Starting phenix.real_space_refine on Tue Jul 7 01:54:03 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7y59_33613/07_2026/7y59_33613.cif Found real_map, /net/cci-nas-00/data/ceres_data/7y59_33613/07_2026/7y59_33613.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.51 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7y59_33613/07_2026/7y59_33613.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7y59_33613/07_2026/7y59_33613.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7y59_33613/07_2026/7y59_33613.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7y59_33613/07_2026/7y59_33613.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7y59_33613/07_2026/7y59_33613.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7y59_33613/07_2026/7y59_33613.map" } resolution = 4.51 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 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 P 30 5.49 5 S 208 5.16 5 C 26100 2.51 5 N 7345 2.21 5 O 7881 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 41564 Number of models: 1 Model: "" Number of chains: 16 Chain: "W" Number of atoms: 1870 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1870 Classifications: {'peptide': 225} Link IDs: {'PTRANS': 13, 'TRANS': 211} Chain: "X" Number of atoms: 1870 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1870 Classifications: {'peptide': 225} Link IDs: {'PTRANS': 13, 'TRANS': 211} Chain: "Y" Number of atoms: 1144 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1144 Classifications: {'peptide': 225} Incomplete info: {'truncation_to_alanine': 185} Link IDs: {'PTRANS': 13, 'TRANS': 211} Unresolved chain link angles: 13 Unresolved non-hydrogen bonds: 794 Unresolved non-hydrogen angles: 1045 Unresolved non-hydrogen dihedrals: 708 Unresolved non-hydrogen chiralities: 69 Planarities with less than four sites: {'ASP:plan': 7, 'TRP:plan': 9, 'PHE:plan': 21, 'ARG:plan': 13, 'TYR:plan': 15, 'GLU:plan': 3, 'GLN:plan1': 5, 'ASN:plan1': 7, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 456 Chain: "Z" Number of atoms: 1144 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1144 Classifications: {'peptide': 225} Incomplete info: {'truncation_to_alanine': 185} Link IDs: {'PTRANS': 13, 'TRANS': 211} Unresolved chain link angles: 13 Unresolved non-hydrogen bonds: 794 Unresolved non-hydrogen angles: 1045 Unresolved non-hydrogen dihedrals: 708 Unresolved non-hydrogen chiralities: 69 Planarities with less than four sites: {'ASP:plan': 7, 'TRP:plan': 9, 'PHE:plan': 21, 'ARG:plan': 13, 'TYR:plan': 15, 'GLU:plan': 3, 'GLN:plan1': 5, 'ASN:plan1': 7, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 456 Chain: "A" Number of atoms: 5846 Number of conformers: 1 Conformer: "" Number of residues, atoms: 745, 5846 Classifications: {'peptide': 745} Link IDs: {'PCIS': 3, 'PTRANS': 38, 'TRANS': 703} Chain: "B" Number of atoms: 5846 Number of conformers: 1 Conformer: "" Number of residues, atoms: 745, 5846 Classifications: {'peptide': 745} Link IDs: {'PCIS': 3, 'PTRANS': 38, 'TRANS': 703} Chain: "C" Number of atoms: 5835 Number of conformers: 1 Conformer: "" Number of residues, atoms: 744, 5835 Classifications: {'peptide': 744} Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 38, 'TRANS': 702} Chain: "D" Number of atoms: 5829 Number of conformers: 1 Conformer: "" Number of residues, atoms: 743, 5829 Classifications: {'peptide': 743} Link IDs: {'PCIS': 3, 'PTRANS': 38, 'TRANS': 701} Chain: "E" Number of atoms: 5911 Number of conformers: 1 Conformer: "" Number of residues, atoms: 753, 5911 Classifications: {'peptide': 753} Link IDs: {'PCIS': 3, 'PTRANS': 39, 'TRANS': 710} Chain: "F" Number of atoms: 5921 Number of conformers: 1 Conformer: "" Number of residues, atoms: 755, 5921 Classifications: {'peptide': 755} Link IDs: {'PCIS': 3, 'PTRANS': 39, 'TRANS': 712} Chain: "A" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 58 Unusual residues: {'ADP': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 58 Unusual residues: {'ADP': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 58 Unusual residues: {'ADP': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 58 Unusual residues: {'ADP': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 58 Unusual residues: {'ADP': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 58 Unusual residues: {'ADP': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 9.51, per 1000 atoms: 0.23 Number of scatterers: 41564 At special positions: 0 Unit cell: (172.7, 179.3, 189.2, 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 208 16.00 P 30 15.00 O 7881 8.00 N 7345 7.00 C 26100 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.09 Conformation dependent library (CDL) restraints added in 1.7 seconds 10730 Ramachandran restraints generated. 5365 Oldfield, 0 Emsley, 5365 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 10024 Finding SS restraints... Secondary structure from input PDB file: 250 helices and 33 sheets defined 53.0% alpha, 9.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.37 Creating SS restraints... Processing helix chain 'W' and resid 2 through 10 removed outlier: 4.202A pdb=" N ASP W 6 " --> pdb=" O SER W 2 " (cutoff:3.500A) Processing helix chain 'W' and resid 12 through 32 Proline residue: W 26 - end of helix removed outlier: 4.526A pdb=" N GLY W 32 " --> pdb=" O VAL W 28 " (cutoff:3.500A) Processing helix chain 'W' and resid 35 through 39 removed outlier: 3.693A pdb=" N TYR W 38 " --> pdb=" O SER W 35 " (cutoff:3.500A) Processing helix chain 'W' and resid 42 through 48 removed outlier: 3.505A pdb=" N TYR W 48 " --> pdb=" O GLU W 44 " (cutoff:3.500A) Processing helix chain 'W' and resid 68 through 88 removed outlier: 6.550A pdb=" N THR W 84 " --> pdb=" O TYR W 80 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N ARG W 85 " --> pdb=" O GLN W 81 " (cutoff:3.500A) Processing helix chain 'W' and resid 94 through 116 Processing helix chain 'W' and resid 122 through 137 removed outlier: 4.052A pdb=" N ILE W 126 " --> pdb=" O MET W 122 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ASN W 137 " --> pdb=" O TRP W 133 " (cutoff:3.500A) Processing helix chain 'W' and resid 154 through 166 Processing helix chain 'W' and resid 170 through 194 removed outlier: 3.613A pdb=" N LEU W 174 " --> pdb=" O VAL W 170 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N PHE W 188 " --> pdb=" O PHE W 184 " (cutoff:3.500A) Proline residue: W 191 - end of helix removed outlier: 3.568A pdb=" N LEU W 194 " --> pdb=" O TYR W 190 " (cutoff:3.500A) Processing helix chain 'W' and resid 204 through 210 Processing helix chain 'X' and resid 2 through 10 removed outlier: 3.799A pdb=" N ASP X 6 " --> pdb=" O SER X 2 " (cutoff:3.500A) Processing helix chain 'X' and resid 12 through 32 Proline residue: X 26 - end of helix removed outlier: 3.802A pdb=" N GLY X 32 " --> pdb=" O VAL X 28 " (cutoff:3.500A) Processing helix chain 'X' and resid 35 through 39 Processing helix chain 'X' and resid 42 through 49 Processing helix chain 'X' and resid 68 through 89 removed outlier: 3.787A pdb=" N TYR X 72 " --> pdb=" O THR X 68 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N GLY X 89 " --> pdb=" O ARG X 85 " (cutoff:3.500A) Processing helix chain 'X' and resid 94 through 116 removed outlier: 3.829A pdb=" N TYR X 98 " --> pdb=" O ARG X 94 " (cutoff:3.500A) Processing helix chain 'X' and resid 122 through 137 removed outlier: 3.810A pdb=" N ASN X 137 " --> pdb=" O TRP X 133 " (cutoff:3.500A) Processing helix chain 'X' and resid 154 through 166 Processing helix chain 'X' and resid 170 through 188 Processing helix chain 'X' and resid 188 through 194 removed outlier: 4.540A pdb=" N MET X 192 " --> pdb=" O PHE X 188 " (cutoff:3.500A) Processing helix chain 'X' and resid 203 through 210 Processing helix chain 'Y' and resid 3 through 10 Processing helix chain 'Y' and resid 12 through 32 Proline residue: Y 26 - end of helix removed outlier: 4.348A pdb=" N GLY Y 32 " --> pdb=" O VAL Y 28 " (cutoff:3.500A) Processing helix chain 'Y' and resid 35 through 39 Processing helix chain 'Y' and resid 42 through 49 removed outlier: 3.783A pdb=" N PHE Y 46 " --> pdb=" O TRP Y 42 " (cutoff:3.500A) Processing helix chain 'Y' and resid 56 through 60 removed outlier: 3.614A pdb=" N THR Y 59 " --> pdb=" O ILE Y 56 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N PHE Y 60 " --> pdb=" O THR Y 57 " (cutoff:3.500A) No H-bonds generated for 'chain 'Y' and resid 56 through 60' Processing helix chain 'Y' and resid 65 through 67 No H-bonds generated for 'chain 'Y' and resid 65 through 67' Processing helix chain 'Y' and resid 68 through 89 removed outlier: 4.001A pdb=" N TYR Y 72 " --> pdb=" O THR Y 68 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N THR Y 84 " --> pdb=" O TYR Y 80 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N ARG Y 85 " --> pdb=" O GLN Y 81 " (cutoff:3.500A) Processing helix chain 'Y' and resid 95 through 116 Processing helix chain 'Y' and resid 122 through 137 Processing helix chain 'Y' and resid 154 through 162 Processing helix chain 'Y' and resid 169 through 188 removed outlier: 4.042A pdb=" N GLU Y 173 " --> pdb=" O SER Y 169 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N MET Y 187 " --> pdb=" O TYR Y 183 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N PHE Y 188 " --> pdb=" O PHE Y 184 " (cutoff:3.500A) Processing helix chain 'Y' and resid 189 through 194 Processing helix chain 'Z' and resid 3 through 11 removed outlier: 3.598A pdb=" N TRP Z 7 " --> pdb=" O ASP Z 3 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ILE Z 11 " --> pdb=" O TRP Z 7 " (cutoff:3.500A) Processing helix chain 'Z' and resid 12 through 30 Proline residue: Z 26 - end of helix Processing helix chain 'Z' and resid 35 through 40 removed outlier: 4.031A pdb=" N PHE Z 40 " --> pdb=" O ALA Z 37 " (cutoff:3.500A) Processing helix chain 'Z' and resid 42 through 49 Processing helix chain 'Z' and resid 56 through 61 removed outlier: 4.093A pdb=" N TYR Z 61 " --> pdb=" O ALA Z 58 " (cutoff:3.500A) Processing helix chain 'Z' and resid 68 through 89 removed outlier: 3.597A pdb=" N VAL Z 74 " --> pdb=" O PHE Z 70 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N ARG Z 85 " --> pdb=" O GLN Z 81 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N THR Z 88 " --> pdb=" O THR Z 84 " (cutoff:3.500A) Processing helix chain 'Z' and resid 94 through 116 Processing helix chain 'Z' and resid 121 through 135 Processing helix chain 'Z' and resid 154 through 166 removed outlier: 3.733A pdb=" N ILE Z 166 " --> pdb=" O PHE Z 162 " (cutoff:3.500A) Processing helix chain 'Z' and resid 171 through 189 removed outlier: 3.715A pdb=" N ILE Z 175 " --> pdb=" O ILE Z 171 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N GLY Z 176 " --> pdb=" O ASN Z 172 " (cutoff:3.500A) Processing helix chain 'Z' and resid 189 through 194 removed outlier: 4.191A pdb=" N ASP Z 193 " --> pdb=" O ARG Z 189 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N LEU Z 194 " --> pdb=" O TYR Z 190 " (cutoff:3.500A) No H-bonds generated for 'chain 'Z' and resid 189 through 194' Processing helix chain 'Z' and resid 204 through 210 removed outlier: 4.172A pdb=" N TRP Z 209 " --> pdb=" O PHE Z 205 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N LEU Z 210 " --> pdb=" O LEU Z 206 " (cutoff:3.500A) Processing helix chain 'A' and resid 42 through 49 Processing helix chain 'A' and resid 62 through 64 No H-bonds generated for 'chain 'A' and resid 62 through 64' Processing helix chain 'A' and resid 85 through 92 Processing helix chain 'A' and resid 119 through 123 removed outlier: 3.929A pdb=" N VAL A 123 " --> pdb=" O ASP A 120 " (cutoff:3.500A) Processing helix chain 'A' and resid 129 through 134 removed outlier: 3.743A pdb=" N VAL A 133 " --> pdb=" O ASN A 129 " (cutoff:3.500A) Processing helix chain 'A' and resid 134 through 139 Processing helix chain 'A' and resid 202 through 206 removed outlier: 4.022A pdb=" N ILE A 206 " --> pdb=" O TYR A 203 " (cutoff:3.500A) Processing helix chain 'A' and resid 209 through 226 Proline residue: A 223 - end of helix removed outlier: 3.940A pdb=" N HIS A 226 " --> pdb=" O LEU A 222 " (cutoff:3.500A) Processing helix chain 'A' and resid 226 through 234 removed outlier: 3.535A pdb=" N PHE A 230 " --> pdb=" O HIS A 226 " (cutoff:3.500A) Processing helix chain 'A' and resid 250 through 263 Processing helix chain 'A' and resid 271 through 276 removed outlier: 3.786A pdb=" N MET A 275 " --> pdb=" O GLY A 271 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N SER A 276 " --> pdb=" O PRO A 272 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 271 through 276' Processing helix chain 'A' and resid 279 through 295 removed outlier: 4.116A pdb=" N GLU A 283 " --> pdb=" O ALA A 279 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LEU A 286 " --> pdb=" O SER A 282 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LYS A 295 " --> pdb=" O GLU A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 305 through 310 Processing helix chain 'A' and resid 319 through 335 Processing helix chain 'A' and resid 354 through 359 removed outlier: 3.797A pdb=" N ARG A 359 " --> pdb=" O ALA A 356 " (cutoff:3.500A) Processing helix chain 'A' and resid 373 through 385 Processing helix chain 'A' and resid 395 through 403 Processing helix chain 'A' and resid 407 through 425 Processing helix chain 'A' and resid 438 through 444 Processing helix chain 'A' and resid 448 through 458 Processing helix chain 'A' and resid 475 through 479 Processing helix chain 'A' and resid 482 through 499 removed outlier: 3.803A pdb=" N TYR A 495 " --> pdb=" O GLU A 491 " (cutoff:3.500A) Proline residue: A 496 - end of helix Processing helix chain 'A' and resid 499 through 507 removed outlier: 4.082A pdb=" N PHE A 503 " --> pdb=" O HIS A 499 " (cutoff:3.500A) Processing helix chain 'A' and resid 523 through 536 Processing helix chain 'A' and resid 543 through 552 Processing helix chain 'A' and resid 556 through 569 removed outlier: 3.829A pdb=" N ARG A 560 " --> pdb=" O GLU A 556 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N GLU A 561 " --> pdb=" O ALA A 557 " (cutoff:3.500A) Processing helix chain 'A' and resid 580 through 587 Processing helix chain 'A' and resid 593 through 611 removed outlier: 3.650A pdb=" N MET A 611 " --> pdb=" O GLU A 607 " (cutoff:3.500A) Processing helix chain 'A' and resid 650 through 660 Processing helix chain 'A' and resid 671 through 679 Processing helix chain 'A' and resid 683 through 716 removed outlier: 3.542A pdb=" N ASN A 716 " --> pdb=" O GLU A 712 " (cutoff:3.500A) Processing helix chain 'A' and resid 732 through 742 removed outlier: 3.798A pdb=" N PHE A 736 " --> pdb=" O ARG A 732 " (cutoff:3.500A) Processing helix chain 'A' and resid 748 through 766 Processing helix chain 'B' and resid 42 through 50 removed outlier: 3.567A pdb=" N MET B 46 " --> pdb=" O SER B 42 " (cutoff:3.500A) Processing helix chain 'B' and resid 61 through 65 Processing helix chain 'B' and resid 85 through 93 Processing helix chain 'B' and resid 120 through 123 Processing helix chain 'B' and resid 129 through 134 Processing helix chain 'B' and resid 134 through 139 Processing helix chain 'B' and resid 202 through 206 Processing helix chain 'B' and resid 209 through 219 Processing helix chain 'B' and resid 220 through 226 removed outlier: 3.518A pdb=" N LEU B 224 " --> pdb=" O VAL B 220 " (cutoff:3.500A) Processing helix chain 'B' and resid 226 through 234 Processing helix chain 'B' and resid 250 through 263 Processing helix chain 'B' and resid 270 through 276 removed outlier: 3.572A pdb=" N ILE B 274 " --> pdb=" O ASN B 270 " (cutoff:3.500A) Processing helix chain 'B' and resid 281 through 295 removed outlier: 3.812A pdb=" N ASN B 285 " --> pdb=" O GLU B 281 " (cutoff:3.500A) Processing helix chain 'B' and resid 305 through 310 removed outlier: 3.717A pdb=" N ILE B 309 " --> pdb=" O GLU B 305 " (cutoff:3.500A) Processing helix chain 'B' and resid 319 through 334 Processing helix chain 'B' and resid 349 through 353 Processing helix chain 'B' and resid 354 through 359 removed outlier: 3.945A pdb=" N ARG B 359 " --> pdb=" O ALA B 356 " (cutoff:3.500A) Processing helix chain 'B' and resid 373 through 385 Processing helix chain 'B' and resid 395 through 403 Processing helix chain 'B' and resid 407 through 425 Processing helix chain 'B' and resid 438 through 445 removed outlier: 3.694A pdb=" N MET B 442 " --> pdb=" O ASP B 438 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LEU B 445 " --> pdb=" O VAL B 441 " (cutoff:3.500A) Processing helix chain 'B' and resid 448 through 458 Processing helix chain 'B' and resid 482 through 499 removed outlier: 4.291A pdb=" N TYR B 495 " --> pdb=" O GLU B 491 " (cutoff:3.500A) Proline residue: B 496 - end of helix Processing helix chain 'B' and resid 499 through 507 removed outlier: 3.864A pdb=" N PHE B 503 " --> pdb=" O HIS B 499 " (cutoff:3.500A) Processing helix chain 'B' and resid 523 through 536 Processing helix chain 'B' and resid 543 through 552 removed outlier: 4.379A pdb=" N PHE B 552 " --> pdb=" O LEU B 548 " (cutoff:3.500A) Processing helix chain 'B' and resid 555 through 569 Processing helix chain 'B' and resid 580 through 587 Processing helix chain 'B' and resid 593 through 609 removed outlier: 3.527A pdb=" N ASP B 609 " --> pdb=" O LEU B 605 " (cutoff:3.500A) Processing helix chain 'B' and resid 625 through 629 Processing helix chain 'B' and resid 650 through 662 Processing helix chain 'B' and resid 671 through 679 Processing helix chain 'B' and resid 683 through 716 removed outlier: 3.903A pdb=" N GLN B 714 " --> pdb=" O GLU B 710 " (cutoff:3.500A) Processing helix chain 'B' and resid 732 through 742 removed outlier: 3.643A pdb=" N PHE B 736 " --> pdb=" O ARG B 732 " (cutoff:3.500A) Processing helix chain 'B' and resid 748 through 766 Processing helix chain 'C' and resid 43 through 49 Processing helix chain 'C' and resid 62 through 64 No H-bonds generated for 'chain 'C' and resid 62 through 64' Processing helix chain 'C' and resid 85 through 93 Processing helix chain 'C' and resid 120 through 124 removed outlier: 3.571A pdb=" N VAL C 123 " --> pdb=" O ASP C 120 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N GLU C 124 " --> pdb=" O ASP C 121 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 120 through 124' Processing helix chain 'C' and resid 129 through 134 removed outlier: 3.559A pdb=" N VAL C 133 " --> pdb=" O ASN C 129 " (cutoff:3.500A) Processing helix chain 'C' and resid 134 through 139 Processing helix chain 'C' and resid 192 through 201 removed outlier: 4.244A pdb=" N GLU C 196 " --> pdb=" O GLU C 192 " (cutoff:3.500A) Processing helix chain 'C' and resid 202 through 206 Processing helix chain 'C' and resid 209 through 219 removed outlier: 3.570A pdb=" N MET C 219 " --> pdb=" O GLN C 215 " (cutoff:3.500A) Processing helix chain 'C' and resid 220 through 226 Processing helix chain 'C' and resid 226 through 234 Processing helix chain 'C' and resid 250 through 263 Processing helix chain 'C' and resid 271 through 276 Processing helix chain 'C' and resid 281 through 294 removed outlier: 3.899A pdb=" N ASN C 285 " --> pdb=" O GLU C 281 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LEU C 286 " --> pdb=" O SER C 282 " (cutoff:3.500A) Processing helix chain 'C' and resid 305 through 309 Processing helix chain 'C' and resid 319 through 335 removed outlier: 3.526A pdb=" N LEU C 335 " --> pdb=" O LEU C 331 " (cutoff:3.500A) Processing helix chain 'C' and resid 349 through 353 removed outlier: 3.700A pdb=" N ILE C 353 " --> pdb=" O PRO C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 354 through 359 removed outlier: 3.834A pdb=" N ARG C 359 " --> pdb=" O ALA C 356 " (cutoff:3.500A) Processing helix chain 'C' and resid 373 through 385 Processing helix chain 'C' and resid 395 through 403 Processing helix chain 'C' and resid 407 through 425 Processing helix chain 'C' and resid 440 through 445 removed outlier: 3.664A pdb=" N SER C 444 " --> pdb=" O GLU C 440 " (cutoff:3.500A) Processing helix chain 'C' and resid 448 through 458 Processing helix chain 'C' and resid 475 through 479 Processing helix chain 'C' and resid 482 through 494 Processing helix chain 'C' and resid 494 through 499 removed outlier: 4.122A pdb=" N GLU C 498 " --> pdb=" O GLN C 494 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N HIS C 499 " --> pdb=" O TYR C 495 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 494 through 499' Processing helix chain 'C' and resid 499 through 506 removed outlier: 3.760A pdb=" N PHE C 503 " --> pdb=" O HIS C 499 " (cutoff:3.500A) Processing helix chain 'C' and resid 524 through 536 Processing helix chain 'C' and resid 543 through 550 Processing helix chain 'C' and resid 558 through 569 Processing helix chain 'C' and resid 579 through 587 removed outlier: 4.382A pdb=" N ALA C 583 " --> pdb=" O LEU C 579 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N GLY C 587 " --> pdb=" O ALA C 583 " (cutoff:3.500A) Processing helix chain 'C' and resid 595 through 610 removed outlier: 3.649A pdb=" N ARG C 599 " --> pdb=" O GLY C 595 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N ILE C 601 " --> pdb=" O ALA C 597 " (cutoff:3.500A) Processing helix chain 'C' and resid 625 through 629 Processing helix chain 'C' and resid 650 through 661 Processing helix chain 'C' and resid 673 through 678 Processing helix chain 'C' and resid 683 through 716 Processing helix chain 'C' and resid 732 through 742 removed outlier: 3.921A pdb=" N PHE C 742 " --> pdb=" O GLU C 738 " (cutoff:3.500A) Processing helix chain 'C' and resid 748 through 762 Processing helix chain 'D' and resid 42 through 50 Processing helix chain 'D' and resid 85 through 93 Processing helix chain 'D' and resid 129 through 134 removed outlier: 3.572A pdb=" N VAL D 133 " --> pdb=" O ASN D 129 " (cutoff:3.500A) Processing helix chain 'D' and resid 134 through 140 Processing helix chain 'D' and resid 192 through 200 removed outlier: 3.781A pdb=" N SER D 197 " --> pdb=" O GLU D 194 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ASN D 199 " --> pdb=" O GLU D 196 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N GLU D 200 " --> pdb=" O SER D 197 " (cutoff:3.500A) Processing helix chain 'D' and resid 202 through 206 removed outlier: 3.506A pdb=" N ILE D 206 " --> pdb=" O TYR D 203 " (cutoff:3.500A) Processing helix chain 'D' and resid 209 through 226 removed outlier: 4.719A pdb=" N LEU D 222 " --> pdb=" O GLU D 218 " (cutoff:3.500A) Proline residue: D 223 - end of helix Processing helix chain 'D' and resid 226 through 234 Processing helix chain 'D' and resid 250 through 263 Processing helix chain 'D' and resid 271 through 276 removed outlier: 4.014A pdb=" N MET D 275 " --> pdb=" O GLY D 271 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N SER D 276 " --> pdb=" O PRO D 272 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 271 through 276' Processing helix chain 'D' and resid 281 through 296 removed outlier: 3.604A pdb=" N ASN D 285 " --> pdb=" O GLU D 281 " (cutoff:3.500A) Processing helix chain 'D' and resid 305 through 310 removed outlier: 3.667A pdb=" N ILE D 309 " --> pdb=" O GLU D 305 " (cutoff:3.500A) Processing helix chain 'D' and resid 312 through 316 Processing helix chain 'D' and resid 319 through 334 Processing helix chain 'D' and resid 354 through 359 removed outlier: 3.911A pdb=" N ARG D 359 " --> pdb=" O ALA D 356 " (cutoff:3.500A) Processing helix chain 'D' and resid 373 through 385 Processing helix chain 'D' and resid 395 through 403 removed outlier: 3.978A pdb=" N VAL D 399 " --> pdb=" O ASP D 395 " (cutoff:3.500A) Processing helix chain 'D' and resid 407 through 427 Processing helix chain 'D' and resid 437 through 443 Processing helix chain 'D' and resid 448 through 458 removed outlier: 3.653A pdb=" N PHE D 452 " --> pdb=" O THR D 448 " (cutoff:3.500A) Processing helix chain 'D' and resid 475 through 480 removed outlier: 3.785A pdb=" N ILE D 479 " --> pdb=" O THR D 475 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N GLY D 480 " --> pdb=" O TRP D 476 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 475 through 480' Processing helix chain 'D' and resid 482 through 499 removed outlier: 3.730A pdb=" N TYR D 495 " --> pdb=" O GLU D 491 " (cutoff:3.500A) Proline residue: D 496 - end of helix Processing helix chain 'D' and resid 499 through 507 removed outlier: 4.005A pdb=" N PHE D 503 " --> pdb=" O HIS D 499 " (cutoff:3.500A) Processing helix chain 'D' and resid 523 through 536 Processing helix chain 'D' and resid 543 through 552 removed outlier: 4.280A pdb=" N PHE D 552 " --> pdb=" O LEU D 548 " (cutoff:3.500A) Processing helix chain 'D' and resid 555 through 569 Processing helix chain 'D' and resid 580 through 587 Processing helix chain 'D' and resid 593 through 610 Processing helix chain 'D' and resid 625 through 629 removed outlier: 3.528A pdb=" N ILE D 628 " --> pdb=" O ARG D 625 " (cutoff:3.500A) Processing helix chain 'D' and resid 650 through 661 Processing helix chain 'D' and resid 671 through 679 removed outlier: 3.737A pdb=" N LEU D 675 " --> pdb=" O ASP D 671 " (cutoff:3.500A) Processing helix chain 'D' and resid 683 through 716 removed outlier: 3.526A pdb=" N LEU D 687 " --> pdb=" O SER D 683 " (cutoff:3.500A) Processing helix chain 'D' and resid 732 through 741 Processing helix chain 'D' and resid 749 through 763 removed outlier: 3.586A pdb=" N ARG D 753 " --> pdb=" O ASP D 749 " (cutoff:3.500A) Processing helix chain 'E' and resid 42 through 49 Processing helix chain 'E' and resid 62 through 64 No H-bonds generated for 'chain 'E' and resid 62 through 64' Processing helix chain 'E' and resid 85 through 92 Processing helix chain 'E' and resid 120 through 123 removed outlier: 4.025A pdb=" N VAL E 123 " --> pdb=" O ASP E 120 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 120 through 123' Processing helix chain 'E' and resid 129 through 134 removed outlier: 3.558A pdb=" N VAL E 133 " --> pdb=" O ASN E 129 " (cutoff:3.500A) Processing helix chain 'E' and resid 134 through 139 Processing helix chain 'E' and resid 202 through 206 Processing helix chain 'E' and resid 209 through 226 removed outlier: 4.693A pdb=" N LEU E 222 " --> pdb=" O GLU E 218 " (cutoff:3.500A) Proline residue: E 223 - end of helix Processing helix chain 'E' and resid 226 through 234 Processing helix chain 'E' and resid 250 through 263 Processing helix chain 'E' and resid 271 through 276 Processing helix chain 'E' and resid 280 through 295 removed outlier: 4.042A pdb=" N SER E 284 " --> pdb=" O GLY E 280 " (cutoff:3.500A) Processing helix chain 'E' and resid 306 through 309 Processing helix chain 'E' and resid 319 through 334 Processing helix chain 'E' and resid 354 through 359 Processing helix chain 'E' and resid 373 through 385 Processing helix chain 'E' and resid 395 through 403 Processing helix chain 'E' and resid 407 through 425 Processing helix chain 'E' and resid 438 through 445 Processing helix chain 'E' and resid 448 through 458 Processing helix chain 'E' and resid 475 through 479 Processing helix chain 'E' and resid 482 through 499 removed outlier: 3.784A pdb=" N TYR E 495 " --> pdb=" O GLU E 491 " (cutoff:3.500A) Proline residue: E 496 - end of helix Processing helix chain 'E' and resid 499 through 507 removed outlier: 3.735A pdb=" N PHE E 503 " --> pdb=" O HIS E 499 " (cutoff:3.500A) Processing helix chain 'E' and resid 523 through 536 Processing helix chain 'E' and resid 543 through 552 removed outlier: 4.136A pdb=" N PHE E 552 " --> pdb=" O LEU E 548 " (cutoff:3.500A) Processing helix chain 'E' and resid 555 through 569 removed outlier: 3.514A pdb=" N VAL E 559 " --> pdb=" O SER E 555 " (cutoff:3.500A) Processing helix chain 'E' and resid 580 through 587 Processing helix chain 'E' and resid 593 through 611 Processing helix chain 'E' and resid 652 through 662 Processing helix chain 'E' and resid 671 through 679 removed outlier: 3.789A pdb=" N LEU E 675 " --> pdb=" O ASP E 671 " (cutoff:3.500A) Processing helix chain 'E' and resid 683 through 714 removed outlier: 3.513A pdb=" N LEU E 687 " --> pdb=" O SER E 683 " (cutoff:3.500A) Processing helix chain 'E' and resid 732 through 742 removed outlier: 3.550A pdb=" N PHE E 736 " --> pdb=" O ARG E 732 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N PHE E 742 " --> pdb=" O GLU E 738 " (cutoff:3.500A) Processing helix chain 'E' and resid 748 through 767 Processing helix chain 'F' and resid 42 through 50 Processing helix chain 'F' and resid 62 through 64 No H-bonds generated for 'chain 'F' and resid 62 through 64' Processing helix chain 'F' and resid 85 through 92 Processing helix chain 'F' and resid 120 through 123 removed outlier: 4.245A pdb=" N VAL F 123 " --> pdb=" O ASP F 120 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 120 through 123' Processing helix chain 'F' and resid 129 through 134 removed outlier: 3.602A pdb=" N VAL F 133 " --> pdb=" O ASN F 129 " (cutoff:3.500A) Processing helix chain 'F' and resid 134 through 140 Processing helix chain 'F' and resid 202 through 206 Processing helix chain 'F' and resid 209 through 226 removed outlier: 3.661A pdb=" N MET F 219 " --> pdb=" O GLN F 215 " (cutoff:3.500A) removed outlier: 4.649A pdb=" N LEU F 222 " --> pdb=" O GLU F 218 " (cutoff:3.500A) Proline residue: F 223 - end of helix Processing helix chain 'F' and resid 228 through 234 Processing helix chain 'F' and resid 250 through 263 Processing helix chain 'F' and resid 271 through 277 removed outlier: 3.613A pdb=" N LYS F 277 " --> pdb=" O GLU F 273 " (cutoff:3.500A) Processing helix chain 'F' and resid 279 through 295 removed outlier: 3.696A pdb=" N GLU F 283 " --> pdb=" O ALA F 279 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N LYS F 295 " --> pdb=" O GLU F 291 " (cutoff:3.500A) Processing helix chain 'F' and resid 319 through 335 removed outlier: 3.548A pdb=" N LEU F 335 " --> pdb=" O LEU F 331 " (cutoff:3.500A) Processing helix chain 'F' and resid 374 through 385 Processing helix chain 'F' and resid 395 through 403 removed outlier: 3.569A pdb=" N VAL F 399 " --> pdb=" O ASP F 395 " (cutoff:3.500A) Processing helix chain 'F' and resid 407 through 425 Processing helix chain 'F' and resid 438 through 444 removed outlier: 3.519A pdb=" N SER F 444 " --> pdb=" O GLU F 440 " (cutoff:3.500A) Processing helix chain 'F' and resid 448 through 458 Processing helix chain 'F' and resid 475 through 479 Processing helix chain 'F' and resid 482 through 499 removed outlier: 4.392A pdb=" N TYR F 495 " --> pdb=" O GLU F 491 " (cutoff:3.500A) Proline residue: F 496 - end of helix Processing helix chain 'F' and resid 499 through 507 removed outlier: 4.308A pdb=" N PHE F 503 " --> pdb=" O HIS F 499 " (cutoff:3.500A) Processing helix chain 'F' and resid 523 through 536 Processing helix chain 'F' and resid 543 through 552 removed outlier: 3.586A pdb=" N PHE F 552 " --> pdb=" O LEU F 548 " (cutoff:3.500A) Processing helix chain 'F' and resid 556 through 569 Processing helix chain 'F' and resid 579 through 587 removed outlier: 4.003A pdb=" N ALA F 583 " --> pdb=" O LEU F 579 " (cutoff:3.500A) Processing helix chain 'F' and resid 593 through 611 removed outlier: 3.970A pdb=" N ALA F 597 " --> pdb=" O GLY F 593 " (cutoff:3.500A) Processing helix chain 'F' and resid 630 through 634 Processing helix chain 'F' and resid 650 through 662 Processing helix chain 'F' and resid 671 through 679 Processing helix chain 'F' and resid 683 through 716 Processing helix chain 'F' and resid 732 through 742 removed outlier: 3.881A pdb=" N PHE F 742 " --> pdb=" O GLU F 738 " (cutoff:3.500A) Processing helix chain 'F' and resid 748 through 766 removed outlier: 3.533A pdb=" N ILE F 752 " --> pdb=" O SER F 748 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'X' and resid 246 through 247 removed outlier: 6.713A pdb=" N ILE B 114 " --> pdb=" O HIS B 183 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N HIS B 115 " --> pdb=" O VAL B 166 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'Y' and resid 245 through 247 removed outlier: 6.781A pdb=" N ARG C 113 " --> pdb=" O THR C 168 " (cutoff:3.500A) removed outlier: 4.793A pdb=" N THR C 168 " --> pdb=" O ARG C 113 " (cutoff:3.500A) removed outlier: 7.123A pdb=" N HIS C 115 " --> pdb=" O VAL C 166 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'Z' and resid 246 through 247 removed outlier: 6.468A pdb=" N ARG D 113 " --> pdb=" O THR D 168 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N THR D 168 " --> pdb=" O ARG D 113 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N HIS D 115 " --> pdb=" O VAL D 166 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 25 through 29 removed outlier: 5.553A pdb=" N VAL A 39 " --> pdb=" O LEU A 72 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N LEU A 26 " --> pdb=" O ILE A 100 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 151 through 155 removed outlier: 6.658A pdb=" N HIS A 115 " --> pdb=" O VAL A 166 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N ILE A 114 " --> pdb=" O HIS A 183 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 145 through 146 Processing sheet with id=AA7, first strand: chain 'A' and resid 267 through 269 removed outlier: 3.910A pdb=" N PHE A 302 " --> pdb=" O PHE A 267 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N ALA A 299 " --> pdb=" O ILE A 342 " (cutoff:3.500A) removed outlier: 8.144A pdb=" N MET A 344 " --> pdb=" O ALA A 299 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N ILE A 301 " --> pdb=" O MET A 344 " (cutoff:3.500A) removed outlier: 8.043A pdb=" N ALA A 346 " --> pdb=" O ILE A 301 " (cutoff:3.500A) removed outlier: 7.153A pdb=" N ILE A 303 " --> pdb=" O ALA A 346 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 538 through 542 removed outlier: 7.007A pdb=" N ASN A 538 " --> pdb=" O VAL A 573 " (cutoff:3.500A) removed outlier: 7.636A pdb=" N PHE A 575 " --> pdb=" O ASN A 538 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N ILE A 540 " --> pdb=" O PHE A 575 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N CYS A 572 " --> pdb=" O PHE A 618 " (cutoff:3.500A) removed outlier: 8.097A pdb=" N ILE A 620 " --> pdb=" O CYS A 572 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N LEU A 574 " --> pdb=" O ILE A 620 " (cutoff:3.500A) removed outlier: 8.204A pdb=" N ALA A 622 " --> pdb=" O LEU A 574 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N PHE A 576 " --> pdb=" O ALA A 622 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N VAL A 514 " --> pdb=" O ILE A 619 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 57 through 60 removed outlier: 3.517A pdb=" N SER B 101 " --> pdb=" O LYS B 60 " (cutoff:3.500A) removed outlier: 7.636A pdb=" N ILE B 82 " --> pdb=" O ARG B 25 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N ILE B 27 " --> pdb=" O ILE B 82 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 38 through 41 Processing sheet with id=AB2, first strand: chain 'B' and resid 145 through 147 Processing sheet with id=AB3, first strand: chain 'B' and resid 267 through 269 removed outlier: 6.181A pdb=" N PHE B 267 " --> pdb=" O PHE B 302 " (cutoff:3.500A) removed outlier: 7.942A pdb=" N ASP B 304 " --> pdb=" O PHE B 267 " (cutoff:3.500A) removed outlier: 7.154A pdb=" N ILE B 269 " --> pdb=" O ASP B 304 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ILE B 241 " --> pdb=" O VAL B 343 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N GLY B 240 " --> pdb=" O ARG B 365 " (cutoff:3.500A) removed outlier: 7.740A pdb=" N VAL B 367 " --> pdb=" O GLY B 240 " (cutoff:3.500A) removed outlier: 5.958A pdb=" N LEU B 242 " --> pdb=" O VAL B 367 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 538 through 542 removed outlier: 6.258A pdb=" N VAL B 514 " --> pdb=" O GLY B 621 " (cutoff:3.500A) removed outlier: 8.030A pdb=" N THR B 623 " --> pdb=" O VAL B 514 " (cutoff:3.500A) removed outlier: 5.743A pdb=" N PHE B 516 " --> pdb=" O THR B 623 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N GLY B 513 " --> pdb=" O LEU B 639 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 26 through 29 removed outlier: 6.131A pdb=" N ILE C 27 " --> pdb=" O ILE C 82 " (cutoff:3.500A) removed outlier: 7.997A pdb=" N LYS C 81 " --> pdb=" O SER C 42 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N SER C 42 " --> pdb=" O LYS C 81 " (cutoff:3.500A) removed outlier: 5.890A pdb=" N VAL C 39 " --> pdb=" O LEU C 72 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N ASP C 74 " --> pdb=" O VAL C 39 " (cutoff:3.500A) removed outlier: 5.370A pdb=" N LEU C 41 " --> pdb=" O ASP C 74 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N SER C 101 " --> pdb=" O LYS C 60 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ILE C 100 " --> pdb=" O LEU C 26 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N LEU C 26 " --> pdb=" O ILE C 100 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 145 through 147 Processing sheet with id=AB7, first strand: chain 'C' and resid 267 through 270 removed outlier: 6.759A pdb=" N ALA C 299 " --> pdb=" O ILE C 342 " (cutoff:3.500A) removed outlier: 7.996A pdb=" N MET C 344 " --> pdb=" O ALA C 299 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N ILE C 301 " --> pdb=" O MET C 344 " (cutoff:3.500A) removed outlier: 7.834A pdb=" N ALA C 346 " --> pdb=" O ILE C 301 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N ILE C 303 " --> pdb=" O ALA C 346 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ILE C 241 " --> pdb=" O VAL C 343 " (cutoff:3.500A) removed outlier: 6.133A pdb=" N LEU C 242 " --> pdb=" O VAL C 367 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 538 through 542 removed outlier: 6.520A pdb=" N CYS C 572 " --> pdb=" O PHE C 618 " (cutoff:3.500A) removed outlier: 8.144A pdb=" N ILE C 620 " --> pdb=" O CYS C 572 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N LEU C 574 " --> pdb=" O ILE C 620 " (cutoff:3.500A) removed outlier: 7.925A pdb=" N ALA C 622 " --> pdb=" O LEU C 574 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N PHE C 576 " --> pdb=" O ALA C 622 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N VAL C 514 " --> pdb=" O GLY C 621 " (cutoff:3.500A) removed outlier: 7.985A pdb=" N THR C 623 " --> pdb=" O VAL C 514 " (cutoff:3.500A) removed outlier: 6.001A pdb=" N PHE C 516 " --> pdb=" O THR C 623 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 81 through 83 removed outlier: 8.199A pdb=" N ILE D 82 " --> pdb=" O ARG D 25 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N ILE D 27 " --> pdb=" O ILE D 82 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ILE D 100 " --> pdb=" O LEU D 26 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 38 through 41 Processing sheet with id=AC2, first strand: chain 'D' and resid 145 through 146 Processing sheet with id=AC3, first strand: chain 'D' and resid 267 through 269 removed outlier: 3.594A pdb=" N PHE D 302 " --> pdb=" O PHE D 267 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N ILE D 301 " --> pdb=" O MET D 344 " (cutoff:3.500A) removed outlier: 7.938A pdb=" N ALA D 346 " --> pdb=" O ILE D 301 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N ILE D 303 " --> pdb=" O ALA D 346 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N ILE D 241 " --> pdb=" O ALA D 345 " (cutoff:3.500A) removed outlier: 8.096A pdb=" N THR D 347 " --> pdb=" O ILE D 241 " (cutoff:3.500A) removed outlier: 6.118A pdb=" N LEU D 243 " --> pdb=" O THR D 347 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 538 through 540 removed outlier: 6.788A pdb=" N ASN D 538 " --> pdb=" O VAL D 573 " (cutoff:3.500A) removed outlier: 7.478A pdb=" N PHE D 575 " --> pdb=" O ASN D 538 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N ILE D 540 " --> pdb=" O PHE D 575 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N VAL D 514 " --> pdb=" O GLY D 621 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N GLN D 641 " --> pdb=" O GLY D 513 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 27 through 29 removed outlier: 6.263A pdb=" N ILE E 27 " --> pdb=" O ILE E 82 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC5 Processing sheet with id=AC6, first strand: chain 'E' and resid 38 through 40 removed outlier: 5.716A pdb=" N VAL E 39 " --> pdb=" O LEU E 72 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N LEU E 58 " --> pdb=" O GLN E 103 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 113 through 118 removed outlier: 3.827A pdb=" N ARG E 113 " --> pdb=" O ASP E 169 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N ASP E 169 " --> pdb=" O ARG E 113 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N HIS E 115 " --> pdb=" O GLU E 167 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N GLU E 167 " --> pdb=" O HIS E 115 " (cutoff:3.500A) removed outlier: 8.388A pdb=" N LEU E 117 " --> pdb=" O VAL E 165 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N VAL E 165 " --> pdb=" O LEU E 117 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 145 through 147 Processing sheet with id=AC9, first strand: chain 'E' and resid 267 through 270 removed outlier: 6.325A pdb=" N PHE E 267 " --> pdb=" O PHE E 302 " (cutoff:3.500A) removed outlier: 7.773A pdb=" N ASP E 304 " --> pdb=" O PHE E 267 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N ILE E 269 " --> pdb=" O ASP E 304 " (cutoff:3.500A) removed outlier: 5.729A pdb=" N ILE E 301 " --> pdb=" O MET E 344 " (cutoff:3.500A) removed outlier: 7.556A pdb=" N ALA E 346 " --> pdb=" O ILE E 301 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N ILE E 303 " --> pdb=" O ALA E 346 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N ILE E 241 " --> pdb=" O ALA E 345 " (cutoff:3.500A) removed outlier: 8.101A pdb=" N THR E 347 " --> pdb=" O ILE E 241 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N LEU E 243 " --> pdb=" O THR E 347 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N GLY E 240 " --> pdb=" O ARG E 365 " (cutoff:3.500A) removed outlier: 7.926A pdb=" N VAL E 367 " --> pdb=" O GLY E 240 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N LEU E 242 " --> pdb=" O VAL E 367 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC9 Processing sheet with id=AD1, first strand: chain 'E' and resid 538 through 540 removed outlier: 6.631A pdb=" N ASN E 538 " --> pdb=" O VAL E 573 " (cutoff:3.500A) removed outlier: 7.347A pdb=" N PHE E 575 " --> pdb=" O ASN E 538 " (cutoff:3.500A) removed outlier: 6.192A pdb=" N ILE E 540 " --> pdb=" O PHE E 575 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N PHE E 618 " --> pdb=" O CYS E 572 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N GLN E 641 " --> pdb=" O GLY E 513 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'F' and resid 25 through 29 removed outlier: 7.631A pdb=" N ILE F 82 " --> pdb=" O ARG F 25 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N ILE F 27 " --> pdb=" O ILE F 82 " (cutoff:3.500A) removed outlier: 7.755A pdb=" N MET F 84 " --> pdb=" O ILE F 27 " (cutoff:3.500A) removed outlier: 5.920A pdb=" N ASP F 29 " --> pdb=" O MET F 84 " (cutoff:3.500A) removed outlier: 5.733A pdb=" N VAL F 39 " --> pdb=" O LEU F 72 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'F' and resid 151 through 155 removed outlier: 5.621A pdb=" N VAL F 165 " --> pdb=" O LEU F 117 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N LEU F 117 " --> pdb=" O VAL F 165 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'F' and resid 145 through 147 Processing sheet with id=AD5, first strand: chain 'F' and resid 267 through 270 removed outlier: 3.741A pdb=" N ASP F 304 " --> pdb=" O ILE F 269 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N ILE F 241 " --> pdb=" O ALA F 345 " (cutoff:3.500A) removed outlier: 7.971A pdb=" N THR F 347 " --> pdb=" O ILE F 241 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N LEU F 243 " --> pdb=" O THR F 347 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N GLY F 240 " --> pdb=" O PHE F 363 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N ARG F 365 " --> pdb=" O GLY F 240 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'F' and resid 538 through 542 removed outlier: 3.545A pdb=" N PHE F 618 " --> pdb=" O CYS F 572 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N GLY F 513 " --> pdb=" O LEU F 639 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N GLN F 641 " --> pdb=" O GLY F 513 " (cutoff:3.500A) 1928 hydrogen bonds defined for protein. 5562 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: 8.94 Time building geometry restraints manager: 3.98 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 14228 1.34 - 1.46: 8246 1.46 - 1.58: 19465 1.58 - 1.70: 35 1.70 - 1.81: 340 Bond restraints: 42314 Sorted by residual: bond pdb=" C LEU X 155 " pdb=" N PRO X 156 " ideal model delta sigma weight residual 1.335 1.361 -0.026 1.36e-02 5.41e+03 3.65e+00 bond pdb=" CA PRO A 246 " pdb=" C PRO A 246 " ideal model delta sigma weight residual 1.514 1.523 -0.008 5.50e-03 3.31e+04 2.35e+00 bond pdb=" C ASP E 726 " pdb=" O ASP E 726 " ideal model delta sigma weight residual 1.235 1.228 0.006 4.70e-03 4.53e+04 1.89e+00 bond pdb=" CG ARG C 711 " pdb=" CD ARG C 711 " ideal model delta sigma weight residual 1.520 1.484 0.036 3.00e-02 1.11e+03 1.45e+00 bond pdb=" CA GLU C 554 " pdb=" CB GLU C 554 " ideal model delta sigma weight residual 1.522 1.538 -0.016 1.32e-02 5.74e+03 1.44e+00 ... (remaining 42309 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.10: 56308 2.10 - 4.20: 880 4.20 - 6.31: 140 6.31 - 8.41: 19 8.41 - 10.51: 5 Bond angle restraints: 57352 Sorted by residual: angle pdb=" C GLU B 712 " pdb=" N ARG B 713 " pdb=" CA ARG B 713 " ideal model delta sigma weight residual 122.38 111.87 10.51 1.81e+00 3.05e-01 3.37e+01 angle pdb=" N VAL D 123 " pdb=" CA VAL D 123 " pdb=" C VAL D 123 " ideal model delta sigma weight residual 111.91 108.51 3.40 8.90e-01 1.26e+00 1.46e+01 angle pdb=" C PHE W 100 " pdb=" N MET W 101 " pdb=" CA MET W 101 " ideal model delta sigma weight residual 121.58 114.19 7.39 1.95e+00 2.63e-01 1.44e+01 angle pdb=" C LEU Z 186 " pdb=" N MET Z 187 " pdb=" CA MET Z 187 " ideal model delta sigma weight residual 122.23 116.33 5.90 1.57e+00 4.06e-01 1.41e+01 angle pdb=" N ILE F 309 " pdb=" CA ILE F 309 " pdb=" C ILE F 309 " ideal model delta sigma weight residual 113.53 109.99 3.54 9.80e-01 1.04e+00 1.30e+01 ... (remaining 57347 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.55: 25390 35.55 - 71.10: 391 71.10 - 106.65: 47 106.65 - 142.20: 5 142.20 - 177.76: 2 Dihedral angle restraints: 25835 sinusoidal: 10340 harmonic: 15495 Sorted by residual: dihedral pdb=" O2A ADP A 902 " pdb=" O3A ADP A 902 " pdb=" PA ADP A 902 " pdb=" PB ADP A 902 " ideal model delta sinusoidal sigma weight residual -60.00 117.76 -177.76 1 2.00e+01 2.50e-03 4.80e+01 dihedral pdb=" C5' ADP A 902 " pdb=" O5' ADP A 902 " pdb=" PA ADP A 902 " pdb=" O2A ADP A 902 " ideal model delta sinusoidal sigma weight residual -60.00 97.03 -157.03 1 2.00e+01 2.50e-03 4.61e+01 dihedral pdb=" O2A ADP C 902 " pdb=" O3A ADP C 902 " pdb=" PA ADP C 902 " pdb=" PB ADP C 902 " ideal model delta sinusoidal sigma weight residual -60.00 69.57 -129.57 1 2.00e+01 2.50e-03 3.93e+01 ... (remaining 25832 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 4280 0.035 - 0.070: 1346 0.070 - 0.105: 616 0.105 - 0.140: 172 0.140 - 0.175: 18 Chirality restraints: 6432 Sorted by residual: chirality pdb=" CA ASP W 139 " pdb=" N ASP W 139 " pdb=" C ASP W 139 " pdb=" CB ASP W 139 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.62e-01 chirality pdb=" C2' ADP E 902 " pdb=" C1' ADP E 902 " pdb=" C3' ADP E 902 " pdb=" O2' ADP E 902 " both_signs ideal model delta sigma weight residual False -2.51 -2.68 0.17 2.00e-01 2.50e+01 7.55e-01 chirality pdb=" CA GLU B 195 " pdb=" N GLU B 195 " pdb=" C GLU B 195 " pdb=" CB GLU B 195 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.37e-01 ... (remaining 6429 not shown) Planarity restraints: 7554 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA C 297 " 0.044 5.00e-02 4.00e+02 6.59e-02 6.95e+00 pdb=" N PRO C 298 " -0.114 5.00e-02 4.00e+02 pdb=" CA PRO C 298 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO C 298 " 0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA B 297 " -0.040 5.00e-02 4.00e+02 6.11e-02 5.97e+00 pdb=" N PRO B 298 " 0.106 5.00e-02 4.00e+02 pdb=" CA PRO B 298 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO B 298 " -0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY C 544 " 0.037 5.00e-02 4.00e+02 5.66e-02 5.12e+00 pdb=" N PRO C 545 " -0.098 5.00e-02 4.00e+02 pdb=" CA PRO C 545 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO C 545 " 0.032 5.00e-02 4.00e+02 ... (remaining 7551 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.67: 971 2.67 - 3.23: 43784 3.23 - 3.79: 68190 3.79 - 4.34: 86325 4.34 - 4.90: 134999 Nonbonded interactions: 334269 Sorted by model distance: nonbonded pdb=" OG1 THR B 127 " pdb=" OG1 THR B 436 " model vdw 2.117 3.040 nonbonded pdb=" OG SER F 748 " pdb=" OD1 ASN F 750 " model vdw 2.127 3.040 nonbonded pdb=" O TRP A 454 " pdb=" OG SER A 457 " model vdw 2.179 3.040 nonbonded pdb=" NH1 ARG B 147 " pdb=" O LYS B 148 " model vdw 2.185 3.120 nonbonded pdb=" OD1 ASN F 624 " pdb=" OH TYR F 755 " model vdw 2.189 3.040 ... (remaining 334264 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 23 through 764 or resid 901 through 902)) selection = (chain 'B' and (resid 23 through 764 or resid 901 through 902)) selection = (chain 'C' and (resid 23 through 764 or resid 901 through 902)) selection = (chain 'D' and resid 23 through 902) selection = (chain 'E' and (resid 23 through 764 or resid 901 through 902)) selection = (chain 'F' and (resid 23 through 764 or resid 901 through 902)) } ncs_group { reference = (chain 'W' and ((resid 1 through 4 and (name N or name CA or name C or name O or \ name CB )) or resid 5 or (resid 6 through 28 and (name N or name CA or name C o \ r name O or name CB )) or resid 29 or (resid 30 through 31 and (name N or name C \ A or name C or name O or name CB )) or resid 32 or (resid 33 through 64 and (nam \ e N or name CA or name C or name O or name CB )) or resid 65 or (resid 66 and (n \ ame N or name CA or name C or name O or name CB )) or resid 67 or (resid 68 and \ (name N or name CA or name C or name O or name CB )) or resid 69 or (resid 70 th \ rough 88 and (name N or name CA or name C or name O or name CB )) or (resid 89 t \ hrough 92 and (name N or name CA or name C or name O or name CB )) or resid 93 o \ r (resid 94 through 112 and (name N or name CA or name C or name O or name CB )) \ or resid 113 or (resid 114 through 146 and (name N or name CA or name C or name \ O or name CB )) or resid 147 or (resid 148 through 160 and (name N or name CA o \ r name C or name O or name CB )) or resid 161 or (resid 162 through 166 and (nam \ e N or name CA or name C or name O or name CB )) or resid 167 through 168 or (re \ sid 169 through 175 and (name N or name CA or name C or name O or name CB )) or \ resid 176 or (resid 177 through 179 and (name N or name CA or name C or name O o \ r name CB )) or resid 180 or (resid 181 through 194 and (name N or name CA or na \ me C or name O or name CB )) or resid 195 through 196 or (resid 197 through 214 \ and (name N or name CA or name C or name O or name CB )) or resid 240 through 25 \ 0)) selection = (chain 'X' and ((resid 1 through 4 and (name N or name CA or name C or name O or \ name CB )) or resid 5 or (resid 6 through 28 and (name N or name CA or name C o \ r name O or name CB )) or resid 29 or (resid 30 through 31 and (name N or name C \ A or name C or name O or name CB )) or resid 32 or (resid 33 through 64 and (nam \ e N or name CA or name C or name O or name CB )) or resid 65 or (resid 66 and (n \ ame N or name CA or name C or name O or name CB )) or resid 67 or (resid 68 and \ (name N or name CA or name C or name O or name CB )) or resid 69 or (resid 70 th \ rough 88 and (name N or name CA or name C or name O or name CB )) or (resid 89 t \ hrough 92 and (name N or name CA or name C or name O or name CB )) or resid 93 o \ r (resid 94 through 112 and (name N or name CA or name C or name O or name CB )) \ or resid 113 or (resid 114 through 146 and (name N or name CA or name C or name \ O or name CB )) or resid 147 or (resid 148 through 160 and (name N or name CA o \ r name C or name O or name CB )) or resid 161 or (resid 162 through 166 and (nam \ e N or name CA or name C or name O or name CB )) or resid 167 through 168 or (re \ sid 169 through 175 and (name N or name CA or name C or name O or name CB )) or \ resid 176 or (resid 177 through 179 and (name N or name CA or name C or name O o \ r name CB )) or resid 180 or (resid 181 through 194 and (name N or name CA or na \ me C or name O or name CB )) or resid 195 through 196 or (resid 197 through 214 \ and (name N or name CA or name C or name O or name CB )) or resid 240 through 25 \ 0)) selection = chain 'Y' selection = chain 'Z' } 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 group one per residue 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: 2.700 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: 0.050 Extract box with map and model: 0.700 Check model and map are aligned: 0.140 Set scattering table: 0.100 Process input model: 37.170 Find NCS groups from input model: 1.040 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.260 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7302 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 : 0.003 0.036 42314 Z= 0.151 Angle : 0.642 10.509 57352 Z= 0.336 Chirality : 0.043 0.175 6432 Planarity : 0.004 0.066 7554 Dihedral : 14.317 177.755 15811 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 15.87 Ramachandran Plot: Outliers : 0.41 % Allowed : 8.09 % Favored : 91.50 % Rotamer: Outliers : 0.00 % Allowed : 0.33 % Favored : 99.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.69 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.24 (0.12), residues: 5365 helix: 0.95 (0.11), residues: 2419 sheet: 0.06 (0.20), residues: 685 loop : -1.47 (0.14), residues: 2261 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 653 TYR 0.011 0.001 TYR X 80 PHE 0.021 0.001 PHE E 742 TRP 0.028 0.001 TRP W 209 HIS 0.007 0.001 HIS A 183 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.15 (42314) covalent geometry : angle 0.64216 / 0.34 (57352) hydrogen bonds : bond 0.16130 / 10.51 ( 1928) hydrogen bonds : angle 6.27816 / 4.52 ( 5562) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10730 Ramachandran restraints generated. 5365 Oldfield, 0 Emsley, 5365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10730 Ramachandran restraints generated. 5365 Oldfield, 0 Emsley, 5365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1531 residues out of total 4598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 1531 time to evaluate : 1.506 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: 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: W 1 MET cc_start: 0.5228 (ppp) cc_final: 0.4770 (ppp) REVERT: W 53 TRP cc_start: 0.3776 (t-100) cc_final: 0.3114 (t60) REVERT: W 106 TRP cc_start: 0.6228 (t60) cc_final: 0.5600 (t-100) REVERT: W 112 THR cc_start: 0.8563 (m) cc_final: 0.8261 (p) REVERT: W 192 MET cc_start: 0.7908 (ppp) cc_final: 0.7703 (ppp) REVERT: W 208 ARG cc_start: 0.6630 (mtt180) cc_final: 0.5648 (tmt-80) REVERT: X 110 VAL cc_start: 0.8514 (p) cc_final: 0.8200 (t) REVERT: A 36 ASN cc_start: 0.8899 (m-40) cc_final: 0.8497 (p0) REVERT: A 150 ASP cc_start: 0.8952 (t0) cc_final: 0.8704 (t70) REVERT: A 205 ASP cc_start: 0.9313 (m-30) cc_final: 0.8943 (m-30) REVERT: A 224 LEU cc_start: 0.8991 (mt) cc_final: 0.8591 (mt) REVERT: A 241 ILE cc_start: 0.9132 (mt) cc_final: 0.8706 (mm) REVERT: A 306 LEU cc_start: 0.8598 (mm) cc_final: 0.8323 (mm) REVERT: A 315 LYS cc_start: 0.9299 (mmtt) cc_final: 0.9086 (mmmt) REVERT: A 326 SER cc_start: 0.9362 (m) cc_final: 0.8921 (t) REVERT: A 368 ASP cc_start: 0.8893 (p0) cc_final: 0.8640 (p0) REVERT: A 369 ILE cc_start: 0.7179 (mm) cc_final: 0.6253 (mt) REVERT: A 415 CYS cc_start: 0.9321 (m) cc_final: 0.9103 (t) REVERT: A 494 GLN cc_start: 0.8608 (tp40) cc_final: 0.8002 (tp-100) REVERT: A 495 TYR cc_start: 0.9026 (m-10) cc_final: 0.8772 (m-80) REVERT: A 535 CYS cc_start: 0.8934 (t) cc_final: 0.8649 (p) REVERT: A 615 LYS cc_start: 0.9031 (mmtt) cc_final: 0.8742 (mmtm) REVERT: A 620 ILE cc_start: 0.9221 (mt) cc_final: 0.9002 (tt) REVERT: A 657 LEU cc_start: 0.9712 (mt) cc_final: 0.9342 (mt) REVERT: A 687 LEU cc_start: 0.8988 (mm) cc_final: 0.8722 (tp) REVERT: A 697 LEU cc_start: 0.9108 (mm) cc_final: 0.8798 (tp) REVERT: A 701 GLU cc_start: 0.9215 (mm-30) cc_final: 0.8789 (tt0) REVERT: A 760 GLN cc_start: 0.8964 (mm110) cc_final: 0.8471 (pp30) REVERT: B 96 LEU cc_start: 0.8697 (mt) cc_final: 0.8390 (mt) REVERT: B 200 GLU cc_start: 0.8605 (mm-30) cc_final: 0.7858 (mp0) REVERT: B 203 TYR cc_start: 0.8039 (m-80) cc_final: 0.7561 (m-10) REVERT: B 219 MET cc_start: 0.8531 (ppp) cc_final: 0.8129 (ppp) REVERT: B 277 LYS cc_start: 0.8512 (tppt) cc_final: 0.8209 (tttt) REVERT: B 278 LEU cc_start: 0.8966 (tp) cc_final: 0.8572 (tt) REVERT: B 291 GLU cc_start: 0.8624 (pp20) cc_final: 0.8403 (pp20) REVERT: B 321 GLU cc_start: 0.9369 (mp0) cc_final: 0.9073 (pm20) REVERT: B 331 LEU cc_start: 0.9147 (mt) cc_final: 0.8783 (mt) REVERT: B 336 LYS cc_start: 0.8987 (mmtt) cc_final: 0.8612 (mmmt) REVERT: B 401 ASN cc_start: 0.8911 (m110) cc_final: 0.8679 (t0) REVERT: B 424 ARG cc_start: 0.8589 (ttm110) cc_final: 0.8133 (ttp80) REVERT: B 484 ASP cc_start: 0.8901 (m-30) cc_final: 0.8377 (p0) REVERT: B 563 PHE cc_start: 0.9319 (m-10) cc_final: 0.9082 (m-80) REVERT: B 578 GLU cc_start: 0.8222 (mt-10) cc_final: 0.7928 (mt-10) REVERT: B 607 GLU cc_start: 0.8933 (mm-30) cc_final: 0.8658 (tp30) REVERT: B 611 MET cc_start: 0.7744 (mmp) cc_final: 0.6904 (mmp) REVERT: B 686 ASP cc_start: 0.9200 (t70) cc_final: 0.8960 (m-30) REVERT: B 691 CYS cc_start: 0.9648 (m) cc_final: 0.9286 (m) REVERT: B 695 CYS cc_start: 0.9328 (m) cc_final: 0.9112 (m) REVERT: B 725 ASP cc_start: 0.6066 (p0) cc_final: 0.5320 (t0) REVERT: C 46 MET cc_start: 0.8530 (ppp) cc_final: 0.8296 (ppp) REVERT: C 162 GLU cc_start: 0.8290 (mt-10) cc_final: 0.7803 (tm-30) REVERT: C 168 THR cc_start: 0.5633 (p) cc_final: 0.4920 (p) REVERT: C 325 VAL cc_start: 0.9543 (t) cc_final: 0.9295 (p) REVERT: C 331 LEU cc_start: 0.8993 (mt) cc_final: 0.8589 (mt) REVERT: C 340 HIS cc_start: 0.8138 (m-70) cc_final: 0.7374 (m-70) REVERT: C 341 VAL cc_start: 0.8667 (t) cc_final: 0.8177 (t) REVERT: C 388 MET cc_start: 0.7482 (mmp) cc_final: 0.7222 (tpt) REVERT: C 398 GLN cc_start: 0.8903 (tt0) cc_final: 0.8469 (tm-30) REVERT: C 401 ASN cc_start: 0.9335 (m110) cc_final: 0.9074 (p0) REVERT: C 421 GLN cc_start: 0.9380 (tp-100) cc_final: 0.8342 (tm-30) REVERT: C 438 ASP cc_start: 0.8179 (p0) cc_final: 0.7841 (p0) REVERT: C 450 ASP cc_start: 0.8816 (t70) cc_final: 0.8529 (t0) REVERT: C 491 GLU cc_start: 0.8440 (mt-10) cc_final: 0.8097 (mt-10) REVERT: C 515 LEU cc_start: 0.9353 (mt) cc_final: 0.8733 (pp) REVERT: C 522 CYS cc_start: 0.7588 (m) cc_final: 0.6737 (p) REVERT: C 524 LYS cc_start: 0.8688 (mttm) cc_final: 0.8440 (mtmt) REVERT: C 565 LYS cc_start: 0.9365 (ttmt) cc_final: 0.9124 (tptp) REVERT: C 575 PHE cc_start: 0.8159 (t80) cc_final: 0.7472 (t80) REVERT: C 636 PRO cc_start: 0.9020 (Cg_exo) cc_final: 0.8693 (Cg_endo) REVERT: C 695 CYS cc_start: 0.9410 (m) cc_final: 0.9076 (t) REVERT: D 62 LYS cc_start: 0.8386 (mttt) cc_final: 0.8025 (mtmm) REVERT: D 326 SER cc_start: 0.9530 (m) cc_final: 0.8650 (t) REVERT: D 410 ASP cc_start: 0.8844 (m-30) cc_final: 0.8628 (t70) REVERT: D 491 GLU cc_start: 0.7840 (tt0) cc_final: 0.7365 (tt0) REVERT: D 495 TYR cc_start: 0.8692 (m-10) cc_final: 0.8398 (m-10) REVERT: D 517 TYR cc_start: 0.8932 (p90) cc_final: 0.8595 (p90) REVERT: D 527 LEU cc_start: 0.9278 (mm) cc_final: 0.9024 (tp) REVERT: D 560 ARG cc_start: 0.9222 (mtt90) cc_final: 0.8783 (ptp-110) REVERT: D 603 GLN cc_start: 0.8403 (mt0) cc_final: 0.8063 (mt0) REVERT: D 661 LEU cc_start: 0.9288 (mt) cc_final: 0.8850 (pp) REVERT: D 720 MET cc_start: 0.0906 (ppp) cc_final: 0.0432 (ppp) REVERT: E 84 MET cc_start: 0.5783 (tmm) cc_final: 0.5260 (tmm) REVERT: E 90 ASN cc_start: 0.8433 (m110) cc_final: 0.8180 (t0) REVERT: E 105 CYS cc_start: 0.6735 (t) cc_final: 0.6395 (m) REVERT: E 219 MET cc_start: 0.7484 (mpp) cc_final: 0.7193 (mpp) REVERT: E 231 LYS cc_start: 0.8294 (mmtt) cc_final: 0.8087 (tptt) REVERT: E 270 ASN cc_start: 0.7884 (m-40) cc_final: 0.7654 (t0) REVERT: E 302 PHE cc_start: 0.8694 (t80) cc_final: 0.8263 (t80) REVERT: E 469 VAL cc_start: 0.7850 (p) cc_final: 0.7619 (m) REVERT: E 488 GLU cc_start: 0.8600 (mm-30) cc_final: 0.8046 (mm-30) REVERT: E 563 PHE cc_start: 0.9175 (m-80) cc_final: 0.8825 (m-80) REVERT: E 573 VAL cc_start: 0.8971 (t) cc_final: 0.8664 (m) REVERT: E 603 GLN cc_start: 0.9000 (mm-40) cc_final: 0.8417 (mm110) REVERT: E 607 GLU cc_start: 0.8774 (mm-30) cc_final: 0.8530 (mm-30) REVERT: E 720 MET cc_start: 0.4236 (mmm) cc_final: 0.3754 (ptt) REVERT: E 740 MET cc_start: 0.5035 (ppp) cc_final: 0.4496 (ppp) REVERT: F 84 MET cc_start: 0.5697 (tmm) cc_final: 0.5088 (tmm) REVERT: F 158 MET cc_start: 0.6241 (ptt) cc_final: 0.5944 (ptt) REVERT: F 194 GLU cc_start: 0.6472 (pm20) cc_final: 0.6111 (tp30) REVERT: F 203 TYR cc_start: 0.7150 (m-80) cc_final: 0.6288 (m-80) REVERT: F 283 GLU cc_start: 0.8788 (mt-10) cc_final: 0.7577 (mm-30) REVERT: F 305 GLU cc_start: 0.8961 (mt-10) cc_final: 0.8667 (mt-10) REVERT: F 312 LYS cc_start: 0.9350 (tppp) cc_final: 0.9040 (tptp) REVERT: F 330 THR cc_start: 0.8927 (m) cc_final: 0.8555 (p) REVERT: F 331 LEU cc_start: 0.9486 (mt) cc_final: 0.9211 (mt) REVERT: F 362 ARG cc_start: 0.7900 (mtt180) cc_final: 0.7207 (mmt90) REVERT: F 404 HIS cc_start: 0.8821 (p90) cc_final: 0.8311 (p-80) REVERT: F 411 LEU cc_start: 0.9578 (mt) cc_final: 0.9047 (mt) REVERT: F 417 GLU cc_start: 0.7518 (pt0) cc_final: 0.7267 (pt0) REVERT: F 442 MET cc_start: 0.8493 (ppp) cc_final: 0.7977 (ppp) REVERT: F 460 ASN cc_start: 0.9064 (t0) cc_final: 0.8807 (t0) REVERT: F 524 LYS cc_start: 0.8431 (mttp) cc_final: 0.7736 (mttt) REVERT: F 529 LYS cc_start: 0.8832 (mtpp) cc_final: 0.8575 (ptpt) REVERT: F 551 TRP cc_start: 0.8387 (t60) cc_final: 0.8110 (t60) REVERT: F 611 MET cc_start: 0.8399 (mmp) cc_final: 0.8036 (tpt) REVERT: F 678 MET cc_start: 0.8115 (ptp) cc_final: 0.7881 (ptp) REVERT: F 736 PHE cc_start: 0.8899 (m-80) cc_final: 0.8360 (m-80) outliers start: 0 outliers final: 0 residues processed: 1531 average time/residue: 0.2758 time to fit residues: 671.4552 Evaluate side-chains 898 residues out of total 4598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 898 time to evaluate : 1.686 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 534 random chunks: chunk 394 optimal weight: 9.9990 chunk 430 optimal weight: 2.9990 chunk 41 optimal weight: 20.0000 chunk 265 optimal weight: 1.9990 chunk 523 optimal weight: 7.9990 chunk 497 optimal weight: 3.9990 chunk 414 optimal weight: 0.8980 chunk 310 optimal weight: 5.9990 chunk 488 optimal weight: 5.9990 chunk 366 optimal weight: 6.9990 chunk 223 optimal weight: 20.0000 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... X 51 GLN X 105 ASN X 181 HIS A 317 HIS A 384 HIS A 398 GLN A 568 GLN ** A 735 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 36 ASN B 401 ASN B 602 ASN C 43 GLN C 91 ASN C 260 ASN C 296 ASN C 382 GLN C 384 HIS ** C 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 624 ASN C 714 GLN D 327 GLN D 490 GLN D 603 GLN E 536 GLN F 317 HIS F 340 HIS Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4038 r_free = 0.4038 target = 0.123921 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.087109 restraints weight = 142979.342| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.090044 restraints weight = 84521.320| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.092045 restraints weight = 59365.295| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 51)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.093343 restraints weight = 46608.089| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.094196 restraints weight = 39614.283| |-----------------------------------------------------------------------------| r_work (final): 0.3530 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7585 moved from start: 0.3167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.084 42314 Z= 0.209 Angle : 0.713 8.764 57352 Z= 0.368 Chirality : 0.046 0.343 6432 Planarity : 0.006 0.084 7554 Dihedral : 7.383 164.977 5927 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 15.40 Ramachandran Plot: Outliers : 0.41 % Allowed : 7.94 % Favored : 91.65 % Rotamer: Outliers : 0.07 % Allowed : 5.89 % Favored : 94.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.69 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.46 (0.12), residues: 5365 helix: 0.69 (0.10), residues: 2504 sheet: 0.08 (0.20), residues: 650 loop : -1.58 (0.14), residues: 2211 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.022 0.001 ARG D 349 TYR 0.021 0.002 TYR E 203 PHE 0.038 0.002 PHE F 674 TRP 0.040 0.003 TRP W 42 HIS 0.006 0.001 HIS C 115 Details of bonding type rmsd/Z covalent geometry : bond 0.00450 / 0.21 (42314) covalent geometry : angle 0.71347 / 0.37 (57352) hydrogen bonds : bond 0.04596 / 3.06 ( 1928) hydrogen bonds : angle 5.10907 / 3.69 ( 5562) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10730 Ramachandran restraints generated. 5365 Oldfield, 0 Emsley, 5365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10730 Ramachandran restraints generated. 5365 Oldfield, 0 Emsley, 5365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1071 residues out of total 4598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 1068 time to evaluate : 1.657 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: 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: W 53 TRP cc_start: 0.3775 (t-100) cc_final: 0.3267 (t60) REVERT: W 76 LEU cc_start: 0.8234 (tt) cc_final: 0.7756 (mm) REVERT: W 105 ASN cc_start: 0.1629 (m110) cc_final: 0.1306 (m110) REVERT: W 106 TRP cc_start: 0.5636 (t60) cc_final: 0.5430 (t60) REVERT: W 186 LEU cc_start: 0.7202 (tt) cc_final: 0.6852 (mm) REVERT: W 208 ARG cc_start: 0.6536 (mtt180) cc_final: 0.5580 (tmt-80) REVERT: X 1 MET cc_start: 0.1771 (ttt) cc_final: 0.1568 (mtt) REVERT: X 181 HIS cc_start: 0.8560 (t70) cc_final: 0.8030 (p-80) REVERT: Y 247 ARG cc_start: 0.6126 (mmp80) cc_final: 0.5374 (mmm160) REVERT: A 36 ASN cc_start: 0.9003 (m-40) cc_final: 0.8474 (p0) REVERT: A 84 MET cc_start: 0.8363 (tmm) cc_final: 0.8139 (tmm) REVERT: A 96 LEU cc_start: 0.9144 (tt) cc_final: 0.8906 (tp) REVERT: A 150 ASP cc_start: 0.8959 (t0) cc_final: 0.8606 (t70) REVERT: A 204 ASP cc_start: 0.9286 (p0) cc_final: 0.8940 (p0) REVERT: A 205 ASP cc_start: 0.9071 (m-30) cc_final: 0.8870 (m-30) REVERT: A 241 ILE cc_start: 0.9181 (mt) cc_final: 0.8849 (mm) REVERT: A 326 SER cc_start: 0.9465 (m) cc_final: 0.9070 (p) REVERT: A 410 ASP cc_start: 0.8930 (t0) cc_final: 0.8662 (t70) REVERT: A 491 GLU cc_start: 0.8946 (mt-10) cc_final: 0.8171 (mm-30) REVERT: A 494 GLN cc_start: 0.8263 (tp40) cc_final: 0.7832 (tp-100) REVERT: A 495 TYR cc_start: 0.9132 (m-10) cc_final: 0.8338 (m-80) REVERT: A 561 GLU cc_start: 0.9081 (pm20) cc_final: 0.8856 (pm20) REVERT: A 564 ASP cc_start: 0.9083 (m-30) cc_final: 0.8586 (m-30) REVERT: A 575 PHE cc_start: 0.8987 (t80) cc_final: 0.8550 (t80) REVERT: A 608 MET cc_start: 0.9179 (tmm) cc_final: 0.8848 (tmm) REVERT: A 609 ASP cc_start: 0.8945 (p0) cc_final: 0.8744 (p0) REVERT: A 634 LEU cc_start: 0.9055 (mm) cc_final: 0.8248 (tt) REVERT: A 701 GLU cc_start: 0.9233 (mm-30) cc_final: 0.8821 (tt0) REVERT: A 740 MET cc_start: 0.8014 (tmm) cc_final: 0.7683 (tmm) REVERT: A 749 ASP cc_start: 0.8539 (t0) cc_final: 0.8337 (t0) REVERT: A 760 GLN cc_start: 0.8923 (mm110) cc_final: 0.8408 (pp30) REVERT: B 36 ASN cc_start: 0.9393 (m-40) cc_final: 0.9030 (p0) REVERT: B 120 ASP cc_start: 0.9186 (t70) cc_final: 0.8812 (p0) REVERT: B 121 ASP cc_start: 0.9317 (m-30) cc_final: 0.9044 (m-30) REVERT: B 162 GLU cc_start: 0.9329 (pt0) cc_final: 0.8932 (pm20) REVERT: B 200 GLU cc_start: 0.8596 (mm-30) cc_final: 0.7988 (mp0) REVERT: B 219 MET cc_start: 0.8586 (ppp) cc_final: 0.8296 (ppp) REVERT: B 236 LYS cc_start: 0.9095 (tptm) cc_final: 0.8811 (tptm) REVERT: B 267 PHE cc_start: 0.8435 (t80) cc_final: 0.7787 (t80) REVERT: B 291 GLU cc_start: 0.8243 (pp20) cc_final: 0.7802 (pp20) REVERT: B 321 GLU cc_start: 0.9490 (mp0) cc_final: 0.9144 (pm20) REVERT: B 332 MET cc_start: 0.8970 (ttp) cc_final: 0.8460 (ppp) REVERT: B 484 ASP cc_start: 0.9069 (m-30) cc_final: 0.8507 (p0) REVERT: B 563 PHE cc_start: 0.9358 (m-10) cc_final: 0.9094 (m-80) REVERT: B 602 ASN cc_start: 0.8297 (t160) cc_final: 0.7673 (t0) REVERT: B 607 GLU cc_start: 0.8977 (mm-30) cc_final: 0.8668 (tp30) REVERT: B 611 MET cc_start: 0.8118 (mmp) cc_final: 0.6832 (mmp) REVERT: B 686 ASP cc_start: 0.9153 (t70) cc_final: 0.8719 (m-30) REVERT: B 695 CYS cc_start: 0.9392 (m) cc_final: 0.9184 (m) REVERT: B 757 MET cc_start: 0.9369 (mmt) cc_final: 0.9096 (mmm) REVERT: C 46 MET cc_start: 0.8629 (ppp) cc_final: 0.8276 (ppp) REVERT: C 153 LEU cc_start: 0.9076 (tt) cc_final: 0.8807 (tt) REVERT: C 218 GLU cc_start: 0.9121 (tp30) cc_final: 0.8878 (tp30) REVERT: C 331 LEU cc_start: 0.9278 (mt) cc_final: 0.8879 (mt) REVERT: C 340 HIS cc_start: 0.7611 (m-70) cc_final: 0.7387 (m-70) REVERT: C 344 MET cc_start: 0.9142 (mmp) cc_final: 0.8895 (mmp) REVERT: C 385 THR cc_start: 0.9204 (p) cc_final: 0.8899 (t) REVERT: C 388 MET cc_start: 0.7320 (mmp) cc_final: 0.6932 (tpp) REVERT: C 401 ASN cc_start: 0.9300 (m110) cc_final: 0.8955 (p0) REVERT: C 421 GLN cc_start: 0.9490 (tp-100) cc_final: 0.8442 (tm-30) REVERT: C 488 GLU cc_start: 0.9258 (mt-10) cc_final: 0.9032 (mp0) REVERT: C 489 LEU cc_start: 0.9483 (mt) cc_final: 0.9270 (mt) REVERT: C 515 LEU cc_start: 0.9269 (mt) cc_final: 0.8564 (pp) REVERT: C 522 CYS cc_start: 0.7945 (m) cc_final: 0.7228 (p) REVERT: C 607 GLU cc_start: 0.9302 (tp30) cc_final: 0.9094 (tp30) REVERT: C 689 GLU cc_start: 0.9515 (mt-10) cc_final: 0.9194 (mt-10) REVERT: C 695 CYS cc_start: 0.9442 (m) cc_final: 0.9241 (t) REVERT: C 697 LEU cc_start: 0.9426 (tp) cc_final: 0.9213 (tt) REVERT: D 283 GLU cc_start: 0.9293 (pp20) cc_final: 0.8592 (pp20) REVERT: D 312 LYS cc_start: 0.8928 (mtpp) cc_final: 0.8701 (mtpt) REVERT: D 316 THR cc_start: 0.7964 (p) cc_final: 0.6763 (p) REVERT: D 495 TYR cc_start: 0.8955 (m-10) cc_final: 0.8684 (m-10) REVERT: D 515 LEU cc_start: 0.9388 (tt) cc_final: 0.9158 (tt) REVERT: D 517 TYR cc_start: 0.9140 (p90) cc_final: 0.8573 (p90) REVERT: D 560 ARG cc_start: 0.9141 (mtt90) cc_final: 0.8822 (mtt90) REVERT: D 564 ASP cc_start: 0.9035 (m-30) cc_final: 0.8815 (m-30) REVERT: D 604 ILE cc_start: 0.9776 (mt) cc_final: 0.9540 (mt) REVERT: D 642 LEU cc_start: 0.8923 (tp) cc_final: 0.8428 (tt) REVERT: D 660 ASN cc_start: 0.8237 (p0) cc_final: 0.7953 (p0) REVERT: E 90 ASN cc_start: 0.8460 (m110) cc_final: 0.7981 (t0) REVERT: E 105 CYS cc_start: 0.6703 (t) cc_final: 0.5987 (m) REVERT: E 261 GLU cc_start: 0.8217 (tp30) cc_final: 0.7792 (tp30) REVERT: E 275 MET cc_start: 0.9011 (tmm) cc_final: 0.8626 (tmm) REVERT: E 302 PHE cc_start: 0.8891 (t80) cc_final: 0.8531 (t80) REVERT: E 315 LYS cc_start: 0.9389 (mmpt) cc_final: 0.9147 (mmmt) REVERT: E 321 GLU cc_start: 0.9294 (mp0) cc_final: 0.8853 (pm20) REVERT: E 332 MET cc_start: 0.9018 (tmm) cc_final: 0.8766 (tmm) REVERT: E 379 GLU cc_start: 0.9244 (mp0) cc_final: 0.8931 (mm-30) REVERT: E 548 LEU cc_start: 0.8930 (tt) cc_final: 0.8694 (tp) REVERT: E 551 TRP cc_start: 0.6999 (m-10) cc_final: 0.6129 (m100) REVERT: E 563 PHE cc_start: 0.9096 (m-80) cc_final: 0.8863 (m-80) REVERT: E 573 VAL cc_start: 0.9435 (t) cc_final: 0.9232 (m) REVERT: E 603 GLN cc_start: 0.9537 (mm-40) cc_final: 0.8596 (mm-40) REVERT: E 607 GLU cc_start: 0.9156 (mm-30) cc_final: 0.8549 (mm-30) REVERT: E 673 GLU cc_start: 0.8954 (mm-30) cc_final: 0.8712 (mp0) REVERT: E 720 MET cc_start: 0.4524 (mmm) cc_final: 0.3845 (ptt) REVERT: E 740 MET cc_start: 0.5513 (ppp) cc_final: 0.5277 (ppp) REVERT: F 84 MET cc_start: 0.6163 (tmm) cc_final: 0.5416 (tmm) REVERT: F 273 GLU cc_start: 0.8911 (mt-10) cc_final: 0.8661 (mt-10) REVERT: F 312 LYS cc_start: 0.9386 (tppp) cc_final: 0.9180 (tptp) REVERT: F 321 GLU cc_start: 0.8301 (pm20) cc_final: 0.8097 (pm20) REVERT: F 329 LEU cc_start: 0.9734 (tp) cc_final: 0.9491 (tp) REVERT: F 331 LEU cc_start: 0.9606 (mt) cc_final: 0.9391 (mt) REVERT: F 344 MET cc_start: 0.9327 (ptp) cc_final: 0.9092 (ptp) REVERT: F 403 THR cc_start: 0.8800 (m) cc_final: 0.8167 (m) REVERT: F 404 HIS cc_start: 0.8772 (p90) cc_final: 0.8380 (p-80) REVERT: F 411 LEU cc_start: 0.9399 (mt) cc_final: 0.8914 (tp) REVERT: F 442 MET cc_start: 0.8453 (ppp) cc_final: 0.8121 (ppp) REVERT: F 529 LYS cc_start: 0.9016 (mtpp) cc_final: 0.8752 (ptpt) REVERT: F 663 LYS cc_start: 0.8623 (mmtm) cc_final: 0.8286 (mmtm) REVERT: F 736 PHE cc_start: 0.8839 (m-80) cc_final: 0.8193 (m-80) outliers start: 3 outliers final: 1 residues processed: 1070 average time/residue: 0.2677 time to fit residues: 465.7940 Evaluate side-chains 761 residues out of total 4598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 760 time to evaluate : 1.676 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 534 random chunks: chunk 228 optimal weight: 9.9990 chunk 161 optimal weight: 6.9990 chunk 390 optimal weight: 10.0000 chunk 167 optimal weight: 20.0000 chunk 478 optimal weight: 3.9990 chunk 106 optimal weight: 3.9990 chunk 62 optimal weight: 50.0000 chunk 389 optimal weight: 5.9990 chunk 82 optimal weight: 30.0000 chunk 133 optimal weight: 0.2980 chunk 360 optimal weight: 5.9990 overall best weight: 4.0588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 260 ASN A 494 GLN A 499 HIS A 568 GLN ** B 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 603 GLN C 317 HIS C 384 HIS ** C 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 494 GLN ** D 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 536 GLN ** D 602 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 296 ASN ** E 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 602 ASN ** F 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 317 HIS F 327 GLN F 340 HIS ** F 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.121236 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.085204 restraints weight = 145989.989| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.087849 restraints weight = 88449.517| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.089222 restraints weight = 58062.814| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.089834 restraints weight = 47607.234| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.089960 restraints weight = 44862.033| |-----------------------------------------------------------------------------| r_work (final): 0.3436 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7754 moved from start: 0.4058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.135 42314 Z= 0.232 Angle : 0.736 9.572 57352 Z= 0.377 Chirality : 0.047 0.421 6432 Planarity : 0.006 0.085 7554 Dihedral : 7.327 147.685 5927 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 16.60 Ramachandran Plot: Outliers : 0.41 % Allowed : 8.46 % Favored : 91.13 % Rotamer: Outliers : 0.07 % Allowed : 5.61 % Favored : 94.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.69 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.79 (0.11), residues: 5365 helix: 0.46 (0.10), residues: 2502 sheet: -0.12 (0.20), residues: 657 loop : -1.80 (0.13), residues: 2206 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG E 89 TYR 0.021 0.002 TYR C 143 PHE 0.050 0.002 PHE F 552 TRP 0.047 0.003 TRP D 476 HIS 0.006 0.001 HIS C 384 Details of bonding type rmsd/Z covalent geometry : bond 0.00495 / 0.23 (42314) covalent geometry : angle 0.73568 / 0.38 (57352) hydrogen bonds : bond 0.04613 / 3.06 ( 1928) hydrogen bonds : angle 5.10867 / 3.70 ( 5562) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10730 Ramachandran restraints generated. 5365 Oldfield, 0 Emsley, 5365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10730 Ramachandran restraints generated. 5365 Oldfield, 0 Emsley, 5365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 952 residues out of total 4598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 949 time to evaluate : 2.039 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: 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: W 53 TRP cc_start: 0.3780 (t-100) cc_final: 0.3259 (t60) REVERT: W 75 ASN cc_start: 0.8019 (m110) cc_final: 0.7623 (m110) REVERT: W 76 LEU cc_start: 0.8280 (tt) cc_final: 0.7800 (mm) REVERT: W 116 MET cc_start: 0.6915 (mtm) cc_final: 0.6385 (ttt) REVERT: W 118 MET cc_start: 0.1548 (pmm) cc_final: 0.0767 (pmm) REVERT: W 186 LEU cc_start: 0.7151 (tt) cc_final: 0.6876 (mm) REVERT: X 99 LEU cc_start: 0.8866 (mm) cc_final: 0.8354 (tp) REVERT: X 103 LEU cc_start: 0.9268 (mm) cc_final: 0.9052 (mm) REVERT: Y 247 ARG cc_start: 0.6473 (mmp80) cc_final: 0.5671 (mmm160) REVERT: A 150 ASP cc_start: 0.9072 (t0) cc_final: 0.8761 (t70) REVERT: A 198 LEU cc_start: 0.9395 (tt) cc_final: 0.9176 (tt) REVERT: A 204 ASP cc_start: 0.9340 (p0) cc_final: 0.8895 (p0) REVERT: A 291 GLU cc_start: 0.9018 (tp30) cc_final: 0.8797 (tm-30) REVERT: A 326 SER cc_start: 0.9521 (m) cc_final: 0.9080 (t) REVERT: A 410 ASP cc_start: 0.8941 (t0) cc_final: 0.8691 (t70) REVERT: A 494 GLN cc_start: 0.8379 (tp-100) cc_final: 0.7866 (tp-100) REVERT: A 495 TYR cc_start: 0.9124 (m-10) cc_final: 0.8815 (m-80) REVERT: A 564 ASP cc_start: 0.9130 (m-30) cc_final: 0.8454 (m-30) REVERT: A 608 MET cc_start: 0.9225 (tmm) cc_final: 0.8394 (tmm) REVERT: A 613 THR cc_start: 0.8305 (p) cc_final: 0.8024 (t) REVERT: A 634 LEU cc_start: 0.9066 (mm) cc_final: 0.8275 (tt) REVERT: A 701 GLU cc_start: 0.9276 (mm-30) cc_final: 0.8941 (tt0) REVERT: A 740 MET cc_start: 0.8019 (tmm) cc_final: 0.7668 (tmm) REVERT: A 760 GLN cc_start: 0.9075 (mm110) cc_final: 0.8458 (pp30) REVERT: B 36 ASN cc_start: 0.9303 (m-40) cc_final: 0.9039 (p0) REVERT: B 120 ASP cc_start: 0.9213 (t70) cc_final: 0.8940 (p0) REVERT: B 121 ASP cc_start: 0.9305 (m-30) cc_final: 0.9060 (m-30) REVERT: B 133 VAL cc_start: 0.9209 (t) cc_final: 0.8983 (m) REVERT: B 162 GLU cc_start: 0.9320 (pt0) cc_final: 0.8939 (pm20) REVERT: B 200 GLU cc_start: 0.8686 (mm-30) cc_final: 0.8181 (mp0) REVERT: B 236 LYS cc_start: 0.9243 (tptm) cc_final: 0.8997 (tptm) REVERT: B 267 PHE cc_start: 0.8567 (t80) cc_final: 0.7706 (t80) REVERT: B 291 GLU cc_start: 0.8048 (pp20) cc_final: 0.7847 (pp20) REVERT: B 321 GLU cc_start: 0.9560 (mp0) cc_final: 0.9172 (pm20) REVERT: B 332 MET cc_start: 0.8911 (ttp) cc_final: 0.8467 (tpp) REVERT: B 398 GLN cc_start: 0.9202 (tt0) cc_final: 0.8875 (tp-100) REVERT: B 401 ASN cc_start: 0.8845 (t0) cc_final: 0.8614 (t0) REVERT: B 484 ASP cc_start: 0.9201 (m-30) cc_final: 0.8568 (p0) REVERT: B 542 ILE cc_start: 0.8886 (mm) cc_final: 0.8561 (mt) REVERT: B 578 GLU cc_start: 0.8450 (mt-10) cc_final: 0.7588 (mt-10) REVERT: B 602 ASN cc_start: 0.8187 (t0) cc_final: 0.7963 (t0) REVERT: B 686 ASP cc_start: 0.9220 (t70) cc_final: 0.8760 (m-30) REVERT: B 691 CYS cc_start: 0.9465 (m) cc_final: 0.9233 (m) REVERT: B 695 CYS cc_start: 0.9454 (m) cc_final: 0.9136 (m) REVERT: B 757 MET cc_start: 0.9440 (mmt) cc_final: 0.9224 (mmm) REVERT: C 46 MET cc_start: 0.8729 (ppp) cc_final: 0.8363 (ppp) REVERT: C 84 MET cc_start: 0.7732 (ppp) cc_final: 0.7474 (ppp) REVERT: C 218 GLU cc_start: 0.9096 (tp30) cc_final: 0.8855 (tp30) REVERT: C 251 LYS cc_start: 0.9506 (ptpp) cc_final: 0.9255 (pttt) REVERT: C 270 ASN cc_start: 0.8905 (p0) cc_final: 0.8598 (p0) REVERT: C 331 LEU cc_start: 0.9297 (mt) cc_final: 0.8948 (mt) REVERT: C 417 GLU cc_start: 0.8784 (pt0) cc_final: 0.8578 (pt0) REVERT: C 421 GLN cc_start: 0.9498 (tp-100) cc_final: 0.9236 (tp40) REVERT: C 488 GLU cc_start: 0.9132 (mt-10) cc_final: 0.8877 (mp0) REVERT: C 489 LEU cc_start: 0.9489 (mt) cc_final: 0.9281 (mt) REVERT: C 517 TYR cc_start: 0.8883 (p90) cc_final: 0.8630 (p90) REVERT: C 522 CYS cc_start: 0.8048 (m) cc_final: 0.7416 (p) REVERT: C 689 GLU cc_start: 0.9519 (mt-10) cc_final: 0.9162 (mt-10) REVERT: D 283 GLU cc_start: 0.9251 (pp20) cc_final: 0.8369 (pp20) REVERT: D 285 ASN cc_start: 0.9140 (m110) cc_final: 0.8923 (m110) REVERT: D 312 LYS cc_start: 0.9004 (mtpp) cc_final: 0.8746 (mtpt) REVERT: D 326 SER cc_start: 0.9619 (m) cc_final: 0.8769 (t) REVERT: D 351 ASN cc_start: 0.8708 (m-40) cc_final: 0.8258 (m110) REVERT: D 354 ASP cc_start: 0.8999 (t0) cc_final: 0.8731 (t0) REVERT: D 460 ASN cc_start: 0.9391 (t0) cc_final: 0.9062 (p0) REVERT: D 495 TYR cc_start: 0.8972 (m-10) cc_final: 0.8770 (m-10) REVERT: D 515 LEU cc_start: 0.9406 (tt) cc_final: 0.9141 (tt) REVERT: D 517 TYR cc_start: 0.9080 (p90) cc_final: 0.8325 (p90) REVERT: D 560 ARG cc_start: 0.9194 (mtt90) cc_final: 0.8766 (mtt90) REVERT: D 572 CYS cc_start: 0.8370 (p) cc_final: 0.8106 (p) REVERT: E 90 ASN cc_start: 0.8423 (m110) cc_final: 0.8010 (t0) REVERT: E 158 MET cc_start: 0.6196 (mtp) cc_final: 0.5867 (mtm) REVERT: E 275 MET cc_start: 0.8915 (tmm) cc_final: 0.8634 (tpt) REVERT: E 306 LEU cc_start: 0.9455 (pp) cc_final: 0.9249 (pp) REVERT: E 314 GLU cc_start: 0.8699 (tm-30) cc_final: 0.8411 (tm-30) REVERT: E 315 LYS cc_start: 0.9482 (mmpt) cc_final: 0.9027 (mmmt) REVERT: E 321 GLU cc_start: 0.9330 (mp0) cc_final: 0.8897 (pm20) REVERT: E 332 MET cc_start: 0.8932 (tmm) cc_final: 0.8729 (tmm) REVERT: E 548 LEU cc_start: 0.9177 (tt) cc_final: 0.8831 (mt) REVERT: E 551 TRP cc_start: 0.7179 (m-10) cc_final: 0.5721 (m100) REVERT: E 603 GLN cc_start: 0.9591 (mm-40) cc_final: 0.8628 (mm-40) REVERT: E 607 GLU cc_start: 0.9184 (mm-30) cc_final: 0.8501 (mm-30) REVERT: E 720 MET cc_start: 0.4638 (mmm) cc_final: 0.4080 (ptt) REVERT: F 84 MET cc_start: 0.6173 (tmm) cc_final: 0.5188 (tmm) REVERT: F 273 GLU cc_start: 0.8917 (mt-10) cc_final: 0.8684 (mt-10) REVERT: F 275 MET cc_start: 0.9607 (mmm) cc_final: 0.9357 (tpp) REVERT: F 278 LEU cc_start: 0.9239 (tp) cc_final: 0.9034 (tt) REVERT: F 285 ASN cc_start: 0.9633 (m-40) cc_final: 0.9385 (m110) REVERT: F 291 GLU cc_start: 0.9001 (pt0) cc_final: 0.8790 (pt0) REVERT: F 312 LYS cc_start: 0.9397 (tppp) cc_final: 0.9174 (tptp) REVERT: F 321 GLU cc_start: 0.8334 (pm20) cc_final: 0.7967 (pm20) REVERT: F 331 LEU cc_start: 0.9646 (mt) cc_final: 0.9403 (mt) REVERT: F 404 HIS cc_start: 0.8891 (p90) cc_final: 0.8413 (p-80) REVERT: F 411 LEU cc_start: 0.9420 (mt) cc_final: 0.8942 (tp) REVERT: F 442 MET cc_start: 0.8476 (ppp) cc_final: 0.8120 (ppp) REVERT: F 460 ASN cc_start: 0.8966 (t0) cc_final: 0.8760 (t0) REVERT: F 492 LEU cc_start: 0.9216 (mt) cc_final: 0.9015 (mt) REVERT: F 529 LYS cc_start: 0.9097 (mtpp) cc_final: 0.8847 (ptpt) REVERT: F 577 ASP cc_start: 0.9163 (t70) cc_final: 0.8501 (t70) REVERT: F 640 ASP cc_start: 0.6953 (m-30) cc_final: 0.6649 (m-30) REVERT: F 736 PHE cc_start: 0.8896 (m-80) cc_final: 0.8182 (m-80) REVERT: F 738 GLU cc_start: 0.9178 (mm-30) cc_final: 0.8729 (tp30) outliers start: 3 outliers final: 2 residues processed: 950 average time/residue: 0.2620 time to fit residues: 407.5452 Evaluate side-chains 723 residues out of total 4598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 721 time to evaluate : 1.631 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 534 random chunks: chunk 232 optimal weight: 8.9990 chunk 384 optimal weight: 8.9990 chunk 217 optimal weight: 2.9990 chunk 15 optimal weight: 8.9990 chunk 438 optimal weight: 0.9990 chunk 143 optimal weight: 3.9990 chunk 43 optimal weight: 10.0000 chunk 90 optimal weight: 6.9990 chunk 299 optimal weight: 5.9990 chunk 510 optimal weight: 6.9990 chunk 339 optimal weight: 5.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... W 51 GLN A 36 ASN A 260 ASN A 337 GLN ** A 499 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 568 GLN A 692 GLN B 24 ASN ** B 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 406 HIS ** B 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 260 ASN ** C 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 494 GLN ** C 589 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 327 GLN ** D 490 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 602 ASN ** E 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 760 GLN F 317 HIS F 340 HIS ** F 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 421 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.119870 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.083786 restraints weight = 146205.020| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.085591 restraints weight = 92065.662| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.087299 restraints weight = 63742.654| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.088296 restraints weight = 49107.663| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.088335 restraints weight = 45583.773| |-----------------------------------------------------------------------------| r_work (final): 0.3406 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7816 moved from start: 0.4709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 42314 Z= 0.224 Angle : 0.722 9.708 57352 Z= 0.372 Chirality : 0.047 0.270 6432 Planarity : 0.005 0.063 7554 Dihedral : 7.246 134.912 5927 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 16.09 Ramachandran Plot: Outliers : 0.37 % Allowed : 8.70 % Favored : 90.92 % Rotamer: Outliers : 0.05 % Allowed : 4.82 % Favored : 95.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.69 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.88 (0.11), residues: 5365 helix: 0.45 (0.10), residues: 2484 sheet: -0.19 (0.20), residues: 641 loop : -1.89 (0.13), residues: 2240 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.033 0.001 ARG E 144 TYR 0.019 0.002 TYR W 154 PHE 0.045 0.002 PHE F 552 TRP 0.034 0.002 TRP W 133 HIS 0.007 0.001 HIS C 384 Details of bonding type rmsd/Z covalent geometry : bond 0.00475 / 0.22 (42314) covalent geometry : angle 0.72227 / 0.37 (57352) hydrogen bonds : bond 0.04312 / 2.86 ( 1928) hydrogen bonds : angle 5.02056 / 3.63 ( 5562) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10730 Ramachandran restraints generated. 5365 Oldfield, 0 Emsley, 5365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10730 Ramachandran restraints generated. 5365 Oldfield, 0 Emsley, 5365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 889 residues out of total 4598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 887 time to evaluate : 1.698 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: W 53 TRP cc_start: 0.3726 (t-100) cc_final: 0.3195 (t60) REVERT: W 75 ASN cc_start: 0.8017 (m110) cc_final: 0.7762 (m110) REVERT: W 76 LEU cc_start: 0.8138 (tt) cc_final: 0.7606 (mm) REVERT: W 112 THR cc_start: 0.8306 (m) cc_final: 0.8020 (m) REVERT: W 118 MET cc_start: 0.0679 (pmm) cc_final: 0.0348 (pmm) REVERT: W 186 LEU cc_start: 0.7019 (tt) cc_final: 0.6766 (mm) REVERT: X 1 MET cc_start: 0.2749 (mtt) cc_final: 0.2525 (mtt) REVERT: X 99 LEU cc_start: 0.8831 (mm) cc_final: 0.8254 (tp) REVERT: X 103 LEU cc_start: 0.9315 (mm) cc_final: 0.9014 (mm) REVERT: X 181 HIS cc_start: 0.8678 (t70) cc_final: 0.8202 (p-80) REVERT: Y 247 ARG cc_start: 0.6391 (mmp80) cc_final: 0.5683 (mmm160) REVERT: A 150 ASP cc_start: 0.9008 (t0) cc_final: 0.8767 (t70) REVERT: A 204 ASP cc_start: 0.9324 (p0) cc_final: 0.8788 (p0) REVERT: A 265 PHE cc_start: 0.8330 (t80) cc_final: 0.7940 (t80) REVERT: A 291 GLU cc_start: 0.8992 (tp30) cc_final: 0.8756 (tm-30) REVERT: A 326 SER cc_start: 0.9521 (m) cc_final: 0.9081 (p) REVERT: A 383 ILE cc_start: 0.9513 (tp) cc_final: 0.9266 (tt) REVERT: A 494 GLN cc_start: 0.8298 (tp-100) cc_final: 0.7798 (tp-100) REVERT: A 495 TYR cc_start: 0.8910 (m-10) cc_final: 0.8642 (m-80) REVERT: A 541 SER cc_start: 0.8388 (p) cc_final: 0.8103 (t) REVERT: A 561 GLU cc_start: 0.8996 (mp0) cc_final: 0.8710 (pm20) REVERT: A 564 ASP cc_start: 0.9174 (m-30) cc_final: 0.8666 (m-30) REVERT: A 608 MET cc_start: 0.9308 (tmm) cc_final: 0.8471 (tmm) REVERT: A 613 THR cc_start: 0.8440 (p) cc_final: 0.8104 (t) REVERT: B 36 ASN cc_start: 0.9332 (m-40) cc_final: 0.8920 (p0) REVERT: B 69 CYS cc_start: 0.8666 (m) cc_final: 0.8281 (m) REVERT: B 162 GLU cc_start: 0.9264 (pt0) cc_final: 0.8989 (pm20) REVERT: B 218 GLU cc_start: 0.8154 (tm-30) cc_final: 0.7381 (tp30) REVERT: B 267 PHE cc_start: 0.8530 (t80) cc_final: 0.7965 (t80) REVERT: B 283 GLU cc_start: 0.9295 (pt0) cc_final: 0.8893 (pt0) REVERT: B 386 LYS cc_start: 0.9225 (ttmt) cc_final: 0.8954 (ttpt) REVERT: B 449 MET cc_start: 0.8402 (ttt) cc_final: 0.7846 (ttt) REVERT: B 484 ASP cc_start: 0.9106 (m-30) cc_final: 0.8514 (p0) REVERT: B 542 ILE cc_start: 0.9160 (mm) cc_final: 0.8901 (mt) REVERT: B 577 ASP cc_start: 0.8806 (t70) cc_final: 0.8393 (t70) REVERT: B 578 GLU cc_start: 0.8365 (mt-10) cc_final: 0.7934 (mt-10) REVERT: B 602 ASN cc_start: 0.8259 (t0) cc_final: 0.8027 (t0) REVERT: B 608 MET cc_start: 0.8259 (tmm) cc_final: 0.8021 (tmm) REVERT: B 686 ASP cc_start: 0.9233 (t70) cc_final: 0.8743 (m-30) REVERT: B 691 CYS cc_start: 0.9467 (m) cc_final: 0.9233 (m) REVERT: B 757 MET cc_start: 0.9474 (mmt) cc_final: 0.9161 (mpp) REVERT: C 35 ASP cc_start: 0.9077 (t0) cc_final: 0.8693 (t70) REVERT: C 46 MET cc_start: 0.8746 (ppp) cc_final: 0.8373 (ppp) REVERT: C 84 MET cc_start: 0.7766 (ppp) cc_final: 0.7440 (ppp) REVERT: C 218 GLU cc_start: 0.9179 (tp30) cc_final: 0.8911 (tp30) REVERT: C 251 LYS cc_start: 0.9511 (ptpp) cc_final: 0.9294 (pttt) REVERT: C 281 GLU cc_start: 0.8407 (pm20) cc_final: 0.8181 (pm20) REVERT: C 292 GLU cc_start: 0.8435 (mm-30) cc_final: 0.8171 (mp0) REVERT: C 331 LEU cc_start: 0.9356 (mt) cc_final: 0.9107 (mt) REVERT: C 385 THR cc_start: 0.9231 (p) cc_final: 0.8934 (t) REVERT: C 421 GLN cc_start: 0.9581 (tp-100) cc_final: 0.9199 (tp40) REVERT: C 489 LEU cc_start: 0.9525 (mt) cc_final: 0.9318 (mt) REVERT: C 522 CYS cc_start: 0.7775 (m) cc_final: 0.7254 (p) REVERT: C 524 LYS cc_start: 0.9110 (mttm) cc_final: 0.8705 (mtmt) REVERT: C 689 GLU cc_start: 0.9505 (mt-10) cc_final: 0.9159 (mt-10) REVERT: D 242 LEU cc_start: 0.9100 (tt) cc_final: 0.8839 (tt) REVERT: D 283 GLU cc_start: 0.9248 (pp20) cc_final: 0.8378 (pp20) REVERT: D 304 ASP cc_start: 0.8732 (p0) cc_final: 0.8516 (p0) REVERT: D 312 LYS cc_start: 0.8988 (mtpp) cc_final: 0.8681 (mtpt) REVERT: D 351 ASN cc_start: 0.8734 (m-40) cc_final: 0.7833 (m-40) REVERT: D 354 ASP cc_start: 0.9080 (t0) cc_final: 0.8879 (t0) REVERT: D 460 ASN cc_start: 0.9371 (t0) cc_final: 0.9076 (p0) REVERT: D 495 TYR cc_start: 0.8922 (m-10) cc_final: 0.8662 (m-10) REVERT: D 517 TYR cc_start: 0.9052 (p90) cc_final: 0.8258 (p90) REVERT: D 560 ARG cc_start: 0.9192 (mtt90) cc_final: 0.8799 (mtt90) REVERT: D 577 ASP cc_start: 0.8270 (t0) cc_final: 0.7788 (t0) REVERT: E 90 ASN cc_start: 0.8425 (m110) cc_final: 0.8020 (t0) REVERT: E 158 MET cc_start: 0.6332 (mtp) cc_final: 0.5987 (mtm) REVERT: E 314 GLU cc_start: 0.8596 (tm-30) cc_final: 0.8341 (tm-30) REVERT: E 315 LYS cc_start: 0.9487 (mmpt) cc_final: 0.9070 (mmmt) REVERT: E 321 GLU cc_start: 0.9350 (mp0) cc_final: 0.8937 (pm20) REVERT: E 326 SER cc_start: 0.9451 (m) cc_final: 0.9161 (p) REVERT: E 564 ASP cc_start: 0.9304 (m-30) cc_final: 0.9085 (m-30) REVERT: E 603 GLN cc_start: 0.9640 (mm-40) cc_final: 0.8560 (mm110) REVERT: E 607 GLU cc_start: 0.9244 (mm-30) cc_final: 0.8730 (mm-30) REVERT: E 720 MET cc_start: 0.4562 (mmm) cc_final: 0.3955 (ptt) REVERT: F 84 MET cc_start: 0.6111 (tmm) cc_final: 0.4937 (tmm) REVERT: F 198 LEU cc_start: 0.7888 (tp) cc_final: 0.7349 (tp) REVERT: F 291 GLU cc_start: 0.9087 (pt0) cc_final: 0.8873 (pt0) REVERT: F 312 LYS cc_start: 0.9390 (tppp) cc_final: 0.9126 (tptp) REVERT: F 317 HIS cc_start: 0.8140 (t-170) cc_final: 0.7677 (t-170) REVERT: F 321 GLU cc_start: 0.8314 (pm20) cc_final: 0.8012 (pm20) REVERT: F 331 LEU cc_start: 0.9614 (mt) cc_final: 0.9271 (mt) REVERT: F 359 ARG cc_start: 0.8644 (mpp-170) cc_final: 0.8316 (mpt-90) REVERT: F 410 ASP cc_start: 0.8917 (t0) cc_final: 0.8663 (t0) REVERT: F 411 LEU cc_start: 0.9461 (mt) cc_final: 0.8992 (tp) REVERT: F 442 MET cc_start: 0.8470 (ppp) cc_final: 0.8091 (ppp) REVERT: F 492 LEU cc_start: 0.9216 (mt) cc_final: 0.8988 (mt) REVERT: F 561 GLU cc_start: 0.9221 (pm20) cc_final: 0.9018 (pm20) REVERT: F 577 ASP cc_start: 0.8926 (t70) cc_final: 0.8324 (t70) REVERT: F 640 ASP cc_start: 0.7070 (m-30) cc_final: 0.6779 (m-30) REVERT: F 736 PHE cc_start: 0.8910 (m-80) cc_final: 0.8229 (m-80) outliers start: 2 outliers final: 2 residues processed: 888 average time/residue: 0.2499 time to fit residues: 368.0334 Evaluate side-chains 687 residues out of total 4598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 685 time to evaluate : 1.674 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 534 random chunks: chunk 457 optimal weight: 6.9990 chunk 111 optimal weight: 0.9980 chunk 424 optimal weight: 6.9990 chunk 292 optimal weight: 8.9990 chunk 45 optimal weight: 50.0000 chunk 349 optimal weight: 0.9990 chunk 304 optimal weight: 2.9990 chunk 415 optimal weight: 3.9990 chunk 177 optimal weight: 10.0000 chunk 141 optimal weight: 0.0070 chunk 281 optimal weight: 0.0000 overall best weight: 1.0006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 36 ASN A 340 HIS ** A 499 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 692 GLN ** B 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 499 HIS C 384 HIS ** C 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 568 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 490 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 602 ASN E 337 GLN E 340 HIS E 384 HIS E 602 ASN ** F 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 317 HIS F 340 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4021 r_free = 0.4021 target = 0.123168 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.085905 restraints weight = 142443.400| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.088720 restraints weight = 85264.102| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.090597 restraints weight = 60344.995| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.091737 restraints weight = 47873.920| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.092652 restraints weight = 41227.675| |-----------------------------------------------------------------------------| r_work (final): 0.3488 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7706 moved from start: 0.4931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.077 42314 Z= 0.130 Angle : 0.673 10.179 57352 Z= 0.337 Chirality : 0.046 0.230 6432 Planarity : 0.005 0.069 7554 Dihedral : 6.998 129.314 5927 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 13.20 Ramachandran Plot: Outliers : 0.35 % Allowed : 7.74 % Favored : 91.91 % Rotamer: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.69 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.67 (0.12), residues: 5365 helix: 0.64 (0.11), residues: 2486 sheet: -0.10 (0.20), residues: 648 loop : -1.81 (0.13), residues: 2231 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 89 TYR 0.023 0.001 TYR W 154 PHE 0.028 0.001 PHE F 552 TRP 0.037 0.002 TRP W 133 HIS 0.015 0.001 HIS F 406 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.13 (42314) covalent geometry : angle 0.67347 / 0.34 (57352) hydrogen bonds : bond 0.03796 / 2.52 ( 1928) hydrogen bonds : angle 4.75531 / 3.44 ( 5562) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10730 Ramachandran restraints generated. 5365 Oldfield, 0 Emsley, 5365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10730 Ramachandran restraints generated. 5365 Oldfield, 0 Emsley, 5365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 925 residues out of total 4598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 925 time to evaluate : 1.399 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: W 44 GLU cc_start: 0.7387 (tt0) cc_final: 0.6847 (mp0) REVERT: W 53 TRP cc_start: 0.3896 (t-100) cc_final: 0.3228 (t60) REVERT: W 75 ASN cc_start: 0.8031 (m110) cc_final: 0.7746 (m110) REVERT: W 76 LEU cc_start: 0.8191 (tt) cc_final: 0.7689 (mm) REVERT: W 116 MET cc_start: 0.6978 (mtm) cc_final: 0.6438 (ttt) REVERT: W 118 MET cc_start: 0.0614 (pmm) cc_final: 0.0344 (pmm) REVERT: W 186 LEU cc_start: 0.7192 (tt) cc_final: 0.6940 (mm) REVERT: X 181 HIS cc_start: 0.8596 (t70) cc_final: 0.8121 (p-80) REVERT: Y 247 ARG cc_start: 0.6288 (mmp80) cc_final: 0.5626 (mmm160) REVERT: A 150 ASP cc_start: 0.9034 (t0) cc_final: 0.8794 (t70) REVERT: A 198 LEU cc_start: 0.9320 (tt) cc_final: 0.9087 (tt) REVERT: A 265 PHE cc_start: 0.8183 (t80) cc_final: 0.7667 (t80) REVERT: A 291 GLU cc_start: 0.8950 (tp30) cc_final: 0.8704 (tm-30) REVERT: A 326 SER cc_start: 0.9357 (m) cc_final: 0.8945 (p) REVERT: A 494 GLN cc_start: 0.8281 (tp-100) cc_final: 0.7754 (tp-100) REVERT: A 495 TYR cc_start: 0.8890 (m-10) cc_final: 0.8577 (m-80) REVERT: A 541 SER cc_start: 0.8290 (p) cc_final: 0.7995 (t) REVERT: A 561 GLU cc_start: 0.8997 (mp0) cc_final: 0.8713 (pm20) REVERT: A 564 ASP cc_start: 0.9136 (m-30) cc_final: 0.8453 (m-30) REVERT: A 608 MET cc_start: 0.9275 (tmm) cc_final: 0.8928 (tmm) REVERT: A 634 LEU cc_start: 0.8978 (mm) cc_final: 0.8125 (tt) REVERT: A 740 MET cc_start: 0.7973 (tmm) cc_final: 0.7451 (tmm) REVERT: B 36 ASN cc_start: 0.9327 (m-40) cc_final: 0.8945 (p0) REVERT: B 120 ASP cc_start: 0.9208 (t70) cc_final: 0.8978 (p0) REVERT: B 162 GLU cc_start: 0.9197 (pt0) cc_final: 0.8934 (pm20) REVERT: B 200 GLU cc_start: 0.8679 (mm-30) cc_final: 0.8204 (mp0) REVERT: B 233 ILE cc_start: 0.9719 (mm) cc_final: 0.9458 (mm) REVERT: B 275 MET cc_start: 0.9016 (tmm) cc_final: 0.8626 (tmm) REVERT: B 283 GLU cc_start: 0.9284 (pt0) cc_final: 0.8838 (pt0) REVERT: B 292 GLU cc_start: 0.7946 (mt-10) cc_final: 0.7592 (mt-10) REVERT: B 366 GLU cc_start: 0.9076 (mm-30) cc_final: 0.8840 (mm-30) REVERT: B 398 GLN cc_start: 0.9151 (tt0) cc_final: 0.8744 (pp30) REVERT: B 449 MET cc_start: 0.8384 (ttt) cc_final: 0.7591 (ttt) REVERT: B 484 ASP cc_start: 0.9107 (m-30) cc_final: 0.8460 (p0) REVERT: B 577 ASP cc_start: 0.8759 (t70) cc_final: 0.8264 (t70) REVERT: B 578 GLU cc_start: 0.8209 (mt-10) cc_final: 0.7948 (mt-10) REVERT: B 608 MET cc_start: 0.8128 (tmm) cc_final: 0.7797 (tmm) REVERT: B 686 ASP cc_start: 0.9171 (t70) cc_final: 0.8650 (m-30) REVERT: B 757 MET cc_start: 0.9420 (mmt) cc_final: 0.9155 (mpp) REVERT: C 35 ASP cc_start: 0.9013 (t0) cc_final: 0.8679 (t70) REVERT: C 46 MET cc_start: 0.8726 (ppp) cc_final: 0.8316 (ppp) REVERT: C 84 MET cc_start: 0.7930 (ppp) cc_final: 0.7630 (ppp) REVERT: C 218 GLU cc_start: 0.9173 (tp30) cc_final: 0.8849 (tp30) REVERT: C 251 LYS cc_start: 0.9353 (ptpp) cc_final: 0.9062 (pttt) REVERT: C 278 LEU cc_start: 0.9164 (tp) cc_final: 0.8773 (tt) REVERT: C 327 GLN cc_start: 0.9276 (tp-100) cc_final: 0.8685 (tp-100) REVERT: C 331 LEU cc_start: 0.9347 (mt) cc_final: 0.8581 (mt) REVERT: C 385 THR cc_start: 0.9080 (p) cc_final: 0.8838 (t) REVERT: C 388 MET cc_start: 0.7916 (tpt) cc_final: 0.7626 (tpt) REVERT: C 421 GLN cc_start: 0.9562 (tp-100) cc_final: 0.8482 (tm-30) REVERT: C 489 LEU cc_start: 0.9513 (mt) cc_final: 0.9292 (mt) REVERT: C 522 CYS cc_start: 0.7780 (m) cc_final: 0.7124 (p) REVERT: C 524 LYS cc_start: 0.8994 (mttm) cc_final: 0.8558 (mtpt) REVERT: C 689 GLU cc_start: 0.9514 (mt-10) cc_final: 0.9150 (mt-10) REVERT: D 182 ILE cc_start: 0.8921 (pt) cc_final: 0.8582 (tp) REVERT: D 225 ARG cc_start: 0.8340 (tpp80) cc_final: 0.8066 (tpp80) REVERT: D 283 GLU cc_start: 0.9137 (pp20) cc_final: 0.8269 (pp20) REVERT: D 304 ASP cc_start: 0.8722 (p0) cc_final: 0.8393 (p0) REVERT: D 312 LYS cc_start: 0.9013 (mtpp) cc_final: 0.8543 (mtpt) REVERT: D 315 LYS cc_start: 0.9547 (mmmm) cc_final: 0.9136 (mmmm) REVERT: D 351 ASN cc_start: 0.8607 (m-40) cc_final: 0.8217 (m-40) REVERT: D 354 ASP cc_start: 0.8958 (t0) cc_final: 0.8735 (t0) REVERT: D 460 ASN cc_start: 0.9347 (t0) cc_final: 0.9031 (p0) REVERT: D 495 TYR cc_start: 0.8902 (m-10) cc_final: 0.8633 (m-80) REVERT: D 604 ILE cc_start: 0.9776 (mt) cc_final: 0.9528 (mt) REVERT: D 697 LEU cc_start: 0.9234 (mm) cc_final: 0.8937 (pp) REVERT: D 708 ARG cc_start: 0.9141 (tmt-80) cc_final: 0.8933 (tpt90) REVERT: E 90 ASN cc_start: 0.8412 (m110) cc_final: 0.7978 (t0) REVERT: E 158 MET cc_start: 0.6263 (mtp) cc_final: 0.5926 (mtm) REVERT: E 295 LYS cc_start: 0.8849 (ptpp) cc_final: 0.8510 (ptpp) REVERT: E 314 GLU cc_start: 0.8541 (tm-30) cc_final: 0.8255 (tm-30) REVERT: E 315 LYS cc_start: 0.9450 (mmpt) cc_final: 0.8961 (mmmt) REVERT: E 321 GLU cc_start: 0.9332 (mp0) cc_final: 0.8874 (pm20) REVERT: E 494 GLN cc_start: 0.8963 (tp40) cc_final: 0.8577 (mm-40) REVERT: E 495 TYR cc_start: 0.9082 (m-80) cc_final: 0.8687 (m-80) REVERT: E 499 HIS cc_start: 0.8470 (m-70) cc_final: 0.8254 (m170) REVERT: E 535 CYS cc_start: 0.8195 (t) cc_final: 0.7976 (p) REVERT: E 551 TRP cc_start: 0.6996 (m-10) cc_final: 0.5709 (m100) REVERT: E 564 ASP cc_start: 0.9251 (m-30) cc_final: 0.9003 (m-30) REVERT: E 603 GLN cc_start: 0.9652 (mm-40) cc_final: 0.9092 (mm110) REVERT: E 607 GLU cc_start: 0.9201 (mm-30) cc_final: 0.8780 (mm-30) REVERT: E 720 MET cc_start: 0.4721 (mmm) cc_final: 0.3946 (ptt) REVERT: F 244 TYR cc_start: 0.8838 (p90) cc_final: 0.8362 (p90) REVERT: F 291 GLU cc_start: 0.9028 (pt0) cc_final: 0.8828 (pt0) REVERT: F 312 LYS cc_start: 0.9427 (tppp) cc_final: 0.9172 (tptp) REVERT: F 321 GLU cc_start: 0.8336 (pm20) cc_final: 0.8001 (pm20) REVERT: F 331 LEU cc_start: 0.9559 (mt) cc_final: 0.9312 (mt) REVERT: F 332 MET cc_start: 0.9264 (tmm) cc_final: 0.8920 (tmm) REVERT: F 403 THR cc_start: 0.8622 (m) cc_final: 0.8408 (m) REVERT: F 411 LEU cc_start: 0.9445 (mt) cc_final: 0.8987 (tp) REVERT: F 442 MET cc_start: 0.8436 (ppp) cc_final: 0.8109 (ppp) REVERT: F 492 LEU cc_start: 0.9259 (mt) cc_final: 0.9024 (mt) REVERT: F 577 ASP cc_start: 0.9013 (t70) cc_final: 0.8469 (t70) REVERT: F 620 ILE cc_start: 0.9173 (mt) cc_final: 0.8972 (pt) REVERT: F 640 ASP cc_start: 0.7007 (m-30) cc_final: 0.6757 (m-30) REVERT: F 663 LYS cc_start: 0.8753 (mmtm) cc_final: 0.8534 (mmtm) REVERT: F 736 PHE cc_start: 0.8825 (m-80) cc_final: 0.8176 (m-80) REVERT: F 738 GLU cc_start: 0.9094 (mm-30) cc_final: 0.8697 (tp30) outliers start: 0 outliers final: 0 residues processed: 925 average time/residue: 0.2482 time to fit residues: 377.5761 Evaluate side-chains 728 residues out of total 4598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 728 time to evaluate : 1.711 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 534 random chunks: chunk 475 optimal weight: 6.9990 chunk 306 optimal weight: 0.9980 chunk 228 optimal weight: 5.9990 chunk 230 optimal weight: 0.8980 chunk 2 optimal weight: 2.9990 chunk 327 optimal weight: 3.9990 chunk 262 optimal weight: 4.9990 chunk 5 optimal weight: 30.0000 chunk 145 optimal weight: 7.9990 chunk 37 optimal weight: 1.9990 chunk 237 optimal weight: 5.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 36 ASN A 340 HIS ** A 499 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 568 GLN ** B 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 260 ASN C 384 HIS ** C 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 490 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 602 ASN E 384 HIS ** F 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 285 ASN F 340 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4004 r_free = 0.4004 target = 0.121853 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.084153 restraints weight = 143433.760| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.086921 restraints weight = 86322.255| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.088768 restraints weight = 61564.246| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.089998 restraints weight = 49035.449| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.090830 restraints weight = 42078.437| |-----------------------------------------------------------------------------| r_work (final): 0.3463 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7759 moved from start: 0.5205 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 42314 Z= 0.151 Angle : 0.682 10.880 57352 Z= 0.342 Chirality : 0.046 0.188 6432 Planarity : 0.005 0.080 7554 Dihedral : 6.870 124.358 5927 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 13.91 Ramachandran Plot: Outliers : 0.34 % Allowed : 8.31 % Favored : 91.35 % Rotamer: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.69 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.65 (0.12), residues: 5365 helix: 0.64 (0.11), residues: 2482 sheet: -0.15 (0.20), residues: 642 loop : -1.75 (0.13), residues: 2241 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG E 89 TYR 0.024 0.001 TYR D 517 PHE 0.040 0.002 PHE B 674 TRP 0.047 0.002 TRP A 454 HIS 0.012 0.001 HIS F 406 Details of bonding type rmsd/Z covalent geometry : bond 0.00333 / 0.15 (42314) covalent geometry : angle 0.68183 / 0.34 (57352) hydrogen bonds : bond 0.03792 / 2.53 ( 1928) hydrogen bonds : angle 4.75331 / 3.43 ( 5562) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10730 Ramachandran restraints generated. 5365 Oldfield, 0 Emsley, 5365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10730 Ramachandran restraints generated. 5365 Oldfield, 0 Emsley, 5365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 900 residues out of total 4598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 900 time to evaluate : 1.763 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: 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: W 44 GLU cc_start: 0.7378 (tt0) cc_final: 0.6837 (mp0) REVERT: W 53 TRP cc_start: 0.3843 (t-100) cc_final: 0.3192 (t60) REVERT: W 75 ASN cc_start: 0.8032 (m110) cc_final: 0.7769 (m110) REVERT: W 76 LEU cc_start: 0.8098 (tt) cc_final: 0.7547 (mm) REVERT: W 116 MET cc_start: 0.7004 (mtm) cc_final: 0.6552 (ttt) REVERT: W 118 MET cc_start: 0.1066 (pmm) cc_final: 0.0365 (pmm) REVERT: W 186 LEU cc_start: 0.7231 (tt) cc_final: 0.6995 (mm) REVERT: X 99 LEU cc_start: 0.8869 (mm) cc_final: 0.8370 (tp) REVERT: X 103 LEU cc_start: 0.9317 (mm) cc_final: 0.9061 (mm) REVERT: X 181 HIS cc_start: 0.8617 (t70) cc_final: 0.8347 (t70) REVERT: X 183 TYR cc_start: 0.7546 (t80) cc_final: 0.7274 (t80) REVERT: Y 247 ARG cc_start: 0.6312 (mmp80) cc_final: 0.5632 (mmm160) REVERT: A 35 ASP cc_start: 0.8565 (t0) cc_final: 0.8211 (t70) REVERT: A 150 ASP cc_start: 0.8926 (t0) cc_final: 0.8687 (t70) REVERT: A 198 LEU cc_start: 0.9390 (tt) cc_final: 0.9127 (tt) REVERT: A 265 PHE cc_start: 0.8316 (t80) cc_final: 0.8001 (t80) REVERT: A 315 LYS cc_start: 0.9524 (mmtp) cc_final: 0.9266 (mmmt) REVERT: A 326 SER cc_start: 0.9417 (m) cc_final: 0.9016 (p) REVERT: A 415 CYS cc_start: 0.9513 (m) cc_final: 0.9163 (t) REVERT: A 434 ASP cc_start: 0.8181 (t0) cc_final: 0.7904 (t70) REVERT: A 457 SER cc_start: 0.9007 (m) cc_final: 0.8800 (p) REVERT: A 494 GLN cc_start: 0.8248 (tp-100) cc_final: 0.7730 (tp-100) REVERT: A 495 TYR cc_start: 0.8886 (m-10) cc_final: 0.8550 (m-80) REVERT: A 541 SER cc_start: 0.8259 (p) cc_final: 0.8016 (t) REVERT: A 561 GLU cc_start: 0.9015 (mp0) cc_final: 0.8705 (mp0) REVERT: A 564 ASP cc_start: 0.9159 (m-30) cc_final: 0.8501 (m-30) REVERT: A 602 ASN cc_start: 0.8170 (m110) cc_final: 0.7969 (m110) REVERT: A 608 MET cc_start: 0.9278 (tmm) cc_final: 0.8795 (tmm) REVERT: A 614 LYS cc_start: 0.9544 (mmmt) cc_final: 0.9319 (pptt) REVERT: A 634 LEU cc_start: 0.8948 (mm) cc_final: 0.8115 (tt) REVERT: A 740 MET cc_start: 0.7899 (tmm) cc_final: 0.7345 (tmm) REVERT: B 36 ASN cc_start: 0.9343 (m-40) cc_final: 0.8892 (p0) REVERT: B 84 MET cc_start: 0.9116 (tmm) cc_final: 0.8780 (tmm) REVERT: B 162 GLU cc_start: 0.9263 (pt0) cc_final: 0.8928 (pm20) REVERT: B 198 LEU cc_start: 0.8987 (tt) cc_final: 0.8718 (tp) REVERT: B 200 GLU cc_start: 0.8673 (mm-30) cc_final: 0.8229 (mp0) REVERT: B 275 MET cc_start: 0.9056 (tmm) cc_final: 0.8701 (tmm) REVERT: B 283 GLU cc_start: 0.9289 (pt0) cc_final: 0.9077 (mp0) REVERT: B 292 GLU cc_start: 0.7971 (mt-10) cc_final: 0.7571 (mt-10) REVERT: B 331 LEU cc_start: 0.9592 (mm) cc_final: 0.9301 (mm) REVERT: B 335 LEU cc_start: 0.9082 (tp) cc_final: 0.8800 (tp) REVERT: B 398 GLN cc_start: 0.9129 (tt0) cc_final: 0.8825 (pp30) REVERT: B 484 ASP cc_start: 0.9144 (m-30) cc_final: 0.8442 (p0) REVERT: B 546 GLU cc_start: 0.9454 (mm-30) cc_final: 0.8865 (tp30) REVERT: B 550 MET cc_start: 0.8375 (ptp) cc_final: 0.8036 (ptp) REVERT: B 577 ASP cc_start: 0.8709 (t70) cc_final: 0.8140 (t70) REVERT: B 607 GLU cc_start: 0.9063 (mm-30) cc_final: 0.8718 (tp30) REVERT: B 686 ASP cc_start: 0.9187 (t70) cc_final: 0.8684 (m-30) REVERT: B 757 MET cc_start: 0.9397 (mmt) cc_final: 0.9159 (mpp) REVERT: C 35 ASP cc_start: 0.8958 (t0) cc_final: 0.8690 (t70) REVERT: C 46 MET cc_start: 0.8736 (ppp) cc_final: 0.8345 (ppp) REVERT: C 84 MET cc_start: 0.7752 (ppp) cc_final: 0.7548 (ppp) REVERT: C 218 GLU cc_start: 0.9188 (tp30) cc_final: 0.8908 (tp30) REVERT: C 221 GLU cc_start: 0.8357 (mp0) cc_final: 0.8094 (mp0) REVERT: C 278 LEU cc_start: 0.9108 (tp) cc_final: 0.8696 (tt) REVERT: C 326 SER cc_start: 0.9291 (m) cc_final: 0.8672 (t) REVERT: C 331 LEU cc_start: 0.9360 (mt) cc_final: 0.9135 (mt) REVERT: C 385 THR cc_start: 0.9161 (p) cc_final: 0.8873 (t) REVERT: C 421 GLN cc_start: 0.9563 (tp-100) cc_final: 0.9209 (tp40) REVERT: C 489 LEU cc_start: 0.9525 (mt) cc_final: 0.9296 (mt) REVERT: C 522 CYS cc_start: 0.7810 (m) cc_final: 0.7164 (p) REVERT: C 524 LYS cc_start: 0.8990 (mttm) cc_final: 0.8685 (mtmt) REVERT: C 689 GLU cc_start: 0.9520 (mt-10) cc_final: 0.9151 (mt-10) REVERT: D 242 LEU cc_start: 0.9074 (tt) cc_final: 0.8864 (tt) REVERT: D 283 GLU cc_start: 0.9159 (pp20) cc_final: 0.8311 (pp20) REVERT: D 304 ASP cc_start: 0.8753 (p0) cc_final: 0.8254 (p0) REVERT: D 305 GLU cc_start: 0.8675 (pm20) cc_final: 0.7829 (pm20) REVERT: D 312 LYS cc_start: 0.9076 (mtpp) cc_final: 0.8723 (mtpt) REVERT: D 460 ASN cc_start: 0.9351 (t0) cc_final: 0.9071 (p0) REVERT: D 495 TYR cc_start: 0.8957 (m-10) cc_final: 0.8730 (m-80) REVERT: D 517 TYR cc_start: 0.9098 (p90) cc_final: 0.8071 (p90) REVERT: D 546 GLU cc_start: 0.9425 (tp30) cc_final: 0.9200 (tp30) REVERT: D 604 ILE cc_start: 0.9773 (mt) cc_final: 0.9540 (mt) REVERT: D 697 LEU cc_start: 0.9254 (mm) cc_final: 0.8983 (pp) REVERT: D 708 ARG cc_start: 0.9138 (tmt-80) cc_final: 0.8927 (tpt90) REVERT: E 90 ASN cc_start: 0.8340 (m110) cc_final: 0.7907 (t0) REVERT: E 158 MET cc_start: 0.6388 (mtp) cc_final: 0.6032 (mtm) REVERT: E 295 LYS cc_start: 0.8864 (ptpp) cc_final: 0.8547 (ptpp) REVERT: E 315 LYS cc_start: 0.9371 (mmpt) cc_final: 0.9037 (mmmt) REVERT: E 321 GLU cc_start: 0.9343 (mp0) cc_final: 0.8731 (pm20) REVERT: E 326 SER cc_start: 0.9514 (m) cc_final: 0.9189 (p) REVERT: E 494 GLN cc_start: 0.8461 (tp40) cc_final: 0.8157 (tp40) REVERT: E 495 TYR cc_start: 0.9038 (m-80) cc_final: 0.8578 (m-80) REVERT: E 535 CYS cc_start: 0.8258 (t) cc_final: 0.7976 (p) REVERT: E 548 LEU cc_start: 0.9200 (tt) cc_final: 0.8933 (tp) REVERT: E 551 TRP cc_start: 0.7236 (m-10) cc_final: 0.6106 (m100) REVERT: E 564 ASP cc_start: 0.9279 (m-30) cc_final: 0.9039 (m-30) REVERT: E 603 GLN cc_start: 0.9664 (mm-40) cc_final: 0.9125 (mm110) REVERT: E 607 GLU cc_start: 0.9196 (mm-30) cc_final: 0.8975 (mm-30) REVERT: E 720 MET cc_start: 0.4642 (mmm) cc_final: 0.3837 (ptt) REVERT: F 244 TYR cc_start: 0.8836 (p90) cc_final: 0.8267 (p90) REVERT: F 275 MET cc_start: 0.9484 (tpp) cc_final: 0.9223 (tpp) REVERT: F 291 GLU cc_start: 0.9082 (pt0) cc_final: 0.8862 (pt0) REVERT: F 312 LYS cc_start: 0.9424 (tppp) cc_final: 0.9168 (tptp) REVERT: F 321 GLU cc_start: 0.8322 (pm20) cc_final: 0.7959 (pm20) REVERT: F 331 LEU cc_start: 0.9597 (mt) cc_final: 0.9293 (mt) REVERT: F 411 LEU cc_start: 0.9453 (mt) cc_final: 0.8997 (tp) REVERT: F 442 MET cc_start: 0.8495 (ppp) cc_final: 0.8162 (ppp) REVERT: F 492 LEU cc_start: 0.9268 (mt) cc_final: 0.9028 (mt) REVERT: F 574 LEU cc_start: 0.8202 (tt) cc_final: 0.7984 (tt) REVERT: F 577 ASP cc_start: 0.9001 (t70) cc_final: 0.8441 (t70) REVERT: F 620 ILE cc_start: 0.9238 (mt) cc_final: 0.9032 (pt) REVERT: F 640 ASP cc_start: 0.7149 (m-30) cc_final: 0.6914 (m-30) REVERT: F 736 PHE cc_start: 0.8823 (m-80) cc_final: 0.8182 (m-80) REVERT: F 738 GLU cc_start: 0.9107 (mm-30) cc_final: 0.8744 (tp30) outliers start: 0 outliers final: 0 residues processed: 900 average time/residue: 0.2525 time to fit residues: 376.1865 Evaluate side-chains 706 residues out of total 4598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 706 time to evaluate : 1.661 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 534 random chunks: chunk 459 optimal weight: 4.9990 chunk 139 optimal weight: 1.9990 chunk 397 optimal weight: 10.0000 chunk 44 optimal weight: 0.7980 chunk 164 optimal weight: 5.9990 chunk 268 optimal weight: 1.9990 chunk 379 optimal weight: 20.0000 chunk 87 optimal weight: 7.9990 chunk 361 optimal weight: 4.9990 chunk 92 optimal weight: 7.9990 chunk 489 optimal weight: 0.8980 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 317 HIS A 340 HIS ** A 499 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 735 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 260 ASN ** C 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 384 HIS ** C 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 490 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 384 HIS E 602 ASN ** F 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 340 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.121590 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.084798 restraints weight = 144220.034| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.087302 restraints weight = 88778.817| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.089389 restraints weight = 59243.294| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.089765 restraints weight = 45233.561| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.089839 restraints weight = 44496.383| |-----------------------------------------------------------------------------| r_work (final): 0.3431 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7801 moved from start: 0.5428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 42314 Z= 0.150 Angle : 0.683 10.566 57352 Z= 0.345 Chirality : 0.046 0.230 6432 Planarity : 0.005 0.063 7554 Dihedral : 6.754 121.166 5927 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 13.52 Ramachandran Plot: Outliers : 0.32 % Allowed : 8.46 % Favored : 91.22 % Rotamer: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.69 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.68 (0.12), residues: 5365 helix: 0.62 (0.11), residues: 2486 sheet: -0.16 (0.20), residues: 642 loop : -1.79 (0.13), residues: 2237 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D 365 TYR 0.026 0.002 TYR B 203 PHE 0.036 0.002 PHE B 674 TRP 0.048 0.002 TRP W 133 HIS 0.012 0.001 HIS F 406 Details of bonding type rmsd/Z covalent geometry : bond 0.00328 / 0.15 (42314) covalent geometry : angle 0.68291 / 0.35 (57352) hydrogen bonds : bond 0.03751 / 2.51 ( 1928) hydrogen bonds : angle 4.75874 / 3.44 ( 5562) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10730 Ramachandran restraints generated. 5365 Oldfield, 0 Emsley, 5365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10730 Ramachandran restraints generated. 5365 Oldfield, 0 Emsley, 5365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 881 residues out of total 4598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 881 time to evaluate : 1.736 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: W 44 GLU cc_start: 0.7361 (tt0) cc_final: 0.6822 (mp0) REVERT: W 53 TRP cc_start: 0.3848 (t-100) cc_final: 0.3207 (t60) REVERT: W 75 ASN cc_start: 0.8042 (m110) cc_final: 0.7771 (m110) REVERT: W 76 LEU cc_start: 0.8044 (tt) cc_final: 0.7489 (mm) REVERT: W 118 MET cc_start: 0.1007 (pmm) cc_final: 0.0766 (pmm) REVERT: W 186 LEU cc_start: 0.7207 (tt) cc_final: 0.6984 (mm) REVERT: X 99 LEU cc_start: 0.8886 (mm) cc_final: 0.8388 (tp) REVERT: X 103 LEU cc_start: 0.9286 (mm) cc_final: 0.9032 (mm) REVERT: X 181 HIS cc_start: 0.8610 (t70) cc_final: 0.8345 (t70) REVERT: X 183 TYR cc_start: 0.7638 (t80) cc_final: 0.7338 (t80) REVERT: Y 247 ARG cc_start: 0.6596 (mmp80) cc_final: 0.5816 (mmm160) REVERT: A 35 ASP cc_start: 0.8500 (t0) cc_final: 0.8125 (t70) REVERT: A 150 ASP cc_start: 0.8904 (t0) cc_final: 0.8657 (t70) REVERT: A 198 LEU cc_start: 0.9380 (tt) cc_final: 0.9175 (tt) REVERT: A 265 PHE cc_start: 0.8340 (t80) cc_final: 0.7832 (t80) REVERT: A 267 PHE cc_start: 0.7823 (m-80) cc_final: 0.6524 (m-80) REVERT: A 302 PHE cc_start: 0.9387 (t80) cc_final: 0.9141 (t80) REVERT: A 315 LYS cc_start: 0.9504 (mmtp) cc_final: 0.9217 (mmmt) REVERT: A 326 SER cc_start: 0.9426 (m) cc_final: 0.8994 (p) REVERT: A 415 CYS cc_start: 0.9513 (m) cc_final: 0.9125 (t) REVERT: A 494 GLN cc_start: 0.8227 (tp-100) cc_final: 0.7687 (tp-100) REVERT: A 495 TYR cc_start: 0.8923 (m-10) cc_final: 0.8526 (m-10) REVERT: A 541 SER cc_start: 0.8357 (p) cc_final: 0.8155 (t) REVERT: A 561 GLU cc_start: 0.9062 (mp0) cc_final: 0.8725 (mp0) REVERT: A 564 ASP cc_start: 0.9224 (m-30) cc_final: 0.8549 (m-30) REVERT: A 602 ASN cc_start: 0.8431 (m110) cc_final: 0.8092 (m110) REVERT: A 608 MET cc_start: 0.9349 (tmm) cc_final: 0.8839 (tmm) REVERT: A 614 LYS cc_start: 0.9567 (mmmt) cc_final: 0.9331 (pptt) REVERT: A 634 LEU cc_start: 0.8935 (mm) cc_final: 0.8093 (tt) REVERT: A 740 MET cc_start: 0.7897 (tmm) cc_final: 0.7341 (tmm) REVERT: B 36 ASN cc_start: 0.9332 (m-40) cc_final: 0.8908 (p0) REVERT: B 84 MET cc_start: 0.9057 (tmm) cc_final: 0.8810 (tmm) REVERT: B 120 ASP cc_start: 0.9031 (p0) cc_final: 0.8831 (p0) REVERT: B 162 GLU cc_start: 0.9303 (pt0) cc_final: 0.8952 (pm20) REVERT: B 198 LEU cc_start: 0.9019 (tt) cc_final: 0.8550 (tp) REVERT: B 200 GLU cc_start: 0.8646 (mm-30) cc_final: 0.8057 (mp0) REVERT: B 273 GLU cc_start: 0.8851 (pt0) cc_final: 0.8164 (pt0) REVERT: B 274 ILE cc_start: 0.9436 (tp) cc_final: 0.9217 (tp) REVERT: B 275 MET cc_start: 0.9105 (tmm) cc_final: 0.8725 (tmm) REVERT: B 292 GLU cc_start: 0.7931 (mt-10) cc_final: 0.7532 (mt-10) REVERT: B 317 HIS cc_start: 0.8603 (m-70) cc_final: 0.8352 (m-70) REVERT: B 335 LEU cc_start: 0.9036 (tp) cc_final: 0.8729 (tp) REVERT: B 364 ASP cc_start: 0.9586 (p0) cc_final: 0.9326 (p0) REVERT: B 398 GLN cc_start: 0.9131 (tt0) cc_final: 0.8796 (pp30) REVERT: B 401 ASN cc_start: 0.8920 (t0) cc_final: 0.8686 (t0) REVERT: B 484 ASP cc_start: 0.9144 (m-30) cc_final: 0.8390 (p0) REVERT: B 546 GLU cc_start: 0.9510 (mm-30) cc_final: 0.9235 (tp30) REVERT: B 572 CYS cc_start: 0.8138 (p) cc_final: 0.7610 (p) REVERT: B 686 ASP cc_start: 0.9244 (t70) cc_final: 0.8577 (m-30) REVERT: B 757 MET cc_start: 0.9461 (mmt) cc_final: 0.9248 (mpp) REVERT: C 35 ASP cc_start: 0.8943 (t0) cc_final: 0.8680 (t70) REVERT: C 46 MET cc_start: 0.8768 (ppp) cc_final: 0.8396 (ppp) REVERT: C 218 GLU cc_start: 0.9208 (tp30) cc_final: 0.8857 (tp30) REVERT: C 326 SER cc_start: 0.9309 (m) cc_final: 0.8689 (t) REVERT: C 331 LEU cc_start: 0.9363 (mt) cc_final: 0.9127 (mt) REVERT: C 385 THR cc_start: 0.9162 (p) cc_final: 0.8876 (t) REVERT: C 388 MET cc_start: 0.8359 (tpt) cc_final: 0.8100 (tpt) REVERT: C 421 GLN cc_start: 0.9604 (tp-100) cc_final: 0.9156 (tp40) REVERT: C 449 MET cc_start: 0.8367 (tmm) cc_final: 0.8143 (tmm) REVERT: C 489 LEU cc_start: 0.9521 (mt) cc_final: 0.9307 (mt) REVERT: C 522 CYS cc_start: 0.7806 (m) cc_final: 0.7119 (p) REVERT: C 564 ASP cc_start: 0.8790 (m-30) cc_final: 0.8527 (m-30) REVERT: C 689 GLU cc_start: 0.9543 (mt-10) cc_final: 0.9163 (mt-10) REVERT: C 708 ARG cc_start: 0.9293 (pmt-80) cc_final: 0.9061 (pmt-80) REVERT: C 736 PHE cc_start: 0.7748 (m-10) cc_final: 0.7515 (m-10) REVERT: D 89 ARG cc_start: 0.9008 (ttm170) cc_final: 0.8776 (ttm170) REVERT: D 242 LEU cc_start: 0.9102 (tt) cc_final: 0.8896 (tt) REVERT: D 283 GLU cc_start: 0.9103 (pp20) cc_final: 0.8452 (pp20) REVERT: D 304 ASP cc_start: 0.8731 (p0) cc_final: 0.8246 (p0) REVERT: D 305 GLU cc_start: 0.8607 (pm20) cc_final: 0.7813 (pm20) REVERT: D 312 LYS cc_start: 0.9096 (mtpp) cc_final: 0.8742 (mtpt) REVERT: D 460 ASN cc_start: 0.9286 (t0) cc_final: 0.9046 (p0) REVERT: D 495 TYR cc_start: 0.9063 (m-10) cc_final: 0.8792 (m-80) REVERT: D 517 TYR cc_start: 0.9068 (p90) cc_final: 0.8042 (p90) REVERT: D 578 GLU cc_start: 0.8173 (pt0) cc_final: 0.7819 (pt0) REVERT: D 604 ILE cc_start: 0.9778 (mt) cc_final: 0.9509 (mt) REVERT: D 615 LYS cc_start: 0.8895 (mmtt) cc_final: 0.8605 (mmtm) REVERT: D 697 LEU cc_start: 0.9263 (mm) cc_final: 0.8954 (pp) REVERT: D 708 ARG cc_start: 0.9136 (tmt-80) cc_final: 0.8932 (tpt90) REVERT: E 90 ASN cc_start: 0.8405 (m110) cc_final: 0.7995 (t0) REVERT: E 158 MET cc_start: 0.6448 (mtp) cc_final: 0.6101 (mtm) REVERT: E 314 GLU cc_start: 0.8499 (tm-30) cc_final: 0.8201 (tm-30) REVERT: E 315 LYS cc_start: 0.9370 (mmpt) cc_final: 0.9078 (mmmt) REVERT: E 321 GLU cc_start: 0.9335 (mp0) cc_final: 0.8960 (pm20) REVERT: E 326 SER cc_start: 0.9494 (m) cc_final: 0.9170 (p) REVERT: E 379 GLU cc_start: 0.8965 (mp0) cc_final: 0.8564 (mp0) REVERT: E 495 TYR cc_start: 0.9033 (m-80) cc_final: 0.8647 (m-80) REVERT: E 527 LEU cc_start: 0.9438 (mm) cc_final: 0.9160 (mp) REVERT: E 551 TRP cc_start: 0.7197 (m-10) cc_final: 0.5990 (m100) REVERT: E 564 ASP cc_start: 0.9294 (m-30) cc_final: 0.9058 (m-30) REVERT: E 603 GLN cc_start: 0.9680 (mm-40) cc_final: 0.9138 (mm110) REVERT: E 607 GLU cc_start: 0.9229 (mm-30) cc_final: 0.9005 (mm-30) REVERT: E 720 MET cc_start: 0.4487 (mmm) cc_final: 0.3934 (ptt) REVERT: F 244 TYR cc_start: 0.8835 (p90) cc_final: 0.8160 (p90) REVERT: F 291 GLU cc_start: 0.9081 (pt0) cc_final: 0.8852 (pt0) REVERT: F 312 LYS cc_start: 0.9386 (tppp) cc_final: 0.9103 (tptp) REVERT: F 321 GLU cc_start: 0.8179 (pm20) cc_final: 0.7907 (pm20) REVERT: F 331 LEU cc_start: 0.9610 (mt) cc_final: 0.9306 (mt) REVERT: F 336 LYS cc_start: 0.7710 (tmmt) cc_final: 0.7016 (tmmt) REVERT: F 411 LEU cc_start: 0.9435 (mt) cc_final: 0.9002 (tp) REVERT: F 425 LYS cc_start: 0.8033 (tppt) cc_final: 0.7531 (ptpp) REVERT: F 442 MET cc_start: 0.8608 (ppp) cc_final: 0.8191 (ppp) REVERT: F 492 LEU cc_start: 0.9301 (mt) cc_final: 0.9053 (mt) REVERT: F 561 GLU cc_start: 0.9305 (pm20) cc_final: 0.9083 (pm20) REVERT: F 577 ASP cc_start: 0.8969 (t70) cc_final: 0.8417 (t70) REVERT: F 620 ILE cc_start: 0.9239 (mt) cc_final: 0.9031 (pt) REVERT: F 640 ASP cc_start: 0.7164 (m-30) cc_final: 0.6898 (m-30) REVERT: F 736 PHE cc_start: 0.8838 (m-80) cc_final: 0.8239 (m-80) REVERT: F 738 GLU cc_start: 0.9222 (mm-30) cc_final: 0.8808 (tp30) outliers start: 0 outliers final: 0 residues processed: 881 average time/residue: 0.2442 time to fit residues: 356.9452 Evaluate side-chains 685 residues out of total 4598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 685 time to evaluate : 1.717 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 534 random chunks: chunk 380 optimal weight: 1.9990 chunk 417 optimal weight: 0.9990 chunk 407 optimal weight: 6.9990 chunk 276 optimal weight: 1.9990 chunk 219 optimal weight: 10.0000 chunk 294 optimal weight: 9.9990 chunk 8 optimal weight: 4.9990 chunk 232 optimal weight: 7.9990 chunk 179 optimal weight: 0.5980 chunk 181 optimal weight: 1.9990 chunk 528 optimal weight: 7.9990 overall best weight: 1.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 317 HIS A 340 HIS ** A 499 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 538 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 603 GLN ** A 735 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 260 ASN C 317 HIS ** C 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 384 HIS C 406 HIS D 490 GLN E 103 GLN E 384 HIS ** E 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 285 ASN F 317 HIS F 340 HIS ** F 490 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4009 r_free = 0.4009 target = 0.122114 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.085324 restraints weight = 142749.413| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.087270 restraints weight = 90708.185| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.088856 restraints weight = 64154.724| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.089831 restraints weight = 48535.564| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.090004 restraints weight = 44094.977| |-----------------------------------------------------------------------------| r_work (final): 0.3465 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7791 moved from start: 0.5603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 42314 Z= 0.135 Angle : 0.691 11.432 57352 Z= 0.346 Chirality : 0.046 0.212 6432 Planarity : 0.005 0.067 7554 Dihedral : 6.612 120.497 5927 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 13.30 Ramachandran Plot: Outliers : 0.32 % Allowed : 8.09 % Favored : 91.59 % Rotamer: Outliers : 0.05 % Allowed : 0.80 % Favored : 99.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.69 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.62 (0.12), residues: 5365 helix: 0.66 (0.11), residues: 2487 sheet: -0.10 (0.21), residues: 632 loop : -1.74 (0.13), residues: 2246 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG F 239 TYR 0.017 0.001 TYR X 183 PHE 0.034 0.001 PHE B 674 TRP 0.051 0.002 TRP W 133 HIS 0.010 0.001 HIS F 406 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.13 (42314) covalent geometry : angle 0.69143 / 0.35 (57352) hydrogen bonds : bond 0.03687 / 2.47 ( 1928) hydrogen bonds : angle 4.69992 / 3.41 ( 5562) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10730 Ramachandran restraints generated. 5365 Oldfield, 0 Emsley, 5365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10730 Ramachandran restraints generated. 5365 Oldfield, 0 Emsley, 5365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 877 residues out of total 4598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 875 time to evaluate : 1.744 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: symmetry clash REVERT: W 44 GLU cc_start: 0.7345 (tt0) cc_final: 0.6813 (mp0) REVERT: W 75 ASN cc_start: 0.7985 (m110) cc_final: 0.7700 (m110) REVERT: W 76 LEU cc_start: 0.8086 (tt) cc_final: 0.7527 (mm) REVERT: W 116 MET cc_start: 0.7056 (mtm) cc_final: 0.6607 (ttt) REVERT: W 118 MET cc_start: 0.0898 (pmm) cc_final: 0.0267 (pmm) REVERT: X 99 LEU cc_start: 0.8856 (mm) cc_final: 0.8352 (tp) REVERT: X 103 LEU cc_start: 0.9273 (mm) cc_final: 0.9022 (mm) REVERT: X 181 HIS cc_start: 0.8621 (t70) cc_final: 0.8344 (t70) REVERT: X 187 MET cc_start: 0.3152 (mpp) cc_final: 0.2648 (mpp) REVERT: Y 247 ARG cc_start: 0.6591 (mmp80) cc_final: 0.5844 (mmm160) REVERT: A 52 PHE cc_start: 0.8391 (t80) cc_final: 0.8054 (t80) REVERT: A 150 ASP cc_start: 0.8842 (t0) cc_final: 0.8595 (t70) REVERT: A 265 PHE cc_start: 0.8281 (t80) cc_final: 0.7874 (t80) REVERT: A 267 PHE cc_start: 0.7556 (m-80) cc_final: 0.7055 (m-80) REVERT: A 274 ILE cc_start: 0.9806 (mm) cc_final: 0.9562 (mm) REVERT: A 315 LYS cc_start: 0.9469 (mmtp) cc_final: 0.9209 (mmmt) REVERT: A 326 SER cc_start: 0.9409 (m) cc_final: 0.8956 (p) REVERT: A 415 CYS cc_start: 0.9495 (m) cc_final: 0.9094 (t) REVERT: A 494 GLN cc_start: 0.8223 (tp-100) cc_final: 0.7672 (tp-100) REVERT: A 495 TYR cc_start: 0.8990 (m-10) cc_final: 0.8633 (m-10) REVERT: A 561 GLU cc_start: 0.9083 (mp0) cc_final: 0.8697 (mp0) REVERT: A 564 ASP cc_start: 0.9211 (m-30) cc_final: 0.8547 (m-30) REVERT: A 602 ASN cc_start: 0.8324 (m110) cc_final: 0.8079 (m110) REVERT: A 608 MET cc_start: 0.9409 (tmm) cc_final: 0.8923 (tmm) REVERT: A 614 LYS cc_start: 0.9570 (mmmt) cc_final: 0.9310 (pptt) REVERT: A 634 LEU cc_start: 0.8924 (mm) cc_final: 0.8065 (tt) REVERT: A 740 MET cc_start: 0.7685 (tmm) cc_final: 0.7114 (tmm) REVERT: B 36 ASN cc_start: 0.9324 (m-40) cc_final: 0.8895 (p0) REVERT: B 162 GLU cc_start: 0.9295 (pt0) cc_final: 0.8929 (pm20) REVERT: B 198 LEU cc_start: 0.8848 (tt) cc_final: 0.8505 (tp) REVERT: B 218 GLU cc_start: 0.7787 (tm-30) cc_final: 0.6917 (tm-30) REVERT: B 244 TYR cc_start: 0.8673 (p90) cc_final: 0.8409 (p90) REVERT: B 273 GLU cc_start: 0.8819 (pt0) cc_final: 0.8111 (pt0) REVERT: B 274 ILE cc_start: 0.9309 (tp) cc_final: 0.9103 (tp) REVERT: B 275 MET cc_start: 0.9053 (tmm) cc_final: 0.8711 (tmm) REVERT: B 292 GLU cc_start: 0.7852 (mt-10) cc_final: 0.7427 (mt-10) REVERT: B 335 LEU cc_start: 0.9078 (tp) cc_final: 0.8805 (tp) REVERT: B 398 GLN cc_start: 0.9159 (tt0) cc_final: 0.8764 (pp30) REVERT: B 401 ASN cc_start: 0.8904 (t0) cc_final: 0.8669 (t0) REVERT: B 484 ASP cc_start: 0.9156 (m-30) cc_final: 0.8394 (p0) REVERT: B 546 GLU cc_start: 0.9478 (mm-30) cc_final: 0.9205 (tp30) REVERT: B 572 CYS cc_start: 0.8159 (p) cc_final: 0.7577 (p) REVERT: B 607 GLU cc_start: 0.8895 (tp30) cc_final: 0.8665 (tp30) REVERT: B 686 ASP cc_start: 0.9227 (t70) cc_final: 0.8558 (m-30) REVERT: C 35 ASP cc_start: 0.8933 (t0) cc_final: 0.8660 (t70) REVERT: C 46 MET cc_start: 0.8779 (ppp) cc_final: 0.8402 (ppp) REVERT: C 218 GLU cc_start: 0.9196 (tp30) cc_final: 0.8852 (tp30) REVERT: C 221 GLU cc_start: 0.8425 (mp0) cc_final: 0.8156 (mp0) REVERT: C 326 SER cc_start: 0.9294 (m) cc_final: 0.8663 (t) REVERT: C 331 LEU cc_start: 0.9383 (mt) cc_final: 0.9173 (mt) REVERT: C 385 THR cc_start: 0.9147 (p) cc_final: 0.8870 (t) REVERT: C 421 GLN cc_start: 0.9580 (tp-100) cc_final: 0.9177 (tp40) REVERT: C 449 MET cc_start: 0.8334 (tmm) cc_final: 0.8098 (tmm) REVERT: C 489 LEU cc_start: 0.9545 (mt) cc_final: 0.9289 (mt) REVERT: C 522 CYS cc_start: 0.7717 (m) cc_final: 0.7021 (p) REVERT: C 564 ASP cc_start: 0.8790 (m-30) cc_final: 0.8559 (m-30) REVERT: C 689 GLU cc_start: 0.9526 (mt-10) cc_final: 0.9143 (mt-10) REVERT: C 736 PHE cc_start: 0.7781 (m-10) cc_final: 0.7578 (m-10) REVERT: D 89 ARG cc_start: 0.9033 (ttm170) cc_final: 0.8786 (ttm170) REVERT: D 182 ILE cc_start: 0.8796 (pt) cc_final: 0.8436 (tp) REVERT: D 242 LEU cc_start: 0.9093 (tt) cc_final: 0.8871 (tt) REVERT: D 283 GLU cc_start: 0.9011 (pp20) cc_final: 0.8320 (pp20) REVERT: D 304 ASP cc_start: 0.8716 (p0) cc_final: 0.8177 (p0) REVERT: D 305 GLU cc_start: 0.8670 (pm20) cc_final: 0.7856 (pm20) REVERT: D 312 LYS cc_start: 0.9179 (mtpp) cc_final: 0.8812 (mttt) REVERT: D 351 ASN cc_start: 0.8679 (m-40) cc_final: 0.8473 (m-40) REVERT: D 460 ASN cc_start: 0.9273 (t0) cc_final: 0.9064 (p0) REVERT: D 495 TYR cc_start: 0.9147 (m-10) cc_final: 0.8751 (m-10) REVERT: D 517 TYR cc_start: 0.9057 (p90) cc_final: 0.8049 (p90) REVERT: D 604 ILE cc_start: 0.9761 (mt) cc_final: 0.9507 (mt) REVERT: D 697 LEU cc_start: 0.9269 (mm) cc_final: 0.8962 (pp) REVERT: D 708 ARG cc_start: 0.9125 (tmt-80) cc_final: 0.8914 (tpt90) REVERT: E 90 ASN cc_start: 0.8448 (m110) cc_final: 0.8062 (t0) REVERT: E 158 MET cc_start: 0.6436 (mtp) cc_final: 0.6081 (mtm) REVERT: E 314 GLU cc_start: 0.8506 (tm-30) cc_final: 0.8266 (tm-30) REVERT: E 315 LYS cc_start: 0.9360 (mmpt) cc_final: 0.9057 (mmmt) REVERT: E 321 GLU cc_start: 0.9333 (mp0) cc_final: 0.8941 (pm20) REVERT: E 326 SER cc_start: 0.9485 (m) cc_final: 0.9155 (p) REVERT: E 449 MET cc_start: 0.8159 (tpp) cc_final: 0.7441 (tpp) REVERT: E 450 ASP cc_start: 0.8761 (t70) cc_final: 0.8478 (t0) REVERT: E 484 ASP cc_start: 0.8807 (p0) cc_final: 0.8591 (p0) REVERT: E 495 TYR cc_start: 0.9009 (m-80) cc_final: 0.8619 (m-80) REVERT: E 551 TRP cc_start: 0.7135 (m-10) cc_final: 0.5973 (m100) REVERT: E 603 GLN cc_start: 0.9681 (mm-40) cc_final: 0.9110 (mm110) REVERT: E 607 GLU cc_start: 0.9205 (mm-30) cc_final: 0.8955 (mm-30) REVERT: E 608 MET cc_start: 0.8762 (tmm) cc_final: 0.8489 (tmm) REVERT: E 720 MET cc_start: 0.4518 (mmm) cc_final: 0.3960 (ptt) REVERT: F 218 GLU cc_start: 0.8654 (mm-30) cc_final: 0.8438 (mp0) REVERT: F 244 TYR cc_start: 0.8799 (p90) cc_final: 0.8009 (p90) REVERT: F 285 ASN cc_start: 0.9632 (m-40) cc_final: 0.8894 (t0) REVERT: F 312 LYS cc_start: 0.9391 (tppp) cc_final: 0.9105 (tptp) REVERT: F 321 GLU cc_start: 0.8213 (pm20) cc_final: 0.7907 (pm20) REVERT: F 331 LEU cc_start: 0.9612 (mt) cc_final: 0.9299 (mt) REVERT: F 403 THR cc_start: 0.8814 (m) cc_final: 0.8490 (m) REVERT: F 411 LEU cc_start: 0.9439 (mt) cc_final: 0.9008 (tp) REVERT: F 425 LYS cc_start: 0.8105 (tppt) cc_final: 0.7585 (ptpp) REVERT: F 442 MET cc_start: 0.8537 (ppp) cc_final: 0.8249 (ppp) REVERT: F 492 LEU cc_start: 0.9286 (mt) cc_final: 0.9052 (mt) REVERT: F 561 GLU cc_start: 0.9291 (pm20) cc_final: 0.9078 (pm20) REVERT: F 577 ASP cc_start: 0.8975 (t70) cc_final: 0.8469 (t70) REVERT: F 620 ILE cc_start: 0.9248 (mt) cc_final: 0.9037 (pt) REVERT: F 640 ASP cc_start: 0.7192 (m-30) cc_final: 0.6922 (m-30) REVERT: F 736 PHE cc_start: 0.8791 (m-80) cc_final: 0.8234 (m-80) REVERT: F 738 GLU cc_start: 0.9220 (mm-30) cc_final: 0.8826 (tp30) outliers start: 2 outliers final: 1 residues processed: 876 average time/residue: 0.2396 time to fit residues: 350.0989 Evaluate side-chains 690 residues out of total 4598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 689 time to evaluate : 1.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 534 random chunks: chunk 395 optimal weight: 9.9990 chunk 429 optimal weight: 0.3980 chunk 267 optimal weight: 5.9990 chunk 43 optimal weight: 0.0570 chunk 266 optimal weight: 0.8980 chunk 330 optimal weight: 8.9990 chunk 321 optimal weight: 1.9990 chunk 431 optimal weight: 5.9990 chunk 519 optimal weight: 8.9990 chunk 175 optimal weight: 0.9980 chunk 109 optimal weight: 0.9990 overall best weight: 0.6700 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 317 HIS A 340 HIS ** A 499 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 692 GLN A 735 HIS ** B 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 317 HIS ** C 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 384 HIS D 384 HIS E 103 GLN E 384 HIS ** E 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 602 ASN ** F 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 91 ASN F 296 ASN F 317 HIS ** F 490 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4028 r_free = 0.4028 target = 0.123595 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.086039 restraints weight = 141666.721| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.088883 restraints weight = 84743.682| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 56)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.090782 restraints weight = 60076.983| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.092033 restraints weight = 47550.632| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.092877 restraints weight = 40680.544| |-----------------------------------------------------------------------------| r_work (final): 0.3498 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7721 moved from start: 0.5731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.078 42314 Z= 0.126 Angle : 0.697 12.266 57352 Z= 0.347 Chirality : 0.046 0.245 6432 Planarity : 0.005 0.124 7554 Dihedral : 6.489 121.430 5927 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 12.66 Ramachandran Plot: Outliers : 0.32 % Allowed : 7.53 % Favored : 92.15 % Rotamer: Outliers : 0.00 % Allowed : 0.69 % Favored : 99.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.69 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.52 (0.12), residues: 5365 helix: 0.75 (0.11), residues: 2469 sheet: -0.01 (0.21), residues: 632 loop : -1.69 (0.13), residues: 2264 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG E 772 TYR 0.042 0.001 TYR X 183 PHE 0.031 0.001 PHE B 674 TRP 0.052 0.002 TRP W 133 HIS 0.009 0.001 HIS F 406 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.13 (42314) covalent geometry : angle 0.69727 / 0.35 (57352) hydrogen bonds : bond 0.03567 / 2.40 ( 1928) hydrogen bonds : angle 4.66603 / 3.38 ( 5562) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10730 Ramachandran restraints generated. 5365 Oldfield, 0 Emsley, 5365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10730 Ramachandran restraints generated. 5365 Oldfield, 0 Emsley, 5365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 879 residues out of total 4598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 879 time to evaluate : 1.671 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: W 44 GLU cc_start: 0.7348 (tt0) cc_final: 0.6825 (mp0) REVERT: W 75 ASN cc_start: 0.7966 (m110) cc_final: 0.7601 (m110) REVERT: W 76 LEU cc_start: 0.8165 (tt) cc_final: 0.7606 (mm) REVERT: W 116 MET cc_start: 0.6968 (mtm) cc_final: 0.6533 (ttt) REVERT: W 118 MET cc_start: 0.0488 (pmm) cc_final: -0.0073 (pmm) REVERT: X 181 HIS cc_start: 0.8557 (t70) cc_final: 0.8245 (t70) REVERT: Y 247 ARG cc_start: 0.6468 (mmp80) cc_final: 0.5761 (mmm160) REVERT: A 52 PHE cc_start: 0.8536 (t80) cc_final: 0.8114 (t80) REVERT: A 150 ASP cc_start: 0.8803 (t0) cc_final: 0.8555 (t70) REVERT: A 274 ILE cc_start: 0.9783 (mm) cc_final: 0.9539 (mm) REVERT: A 326 SER cc_start: 0.9391 (m) cc_final: 0.8941 (p) REVERT: A 364 ASP cc_start: 0.9108 (p0) cc_final: 0.8690 (p0) REVERT: A 388 MET cc_start: 0.8914 (ptp) cc_final: 0.8467 (ptp) REVERT: A 415 CYS cc_start: 0.9508 (m) cc_final: 0.9131 (t) REVERT: A 494 GLN cc_start: 0.8222 (tp-100) cc_final: 0.7651 (tp-100) REVERT: A 495 TYR cc_start: 0.8982 (m-10) cc_final: 0.8649 (m-80) REVERT: A 561 GLU cc_start: 0.9095 (mp0) cc_final: 0.8712 (mp0) REVERT: A 564 ASP cc_start: 0.9226 (m-30) cc_final: 0.8602 (m-30) REVERT: A 602 ASN cc_start: 0.8432 (m110) cc_final: 0.8193 (m110) REVERT: A 608 MET cc_start: 0.9336 (tmm) cc_final: 0.8873 (tmm) REVERT: A 614 LYS cc_start: 0.9562 (mmmt) cc_final: 0.9320 (pptt) REVERT: A 634 LEU cc_start: 0.8909 (mm) cc_final: 0.8066 (tt) REVERT: A 740 MET cc_start: 0.7614 (tmm) cc_final: 0.7023 (tmm) REVERT: B 36 ASN cc_start: 0.9274 (m-40) cc_final: 0.8799 (p0) REVERT: B 84 MET cc_start: 0.9063 (tmm) cc_final: 0.8702 (tmm) REVERT: B 120 ASP cc_start: 0.8920 (p0) cc_final: 0.8685 (p0) REVERT: B 162 GLU cc_start: 0.9239 (pt0) cc_final: 0.8951 (pm20) REVERT: B 218 GLU cc_start: 0.7736 (tm-30) cc_final: 0.7001 (tm-30) REVERT: B 244 TYR cc_start: 0.8668 (p90) cc_final: 0.8399 (p90) REVERT: B 273 GLU cc_start: 0.8767 (pt0) cc_final: 0.7970 (pt0) REVERT: B 274 ILE cc_start: 0.9183 (tp) cc_final: 0.8963 (tp) REVERT: B 275 MET cc_start: 0.9042 (tmm) cc_final: 0.8673 (tmm) REVERT: B 292 GLU cc_start: 0.7881 (mt-10) cc_final: 0.7498 (mt-10) REVERT: B 317 HIS cc_start: 0.8357 (m90) cc_final: 0.7938 (m90) REVERT: B 335 LEU cc_start: 0.9049 (tp) cc_final: 0.8774 (tp) REVERT: B 398 GLN cc_start: 0.9163 (tt0) cc_final: 0.8768 (pp30) REVERT: B 401 ASN cc_start: 0.8898 (t0) cc_final: 0.8675 (t0) REVERT: B 484 ASP cc_start: 0.9126 (m-30) cc_final: 0.8382 (p0) REVERT: B 525 THR cc_start: 0.9019 (p) cc_final: 0.8525 (p) REVERT: B 529 LYS cc_start: 0.9463 (mmtm) cc_final: 0.9160 (mmtp) REVERT: B 546 GLU cc_start: 0.9476 (mm-30) cc_final: 0.9168 (tp30) REVERT: B 686 ASP cc_start: 0.9200 (t70) cc_final: 0.8544 (m-30) REVERT: B 757 MET cc_start: 0.9244 (mpp) cc_final: 0.9007 (mpp) REVERT: C 35 ASP cc_start: 0.8873 (t0) cc_final: 0.8610 (t70) REVERT: C 46 MET cc_start: 0.8738 (ppp) cc_final: 0.8353 (ppp) REVERT: C 218 GLU cc_start: 0.9194 (tp30) cc_final: 0.8796 (tp30) REVERT: C 221 GLU cc_start: 0.8427 (mp0) cc_final: 0.8133 (mp0) REVERT: C 326 SER cc_start: 0.9276 (m) cc_final: 0.8609 (t) REVERT: C 327 GLN cc_start: 0.9183 (tp-100) cc_final: 0.8579 (tp-100) REVERT: C 331 LEU cc_start: 0.9342 (mt) cc_final: 0.8442 (mt) REVERT: C 340 HIS cc_start: 0.6928 (p-80) cc_final: 0.6651 (p90) REVERT: C 385 THR cc_start: 0.9116 (p) cc_final: 0.8843 (t) REVERT: C 421 GLN cc_start: 0.9564 (tp-100) cc_final: 0.9163 (tp40) REVERT: C 449 MET cc_start: 0.8314 (tmm) cc_final: 0.8099 (tmm) REVERT: C 489 LEU cc_start: 0.9531 (mt) cc_final: 0.9273 (mt) REVERT: C 564 ASP cc_start: 0.8775 (m-30) cc_final: 0.8512 (m-30) REVERT: C 615 LYS cc_start: 0.8751 (mtmm) cc_final: 0.8206 (tppt) REVERT: C 689 GLU cc_start: 0.9523 (mt-10) cc_final: 0.9126 (mt-10) REVERT: D 89 ARG cc_start: 0.9022 (ttm170) cc_final: 0.8766 (ttm170) REVERT: D 283 GLU cc_start: 0.9154 (pp20) cc_final: 0.8240 (pp20) REVERT: D 296 ASN cc_start: 0.9227 (t0) cc_final: 0.8520 (t0) REVERT: D 312 LYS cc_start: 0.9139 (mtpp) cc_final: 0.8929 (ttpt) REVERT: D 460 ASN cc_start: 0.9234 (t0) cc_final: 0.9020 (p0) REVERT: D 489 LEU cc_start: 0.9396 (mt) cc_final: 0.9008 (mt) REVERT: D 495 TYR cc_start: 0.9179 (m-10) cc_final: 0.8790 (m-10) REVERT: D 517 TYR cc_start: 0.9097 (p90) cc_final: 0.8072 (p90) REVERT: D 697 LEU cc_start: 0.9245 (mm) cc_final: 0.8963 (pp) REVERT: D 708 ARG cc_start: 0.9083 (tmt-80) cc_final: 0.8741 (ttp80) REVERT: E 90 ASN cc_start: 0.8415 (m110) cc_final: 0.7950 (t0) REVERT: E 158 MET cc_start: 0.6359 (mtp) cc_final: 0.6008 (mtm) REVERT: E 314 GLU cc_start: 0.8428 (tm-30) cc_final: 0.8185 (tm-30) REVERT: E 315 LYS cc_start: 0.9289 (mmpt) cc_final: 0.8953 (mmmt) REVERT: E 321 GLU cc_start: 0.9278 (mp0) cc_final: 0.8924 (pm20) REVERT: E 326 SER cc_start: 0.9507 (m) cc_final: 0.9156 (p) REVERT: E 366 GLU cc_start: 0.8287 (mt-10) cc_final: 0.8025 (mp0) REVERT: E 379 GLU cc_start: 0.8999 (mp0) cc_final: 0.8552 (mp0) REVERT: E 449 MET cc_start: 0.8149 (tpp) cc_final: 0.7443 (tpp) REVERT: E 450 ASP cc_start: 0.8650 (t70) cc_final: 0.8362 (t0) REVERT: E 495 TYR cc_start: 0.9030 (m-80) cc_final: 0.8779 (m-80) REVERT: E 527 LEU cc_start: 0.9391 (mm) cc_final: 0.9157 (mp) REVERT: E 548 LEU cc_start: 0.9236 (mp) cc_final: 0.8924 (tp) REVERT: E 551 TRP cc_start: 0.6835 (m-10) cc_final: 0.5909 (m100) REVERT: E 561 GLU cc_start: 0.9041 (pp20) cc_final: 0.8833 (pp20) REVERT: E 564 ASP cc_start: 0.9264 (m-30) cc_final: 0.9037 (m-30) REVERT: E 603 GLN cc_start: 0.9685 (mm-40) cc_final: 0.9141 (mm110) REVERT: E 607 GLU cc_start: 0.9212 (mm-30) cc_final: 0.8953 (mm-30) REVERT: E 608 MET cc_start: 0.8702 (tmm) cc_final: 0.8422 (tmm) REVERT: E 720 MET cc_start: 0.4339 (mmm) cc_final: 0.3755 (ptt) REVERT: F 218 GLU cc_start: 0.8658 (mm-30) cc_final: 0.8433 (mp0) REVERT: F 244 TYR cc_start: 0.8773 (p90) cc_final: 0.7993 (p90) REVERT: F 312 LYS cc_start: 0.9388 (tppp) cc_final: 0.9137 (tptp) REVERT: F 321 GLU cc_start: 0.8270 (pm20) cc_final: 0.7934 (pm20) REVERT: F 331 LEU cc_start: 0.9603 (mt) cc_final: 0.9267 (mt) REVERT: F 403 THR cc_start: 0.8682 (m) cc_final: 0.8449 (m) REVERT: F 411 LEU cc_start: 0.9418 (mt) cc_final: 0.9017 (tp) REVERT: F 442 MET cc_start: 0.8477 (ppp) cc_final: 0.8199 (ppp) REVERT: F 492 LEU cc_start: 0.9318 (mt) cc_final: 0.9087 (mt) REVERT: F 577 ASP cc_start: 0.9020 (t70) cc_final: 0.8620 (t70) REVERT: F 640 ASP cc_start: 0.7134 (m-30) cc_final: 0.6879 (m-30) REVERT: F 736 PHE cc_start: 0.8706 (m-80) cc_final: 0.8174 (m-80) REVERT: F 738 GLU cc_start: 0.9110 (mm-30) cc_final: 0.8752 (tp30) outliers start: 0 outliers final: 0 residues processed: 879 average time/residue: 0.2385 time to fit residues: 350.6307 Evaluate side-chains 713 residues out of total 4598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 713 time to evaluate : 1.672 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 534 random chunks: chunk 290 optimal weight: 5.9990 chunk 314 optimal weight: 6.9990 chunk 271 optimal weight: 5.9990 chunk 244 optimal weight: 7.9990 chunk 103 optimal weight: 0.3980 chunk 28 optimal weight: 10.0000 chunk 3 optimal weight: 0.0270 chunk 189 optimal weight: 0.0770 chunk 42 optimal weight: 2.9990 chunk 120 optimal weight: 3.9990 chunk 107 optimal weight: 3.9990 overall best weight: 1.5000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... X 105 ASN A 36 ASN A 317 HIS A 340 HIS ** A 499 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 317 HIS ** C 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 384 HIS D 384 HIS E 103 GLN E 384 HIS ** E 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 499 HIS ** F 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 285 ASN F 317 HIS ** F 490 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4022 r_free = 0.4022 target = 0.123217 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.085813 restraints weight = 142478.184| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.088552 restraints weight = 85644.263| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.090447 restraints weight = 60964.276| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.091722 restraints weight = 48379.655| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.092580 restraints weight = 41289.422| |-----------------------------------------------------------------------------| r_work (final): 0.3506 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7748 moved from start: 0.5861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.076 42314 Z= 0.134 Angle : 0.702 11.743 57352 Z= 0.351 Chirality : 0.046 0.219 6432 Planarity : 0.005 0.067 7554 Dihedral : 6.402 125.376 5927 Min Nonbonded Distance : 2.310 Molprobity Statistics. All-atom Clashscore : 13.09 Ramachandran Plot: Outliers : 0.32 % Allowed : 7.75 % Favored : 91.93 % Rotamer: Outliers : 0.02 % Allowed : 0.35 % Favored : 99.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.69 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.51 (0.12), residues: 5365 helix: 0.75 (0.11), residues: 2479 sheet: -0.08 (0.21), residues: 640 loop : -1.67 (0.13), residues: 2246 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 86 TYR 0.037 0.001 TYR X 183 PHE 0.031 0.001 PHE B 674 TRP 0.057 0.002 TRP C 476 HIS 0.008 0.001 HIS F 406 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.13 (42314) covalent geometry : angle 0.70245 / 0.35 (57352) hydrogen bonds : bond 0.03578 / 2.40 ( 1928) hydrogen bonds : angle 4.69006 / 3.38 ( 5562) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10730 Ramachandran restraints generated. 5365 Oldfield, 0 Emsley, 5365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10730 Ramachandran restraints generated. 5365 Oldfield, 0 Emsley, 5365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 863 residues out of total 4598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 862 time to evaluate : 1.532 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: W 44 GLU cc_start: 0.7364 (tt0) cc_final: 0.6845 (mp0) REVERT: W 75 ASN cc_start: 0.8012 (m110) cc_final: 0.7648 (m110) REVERT: W 76 LEU cc_start: 0.8073 (tt) cc_final: 0.7472 (mm) REVERT: W 116 MET cc_start: 0.6929 (mtm) cc_final: 0.6604 (ttt) REVERT: W 118 MET cc_start: 0.0042 (pmm) cc_final: -0.0503 (pmm) REVERT: X 181 HIS cc_start: 0.8540 (t70) cc_final: 0.8213 (t70) REVERT: X 187 MET cc_start: 0.3361 (mpp) cc_final: 0.2945 (mpp) REVERT: A 35 ASP cc_start: 0.8386 (t0) cc_final: 0.8124 (t70) REVERT: A 52 PHE cc_start: 0.8589 (t80) cc_final: 0.8137 (t80) REVERT: A 150 ASP cc_start: 0.8817 (t0) cc_final: 0.8538 (t70) REVERT: A 253 LEU cc_start: 0.9427 (tt) cc_final: 0.9220 (tt) REVERT: A 292 GLU cc_start: 0.9251 (tt0) cc_final: 0.8936 (tt0) REVERT: A 326 SER cc_start: 0.9396 (m) cc_final: 0.8943 (p) REVERT: A 415 CYS cc_start: 0.9511 (m) cc_final: 0.9119 (t) REVERT: A 494 GLN cc_start: 0.8208 (tp-100) cc_final: 0.7608 (tp-100) REVERT: A 495 TYR cc_start: 0.8979 (m-10) cc_final: 0.8638 (m-80) REVERT: A 550 MET cc_start: 0.8745 (mpp) cc_final: 0.8481 (ptp) REVERT: A 561 GLU cc_start: 0.9082 (mp0) cc_final: 0.8668 (mp0) REVERT: A 564 ASP cc_start: 0.9193 (m-30) cc_final: 0.8592 (m-30) REVERT: A 568 GLN cc_start: 0.8856 (mm110) cc_final: 0.8656 (mm110) REVERT: A 602 ASN cc_start: 0.8488 (m110) cc_final: 0.8249 (m110) REVERT: A 608 MET cc_start: 0.9341 (tmm) cc_final: 0.8871 (tmm) REVERT: A 740 MET cc_start: 0.7630 (tmm) cc_final: 0.7021 (tmm) REVERT: B 36 ASN cc_start: 0.9225 (m-40) cc_final: 0.8799 (p0) REVERT: B 84 MET cc_start: 0.9055 (tmm) cc_final: 0.8748 (tmm) REVERT: B 162 GLU cc_start: 0.9292 (pt0) cc_final: 0.8924 (pm20) REVERT: B 218 GLU cc_start: 0.7758 (tm-30) cc_final: 0.6940 (tm-30) REVERT: B 244 TYR cc_start: 0.8661 (p90) cc_final: 0.8258 (p90) REVERT: B 273 GLU cc_start: 0.8787 (pt0) cc_final: 0.7952 (pt0) REVERT: B 274 ILE cc_start: 0.9279 (tp) cc_final: 0.9058 (tp) REVERT: B 275 MET cc_start: 0.9020 (tmm) cc_final: 0.8699 (tmm) REVERT: B 281 GLU cc_start: 0.8151 (pm20) cc_final: 0.7944 (mp0) REVERT: B 292 GLU cc_start: 0.7896 (mt-10) cc_final: 0.7469 (mt-10) REVERT: B 317 HIS cc_start: 0.8312 (m90) cc_final: 0.7962 (m90) REVERT: B 335 LEU cc_start: 0.9039 (tp) cc_final: 0.8728 (tp) REVERT: B 398 GLN cc_start: 0.9186 (tt0) cc_final: 0.8764 (pp30) REVERT: B 401 ASN cc_start: 0.8947 (t0) cc_final: 0.8701 (t0) REVERT: B 484 ASP cc_start: 0.9094 (m-30) cc_final: 0.8334 (p0) REVERT: B 525 THR cc_start: 0.8967 (p) cc_final: 0.8453 (p) REVERT: B 529 LYS cc_start: 0.9446 (mmtm) cc_final: 0.9148 (mmtp) REVERT: B 546 GLU cc_start: 0.9440 (mm-30) cc_final: 0.8776 (tp30) REVERT: B 550 MET cc_start: 0.8233 (ptt) cc_final: 0.7902 (ptp) REVERT: B 572 CYS cc_start: 0.8252 (p) cc_final: 0.7666 (p) REVERT: B 611 MET cc_start: 0.8218 (mmp) cc_final: 0.7665 (mmm) REVERT: B 686 ASP cc_start: 0.9188 (t70) cc_final: 0.8538 (m-30) REVERT: B 757 MET cc_start: 0.9232 (mpp) cc_final: 0.8988 (mpp) REVERT: C 35 ASP cc_start: 0.8866 (t0) cc_final: 0.8593 (t70) REVERT: C 46 MET cc_start: 0.8721 (ppp) cc_final: 0.8342 (ppp) REVERT: C 218 GLU cc_start: 0.9156 (tp30) cc_final: 0.8784 (tp30) REVERT: C 221 GLU cc_start: 0.8406 (mp0) cc_final: 0.8006 (mp0) REVERT: C 326 SER cc_start: 0.9283 (m) cc_final: 0.8645 (t) REVERT: C 327 GLN cc_start: 0.9206 (tp-100) cc_final: 0.8584 (tp-100) REVERT: C 331 LEU cc_start: 0.9332 (mt) cc_final: 0.8440 (mt) REVERT: C 385 THR cc_start: 0.9136 (p) cc_final: 0.8883 (t) REVERT: C 388 MET cc_start: 0.8529 (tpt) cc_final: 0.8291 (tpt) REVERT: C 421 GLN cc_start: 0.9567 (tp-100) cc_final: 0.9125 (tp40) REVERT: C 449 MET cc_start: 0.8285 (tmm) cc_final: 0.8064 (tmm) REVERT: C 491 GLU cc_start: 0.8532 (mt-10) cc_final: 0.8188 (mm-30) REVERT: C 564 ASP cc_start: 0.8731 (m-30) cc_final: 0.8472 (m-30) REVERT: C 615 LYS cc_start: 0.8708 (mtmm) cc_final: 0.8196 (tppt) REVERT: C 689 GLU cc_start: 0.9535 (mt-10) cc_final: 0.9124 (mt-10) REVERT: D 89 ARG cc_start: 0.9001 (ttm170) cc_final: 0.8741 (ttm170) REVERT: D 283 GLU cc_start: 0.9125 (pp20) cc_final: 0.8246 (pp20) REVERT: D 296 ASN cc_start: 0.9273 (t0) cc_final: 0.8567 (t0) REVERT: D 304 ASP cc_start: 0.8603 (p0) cc_final: 0.7898 (p0) REVERT: D 305 GLU cc_start: 0.8814 (pm20) cc_final: 0.8146 (pm20) REVERT: D 312 LYS cc_start: 0.9172 (mtpp) cc_final: 0.8929 (ttpt) REVERT: D 489 LEU cc_start: 0.9398 (mt) cc_final: 0.8909 (mt) REVERT: D 495 TYR cc_start: 0.9206 (m-10) cc_final: 0.8844 (m-10) REVERT: D 517 TYR cc_start: 0.9102 (p90) cc_final: 0.8092 (p90) REVERT: D 697 LEU cc_start: 0.9252 (mm) cc_final: 0.8970 (pp) REVERT: D 708 ARG cc_start: 0.9068 (tmt-80) cc_final: 0.8694 (ttp80) REVERT: E 90 ASN cc_start: 0.8467 (m110) cc_final: 0.8003 (t0) REVERT: E 158 MET cc_start: 0.6413 (mtp) cc_final: 0.5682 (mmm) REVERT: E 315 LYS cc_start: 0.9276 (mmpt) cc_final: 0.8945 (mmmt) REVERT: E 321 GLU cc_start: 0.9314 (mp0) cc_final: 0.8964 (pm20) REVERT: E 326 SER cc_start: 0.9488 (m) cc_final: 0.9162 (p) REVERT: E 366 GLU cc_start: 0.8346 (mt-10) cc_final: 0.7952 (mp0) REVERT: E 379 GLU cc_start: 0.8951 (mp0) cc_final: 0.8671 (mp0) REVERT: E 449 MET cc_start: 0.8067 (tpp) cc_final: 0.7458 (tpp) REVERT: E 450 ASP cc_start: 0.8638 (t70) cc_final: 0.8360 (t0) REVERT: E 527 LEU cc_start: 0.9429 (mm) cc_final: 0.9180 (mp) REVERT: E 548 LEU cc_start: 0.9204 (mp) cc_final: 0.8934 (tp) REVERT: E 551 TRP cc_start: 0.6698 (m-10) cc_final: 0.5716 (m100) REVERT: E 564 ASP cc_start: 0.9260 (m-30) cc_final: 0.9038 (m-30) REVERT: E 603 GLN cc_start: 0.9675 (mm-40) cc_final: 0.9120 (mm110) REVERT: E 607 GLU cc_start: 0.9180 (mm-30) cc_final: 0.8940 (mm-30) REVERT: E 720 MET cc_start: 0.4402 (mmm) cc_final: 0.3782 (ptt) REVERT: F 218 GLU cc_start: 0.8644 (mm-30) cc_final: 0.8407 (mp0) REVERT: F 244 TYR cc_start: 0.8782 (p90) cc_final: 0.7913 (p90) REVERT: F 291 GLU cc_start: 0.9063 (pt0) cc_final: 0.8849 (pt0) REVERT: F 312 LYS cc_start: 0.9360 (tppp) cc_final: 0.9086 (tptp) REVERT: F 321 GLU cc_start: 0.8203 (pm20) cc_final: 0.7894 (pm20) REVERT: F 326 SER cc_start: 0.9316 (m) cc_final: 0.9068 (t) REVERT: F 331 LEU cc_start: 0.9606 (mt) cc_final: 0.9289 (mt) REVERT: F 403 THR cc_start: 0.8611 (m) cc_final: 0.8321 (m) REVERT: F 410 ASP cc_start: 0.9000 (t70) cc_final: 0.8782 (t0) REVERT: F 411 LEU cc_start: 0.9438 (mt) cc_final: 0.9021 (tp) REVERT: F 442 MET cc_start: 0.8476 (ppp) cc_final: 0.8212 (ppp) REVERT: F 492 LEU cc_start: 0.9341 (mt) cc_final: 0.9111 (mt) REVERT: F 577 ASP cc_start: 0.8988 (t70) cc_final: 0.8520 (t70) REVERT: F 640 ASP cc_start: 0.7189 (m-30) cc_final: 0.6944 (m-30) REVERT: F 736 PHE cc_start: 0.8669 (m-80) cc_final: 0.8160 (m-80) REVERT: F 738 GLU cc_start: 0.9104 (mm-30) cc_final: 0.8751 (tp30) outliers start: 1 outliers final: 1 residues processed: 862 average time/residue: 0.2240 time to fit residues: 323.5062 Evaluate side-chains 699 residues out of total 4598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 698 time to evaluate : 2.508 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 534 random chunks: chunk 39 optimal weight: 5.9990 chunk 443 optimal weight: 0.9980 chunk 415 optimal weight: 4.9990 chunk 378 optimal weight: 7.9990 chunk 316 optimal weight: 3.9990 chunk 162 optimal weight: 5.9990 chunk 61 optimal weight: 6.9990 chunk 92 optimal weight: 3.9990 chunk 125 optimal weight: 0.0870 chunk 89 optimal weight: 0.2980 chunk 393 optimal weight: 10.0000 overall best weight: 1.8762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 317 HIS A 340 HIS ** A 499 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 384 HIS C 317 HIS E 103 GLN E 384 HIS ** E 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 602 ASN ** F 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 285 ASN F 317 HIS ** F 490 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4009 r_free = 0.4009 target = 0.122356 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.085948 restraints weight = 144727.350| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.087944 restraints weight = 94806.010| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.089239 restraints weight = 59562.350| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.089845 restraints weight = 50895.065| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.089979 restraints weight = 47284.200| |-----------------------------------------------------------------------------| r_work (final): 0.3449 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7809 moved from start: 0.6008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.076 42314 Z= 0.142 Angle : 0.702 11.311 57352 Z= 0.352 Chirality : 0.046 0.210 6432 Planarity : 0.005 0.099 7554 Dihedral : 6.374 131.733 5927 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 13.01 Ramachandran Plot: Outliers : 0.32 % Allowed : 7.90 % Favored : 91.78 % Rotamer: Outliers : 0.00 % Allowed : 0.45 % Favored : 99.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.69 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.52 (0.12), residues: 5365 helix: 0.74 (0.11), residues: 2472 sheet: -0.16 (0.20), residues: 652 loop : -1.65 (0.13), residues: 2241 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG E 89 TYR 0.038 0.002 TYR X 183 PHE 0.031 0.001 PHE B 674 TRP 0.048 0.002 TRP C 476 HIS 0.008 0.001 HIS F 406 Details of bonding type rmsd/Z covalent geometry : bond 0.00313 / 0.14 (42314) covalent geometry : angle 0.70213 / 0.35 (57352) hydrogen bonds : bond 0.03617 / 2.43 ( 1928) hydrogen bonds : angle 4.70764 / 3.39 ( 5562) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9851.66 seconds wall clock time: 169 minutes 53.25 seconds (10193.25 seconds total)