removed outlier: 3.711A pdb=" N GLN C 26 " --> pdb=" O ILE C 22 " (cutoff:3.500A) Processing helix chain 'C' and resid 64 through 89 removed outlier: 3.829A pdb=" N ARG C 77 " --> pdb=" O ARG C 73 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N LEU C 78 " --> pdb=" O LEU C 74 " (cutoff:3.500A) Proline residue: C 81 - end of helix removed outlier: 3.505A pdb=" N GLN C 89 " --> pdb=" O GLY C 85 " (cutoff:3.500A) Processing helix chain 'C' and resid 125 through 138 removed outlier: 4.045A pdb=" N ALA C 130 " --> pdb=" O ALA C 126 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N LYS C 138 " --> pdb=" O LEU C 134 " (cutoff:3.500A) Processing helix chain 'C' and resid 140 through 151 Processing helix chain 'C' and resid 175 through 183 Processing helix chain 'C' and resid 191 through 210 Processing helix chain 'C' and resid 227 through 236 removed outlier: 3.602A pdb=" N ILE C 231 " --> pdb=" O LYS C 227 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N ARG C 236 " --> pdb=" O ALA C 232 " (cutoff:3.500A) Processing helix chain 'C' and resid 246 through 251 removed outlier: 3.870A pdb=" N ASP C 249 " --> pdb=" O SER C 246 " (cutoff:3.500A) Processing helix chain 'C' and resid 252 through 262 removed outlier: 3.623A pdb=" N LEU C 257 " --> pdb=" O ILE C 253 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ILE C 262 " --> pdb=" O PHE C 258 " (cutoff:3.500A) Processing helix chain 'C' and resid 349 through 357 Processing helix chain 'C' and resid 359 through 363 removed outlier: 3.583A pdb=" N GLN C 362 " --> pdb=" O ASN C 359 " (cutoff:3.500A) Processing helix chain 'C' and resid 452 through 472 Processing sheet with id=AA1, first strand: chain 'D' and resid 19 through 23 removed outlier: 3.632A pdb=" N THR D 77 " --> pdb=" O ASP D 72 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ASP D 79 " --> pdb=" O SER D 70 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 58 through 59 removed outlier: 4.048A pdb=" N SER D 50 " --> pdb=" O PHE D 58 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N TRP D 36 " --> pdb=" O VAL D 48 " (cutoff:3.500A) removed outlier: 4.882A pdb=" N SER D 50 " --> pdb=" O MET D 34 " (cutoff:3.500A) removed outlier: 7.108A pdb=" N MET D 34 " --> pdb=" O SER D 50 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'E' and resid 4 through 7 removed outlier: 3.662A pdb=" N THR E 22 " --> pdb=" O SER E 7 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N VAL E 19 " --> pdb=" O ILE E 75 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N SER E 67 " --> pdb=" O GLU E 70 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N THR E 72 " --> pdb=" O SER E 65 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N SER E 65 " --> pdb=" O THR E 72 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'E' and resid 10 through 11 Processing sheet with id=AA5, first strand: chain 'E' and resid 45 through 48 removed outlier: 5.798A pdb=" N ILE E 46 " --> pdb=" O GLN E 37 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N GLN E 37 " --> pdb=" O ILE E 46 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N ILE E 48 " --> pdb=" O TRP E 35 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'F' and resid 3 through 4 Processing sheet with id=AA7, first strand: chain 'F' and resid 58 through 59 removed outlier: 5.108A pdb=" N TRP F 47 " --> pdb=" O ARG F 38 " (cutoff:3.500A) removed outlier: 5.536A pdb=" N ARG F 38 " --> pdb=" O TRP F 47 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N SER F 49 " --> pdb=" O TRP F 36 " (cutoff:3.500A) removed outlier: 4.649A pdb=" N VAL F 33 " --> pdb=" O MET F 95 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'G' and resid 4 through 5 removed outlier: 3.682A pdb=" N VAL G 19 " --> pdb=" O ILE G 75 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N CYS G 23 " --> pdb=" O PHE G 71 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N PHE G 71 " --> pdb=" O CYS G 23 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'G' and resid 45 through 48 removed outlier: 6.701A pdb=" N TRP G 35 " --> pdb=" O LEU G 47 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'H' and resid 3 through 7 removed outlier: 3.525A pdb=" N SER H 25 " --> pdb=" O GLN H 3 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'H' and resid 58 through 59 removed outlier: 5.161A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) removed outlier: 5.344A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N SER H 49 " --> pdb=" O TRP H 36 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N VAL H 33 " --> pdb=" O MET H 95 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ALA H 35 " --> pdb=" O ALA H 93 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'L' and resid 4 through 7 removed outlier: 3.521A pdb=" N THR L 22 " --> pdb=" O SER L 7 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N VAL L 19 " --> pdb=" O ILE L 75 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N GLU L 70 " --> pdb=" O SER L 67 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'L' and resid 34 through 38 removed outlier: 3.587A pdb=" N THR L 85 " --> pdb=" O HIS L 38 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N TYR L 86 " --> pdb=" O THR L 102 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N THR L 102 " --> pdb=" O TYR L 86 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 30 through 32 removed outlier: 3.608A pdb=" N ILE A 316 " --> pdb=" O TYR A 294 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N HIS A 315 " --> pdb=" O ALA A 326 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ALA A 326 " --> pdb=" O HIS A 315 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N GLY A 325 " --> pdb=" O PHE A 346 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 158 through 161 removed outlier: 8.767A pdb=" N VAL A 170 " --> pdb=" O THR A 46 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N TYR A 48 " --> pdb=" O VAL A 170 " (cutoff:3.500A) removed outlier: 7.893A pdb=" N ILE A 172 " --> pdb=" O TYR A 48 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N ILE A 50 " --> pdb=" O ILE A 172 " (cutoff:3.500A) removed outlier: 5.766A pdb=" N SER A 41 " --> pdb=" O THR A 286 " (cutoff:3.500A) removed outlier: 7.620A pdb=" N THR A 286 " --> pdb=" O SER A 41 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N ASN A 43 " --> pdb=" O LEU A 284 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N ASP A 268 " --> pdb=" O THR A 277 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N GLN A 279 " --> pdb=" O VAL A 266 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N VAL A 266 " --> pdb=" O GLN A 279 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 158 through 161 removed outlier: 8.767A pdb=" N VAL A 170 " --> pdb=" O THR A 46 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N TYR A 48 " --> pdb=" O VAL A 170 " (cutoff:3.500A) removed outlier: 7.893A pdb=" N ILE A 172 " --> pdb=" O TYR A 48 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N ILE A 50 " --> pdb=" O ILE A 172 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N SER A 41 " --> pdb=" O CYS A 340 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 123 through 124 removed outlier: 3.856A pdb=" N VAL C 383 " --> pdb=" O ILE C 412 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 301 through 302 Processing sheet with id=AC1, first strand: chain 'A' and resid 378 through 380 removed outlier: 5.279A pdb=" N VAL A 379 " --> pdb=" O GLY B 121 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 383 through 385 removed outlier: 3.645A pdb=" N VAL A 383 " --> pdb=" O ILE A 412 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ALA A 385 " --> pdb=" O LYS A 410 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'A' and resid 392 through 393 Processing sheet with id=AC4, first strand: chain 'B' and resid 31 through 32 removed outlier: 4.357A pdb=" N HIS B 315 " --> pdb=" O ALA B 326 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ALA B 326 " --> pdb=" O HIS B 315 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 285 through 287 removed outlier: 3.560A pdb=" N ILE B 40 " --> pdb=" O THR B 286 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N LYS B 39 " --> pdb=" O CYS B 340 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 158 through 159 removed outlier: 3.646A pdb=" N ALA B 171 " --> pdb=" O GLN B 159 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N VAL B 170 " --> pdb=" O TYR B 48 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N ASP B 268 " --> pdb=" O THR B 277 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N GLN B 279 " --> pdb=" O VAL B 266 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N VAL B 266 " --> pdb=" O GLN B 279 " (cutoff:3.500A) removed outlier: 8.809A pdb=" N ARG B 281 " --> pdb=" O VAL B 264 " (cutoff:3.500A) removed outlier: 8.378A pdb=" N VAL B 264 " --> pdb=" O ARG B 281 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 301 through 302 Processing sheet with id=AC8, first strand: chain 'B' and resid 410 through 411 removed outlier: 4.285A pdb=" N ASN B 380 " --> pdb=" O GLY C 121 " (cutoff:3.500A) removed outlier: 7.214A pdb=" N GLY C 121 " --> pdb=" O ASN B 380 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 420 through 421 Processing sheet with id=AD1, first strand: chain 'C' and resid 30 through 32 removed outlier: 3.648A pdb=" N ILE C 316 " --> pdb=" O TYR C 294 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N HIS C 315 " --> pdb=" O ALA C 326 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ALA C 326 " --> pdb=" O HIS C 315 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLY C 325 " --> pdb=" O PHE C 346 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 285 through 287 removed outlier: 3.590A pdb=" N ILE C 40 " --> pdb=" O THR C 286 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N GLY C 37 " --> pdb=" O TYR C 338 " (cutoff:3.500A) removed outlier: 8.167A pdb=" N CYS C 340 " --> pdb=" O GLY C 37 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N LYS C 39 " --> pdb=" O CYS C 340 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 158 through 161 removed outlier: 7.021A pdb=" N SER C 275 " --> pdb=" O VAL C 269 " (cutoff:3.500A) removed outlier: 4.625A pdb=" N VAL C 269 " --> pdb=" O SER C 275 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N THR C 277 " --> pdb=" O ILE C 267 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ARG C 265 " --> pdb=" O GLN C 279 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 301 through 303 Processing sheet with id=AD5, first strand: chain 'C' and resid 419 through 421 519 hydrogen bonds defined for protein. 1383 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: 9.71 Time building geometry restraints manager: 8.35 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.82 - 1.02: 14502 1.02 - 1.22: 19 1.22 - 1.43: 6105 1.43 - 1.63: 8746 1.63 - 1.83: 100 Bond restraints: 29472 Sorted by residual: bond pdb=" N PRO D 14 " pdb=" CD PRO D 14 " ideal model delta sigma weight residual 1.473 1.545 -0.072 1.40e-02 5.10e+03 2.68e+01 bond pdb=" CA ASN C 305 " pdb=" C ASN C 305 " ideal model delta sigma weight residual 1.524 1.590 -0.066 1.50e-02 4.44e+03 1.93e+01 bond pdb=" N LYS A 227 " pdb=" CA LYS A 227 " ideal model delta sigma weight residual 1.457 1.506 -0.049 1.29e-02 6.01e+03 1.44e+01 bond pdb=" CA GLN B 362 " pdb=" C GLN B 362 " ideal model delta sigma weight residual 1.523 1.574 -0.051 1.34e-02 5.57e+03 1.43e+01 bond pdb=" N THR B 429 " pdb=" CA THR B 429 " ideal model delta sigma weight residual 1.457 1.504 -0.047 1.29e-02 6.01e+03 1.30e+01 ... (remaining 29467 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.53: 52193 2.53 - 5.06: 870 5.06 - 7.58: 106 7.58 - 10.11: 31 10.11 - 12.64: 10 Bond angle restraints: 53210 Sorted by residual: angle pdb=" N GLY E 101 " pdb=" CA GLY E 101 " pdb=" C GLY E 101 " ideal model delta sigma weight residual 112.08 123.55 -11.47 1.01e+00 9.80e-01 1.29e+02 angle pdb=" C GLU B 432 " pdb=" N GLY B 433 " pdb=" CA GLY B 433 " ideal model delta sigma weight residual 120.10 127.58 -7.48 9.50e-01 1.11e+00 6.20e+01 angle pdb=" N CYS B 363 " pdb=" CA CYS B 363 " pdb=" C CYS B 363 " ideal model delta sigma weight residual 109.93 100.29 9.64 1.24e+00 6.50e-01 6.04e+01 angle pdb=" N ILE B 456 " pdb=" CA ILE B 456 " pdb=" C ILE B 456 " ideal model delta sigma weight residual 110.62 118.64 -8.02 1.14e+00 7.69e-01 4.95e+01 angle pdb=" CA THR A 237 " pdb=" C THR A 237 " pdb=" O THR A 237 " ideal model delta sigma weight residual 120.51 110.70 9.81 1.43e+00 4.89e-01 4.71e+01 ... (remaining 53205 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 12089 17.99 - 35.97: 1285 35.97 - 53.96: 437 53.96 - 71.95: 92 71.95 - 89.94: 25 Dihedral angle restraints: 13928 sinusoidal: 7640 harmonic: 6288 Sorted by residual: dihedral pdb=" CB CYS B 394 " pdb=" SG CYS B 394 " pdb=" SG CYS B 417 " pdb=" CB CYS B 417 " ideal model delta sinusoidal sigma weight residual 93.00 -178.93 -88.07 1 1.00e+01 1.00e-02 9.28e+01 dihedral pdb=" CB CYS C 394 " pdb=" SG CYS C 394 " pdb=" SG CYS C 417 " pdb=" CB CYS C 417 " ideal model delta sinusoidal sigma weight residual -86.00 -170.95 84.95 1 1.00e+01 1.00e-02 8.76e+01 dihedral pdb=" CB CYS F 22 " pdb=" SG CYS F 22 " pdb=" SG CYS F 92 " pdb=" CB CYS F 92 " ideal model delta sinusoidal sigma weight residual -86.00 -16.67 -69.33 1 1.00e+01 1.00e-02 6.21e+01 ... (remaining 13925 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.082: 2075 0.082 - 0.164: 269 0.164 - 0.246: 31 0.246 - 0.328: 11 0.328 - 0.410: 2 Chirality restraints: 2388 Sorted by residual: chirality pdb=" CA ASN C 305 " pdb=" N ASN C 305 " pdb=" C ASN C 305 " pdb=" CB ASN C 305 " both_signs ideal model delta sigma weight residual False 2.51 2.10 0.41 2.00e-01 2.50e+01 4.21e+00 chirality pdb=" CA GLU A 182 " pdb=" N GLU A 182 " pdb=" C GLU A 182 " pdb=" CB GLU A 182 " both_signs ideal model delta sigma weight residual False 2.51 2.11 0.40 2.00e-01 2.50e+01 4.07e+00 chirality pdb=" CA ASN A 180 " pdb=" N ASN A 180 " pdb=" C ASN A 180 " pdb=" CB ASN A 180 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.56e+00 ... (remaining 2385 not shown) Planarity restraints: 4384 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN G 92 " -0.237 2.00e-02 2.50e+03 3.88e-01 2.26e+03 pdb=" CG ASN G 92 " 0.020 2.00e-02 2.50e+03 pdb=" OD1 ASN G 92 " 0.230 2.00e-02 2.50e+03 pdb=" ND2 ASN G 92 " -0.000 2.00e-02 2.50e+03 pdb="HD21 ASN G 92 " -0.637 2.00e-02 2.50e+03 pdb="HD22 ASN G 92 " 0.624 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN C 176 " 0.196 2.00e-02 2.50e+03 2.19e-01 7.20e+02 pdb=" CD GLN C 176 " -0.014 2.00e-02 2.50e+03 pdb=" OE1 GLN C 176 " -0.188 2.00e-02 2.50e+03 pdb=" NE2 GLN C 176 " 0.000 2.00e-02 2.50e+03 pdb="HE21 GLN C 176 " -0.324 2.00e-02 2.50e+03 pdb="HE22 GLN C 176 " 0.330 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 238 " -0.123 2.00e-02 2.50e+03 1.32e-01 2.61e+02 pdb=" CG ASN C 238 " 0.009 2.00e-02 2.50e+03 pdb=" OD1 ASN C 238 " 0.118 2.00e-02 2.50e+03 pdb=" ND2 ASN C 238 " 0.000 2.00e-02 2.50e+03 pdb="HD21 ASN C 238 " -0.196 2.00e-02 2.50e+03 pdb="HD22 ASN C 238 " 0.192 2.00e-02 2.50e+03 ... (remaining 4381 not shown) Histogram of nonbonded interaction distances: 0.98 - 1.70: 31 1.70 - 2.43: 14739 2.43 - 3.15: 84203 3.15 - 3.88: 104174 3.88 - 4.60: 166230 Warning: very small nonbonded interaction distances. Nonbonded interactions: 369377 Sorted by model distance: nonbonded pdb="HD22 ASN G 92 " pdb=" HA3 GLY C 191 " model vdw 0.981 2.270 nonbonded pdb="HG22 ILE B 422 " pdb=" H ASN B 423 " model vdw 1.242 2.270 nonbonded pdb="HD21 ASN G 92 " pdb=" H CYS C 192 " model vdw 1.284 2.100 nonbonded pdb=" OE1 GLU A 58 " pdb=" H GLU A 58 " model vdw 1.407 2.450 nonbonded pdb="HG23 THR C 244 " pdb=" H THR C 245 " model vdw 1.432 2.270 ... (remaining 369372 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 161 or (resid 169 and (name N or name CA or nam \ e C or name O or name CB or name CG1 or name CG2 or name CD1 or name HA or name \ HB or name HG12 or name HG13 or name HG21 or name HG22 or name HG23 or name HD11 \ or name HD12 or name HD13)) or resid 170 through 472)) selection = (chain 'B' and (resid 19 through 71 or (resid 72 and (name N or name CA or name \ C or name O or name CB or name CG or name CD or name CE or name NZ or name H or \ name HA )) or resid 73 through 89 or (resid 90 and (name N or name CA or name C \ or name O or name CB or name CG or name CD or name CE or name NZ or name H or na \ me HA )) or resid 91 through 94 or resid 114 through 212 or (resid 213 and (name \ N or name CA or name C or name O or name CB or name SG or name H or name HA or \ name HB2 or name HB3)) or resid 214 through 229 or (resid 230 and (name N or nam \ e CA or name C or name O or name CB or name SG or name H or name HA or name HB2 \ or name HB3)) or resid 231 through 336 or (resid 337 and (name N or name CA or n \ ame C or name O or name CB or name H or name HA )) or resid 338 through 413 or ( \ resid 415 and (name N or name CA or name C or name O or name CB or name CG or na \ me CD or name CE or name NZ or name HA or name HB2 or name HB3 or name HG2 or na \ me HG3 or name HD2 or name HD3 or name HE2 or name HE3 or name HZ1 or name HZ2 o \ r name HZ3)) or resid 416 through 430 or (resid 431 and (name N or name CA or na \ me C or name O or name CB or name H or name HA )) or resid 432 through 472)) selection = (chain 'C' and (resid 19 through 71 or (resid 72 and (name N or name CA or name \ C or name O or name CB or name CG or name CD or name CE or name NZ or name H or \ name HA )) or resid 73 through 89 or (resid 90 and (name N or name CA or name C \ or name O or name CB or name CG or name CD or name CE or name NZ or name H or na \ me HA )) or resid 91 through 94 or resid 114 through 161 or (resid 169 and (name \ N or name CA or name C or name O or name CB or name CG1 or name CG2 or name CD1 \ or name HA or name HB or name HG12 or name HG13 or name HG21 or name HG22 or na \ me HG23 or name HD11 or name HD12 or name HD13)) or resid 170 through 336 or (re \ sid 337 and (name N or name CA or name C or name O or name CB or name H or name \ HA )) or resid 338 through 430 or (resid 431 and (name N or name CA or name C or \ name O or name CB or name H or name HA )) or resid 432 through 472)) } ncs_group { reference = (chain 'D' and (resid 2 through 82C or (resid 83 and (name N or name CA or name \ C or name O or name CB or name H or name HA )) or resid 84 through 109)) selection = (chain 'F' and (resid 2 through 5 or (resid 6 and (name N or name CA or name C o \ r name O or name CB or name H or name HA )) or resid 7 through 82C or (resid 83 \ and (name N or name CA or name C or name O or name CB or name H or name HA )) or \ resid 84 through 109)) selection = chain 'H' } ncs_group { reference = (chain 'E' and ((resid 2 and (name N or name CA or name C or name O or name CB o \ r name CG or name CD1 or name CD2 or name CE1 or name CE2 or name CZ or name HA \ or name HB2 or name HB3 or name HD1 or name HD2 or name HE1 or name HE2 or name \ HZ )) or resid 3 through 23 or (resid 24 and (name N or name CA or name C or nam \ e O or name CB or name H or name HA )) or resid 25 through 89 or (resid 90 and ( \ name N or name CA or name C or name O or name CB or name CG or name CD or name O \ E1 or name NE2 or name H or name HA )) or resid 91 through 105)) selection = (chain 'G' and ((resid 2 and (name N or name CA or name C or name O or name CB o \ r name CG or name CD1 or name CD2 or name CE1 or name CE2 or name CZ or name HA \ or name HB2 or name HB3 or name HD1 or name HD2 or name HE1 or name HE2 or name \ HZ )) or resid 3 through 23 or (resid 24 and (name N or name CA or name C or nam \ e O or name CB or name H or name HA )) or resid 25 through 105)) selection = (chain 'L' and (resid 2 through 82 or (resid 83 and (name N or name CA or name C \ or name O or name CB or name H or name HA )) or resid 84 through 89 or (resid 9 \ 0 and (name N or name CA or name C or name O or name CB or name CG or name CD or \ name OE1 or name NE2 or name H or name HA )) or resid 91 through 105)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.540 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.500 Extract box with map and model: 0.980 Check model and map are aligned: 0.180 Set scattering table: 0.230 Process input model: 56.710 Find NCS groups from input model: 1.070 Set up NCS constraints: 0.080 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:2.470 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 64.760 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7834 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 : 0.013 0.766 14995 Z= 0.731 Angle : 1.109 40.008 20336 Z= 0.691 Chirality : 0.057 0.410 2388 Planarity : 0.005 0.060 2562 Dihedral : 17.677 89.937 5438 Min Nonbonded Distance : 1.627 Molprobity Statistics. All-atom Clashscore : 12.45 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.31 % Favored : 94.53 % Rotamer: Outliers : 2.37 % Allowed : 33.50 % Favored : 64.13 % Cbeta Deviations : 0.17 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.26 (0.19), residues: 1866 helix: 0.88 (0.27), residues: 402 sheet: -0.44 (0.25), residues: 431 loop : -1.77 (0.17), residues: 1033 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP D 103 HIS 0.005 0.001 HIS B 414 PHE 0.021 0.002 PHE L 91 TYR 0.015 0.001 TYR G 94 ARG 0.003 0.000 ARG D 38 Details of bonding type rmsd hydrogen bonds : bond 0.25867 ( 515) hydrogen bonds : angle 8.44328 ( 1383) SS BOND : bond 0.26975 ( 26) SS BOND : angle 9.73547 ( 52) covalent geometry : bond 0.00505 (14968) covalent geometry : angle 0.99525 (20284) Misc. bond : bond 0.41125 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3732 Ramachandran restraints generated. 1866 Oldfield, 0 Emsley, 1866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3732 Ramachandran restraints generated. 1866 Oldfield, 0 Emsley, 1866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 108 is missing expected H atoms. Skipping. Residue THR 93 is missing expected H atoms. Skipping. Residue SER 95 is missing expected H atoms. Skipping. Residue VAL 104 is missing expected H atoms. Skipping. Residue LEU 108 is missing expected H atoms. Skipping. Residue THR 93 is missing expected H atoms. Skipping. Residue SER 95 is missing expected H atoms. Skipping. Residue VAL 104 is missing expected H atoms. Skipping. Residue LEU 108 is missing expected H atoms. Skipping. Residue THR 93 is missing expected H atoms. Skipping. Residue SER 95 is missing expected H atoms. Skipping. Residue VAL 104 is missing expected H atoms. Skipping. Residue LYS 72 is missing expected H atoms. Skipping. Residue LYS 90 is missing expected H atoms. Skipping. Residue SER 337 is missing expected H atoms. Skipping. Residue LYS 431 is missing expected H atoms. Skipping. Evaluate side-chains 247 residues out of total 1666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 208 time to evaluate : 2.290 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 75 ILE cc_start: 0.7988 (pt) cc_final: 0.7482 (tt) REVERT: L 105 GLU cc_start: 0.6446 (OUTLIER) cc_final: 0.5491 (tp30) outliers start: 39 outliers final: 10 residues processed: 246 average time/residue: 0.7374 time to fit residues: 246.5054 Evaluate side-chains 129 residues out of total 1666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 118 time to evaluate : 2.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 78 LEU Chi-restraints excluded: chain L residue 105 GLU Chi-restraints excluded: chain A residue 161 VAL Chi-restraints excluded: chain B residue 161 VAL Chi-restraints excluded: chain B residue 414 HIS Chi-restraints excluded: chain B residue 419 THR Chi-restraints excluded: chain B residue 443 ILE Chi-restraints excluded: chain C residue 209 GLU Chi-restraints excluded: chain C residue 239 ILE Chi-restraints excluded: chain C residue 361 SER Chi-restraints excluded: chain C residue 401 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 157 optimal weight: 0.8980 chunk 140 optimal weight: 0.9990 chunk 78 optimal weight: 1.9990 chunk 48 optimal weight: 6.9990 chunk 95 optimal weight: 4.9990 chunk 75 optimal weight: 0.0980 chunk 145 optimal weight: 4.9990 chunk 56 optimal weight: 2.9990 chunk 88 optimal weight: 0.8980 chunk 108 optimal weight: 10.0000 chunk 168 optimal weight: 4.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 89 GLN L 6 GLN A 407 GLN ** C 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 238 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.059485 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.047822 restraints weight = 198655.807| |-----------------------------------------------------------------------------| r_work (start): 0.3019 rms_B_bonded: 4.98 r_work: 0.2893 rms_B_bonded: 4.91 restraints_weight: 0.5000 r_work (final): 0.2893 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8459 moved from start: 0.2022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 14995 Z= 0.136 Angle : 0.637 6.502 20336 Z= 0.342 Chirality : 0.044 0.183 2388 Planarity : 0.004 0.056 2562 Dihedral : 5.476 59.766 2057 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.68 % Favored : 94.16 % Rotamer: Outliers : 1.88 % Allowed : 32.71 % Favored : 65.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.88 (0.19), residues: 1866 helix: 1.12 (0.26), residues: 418 sheet: -0.09 (0.25), residues: 447 loop : -1.61 (0.18), residues: 1001 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 308 HIS 0.003 0.001 HIS B 414 PHE 0.021 0.001 PHE G 98 TYR 0.016 0.001 TYR B 294 ARG 0.005 0.000 ARG F 71 Details of bonding type rmsd hydrogen bonds : bond 0.05835 ( 515) hydrogen bonds : angle 6.37970 ( 1383) SS BOND : bond 0.00437 ( 26) SS BOND : angle 1.56395 ( 52) covalent geometry : bond 0.00299 (14968) covalent geometry : angle 0.63263 (20284) Misc. bond : bond 0.00560 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3732 Ramachandran restraints generated. 1866 Oldfield, 0 Emsley, 1866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3732 Ramachandran restraints generated. 1866 Oldfield, 0 Emsley, 1866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 108 is missing expected H atoms. Skipping. Residue THR 93 is missing expected H atoms. Skipping. Residue SER 95 is missing expected H atoms. Skipping. Residue VAL 104 is missing expected H atoms. Skipping. Residue LEU 108 is missing expected H atoms. Skipping. Residue THR 93 is missing expected H atoms. Skipping. Residue SER 95 is missing expected H atoms. Skipping. Residue VAL 104 is missing expected H atoms. Skipping. Residue LEU 108 is missing expected H atoms. Skipping. Residue THR 93 is missing expected H atoms. Skipping. Residue SER 95 is missing expected H atoms. Skipping. Residue VAL 104 is missing expected H atoms. Skipping. Residue LYS 72 is missing expected H atoms. Skipping. Residue LYS 90 is missing expected H atoms. Skipping. Residue SER 337 is missing expected H atoms. Skipping. Residue LYS 431 is missing expected H atoms. Skipping. Evaluate side-chains 152 residues out of total 1666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 121 time to evaluate : 2.250 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 50 LYS cc_start: 0.8608 (mttp) cc_final: 0.8275 (ttmt) REVERT: F 46 GLU cc_start: 0.8736 (tt0) cc_final: 0.8299 (tt0) REVERT: H 72 ASP cc_start: 0.8910 (t0) cc_final: 0.8456 (t0) REVERT: L 54 LEU cc_start: 0.8975 (OUTLIER) cc_final: 0.8740 (tm) REVERT: L 78 LEU cc_start: 0.8291 (OUTLIER) cc_final: 0.7862 (mp) REVERT: L 105 GLU cc_start: 0.5670 (OUTLIER) cc_final: 0.4794 (tp30) REVERT: B 435 LEU cc_start: 0.8995 (OUTLIER) cc_final: 0.8613 (tp) REVERT: C 459 GLU cc_start: 0.9427 (mm-30) cc_final: 0.9146 (mt-10) REVERT: C 469 GLU cc_start: 0.9426 (tt0) cc_final: 0.9128 (tm-30) outliers start: 31 outliers final: 14 residues processed: 151 average time/residue: 0.7605 time to fit residues: 155.7022 Evaluate side-chains 126 residues out of total 1666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 108 time to evaluate : 2.739 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 6 GLU Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain L residue 54 LEU Chi-restraints excluded: chain L residue 78 LEU Chi-restraints excluded: chain L residue 105 GLU Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain A residue 141 LYS Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 465 SER Chi-restraints excluded: chain B residue 79 ILE Chi-restraints excluded: chain B residue 141 LYS Chi-restraints excluded: chain B residue 414 HIS Chi-restraints excluded: chain B residue 419 THR Chi-restraints excluded: chain B residue 435 LEU Chi-restraints excluded: chain C residue 209 GLU Chi-restraints excluded: chain C residue 230 CYS Chi-restraints excluded: chain C residue 302 ASN Chi-restraints excluded: chain C residue 401 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 10 optimal weight: 2.9990 chunk 3 optimal weight: 10.0000 chunk 7 optimal weight: 7.9990 chunk 63 optimal weight: 4.9990 chunk 134 optimal weight: 5.9990 chunk 39 optimal weight: 3.9990 chunk 109 optimal weight: 2.9990 chunk 43 optimal weight: 2.9990 chunk 162 optimal weight: 6.9990 chunk 148 optimal weight: 4.9990 chunk 15 optimal weight: 0.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 6 GLN C 205 GLN C 229 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.057980 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.046271 restraints weight = 202552.241| |-----------------------------------------------------------------------------| r_work (start): 0.2981 rms_B_bonded: 4.96 r_work: 0.2855 rms_B_bonded: 4.89 restraints_weight: 0.5000 r_work (final): 0.2855 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8508 moved from start: 0.2499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 14995 Z= 0.174 Angle : 0.595 9.249 20336 Z= 0.317 Chirality : 0.042 0.180 2388 Planarity : 0.003 0.049 2562 Dihedral : 5.304 59.440 2050 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.89 % Favored : 94.00 % Rotamer: Outliers : 2.07 % Allowed : 30.88 % Favored : 67.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.93 (0.19), residues: 1866 helix: 1.05 (0.26), residues: 423 sheet: -0.24 (0.25), residues: 454 loop : -1.59 (0.18), residues: 989 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 32 HIS 0.004 0.001 HIS B 414 PHE 0.012 0.001 PHE A 378 TYR 0.011 0.001 TYR C 235 ARG 0.004 0.000 ARG F 56 Details of bonding type rmsd hydrogen bonds : bond 0.04876 ( 515) hydrogen bonds : angle 5.88909 ( 1383) SS BOND : bond 0.00490 ( 26) SS BOND : angle 1.39609 ( 52) covalent geometry : bond 0.00372 (14968) covalent geometry : angle 0.59134 (20284) Misc. bond : bond 0.00035 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3732 Ramachandran restraints generated. 1866 Oldfield, 0 Emsley, 1866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3732 Ramachandran restraints generated. 1866 Oldfield, 0 Emsley, 1866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 108 is missing expected H atoms. Skipping. Residue THR 93 is missing expected H atoms. Skipping. Residue SER 95 is missing expected H atoms. Skipping. Residue VAL 104 is missing expected H atoms. Skipping. Residue LEU 108 is missing expected H atoms. Skipping. Residue THR 93 is missing expected H atoms. Skipping. Residue SER 95 is missing expected H atoms. Skipping. Residue VAL 104 is missing expected H atoms. Skipping. Residue LEU 108 is missing expected H atoms. Skipping. Residue THR 93 is missing expected H atoms. Skipping. Residue SER 95 is missing expected H atoms. Skipping. Residue VAL 104 is missing expected H atoms. Skipping. Residue LYS 72 is missing expected H atoms. Skipping. Residue LYS 90 is missing expected H atoms. Skipping. Residue SER 337 is missing expected H atoms. Skipping. Residue LYS 431 is missing expected H atoms. Skipping. Evaluate side-chains 138 residues out of total 1666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 104 time to evaluate : 2.656 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 34 MET cc_start: 0.7049 (mmm) cc_final: 0.6840 (mmm) REVERT: E 36 TYR cc_start: 0.6395 (m-80) cc_final: 0.6093 (m-80) REVERT: E 95 SER cc_start: 0.8907 (OUTLIER) cc_final: 0.8572 (m) REVERT: F 31 LYS cc_start: 0.9448 (tppt) cc_final: 0.9182 (ptmm) REVERT: F 46 GLU cc_start: 0.8777 (tt0) cc_final: 0.8298 (tt0) REVERT: H 43 LYS cc_start: 0.8717 (ttmm) cc_final: 0.8397 (mtmm) REVERT: H 61 ASP cc_start: 0.9176 (p0) cc_final: 0.8911 (p0) REVERT: H 97 LYS cc_start: 0.9086 (mtpp) cc_final: 0.8827 (mtmm) REVERT: L 54 LEU cc_start: 0.8980 (OUTLIER) cc_final: 0.8724 (tm) REVERT: L 78 LEU cc_start: 0.8305 (OUTLIER) cc_final: 0.7871 (mp) REVERT: L 105 GLU cc_start: 0.5802 (OUTLIER) cc_final: 0.4724 (tp30) REVERT: C 459 GLU cc_start: 0.9442 (mm-30) cc_final: 0.9190 (mt-10) REVERT: C 469 GLU cc_start: 0.9461 (tt0) cc_final: 0.9168 (tm-30) outliers start: 34 outliers final: 22 residues processed: 136 average time/residue: 0.7767 time to fit residues: 144.9951 Evaluate side-chains 126 residues out of total 1666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 100 time to evaluate : 2.007 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 18 LEU Chi-restraints excluded: chain D residue 82 MET Chi-restraints excluded: chain E residue 95 SER Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain L residue 54 LEU Chi-restraints excluded: chain L residue 78 LEU Chi-restraints excluded: chain L residue 105 GLU Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain A residue 161 VAL Chi-restraints excluded: chain A residue 236 ARG Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 342 SER Chi-restraints excluded: chain A residue 356 LEU Chi-restraints excluded: chain A residue 357 SER Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain A residue 465 SER Chi-restraints excluded: chain B residue 79 ILE Chi-restraints excluded: chain B residue 141 LYS Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 414 HIS Chi-restraints excluded: chain B residue 419 THR Chi-restraints excluded: chain B residue 434 THR Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain C residue 183 ILE Chi-restraints excluded: chain C residue 302 ASN Chi-restraints excluded: chain C residue 401 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 6 optimal weight: 0.0870 chunk 137 optimal weight: 0.9990 chunk 24 optimal weight: 5.9990 chunk 148 optimal weight: 4.9990 chunk 85 optimal weight: 4.9990 chunk 10 optimal weight: 10.0000 chunk 157 optimal weight: 0.7980 chunk 58 optimal weight: 10.0000 chunk 59 optimal weight: 8.9990 chunk 0 optimal weight: 9.9990 chunk 175 optimal weight: 4.9990 overall best weight: 2.3764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.057622 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.045945 restraints weight = 203489.566| |-----------------------------------------------------------------------------| r_work (start): 0.2973 rms_B_bonded: 4.96 r_work: 0.2848 rms_B_bonded: 4.91 restraints_weight: 0.5000 r_work (final): 0.2848 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8510 moved from start: 0.2813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 14995 Z= 0.139 Angle : 0.547 6.000 20336 Z= 0.292 Chirality : 0.042 0.177 2388 Planarity : 0.003 0.039 2562 Dihedral : 4.992 58.762 2047 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.41 % Favored : 94.48 % Rotamer: Outliers : 2.37 % Allowed : 29.30 % Favored : 68.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.72 (0.19), residues: 1866 helix: 1.34 (0.26), residues: 423 sheet: -0.07 (0.25), residues: 441 loop : -1.53 (0.18), residues: 1002 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 32 HIS 0.003 0.001 HIS B 414 PHE 0.010 0.001 PHE A 378 TYR 0.010 0.001 TYR C 235 ARG 0.004 0.000 ARG F 56 Details of bonding type rmsd hydrogen bonds : bond 0.03943 ( 515) hydrogen bonds : angle 5.49429 ( 1383) SS BOND : bond 0.00386 ( 26) SS BOND : angle 1.26808 ( 52) covalent geometry : bond 0.00302 (14968) covalent geometry : angle 0.54390 (20284) Misc. bond : bond 0.00008 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3732 Ramachandran restraints generated. 1866 Oldfield, 0 Emsley, 1866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3732 Ramachandran restraints generated. 1866 Oldfield, 0 Emsley, 1866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 108 is missing expected H atoms. Skipping. Residue THR 93 is missing expected H atoms. Skipping. Residue SER 95 is missing expected H atoms. Skipping. Residue VAL 104 is missing expected H atoms. Skipping. Residue LEU 108 is missing expected H atoms. Skipping. Residue THR 93 is missing expected H atoms. Skipping. Residue SER 95 is missing expected H atoms. Skipping. Residue VAL 104 is missing expected H atoms. Skipping. Residue LEU 108 is missing expected H atoms. Skipping. Residue THR 93 is missing expected H atoms. Skipping. Residue SER 95 is missing expected H atoms. Skipping. Residue VAL 104 is missing expected H atoms. Skipping. Residue LYS 72 is missing expected H atoms. Skipping. Residue LYS 90 is missing expected H atoms. Skipping. Residue SER 337 is missing expected H atoms. Skipping. Residue LYS 431 is missing expected H atoms. Skipping. Evaluate side-chains 142 residues out of total 1666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 103 time to evaluate : 2.200 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 34 MET cc_start: 0.7081 (mmm) cc_final: 0.6865 (mmm) REVERT: E 36 TYR cc_start: 0.6409 (m-80) cc_final: 0.6158 (m-80) REVERT: F 31 LYS cc_start: 0.9464 (tppt) cc_final: 0.9180 (ptmm) REVERT: F 46 GLU cc_start: 0.8781 (tt0) cc_final: 0.8302 (tt0) REVERT: H 61 ASP cc_start: 0.9217 (p0) cc_final: 0.8934 (p0) REVERT: L 54 LEU cc_start: 0.8960 (OUTLIER) cc_final: 0.8713 (tm) REVERT: L 78 LEU cc_start: 0.8309 (OUTLIER) cc_final: 0.7873 (mp) REVERT: L 105 GLU cc_start: 0.5909 (OUTLIER) cc_final: 0.4767 (tp30) REVERT: B 435 LEU cc_start: 0.9024 (OUTLIER) cc_final: 0.8619 (tp) REVERT: C 459 GLU cc_start: 0.9453 (mm-30) cc_final: 0.9190 (mt-10) REVERT: C 469 GLU cc_start: 0.9471 (tt0) cc_final: 0.9208 (tm-30) outliers start: 39 outliers final: 23 residues processed: 141 average time/residue: 0.7329 time to fit residues: 142.2130 Evaluate side-chains 125 residues out of total 1666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 98 time to evaluate : 2.139 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 18 LEU Chi-restraints excluded: chain E residue 93 THR Chi-restraints excluded: chain L residue 54 LEU Chi-restraints excluded: chain L residue 78 LEU Chi-restraints excluded: chain L residue 97 THR Chi-restraints excluded: chain L residue 105 GLU Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain A residue 161 VAL Chi-restraints excluded: chain A residue 236 ARG Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 342 SER Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain A residue 465 SER Chi-restraints excluded: chain B residue 79 ILE Chi-restraints excluded: chain B residue 141 LYS Chi-restraints excluded: chain B residue 414 HIS Chi-restraints excluded: chain B residue 419 THR Chi-restraints excluded: chain B residue 434 THR Chi-restraints excluded: chain B residue 435 LEU Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain C residue 209 GLU Chi-restraints excluded: chain C residue 230 CYS Chi-restraints excluded: chain C residue 261 SER Chi-restraints excluded: chain C residue 302 ASN Chi-restraints excluded: chain C residue 401 ILE Chi-restraints excluded: chain C residue 422 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 156 optimal weight: 7.9990 chunk 160 optimal weight: 5.9990 chunk 109 optimal weight: 5.9990 chunk 52 optimal weight: 9.9990 chunk 26 optimal weight: 6.9990 chunk 113 optimal weight: 4.9990 chunk 71 optimal weight: 5.9990 chunk 66 optimal weight: 4.9990 chunk 33 optimal weight: 7.9990 chunk 8 optimal weight: 0.0030 chunk 153 optimal weight: 8.9990 overall best weight: 4.3998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 90 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.055954 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2945 r_free = 0.2945 target = 0.044333 restraints weight = 208378.139| |-----------------------------------------------------------------------------| r_work (start): 0.2931 rms_B_bonded: 4.88 r_work: 0.2807 rms_B_bonded: 4.83 restraints_weight: 0.5000 r_work (final): 0.2807 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8568 moved from start: 0.3188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 14995 Z= 0.238 Angle : 0.589 5.827 20336 Z= 0.319 Chirality : 0.042 0.185 2388 Planarity : 0.003 0.036 2562 Dihedral : 5.120 59.952 2047 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.59 % Favored : 93.30 % Rotamer: Outliers : 2.43 % Allowed : 29.06 % Favored : 68.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.99 (0.19), residues: 1866 helix: 0.95 (0.25), residues: 419 sheet: -0.21 (0.25), residues: 442 loop : -1.62 (0.18), residues: 1005 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 32 HIS 0.005 0.001 HIS B 414 PHE 0.015 0.001 PHE A 378 TYR 0.020 0.001 TYR C 178 ARG 0.003 0.000 ARG F 71 Details of bonding type rmsd hydrogen bonds : bond 0.04048 ( 515) hydrogen bonds : angle 5.54890 ( 1383) SS BOND : bond 0.00597 ( 26) SS BOND : angle 1.41151 ( 52) covalent geometry : bond 0.00505 (14968) covalent geometry : angle 0.58569 (20284) Misc. bond : bond 0.00018 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3732 Ramachandran restraints generated. 1866 Oldfield, 0 Emsley, 1866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3732 Ramachandran restraints generated. 1866 Oldfield, 0 Emsley, 1866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 108 is missing expected H atoms. Skipping. Residue THR 93 is missing expected H atoms. Skipping. Residue SER 95 is missing expected H atoms. Skipping. Residue VAL 104 is missing expected H atoms. Skipping. Residue LEU 108 is missing expected H atoms. Skipping. Residue THR 93 is missing expected H atoms. Skipping. Residue SER 95 is missing expected H atoms. Skipping. Residue VAL 104 is missing expected H atoms. Skipping. Residue LEU 108 is missing expected H atoms. Skipping. Residue THR 93 is missing expected H atoms. Skipping. Residue SER 95 is missing expected H atoms. Skipping. Residue VAL 104 is missing expected H atoms. Skipping. Residue LYS 72 is missing expected H atoms. Skipping. Residue LYS 90 is missing expected H atoms. Skipping. Residue SER 337 is missing expected H atoms. Skipping. Residue LYS 431 is missing expected H atoms. Skipping. Evaluate side-chains 138 residues out of total 1666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 98 time to evaluate : 2.188 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 31 LYS cc_start: 0.9491 (tppt) cc_final: 0.9203 (ptmm) REVERT: F 46 GLU cc_start: 0.8802 (tt0) cc_final: 0.8367 (tt0) REVERT: H 61 ASP cc_start: 0.9260 (p0) cc_final: 0.8897 (p0) REVERT: H 97 LYS cc_start: 0.9181 (mtpp) cc_final: 0.8707 (mtmm) REVERT: L 54 LEU cc_start: 0.8959 (OUTLIER) cc_final: 0.8713 (tm) REVERT: L 105 GLU cc_start: 0.5860 (OUTLIER) cc_final: 0.4662 (tp30) REVERT: B 435 LEU cc_start: 0.9041 (OUTLIER) cc_final: 0.8618 (tp) REVERT: C 459 GLU cc_start: 0.9444 (mm-30) cc_final: 0.9222 (mt-10) REVERT: C 469 GLU cc_start: 0.9495 (tt0) cc_final: 0.9240 (tm-30) outliers start: 40 outliers final: 32 residues processed: 135 average time/residue: 0.7386 time to fit residues: 137.0578 Evaluate side-chains 129 residues out of total 1666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 94 time to evaluate : 2.165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 18 LEU Chi-restraints excluded: chain D residue 82 MET Chi-restraints excluded: chain E residue 90 GLN Chi-restraints excluded: chain E residue 93 THR Chi-restraints excluded: chain F residue 6 GLU Chi-restraints excluded: chain G residue 26 SER Chi-restraints excluded: chain G residue 78 LEU Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain L residue 54 LEU Chi-restraints excluded: chain L residue 97 THR Chi-restraints excluded: chain L residue 105 GLU Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain A residue 161 VAL Chi-restraints excluded: chain A residue 214 PHE Chi-restraints excluded: chain A residue 236 ARG Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 342 SER Chi-restraints excluded: chain A residue 357 SER Chi-restraints excluded: chain A residue 373 VAL Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain A residue 465 SER Chi-restraints excluded: chain B residue 79 ILE Chi-restraints excluded: chain B residue 141 LYS Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 414 HIS Chi-restraints excluded: chain B residue 419 THR Chi-restraints excluded: chain B residue 434 THR Chi-restraints excluded: chain B residue 435 LEU Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain C residue 162 CYS Chi-restraints excluded: chain C residue 261 SER Chi-restraints excluded: chain C residue 302 ASN Chi-restraints excluded: chain C residue 401 ILE Chi-restraints excluded: chain C residue 422 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 57 optimal weight: 2.9990 chunk 21 optimal weight: 9.9990 chunk 150 optimal weight: 3.9990 chunk 146 optimal weight: 1.9990 chunk 80 optimal weight: 0.9990 chunk 50 optimal weight: 10.0000 chunk 120 optimal weight: 5.9990 chunk 175 optimal weight: 4.9990 chunk 14 optimal weight: 10.0000 chunk 27 optimal weight: 6.9990 chunk 79 optimal weight: 2.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.056384 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2955 r_free = 0.2955 target = 0.044821 restraints weight = 207877.283| |-----------------------------------------------------------------------------| r_work (start): 0.2938 rms_B_bonded: 4.84 r_work: 0.2818 rms_B_bonded: 4.79 restraints_weight: 0.5000 r_work (final): 0.2818 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8554 moved from start: 0.3334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 14995 Z= 0.153 Angle : 0.547 5.649 20336 Z= 0.293 Chirality : 0.041 0.178 2388 Planarity : 0.003 0.037 2562 Dihedral : 4.923 58.994 2045 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.57 % Favored : 94.32 % Rotamer: Outliers : 2.37 % Allowed : 29.12 % Favored : 68.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.77 (0.19), residues: 1866 helix: 1.27 (0.26), residues: 423 sheet: -0.10 (0.25), residues: 437 loop : -1.54 (0.18), residues: 1006 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 32 HIS 0.004 0.001 HIS B 414 PHE 0.010 0.001 PHE A 378 TYR 0.011 0.001 TYR C 235 ARG 0.008 0.000 ARG B 189 Details of bonding type rmsd hydrogen bonds : bond 0.03713 ( 515) hydrogen bonds : angle 5.27394 ( 1383) SS BOND : bond 0.00342 ( 26) SS BOND : angle 1.19326 ( 52) covalent geometry : bond 0.00335 (14968) covalent geometry : angle 0.54428 (20284) Misc. bond : bond 0.00020 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3732 Ramachandran restraints generated. 1866 Oldfield, 0 Emsley, 1866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3732 Ramachandran restraints generated. 1866 Oldfield, 0 Emsley, 1866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 108 is missing expected H atoms. Skipping. Residue THR 93 is missing expected H atoms. Skipping. Residue SER 95 is missing expected H atoms. Skipping. Residue VAL 104 is missing expected H atoms. Skipping. Residue LEU 108 is missing expected H atoms. Skipping. Residue THR 93 is missing expected H atoms. Skipping. Residue SER 95 is missing expected H atoms. Skipping. Residue VAL 104 is missing expected H atoms. Skipping. Residue LEU 108 is missing expected H atoms. Skipping. Residue THR 93 is missing expected H atoms. Skipping. Residue SER 95 is missing expected H atoms. Skipping. Residue VAL 104 is missing expected H atoms. Skipping. Residue LYS 72 is missing expected H atoms. Skipping. Residue LYS 90 is missing expected H atoms. Skipping. Residue SER 337 is missing expected H atoms. Skipping. Residue LYS 431 is missing expected H atoms. Skipping. Evaluate side-chains 132 residues out of total 1666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 93 time to evaluate : 2.286 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 31 LYS cc_start: 0.9488 (tppt) cc_final: 0.9206 (ptmm) REVERT: F 46 GLU cc_start: 0.8791 (tt0) cc_final: 0.8326 (tt0) REVERT: H 61 ASP cc_start: 0.9244 (p0) cc_final: 0.8867 (p0) REVERT: H 97 LYS cc_start: 0.9178 (mtpp) cc_final: 0.8707 (mtmm) REVERT: L 54 LEU cc_start: 0.8959 (OUTLIER) cc_final: 0.8745 (tm) REVERT: L 105 GLU cc_start: 0.5765 (OUTLIER) cc_final: 0.4471 (tp30) REVERT: B 435 LEU cc_start: 0.9027 (OUTLIER) cc_final: 0.8589 (tp) REVERT: C 469 GLU cc_start: 0.9503 (tt0) cc_final: 0.9248 (tm-30) outliers start: 39 outliers final: 34 residues processed: 128 average time/residue: 0.7547 time to fit residues: 132.9215 Evaluate side-chains 127 residues out of total 1666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 90 time to evaluate : 2.100 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 18 LEU Chi-restraints excluded: chain D residue 82 MET Chi-restraints excluded: chain E residue 95 SER Chi-restraints excluded: chain F residue 6 GLU Chi-restraints excluded: chain F residue 85 GLU Chi-restraints excluded: chain G residue 78 LEU Chi-restraints excluded: chain G residue 89 GLN Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain L residue 54 LEU Chi-restraints excluded: chain L residue 97 THR Chi-restraints excluded: chain L residue 105 GLU Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain A residue 214 PHE Chi-restraints excluded: chain A residue 236 ARG Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 342 SER Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain A residue 465 SER Chi-restraints excluded: chain B residue 79 ILE Chi-restraints excluded: chain B residue 141 LYS Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 407 GLN Chi-restraints excluded: chain B residue 414 HIS Chi-restraints excluded: chain B residue 419 THR Chi-restraints excluded: chain B residue 434 THR Chi-restraints excluded: chain B residue 435 LEU Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain C residue 118 ILE Chi-restraints excluded: chain C residue 162 CYS Chi-restraints excluded: chain C residue 209 GLU Chi-restraints excluded: chain C residue 245 THR Chi-restraints excluded: chain C residue 261 SER Chi-restraints excluded: chain C residue 302 ASN Chi-restraints excluded: chain C residue 401 ILE Chi-restraints excluded: chain C residue 422 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 88 optimal weight: 4.9990 chunk 63 optimal weight: 3.9990 chunk 167 optimal weight: 5.9990 chunk 150 optimal weight: 3.9990 chunk 70 optimal weight: 5.9990 chunk 164 optimal weight: 3.9990 chunk 97 optimal weight: 7.9990 chunk 160 optimal weight: 4.9990 chunk 87 optimal weight: 3.9990 chunk 156 optimal weight: 0.9990 chunk 31 optimal weight: 8.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 362 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.055769 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2938 r_free = 0.2938 target = 0.044233 restraints weight = 208605.360| |-----------------------------------------------------------------------------| r_work (start): 0.2923 rms_B_bonded: 4.82 r_work: 0.2800 rms_B_bonded: 4.79 restraints_weight: 0.5000 r_work (final): 0.2800 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8563 moved from start: 0.3645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 14995 Z= 0.198 Angle : 0.561 6.752 20336 Z= 0.301 Chirality : 0.041 0.180 2388 Planarity : 0.003 0.038 2562 Dihedral : 4.928 59.497 2045 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.65 % Favored : 93.19 % Rotamer: Outliers : 2.86 % Allowed : 28.39 % Favored : 68.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.85 (0.19), residues: 1866 helix: 1.20 (0.26), residues: 424 sheet: -0.18 (0.25), residues: 436 loop : -1.57 (0.19), residues: 1006 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 32 HIS 0.005 0.001 HIS B 414 PHE 0.013 0.001 PHE A 378 TYR 0.012 0.001 TYR C 235 ARG 0.011 0.000 ARG B 189 Details of bonding type rmsd hydrogen bonds : bond 0.03625 ( 515) hydrogen bonds : angle 5.20947 ( 1383) SS BOND : bond 0.00419 ( 26) SS BOND : angle 1.19707 ( 52) covalent geometry : bond 0.00422 (14968) covalent geometry : angle 0.55831 (20284) Misc. bond : bond 0.00010 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3732 Ramachandran restraints generated. 1866 Oldfield, 0 Emsley, 1866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3732 Ramachandran restraints generated. 1866 Oldfield, 0 Emsley, 1866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 108 is missing expected H atoms. Skipping. Residue THR 93 is missing expected H atoms. Skipping. Residue SER 95 is missing expected H atoms. Skipping. Residue VAL 104 is missing expected H atoms. Skipping. Residue LEU 108 is missing expected H atoms. Skipping. Residue THR 93 is missing expected H atoms. Skipping. Residue SER 95 is missing expected H atoms. Skipping. Residue VAL 104 is missing expected H atoms. Skipping. Residue LEU 108 is missing expected H atoms. Skipping. Residue THR 93 is missing expected H atoms. Skipping. Residue SER 95 is missing expected H atoms. Skipping. Residue VAL 104 is missing expected H atoms. Skipping. Residue LYS 72 is missing expected H atoms. Skipping. Residue LYS 90 is missing expected H atoms. Skipping. Residue SER 337 is missing expected H atoms. Skipping. Residue LYS 431 is missing expected H atoms. Skipping. Evaluate side-chains 138 residues out of total 1666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 91 time to evaluate : 2.500 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 50 LYS cc_start: 0.8642 (mttp) cc_final: 0.8258 (ttmt) REVERT: F 46 GLU cc_start: 0.8811 (tt0) cc_final: 0.8346 (tt0) REVERT: H 97 LYS cc_start: 0.9187 (mtpp) cc_final: 0.8681 (mtmm) REVERT: L 54 LEU cc_start: 0.8975 (OUTLIER) cc_final: 0.8773 (tm) REVERT: L 105 GLU cc_start: 0.5798 (OUTLIER) cc_final: 0.4508 (tp30) REVERT: B 435 LEU cc_start: 0.9052 (OUTLIER) cc_final: 0.8636 (tp) REVERT: C 469 GLU cc_start: 0.9522 (tt0) cc_final: 0.9212 (tm-30) outliers start: 47 outliers final: 38 residues processed: 133 average time/residue: 0.7572 time to fit residues: 141.0044 Evaluate side-chains 127 residues out of total 1666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 86 time to evaluate : 2.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 18 LEU Chi-restraints excluded: chain D residue 82 MET Chi-restraints excluded: chain E residue 95 SER Chi-restraints excluded: chain F residue 6 GLU Chi-restraints excluded: chain F residue 85 GLU Chi-restraints excluded: chain G residue 17 ASP Chi-restraints excluded: chain G residue 26 SER Chi-restraints excluded: chain G residue 78 LEU Chi-restraints excluded: chain G residue 89 GLN Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain L residue 54 LEU Chi-restraints excluded: chain L residue 97 THR Chi-restraints excluded: chain L residue 105 GLU Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain A residue 161 VAL Chi-restraints excluded: chain A residue 214 PHE Chi-restraints excluded: chain A residue 236 ARG Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 342 SER Chi-restraints excluded: chain A residue 357 SER Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain A residue 465 SER Chi-restraints excluded: chain B residue 79 ILE Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 407 GLN Chi-restraints excluded: chain B residue 414 HIS Chi-restraints excluded: chain B residue 419 THR Chi-restraints excluded: chain B residue 434 THR Chi-restraints excluded: chain B residue 435 LEU Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain C residue 118 ILE Chi-restraints excluded: chain C residue 162 CYS Chi-restraints excluded: chain C residue 209 GLU Chi-restraints excluded: chain C residue 245 THR Chi-restraints excluded: chain C residue 261 SER Chi-restraints excluded: chain C residue 302 ASN Chi-restraints excluded: chain C residue 352 MET Chi-restraints excluded: chain C residue 401 ILE Chi-restraints excluded: chain C residue 422 ILE Chi-restraints excluded: chain C residue 432 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 166 optimal weight: 2.9990 chunk 185 optimal weight: 3.9990 chunk 10 optimal weight: 3.9990 chunk 58 optimal weight: 9.9990 chunk 47 optimal weight: 3.9990 chunk 63 optimal weight: 4.9990 chunk 14 optimal weight: 20.0000 chunk 129 optimal weight: 0.8980 chunk 74 optimal weight: 5.9990 chunk 60 optimal weight: 8.9990 chunk 155 optimal weight: 3.9990 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 206 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.055577 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2935 r_free = 0.2935 target = 0.044061 restraints weight = 208555.485| |-----------------------------------------------------------------------------| r_work (start): 0.2915 rms_B_bonded: 4.83 r_work: 0.2793 rms_B_bonded: 4.79 restraints_weight: 0.5000 r_work (final): 0.2793 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8555 moved from start: 0.3782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 14995 Z= 0.173 Angle : 0.545 5.389 20336 Z= 0.292 Chirality : 0.041 0.175 2388 Planarity : 0.003 0.036 2562 Dihedral : 4.893 58.390 2045 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.27 % Favored : 93.62 % Rotamer: Outliers : 2.55 % Allowed : 28.69 % Favored : 68.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.76 (0.19), residues: 1866 helix: 1.30 (0.26), residues: 425 sheet: -0.19 (0.25), residues: 445 loop : -1.50 (0.19), residues: 996 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 32 HIS 0.004 0.001 HIS B 414 PHE 0.011 0.001 PHE A 378 TYR 0.011 0.001 TYR C 235 ARG 0.006 0.000 ARG B 189 Details of bonding type rmsd hydrogen bonds : bond 0.03507 ( 515) hydrogen bonds : angle 5.11854 ( 1383) SS BOND : bond 0.00385 ( 26) SS BOND : angle 1.19884 ( 52) covalent geometry : bond 0.00373 (14968) covalent geometry : angle 0.54281 (20284) Misc. bond : bond 0.00009 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3732 Ramachandran restraints generated. 1866 Oldfield, 0 Emsley, 1866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3732 Ramachandran restraints generated. 1866 Oldfield, 0 Emsley, 1866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 108 is missing expected H atoms. Skipping. Residue THR 93 is missing expected H atoms. Skipping. Residue SER 95 is missing expected H atoms. Skipping. Residue VAL 104 is missing expected H atoms. Skipping. Residue LEU 108 is missing expected H atoms. Skipping. Residue THR 93 is missing expected H atoms. Skipping. Residue SER 95 is missing expected H atoms. Skipping. Residue VAL 104 is missing expected H atoms. Skipping. Residue LEU 108 is missing expected H atoms. Skipping. Residue THR 93 is missing expected H atoms. Skipping. Residue SER 95 is missing expected H atoms. Skipping. Residue VAL 104 is missing expected H atoms. Skipping. Residue LYS 72 is missing expected H atoms. Skipping. Residue LYS 90 is missing expected H atoms. Skipping. Residue SER 337 is missing expected H atoms. Skipping. Residue LYS 431 is missing expected H atoms. Skipping. Evaluate side-chains 131 residues out of total 1666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 89 time to evaluate : 2.167 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 50 LYS cc_start: 0.8690 (mttp) cc_final: 0.8278 (ttmt) REVERT: F 31 LYS cc_start: 0.9430 (tppt) cc_final: 0.9186 (ptmm) REVERT: F 46 GLU cc_start: 0.8814 (tt0) cc_final: 0.8329 (tt0) REVERT: H 97 LYS cc_start: 0.9184 (mtpp) cc_final: 0.8682 (mtmm) REVERT: L 105 GLU cc_start: 0.5741 (OUTLIER) cc_final: 0.4381 (tp30) REVERT: B 435 LEU cc_start: 0.9036 (OUTLIER) cc_final: 0.8606 (tp) REVERT: C 469 GLU cc_start: 0.9529 (tt0) cc_final: 0.9220 (tm-30) outliers start: 42 outliers final: 37 residues processed: 126 average time/residue: 0.7224 time to fit residues: 126.0117 Evaluate side-chains 124 residues out of total 1666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 85 time to evaluate : 2.170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 18 LEU Chi-restraints excluded: chain D residue 82 MET Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 95 SER Chi-restraints excluded: chain F residue 6 GLU Chi-restraints excluded: chain F residue 85 GLU Chi-restraints excluded: chain G residue 26 SER Chi-restraints excluded: chain G residue 78 LEU Chi-restraints excluded: chain G residue 89 GLN Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain L residue 77 SER Chi-restraints excluded: chain L residue 97 THR Chi-restraints excluded: chain L residue 105 GLU Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain A residue 214 PHE Chi-restraints excluded: chain A residue 236 ARG Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 342 SER Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain A residue 465 SER Chi-restraints excluded: chain B residue 79 ILE Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 407 GLN Chi-restraints excluded: chain B residue 414 HIS Chi-restraints excluded: chain B residue 419 THR Chi-restraints excluded: chain B residue 434 THR Chi-restraints excluded: chain B residue 435 LEU Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain C residue 118 ILE Chi-restraints excluded: chain C residue 162 CYS Chi-restraints excluded: chain C residue 209 GLU Chi-restraints excluded: chain C residue 245 THR Chi-restraints excluded: chain C residue 261 SER Chi-restraints excluded: chain C residue 302 ASN Chi-restraints excluded: chain C residue 352 MET Chi-restraints excluded: chain C residue 401 ILE Chi-restraints excluded: chain C residue 422 ILE Chi-restraints excluded: chain C residue 432 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 4 optimal weight: 7.9990 chunk 82 optimal weight: 3.9990 chunk 24 optimal weight: 4.9990 chunk 20 optimal weight: 9.9990 chunk 1 optimal weight: 0.3980 chunk 65 optimal weight: 4.9990 chunk 174 optimal weight: 0.8980 chunk 120 optimal weight: 4.9990 chunk 56 optimal weight: 6.9990 chunk 152 optimal weight: 5.9990 chunk 32 optimal weight: 9.9990 overall best weight: 3.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.055498 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2932 r_free = 0.2932 target = 0.044032 restraints weight = 208731.363| |-----------------------------------------------------------------------------| r_work (start): 0.2911 rms_B_bonded: 4.79 r_work: 0.2792 rms_B_bonded: 4.75 restraints_weight: 0.5000 r_work (final): 0.2792 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8564 moved from start: 0.3917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 14995 Z= 0.172 Angle : 0.548 6.598 20336 Z= 0.292 Chirality : 0.041 0.175 2388 Planarity : 0.003 0.036 2562 Dihedral : 4.860 57.638 2045 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.59 % Favored : 93.30 % Rotamer: Outliers : 2.55 % Allowed : 28.69 % Favored : 68.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.69 (0.20), residues: 1866 helix: 1.41 (0.26), residues: 420 sheet: -0.18 (0.25), residues: 445 loop : -1.45 (0.19), residues: 1001 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 32 HIS 0.004 0.001 HIS B 414 PHE 0.011 0.001 PHE A 378 TYR 0.012 0.001 TYR C 235 ARG 0.006 0.000 ARG B 189 Details of bonding type rmsd hydrogen bonds : bond 0.03431 ( 515) hydrogen bonds : angle 5.06856 ( 1383) SS BOND : bond 0.00388 ( 26) SS BOND : angle 1.13244 ( 52) covalent geometry : bond 0.00371 (14968) covalent geometry : angle 0.54598 (20284) Misc. bond : bond 0.00009 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3732 Ramachandran restraints generated. 1866 Oldfield, 0 Emsley, 1866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3732 Ramachandran restraints generated. 1866 Oldfield, 0 Emsley, 1866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 108 is missing expected H atoms. Skipping. Residue THR 93 is missing expected H atoms. Skipping. Residue SER 95 is missing expected H atoms. Skipping. Residue VAL 104 is missing expected H atoms. Skipping. Residue LEU 108 is missing expected H atoms. Skipping. Residue THR 93 is missing expected H atoms. Skipping. Residue SER 95 is missing expected H atoms. Skipping. Residue VAL 104 is missing expected H atoms. Skipping. Residue LEU 108 is missing expected H atoms. Skipping. Residue THR 93 is missing expected H atoms. Skipping. Residue SER 95 is missing expected H atoms. Skipping. Residue VAL 104 is missing expected H atoms. Skipping. Residue LYS 72 is missing expected H atoms. Skipping. Residue LYS 90 is missing expected H atoms. Skipping. Residue SER 337 is missing expected H atoms. Skipping. Residue LYS 431 is missing expected H atoms. Skipping. Evaluate side-chains 127 residues out of total 1666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 85 time to evaluate : 2.516 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 50 LYS cc_start: 0.8677 (mttp) cc_final: 0.8230 (ttmt) REVERT: F 31 LYS cc_start: 0.9433 (tppt) cc_final: 0.9194 (ptmm) REVERT: F 46 GLU cc_start: 0.8808 (tt0) cc_final: 0.8350 (tt0) REVERT: L 105 GLU cc_start: 0.5713 (OUTLIER) cc_final: 0.4325 (tp30) REVERT: C 469 GLU cc_start: 0.9531 (tt0) cc_final: 0.9227 (tm-30) outliers start: 42 outliers final: 38 residues processed: 122 average time/residue: 0.7378 time to fit residues: 125.4327 Evaluate side-chains 123 residues out of total 1666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 84 time to evaluate : 2.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 18 LEU Chi-restraints excluded: chain D residue 82 MET Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 93 THR Chi-restraints excluded: chain E residue 95 SER Chi-restraints excluded: chain F residue 6 GLU Chi-restraints excluded: chain F residue 85 GLU Chi-restraints excluded: chain G residue 26 SER Chi-restraints excluded: chain G residue 78 LEU Chi-restraints excluded: chain G residue 89 GLN Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain L residue 77 SER Chi-restraints excluded: chain L residue 97 THR Chi-restraints excluded: chain L residue 105 GLU Chi-restraints excluded: chain A residue 214 PHE Chi-restraints excluded: chain A residue 236 ARG Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 342 SER Chi-restraints excluded: chain A residue 357 SER Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain A residue 465 SER Chi-restraints excluded: chain B residue 79 ILE Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 407 GLN Chi-restraints excluded: chain B residue 414 HIS Chi-restraints excluded: chain B residue 434 THR Chi-restraints excluded: chain B residue 435 LEU Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain C residue 118 ILE Chi-restraints excluded: chain C residue 162 CYS Chi-restraints excluded: chain C residue 209 GLU Chi-restraints excluded: chain C residue 245 THR Chi-restraints excluded: chain C residue 261 SER Chi-restraints excluded: chain C residue 302 ASN Chi-restraints excluded: chain C residue 352 MET Chi-restraints excluded: chain C residue 401 ILE Chi-restraints excluded: chain C residue 422 ILE Chi-restraints excluded: chain C residue 432 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 8 optimal weight: 9.9990 chunk 43 optimal weight: 0.8980 chunk 80 optimal weight: 3.9990 chunk 67 optimal weight: 8.9990 chunk 166 optimal weight: 3.9990 chunk 133 optimal weight: 0.9980 chunk 61 optimal weight: 0.9980 chunk 120 optimal weight: 6.9990 chunk 148 optimal weight: 0.7980 chunk 139 optimal weight: 0.7980 chunk 54 optimal weight: 10.0000 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.056183 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2959 r_free = 0.2959 target = 0.044790 restraints weight = 203980.413| |-----------------------------------------------------------------------------| r_work (start): 0.2944 rms_B_bonded: 4.79 r_work: 0.2825 rms_B_bonded: 4.73 restraints_weight: 0.5000 r_work (final): 0.2825 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8530 moved from start: 0.3955 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 14995 Z= 0.097 Angle : 0.521 6.829 20336 Z= 0.274 Chirality : 0.042 0.171 2388 Planarity : 0.003 0.036 2562 Dihedral : 4.668 55.528 2044 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.20 % Favored : 94.69 % Rotamer: Outliers : 2.07 % Allowed : 29.12 % Favored : 68.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.40 (0.20), residues: 1866 helix: 1.77 (0.27), residues: 420 sheet: -0.09 (0.25), residues: 445 loop : -1.28 (0.19), residues: 1001 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 308 HIS 0.002 0.000 HIS B 414 PHE 0.007 0.001 PHE C 378 TYR 0.010 0.001 TYR C 235 ARG 0.006 0.000 ARG B 189 Details of bonding type rmsd hydrogen bonds : bond 0.03151 ( 515) hydrogen bonds : angle 4.81961 ( 1383) SS BOND : bond 0.00308 ( 26) SS BOND : angle 0.94037 ( 52) covalent geometry : bond 0.00222 (14968) covalent geometry : angle 0.51988 (20284) Misc. bond : bond 0.00002 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3732 Ramachandran restraints generated. 1866 Oldfield, 0 Emsley, 1866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3732 Ramachandran restraints generated. 1866 Oldfield, 0 Emsley, 1866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 108 is missing expected H atoms. Skipping. Residue THR 93 is missing expected H atoms. Skipping. Residue SER 95 is missing expected H atoms. Skipping. Residue VAL 104 is missing expected H atoms. Skipping. Residue LEU 108 is missing expected H atoms. Skipping. Residue THR 93 is missing expected H atoms. Skipping. Residue SER 95 is missing expected H atoms. Skipping. Residue VAL 104 is missing expected H atoms. Skipping. Residue LEU 108 is missing expected H atoms. Skipping. Residue THR 93 is missing expected H atoms. Skipping. Residue SER 95 is missing expected H atoms. Skipping. Residue VAL 104 is missing expected H atoms. Skipping. Residue LYS 72 is missing expected H atoms. Skipping. Residue LYS 90 is missing expected H atoms. Skipping. Residue SER 337 is missing expected H atoms. Skipping. Residue LYS 431 is missing expected H atoms. Skipping. Evaluate side-chains 121 residues out of total 1666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 87 time to evaluate : 2.518 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 50 LYS cc_start: 0.8635 (mttp) cc_final: 0.8189 (ttmt) REVERT: E 95 SER cc_start: 0.8941 (OUTLIER) cc_final: 0.8603 (m) REVERT: F 31 LYS cc_start: 0.9427 (tppt) cc_final: 0.9218 (ptmm) REVERT: F 46 GLU cc_start: 0.8788 (tt0) cc_final: 0.8369 (tt0) REVERT: L 105 GLU cc_start: 0.5791 (OUTLIER) cc_final: 0.4367 (tp30) REVERT: B 435 LEU cc_start: 0.9004 (OUTLIER) cc_final: 0.8579 (tp) REVERT: C 469 GLU cc_start: 0.9536 (tt0) cc_final: 0.9242 (tm-30) outliers start: 34 outliers final: 30 residues processed: 116 average time/residue: 0.7457 time to fit residues: 119.8274 Evaluate side-chains 116 residues out of total 1666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 83 time to evaluate : 2.470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 18 LEU Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 82 MET Chi-restraints excluded: chain E residue 95 SER Chi-restraints excluded: chain F residue 85 GLU Chi-restraints excluded: chain G residue 26 SER Chi-restraints excluded: chain G residue 78 LEU Chi-restraints excluded: chain G residue 89 GLN Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain L residue 77 SER Chi-restraints excluded: chain L residue 97 THR Chi-restraints excluded: chain L residue 105 GLU Chi-restraints excluded: chain A residue 214 PHE Chi-restraints excluded: chain A residue 236 ARG Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 357 SER Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain A residue 465 SER Chi-restraints excluded: chain B residue 79 ILE Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 407 GLN Chi-restraints excluded: chain B residue 414 HIS Chi-restraints excluded: chain B residue 434 THR Chi-restraints excluded: chain B residue 435 LEU Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain C residue 118 ILE Chi-restraints excluded: chain C residue 162 CYS Chi-restraints excluded: chain C residue 209 GLU Chi-restraints excluded: chain C residue 245 THR Chi-restraints excluded: chain C residue 261 SER Chi-restraints excluded: chain C residue 302 ASN Chi-restraints excluded: chain C residue 352 MET Chi-restraints excluded: chain C residue 422 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 184 optimal weight: 4.9990 chunk 140 optimal weight: 6.9990 chunk 159 optimal weight: 0.0040 chunk 79 optimal weight: 4.9990 chunk 32 optimal weight: 2.9990 chunk 52 optimal weight: 10.0000 chunk 38 optimal weight: 8.9990 chunk 43 optimal weight: 3.9990 chunk 22 optimal weight: 0.6980 chunk 162 optimal weight: 5.9990 chunk 42 optimal weight: 7.9990 overall best weight: 2.5398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.055668 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2940 r_free = 0.2940 target = 0.044218 restraints weight = 208734.858| |-----------------------------------------------------------------------------| r_work (start): 0.2927 rms_B_bonded: 4.81 r_work: 0.2804 rms_B_bonded: 4.77 restraints_weight: 0.5000 r_work (final): 0.2804 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8548 moved from start: 0.4041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 14995 Z= 0.147 Angle : 0.529 6.762 20336 Z= 0.280 Chirality : 0.041 0.171 2388 Planarity : 0.003 0.078 2562 Dihedral : 4.662 55.992 2042 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.32 % Favored : 93.57 % Rotamer: Outliers : 2.13 % Allowed : 29.00 % Favored : 68.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.46 (0.20), residues: 1866 helix: 1.68 (0.26), residues: 420 sheet: -0.13 (0.25), residues: 452 loop : -1.30 (0.19), residues: 994 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 32 HIS 0.003 0.000 HIS B 414 PHE 0.010 0.001 PHE A 378 TYR 0.012 0.001 TYR C 235 ARG 0.010 0.000 ARG C 236 Details of bonding type rmsd hydrogen bonds : bond 0.03204 ( 515) hydrogen bonds : angle 4.86827 ( 1383) SS BOND : bond 0.00356 ( 26) SS BOND : angle 1.04988 ( 52) covalent geometry : bond 0.00320 (14968) covalent geometry : angle 0.52721 (20284) Misc. bond : bond 0.00006 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11684.68 seconds wall clock time: 201 minutes 18.68 seconds (12078.68 seconds total)