Starting phenix.real_space_refine on Sat Jul 4 16:01:49 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7s65_24850/07_2026/7s65_24850.cif Found real_map, /net/cci-nas-00/data/ceres_data/7s65_24850/07_2026/7s65_24850.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7s65_24850/07_2026/7s65_24850.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7s65_24850/07_2026/7s65_24850.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7s65_24850/07_2026/7s65_24850.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7s65_24850/07_2026/7s65_24850.cif" model { file = "/net/cci-nas-00/data/ceres_data/7s65_24850/07_2026/7s65_24850.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7s65_24850/07_2026/7s65_24850.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.011 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: 6 Type Number sf(0) Gaussians P 34 5.49 5 Mg 12 5.21 5 S 88 5.16 5 C 13808 2.51 5 N 3854 2.21 5 O 4253 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 22049 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 3579 Number of conformers: 1 Conformer: "" Number of residues, atoms: 456, 3579 Classifications: {'peptide': 456} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 10, 'TRANS': 445} Chain breaks: 1 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "B" Number of atoms: 3627 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 461, 3618 Classifications: {'peptide': 461} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 11, 'TRANS': 449} Chain breaks: 1 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 8 Conformer: "B" Number of residues, atoms: 461, 3618 Classifications: {'peptide': 461} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 11, 'TRANS': 449} Chain breaks: 1 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 8 bond proxies already assigned to first conformer: 3667 Chain: "C" Number of atoms: 3626 Number of conformers: 1 Conformer: "" Number of residues, atoms: 463, 3626 Classifications: {'peptide': 463} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 11, 'TRANS': 451} Chain breaks: 1 Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 14 Chain: "D" Number of atoms: 3579 Number of conformers: 1 Conformer: "" Number of residues, atoms: 456, 3579 Classifications: {'peptide': 456} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 10, 'TRANS': 445} Chain breaks: 1 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "E" Number of atoms: 3636 Number of conformers: 3 Conformer: "A" Number of residues, atoms: 461, 3618 Classifications: {'peptide': 461} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 11, 'TRANS': 449} Chain breaks: 1 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 8 Conformer: "B" Number of residues, atoms: 461, 3618 Classifications: {'peptide': 461} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 11, 'TRANS': 449} Chain breaks: 1 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 8 bond proxies already assigned to first conformer: 3667 Conformer: "C" Number of residues, atoms: 461, 3618 Classifications: {'peptide': 461} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 11, 'TRANS': 449} Chain breaks: 1 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 8 bond proxies already assigned to first conformer: 3667 Chain: "F" Number of atoms: 3626 Number of conformers: 1 Conformer: "" Number of residues, atoms: 463, 3626 Classifications: {'peptide': 463} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 11, 'TRANS': 451} Chain breaks: 1 Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 14 Chain: "A" Number of atoms: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 60 Unusual residues: {' MG': 2, 'ADP': 1, 'ATP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 64 Unusual residues: {' MG': 2, 'ATP': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "C" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 64 Unusual residues: {' MG': 2, 'ATP': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "D" Number of atoms: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 60 Unusual residues: {' MG': 2, 'ADP': 1, 'ATP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "E" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 64 Unusual residues: {' MG': 2, 'ATP': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "F" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 64 Unusual residues: {' MG': 2, 'ATP': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Time building chain proxies: 7.08, per 1000 atoms: 0.32 Number of scatterers: 22049 At special positions: 0 Unit cell: (125.35, 118.45, 110.4, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 88 16.00 P 34 15.00 Mg 12 11.99 O 4253 8.00 N 3854 7.00 C 13808 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.82 Conformation dependent library (CDL) restraints added in 1.4 seconds 5478 Ramachandran restraints generated. 2739 Oldfield, 0 Emsley, 2739 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5070 Finding SS restraints... Secondary structure from input PDB file: 102 helices and 24 sheets defined 39.5% alpha, 21.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.77 Creating SS restraints... Processing helix chain 'A' and resid 27 through 32 Processing helix chain 'A' and resid 51 through 67 removed outlier: 3.894A pdb=" N LEU A 60 " --> pdb=" O SER A 56 " (cutoff:3.500A) Processing helix chain 'A' and resid 79 through 88 Processing helix chain 'A' and resid 89 through 91 No H-bonds generated for 'chain 'A' and resid 89 through 91' Processing helix chain 'A' and resid 93 through 100 removed outlier: 3.643A pdb=" N LEU A 97 " --> pdb=" O ASP A 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 137 removed outlier: 3.584A pdb=" N LEU A 126 " --> pdb=" O ASP A 122 " (cutoff:3.500A) Processing helix chain 'A' and resid 146 through 151 removed outlier: 3.926A pdb=" N VAL A 150 " --> pdb=" O VAL A 147 " (cutoff:3.500A) Processing helix chain 'A' and resid 154 through 158 Processing helix chain 'A' and resid 159 through 175 Processing helix chain 'A' and resid 196 through 201 Processing helix chain 'A' and resid 248 through 252 Processing helix chain 'A' and resid 267 through 274 Processing helix chain 'A' and resid 293 through 308 Processing helix chain 'A' and resid 320 through 332 Processing helix chain 'A' and resid 334 through 341 Processing helix chain 'A' and resid 355 through 371 Processing helix chain 'A' and resid 379 through 383 Processing helix chain 'A' and resid 388 through 406 Processing helix chain 'B' and resid 27 through 32 Processing helix chain 'B' and resid 51 through 66 Processing helix chain 'B' and resid 79 through 88 Processing helix chain 'B' and resid 89 through 91 No H-bonds generated for 'chain 'B' and resid 89 through 91' Processing helix chain 'B' and resid 93 through 100 removed outlier: 3.631A pdb=" N LEU B 97 " --> pdb=" O ASP B 93 " (cutoff:3.500A) Processing helix chain 'B' and resid 123 through 137 removed outlier: 3.899A pdb=" N GLU B 128 " --> pdb=" O SER B 124 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N ARG B 129 " --> pdb=" O ALA B 125 " (cutoff:3.500A) Processing helix chain 'B' and resid 146 through 151 Processing helix chain 'B' and resid 156 through 175 Processing helix chain 'B' and resid 196 through 200 Processing helix chain 'B' and resid 267 through 274 Processing helix chain 'B' and resid 293 through 308 Processing helix chain 'B' and resid 320 through 331 Processing helix chain 'B' and resid 334 through 341 Processing helix chain 'B' and resid 350 through 354 removed outlier: 3.553A pdb=" N ALA B 354 " --> pdb=" O PRO B 351 " (cutoff:3.500A) Processing helix chain 'B' and resid 355 through 371 Processing helix chain 'B' and resid 380 through 385 Processing helix chain 'B' and resid 388 through 406 Processing helix chain 'B' and resid 424 through 434 Processing helix chain 'C' and resid 27 through 32 Processing helix chain 'C' and resid 51 through 67 Processing helix chain 'C' and resid 79 through 88 Processing helix chain 'C' and resid 89 through 91 No H-bonds generated for 'chain 'C' and resid 89 through 91' Processing helix chain 'C' and resid 93 through 100 Processing helix chain 'C' and resid 122 through 137 Processing helix chain 'C' and resid 156 through 175 Processing helix chain 'C' and resid 192 through 196 removed outlier: 4.549A pdb=" N VAL C 196 " --> pdb=" O ARG C 193 " (cutoff:3.500A) Processing helix chain 'C' and resid 267 through 274 Processing helix chain 'C' and resid 293 through 308 Processing helix chain 'C' and resid 320 through 330 Processing helix chain 'C' and resid 334 through 341 Processing helix chain 'C' and resid 350 through 354 Processing helix chain 'C' and resid 355 through 371 Processing helix chain 'C' and resid 388 through 406 Processing helix chain 'D' and resid 27 through 32 Processing helix chain 'D' and resid 51 through 67 removed outlier: 3.893A pdb=" N LEU D 60 " --> pdb=" O SER D 56 " (cutoff:3.500A) Processing helix chain 'D' and resid 79 through 88 Processing helix chain 'D' and resid 89 through 91 No H-bonds generated for 'chain 'D' and resid 89 through 91' Processing helix chain 'D' and resid 93 through 100 removed outlier: 3.643A pdb=" N LEU D 97 " --> pdb=" O ASP D 93 " (cutoff:3.500A) Processing helix chain 'D' and resid 122 through 137 removed outlier: 3.583A pdb=" N LEU D 126 " --> pdb=" O ASP D 122 " (cutoff:3.500A) Processing helix chain 'D' and resid 146 through 151 removed outlier: 3.926A pdb=" N VAL D 150 " --> pdb=" O VAL D 147 " (cutoff:3.500A) Processing helix chain 'D' and resid 154 through 158 Processing helix chain 'D' and resid 159 through 175 Processing helix chain 'D' and resid 196 through 201 Processing helix chain 'D' and resid 248 through 252 Processing helix chain 'D' and resid 267 through 274 Processing helix chain 'D' and resid 293 through 308 Processing helix chain 'D' and resid 320 through 332 Processing helix chain 'D' and resid 334 through 341 Processing helix chain 'D' and resid 355 through 371 Processing helix chain 'D' and resid 379 through 383 Processing helix chain 'D' and resid 388 through 406 Processing helix chain 'E' and resid 27 through 32 Processing helix chain 'E' and resid 51 through 66 Processing helix chain 'E' and resid 79 through 88 Processing helix chain 'E' and resid 89 through 91 No H-bonds generated for 'chain 'E' and resid 89 through 91' Processing helix chain 'E' and resid 93 through 100 removed outlier: 3.630A pdb=" N LEU E 97 " --> pdb=" O ASP E 93 " (cutoff:3.500A) Processing helix chain 'E' and resid 123 through 137 removed outlier: 3.899A pdb=" N GLU E 128 " --> pdb=" O SER E 124 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N ARG E 129 " --> pdb=" O ALA E 125 " (cutoff:3.500A) Processing helix chain 'E' and resid 146 through 151 Processing helix chain 'E' and resid 156 through 175 Processing helix chain 'E' and resid 196 through 200 Processing helix chain 'E' and resid 267 through 274 Processing helix chain 'E' and resid 293 through 308 Processing helix chain 'E' and resid 320 through 331 Processing helix chain 'E' and resid 334 through 341 Processing helix chain 'E' and resid 350 through 354 removed outlier: 3.552A pdb=" N ALA E 354 " --> pdb=" O PRO E 351 " (cutoff:3.500A) Processing helix chain 'E' and resid 355 through 371 Processing helix chain 'E' and resid 380 through 385 Processing helix chain 'E' and resid 388 through 406 Processing helix chain 'E' and resid 424 through 434 Processing helix chain 'F' and resid 27 through 32 Processing helix chain 'F' and resid 51 through 67 Processing helix chain 'F' and resid 79 through 88 Processing helix chain 'F' and resid 89 through 91 No H-bonds generated for 'chain 'F' and resid 89 through 91' Processing helix chain 'F' and resid 93 through 100 Processing helix chain 'F' and resid 122 through 137 Processing helix chain 'F' and resid 156 through 175 Processing helix chain 'F' and resid 192 through 196 removed outlier: 4.550A pdb=" N VAL F 196 " --> pdb=" O ARG F 193 " (cutoff:3.500A) Processing helix chain 'F' and resid 267 through 274 Processing helix chain 'F' and resid 293 through 308 Processing helix chain 'F' and resid 320 through 330 Processing helix chain 'F' and resid 334 through 341 Processing helix chain 'F' and resid 350 through 354 Processing helix chain 'F' and resid 355 through 371 Processing helix chain 'F' and resid 388 through 406 Processing sheet with id=AA1, first strand: chain 'A' and resid 20 through 21 Processing sheet with id=AA2, first strand: chain 'A' and resid 103 through 107 removed outlier: 6.656A pdb=" N GLY A 71 " --> pdb=" O PHE A 104 " (cutoff:3.500A) removed outlier: 7.606A pdb=" N LEU A 106 " --> pdb=" O GLY A 71 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N PHE A 73 " --> pdb=" O LEU A 106 " (cutoff:3.500A) removed outlier: 6.059A pdb=" N THR A 42 " --> pdb=" O MET A 180 " (cutoff:3.500A) removed outlier: 8.346A pdb=" N VAL A 205 " --> pdb=" O SER A 41 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N LEU A 43 " --> pdb=" O VAL A 205 " (cutoff:3.500A) removed outlier: 7.372A pdb=" N LEU A 207 " --> pdb=" O LEU A 43 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N SER A 45 " --> pdb=" O LEU A 207 " (cutoff:3.500A) removed outlier: 8.049A pdb=" N ASN A 209 " --> pdb=" O SER A 45 " (cutoff:3.500A) removed outlier: 13.427A pdb=" N ARG A 216 " --> pdb=" O ILE A 239 " (cutoff:3.500A) removed outlier: 9.923A pdb=" N ILE A 239 " --> pdb=" O ARG A 216 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N ARG A 218 " --> pdb=" O PHE A 237 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 262 through 263 Processing sheet with id=AA4, first strand: chain 'A' and resid 344 through 348 removed outlier: 6.330A pdb=" N ILE A 437 " --> pdb=" O PHE A 456 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 20 through 21 Processing sheet with id=AA6, first strand: chain 'B' and resid 103 through 107 removed outlier: 6.739A pdb=" N VAL B 142 " --> pdb=" O VAL B 179 " (cutoff:3.500A) removed outlier: 8.121A pdb=" N THR B 181 " --> pdb=" O VAL B 142 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N ILE B 144 " --> pdb=" O THR B 181 " (cutoff:3.500A) removed outlier: 8.998A pdb=" N GLU B 183 " --> pdb=" O ILE B 144 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N VAL B 204 " --> pdb=" O LEU B 223 " (cutoff:3.500A) removed outlier: 13.395A pdb=" N ARG B 216 " --> pdb=" O ILE B 239 " (cutoff:3.500A) removed outlier: 9.784A pdb=" N ILE B 239 " --> pdb=" O ARG B 216 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N ARG B 218 " --> pdb=" O PHE B 237 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 262 through 263 Processing sheet with id=AA8, first strand: chain 'B' and resid 344 through 348 removed outlier: 6.771A pdb=" N ILE B 375 " --> pdb=" O LEU B 411 " (cutoff:3.500A) removed outlier: 8.439A pdb=" N THR B 413 " --> pdb=" O ILE B 375 " (cutoff:3.500A) removed outlier: 7.109A pdb=" N ILE B 377 " --> pdb=" O THR B 413 " (cutoff:3.500A) removed outlier: 9.282A pdb=" N THR B 415 " --> pdb=" O ILE B 377 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N ILE B 437 " --> pdb=" O PHE B 456 " (cutoff:3.500A) removed outlier: 12.868A pdb=" N MET B 449 " --> pdb=" O ILE B 472 " (cutoff:3.500A) removed outlier: 9.667A pdb=" N ILE B 472 " --> pdb=" O MET B 449 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N ARG B 451 " --> pdb=" O PHE B 470 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 20 through 21 Processing sheet with id=AB1, first strand: chain 'C' and resid 103 through 107 removed outlier: 6.576A pdb=" N VAL C 204 " --> pdb=" O LEU C 223 " (cutoff:3.500A) removed outlier: 13.400A pdb=" N ARG C 216 " --> pdb=" O ILE C 239 " (cutoff:3.500A) removed outlier: 9.917A pdb=" N ILE C 239 " --> pdb=" O ARG C 216 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N ARG C 218 " --> pdb=" O PHE C 237 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 262 through 263 Processing sheet with id=AB3, first strand: chain 'C' and resid 344 through 348 removed outlier: 6.191A pdb=" N ILE C 437 " --> pdb=" O PHE C 456 " (cutoff:3.500A) removed outlier: 12.302A pdb=" N MET C 449 " --> pdb=" O ILE C 472 " (cutoff:3.500A) removed outlier: 9.000A pdb=" N ILE C 472 " --> pdb=" O MET C 449 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N ARG C 451 " --> pdb=" O PHE C 470 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 20 through 21 Processing sheet with id=AB5, first strand: chain 'D' and resid 103 through 107 removed outlier: 6.655A pdb=" N GLY D 71 " --> pdb=" O PHE D 104 " (cutoff:3.500A) removed outlier: 7.605A pdb=" N LEU D 106 " --> pdb=" O GLY D 71 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N PHE D 73 " --> pdb=" O LEU D 106 " (cutoff:3.500A) removed outlier: 6.058A pdb=" N THR D 42 " --> pdb=" O MET D 180 " (cutoff:3.500A) removed outlier: 8.346A pdb=" N VAL D 205 " --> pdb=" O SER D 41 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N LEU D 43 " --> pdb=" O VAL D 205 " (cutoff:3.500A) removed outlier: 7.372A pdb=" N LEU D 207 " --> pdb=" O LEU D 43 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N SER D 45 " --> pdb=" O LEU D 207 " (cutoff:3.500A) removed outlier: 8.049A pdb=" N ASN D 209 " --> pdb=" O SER D 45 " (cutoff:3.500A) removed outlier: 13.428A pdb=" N ARG D 216 " --> pdb=" O ILE D 239 " (cutoff:3.500A) removed outlier: 9.922A pdb=" N ILE D 239 " --> pdb=" O ARG D 216 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N ARG D 218 " --> pdb=" O PHE D 237 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 262 through 263 Processing sheet with id=AB7, first strand: chain 'D' and resid 344 through 348 removed outlier: 6.329A pdb=" N ILE D 437 " --> pdb=" O PHE D 456 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 20 through 21 Processing sheet with id=AB9, first strand: chain 'E' and resid 103 through 107 removed outlier: 6.739A pdb=" N VAL E 142 " --> pdb=" O VAL E 179 " (cutoff:3.500A) removed outlier: 8.121A pdb=" N THR E 181 " --> pdb=" O VAL E 142 " (cutoff:3.500A) removed outlier: 6.973A pdb=" N ILE E 144 " --> pdb=" O THR E 181 " (cutoff:3.500A) removed outlier: 8.998A pdb=" N GLU E 183 " --> pdb=" O ILE E 144 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N VAL E 204 " --> pdb=" O LEU E 223 " (cutoff:3.500A) removed outlier: 13.396A pdb=" N ARG E 216 " --> pdb=" O ILE E 239 " (cutoff:3.500A) removed outlier: 9.785A pdb=" N ILE E 239 " --> pdb=" O ARG E 216 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N ARG E 218 " --> pdb=" O PHE E 237 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 262 through 263 Processing sheet with id=AC2, first strand: chain 'E' and resid 344 through 348 removed outlier: 6.772A pdb=" N ILE E 375 " --> pdb=" O LEU E 411 " (cutoff:3.500A) removed outlier: 8.439A pdb=" N THR E 413 " --> pdb=" O ILE E 375 " (cutoff:3.500A) removed outlier: 7.109A pdb=" N ILE E 377 " --> pdb=" O THR E 413 " (cutoff:3.500A) removed outlier: 9.281A pdb=" N THR E 415 " --> pdb=" O ILE E 377 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N ILE E 437 " --> pdb=" O PHE E 456 " (cutoff:3.500A) removed outlier: 12.868A pdb=" N MET E 449 " --> pdb=" O ILE E 472 " (cutoff:3.500A) removed outlier: 9.667A pdb=" N ILE E 472 " --> pdb=" O MET E 449 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N ARG E 451 " --> pdb=" O PHE E 470 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 20 through 21 Processing sheet with id=AC4, first strand: chain 'F' and resid 103 through 107 removed outlier: 6.575A pdb=" N VAL F 204 " --> pdb=" O LEU F 223 " (cutoff:3.500A) removed outlier: 13.399A pdb=" N ARG F 216 " --> pdb=" O ILE F 239 " (cutoff:3.500A) removed outlier: 9.916A pdb=" N ILE F 239 " --> pdb=" O ARG F 216 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N ARG F 218 " --> pdb=" O PHE F 237 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 262 through 263 Processing sheet with id=AC6, first strand: chain 'F' and resid 344 through 348 removed outlier: 6.191A pdb=" N ILE F 437 " --> pdb=" O PHE F 456 " (cutoff:3.500A) removed outlier: 12.302A pdb=" N MET F 449 " --> pdb=" O ILE F 472 " (cutoff:3.500A) removed outlier: 9.000A pdb=" N ILE F 472 " --> pdb=" O MET F 449 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N ARG F 451 " --> pdb=" O PHE F 470 " (cutoff:3.500A) 1102 hydrogen bonds defined for protein. 3040 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: 4.10 Time building geometry restraints manager: 2.38 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 4320 1.32 - 1.45: 5522 1.45 - 1.57: 12373 1.57 - 1.70: 52 1.70 - 1.83: 158 Bond restraints: 22425 Sorted by residual: bond pdb=" C4 ATP E 602 " pdb=" C5 ATP E 602 " ideal model delta sigma weight residual 1.388 1.471 -0.083 1.00e-02 1.00e+04 6.88e+01 bond pdb=" C4 ATP C 602 " pdb=" C5 ATP C 602 " ideal model delta sigma weight residual 1.388 1.470 -0.082 1.00e-02 1.00e+04 6.77e+01 bond pdb=" C4 ATP B 602 " pdb=" C5 ATP B 602 " ideal model delta sigma weight residual 1.388 1.470 -0.082 1.00e-02 1.00e+04 6.76e+01 bond pdb=" C4 ATP B 603 " pdb=" C5 ATP B 603 " ideal model delta sigma weight residual 1.388 1.470 -0.082 1.00e-02 1.00e+04 6.75e+01 bond pdb=" C4 ATP E 603 " pdb=" C5 ATP E 603 " ideal model delta sigma weight residual 1.388 1.470 -0.082 1.00e-02 1.00e+04 6.74e+01 ... (remaining 22420 not shown) Histogram of bond angle deviations from ideal: 0.00 - 6.42: 30174 6.42 - 12.84: 113 12.84 - 19.25: 14 19.25 - 25.67: 10 25.67 - 32.09: 4 Bond angle restraints: 30315 Sorted by residual: angle pdb=" PA ATP D 603 " pdb=" O3A ATP D 603 " pdb=" PB ATP D 603 " ideal model delta sigma weight residual 136.83 104.74 32.09 1.00e+00 1.00e+00 1.03e+03 angle pdb=" PA ATP A 603 " pdb=" O3A ATP A 603 " pdb=" PB ATP A 603 " ideal model delta sigma weight residual 136.83 104.75 32.08 1.00e+00 1.00e+00 1.03e+03 angle pdb=" PB ATP A 603 " pdb=" O3B ATP A 603 " pdb=" PG ATP A 603 " ideal model delta sigma weight residual 139.87 108.19 31.68 1.00e+00 1.00e+00 1.00e+03 angle pdb=" PB ATP D 603 " pdb=" O3B ATP D 603 " pdb=" PG ATP D 603 " ideal model delta sigma weight residual 139.87 108.21 31.66 1.00e+00 1.00e+00 1.00e+03 angle pdb=" PB ATP E 603 " pdb=" O3B ATP E 603 " pdb=" PG ATP E 603 " ideal model delta sigma weight residual 139.87 119.19 20.68 1.00e+00 1.00e+00 4.28e+02 ... (remaining 30310 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.91: 13107 30.91 - 61.83: 170 61.83 - 92.74: 26 92.74 - 123.66: 4 123.66 - 154.57: 4 Dihedral angle restraints: 13311 sinusoidal: 5412 harmonic: 7899 Sorted by residual: dihedral pdb=" O2A ADP D 602 " pdb=" O3A ADP D 602 " pdb=" PA ADP D 602 " pdb=" PB ADP D 602 " ideal model delta sinusoidal sigma weight residual -60.00 94.57 -154.57 1 2.00e+01 2.50e-03 4.57e+01 dihedral pdb=" O2A ADP A 602 " pdb=" O3A ADP A 602 " pdb=" PA ADP A 602 " pdb=" PB ADP A 602 " ideal model delta sinusoidal sigma weight residual -60.00 94.56 -154.56 1 2.00e+01 2.50e-03 4.57e+01 dihedral pdb=" O1B ADP A 602 " pdb=" O3A ADP A 602 " pdb=" PB ADP A 602 " pdb=" PA ADP A 602 " ideal model delta sinusoidal sigma weight residual -60.00 86.80 -146.80 1 2.00e+01 2.50e-03 4.41e+01 ... (remaining 13308 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.071: 2495 0.071 - 0.143: 758 0.143 - 0.214: 118 0.214 - 0.286: 4 0.286 - 0.357: 10 Chirality restraints: 3385 Sorted by residual: chirality pdb=" CA GLU B 77 " pdb=" N GLU B 77 " pdb=" C GLU B 77 " pdb=" CB GLU B 77 " both_signs ideal model delta sigma weight residual False 2.51 2.15 0.36 2.00e-01 2.50e+01 3.19e+00 chirality pdb=" CA GLU E 77 " pdb=" N GLU E 77 " pdb=" C GLU E 77 " pdb=" CB GLU E 77 " both_signs ideal model delta sigma weight residual False 2.51 2.16 0.35 2.00e-01 2.50e+01 3.13e+00 chirality pdb=" CA BTYR E 402 " pdb=" N TYR E 402 " pdb=" C TYR E 402 " pdb=" CB BTYR E 402 " both_signs ideal model delta sigma weight residual False 2.51 2.17 0.34 2.00e-01 2.50e+01 2.86e+00 ... (remaining 3382 not shown) Planarity restraints: 3868 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 235 " 0.089 2.00e-02 2.50e+03 4.88e-02 4.76e+01 pdb=" CG TYR A 235 " -0.030 2.00e-02 2.50e+03 pdb=" CD1 TYR A 235 " -0.037 2.00e-02 2.50e+03 pdb=" CD2 TYR A 235 " -0.039 2.00e-02 2.50e+03 pdb=" CE1 TYR A 235 " -0.028 2.00e-02 2.50e+03 pdb=" CE2 TYR A 235 " -0.025 2.00e-02 2.50e+03 pdb=" CZ TYR A 235 " -0.007 2.00e-02 2.50e+03 pdb=" OH TYR A 235 " 0.076 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR D 235 " -0.089 2.00e-02 2.50e+03 4.85e-02 4.71e+01 pdb=" CG TYR D 235 " 0.030 2.00e-02 2.50e+03 pdb=" CD1 TYR D 235 " 0.036 2.00e-02 2.50e+03 pdb=" CD2 TYR D 235 " 0.039 2.00e-02 2.50e+03 pdb=" CE1 TYR D 235 " 0.028 2.00e-02 2.50e+03 pdb=" CE2 TYR D 235 " 0.024 2.00e-02 2.50e+03 pdb=" CZ TYR D 235 " 0.006 2.00e-02 2.50e+03 pdb=" OH TYR D 235 " -0.076 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR E 235 " -0.082 2.00e-02 2.50e+03 4.47e-02 4.00e+01 pdb=" CG TYR E 235 " 0.029 2.00e-02 2.50e+03 pdb=" CD1 TYR E 235 " 0.035 2.00e-02 2.50e+03 pdb=" CD2 TYR E 235 " 0.034 2.00e-02 2.50e+03 pdb=" CE1 TYR E 235 " 0.024 2.00e-02 2.50e+03 pdb=" CE2 TYR E 235 " 0.023 2.00e-02 2.50e+03 pdb=" CZ TYR E 235 " 0.008 2.00e-02 2.50e+03 pdb=" OH TYR E 235 " -0.070 2.00e-02 2.50e+03 ... (remaining 3865 not shown) Histogram of nonbonded interaction distances: 1.39 - 2.09: 14 2.09 - 2.79: 5831 2.79 - 3.49: 29748 3.49 - 4.20: 55902 4.20 - 4.90: 97511 Nonbonded interactions: 189006 Sorted by model distance: nonbonded pdb=" O1G ATP A 603 " pdb="MG MG A 604 " model vdw 1.385 2.170 nonbonded pdb=" O1G ATP D 603 " pdb="MG MG D 604 " model vdw 1.386 2.170 nonbonded pdb=" O GLU D 198 " pdb=" NZ LYS D 224 " model vdw 1.596 3.120 nonbonded pdb=" O GLU A 198 " pdb=" NZ LYS A 224 " model vdw 1.597 3.120 nonbonded pdb=" OG1 THR D 290 " pdb=" O3B ADP D 602 " model vdw 1.641 3.040 ... (remaining 189001 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 15 through 120 or (resid 121 and (name N or name CA or nam \ e C or name O or name CB )) or resid 122 through 401 or resid 403 through 416 or \ resid 427 through 601 or resid 603 through 604)) selection = (chain 'B' and (resid 15 through 120 or (resid 121 and (name N or name CA or nam \ e C or name O or name CB )) or resid 122 through 401 or resid 403 through 416 or \ resid 427 through 444 or resid 449 through 473 or resid 601 or resid 603 throug \ h 604)) selection = (chain 'C' and (resid 15 through 401 or resid 403 through 416 or resid 427 throu \ gh 444 or resid 449 through 473 or resid 601 or resid 603 through 604)) selection = (chain 'D' and (resid 15 through 120 or (resid 121 and (name N or name CA or nam \ e C or name O or name CB )) or resid 122 through 401 or resid 403 through 416 or \ resid 427 through 601 or resid 603 through 604)) selection = (chain 'E' and (resid 15 through 120 or (resid 121 and (name N or name CA or nam \ e C or name O or name CB )) or resid 122 through 401 or resid 403 through 416 or \ resid 427 through 444 or resid 449 through 473 or resid 601 or resid 603 throug \ h 604)) selection = (chain 'F' and (resid 15 through 401 or resid 403 through 416 or resid 427 throu \ gh 444 or resid 449 through 473 or resid 601 or resid 603 through 604)) } 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=0.25 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.460 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: 0.350 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 23.400 Find NCS groups from input model: 0.640 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: 0.010 Load rotamer database and sin/cos tables:1.460 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.510 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7430 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 : 0.016 0.773 22427 Z= 1.072 Angle : 1.457 32.091 30315 Z= 1.071 Chirality : 0.067 0.357 3385 Planarity : 0.010 0.056 3868 Dihedral : 11.661 154.571 8241 Min Nonbonded Distance : 1.385 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 0.26 % Allowed : 0.86 % Favored : 98.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.19 (0.15), residues: 2739 helix: -0.19 (0.14), residues: 1033 sheet: 1.03 (0.20), residues: 710 loop : 0.02 (0.18), residues: 996 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.002 ARG F 161 TYR 0.089 0.010 TYR A 235 PHE 0.054 0.009 PHE F 237 TRP 0.052 0.011 TRP E 92 HIS 0.007 0.003 HIS C 429 Details of bonding type rmsd/Z covalent geometry : bond 0.01421 / 0.81 (22425) covalent geometry : angle 1.45699 / 1.07 (30315) hydrogen bonds : bond 0.17776 / 11.74 ( 1102) hydrogen bonds : angle 7.14441 / 5.06 ( 3040) Misc. bond : bond 0.74976 / 37.75 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5478 Ramachandran restraints generated. 2739 Oldfield, 0 Emsley, 2739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5478 Ramachandran restraints generated. 2739 Oldfield, 0 Emsley, 2739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 628 residues out of total 2334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 622 time to evaluate : 0.839 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 85 LYS cc_start: 0.7596 (tptt) cc_final: 0.7376 (tttt) REVERT: A 458 MET cc_start: 0.7119 (tpt) cc_final: 0.6658 (tpt) REVERT: B 471 MET cc_start: 0.6373 (mpt) cc_final: 0.5995 (mpp) REVERT: C 172 LYS cc_start: 0.7640 (ttpt) cc_final: 0.7157 (tttt) REVERT: C 420 MET cc_start: 0.4519 (ttm) cc_final: 0.4304 (ttm) REVERT: D 85 LYS cc_start: 0.7780 (tptt) cc_final: 0.7512 (tttt) REVERT: D 193 ARG cc_start: 0.7453 (ttm-80) cc_final: 0.7221 (ttt180) REVERT: D 309 LYS cc_start: 0.7636 (mmtm) cc_final: 0.7414 (mppt) REVERT: D 458 MET cc_start: 0.7055 (tpt) cc_final: 0.6592 (tpt) REVERT: E 471 MET cc_start: 0.6337 (mpt) cc_final: 0.6025 (mpp) REVERT: F 172 LYS cc_start: 0.7721 (ttpt) cc_final: 0.7247 (tttt) outliers start: 6 outliers final: 1 residues processed: 628 average time/residue: 0.1972 time to fit residues: 180.7258 Evaluate side-chains 403 residues out of total 2334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 402 time to evaluate : 0.844 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 427 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 274 random chunks: chunk 197 optimal weight: 3.9990 chunk 215 optimal weight: 7.9990 chunk 20 optimal weight: 5.9990 chunk 132 optimal weight: 0.9980 chunk 261 optimal weight: 0.8980 chunk 248 optimal weight: 1.9990 chunk 207 optimal weight: 6.9990 chunk 155 optimal weight: 2.9990 chunk 244 optimal weight: 0.7980 chunk 183 optimal weight: 0.6980 chunk 111 optimal weight: 0.6980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 341 GLN A 414 ASN B 15 HIS B 86 ASN C 308 ASN ** C 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 441 GLN D 341 GLN D 414 ASN ** E 15 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 86 ASN E 245 ASN F 308 ASN ** F 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 441 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.159299 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.134914 restraints weight = 50159.563| |-----------------------------------------------------------------------------| r_work (start): 0.3469 rms_B_bonded: 2.48 r_work: 0.3291 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3291 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3378 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3378 r_free = 0.3378 target_work(ls_wunit_k1) = 0.125 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3378 r_free = 0.3378 target_work(ls_wunit_k1) = 0.125 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (5 function evaluations) r_final: 0.3378 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7646 moved from start: 0.2280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.088 22427 Z= 0.158 Angle : 0.677 14.020 30315 Z= 0.353 Chirality : 0.046 0.259 3385 Planarity : 0.004 0.056 3868 Dihedral : 8.885 146.850 3091 Min Nonbonded Distance : 1.818 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.10 % Favored : 98.90 % Rotamer: Outliers : 1.12 % Allowed : 7.96 % Favored : 90.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.88 (0.16), residues: 2739 helix: 0.95 (0.16), residues: 1039 sheet: 0.93 (0.19), residues: 722 loop : 0.08 (0.19), residues: 978 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG F 393 TYR 0.013 0.001 TYR A 132 PHE 0.034 0.002 PHE E 59 TRP 0.017 0.001 TRP E 92 HIS 0.008 0.001 HIS F 463 Details of bonding type rmsd/Z covalent geometry : bond 0.00336 / 0.16 (22425) covalent geometry : angle 0.67682 / 0.35 (30315) hydrogen bonds : bond 0.04876 / 3.20 ( 1102) hydrogen bonds : angle 5.08117 / 3.57 ( 3040) Misc. bond : bond 0.00221 / 0.11 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5478 Ramachandran restraints generated. 2739 Oldfield, 0 Emsley, 2739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5478 Ramachandran restraints generated. 2739 Oldfield, 0 Emsley, 2739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 472 residues out of total 2334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 446 time to evaluate : 0.838 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 85 LYS cc_start: 0.7532 (tptt) cc_final: 0.7057 (tttt) REVERT: A 172 LYS cc_start: 0.8172 (OUTLIER) cc_final: 0.7894 (mmtt) REVERT: A 323 GLN cc_start: 0.7272 (mm110) cc_final: 0.6787 (mm-40) REVERT: A 458 MET cc_start: 0.7106 (tpt) cc_final: 0.6698 (tpt) REVERT: B 21 MET cc_start: 0.6623 (ttm) cc_final: 0.6420 (ttp) REVERT: B 435 ASP cc_start: 0.7618 (m-30) cc_final: 0.7418 (t0) REVERT: B 471 MET cc_start: 0.6274 (mpt) cc_final: 0.5900 (mpp) REVERT: C 138 ARG cc_start: 0.7993 (mmm-85) cc_final: 0.7755 (mmm160) REVERT: C 172 LYS cc_start: 0.7900 (ttpt) cc_final: 0.7309 (ttmt) REVERT: C 329 TYR cc_start: 0.7347 (t80) cc_final: 0.7122 (t80) REVERT: C 420 MET cc_start: 0.4766 (ttm) cc_final: 0.4459 (ttm) REVERT: C 431 GLU cc_start: 0.7452 (mp0) cc_final: 0.7167 (mt-10) REVERT: C 448 GLU cc_start: 0.7126 (mt-10) cc_final: 0.6299 (pt0) REVERT: D 85 LYS cc_start: 0.7558 (tptt) cc_final: 0.7063 (tttt) REVERT: D 127 ILE cc_start: 0.7794 (mt) cc_final: 0.7582 (tp) REVERT: D 172 LYS cc_start: 0.8162 (OUTLIER) cc_final: 0.7898 (mmtt) REVERT: D 193 ARG cc_start: 0.7795 (ttm-80) cc_final: 0.7546 (ttt180) REVERT: D 257 ARG cc_start: 0.7603 (mtp-110) cc_final: 0.7332 (mtp-110) REVERT: D 309 LYS cc_start: 0.7741 (mmtm) cc_final: 0.7441 (mppt) REVERT: D 458 MET cc_start: 0.7065 (tpt) cc_final: 0.6660 (tpt) REVERT: E 217 ARG cc_start: 0.7572 (mtp180) cc_final: 0.7358 (mtp180) REVERT: F 138 ARG cc_start: 0.7916 (mmm-85) cc_final: 0.7686 (mmm160) REVERT: F 172 LYS cc_start: 0.7889 (ttpt) cc_final: 0.7328 (ttmt) REVERT: F 336 GLU cc_start: 0.8351 (tp30) cc_final: 0.8129 (tp30) outliers start: 26 outliers final: 14 residues processed: 452 average time/residue: 0.1870 time to fit residues: 124.3933 Evaluate side-chains 379 residues out of total 2334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 363 time to evaluate : 0.840 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 172 LYS Chi-restraints excluded: chain A residue 377 ILE Chi-restraints excluded: chain B residue 166 ARG Chi-restraints excluded: chain B residue 241 ASP Chi-restraints excluded: chain B residue 454 ASN Chi-restraints excluded: chain C residue 182 THR Chi-restraints excluded: chain C residue 228 THR Chi-restraints excluded: chain C residue 439 LEU Chi-restraints excluded: chain D residue 172 LYS Chi-restraints excluded: chain D residue 377 ILE Chi-restraints excluded: chain E residue 166 ARG Chi-restraints excluded: chain E residue 241 ASP Chi-restraints excluded: chain E residue 454 ASN Chi-restraints excluded: chain F residue 182 THR Chi-restraints excluded: chain F residue 228 THR Chi-restraints excluded: chain F residue 439 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 274 random chunks: chunk 272 optimal weight: 0.8980 chunk 162 optimal weight: 9.9990 chunk 207 optimal weight: 10.0000 chunk 248 optimal weight: 6.9990 chunk 246 optimal weight: 10.0000 chunk 114 optimal weight: 7.9990 chunk 53 optimal weight: 9.9990 chunk 4 optimal weight: 0.9980 chunk 166 optimal weight: 10.0000 chunk 227 optimal weight: 8.9990 chunk 83 optimal weight: 7.9990 overall best weight: 4.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 86 ASN A 203 ASN A 463 HIS B 15 HIS B 58 GLN B 173 GLN B 423 HIS D 203 ASN ** D 323 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 463 HIS E 58 GLN E 423 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.145866 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.119258 restraints weight = 69718.064| |-----------------------------------------------------------------------------| r_work (start): 0.3283 rms_B_bonded: 3.20 r_work: 0.3084 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.3084 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3123 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3123 r_free = 0.3123 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3123 r_free = 0.3123 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (5 function evaluations) r_final: 0.3123 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7798 moved from start: 0.3184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.098 22427 Z= 0.283 Angle : 0.752 10.933 30315 Z= 0.388 Chirality : 0.050 0.247 3385 Planarity : 0.005 0.048 3868 Dihedral : 9.136 155.326 3089 Min Nonbonded Distance : 1.742 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 2.03 % Allowed : 9.08 % Favored : 88.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.29 (0.15), residues: 2739 helix: 0.63 (0.16), residues: 1045 sheet: 0.58 (0.19), residues: 712 loop : -0.43 (0.18), residues: 982 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 193 TYR 0.023 0.002 TYR C 350 PHE 0.036 0.003 PHE A 301 TRP 0.017 0.003 TRP E 92 HIS 0.009 0.002 HIS A 230 Details of bonding type rmsd/Z covalent geometry : bond 0.00692 / 0.28 (22425) covalent geometry : angle 0.75222 / 0.39 (30315) hydrogen bonds : bond 0.04933 / 3.28 ( 1102) hydrogen bonds : angle 4.88837 / 3.43 ( 3040) Misc. bond : bond 0.00290 / 0.15 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5478 Ramachandran restraints generated. 2739 Oldfield, 0 Emsley, 2739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5478 Ramachandran restraints generated. 2739 Oldfield, 0 Emsley, 2739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 454 residues out of total 2334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 407 time to evaluate : 0.968 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 85 LYS cc_start: 0.7572 (tptt) cc_final: 0.6915 (mtpp) REVERT: A 96 LYS cc_start: 0.8057 (tttm) cc_final: 0.7855 (tttm) REVERT: A 310 GLU cc_start: 0.7695 (mt-10) cc_final: 0.7463 (mt-10) REVERT: A 361 GLN cc_start: 0.8133 (tm-30) cc_final: 0.7785 (tm-30) REVERT: A 419 PHE cc_start: 0.7907 (p90) cc_final: 0.7701 (p90) REVERT: A 465 LYS cc_start: 0.5627 (pttt) cc_final: 0.4980 (mmtm) REVERT: B 24 MET cc_start: 0.6515 (mtt) cc_final: 0.6186 (mtp) REVERT: B 471 MET cc_start: 0.6652 (mpt) cc_final: 0.6425 (mpp) REVERT: C 24 MET cc_start: 0.6952 (OUTLIER) cc_final: 0.6390 (mtm) REVERT: C 431 GLU cc_start: 0.7596 (mp0) cc_final: 0.7335 (mt-10) REVERT: C 448 GLU cc_start: 0.7352 (mt-10) cc_final: 0.6302 (pt0) REVERT: C 458 MET cc_start: 0.7956 (tpt) cc_final: 0.7738 (ttt) REVERT: D 85 LYS cc_start: 0.7616 (tptt) cc_final: 0.6903 (mtpt) REVERT: D 193 ARG cc_start: 0.8090 (ttm-80) cc_final: 0.7604 (ttt180) REVERT: D 257 ARG cc_start: 0.7668 (mtp-110) cc_final: 0.7341 (mtp-110) REVERT: D 310 GLU cc_start: 0.7722 (mt-10) cc_final: 0.7499 (mt-10) REVERT: D 361 GLN cc_start: 0.8280 (tm-30) cc_final: 0.7912 (tm-30) REVERT: E 217 ARG cc_start: 0.7858 (mtp180) cc_final: 0.7533 (mtp180) REVERT: E 303 GLU cc_start: 0.7987 (tp30) cc_final: 0.7785 (tp30) REVERT: E 471 MET cc_start: 0.6404 (mpp) cc_final: 0.6142 (mtm) REVERT: F 24 MET cc_start: 0.6928 (OUTLIER) cc_final: 0.6349 (mtm) REVERT: F 257 ARG cc_start: 0.7650 (tpt170) cc_final: 0.7380 (ttp-110) REVERT: F 448 GLU cc_start: 0.7245 (mt-10) cc_final: 0.6378 (pt0) REVERT: F 458 MET cc_start: 0.8047 (tpt) cc_final: 0.7793 (ttt) outliers start: 47 outliers final: 33 residues processed: 424 average time/residue: 0.1846 time to fit residues: 115.2679 Evaluate side-chains 390 residues out of total 2334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 355 time to evaluate : 0.785 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 287 THR Chi-restraints excluded: chain A residue 333 MET Chi-restraints excluded: chain A residue 377 ILE Chi-restraints excluded: chain A residue 450 SER Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 166 ARG Chi-restraints excluded: chain B residue 207 LEU Chi-restraints excluded: chain B residue 210 VAL Chi-restraints excluded: chain B residue 228 THR Chi-restraints excluded: chain B residue 241 ASP Chi-restraints excluded: chain B residue 454 ASN Chi-restraints excluded: chain C residue 24 MET Chi-restraints excluded: chain C residue 60 LEU Chi-restraints excluded: chain C residue 147 VAL Chi-restraints excluded: chain C residue 228 THR Chi-restraints excluded: chain C residue 415 THR Chi-restraints excluded: chain C residue 433 ILE Chi-restraints excluded: chain C residue 439 LEU Chi-restraints excluded: chain D residue 79 THR Chi-restraints excluded: chain D residue 223 LEU Chi-restraints excluded: chain D residue 287 THR Chi-restraints excluded: chain D residue 333 MET Chi-restraints excluded: chain D residue 377 ILE Chi-restraints excluded: chain D residue 450 SER Chi-restraints excluded: chain E residue 166 ARG Chi-restraints excluded: chain E residue 210 VAL Chi-restraints excluded: chain E residue 241 ASP Chi-restraints excluded: chain E residue 454 ASN Chi-restraints excluded: chain F residue 24 MET Chi-restraints excluded: chain F residue 147 VAL Chi-restraints excluded: chain F residue 228 THR Chi-restraints excluded: chain F residue 387 VAL Chi-restraints excluded: chain F residue 415 THR Chi-restraints excluded: chain F residue 439 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 274 random chunks: chunk 11 optimal weight: 10.0000 chunk 123 optimal weight: 4.9990 chunk 270 optimal weight: 10.0000 chunk 248 optimal weight: 6.9990 chunk 85 optimal weight: 10.0000 chunk 206 optimal weight: 8.9990 chunk 249 optimal weight: 7.9990 chunk 216 optimal weight: 3.9990 chunk 238 optimal weight: 0.2980 chunk 60 optimal weight: 0.9990 chunk 204 optimal weight: 0.8980 overall best weight: 2.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 86 ASN A 341 GLN B 86 ASN B 308 ASN ** D 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 203 ASN E 86 ASN E 308 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.148970 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.123394 restraints weight = 52274.499| |-----------------------------------------------------------------------------| r_work (start): 0.3348 rms_B_bonded: 2.62 r_work: 0.3165 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.3165 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3153 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3153 r_free = 0.3153 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3153 r_free = 0.3153 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (5 function evaluations) r_final: 0.3153 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7798 moved from start: 0.3418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 22427 Z= 0.155 Angle : 0.583 10.172 30315 Z= 0.303 Chirality : 0.045 0.235 3385 Planarity : 0.004 0.056 3868 Dihedral : 8.883 156.224 3089 Min Nonbonded Distance : 1.848 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 1.69 % Allowed : 10.42 % Favored : 87.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.48 (0.15), residues: 2739 helix: 0.96 (0.16), residues: 1037 sheet: 0.45 (0.19), residues: 726 loop : -0.33 (0.18), residues: 976 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 468 TYR 0.013 0.001 TYR C 132 PHE 0.025 0.002 PHE E 59 TRP 0.014 0.002 TRP E 92 HIS 0.004 0.001 HIS A 423 Details of bonding type rmsd/Z covalent geometry : bond 0.00365 / 0.16 (22425) covalent geometry : angle 0.58269 / 0.30 (30315) hydrogen bonds : bond 0.03884 / 2.59 ( 1102) hydrogen bonds : angle 4.48755 / 3.15 ( 3040) Misc. bond : bond 0.00122 / 0.06 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5478 Ramachandran restraints generated. 2739 Oldfield, 0 Emsley, 2739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5478 Ramachandran restraints generated. 2739 Oldfield, 0 Emsley, 2739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 430 residues out of total 2334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 391 time to evaluate : 0.849 Fit side-chains revert: symmetry clash REVERT: A 85 LYS cc_start: 0.7733 (tptt) cc_final: 0.7193 (mtpp) REVERT: A 310 GLU cc_start: 0.7739 (mt-10) cc_final: 0.7464 (mt-10) REVERT: A 366 GLU cc_start: 0.7377 (mm-30) cc_final: 0.7155 (tp30) REVERT: B 24 MET cc_start: 0.6137 (mtt) cc_final: 0.5819 (mtp) REVERT: C 338 MET cc_start: 0.8618 (mtm) cc_final: 0.8236 (mtt) REVERT: C 448 GLU cc_start: 0.7255 (mt-10) cc_final: 0.6315 (pt0) REVERT: D 85 LYS cc_start: 0.7713 (tptt) cc_final: 0.7166 (mtpp) REVERT: D 127 ILE cc_start: 0.7967 (mt) cc_final: 0.7508 (tp) REVERT: D 193 ARG cc_start: 0.7953 (ttm-80) cc_final: 0.7567 (ttt180) REVERT: D 257 ARG cc_start: 0.7663 (mtp-110) cc_final: 0.7429 (mtp-110) REVERT: D 310 GLU cc_start: 0.7803 (mt-10) cc_final: 0.7554 (mt-10) REVERT: D 361 GLN cc_start: 0.8346 (tm-30) cc_final: 0.7979 (tm-30) REVERT: D 366 GLU cc_start: 0.7357 (mm-30) cc_final: 0.7122 (tp30) REVERT: E 217 ARG cc_start: 0.7791 (mtp180) cc_final: 0.7497 (mtp180) REVERT: E 303 GLU cc_start: 0.8099 (tp30) cc_final: 0.7892 (tp30) REVERT: E 471 MET cc_start: 0.6700 (mpp) cc_final: 0.6044 (mtm) REVERT: F 24 MET cc_start: 0.6710 (OUTLIER) cc_final: 0.6117 (mtm) REVERT: F 26 GLU cc_start: 0.7209 (mp0) cc_final: 0.6893 (mp0) REVERT: F 172 LYS cc_start: 0.7880 (ttmt) cc_final: 0.7276 (ttmt) REVERT: F 431 GLU cc_start: 0.7530 (mp0) cc_final: 0.7208 (mt-10) REVERT: F 433 ILE cc_start: 0.8609 (OUTLIER) cc_final: 0.8181 (pt) REVERT: F 448 GLU cc_start: 0.7153 (mt-10) cc_final: 0.6225 (pt0) outliers start: 39 outliers final: 27 residues processed: 406 average time/residue: 0.1936 time to fit residues: 116.0053 Evaluate side-chains 389 residues out of total 2334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 360 time to evaluate : 0.948 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 201 SER Chi-restraints excluded: chain A residue 333 MET Chi-restraints excluded: chain A residue 379 SER Chi-restraints excluded: chain A residue 427 ASP Chi-restraints excluded: chain B residue 79 THR Chi-restraints excluded: chain B residue 183 GLU Chi-restraints excluded: chain B residue 241 ASP Chi-restraints excluded: chain B residue 454 ASN Chi-restraints excluded: chain C residue 147 VAL Chi-restraints excluded: chain C residue 182 THR Chi-restraints excluded: chain C residue 228 THR Chi-restraints excluded: chain C residue 387 VAL Chi-restraints excluded: chain C residue 439 LEU Chi-restraints excluded: chain D residue 333 MET Chi-restraints excluded: chain D residue 365 SER Chi-restraints excluded: chain D residue 377 ILE Chi-restraints excluded: chain D residue 379 SER Chi-restraints excluded: chain D residue 427 ASP Chi-restraints excluded: chain D residue 450 SER Chi-restraints excluded: chain E residue 50 THR Chi-restraints excluded: chain E residue 241 ASP Chi-restraints excluded: chain E residue 454 ASN Chi-restraints excluded: chain E residue 467 ILE Chi-restraints excluded: chain F residue 24 MET Chi-restraints excluded: chain F residue 147 VAL Chi-restraints excluded: chain F residue 182 THR Chi-restraints excluded: chain F residue 228 THR Chi-restraints excluded: chain F residue 433 ILE Chi-restraints excluded: chain F residue 439 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 274 random chunks: chunk 183 optimal weight: 5.9990 chunk 169 optimal weight: 4.9990 chunk 216 optimal weight: 8.9990 chunk 108 optimal weight: 8.9990 chunk 251 optimal weight: 6.9990 chunk 92 optimal weight: 5.9990 chunk 14 optimal weight: 0.0970 chunk 149 optimal weight: 6.9990 chunk 121 optimal weight: 9.9990 chunk 145 optimal weight: 5.9990 chunk 223 optimal weight: 1.9990 overall best weight: 3.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 341 GLN B 86 ASN E 58 GLN E 86 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.146338 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.121745 restraints weight = 53475.688| |-----------------------------------------------------------------------------| r_work (start): 0.3315 rms_B_bonded: 2.49 r_work: 0.3142 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3142 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3129 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3129 r_free = 0.3129 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3129 r_free = 0.3129 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3129 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7830 moved from start: 0.3650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.076 22427 Z= 0.222 Angle : 0.639 12.181 30315 Z= 0.331 Chirality : 0.046 0.234 3385 Planarity : 0.004 0.048 3868 Dihedral : 8.971 163.794 3089 Min Nonbonded Distance : 1.765 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 2.08 % Allowed : 10.85 % Favored : 87.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.24 (0.15), residues: 2739 helix: 0.85 (0.16), residues: 1037 sheet: 0.40 (0.19), residues: 712 loop : -0.63 (0.17), residues: 990 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG E 184 TYR 0.015 0.002 TYR F 442 PHE 0.031 0.003 PHE E 59 TRP 0.013 0.002 TRP E 92 HIS 0.005 0.001 HIS D 230 Details of bonding type rmsd/Z covalent geometry : bond 0.00540 / 0.22 (22425) covalent geometry : angle 0.63915 / 0.33 (30315) hydrogen bonds : bond 0.04175 / 2.79 ( 1102) hydrogen bonds : angle 4.52777 / 3.17 ( 3040) Misc. bond : bond 0.00200 / 0.10 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5478 Ramachandran restraints generated. 2739 Oldfield, 0 Emsley, 2739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5478 Ramachandran restraints generated. 2739 Oldfield, 0 Emsley, 2739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 427 residues out of total 2334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 379 time to evaluate : 0.856 Fit side-chains revert: symmetry clash REVERT: A 85 LYS cc_start: 0.7644 (tptt) cc_final: 0.7086 (mtpp) REVERT: A 310 GLU cc_start: 0.7744 (mt-10) cc_final: 0.7503 (mt-10) REVERT: A 366 GLU cc_start: 0.7270 (mm-30) cc_final: 0.7047 (tp30) REVERT: A 420 MET cc_start: 0.6274 (mmt) cc_final: 0.5874 (mmt) REVERT: A 458 MET cc_start: 0.6856 (tpt) cc_final: 0.6586 (tpt) REVERT: A 465 LYS cc_start: 0.5777 (pttt) cc_final: 0.5186 (mmtm) REVERT: B 24 MET cc_start: 0.6608 (mtt) cc_final: 0.6337 (mtp) REVERT: B 163 GLU cc_start: 0.7387 (mm-30) cc_final: 0.7187 (mm-30) REVERT: B 430 ILE cc_start: 0.7081 (mt) cc_final: 0.6815 (mm) REVERT: B 471 MET cc_start: 0.6666 (mpp) cc_final: 0.6045 (mtm) REVERT: C 24 MET cc_start: 0.6731 (OUTLIER) cc_final: 0.6061 (mtm) REVERT: C 26 GLU cc_start: 0.7177 (mp0) cc_final: 0.6921 (mp0) REVERT: C 448 GLU cc_start: 0.7303 (mt-10) cc_final: 0.6432 (pt0) REVERT: D 85 LYS cc_start: 0.7577 (tptt) cc_final: 0.7112 (mtpp) REVERT: D 127 ILE cc_start: 0.8074 (mt) cc_final: 0.7581 (tp) REVERT: D 193 ARG cc_start: 0.7961 (ttm-80) cc_final: 0.7601 (ttt180) REVERT: D 257 ARG cc_start: 0.7619 (mtp-110) cc_final: 0.7382 (mtp-110) REVERT: D 310 GLU cc_start: 0.7742 (mt-10) cc_final: 0.7480 (mt-10) REVERT: D 366 GLU cc_start: 0.7256 (mm-30) cc_final: 0.7015 (tp30) REVERT: D 420 MET cc_start: 0.6174 (mmt) cc_final: 0.5778 (mmt) REVERT: D 458 MET cc_start: 0.6901 (tpt) cc_final: 0.6626 (tpt) REVERT: D 465 LYS cc_start: 0.5768 (pttt) cc_final: 0.5225 (mmtm) REVERT: E 471 MET cc_start: 0.6604 (mpp) cc_final: 0.6008 (mtm) REVERT: F 24 MET cc_start: 0.6799 (OUTLIER) cc_final: 0.6165 (mtm) REVERT: F 26 GLU cc_start: 0.7226 (mp0) cc_final: 0.6933 (mp0) REVERT: F 431 GLU cc_start: 0.7425 (mp0) cc_final: 0.7201 (mt-10) REVERT: F 448 GLU cc_start: 0.7164 (mt-10) cc_final: 0.6249 (pt0) outliers start: 48 outliers final: 40 residues processed: 400 average time/residue: 0.1931 time to fit residues: 113.4631 Evaluate side-chains 408 residues out of total 2334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 366 time to evaluate : 0.871 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 THR Chi-restraints excluded: chain A residue 201 SER Chi-restraints excluded: chain A residue 257 ARG Chi-restraints excluded: chain A residue 333 MET Chi-restraints excluded: chain A residue 377 ILE Chi-restraints excluded: chain A residue 379 SER Chi-restraints excluded: chain A residue 427 ASP Chi-restraints excluded: chain A residue 450 SER Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 79 THR Chi-restraints excluded: chain B residue 207 LEU Chi-restraints excluded: chain B residue 228 THR Chi-restraints excluded: chain B residue 241 ASP Chi-restraints excluded: chain B residue 333 MET Chi-restraints excluded: chain B residue 454 ASN Chi-restraints excluded: chain C residue 24 MET Chi-restraints excluded: chain C residue 147 VAL Chi-restraints excluded: chain C residue 228 THR Chi-restraints excluded: chain C residue 292 THR Chi-restraints excluded: chain C residue 415 THR Chi-restraints excluded: chain C residue 439 LEU Chi-restraints excluded: chain D residue 186 GLU Chi-restraints excluded: chain D residue 333 MET Chi-restraints excluded: chain D residue 365 SER Chi-restraints excluded: chain D residue 377 ILE Chi-restraints excluded: chain D residue 379 SER Chi-restraints excluded: chain D residue 427 ASP Chi-restraints excluded: chain D residue 471 MET Chi-restraints excluded: chain E residue 50 THR Chi-restraints excluded: chain E residue 79 THR Chi-restraints excluded: chain E residue 210 VAL Chi-restraints excluded: chain E residue 228 THR Chi-restraints excluded: chain E residue 241 ASP Chi-restraints excluded: chain E residue 454 ASN Chi-restraints excluded: chain E residue 467 ILE Chi-restraints excluded: chain F residue 24 MET Chi-restraints excluded: chain F residue 147 VAL Chi-restraints excluded: chain F residue 182 THR Chi-restraints excluded: chain F residue 228 THR Chi-restraints excluded: chain F residue 292 THR Chi-restraints excluded: chain F residue 415 THR Chi-restraints excluded: chain F residue 439 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 274 random chunks: chunk 68 optimal weight: 3.9990 chunk 199 optimal weight: 0.0040 chunk 228 optimal weight: 8.9990 chunk 132 optimal weight: 0.7980 chunk 232 optimal weight: 0.7980 chunk 127 optimal weight: 1.9990 chunk 179 optimal weight: 3.9990 chunk 77 optimal weight: 9.9990 chunk 185 optimal weight: 0.9990 chunk 251 optimal weight: 0.9990 chunk 175 optimal weight: 0.9990 overall best weight: 0.7196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 86 ASN ** B 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 203 ASN D 256 GLN ** E 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 359 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.150077 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.124107 restraints weight = 55149.949| |-----------------------------------------------------------------------------| r_work (start): 0.3365 rms_B_bonded: 2.80 r_work: 0.3183 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.3183 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3164 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3164 r_free = 0.3164 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3164 r_free = 0.3164 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3164 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7739 moved from start: 0.3813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 22427 Z= 0.108 Angle : 0.525 8.348 30315 Z= 0.274 Chirality : 0.043 0.203 3385 Planarity : 0.003 0.058 3868 Dihedral : 8.653 165.363 3089 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 1.12 % Allowed : 12.54 % Favored : 86.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.59 (0.16), residues: 2739 helix: 1.16 (0.16), residues: 1049 sheet: 0.43 (0.19), residues: 720 loop : -0.35 (0.18), residues: 970 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 22 TYR 0.011 0.001 TYR B 235 PHE 0.019 0.001 PHE C 59 TRP 0.013 0.001 TRP E 92 HIS 0.003 0.001 HIS B 463 Details of bonding type rmsd/Z covalent geometry : bond 0.00232 / 0.11 (22425) covalent geometry : angle 0.52539 / 0.27 (30315) hydrogen bonds : bond 0.03331 / 2.22 ( 1102) hydrogen bonds : angle 4.20006 / 2.95 ( 3040) Misc. bond : bond 0.00061 / 0.03 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5478 Ramachandran restraints generated. 2739 Oldfield, 0 Emsley, 2739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5478 Ramachandran restraints generated. 2739 Oldfield, 0 Emsley, 2739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 429 residues out of total 2334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 403 time to evaluate : 0.753 Fit side-chains REVERT: A 85 LYS cc_start: 0.7458 (tptt) cc_final: 0.7000 (mtpt) REVERT: A 86 ASN cc_start: 0.8095 (m110) cc_final: 0.7673 (m-40) REVERT: A 180 MET cc_start: 0.8086 (mtp) cc_final: 0.7881 (mtp) REVERT: A 310 GLU cc_start: 0.7744 (mt-10) cc_final: 0.7530 (mt-10) REVERT: A 420 MET cc_start: 0.6167 (mmt) cc_final: 0.5937 (mmt) REVERT: A 458 MET cc_start: 0.6733 (tpt) cc_final: 0.6452 (tpt) REVERT: B 471 MET cc_start: 0.6764 (mpp) cc_final: 0.6149 (mtm) REVERT: C 16 GLN cc_start: 0.6124 (tm-30) cc_final: 0.5626 (tm-30) REVERT: C 24 MET cc_start: 0.6757 (OUTLIER) cc_final: 0.6206 (mtm) REVERT: C 338 MET cc_start: 0.8571 (mtm) cc_final: 0.8166 (mtt) REVERT: C 448 GLU cc_start: 0.7196 (mt-10) cc_final: 0.6286 (pt0) REVERT: D 85 LYS cc_start: 0.7437 (tptt) cc_final: 0.6942 (mtpt) REVERT: D 86 ASN cc_start: 0.8117 (m110) cc_final: 0.7718 (m-40) REVERT: D 127 ILE cc_start: 0.7973 (mt) cc_final: 0.7544 (tp) REVERT: D 193 ARG cc_start: 0.7918 (ttm-80) cc_final: 0.7565 (ttt180) REVERT: D 256 GLN cc_start: 0.8448 (mp10) cc_final: 0.7835 (mm-40) REVERT: D 366 GLU cc_start: 0.7352 (mm-30) cc_final: 0.7125 (tp30) REVERT: D 420 MET cc_start: 0.5889 (mmt) cc_final: 0.5555 (mmt) REVERT: D 425 ILE cc_start: 0.7732 (mt) cc_final: 0.7527 (mm) REVERT: E 446 ARG cc_start: 0.5850 (ttm110) cc_final: 0.5632 (mtt180) REVERT: E 471 MET cc_start: 0.6527 (mpp) cc_final: 0.6011 (mtm) REVERT: F 16 GLN cc_start: 0.6028 (tm-30) cc_final: 0.5551 (tm-30) REVERT: F 24 MET cc_start: 0.6644 (OUTLIER) cc_final: 0.6071 (mtm) REVERT: F 172 LYS cc_start: 0.7948 (ttmt) cc_final: 0.7299 (ttmt) REVERT: F 433 ILE cc_start: 0.8601 (OUTLIER) cc_final: 0.8174 (pt) REVERT: F 448 GLU cc_start: 0.7134 (mt-10) cc_final: 0.6409 (pt0) outliers start: 26 outliers final: 18 residues processed: 416 average time/residue: 0.1841 time to fit residues: 112.1730 Evaluate side-chains 393 residues out of total 2334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 372 time to evaluate : 0.875 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 333 MET Chi-restraints excluded: chain A residue 379 SER Chi-restraints excluded: chain B residue 79 THR Chi-restraints excluded: chain B residue 207 LEU Chi-restraints excluded: chain B residue 241 ASP Chi-restraints excluded: chain B residue 454 ASN Chi-restraints excluded: chain C residue 24 MET Chi-restraints excluded: chain C residue 60 LEU Chi-restraints excluded: chain C residue 182 THR Chi-restraints excluded: chain C residue 439 LEU Chi-restraints excluded: chain D residue 79 THR Chi-restraints excluded: chain D residue 333 MET Chi-restraints excluded: chain D residue 365 SER Chi-restraints excluded: chain D residue 379 SER Chi-restraints excluded: chain D residue 450 SER Chi-restraints excluded: chain E residue 36 LEU Chi-restraints excluded: chain E residue 241 ASP Chi-restraints excluded: chain E residue 454 ASN Chi-restraints excluded: chain F residue 24 MET Chi-restraints excluded: chain F residue 433 ILE Chi-restraints excluded: chain F residue 439 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 274 random chunks: chunk 173 optimal weight: 10.0000 chunk 250 optimal weight: 4.9990 chunk 23 optimal weight: 6.9990 chunk 47 optimal weight: 10.0000 chunk 196 optimal weight: 0.7980 chunk 114 optimal weight: 4.9990 chunk 164 optimal weight: 5.9990 chunk 87 optimal weight: 8.9990 chunk 76 optimal weight: 5.9990 chunk 205 optimal weight: 1.9990 chunk 256 optimal weight: 0.8980 overall best weight: 2.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 203 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.147278 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.124223 restraints weight = 42801.443| |-----------------------------------------------------------------------------| r_work (start): 0.3369 rms_B_bonded: 2.11 r_work: 0.3196 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3196 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3163 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3163 r_free = 0.3163 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3163 r_free = 0.3163 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3163 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7812 moved from start: 0.3906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 22427 Z= 0.174 Angle : 0.585 10.129 30315 Z= 0.303 Chirality : 0.044 0.206 3385 Planarity : 0.004 0.052 3868 Dihedral : 8.726 173.220 3089 Min Nonbonded Distance : 1.813 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 1.38 % Allowed : 13.27 % Favored : 85.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.46 (0.16), residues: 2739 helix: 1.07 (0.16), residues: 1051 sheet: 0.35 (0.19), residues: 722 loop : -0.44 (0.18), residues: 966 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG D 326 TYR 0.016 0.002 TYR C 442 PHE 0.025 0.002 PHE A 301 TRP 0.009 0.002 TRP E 92 HIS 0.004 0.001 HIS D 423 Details of bonding type rmsd/Z covalent geometry : bond 0.00421 / 0.17 (22425) covalent geometry : angle 0.58500 / 0.30 (30315) hydrogen bonds : bond 0.03712 / 2.48 ( 1102) hydrogen bonds : angle 4.27070 / 3.00 ( 3040) Misc. bond : bond 0.00138 / 0.07 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5478 Ramachandran restraints generated. 2739 Oldfield, 0 Emsley, 2739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5478 Ramachandran restraints generated. 2739 Oldfield, 0 Emsley, 2739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 422 residues out of total 2334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 390 time to evaluate : 0.874 Fit side-chains REVERT: A 85 LYS cc_start: 0.7530 (tptt) cc_final: 0.7130 (mtpt) REVERT: A 86 ASN cc_start: 0.8079 (m110) cc_final: 0.7733 (m-40) REVERT: A 458 MET cc_start: 0.6755 (tpt) cc_final: 0.6432 (tpt) REVERT: B 430 ILE cc_start: 0.7045 (mt) cc_final: 0.6796 (mm) REVERT: B 471 MET cc_start: 0.6688 (mpp) cc_final: 0.6078 (mtm) REVERT: C 16 GLN cc_start: 0.6319 (tm-30) cc_final: 0.5849 (tm-30) REVERT: C 24 MET cc_start: 0.6870 (OUTLIER) cc_final: 0.6193 (mtm) REVERT: C 26 GLU cc_start: 0.7064 (mp0) cc_final: 0.6783 (mp0) REVERT: C 338 MET cc_start: 0.8586 (mtm) cc_final: 0.8192 (mtt) REVERT: C 448 GLU cc_start: 0.7216 (mt-10) cc_final: 0.6386 (pt0) REVERT: D 85 LYS cc_start: 0.7481 (tptt) cc_final: 0.7075 (mtpt) REVERT: D 127 ILE cc_start: 0.8085 (mt) cc_final: 0.7595 (tp) REVERT: D 193 ARG cc_start: 0.7877 (ttm-80) cc_final: 0.7492 (ttt180) REVERT: D 366 GLU cc_start: 0.7283 (mm-30) cc_final: 0.7079 (tp30) REVERT: D 458 MET cc_start: 0.6783 (tpt) cc_final: 0.6465 (tpt) REVERT: E 368 ASN cc_start: 0.8231 (m-40) cc_final: 0.7924 (m-40) REVERT: E 471 MET cc_start: 0.6684 (mpp) cc_final: 0.5913 (mtm) REVERT: F 16 GLN cc_start: 0.6173 (tm-30) cc_final: 0.5724 (tm-30) REVERT: F 172 LYS cc_start: 0.7925 (ttmt) cc_final: 0.7311 (ttmt) REVERT: F 448 GLU cc_start: 0.7219 (mt-10) cc_final: 0.6485 (pt0) outliers start: 32 outliers final: 29 residues processed: 406 average time/residue: 0.1757 time to fit residues: 105.6147 Evaluate side-chains 403 residues out of total 2334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 373 time to evaluate : 0.742 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 201 SER Chi-restraints excluded: chain A residue 333 MET Chi-restraints excluded: chain A residue 377 ILE Chi-restraints excluded: chain A residue 379 SER Chi-restraints excluded: chain A residue 427 ASP Chi-restraints excluded: chain A residue 450 SER Chi-restraints excluded: chain B residue 79 THR Chi-restraints excluded: chain B residue 207 LEU Chi-restraints excluded: chain B residue 241 ASP Chi-restraints excluded: chain B residue 454 ASN Chi-restraints excluded: chain C residue 24 MET Chi-restraints excluded: chain C residue 147 VAL Chi-restraints excluded: chain C residue 182 THR Chi-restraints excluded: chain C residue 292 THR Chi-restraints excluded: chain C residue 433 ILE Chi-restraints excluded: chain C residue 439 LEU Chi-restraints excluded: chain D residue 79 THR Chi-restraints excluded: chain D residue 333 MET Chi-restraints excluded: chain D residue 365 SER Chi-restraints excluded: chain D residue 379 SER Chi-restraints excluded: chain D residue 427 ASP Chi-restraints excluded: chain D residue 450 SER Chi-restraints excluded: chain D residue 471 MET Chi-restraints excluded: chain E residue 79 THR Chi-restraints excluded: chain E residue 241 ASP Chi-restraints excluded: chain E residue 454 ASN Chi-restraints excluded: chain F residue 147 VAL Chi-restraints excluded: chain F residue 182 THR Chi-restraints excluded: chain F residue 433 ILE Chi-restraints excluded: chain F residue 439 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 274 random chunks: chunk 31 optimal weight: 9.9990 chunk 259 optimal weight: 9.9990 chunk 95 optimal weight: 0.9980 chunk 90 optimal weight: 1.9990 chunk 48 optimal weight: 5.9990 chunk 227 optimal weight: 1.9990 chunk 130 optimal weight: 3.9990 chunk 209 optimal weight: 0.8980 chunk 212 optimal weight: 7.9990 chunk 43 optimal weight: 9.9990 chunk 193 optimal weight: 6.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 203 ASN D 256 GLN E 173 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.148339 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.122106 restraints weight = 66854.441| |-----------------------------------------------------------------------------| r_work (start): 0.3341 rms_B_bonded: 3.06 r_work: 0.3142 rms_B_bonded: 4.17 restraints_weight: 0.5000 r_work (final): 0.3142 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3112 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3112 r_free = 0.3112 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3112 r_free = 0.3112 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3112 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7826 moved from start: 0.3999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 22427 Z= 0.139 Angle : 0.556 8.866 30315 Z= 0.288 Chirality : 0.043 0.203 3385 Planarity : 0.004 0.060 3868 Dihedral : 8.699 177.826 3089 Min Nonbonded Distance : 1.850 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 1.73 % Allowed : 13.36 % Favored : 84.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.51 (0.16), residues: 2739 helix: 1.17 (0.16), residues: 1051 sheet: 0.33 (0.19), residues: 718 loop : -0.45 (0.18), residues: 970 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 446 TYR 0.010 0.001 TYR B 235 PHE 0.022 0.002 PHE E 301 TRP 0.010 0.001 TRP E 92 HIS 0.004 0.001 HIS A 423 Details of bonding type rmsd/Z covalent geometry : bond 0.00328 / 0.14 (22425) covalent geometry : angle 0.55620 / 0.29 (30315) hydrogen bonds : bond 0.03481 / 2.32 ( 1102) hydrogen bonds : angle 4.18171 / 2.94 ( 3040) Misc. bond : bond 0.00096 / 0.05 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5478 Ramachandran restraints generated. 2739 Oldfield, 0 Emsley, 2739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5478 Ramachandran restraints generated. 2739 Oldfield, 0 Emsley, 2739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 421 residues out of total 2334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 381 time to evaluate : 0.785 Fit side-chains REVERT: A 85 LYS cc_start: 0.7443 (tptt) cc_final: 0.7006 (mtpt) REVERT: A 309 LYS cc_start: 0.7812 (mppt) cc_final: 0.7314 (mmtt) REVERT: A 358 ASP cc_start: 0.8322 (t0) cc_final: 0.7966 (t0) REVERT: A 394 GLN cc_start: 0.7729 (mt0) cc_final: 0.7524 (mt0) REVERT: A 420 MET cc_start: 0.6096 (mmt) cc_final: 0.5808 (mmt) REVERT: A 458 MET cc_start: 0.6760 (tpt) cc_final: 0.6422 (tpt) REVERT: B 111 ASP cc_start: 0.5638 (t0) cc_final: 0.5286 (t0) REVERT: B 185 ILE cc_start: 0.8972 (mm) cc_final: 0.8490 (mt) REVERT: B 430 ILE cc_start: 0.7057 (mt) cc_final: 0.6809 (mm) REVERT: B 471 MET cc_start: 0.6654 (mpp) cc_final: 0.6125 (mtm) REVERT: C 16 GLN cc_start: 0.6147 (tm-30) cc_final: 0.5622 (tm-30) REVERT: C 24 MET cc_start: 0.6814 (OUTLIER) cc_final: 0.6254 (mtm) REVERT: C 338 MET cc_start: 0.8640 (mtm) cc_final: 0.8226 (mtt) REVERT: C 448 GLU cc_start: 0.7368 (mt-10) cc_final: 0.6398 (pt0) REVERT: D 85 LYS cc_start: 0.7434 (tptt) cc_final: 0.7003 (mtpt) REVERT: D 86 ASN cc_start: 0.8028 (m110) cc_final: 0.7635 (m-40) REVERT: D 127 ILE cc_start: 0.8016 (mt) cc_final: 0.7554 (tp) REVERT: D 193 ARG cc_start: 0.7912 (ttm-80) cc_final: 0.7520 (ttt180) REVERT: D 256 GLN cc_start: 0.8225 (mp10) cc_final: 0.7772 (mm-40) REVERT: D 309 LYS cc_start: 0.7889 (mmtp) cc_final: 0.7652 (mmtt) REVERT: D 358 ASP cc_start: 0.8329 (t0) cc_final: 0.8013 (t0) REVERT: D 366 GLU cc_start: 0.7515 (mm-30) cc_final: 0.7276 (tp30) REVERT: D 458 MET cc_start: 0.6763 (tpt) cc_final: 0.6434 (tpt) REVERT: E 129 ARG cc_start: 0.7720 (mtp85) cc_final: 0.7216 (mtm110) REVERT: E 368 ASN cc_start: 0.8240 (m-40) cc_final: 0.7888 (m-40) REVERT: E 471 MET cc_start: 0.6708 (mpp) cc_final: 0.5952 (mtm) REVERT: F 16 GLN cc_start: 0.6165 (tm-30) cc_final: 0.5670 (tm-30) REVERT: F 172 LYS cc_start: 0.7910 (ttmt) cc_final: 0.7317 (ttmt) outliers start: 40 outliers final: 34 residues processed: 402 average time/residue: 0.1791 time to fit residues: 106.5533 Evaluate side-chains 403 residues out of total 2334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 368 time to evaluate : 0.770 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 201 SER Chi-restraints excluded: chain A residue 333 MET Chi-restraints excluded: chain A residue 379 SER Chi-restraints excluded: chain A residue 427 ASP Chi-restraints excluded: chain A residue 450 SER Chi-restraints excluded: chain A residue 461 SER Chi-restraints excluded: chain B residue 79 THR Chi-restraints excluded: chain B residue 241 ASP Chi-restraints excluded: chain B residue 454 ASN Chi-restraints excluded: chain C residue 24 MET Chi-restraints excluded: chain C residue 60 LEU Chi-restraints excluded: chain C residue 147 VAL Chi-restraints excluded: chain C residue 182 THR Chi-restraints excluded: chain C residue 228 THR Chi-restraints excluded: chain C residue 292 THR Chi-restraints excluded: chain C residue 439 LEU Chi-restraints excluded: chain D residue 79 THR Chi-restraints excluded: chain D residue 186 GLU Chi-restraints excluded: chain D residue 287 THR Chi-restraints excluded: chain D residue 333 MET Chi-restraints excluded: chain D residue 365 SER Chi-restraints excluded: chain D residue 379 SER Chi-restraints excluded: chain D residue 427 ASP Chi-restraints excluded: chain D residue 450 SER Chi-restraints excluded: chain D residue 461 SER Chi-restraints excluded: chain E residue 36 LEU Chi-restraints excluded: chain E residue 79 THR Chi-restraints excluded: chain E residue 241 ASP Chi-restraints excluded: chain E residue 454 ASN Chi-restraints excluded: chain F residue 24 MET Chi-restraints excluded: chain F residue 147 VAL Chi-restraints excluded: chain F residue 228 THR Chi-restraints excluded: chain F residue 292 THR Chi-restraints excluded: chain F residue 433 ILE Chi-restraints excluded: chain F residue 439 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 274 random chunks: chunk 14 optimal weight: 8.9990 chunk 161 optimal weight: 5.9990 chunk 62 optimal weight: 1.9990 chunk 247 optimal weight: 0.9980 chunk 142 optimal weight: 0.5980 chunk 50 optimal weight: 2.9990 chunk 132 optimal weight: 3.9990 chunk 101 optimal weight: 40.0000 chunk 268 optimal weight: 10.0000 chunk 28 optimal weight: 0.9990 chunk 150 optimal weight: 1.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 423 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 423 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 359 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.149171 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.122673 restraints weight = 61076.050| |-----------------------------------------------------------------------------| r_work (start): 0.3334 rms_B_bonded: 3.01 r_work: 0.3151 rms_B_bonded: 3.91 restraints_weight: 0.5000 r_work (final): 0.3151 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3154 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3154 r_free = 0.3154 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3154 r_free = 0.3154 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3154 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7741 moved from start: 0.4082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 22427 Z= 0.118 Angle : 0.533 7.677 30315 Z= 0.276 Chirality : 0.043 0.190 3385 Planarity : 0.003 0.058 3868 Dihedral : 8.579 179.576 3089 Min Nonbonded Distance : 1.885 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 1.51 % Allowed : 13.79 % Favored : 84.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.60 (0.16), residues: 2739 helix: 1.29 (0.16), residues: 1057 sheet: 0.35 (0.19), residues: 718 loop : -0.45 (0.18), residues: 964 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 326 TYR 0.012 0.001 TYR A 132 PHE 0.020 0.002 PHE E 301 TRP 0.010 0.001 TRP B 462 HIS 0.003 0.001 HIS A 423 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.12 (22425) covalent geometry : angle 0.53297 / 0.28 (30315) hydrogen bonds : bond 0.03268 / 2.18 ( 1102) hydrogen bonds : angle 4.09317 / 2.88 ( 3040) Misc. bond : bond 0.00069 / 0.03 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5478 Ramachandran restraints generated. 2739 Oldfield, 0 Emsley, 2739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5478 Ramachandran restraints generated. 2739 Oldfield, 0 Emsley, 2739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 427 residues out of total 2334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 392 time to evaluate : 0.840 Fit side-chains REVERT: A 85 LYS cc_start: 0.7177 (tptt) cc_final: 0.6789 (mtpt) REVERT: A 86 ASN cc_start: 0.8192 (m110) cc_final: 0.7697 (m-40) REVERT: A 309 LYS cc_start: 0.7786 (mppt) cc_final: 0.7223 (mmtt) REVERT: A 358 ASP cc_start: 0.8300 (t0) cc_final: 0.7968 (t0) REVERT: A 420 MET cc_start: 0.5903 (mmt) cc_final: 0.5499 (mmt) REVERT: A 425 ILE cc_start: 0.7747 (mt) cc_final: 0.7504 (mm) REVERT: A 458 MET cc_start: 0.6667 (tpt) cc_final: 0.6285 (tpt) REVERT: B 111 ASP cc_start: 0.5892 (t0) cc_final: 0.5538 (t0) REVERT: B 430 ILE cc_start: 0.6896 (mt) cc_final: 0.6661 (mm) REVERT: B 471 MET cc_start: 0.6623 (mpp) cc_final: 0.6124 (mtm) REVERT: C 16 GLN cc_start: 0.6038 (tm-30) cc_final: 0.5484 (tm-30) REVERT: C 24 MET cc_start: 0.6803 (OUTLIER) cc_final: 0.6212 (mtm) REVERT: C 338 MET cc_start: 0.8680 (mtm) cc_final: 0.8239 (mtt) REVERT: D 85 LYS cc_start: 0.7228 (tptt) cc_final: 0.6785 (mtpt) REVERT: D 86 ASN cc_start: 0.8071 (m110) cc_final: 0.7665 (m-40) REVERT: D 127 ILE cc_start: 0.7925 (mt) cc_final: 0.7649 (tp) REVERT: D 193 ARG cc_start: 0.7942 (ttm-80) cc_final: 0.7488 (ttt180) REVERT: D 256 GLN cc_start: 0.8138 (mp10) cc_final: 0.7667 (mm-40) REVERT: D 309 LYS cc_start: 0.7743 (mmtp) cc_final: 0.7490 (mmtt) REVERT: D 358 ASP cc_start: 0.8305 (t0) cc_final: 0.8018 (t0) REVERT: D 366 GLU cc_start: 0.7491 (mm-30) cc_final: 0.7217 (tp30) REVERT: D 458 MET cc_start: 0.6682 (tpt) cc_final: 0.6308 (tpt) REVERT: E 111 ASP cc_start: 0.5871 (t0) cc_final: 0.5505 (t0) REVERT: E 129 ARG cc_start: 0.7561 (mtp85) cc_final: 0.7033 (mtm110) REVERT: E 368 ASN cc_start: 0.8154 (m-40) cc_final: 0.7808 (m-40) REVERT: E 471 MET cc_start: 0.6693 (mpp) cc_final: 0.6004 (mtm) REVERT: F 16 GLN cc_start: 0.6067 (tm-30) cc_final: 0.5544 (tm-30) REVERT: F 172 LYS cc_start: 0.7960 (ttmt) cc_final: 0.7278 (tttt) REVERT: F 448 GLU cc_start: 0.7118 (mt-10) cc_final: 0.6384 (pt0) outliers start: 35 outliers final: 30 residues processed: 410 average time/residue: 0.1810 time to fit residues: 109.6202 Evaluate side-chains 404 residues out of total 2334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 373 time to evaluate : 0.587 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 201 SER Chi-restraints excluded: chain A residue 333 MET Chi-restraints excluded: chain A residue 377 ILE Chi-restraints excluded: chain A residue 379 SER Chi-restraints excluded: chain A residue 427 ASP Chi-restraints excluded: chain A residue 461 SER Chi-restraints excluded: chain B residue 79 THR Chi-restraints excluded: chain B residue 241 ASP Chi-restraints excluded: chain B residue 454 ASN Chi-restraints excluded: chain C residue 24 MET Chi-restraints excluded: chain C residue 60 LEU Chi-restraints excluded: chain C residue 228 THR Chi-restraints excluded: chain C residue 439 LEU Chi-restraints excluded: chain D residue 79 THR Chi-restraints excluded: chain D residue 186 GLU Chi-restraints excluded: chain D residue 201 SER Chi-restraints excluded: chain D residue 287 THR Chi-restraints excluded: chain D residue 333 MET Chi-restraints excluded: chain D residue 365 SER Chi-restraints excluded: chain D residue 379 SER Chi-restraints excluded: chain D residue 427 ASP Chi-restraints excluded: chain D residue 461 SER Chi-restraints excluded: chain E residue 36 LEU Chi-restraints excluded: chain E residue 79 THR Chi-restraints excluded: chain E residue 241 ASP Chi-restraints excluded: chain E residue 454 ASN Chi-restraints excluded: chain F residue 24 MET Chi-restraints excluded: chain F residue 147 VAL Chi-restraints excluded: chain F residue 228 THR Chi-restraints excluded: chain F residue 292 THR Chi-restraints excluded: chain F residue 439 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 274 random chunks: chunk 135 optimal weight: 0.6980 chunk 191 optimal weight: 8.9990 chunk 76 optimal weight: 0.8980 chunk 48 optimal weight: 8.9990 chunk 221 optimal weight: 3.9990 chunk 265 optimal weight: 0.8980 chunk 142 optimal weight: 8.9990 chunk 46 optimal weight: 4.9990 chunk 50 optimal weight: 1.9990 chunk 269 optimal weight: 0.6980 chunk 37 optimal weight: 1.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 423 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 359 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 423 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 359 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.149774 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.124514 restraints weight = 60740.892| |-----------------------------------------------------------------------------| r_work (start): 0.3367 rms_B_bonded: 2.85 r_work: 0.3180 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.3180 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3183 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3183 r_free = 0.3183 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3183 r_free = 0.3183 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (5 function evaluations) r_final: 0.3183 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7730 moved from start: 0.4150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 22427 Z= 0.110 Angle : 0.535 9.850 30315 Z= 0.276 Chirality : 0.043 0.184 3385 Planarity : 0.003 0.060 3868 Dihedral : 8.457 176.568 3089 Min Nonbonded Distance : 1.904 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 1.43 % Allowed : 14.09 % Favored : 84.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.69 (0.16), residues: 2739 helix: 1.43 (0.16), residues: 1045 sheet: 0.39 (0.19), residues: 718 loop : -0.45 (0.18), residues: 976 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 226 TYR 0.012 0.001 TYR C 442 PHE 0.019 0.002 PHE E 301 TRP 0.010 0.001 TRP B 462 HIS 0.003 0.001 HIS C 242 Details of bonding type rmsd/Z covalent geometry : bond 0.00252 / 0.11 (22425) covalent geometry : angle 0.53458 / 0.28 (30315) hydrogen bonds : bond 0.03187 / 2.13 ( 1102) hydrogen bonds : angle 4.01540 / 2.83 ( 3040) Misc. bond : bond 0.00054 / 0.03 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5478 Ramachandran restraints generated. 2739 Oldfield, 0 Emsley, 2739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5478 Ramachandran restraints generated. 2739 Oldfield, 0 Emsley, 2739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 415 residues out of total 2334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 382 time to evaluate : 0.759 Fit side-chains REVERT: A 85 LYS cc_start: 0.7144 (tptt) cc_final: 0.6786 (mtpt) REVERT: A 86 ASN cc_start: 0.8158 (m110) cc_final: 0.7676 (m-40) REVERT: A 257 ARG cc_start: 0.7560 (mtp-110) cc_final: 0.7232 (mtm110) REVERT: A 358 ASP cc_start: 0.8299 (t0) cc_final: 0.7981 (t0) REVERT: A 458 MET cc_start: 0.6687 (tpt) cc_final: 0.6314 (tpt) REVERT: A 471 MET cc_start: 0.5466 (mmm) cc_final: 0.5227 (mmm) REVERT: B 111 ASP cc_start: 0.5925 (t0) cc_final: 0.5502 (t0) REVERT: B 430 ILE cc_start: 0.6873 (mt) cc_final: 0.6645 (mm) REVERT: B 471 MET cc_start: 0.6624 (mpp) cc_final: 0.6133 (mtm) REVERT: C 16 GLN cc_start: 0.6086 (tm-30) cc_final: 0.5547 (tm-30) REVERT: C 24 MET cc_start: 0.6767 (OUTLIER) cc_final: 0.6201 (mtm) REVERT: C 338 MET cc_start: 0.8668 (mtm) cc_final: 0.8231 (mtt) REVERT: C 449 MET cc_start: 0.7924 (mmt) cc_final: 0.7706 (mmt) REVERT: D 85 LYS cc_start: 0.7224 (tptt) cc_final: 0.6859 (mtpt) REVERT: D 86 ASN cc_start: 0.8038 (m110) cc_final: 0.7649 (m-40) REVERT: D 127 ILE cc_start: 0.7901 (mt) cc_final: 0.7645 (tp) REVERT: D 193 ARG cc_start: 0.7932 (ttm-80) cc_final: 0.7497 (ttt180) REVERT: D 256 GLN cc_start: 0.8152 (mp10) cc_final: 0.7688 (mm-40) REVERT: D 309 LYS cc_start: 0.7718 (mmtp) cc_final: 0.7482 (mmtt) REVERT: D 358 ASP cc_start: 0.8234 (t0) cc_final: 0.7923 (t0) REVERT: D 366 GLU cc_start: 0.7443 (mm-30) cc_final: 0.7175 (tp30) REVERT: D 425 ILE cc_start: 0.7735 (mt) cc_final: 0.7484 (mm) REVERT: D 458 MET cc_start: 0.6708 (tpt) cc_final: 0.6333 (tpt) REVERT: E 111 ASP cc_start: 0.5907 (t0) cc_final: 0.5541 (t0) REVERT: E 129 ARG cc_start: 0.7589 (mtp85) cc_final: 0.7037 (mtm110) REVERT: E 471 MET cc_start: 0.6623 (mpp) cc_final: 0.5947 (mtm) REVERT: F 16 GLN cc_start: 0.6087 (tm-30) cc_final: 0.5567 (tm-30) REVERT: F 172 LYS cc_start: 0.8009 (ttmt) cc_final: 0.7320 (tttt) outliers start: 33 outliers final: 31 residues processed: 399 average time/residue: 0.1744 time to fit residues: 103.1968 Evaluate side-chains 404 residues out of total 2334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 372 time to evaluate : 0.722 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 201 SER Chi-restraints excluded: chain A residue 333 MET Chi-restraints excluded: chain A residue 377 ILE Chi-restraints excluded: chain A residue 379 SER Chi-restraints excluded: chain A residue 427 ASP Chi-restraints excluded: chain A residue 461 SER Chi-restraints excluded: chain B residue 60 LEU Chi-restraints excluded: chain B residue 79 THR Chi-restraints excluded: chain B residue 241 ASP Chi-restraints excluded: chain B residue 454 ASN Chi-restraints excluded: chain C residue 24 MET Chi-restraints excluded: chain C residue 60 LEU Chi-restraints excluded: chain C residue 228 THR Chi-restraints excluded: chain C residue 439 LEU Chi-restraints excluded: chain D residue 79 THR Chi-restraints excluded: chain D residue 186 GLU Chi-restraints excluded: chain D residue 201 SER Chi-restraints excluded: chain D residue 333 MET Chi-restraints excluded: chain D residue 365 SER Chi-restraints excluded: chain D residue 379 SER Chi-restraints excluded: chain D residue 427 ASP Chi-restraints excluded: chain D residue 461 SER Chi-restraints excluded: chain D residue 471 MET Chi-restraints excluded: chain E residue 79 THR Chi-restraints excluded: chain E residue 241 ASP Chi-restraints excluded: chain E residue 454 ASN Chi-restraints excluded: chain F residue 24 MET Chi-restraints excluded: chain F residue 147 VAL Chi-restraints excluded: chain F residue 181 THR Chi-restraints excluded: chain F residue 228 THR Chi-restraints excluded: chain F residue 292 THR Chi-restraints excluded: chain F residue 439 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 274 random chunks: chunk 126 optimal weight: 8.9990 chunk 53 optimal weight: 0.0060 chunk 192 optimal weight: 30.0000 chunk 15 optimal weight: 1.9990 chunk 66 optimal weight: 0.9990 chunk 190 optimal weight: 6.9990 chunk 244 optimal weight: 9.9990 chunk 239 optimal weight: 5.9990 chunk 116 optimal weight: 10.0000 chunk 234 optimal weight: 3.9990 chunk 197 optimal weight: 0.9980 overall best weight: 1.6002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 423 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.148957 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.122747 restraints weight = 59141.091| |-----------------------------------------------------------------------------| r_work (start): 0.3336 rms_B_bonded: 2.99 r_work: 0.3156 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.3156 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3159 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3159 r_free = 0.3159 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3159 r_free = 0.3159 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3159 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7742 moved from start: 0.4185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 22427 Z= 0.126 Angle : 0.551 9.590 30315 Z= 0.283 Chirality : 0.043 0.189 3385 Planarity : 0.004 0.059 3868 Dihedral : 8.393 173.245 3089 Min Nonbonded Distance : 1.864 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 1.51 % Allowed : 14.14 % Favored : 84.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.68 (0.16), residues: 2739 helix: 1.44 (0.16), residues: 1045 sheet: 0.38 (0.19), residues: 718 loop : -0.48 (0.18), residues: 976 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 257 TYR 0.015 0.001 TYR C 442 PHE 0.021 0.002 PHE E 301 TRP 0.010 0.001 TRP E 92 HIS 0.003 0.001 HIS D 423 Details of bonding type rmsd/Z covalent geometry : bond 0.00297 / 0.13 (22425) covalent geometry : angle 0.55073 / 0.28 (30315) hydrogen bonds : bond 0.03259 / 2.18 ( 1102) hydrogen bonds : angle 4.03204 / 2.84 ( 3040) Misc. bond : bond 0.00078 / 0.04 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4923.68 seconds wall clock time: 85 minutes 18.73 seconds (5118.73 seconds total)