Starting phenix.real_space_refine on Mon Dec 30 14:01:41 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zts_60471/12_2024/8zts_60471.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zts_60471/12_2024/8zts_60471.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8zts_60471/12_2024/8zts_60471.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zts_60471/12_2024/8zts_60471.map" model { file = "/net/cci-nas-00/data/ceres_data/8zts_60471/12_2024/8zts_60471.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zts_60471/12_2024/8zts_60471.cif" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 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: 4 Type Number sf(0) Gaussians S 110 5.16 5 C 8765 2.51 5 N 2210 2.21 5 O 2430 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 75 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 13515 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 2689 Number of conformers: 1 Conformer: "" Number of residues, atoms: 348, 2689 Classifications: {'peptide': 348} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 332} Chain breaks: 1 Unresolved non-hydrogen bonds: 71 Unresolved non-hydrogen angles: 86 Unresolved non-hydrogen dihedrals: 58 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 2, 'HIS:plan': 1, 'ARG:plan': 3, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 48 Chain: "B" Number of atoms: 2689 Number of conformers: 1 Conformer: "" Number of residues, atoms: 348, 2689 Classifications: {'peptide': 348} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 332} Chain breaks: 1 Unresolved non-hydrogen bonds: 71 Unresolved non-hydrogen angles: 86 Unresolved non-hydrogen dihedrals: 58 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 2, 'HIS:plan': 1, 'ARG:plan': 3, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 48 Chain: "C" Number of atoms: 2689 Number of conformers: 1 Conformer: "" Number of residues, atoms: 348, 2689 Classifications: {'peptide': 348} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 332} Chain breaks: 1 Unresolved non-hydrogen bonds: 71 Unresolved non-hydrogen angles: 86 Unresolved non-hydrogen dihedrals: 58 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 2, 'HIS:plan': 1, 'ARG:plan': 3, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 48 Chain: "D" Number of atoms: 2689 Number of conformers: 1 Conformer: "" Number of residues, atoms: 348, 2689 Classifications: {'peptide': 348} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 332} Chain breaks: 1 Unresolved non-hydrogen bonds: 71 Unresolved non-hydrogen angles: 86 Unresolved non-hydrogen dihedrals: 58 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 2, 'HIS:plan': 1, 'ARG:plan': 3, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 48 Chain: "E" Number of atoms: 2689 Number of conformers: 1 Conformer: "" Number of residues, atoms: 348, 2689 Classifications: {'peptide': 348} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 332} Chain breaks: 1 Unresolved non-hydrogen bonds: 71 Unresolved non-hydrogen angles: 86 Unresolved non-hydrogen dihedrals: 58 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 2, 'HIS:plan': 1, 'ARG:plan': 3, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 48 Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 8.70, per 1000 atoms: 0.64 Number of scatterers: 13515 At special positions: 0 Unit cell: (86.1, 83.64, 156.62, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 110 16.00 O 2430 8.00 N 2210 7.00 C 8765 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=10, symmetry=0 Simple disulfide: pdb=" SG CYS A 48 " - pdb=" SG CYS A 173 " distance=2.03 Simple disulfide: pdb=" SG CYS A 147 " - pdb=" SG CYS A 161 " distance=2.03 Simple disulfide: pdb=" SG CYS B 48 " - pdb=" SG CYS B 173 " distance=2.03 Simple disulfide: pdb=" SG CYS B 147 " - pdb=" SG CYS B 161 " distance=2.03 Simple disulfide: pdb=" SG CYS C 48 " - pdb=" SG CYS C 173 " distance=2.03 Simple disulfide: pdb=" SG CYS C 147 " - pdb=" SG CYS C 161 " distance=2.03 Simple disulfide: pdb=" SG CYS D 48 " - pdb=" SG CYS D 173 " distance=2.03 Simple disulfide: pdb=" SG CYS D 147 " - pdb=" SG CYS D 161 " distance=2.03 Simple disulfide: pdb=" SG CYS E 48 " - pdb=" SG CYS E 173 " distance=2.03 Simple disulfide: pdb=" SG CYS E 147 " - pdb=" SG CYS E 161 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A 501 " - " ASN A 132 " " NAG B 501 " - " ASN B 132 " " NAG C 501 " - " ASN C 132 " " NAG D 501 " - " ASN D 132 " " NAG E 501 " - " ASN E 132 " Time building additional restraints: 3.27 Conformation dependent library (CDL) restraints added in 1.9 seconds 3440 Ramachandran restraints generated. 1720 Oldfield, 0 Emsley, 1720 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3320 Finding SS restraints... Secondary structure from input PDB file: 42 helices and 25 sheets defined 43.4% alpha, 28.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.56 Creating SS restraints... Processing helix chain 'A' and resid 26 through 38 removed outlier: 3.952A pdb=" N GLU A 38 " --> pdb=" O LEU A 34 " (cutoff:3.500A) Processing helix chain 'A' and resid 84 through 87 Processing helix chain 'A' and resid 103 through 105 No H-bonds generated for 'chain 'A' and resid 103 through 105' Processing helix chain 'A' and resid 217 through 238 removed outlier: 4.827A pdb=" N LEU A 226 " --> pdb=" O MET A 222 " (cutoff:3.500A) Proline residue: A 227 - end of helix Processing helix chain 'A' and resid 239 through 241 No H-bonds generated for 'chain 'A' and resid 239 through 241' Processing helix chain 'A' and resid 248 through 268 Processing helix chain 'A' and resid 279 through 308 Processing helix chain 'A' and resid 351 through 405 removed outlier: 3.609A pdb=" N VAL A 356 " --> pdb=" O MET A 352 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N VAL A 357 " --> pdb=" O LEU A 353 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ALA A 377 " --> pdb=" O LYS A 373 " (cutoff:3.500A) Processing helix chain 'B' and resid 26 through 38 removed outlier: 3.861A pdb=" N GLU B 38 " --> pdb=" O LEU B 34 " (cutoff:3.500A) Processing helix chain 'B' and resid 103 through 105 No H-bonds generated for 'chain 'B' and resid 103 through 105' Processing helix chain 'B' and resid 217 through 224 Processing helix chain 'B' and resid 224 through 238 removed outlier: 3.598A pdb=" N THR B 228 " --> pdb=" O LEU B 224 " (cutoff:3.500A) Processing helix chain 'B' and resid 239 through 241 No H-bonds generated for 'chain 'B' and resid 239 through 241' Processing helix chain 'B' and resid 248 through 269 removed outlier: 3.812A pdb=" N GLN B 269 " --> pdb=" O LEU B 265 " (cutoff:3.500A) Processing helix chain 'B' and resid 278 through 308 removed outlier: 4.519A pdb=" N ILE B 282 " --> pdb=" O PRO B 278 " (cutoff:3.500A) Processing helix chain 'B' and resid 351 through 405 removed outlier: 3.534A pdb=" N VAL B 356 " --> pdb=" O MET B 352 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N VAL B 357 " --> pdb=" O LEU B 353 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ALA B 377 " --> pdb=" O LYS B 373 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ASP B 378 " --> pdb=" O HIS B 374 " (cutoff:3.500A) Processing helix chain 'C' and resid 26 through 38 removed outlier: 3.919A pdb=" N GLU C 38 " --> pdb=" O LEU C 34 " (cutoff:3.500A) Processing helix chain 'C' and resid 84 through 87 Processing helix chain 'C' and resid 103 through 105 No H-bonds generated for 'chain 'C' and resid 103 through 105' Processing helix chain 'C' and resid 217 through 224 Processing helix chain 'C' and resid 224 through 238 removed outlier: 3.588A pdb=" N THR C 228 " --> pdb=" O LEU C 224 " (cutoff:3.500A) Processing helix chain 'C' and resid 239 through 241 No H-bonds generated for 'chain 'C' and resid 239 through 241' Processing helix chain 'C' and resid 248 through 268 Processing helix chain 'C' and resid 279 through 308 Processing helix chain 'C' and resid 351 through 405 removed outlier: 3.626A pdb=" N VAL C 356 " --> pdb=" O MET C 352 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N VAL C 357 " --> pdb=" O LEU C 353 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N ALA C 377 " --> pdb=" O LYS C 373 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ASP C 378 " --> pdb=" O HIS C 374 " (cutoff:3.500A) Processing helix chain 'D' and resid 26 through 38 removed outlier: 3.931A pdb=" N GLU D 38 " --> pdb=" O LEU D 34 " (cutoff:3.500A) Processing helix chain 'D' and resid 84 through 87 Processing helix chain 'D' and resid 103 through 105 No H-bonds generated for 'chain 'D' and resid 103 through 105' Processing helix chain 'D' and resid 217 through 224 Processing helix chain 'D' and resid 224 through 238 removed outlier: 3.518A pdb=" N THR D 228 " --> pdb=" O LEU D 224 " (cutoff:3.500A) Processing helix chain 'D' and resid 239 through 241 No H-bonds generated for 'chain 'D' and resid 239 through 241' Processing helix chain 'D' and resid 248 through 268 removed outlier: 3.525A pdb=" N LEU D 255 " --> pdb=" O PHE D 251 " (cutoff:3.500A) Processing helix chain 'D' and resid 279 through 308 Processing helix chain 'D' and resid 351 through 405 removed outlier: 3.624A pdb=" N VAL D 356 " --> pdb=" O MET D 352 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N VAL D 357 " --> pdb=" O LEU D 353 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N ALA D 377 " --> pdb=" O LYS D 373 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ASP D 378 " --> pdb=" O HIS D 374 " (cutoff:3.500A) Processing helix chain 'E' and resid 26 through 38 removed outlier: 3.947A pdb=" N GLU E 38 " --> pdb=" O LEU E 34 " (cutoff:3.500A) Processing helix chain 'E' and resid 103 through 105 No H-bonds generated for 'chain 'E' and resid 103 through 105' Processing helix chain 'E' and resid 217 through 224 Processing helix chain 'E' and resid 224 through 238 removed outlier: 3.604A pdb=" N THR E 228 " --> pdb=" O LEU E 224 " (cutoff:3.500A) Processing helix chain 'E' and resid 239 through 241 No H-bonds generated for 'chain 'E' and resid 239 through 241' Processing helix chain 'E' and resid 248 through 268 Processing helix chain 'E' and resid 278 through 308 removed outlier: 4.470A pdb=" N ILE E 282 " --> pdb=" O PRO E 278 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ARG E 303 " --> pdb=" O MET E 299 " (cutoff:3.500A) Processing helix chain 'E' and resid 351 through 406 removed outlier: 3.547A pdb=" N VAL E 356 " --> pdb=" O MET E 352 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N VAL E 357 " --> pdb=" O LEU E 353 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N ALA E 377 " --> pdb=" O LYS E 373 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ASP E 378 " --> pdb=" O HIS E 374 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ILE E 390 " --> pdb=" O LEU E 386 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 52 through 54 Processing sheet with id=AA2, first strand: chain 'A' and resid 97 through 101 removed outlier: 8.225A pdb=" N ASP A 126 " --> pdb=" O GLU A 138 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N GLU A 138 " --> pdb=" O ASP A 126 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N THR A 134 " --> pdb=" O TYR A 130 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N GLU A 144 " --> pdb=" O SER A 117 " (cutoff:3.500A) removed outlier: 4.726A pdb=" N SER A 117 " --> pdb=" O GLU A 144 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 97 through 101 removed outlier: 8.225A pdb=" N ASP A 126 " --> pdb=" O GLU A 138 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N GLU A 138 " --> pdb=" O ASP A 126 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N THR A 134 " --> pdb=" O TYR A 130 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N ARG A 70 " --> pdb=" O VAL A 64 " (cutoff:3.500A) removed outlier: 4.702A pdb=" N VAL A 64 " --> pdb=" O ARG A 70 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N ASN A 72 " --> pdb=" O LEU A 62 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 110 through 111 Processing sheet with id=AA5, first strand: chain 'A' and resid 158 through 164 removed outlier: 6.827A pdb=" N PHE A 208 " --> pdb=" O LEU A 199 " (cutoff:3.500A) removed outlier: 4.768A pdb=" N LEU A 199 " --> pdb=" O PHE A 208 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N ALA A 210 " --> pdb=" O ALA A 197 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N ALA A 197 " --> pdb=" O ALA A 210 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N GLY A 212 " --> pdb=" O THR A 195 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N THR A 194 " --> pdb=" O GLY A 187 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N GLY A 187 " --> pdb=" O THR A 194 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 52 through 54 Processing sheet with id=AA7, first strand: chain 'B' and resid 97 through 101 removed outlier: 8.206A pdb=" N ASP B 126 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N GLU B 138 " --> pdb=" O ASP B 126 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N THR B 134 " --> pdb=" O TYR B 130 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N GLU B 144 " --> pdb=" O SER B 117 " (cutoff:3.500A) removed outlier: 4.746A pdb=" N SER B 117 " --> pdb=" O GLU B 144 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 97 through 101 removed outlier: 8.206A pdb=" N ASP B 126 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N GLU B 138 " --> pdb=" O ASP B 126 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N THR B 134 " --> pdb=" O TYR B 130 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N ARG B 70 " --> pdb=" O VAL B 64 " (cutoff:3.500A) removed outlier: 4.698A pdb=" N VAL B 64 " --> pdb=" O ARG B 70 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N ASN B 72 " --> pdb=" O LEU B 62 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 110 through 111 Processing sheet with id=AB1, first strand: chain 'B' and resid 158 through 164 removed outlier: 6.978A pdb=" N PHE B 208 " --> pdb=" O LEU B 199 " (cutoff:3.500A) removed outlier: 4.830A pdb=" N LEU B 199 " --> pdb=" O PHE B 208 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N ALA B 210 " --> pdb=" O ALA B 197 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N ALA B 197 " --> pdb=" O ALA B 210 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N GLY B 212 " --> pdb=" O THR B 195 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 52 through 54 Processing sheet with id=AB3, first strand: chain 'C' and resid 97 through 101 removed outlier: 8.173A pdb=" N ASP C 126 " --> pdb=" O GLU C 138 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N GLU C 138 " --> pdb=" O ASP C 126 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N THR C 134 " --> pdb=" O TYR C 130 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N GLU C 144 " --> pdb=" O SER C 117 " (cutoff:3.500A) removed outlier: 4.728A pdb=" N SER C 117 " --> pdb=" O GLU C 144 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 97 through 101 removed outlier: 8.173A pdb=" N ASP C 126 " --> pdb=" O GLU C 138 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N GLU C 138 " --> pdb=" O ASP C 126 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N THR C 134 " --> pdb=" O TYR C 130 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N ARG C 70 " --> pdb=" O VAL C 64 " (cutoff:3.500A) removed outlier: 4.708A pdb=" N VAL C 64 " --> pdb=" O ARG C 70 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N ASN C 72 " --> pdb=" O LEU C 62 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 110 through 111 Processing sheet with id=AB6, first strand: chain 'C' and resid 158 through 164 removed outlier: 6.934A pdb=" N PHE C 208 " --> pdb=" O LEU C 199 " (cutoff:3.500A) removed outlier: 4.814A pdb=" N LEU C 199 " --> pdb=" O PHE C 208 " (cutoff:3.500A) removed outlier: 6.242A pdb=" N ALA C 210 " --> pdb=" O ALA C 197 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N ALA C 197 " --> pdb=" O ALA C 210 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N GLY C 212 " --> pdb=" O THR C 195 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N THR C 194 " --> pdb=" O GLY C 187 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N GLY C 187 " --> pdb=" O THR C 194 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 52 through 54 Processing sheet with id=AB8, first strand: chain 'D' and resid 97 through 101 removed outlier: 8.082A pdb=" N ASP D 126 " --> pdb=" O GLU D 138 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N GLU D 138 " --> pdb=" O ASP D 126 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N THR D 134 " --> pdb=" O TYR D 130 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N GLU D 144 " --> pdb=" O SER D 117 " (cutoff:3.500A) removed outlier: 4.740A pdb=" N SER D 117 " --> pdb=" O GLU D 144 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 97 through 101 removed outlier: 8.082A pdb=" N ASP D 126 " --> pdb=" O GLU D 138 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N GLU D 138 " --> pdb=" O ASP D 126 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N THR D 134 " --> pdb=" O TYR D 130 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N ARG D 70 " --> pdb=" O VAL D 64 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N VAL D 64 " --> pdb=" O ARG D 70 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N ASN D 72 " --> pdb=" O LEU D 62 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 110 through 111 Processing sheet with id=AC2, first strand: chain 'D' and resid 158 through 164 removed outlier: 6.952A pdb=" N PHE D 208 " --> pdb=" O LEU D 199 " (cutoff:3.500A) removed outlier: 4.828A pdb=" N LEU D 199 " --> pdb=" O PHE D 208 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N ALA D 210 " --> pdb=" O ALA D 197 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N ALA D 197 " --> pdb=" O ALA D 210 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N GLY D 212 " --> pdb=" O THR D 195 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 52 through 54 Processing sheet with id=AC4, first strand: chain 'E' and resid 97 through 101 removed outlier: 8.208A pdb=" N ASP E 126 " --> pdb=" O GLU E 138 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N GLU E 138 " --> pdb=" O ASP E 126 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N THR E 134 " --> pdb=" O TYR E 130 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N GLU E 144 " --> pdb=" O SER E 117 " (cutoff:3.500A) removed outlier: 4.740A pdb=" N SER E 117 " --> pdb=" O GLU E 144 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 97 through 101 removed outlier: 8.208A pdb=" N ASP E 126 " --> pdb=" O GLU E 138 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N GLU E 138 " --> pdb=" O ASP E 126 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N THR E 134 " --> pdb=" O TYR E 130 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N ARG E 70 " --> pdb=" O VAL E 64 " (cutoff:3.500A) removed outlier: 4.670A pdb=" N VAL E 64 " --> pdb=" O ARG E 70 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N ASN E 72 " --> pdb=" O LEU E 62 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 110 through 111 Processing sheet with id=AC7, first strand: chain 'E' and resid 158 through 164 removed outlier: 6.939A pdb=" N PHE E 208 " --> pdb=" O LEU E 199 " (cutoff:3.500A) removed outlier: 4.835A pdb=" N LEU E 199 " --> pdb=" O PHE E 208 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N ALA E 210 " --> pdb=" O ALA E 197 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N ALA E 197 " --> pdb=" O ALA E 210 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N GLY E 212 " --> pdb=" O THR E 195 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N THR E 194 " --> pdb=" O GLY E 187 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N GLY E 187 " --> pdb=" O THR E 194 " (cutoff:3.500A) 812 hydrogen bonds defined for protein. 2412 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: 4.46 Time building geometry restraints manager: 3.79 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4278 1.34 - 1.46: 2959 1.46 - 1.58: 6378 1.58 - 1.70: 0 1.70 - 1.82: 175 Bond restraints: 13790 Sorted by residual: bond pdb=" C1 NAG D 501 " pdb=" O5 NAG D 501 " ideal model delta sigma weight residual 1.406 1.433 -0.027 2.00e-02 2.50e+03 1.83e+00 bond pdb=" C1 NAG C 501 " pdb=" O5 NAG C 501 " ideal model delta sigma weight residual 1.406 1.433 -0.027 2.00e-02 2.50e+03 1.79e+00 bond pdb=" C1 NAG E 501 " pdb=" O5 NAG E 501 " ideal model delta sigma weight residual 1.406 1.432 -0.026 2.00e-02 2.50e+03 1.66e+00 bond pdb=" C1 NAG A 501 " pdb=" O5 NAG A 501 " ideal model delta sigma weight residual 1.406 1.431 -0.025 2.00e-02 2.50e+03 1.60e+00 bond pdb=" C1 NAG B 501 " pdb=" O5 NAG B 501 " ideal model delta sigma weight residual 1.406 1.431 -0.025 2.00e-02 2.50e+03 1.60e+00 ... (remaining 13785 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.19: 18565 2.19 - 4.39: 187 4.39 - 6.58: 30 6.58 - 8.78: 7 8.78 - 10.97: 1 Bond angle restraints: 18790 Sorted by residual: angle pdb=" CB MET A 39 " pdb=" CG MET A 39 " pdb=" SD MET A 39 " ideal model delta sigma weight residual 112.70 123.67 -10.97 3.00e+00 1.11e-01 1.34e+01 angle pdb=" CB MET D 39 " pdb=" CG MET D 39 " pdb=" SD MET D 39 " ideal model delta sigma weight residual 112.70 121.46 -8.76 3.00e+00 1.11e-01 8.52e+00 angle pdb=" C ASN C 153 " pdb=" N TYR C 154 " pdb=" CA TYR C 154 " ideal model delta sigma weight residual 120.69 112.57 8.12 2.95e+00 1.15e-01 7.58e+00 angle pdb=" C ASN B 153 " pdb=" N TYR B 154 " pdb=" CA TYR B 154 " ideal model delta sigma weight residual 120.69 112.79 7.90 2.95e+00 1.15e-01 7.18e+00 angle pdb=" CB MET C 39 " pdb=" CG MET C 39 " pdb=" SD MET C 39 " ideal model delta sigma weight residual 112.70 120.67 -7.97 3.00e+00 1.11e-01 7.05e+00 ... (remaining 18785 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.65: 7152 17.65 - 35.30: 911 35.30 - 52.95: 220 52.95 - 70.60: 34 70.60 - 88.25: 23 Dihedral angle restraints: 8340 sinusoidal: 3235 harmonic: 5105 Sorted by residual: dihedral pdb=" CB CYS B 147 " pdb=" SG CYS B 147 " pdb=" SG CYS B 161 " pdb=" CB CYS B 161 " ideal model delta sinusoidal sigma weight residual 93.00 161.78 -68.78 1 1.00e+01 1.00e-02 6.13e+01 dihedral pdb=" CB CYS A 147 " pdb=" SG CYS A 147 " pdb=" SG CYS A 161 " pdb=" CB CYS A 161 " ideal model delta sinusoidal sigma weight residual 93.00 160.70 -67.70 1 1.00e+01 1.00e-02 5.96e+01 dihedral pdb=" CB CYS D 147 " pdb=" SG CYS D 147 " pdb=" SG CYS D 161 " pdb=" CB CYS D 161 " ideal model delta sinusoidal sigma weight residual 93.00 159.69 -66.69 1 1.00e+01 1.00e-02 5.80e+01 ... (remaining 8337 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 1581 0.037 - 0.073: 503 0.073 - 0.110: 161 0.110 - 0.147: 41 0.147 - 0.183: 4 Chirality restraints: 2290 Sorted by residual: chirality pdb=" CB THR C 358 " pdb=" CA THR C 358 " pdb=" OG1 THR C 358 " pdb=" CG2 THR C 358 " both_signs ideal model delta sigma weight residual False 2.55 2.37 0.18 2.00e-01 2.50e+01 8.40e-01 chirality pdb=" CG LEU B 391 " pdb=" CB LEU B 391 " pdb=" CD1 LEU B 391 " pdb=" CD2 LEU B 391 " both_signs ideal model delta sigma weight residual False -2.59 -2.41 -0.18 2.00e-01 2.50e+01 8.04e-01 chirality pdb=" CG LEU C 391 " pdb=" CB LEU C 391 " pdb=" CD1 LEU C 391 " pdb=" CD2 LEU C 391 " both_signs ideal model delta sigma weight residual False -2.59 -2.41 -0.17 2.00e-01 2.50e+01 7.63e-01 ... (remaining 2287 not shown) Planarity restraints: 2350 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL E 109 " -0.009 2.00e-02 2.50e+03 1.81e-02 3.26e+00 pdb=" C VAL E 109 " 0.031 2.00e-02 2.50e+03 pdb=" O VAL E 109 " -0.012 2.00e-02 2.50e+03 pdb=" N LEU E 110 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN C 125 " 0.008 2.00e-02 2.50e+03 1.57e-02 2.48e+00 pdb=" C ASN C 125 " -0.027 2.00e-02 2.50e+03 pdb=" O ASN C 125 " 0.010 2.00e-02 2.50e+03 pdb=" N ASP C 126 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL E 237 " -0.007 2.00e-02 2.50e+03 1.37e-02 1.88e+00 pdb=" C VAL E 237 " 0.024 2.00e-02 2.50e+03 pdb=" O VAL E 237 " -0.009 2.00e-02 2.50e+03 pdb=" N SER E 238 " -0.008 2.00e-02 2.50e+03 ... (remaining 2347 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 1981 2.76 - 3.29: 12645 3.29 - 3.83: 22761 3.83 - 4.36: 24732 4.36 - 4.90: 44571 Nonbonded interactions: 106690 Sorted by model distance: nonbonded pdb=" O ASN E 125 " pdb=" ND2 ASN E 125 " model vdw 2.225 3.120 nonbonded pdb=" O ASN C 125 " pdb=" ND2 ASN C 125 " model vdw 2.226 3.120 nonbonded pdb=" O THR A 25 " pdb=" OH TYR A 95 " model vdw 2.274 3.040 nonbonded pdb=" O THR D 25 " pdb=" OH TYR D 95 " model vdw 2.281 3.040 nonbonded pdb=" OD1 ASP B 83 " pdb=" NH1 ARG C 28 " model vdw 2.287 3.120 ... (remaining 106685 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' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' } 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: 1.430 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: 0.010 Extract box with map and model: 0.570 Check model and map are aligned: 0.110 Set scattering table: 0.130 Process input model: 32.990 Find NCS groups from input model: 0.510 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7736 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 0.027 13790 Z= 0.192 Angle : 0.609 10.971 18790 Z= 0.311 Chirality : 0.042 0.183 2290 Planarity : 0.004 0.037 2345 Dihedral : 16.786 88.254 4990 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 0.61 % Allowed : 24.73 % Favored : 74.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.19 (0.21), residues: 1720 helix: 2.69 (0.19), residues: 695 sheet: 0.06 (0.25), residues: 465 loop : -1.01 (0.24), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP D 81 HIS 0.004 0.001 HIS D 122 PHE 0.021 0.001 PHE E 387 TYR 0.006 0.001 TYR C 217 ARG 0.008 0.001 ARG E 362 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3440 Ramachandran restraints generated. 1720 Oldfield, 0 Emsley, 1720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3440 Ramachandran restraints generated. 1720 Oldfield, 0 Emsley, 1720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 282 time to evaluate : 1.518 Fit side-chains REVERT: E 223 THR cc_start: 0.7487 (t) cc_final: 0.7281 (m) outliers start: 9 outliers final: 4 residues processed: 287 average time/residue: 0.2822 time to fit residues: 116.5168 Evaluate side-chains 266 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 262 time to evaluate : 1.857 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 ASN Chi-restraints excluded: chain A residue 172 GLU Chi-restraints excluded: chain C residue 398 VAL Chi-restraints excluded: chain D residue 235 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 143 optimal weight: 3.9990 chunk 128 optimal weight: 0.9980 chunk 71 optimal weight: 2.9990 chunk 44 optimal weight: 9.9990 chunk 86 optimal weight: 6.9990 chunk 68 optimal weight: 8.9990 chunk 133 optimal weight: 0.9980 chunk 51 optimal weight: 6.9990 chunk 81 optimal weight: 3.9990 chunk 99 optimal weight: 6.9990 chunk 154 optimal weight: 1.9990 overall best weight: 2.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 125 ASN C 125 ASN D 193 GLN D 216 ASN ** D 369 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7774 moved from start: 0.0994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 13790 Z= 0.252 Angle : 0.592 7.407 18790 Z= 0.298 Chirality : 0.043 0.194 2290 Planarity : 0.004 0.030 2345 Dihedral : 4.438 37.398 1958 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 3.92 % Allowed : 22.97 % Favored : 73.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.17 (0.21), residues: 1720 helix: 2.78 (0.19), residues: 685 sheet: -0.03 (0.25), residues: 480 loop : -1.07 (0.25), residues: 555 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP C 81 HIS 0.003 0.001 HIS D 122 PHE 0.022 0.002 PHE E 359 TYR 0.010 0.001 TYR E 130 ARG 0.004 0.001 ARG C 354 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3440 Ramachandran restraints generated. 1720 Oldfield, 0 Emsley, 1720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3440 Ramachandran restraints generated. 1720 Oldfield, 0 Emsley, 1720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 321 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 263 time to evaluate : 1.520 Fit side-chains REVERT: A 386 LEU cc_start: 0.7666 (mm) cc_final: 0.7460 (mp) REVERT: A 391 LEU cc_start: 0.7960 (OUTLIER) cc_final: 0.7625 (mp) REVERT: B 181 GLN cc_start: 0.7325 (OUTLIER) cc_final: 0.7124 (tt0) REVERT: C 166 GLU cc_start: 0.7163 (tp30) cc_final: 0.6878 (tt0) REVERT: C 295 MET cc_start: 0.8198 (ttp) cc_final: 0.7838 (ttp) REVERT: C 374 HIS cc_start: 0.7661 (m170) cc_final: 0.7435 (m170) REVERT: D 399 MET cc_start: 0.8133 (tpp) cc_final: 0.7726 (tpt) REVERT: E 166 GLU cc_start: 0.7027 (tp30) cc_final: 0.6708 (tt0) REVERT: E 181 GLN cc_start: 0.7149 (OUTLIER) cc_final: 0.6861 (tt0) REVERT: E 374 HIS cc_start: 0.7657 (m170) cc_final: 0.7405 (m170) REVERT: E 400 LEU cc_start: 0.7787 (tt) cc_final: 0.7584 (tt) outliers start: 58 outliers final: 37 residues processed: 301 average time/residue: 0.2683 time to fit residues: 117.1434 Evaluate side-chains 295 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 255 time to evaluate : 1.695 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 362 ARG Chi-restraints excluded: chain A residue 391 LEU Chi-restraints excluded: chain A residue 398 VAL Chi-restraints excluded: chain B residue 90 THR Chi-restraints excluded: chain B residue 111 GLN Chi-restraints excluded: chain B residue 114 ASN Chi-restraints excluded: chain B residue 118 THR Chi-restraints excluded: chain B residue 181 GLN Chi-restraints excluded: chain B residue 215 ILE Chi-restraints excluded: chain B residue 299 MET Chi-restraints excluded: chain B residue 391 LEU Chi-restraints excluded: chain B residue 398 VAL Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain C residue 174 VAL Chi-restraints excluded: chain C residue 235 ASP Chi-restraints excluded: chain C residue 299 MET Chi-restraints excluded: chain C residue 365 ASP Chi-restraints excluded: chain C residue 398 VAL Chi-restraints excluded: chain C residue 400 LEU Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain D residue 114 ASN Chi-restraints excluded: chain D residue 235 ASP Chi-restraints excluded: chain D residue 262 PHE Chi-restraints excluded: chain D residue 299 MET Chi-restraints excluded: chain D residue 302 THR Chi-restraints excluded: chain D residue 389 VAL Chi-restraints excluded: chain D residue 391 LEU Chi-restraints excluded: chain D residue 398 VAL Chi-restraints excluded: chain D residue 400 LEU Chi-restraints excluded: chain E residue 57 ILE Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 114 ASN Chi-restraints excluded: chain E residue 170 SER Chi-restraints excluded: chain E residue 174 VAL Chi-restraints excluded: chain E residue 181 GLN Chi-restraints excluded: chain E residue 235 ASP Chi-restraints excluded: chain E residue 263 LEU Chi-restraints excluded: chain E residue 391 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 85 optimal weight: 1.9990 chunk 47 optimal weight: 2.9990 chunk 128 optimal weight: 0.7980 chunk 105 optimal weight: 2.9990 chunk 42 optimal weight: 3.9990 chunk 154 optimal weight: 3.9990 chunk 167 optimal weight: 0.9990 chunk 137 optimal weight: 8.9990 chunk 153 optimal weight: 6.9990 chunk 52 optimal weight: 4.9990 chunk 124 optimal weight: 10.0000 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 125 ASN ** B 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 369 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7775 moved from start: 0.1367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 13790 Z= 0.226 Angle : 0.563 7.050 18790 Z= 0.285 Chirality : 0.042 0.169 2290 Planarity : 0.004 0.033 2345 Dihedral : 4.277 39.095 1953 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 5.27 % Allowed : 23.04 % Favored : 71.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.96 (0.21), residues: 1720 helix: 2.74 (0.19), residues: 685 sheet: -0.30 (0.25), residues: 490 loop : -1.22 (0.25), residues: 545 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 81 HIS 0.002 0.001 HIS B 137 PHE 0.024 0.002 PHE D 387 TYR 0.008 0.001 TYR E 130 ARG 0.005 0.001 ARG C 354 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3440 Ramachandran restraints generated. 1720 Oldfield, 0 Emsley, 1720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3440 Ramachandran restraints generated. 1720 Oldfield, 0 Emsley, 1720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 342 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 264 time to evaluate : 1.587 Fit side-chains REVERT: A 386 LEU cc_start: 0.7631 (mm) cc_final: 0.7420 (mp) REVERT: A 391 LEU cc_start: 0.7908 (OUTLIER) cc_final: 0.7605 (mp) REVERT: B 125 ASN cc_start: 0.7985 (OUTLIER) cc_final: 0.7780 (t0) REVERT: B 270 LEU cc_start: 0.8090 (OUTLIER) cc_final: 0.7518 (mp) REVERT: C 166 GLU cc_start: 0.7131 (tp30) cc_final: 0.6853 (tt0) REVERT: C 295 MET cc_start: 0.8174 (ttp) cc_final: 0.7838 (ttp) REVERT: C 368 ASN cc_start: 0.6075 (OUTLIER) cc_final: 0.5868 (t0) REVERT: C 374 HIS cc_start: 0.7688 (m170) cc_final: 0.7464 (m170) REVERT: D 122 HIS cc_start: 0.7496 (m-70) cc_final: 0.7276 (m-70) REVERT: D 262 PHE cc_start: 0.8181 (OUTLIER) cc_final: 0.7626 (t80) REVERT: D 310 LEU cc_start: 0.7456 (mp) cc_final: 0.6692 (pp) REVERT: D 399 MET cc_start: 0.8114 (tpp) cc_final: 0.7694 (tpt) REVERT: E 39 MET cc_start: 0.7871 (mmp) cc_final: 0.7448 (mmm) REVERT: E 125 ASN cc_start: 0.7983 (t160) cc_final: 0.7774 (t0) REVERT: E 166 GLU cc_start: 0.7147 (tp30) cc_final: 0.6756 (tt0) REVERT: E 181 GLN cc_start: 0.7187 (OUTLIER) cc_final: 0.6782 (tt0) REVERT: E 230 LEU cc_start: 0.8277 (OUTLIER) cc_final: 0.7817 (mm) REVERT: E 374 HIS cc_start: 0.7679 (m170) cc_final: 0.7433 (m170) outliers start: 78 outliers final: 51 residues processed: 319 average time/residue: 0.2581 time to fit residues: 120.2034 Evaluate side-chains 314 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 256 time to evaluate : 1.560 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 THR Chi-restraints excluded: chain A residue 66 THR Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 114 ASN Chi-restraints excluded: chain A residue 141 ILE Chi-restraints excluded: chain A residue 235 ASP Chi-restraints excluded: chain A residue 362 ARG Chi-restraints excluded: chain A residue 391 LEU Chi-restraints excluded: chain A residue 398 VAL Chi-restraints excluded: chain B residue 49 THR Chi-restraints excluded: chain B residue 72 ASN Chi-restraints excluded: chain B residue 90 THR Chi-restraints excluded: chain B residue 111 GLN Chi-restraints excluded: chain B residue 114 ASN Chi-restraints excluded: chain B residue 118 THR Chi-restraints excluded: chain B residue 125 ASN Chi-restraints excluded: chain B residue 170 SER Chi-restraints excluded: chain B residue 175 THR Chi-restraints excluded: chain B residue 215 ILE Chi-restraints excluded: chain B residue 235 ASP Chi-restraints excluded: chain B residue 262 PHE Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 298 SER Chi-restraints excluded: chain B residue 299 MET Chi-restraints excluded: chain B residue 391 LEU Chi-restraints excluded: chain B residue 398 VAL Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain C residue 114 ASN Chi-restraints excluded: chain C residue 174 VAL Chi-restraints excluded: chain C residue 175 THR Chi-restraints excluded: chain C residue 235 ASP Chi-restraints excluded: chain C residue 299 MET Chi-restraints excluded: chain C residue 365 ASP Chi-restraints excluded: chain C residue 368 ASN Chi-restraints excluded: chain C residue 391 LEU Chi-restraints excluded: chain C residue 398 VAL Chi-restraints excluded: chain C residue 400 LEU Chi-restraints excluded: chain D residue 72 ASN Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain D residue 114 ASN Chi-restraints excluded: chain D residue 235 ASP Chi-restraints excluded: chain D residue 262 PHE Chi-restraints excluded: chain D residue 299 MET Chi-restraints excluded: chain D residue 302 THR Chi-restraints excluded: chain D residue 389 VAL Chi-restraints excluded: chain D residue 398 VAL Chi-restraints excluded: chain D residue 400 LEU Chi-restraints excluded: chain E residue 57 ILE Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 114 ASN Chi-restraints excluded: chain E residue 167 THR Chi-restraints excluded: chain E residue 170 SER Chi-restraints excluded: chain E residue 174 VAL Chi-restraints excluded: chain E residue 181 GLN Chi-restraints excluded: chain E residue 230 LEU Chi-restraints excluded: chain E residue 235 ASP Chi-restraints excluded: chain E residue 263 LEU Chi-restraints excluded: chain E residue 298 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 152 optimal weight: 6.9990 chunk 116 optimal weight: 10.0000 chunk 80 optimal weight: 7.9990 chunk 17 optimal weight: 5.9990 chunk 73 optimal weight: 4.9990 chunk 103 optimal weight: 0.9980 chunk 155 optimal weight: 0.7980 chunk 164 optimal weight: 5.9990 chunk 81 optimal weight: 0.6980 chunk 147 optimal weight: 0.9990 chunk 44 optimal weight: 0.0170 overall best weight: 0.7020 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 44 GLN A 125 ASN ** B 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 207 ASN ** E 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7735 moved from start: 0.1475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 13790 Z= 0.134 Angle : 0.485 8.092 18790 Z= 0.247 Chirality : 0.040 0.162 2290 Planarity : 0.003 0.026 2345 Dihedral : 3.859 26.818 1953 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 3.51 % Allowed : 25.27 % Favored : 71.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.32 (0.21), residues: 1720 helix: 3.07 (0.19), residues: 695 sheet: -0.17 (0.25), residues: 490 loop : -1.10 (0.26), residues: 535 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 81 HIS 0.002 0.000 HIS E 137 PHE 0.016 0.001 PHE B 359 TYR 0.006 0.001 TYR A 95 ARG 0.006 0.000 ARG E 362 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3440 Ramachandran restraints generated. 1720 Oldfield, 0 Emsley, 1720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3440 Ramachandran restraints generated. 1720 Oldfield, 0 Emsley, 1720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 343 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 291 time to evaluate : 1.517 Fit side-chains REVERT: A 295 MET cc_start: 0.8354 (ttp) cc_final: 0.8132 (ttm) REVERT: B 125 ASN cc_start: 0.7976 (OUTLIER) cc_final: 0.7735 (t0) REVERT: B 181 GLN cc_start: 0.7232 (OUTLIER) cc_final: 0.6544 (tt0) REVERT: C 125 ASN cc_start: 0.7992 (OUTLIER) cc_final: 0.7764 (t0) REVERT: C 166 GLU cc_start: 0.7149 (tp30) cc_final: 0.6824 (tt0) REVERT: C 295 MET cc_start: 0.8129 (ttp) cc_final: 0.7715 (ttp) REVERT: C 374 HIS cc_start: 0.7692 (m170) cc_final: 0.7482 (m170) REVERT: D 233 LEU cc_start: 0.8376 (OUTLIER) cc_final: 0.8108 (tt) REVERT: D 262 PHE cc_start: 0.8156 (OUTLIER) cc_final: 0.7683 (t80) REVERT: D 310 LEU cc_start: 0.7454 (mp) cc_final: 0.6488 (pp) REVERT: D 399 MET cc_start: 0.8152 (tpp) cc_final: 0.7910 (tpt) REVERT: E 39 MET cc_start: 0.7890 (mmp) cc_final: 0.7413 (mmm) REVERT: E 125 ASN cc_start: 0.8021 (OUTLIER) cc_final: 0.7811 (t0) REVERT: E 166 GLU cc_start: 0.7180 (tp30) cc_final: 0.6759 (tt0) REVERT: E 230 LEU cc_start: 0.8288 (OUTLIER) cc_final: 0.7870 (mm) REVERT: E 262 PHE cc_start: 0.7963 (OUTLIER) cc_final: 0.7549 (t80) REVERT: E 374 HIS cc_start: 0.7722 (m170) cc_final: 0.7488 (m170) outliers start: 52 outliers final: 27 residues processed: 324 average time/residue: 0.2643 time to fit residues: 124.9232 Evaluate side-chains 314 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 279 time to evaluate : 1.683 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 ASN Chi-restraints excluded: chain A residue 114 ASN Chi-restraints excluded: chain A residue 159 ASP Chi-restraints excluded: chain A residue 235 ASP Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain B residue 114 ASN Chi-restraints excluded: chain B residue 118 THR Chi-restraints excluded: chain B residue 125 ASN Chi-restraints excluded: chain B residue 181 GLN Chi-restraints excluded: chain B residue 298 SER Chi-restraints excluded: chain B residue 391 LEU Chi-restraints excluded: chain B residue 393 LEU Chi-restraints excluded: chain B residue 398 VAL Chi-restraints excluded: chain C residue 57 ILE Chi-restraints excluded: chain C residue 114 ASN Chi-restraints excluded: chain C residue 125 ASN Chi-restraints excluded: chain C residue 235 ASP Chi-restraints excluded: chain C residue 391 LEU Chi-restraints excluded: chain C residue 400 LEU Chi-restraints excluded: chain D residue 114 ASN Chi-restraints excluded: chain D residue 141 ILE Chi-restraints excluded: chain D residue 233 LEU Chi-restraints excluded: chain D residue 262 PHE Chi-restraints excluded: chain D residue 299 MET Chi-restraints excluded: chain D residue 389 VAL Chi-restraints excluded: chain D residue 393 LEU Chi-restraints excluded: chain D residue 398 VAL Chi-restraints excluded: chain D residue 400 LEU Chi-restraints excluded: chain E residue 125 ASN Chi-restraints excluded: chain E residue 167 THR Chi-restraints excluded: chain E residue 170 SER Chi-restraints excluded: chain E residue 174 VAL Chi-restraints excluded: chain E residue 230 LEU Chi-restraints excluded: chain E residue 262 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 136 optimal weight: 9.9990 chunk 93 optimal weight: 8.9990 chunk 2 optimal weight: 0.7980 chunk 122 optimal weight: 3.9990 chunk 67 optimal weight: 0.9990 chunk 140 optimal weight: 8.9990 chunk 113 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 83 optimal weight: 5.9990 chunk 147 optimal weight: 6.9990 chunk 41 optimal weight: 3.9990 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 125 ASN A 137 HIS ** B 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 137 HIS ** D 369 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 193 GLN E 216 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7802 moved from start: 0.1905 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 13790 Z= 0.328 Angle : 0.645 8.151 18790 Z= 0.325 Chirality : 0.044 0.200 2290 Planarity : 0.004 0.032 2345 Dihedral : 4.383 19.970 1950 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 6.49 % Allowed : 23.92 % Favored : 69.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.77 (0.21), residues: 1720 helix: 2.50 (0.19), residues: 685 sheet: -0.35 (0.25), residues: 480 loop : -1.25 (0.25), residues: 555 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP C 81 HIS 0.004 0.001 HIS E 122 PHE 0.019 0.002 PHE E 236 TYR 0.021 0.002 TYR D 59 ARG 0.009 0.001 ARG C 354 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3440 Ramachandran restraints generated. 1720 Oldfield, 0 Emsley, 1720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3440 Ramachandran restraints generated. 1720 Oldfield, 0 Emsley, 1720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 356 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 260 time to evaluate : 1.724 Fit side-chains REVERT: A 386 LEU cc_start: 0.7648 (mm) cc_final: 0.7403 (mp) REVERT: A 391 LEU cc_start: 0.7821 (OUTLIER) cc_final: 0.7510 (mp) REVERT: B 181 GLN cc_start: 0.7408 (OUTLIER) cc_final: 0.6797 (tt0) REVERT: B 270 LEU cc_start: 0.8243 (OUTLIER) cc_final: 0.7725 (mp) REVERT: B 369 GLN cc_start: 0.7343 (mm110) cc_final: 0.7106 (tp40) REVERT: C 125 ASN cc_start: 0.7939 (t160) cc_final: 0.7692 (t0) REVERT: C 166 GLU cc_start: 0.7241 (tp30) cc_final: 0.6921 (tt0) REVERT: C 230 LEU cc_start: 0.8154 (OUTLIER) cc_final: 0.7946 (mm) REVERT: C 262 PHE cc_start: 0.8248 (OUTLIER) cc_final: 0.7808 (t80) REVERT: C 310 LEU cc_start: 0.7576 (mt) cc_final: 0.7301 (mt) REVERT: C 368 ASN cc_start: 0.6260 (OUTLIER) cc_final: 0.6052 (t0) REVERT: D 262 PHE cc_start: 0.8206 (OUTLIER) cc_final: 0.7622 (t80) REVERT: D 310 LEU cc_start: 0.7633 (mp) cc_final: 0.7012 (pp) REVERT: D 374 HIS cc_start: 0.7803 (m170) cc_final: 0.7475 (m170) REVERT: D 399 MET cc_start: 0.8085 (tpp) cc_final: 0.7664 (tpt) REVERT: E 166 GLU cc_start: 0.7175 (tp30) cc_final: 0.6747 (tt0) REVERT: E 230 LEU cc_start: 0.8243 (OUTLIER) cc_final: 0.7790 (mm) REVERT: E 262 PHE cc_start: 0.8076 (OUTLIER) cc_final: 0.7653 (t80) REVERT: E 371 GLU cc_start: 0.6706 (tm-30) cc_final: 0.5984 (mp0) REVERT: E 374 HIS cc_start: 0.7590 (m170) cc_final: 0.7310 (m170) outliers start: 96 outliers final: 72 residues processed: 332 average time/residue: 0.2613 time to fit residues: 128.3915 Evaluate side-chains 338 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 257 time to evaluate : 1.775 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 THR Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 114 ASN Chi-restraints excluded: chain A residue 141 ILE Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 159 ASP Chi-restraints excluded: chain A residue 160 GLU Chi-restraints excluded: chain A residue 235 ASP Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 362 ARG Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 391 LEU Chi-restraints excluded: chain A residue 393 LEU Chi-restraints excluded: chain A residue 398 VAL Chi-restraints excluded: chain B residue 49 THR Chi-restraints excluded: chain B residue 72 ASN Chi-restraints excluded: chain B residue 90 THR Chi-restraints excluded: chain B residue 114 ASN Chi-restraints excluded: chain B residue 118 THR Chi-restraints excluded: chain B residue 170 SER Chi-restraints excluded: chain B residue 175 THR Chi-restraints excluded: chain B residue 176 THR Chi-restraints excluded: chain B residue 181 GLN Chi-restraints excluded: chain B residue 215 ILE Chi-restraints excluded: chain B residue 232 VAL Chi-restraints excluded: chain B residue 235 ASP Chi-restraints excluded: chain B residue 262 PHE Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 298 SER Chi-restraints excluded: chain B residue 299 MET Chi-restraints excluded: chain B residue 391 LEU Chi-restraints excluded: chain B residue 398 VAL Chi-restraints excluded: chain C residue 49 THR Chi-restraints excluded: chain C residue 57 ILE Chi-restraints excluded: chain C residue 72 ASN Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain C residue 114 ASN Chi-restraints excluded: chain C residue 123 ASP Chi-restraints excluded: chain C residue 174 VAL Chi-restraints excluded: chain C residue 175 THR Chi-restraints excluded: chain C residue 230 LEU Chi-restraints excluded: chain C residue 232 VAL Chi-restraints excluded: chain C residue 235 ASP Chi-restraints excluded: chain C residue 262 PHE Chi-restraints excluded: chain C residue 299 MET Chi-restraints excluded: chain C residue 365 ASP Chi-restraints excluded: chain C residue 368 ASN Chi-restraints excluded: chain C residue 389 VAL Chi-restraints excluded: chain C residue 391 LEU Chi-restraints excluded: chain C residue 398 VAL Chi-restraints excluded: chain C residue 400 LEU Chi-restraints excluded: chain C residue 403 MET Chi-restraints excluded: chain D residue 49 THR Chi-restraints excluded: chain D residue 72 ASN Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain D residue 114 ASN Chi-restraints excluded: chain D residue 141 ILE Chi-restraints excluded: chain D residue 235 ASP Chi-restraints excluded: chain D residue 262 PHE Chi-restraints excluded: chain D residue 299 MET Chi-restraints excluded: chain D residue 302 THR Chi-restraints excluded: chain D residue 389 VAL Chi-restraints excluded: chain D residue 391 LEU Chi-restraints excluded: chain D residue 398 VAL Chi-restraints excluded: chain D residue 400 LEU Chi-restraints excluded: chain E residue 49 THR Chi-restraints excluded: chain E residue 57 ILE Chi-restraints excluded: chain E residue 114 ASN Chi-restraints excluded: chain E residue 167 THR Chi-restraints excluded: chain E residue 170 SER Chi-restraints excluded: chain E residue 174 VAL Chi-restraints excluded: chain E residue 230 LEU Chi-restraints excluded: chain E residue 235 ASP Chi-restraints excluded: chain E residue 262 PHE Chi-restraints excluded: chain E residue 298 SER Chi-restraints excluded: chain E residue 299 MET Chi-restraints excluded: chain E residue 364 ASP Chi-restraints excluded: chain E residue 380 LEU Chi-restraints excluded: chain E residue 391 LEU Chi-restraints excluded: chain E residue 398 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 55 optimal weight: 2.9990 chunk 147 optimal weight: 8.9990 chunk 32 optimal weight: 6.9990 chunk 96 optimal weight: 5.9990 chunk 40 optimal weight: 0.5980 chunk 164 optimal weight: 6.9990 chunk 136 optimal weight: 10.0000 chunk 76 optimal weight: 0.9980 chunk 13 optimal weight: 7.9990 chunk 54 optimal weight: 1.9990 chunk 86 optimal weight: 8.9990 overall best weight: 2.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 125 ASN ** B 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 125 ASN ** D 369 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 125 ASN ** E 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 368 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7793 moved from start: 0.2011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 13790 Z= 0.273 Angle : 0.601 10.328 18790 Z= 0.304 Chirality : 0.043 0.174 2290 Planarity : 0.004 0.035 2345 Dihedral : 4.312 21.372 1950 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 7.50 % Allowed : 24.05 % Favored : 68.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.69 (0.21), residues: 1720 helix: 2.48 (0.19), residues: 685 sheet: -0.44 (0.25), residues: 480 loop : -1.29 (0.25), residues: 555 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 81 HIS 0.004 0.001 HIS E 122 PHE 0.018 0.002 PHE E 236 TYR 0.016 0.002 TYR D 59 ARG 0.006 0.001 ARG C 354 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3440 Ramachandran restraints generated. 1720 Oldfield, 0 Emsley, 1720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3440 Ramachandran restraints generated. 1720 Oldfield, 0 Emsley, 1720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 374 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 263 time to evaluate : 1.607 Fit side-chains REVERT: A 364 ASP cc_start: 0.6808 (OUTLIER) cc_final: 0.6474 (m-30) REVERT: A 386 LEU cc_start: 0.7560 (mm) cc_final: 0.7304 (mp) REVERT: A 391 LEU cc_start: 0.7827 (OUTLIER) cc_final: 0.7523 (mp) REVERT: B 181 GLN cc_start: 0.7396 (OUTLIER) cc_final: 0.6819 (tt0) REVERT: B 224 LEU cc_start: 0.7759 (OUTLIER) cc_final: 0.7471 (mp) REVERT: B 270 LEU cc_start: 0.8181 (OUTLIER) cc_final: 0.7639 (mp) REVERT: C 125 ASN cc_start: 0.7927 (OUTLIER) cc_final: 0.7553 (t0) REVERT: C 166 GLU cc_start: 0.7154 (tp30) cc_final: 0.6858 (tt0) REVERT: C 262 PHE cc_start: 0.8200 (OUTLIER) cc_final: 0.7763 (t80) REVERT: C 310 LEU cc_start: 0.7589 (mt) cc_final: 0.7292 (mt) REVERT: C 368 ASN cc_start: 0.6302 (OUTLIER) cc_final: 0.6092 (t0) REVERT: D 233 LEU cc_start: 0.8320 (OUTLIER) cc_final: 0.8060 (tt) REVERT: D 262 PHE cc_start: 0.8185 (OUTLIER) cc_final: 0.7621 (t80) REVERT: D 310 LEU cc_start: 0.7594 (mp) cc_final: 0.7275 (mt) REVERT: D 371 GLU cc_start: 0.6826 (tm-30) cc_final: 0.6121 (mp0) REVERT: D 374 HIS cc_start: 0.7792 (m170) cc_final: 0.7490 (m170) REVERT: D 399 MET cc_start: 0.8074 (tpp) cc_final: 0.7622 (tpt) REVERT: E 166 GLU cc_start: 0.7241 (tp30) cc_final: 0.6793 (tt0) REVERT: E 230 LEU cc_start: 0.8286 (OUTLIER) cc_final: 0.7835 (mm) REVERT: E 262 PHE cc_start: 0.8056 (OUTLIER) cc_final: 0.7611 (t80) REVERT: E 368 ASN cc_start: 0.7036 (t0) cc_final: 0.6831 (t0) REVERT: E 371 GLU cc_start: 0.6793 (tm-30) cc_final: 0.6094 (mp0) REVERT: E 374 HIS cc_start: 0.7632 (m170) cc_final: 0.7395 (m170) outliers start: 111 outliers final: 78 residues processed: 345 average time/residue: 0.2371 time to fit residues: 122.6553 Evaluate side-chains 352 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 262 time to evaluate : 1.561 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 THR Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 114 ASN Chi-restraints excluded: chain A residue 141 ILE Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 159 ASP Chi-restraints excluded: chain A residue 160 GLU Chi-restraints excluded: chain A residue 175 THR Chi-restraints excluded: chain A residue 235 ASP Chi-restraints excluded: chain A residue 262 PHE Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 299 MET Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 362 ARG Chi-restraints excluded: chain A residue 364 ASP Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 391 LEU Chi-restraints excluded: chain A residue 393 LEU Chi-restraints excluded: chain A residue 398 VAL Chi-restraints excluded: chain B residue 49 THR Chi-restraints excluded: chain B residue 90 THR Chi-restraints excluded: chain B residue 114 ASN Chi-restraints excluded: chain B residue 118 THR Chi-restraints excluded: chain B residue 170 SER Chi-restraints excluded: chain B residue 176 THR Chi-restraints excluded: chain B residue 181 GLN Chi-restraints excluded: chain B residue 224 LEU Chi-restraints excluded: chain B residue 232 VAL Chi-restraints excluded: chain B residue 235 ASP Chi-restraints excluded: chain B residue 262 PHE Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 298 SER Chi-restraints excluded: chain B residue 299 MET Chi-restraints excluded: chain B residue 380 LEU Chi-restraints excluded: chain B residue 389 VAL Chi-restraints excluded: chain B residue 391 LEU Chi-restraints excluded: chain B residue 398 VAL Chi-restraints excluded: chain C residue 49 THR Chi-restraints excluded: chain C residue 57 ILE Chi-restraints excluded: chain C residue 72 ASN Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain C residue 114 ASN Chi-restraints excluded: chain C residue 123 ASP Chi-restraints excluded: chain C residue 125 ASN Chi-restraints excluded: chain C residue 174 VAL Chi-restraints excluded: chain C residue 175 THR Chi-restraints excluded: chain C residue 235 ASP Chi-restraints excluded: chain C residue 262 PHE Chi-restraints excluded: chain C residue 298 SER Chi-restraints excluded: chain C residue 299 MET Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 365 ASP Chi-restraints excluded: chain C residue 368 ASN Chi-restraints excluded: chain C residue 389 VAL Chi-restraints excluded: chain C residue 391 LEU Chi-restraints excluded: chain C residue 398 VAL Chi-restraints excluded: chain C residue 400 LEU Chi-restraints excluded: chain C residue 403 MET Chi-restraints excluded: chain D residue 49 THR Chi-restraints excluded: chain D residue 72 ASN Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain D residue 111 GLN Chi-restraints excluded: chain D residue 114 ASN Chi-restraints excluded: chain D residue 141 ILE Chi-restraints excluded: chain D residue 233 LEU Chi-restraints excluded: chain D residue 235 ASP Chi-restraints excluded: chain D residue 262 PHE Chi-restraints excluded: chain D residue 298 SER Chi-restraints excluded: chain D residue 299 MET Chi-restraints excluded: chain D residue 302 THR Chi-restraints excluded: chain D residue 380 LEU Chi-restraints excluded: chain D residue 389 VAL Chi-restraints excluded: chain D residue 393 LEU Chi-restraints excluded: chain D residue 398 VAL Chi-restraints excluded: chain D residue 400 LEU Chi-restraints excluded: chain E residue 49 THR Chi-restraints excluded: chain E residue 57 ILE Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 102 VAL Chi-restraints excluded: chain E residue 111 GLN Chi-restraints excluded: chain E residue 114 ASN Chi-restraints excluded: chain E residue 167 THR Chi-restraints excluded: chain E residue 170 SER Chi-restraints excluded: chain E residue 174 VAL Chi-restraints excluded: chain E residue 230 LEU Chi-restraints excluded: chain E residue 262 PHE Chi-restraints excluded: chain E residue 380 LEU Chi-restraints excluded: chain E residue 391 LEU Chi-restraints excluded: chain E residue 398 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 158 optimal weight: 5.9990 chunk 18 optimal weight: 7.9990 chunk 93 optimal weight: 0.9990 chunk 120 optimal weight: 8.9990 chunk 138 optimal weight: 8.9990 chunk 91 optimal weight: 0.7980 chunk 163 optimal weight: 0.9990 chunk 102 optimal weight: 9.9990 chunk 99 optimal weight: 7.9990 chunk 75 optimal weight: 0.7980 chunk 101 optimal weight: 3.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 125 ASN ** B 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 125 ASN ** D 369 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 125 ASN ** E 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7771 moved from start: 0.2013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 13790 Z= 0.192 Angle : 0.544 11.340 18790 Z= 0.276 Chirality : 0.041 0.161 2290 Planarity : 0.003 0.030 2345 Dihedral : 4.067 20.447 1950 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 6.01 % Allowed : 26.01 % Favored : 67.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.97 (0.21), residues: 1720 helix: 2.87 (0.19), residues: 680 sheet: -0.37 (0.25), residues: 480 loop : -1.26 (0.25), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 81 HIS 0.003 0.001 HIS D 122 PHE 0.015 0.001 PHE B 359 TYR 0.015 0.001 TYR D 59 ARG 0.007 0.000 ARG E 362 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3440 Ramachandran restraints generated. 1720 Oldfield, 0 Emsley, 1720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3440 Ramachandran restraints generated. 1720 Oldfield, 0 Emsley, 1720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 364 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 275 time to evaluate : 1.635 Fit side-chains REVERT: A 364 ASP cc_start: 0.6778 (OUTLIER) cc_final: 0.6500 (m-30) REVERT: A 386 LEU cc_start: 0.7593 (mm) cc_final: 0.7350 (mp) REVERT: A 391 LEU cc_start: 0.7846 (OUTLIER) cc_final: 0.7538 (mp) REVERT: B 181 GLN cc_start: 0.7333 (OUTLIER) cc_final: 0.6745 (tt0) REVERT: B 224 LEU cc_start: 0.7631 (OUTLIER) cc_final: 0.7360 (mp) REVERT: B 270 LEU cc_start: 0.8054 (OUTLIER) cc_final: 0.7471 (mp) REVERT: B 363 LEU cc_start: 0.6401 (mt) cc_final: 0.5876 (tp) REVERT: C 125 ASN cc_start: 0.7892 (OUTLIER) cc_final: 0.7621 (t0) REVERT: C 166 GLU cc_start: 0.7140 (tp30) cc_final: 0.6868 (tt0) REVERT: C 262 PHE cc_start: 0.8117 (OUTLIER) cc_final: 0.7707 (t80) REVERT: C 310 LEU cc_start: 0.7607 (mt) cc_final: 0.7317 (mt) REVERT: C 353 LEU cc_start: 0.6559 (tp) cc_final: 0.6216 (mp) REVERT: D 233 LEU cc_start: 0.8334 (OUTLIER) cc_final: 0.8073 (tt) REVERT: D 371 GLU cc_start: 0.6830 (tm-30) cc_final: 0.6132 (mp0) REVERT: D 374 HIS cc_start: 0.7751 (m170) cc_final: 0.7472 (m170) REVERT: D 399 MET cc_start: 0.8142 (tpp) cc_final: 0.7583 (tpt) REVERT: E 166 GLU cc_start: 0.7227 (tp30) cc_final: 0.6785 (tt0) REVERT: E 230 LEU cc_start: 0.8278 (OUTLIER) cc_final: 0.7877 (mm) REVERT: E 262 PHE cc_start: 0.7991 (OUTLIER) cc_final: 0.7586 (t80) REVERT: E 374 HIS cc_start: 0.7683 (m170) cc_final: 0.7446 (m170) outliers start: 89 outliers final: 68 residues processed: 338 average time/residue: 0.2381 time to fit residues: 120.8866 Evaluate side-chains 346 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 268 time to evaluate : 1.592 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 THR Chi-restraints excluded: chain A residue 114 ASN Chi-restraints excluded: chain A residue 141 ILE Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 159 ASP Chi-restraints excluded: chain A residue 160 GLU Chi-restraints excluded: chain A residue 235 ASP Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 299 MET Chi-restraints excluded: chain A residue 364 ASP Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 391 LEU Chi-restraints excluded: chain A residue 393 LEU Chi-restraints excluded: chain A residue 398 VAL Chi-restraints excluded: chain B residue 49 THR Chi-restraints excluded: chain B residue 72 ASN Chi-restraints excluded: chain B residue 114 ASN Chi-restraints excluded: chain B residue 118 THR Chi-restraints excluded: chain B residue 176 THR Chi-restraints excluded: chain B residue 181 GLN Chi-restraints excluded: chain B residue 224 LEU Chi-restraints excluded: chain B residue 232 VAL Chi-restraints excluded: chain B residue 235 ASP Chi-restraints excluded: chain B residue 262 PHE Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 298 SER Chi-restraints excluded: chain B residue 299 MET Chi-restraints excluded: chain B residue 389 VAL Chi-restraints excluded: chain B residue 391 LEU Chi-restraints excluded: chain B residue 393 LEU Chi-restraints excluded: chain B residue 398 VAL Chi-restraints excluded: chain C residue 57 ILE Chi-restraints excluded: chain C residue 72 ASN Chi-restraints excluded: chain C residue 114 ASN Chi-restraints excluded: chain C residue 125 ASN Chi-restraints excluded: chain C residue 174 VAL Chi-restraints excluded: chain C residue 175 THR Chi-restraints excluded: chain C residue 230 LEU Chi-restraints excluded: chain C residue 232 VAL Chi-restraints excluded: chain C residue 235 ASP Chi-restraints excluded: chain C residue 262 PHE Chi-restraints excluded: chain C residue 298 SER Chi-restraints excluded: chain C residue 299 MET Chi-restraints excluded: chain C residue 365 ASP Chi-restraints excluded: chain C residue 389 VAL Chi-restraints excluded: chain C residue 391 LEU Chi-restraints excluded: chain C residue 398 VAL Chi-restraints excluded: chain C residue 400 LEU Chi-restraints excluded: chain C residue 403 MET Chi-restraints excluded: chain D residue 49 THR Chi-restraints excluded: chain D residue 72 ASN Chi-restraints excluded: chain D residue 114 ASN Chi-restraints excluded: chain D residue 141 ILE Chi-restraints excluded: chain D residue 176 THR Chi-restraints excluded: chain D residue 233 LEU Chi-restraints excluded: chain D residue 298 SER Chi-restraints excluded: chain D residue 299 MET Chi-restraints excluded: chain D residue 380 LEU Chi-restraints excluded: chain D residue 389 VAL Chi-restraints excluded: chain D residue 393 LEU Chi-restraints excluded: chain D residue 398 VAL Chi-restraints excluded: chain D residue 400 LEU Chi-restraints excluded: chain E residue 49 THR Chi-restraints excluded: chain E residue 57 ILE Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 114 ASN Chi-restraints excluded: chain E residue 167 THR Chi-restraints excluded: chain E residue 170 SER Chi-restraints excluded: chain E residue 174 VAL Chi-restraints excluded: chain E residue 175 THR Chi-restraints excluded: chain E residue 230 LEU Chi-restraints excluded: chain E residue 235 ASP Chi-restraints excluded: chain E residue 262 PHE Chi-restraints excluded: chain E residue 298 SER Chi-restraints excluded: chain E residue 380 LEU Chi-restraints excluded: chain E residue 391 LEU Chi-restraints excluded: chain E residue 398 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 65 optimal weight: 7.9990 chunk 97 optimal weight: 9.9990 chunk 49 optimal weight: 0.9990 chunk 32 optimal weight: 1.9990 chunk 31 optimal weight: 4.9990 chunk 104 optimal weight: 6.9990 chunk 111 optimal weight: 0.2980 chunk 81 optimal weight: 6.9990 chunk 15 optimal weight: 0.9990 chunk 128 optimal weight: 0.7980 chunk 149 optimal weight: 1.9990 overall best weight: 1.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 125 ASN ** B 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 125 ASN E 125 ASN ** E 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 267 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7749 moved from start: 0.2059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 13790 Z= 0.159 Angle : 0.526 12.127 18790 Z= 0.264 Chirality : 0.041 0.171 2290 Planarity : 0.003 0.033 2345 Dihedral : 3.853 19.395 1950 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 5.34 % Allowed : 27.03 % Favored : 67.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.10 (0.21), residues: 1720 helix: 2.98 (0.19), residues: 690 sheet: -0.11 (0.26), residues: 435 loop : -1.40 (0.24), residues: 595 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 81 HIS 0.002 0.001 HIS D 122 PHE 0.016 0.001 PHE B 359 TYR 0.015 0.001 TYR D 59 ARG 0.008 0.000 ARG B 362 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3440 Ramachandran restraints generated. 1720 Oldfield, 0 Emsley, 1720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3440 Ramachandran restraints generated. 1720 Oldfield, 0 Emsley, 1720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 362 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 283 time to evaluate : 1.593 Fit side-chains REVERT: A 386 LEU cc_start: 0.7580 (mm) cc_final: 0.7346 (mp) REVERT: B 181 GLN cc_start: 0.7268 (OUTLIER) cc_final: 0.6661 (tt0) REVERT: B 224 LEU cc_start: 0.7609 (OUTLIER) cc_final: 0.7355 (mp) REVERT: B 270 LEU cc_start: 0.7909 (OUTLIER) cc_final: 0.7280 (mp) REVERT: B 362 ARG cc_start: 0.5670 (mtp-110) cc_final: 0.5285 (ttp80) REVERT: B 363 LEU cc_start: 0.6410 (mt) cc_final: 0.5959 (tp) REVERT: C 125 ASN cc_start: 0.7907 (OUTLIER) cc_final: 0.7639 (t0) REVERT: C 166 GLU cc_start: 0.7143 (tp30) cc_final: 0.6926 (tt0) REVERT: C 310 LEU cc_start: 0.7618 (mt) cc_final: 0.7368 (mt) REVERT: C 380 LEU cc_start: 0.8121 (OUTLIER) cc_final: 0.7785 (mp) REVERT: D 233 LEU cc_start: 0.8338 (OUTLIER) cc_final: 0.8080 (tt) REVERT: D 374 HIS cc_start: 0.7758 (m170) cc_final: 0.7484 (m170) REVERT: D 399 MET cc_start: 0.8187 (tpp) cc_final: 0.7563 (tpt) REVERT: E 166 GLU cc_start: 0.7233 (tp30) cc_final: 0.6836 (tt0) REVERT: E 230 LEU cc_start: 0.8264 (OUTLIER) cc_final: 0.7880 (mm) REVERT: E 262 PHE cc_start: 0.8005 (OUTLIER) cc_final: 0.7643 (t80) REVERT: E 310 LEU cc_start: 0.7382 (mt) cc_final: 0.6383 (pp) REVERT: E 371 GLU cc_start: 0.6705 (tm-30) cc_final: 0.6094 (mp0) REVERT: E 374 HIS cc_start: 0.7626 (m170) cc_final: 0.7393 (m170) outliers start: 79 outliers final: 60 residues processed: 338 average time/residue: 0.2736 time to fit residues: 137.5350 Evaluate side-chains 344 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 276 time to evaluate : 1.566 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 THR Chi-restraints excluded: chain A residue 114 ASN Chi-restraints excluded: chain A residue 141 ILE Chi-restraints excluded: chain A residue 159 ASP Chi-restraints excluded: chain A residue 160 GLU Chi-restraints excluded: chain A residue 235 ASP Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 393 LEU Chi-restraints excluded: chain A residue 398 VAL Chi-restraints excluded: chain B residue 49 THR Chi-restraints excluded: chain B residue 72 ASN Chi-restraints excluded: chain B residue 114 ASN Chi-restraints excluded: chain B residue 118 THR Chi-restraints excluded: chain B residue 181 GLN Chi-restraints excluded: chain B residue 224 LEU Chi-restraints excluded: chain B residue 262 PHE Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 298 SER Chi-restraints excluded: chain B residue 299 MET Chi-restraints excluded: chain B residue 365 ASP Chi-restraints excluded: chain B residue 389 VAL Chi-restraints excluded: chain B residue 391 LEU Chi-restraints excluded: chain B residue 393 LEU Chi-restraints excluded: chain B residue 398 VAL Chi-restraints excluded: chain C residue 49 THR Chi-restraints excluded: chain C residue 57 ILE Chi-restraints excluded: chain C residue 72 ASN Chi-restraints excluded: chain C residue 114 ASN Chi-restraints excluded: chain C residue 125 ASN Chi-restraints excluded: chain C residue 174 VAL Chi-restraints excluded: chain C residue 175 THR Chi-restraints excluded: chain C residue 230 LEU Chi-restraints excluded: chain C residue 232 VAL Chi-restraints excluded: chain C residue 235 ASP Chi-restraints excluded: chain C residue 262 PHE Chi-restraints excluded: chain C residue 299 MET Chi-restraints excluded: chain C residue 365 ASP Chi-restraints excluded: chain C residue 380 LEU Chi-restraints excluded: chain C residue 389 VAL Chi-restraints excluded: chain C residue 391 LEU Chi-restraints excluded: chain C residue 400 LEU Chi-restraints excluded: chain D residue 49 THR Chi-restraints excluded: chain D residue 72 ASN Chi-restraints excluded: chain D residue 114 ASN Chi-restraints excluded: chain D residue 233 LEU Chi-restraints excluded: chain D residue 235 ASP Chi-restraints excluded: chain D residue 241 LEU Chi-restraints excluded: chain D residue 285 CYS Chi-restraints excluded: chain D residue 298 SER Chi-restraints excluded: chain D residue 299 MET Chi-restraints excluded: chain D residue 380 LEU Chi-restraints excluded: chain D residue 389 VAL Chi-restraints excluded: chain D residue 393 LEU Chi-restraints excluded: chain D residue 398 VAL Chi-restraints excluded: chain D residue 400 LEU Chi-restraints excluded: chain E residue 49 THR Chi-restraints excluded: chain E residue 57 ILE Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 114 ASN Chi-restraints excluded: chain E residue 167 THR Chi-restraints excluded: chain E residue 170 SER Chi-restraints excluded: chain E residue 174 VAL Chi-restraints excluded: chain E residue 175 THR Chi-restraints excluded: chain E residue 230 LEU Chi-restraints excluded: chain E residue 262 PHE Chi-restraints excluded: chain E residue 364 ASP Chi-restraints excluded: chain E residue 398 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 156 optimal weight: 0.9980 chunk 143 optimal weight: 0.8980 chunk 152 optimal weight: 6.9990 chunk 91 optimal weight: 0.9980 chunk 66 optimal weight: 1.9990 chunk 119 optimal weight: 10.0000 chunk 46 optimal weight: 6.9990 chunk 137 optimal weight: 0.9990 chunk 144 optimal weight: 0.3980 chunk 100 optimal weight: 7.9990 chunk 161 optimal weight: 7.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 125 ASN A 137 HIS ** B 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 125 ASN E 125 ASN ** E 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 267 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7741 moved from start: 0.2134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 13790 Z= 0.147 Angle : 0.523 12.426 18790 Z= 0.260 Chirality : 0.041 0.171 2290 Planarity : 0.003 0.035 2345 Dihedral : 3.741 18.297 1950 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 5.07 % Allowed : 27.57 % Favored : 67.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.24 (0.21), residues: 1720 helix: 3.04 (0.19), residues: 695 sheet: -0.02 (0.26), residues: 435 loop : -1.30 (0.24), residues: 590 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 81 HIS 0.002 0.000 HIS A 137 PHE 0.019 0.001 PHE B 359 TYR 0.015 0.001 TYR D 59 ARG 0.008 0.000 ARG E 362 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3440 Ramachandran restraints generated. 1720 Oldfield, 0 Emsley, 1720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3440 Ramachandran restraints generated. 1720 Oldfield, 0 Emsley, 1720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 356 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 281 time to evaluate : 1.996 Fit side-chains REVERT: A 391 LEU cc_start: 0.7895 (OUTLIER) cc_final: 0.7540 (mp) REVERT: B 181 GLN cc_start: 0.7246 (OUTLIER) cc_final: 0.6679 (tt0) REVERT: B 224 LEU cc_start: 0.7611 (OUTLIER) cc_final: 0.7364 (mp) REVERT: B 270 LEU cc_start: 0.7848 (OUTLIER) cc_final: 0.7221 (mp) REVERT: B 362 ARG cc_start: 0.5623 (mtp-110) cc_final: 0.5275 (ttp80) REVERT: B 363 LEU cc_start: 0.6366 (mt) cc_final: 0.5890 (tp) REVERT: C 34 LEU cc_start: 0.8869 (mp) cc_final: 0.8657 (mp) REVERT: C 125 ASN cc_start: 0.7908 (OUTLIER) cc_final: 0.7658 (t0) REVERT: C 310 LEU cc_start: 0.7636 (mt) cc_final: 0.7415 (mt) REVERT: C 380 LEU cc_start: 0.8134 (OUTLIER) cc_final: 0.7799 (mp) REVERT: D 233 LEU cc_start: 0.8338 (OUTLIER) cc_final: 0.8118 (tp) REVERT: D 399 MET cc_start: 0.8242 (tpp) cc_final: 0.7588 (tpt) REVERT: E 166 GLU cc_start: 0.7258 (tp30) cc_final: 0.6867 (tt0) REVERT: E 170 SER cc_start: 0.8012 (OUTLIER) cc_final: 0.7664 (p) REVERT: E 230 LEU cc_start: 0.8271 (OUTLIER) cc_final: 0.7893 (mm) REVERT: E 262 PHE cc_start: 0.7984 (OUTLIER) cc_final: 0.7632 (t80) REVERT: E 310 LEU cc_start: 0.7483 (mt) cc_final: 0.7141 (mt) REVERT: E 374 HIS cc_start: 0.7620 (m170) cc_final: 0.7396 (m170) outliers start: 75 outliers final: 58 residues processed: 332 average time/residue: 0.2566 time to fit residues: 126.3195 Evaluate side-chains 340 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 272 time to evaluate : 1.705 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 ASN Chi-restraints excluded: chain A residue 141 ILE Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 159 ASP Chi-restraints excluded: chain A residue 175 THR Chi-restraints excluded: chain A residue 235 ASP Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 391 LEU Chi-restraints excluded: chain A residue 393 LEU Chi-restraints excluded: chain A residue 398 VAL Chi-restraints excluded: chain B residue 72 ASN Chi-restraints excluded: chain B residue 114 ASN Chi-restraints excluded: chain B residue 118 THR Chi-restraints excluded: chain B residue 181 GLN Chi-restraints excluded: chain B residue 224 LEU Chi-restraints excluded: chain B residue 262 PHE Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 298 SER Chi-restraints excluded: chain B residue 299 MET Chi-restraints excluded: chain B residue 380 LEU Chi-restraints excluded: chain B residue 389 VAL Chi-restraints excluded: chain B residue 391 LEU Chi-restraints excluded: chain B residue 393 LEU Chi-restraints excluded: chain B residue 398 VAL Chi-restraints excluded: chain C residue 49 THR Chi-restraints excluded: chain C residue 57 ILE Chi-restraints excluded: chain C residue 72 ASN Chi-restraints excluded: chain C residue 114 ASN Chi-restraints excluded: chain C residue 125 ASN Chi-restraints excluded: chain C residue 174 VAL Chi-restraints excluded: chain C residue 175 THR Chi-restraints excluded: chain C residue 230 LEU Chi-restraints excluded: chain C residue 232 VAL Chi-restraints excluded: chain C residue 262 PHE Chi-restraints excluded: chain C residue 298 SER Chi-restraints excluded: chain C residue 299 MET Chi-restraints excluded: chain C residue 365 ASP Chi-restraints excluded: chain C residue 380 LEU Chi-restraints excluded: chain C residue 389 VAL Chi-restraints excluded: chain C residue 391 LEU Chi-restraints excluded: chain C residue 400 LEU Chi-restraints excluded: chain D residue 49 THR Chi-restraints excluded: chain D residue 72 ASN Chi-restraints excluded: chain D residue 114 ASN Chi-restraints excluded: chain D residue 233 LEU Chi-restraints excluded: chain D residue 235 ASP Chi-restraints excluded: chain D residue 241 LEU Chi-restraints excluded: chain D residue 285 CYS Chi-restraints excluded: chain D residue 298 SER Chi-restraints excluded: chain D residue 299 MET Chi-restraints excluded: chain D residue 380 LEU Chi-restraints excluded: chain D residue 389 VAL Chi-restraints excluded: chain D residue 393 LEU Chi-restraints excluded: chain D residue 398 VAL Chi-restraints excluded: chain D residue 400 LEU Chi-restraints excluded: chain E residue 57 ILE Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 114 ASN Chi-restraints excluded: chain E residue 167 THR Chi-restraints excluded: chain E residue 170 SER Chi-restraints excluded: chain E residue 174 VAL Chi-restraints excluded: chain E residue 175 THR Chi-restraints excluded: chain E residue 230 LEU Chi-restraints excluded: chain E residue 235 ASP Chi-restraints excluded: chain E residue 262 PHE Chi-restraints excluded: chain E residue 364 ASP Chi-restraints excluded: chain E residue 398 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 98 optimal weight: 2.9990 chunk 76 optimal weight: 0.5980 chunk 112 optimal weight: 8.9990 chunk 169 optimal weight: 1.9990 chunk 155 optimal weight: 0.7980 chunk 134 optimal weight: 0.9990 chunk 14 optimal weight: 9.9990 chunk 104 optimal weight: 5.9990 chunk 82 optimal weight: 4.9990 chunk 107 optimal weight: 2.9990 chunk 143 optimal weight: 0.7980 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 125 ASN ** B 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 125 ASN C 32 GLN E 125 ASN ** E 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 267 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7746 moved from start: 0.2185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 13790 Z= 0.160 Angle : 0.534 12.371 18790 Z= 0.266 Chirality : 0.041 0.176 2290 Planarity : 0.003 0.037 2345 Dihedral : 3.753 18.676 1950 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 5.00 % Allowed : 27.77 % Favored : 67.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.24 (0.21), residues: 1720 helix: 3.01 (0.19), residues: 695 sheet: -0.00 (0.26), residues: 435 loop : -1.28 (0.24), residues: 590 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 81 HIS 0.002 0.001 HIS C 122 PHE 0.024 0.001 PHE B 359 TYR 0.014 0.001 TYR D 59 ARG 0.008 0.000 ARG E 362 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3440 Ramachandran restraints generated. 1720 Oldfield, 0 Emsley, 1720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3440 Ramachandran restraints generated. 1720 Oldfield, 0 Emsley, 1720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 354 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 280 time to evaluate : 1.583 Fit side-chains REVERT: A 391 LEU cc_start: 0.7913 (OUTLIER) cc_final: 0.7556 (mp) REVERT: A 402 ILE cc_start: 0.8835 (mt) cc_final: 0.8485 (mm) REVERT: B 181 GLN cc_start: 0.7263 (OUTLIER) cc_final: 0.6683 (tt0) REVERT: B 224 LEU cc_start: 0.7643 (OUTLIER) cc_final: 0.7381 (mp) REVERT: B 270 LEU cc_start: 0.7869 (OUTLIER) cc_final: 0.7228 (mp) REVERT: B 362 ARG cc_start: 0.5658 (mtp-110) cc_final: 0.5298 (ttp80) REVERT: C 125 ASN cc_start: 0.7906 (OUTLIER) cc_final: 0.7651 (t0) REVERT: C 310 LEU cc_start: 0.7626 (mt) cc_final: 0.7417 (mt) REVERT: C 380 LEU cc_start: 0.8121 (OUTLIER) cc_final: 0.7789 (mp) REVERT: D 233 LEU cc_start: 0.8337 (OUTLIER) cc_final: 0.8110 (tt) REVERT: D 399 MET cc_start: 0.8234 (tpp) cc_final: 0.7584 (tpt) REVERT: E 39 MET cc_start: 0.7830 (mmp) cc_final: 0.7425 (mmm) REVERT: E 166 GLU cc_start: 0.7263 (tp30) cc_final: 0.6894 (tt0) REVERT: E 170 SER cc_start: 0.8021 (OUTLIER) cc_final: 0.7670 (p) REVERT: E 230 LEU cc_start: 0.8266 (OUTLIER) cc_final: 0.7850 (mm) REVERT: E 262 PHE cc_start: 0.7989 (OUTLIER) cc_final: 0.7638 (t80) REVERT: E 374 HIS cc_start: 0.7645 (m170) cc_final: 0.7429 (m170) outliers start: 74 outliers final: 60 residues processed: 331 average time/residue: 0.2447 time to fit residues: 120.2489 Evaluate side-chains 341 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 271 time to evaluate : 1.774 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 ASN Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 159 ASP Chi-restraints excluded: chain A residue 235 ASP Chi-restraints excluded: chain A residue 299 MET Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 391 LEU Chi-restraints excluded: chain A residue 393 LEU Chi-restraints excluded: chain A residue 398 VAL Chi-restraints excluded: chain B residue 49 THR Chi-restraints excluded: chain B residue 72 ASN Chi-restraints excluded: chain B residue 114 ASN Chi-restraints excluded: chain B residue 118 THR Chi-restraints excluded: chain B residue 181 GLN Chi-restraints excluded: chain B residue 224 LEU Chi-restraints excluded: chain B residue 262 PHE Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 298 SER Chi-restraints excluded: chain B residue 299 MET Chi-restraints excluded: chain B residue 365 ASP Chi-restraints excluded: chain B residue 380 LEU Chi-restraints excluded: chain B residue 389 VAL Chi-restraints excluded: chain B residue 391 LEU Chi-restraints excluded: chain B residue 393 LEU Chi-restraints excluded: chain B residue 398 VAL Chi-restraints excluded: chain C residue 49 THR Chi-restraints excluded: chain C residue 57 ILE Chi-restraints excluded: chain C residue 72 ASN Chi-restraints excluded: chain C residue 114 ASN Chi-restraints excluded: chain C residue 125 ASN Chi-restraints excluded: chain C residue 174 VAL Chi-restraints excluded: chain C residue 175 THR Chi-restraints excluded: chain C residue 230 LEU Chi-restraints excluded: chain C residue 232 VAL Chi-restraints excluded: chain C residue 262 PHE Chi-restraints excluded: chain C residue 298 SER Chi-restraints excluded: chain C residue 299 MET Chi-restraints excluded: chain C residue 365 ASP Chi-restraints excluded: chain C residue 380 LEU Chi-restraints excluded: chain C residue 389 VAL Chi-restraints excluded: chain C residue 391 LEU Chi-restraints excluded: chain C residue 400 LEU Chi-restraints excluded: chain D residue 49 THR Chi-restraints excluded: chain D residue 72 ASN Chi-restraints excluded: chain D residue 114 ASN Chi-restraints excluded: chain D residue 233 LEU Chi-restraints excluded: chain D residue 235 ASP Chi-restraints excluded: chain D residue 241 LEU Chi-restraints excluded: chain D residue 285 CYS Chi-restraints excluded: chain D residue 298 SER Chi-restraints excluded: chain D residue 299 MET Chi-restraints excluded: chain D residue 380 LEU Chi-restraints excluded: chain D residue 389 VAL Chi-restraints excluded: chain D residue 393 LEU Chi-restraints excluded: chain D residue 398 VAL Chi-restraints excluded: chain D residue 400 LEU Chi-restraints excluded: chain E residue 57 ILE Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 114 ASN Chi-restraints excluded: chain E residue 167 THR Chi-restraints excluded: chain E residue 170 SER Chi-restraints excluded: chain E residue 174 VAL Chi-restraints excluded: chain E residue 175 THR Chi-restraints excluded: chain E residue 230 LEU Chi-restraints excluded: chain E residue 235 ASP Chi-restraints excluded: chain E residue 262 PHE Chi-restraints excluded: chain E residue 364 ASP Chi-restraints excluded: chain E residue 391 LEU Chi-restraints excluded: chain E residue 398 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 41 optimal weight: 4.9990 chunk 124 optimal weight: 3.9990 chunk 19 optimal weight: 0.9980 chunk 37 optimal weight: 6.9990 chunk 135 optimal weight: 4.9990 chunk 56 optimal weight: 3.9990 chunk 138 optimal weight: 3.9990 chunk 17 optimal weight: 4.9990 chunk 24 optimal weight: 1.9990 chunk 118 optimal weight: 7.9990 chunk 7 optimal weight: 0.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 125 ASN ** B 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 125 ASN ** D 369 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 125 ASN ** E 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 267 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.109542 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2935 r_free = 0.2935 target = 0.089529 restraints weight = 20427.961| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2979 r_free = 0.2979 target = 0.092579 restraints weight = 10611.512| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.094594 restraints weight = 6800.063| |-----------------------------------------------------------------------------| r_work (final): 0.3100 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7796 moved from start: 0.2267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 13790 Z= 0.268 Angle : 0.621 13.198 18790 Z= 0.310 Chirality : 0.043 0.192 2290 Planarity : 0.004 0.036 2345 Dihedral : 4.165 20.083 1950 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 5.47 % Allowed : 27.57 % Favored : 66.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.94 (0.21), residues: 1720 helix: 2.66 (0.19), residues: 685 sheet: -0.16 (0.25), residues: 475 loop : -1.26 (0.25), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 81 HIS 0.004 0.001 HIS D 122 PHE 0.015 0.002 PHE B 56 TYR 0.012 0.002 TYR D 59 ARG 0.007 0.001 ARG E 362 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2969.30 seconds wall clock time: 55 minutes 48.87 seconds (3348.87 seconds total)