Starting phenix.real_space_refine on Sun Jan 19 01:01:36 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8yx7_39649/01_2025/8yx7_39649.cif Found real_map, /net/cci-nas-00/data/ceres_data/8yx7_39649/01_2025/8yx7_39649.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8yx7_39649/01_2025/8yx7_39649.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8yx7_39649/01_2025/8yx7_39649.map" model { file = "/net/cci-nas-00/data/ceres_data/8yx7_39649/01_2025/8yx7_39649.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8yx7_39649/01_2025/8yx7_39649.cif" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.024 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 55 5.16 5 C 8485 2.51 5 N 2190 2.21 5 O 2340 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 13070 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 2572 Number of conformers: 1 Conformer: "" Number of residues, atoms: 324, 2572 Classifications: {'peptide': 324} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 306} Chain breaks: 1 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Restraints were copied for chains: C, B, E, D, F, I, H, J Residues with excluded nonbonded symmetry interactions: 5 residue: pdb=" C1 NAG F 2 " occ=0.80 ... (12 atoms not shown) pdb=" O7 NAG F 2 " occ=0.80 residue: pdb=" C1 NAG G 2 " occ=0.80 ... (12 atoms not shown) pdb=" O7 NAG G 2 " occ=0.80 residue: pdb=" C1 NAG H 2 " occ=0.80 ... (12 atoms not shown) pdb=" O7 NAG H 2 " occ=0.80 residue: pdb=" C1 NAG I 2 " occ=0.80 ... (12 atoms not shown) pdb=" O7 NAG I 2 " occ=0.80 residue: pdb=" C1 NAG J 2 " occ=0.80 ... (12 atoms not shown) pdb=" O7 NAG J 2 " occ=0.80 Time building chain proxies: 5.97, per 1000 atoms: 0.46 Number of scatterers: 13070 At special positions: 0 Unit cell: (93, 92.07, 122.76, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 55 16.00 O 2340 8.00 N 2190 7.00 C 8485 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 157 " - pdb=" SG CYS A 171 " distance=2.03 Simple disulfide: pdb=" SG CYS A 289 " - pdb=" SG CYS A 394 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " NAG-ASN " NAG A 501 " - " ASN A 170 " " NAG B 501 " - " ASN B 170 " " NAG C 501 " - " ASN C 170 " " NAG D 501 " - " ASN D 170 " " NAG E 501 " - " ASN E 170 " " NAG F 1 " - " ASN A 55 " " NAG G 1 " - " ASN B 55 " " NAG H 1 " - " ASN C 55 " " NAG I 1 " - " ASN D 55 " " NAG J 1 " - " ASN E 55 " Time building additional restraints: 3.69 Conformation dependent library (CDL) restraints added in 1.8 seconds 3200 Ramachandran restraints generated. 1600 Oldfield, 0 Emsley, 1600 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3140 Finding SS restraints... Secondary structure from input PDB file: 40 helices and 15 sheets defined 39.2% alpha, 33.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.57 Creating SS restraints... Processing helix chain 'A' and resid 94 through 97 Processing helix chain 'A' and resid 113 through 115 No H-bonds generated for 'chain 'A' and resid 113 through 115' Processing helix chain 'A' and resid 160 through 164 removed outlier: 4.224A pdb=" N HIS A 163 " --> pdb=" O GLU A 160 " (cutoff:3.500A) Processing helix chain 'A' and resid 231 through 252 removed outlier: 4.692A pdb=" N VAL A 239 " --> pdb=" O ILE A 235 " (cutoff:3.500A) Proline residue: A 240 - end of helix Processing helix chain 'A' and resid 258 through 283 removed outlier: 4.400A pdb=" N ILE A 262 " --> pdb=" O ALA A 258 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N GLY A 263 " --> pdb=" O ILE A 259 " (cutoff:3.500A) Processing helix chain 'A' and resid 291 through 320 removed outlier: 3.859A pdb=" N TYR A 295 " --> pdb=" O PRO A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 361 through 391 Processing helix chain 'A' and resid 399 through 404 Processing helix chain 'B' and resid 94 through 97 Processing helix chain 'B' and resid 113 through 115 No H-bonds generated for 'chain 'B' and resid 113 through 115' Processing helix chain 'B' and resid 160 through 164 removed outlier: 4.224A pdb=" N HIS B 163 " --> pdb=" O GLU B 160 " (cutoff:3.500A) Processing helix chain 'B' and resid 231 through 252 removed outlier: 4.692A pdb=" N VAL B 239 " --> pdb=" O ILE B 235 " (cutoff:3.500A) Proline residue: B 240 - end of helix Processing helix chain 'B' and resid 258 through 283 removed outlier: 4.400A pdb=" N ILE B 262 " --> pdb=" O ALA B 258 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N GLY B 263 " --> pdb=" O ILE B 259 " (cutoff:3.500A) Processing helix chain 'B' and resid 291 through 320 removed outlier: 3.859A pdb=" N TYR B 295 " --> pdb=" O PRO B 291 " (cutoff:3.500A) Processing helix chain 'B' and resid 361 through 391 Processing helix chain 'B' and resid 399 through 404 Processing helix chain 'C' and resid 94 through 97 Processing helix chain 'C' and resid 113 through 115 No H-bonds generated for 'chain 'C' and resid 113 through 115' Processing helix chain 'C' and resid 160 through 164 removed outlier: 4.224A pdb=" N HIS C 163 " --> pdb=" O GLU C 160 " (cutoff:3.500A) Processing helix chain 'C' and resid 231 through 252 removed outlier: 4.693A pdb=" N VAL C 239 " --> pdb=" O ILE C 235 " (cutoff:3.500A) Proline residue: C 240 - end of helix Processing helix chain 'C' and resid 258 through 283 removed outlier: 4.400A pdb=" N ILE C 262 " --> pdb=" O ALA C 258 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N GLY C 263 " --> pdb=" O ILE C 259 " (cutoff:3.500A) Processing helix chain 'C' and resid 291 through 320 removed outlier: 3.858A pdb=" N TYR C 295 " --> pdb=" O PRO C 291 " (cutoff:3.500A) Processing helix chain 'C' and resid 361 through 391 Processing helix chain 'C' and resid 399 through 404 Processing helix chain 'D' and resid 94 through 97 Processing helix chain 'D' and resid 113 through 115 No H-bonds generated for 'chain 'D' and resid 113 through 115' Processing helix chain 'D' and resid 160 through 164 removed outlier: 4.224A pdb=" N HIS D 163 " --> pdb=" O GLU D 160 " (cutoff:3.500A) Processing helix chain 'D' and resid 231 through 252 removed outlier: 4.692A pdb=" N VAL D 239 " --> pdb=" O ILE D 235 " (cutoff:3.500A) Proline residue: D 240 - end of helix Processing helix chain 'D' and resid 258 through 283 removed outlier: 4.400A pdb=" N ILE D 262 " --> pdb=" O ALA D 258 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N GLY D 263 " --> pdb=" O ILE D 259 " (cutoff:3.500A) Processing helix chain 'D' and resid 291 through 320 removed outlier: 3.859A pdb=" N TYR D 295 " --> pdb=" O PRO D 291 " (cutoff:3.500A) Processing helix chain 'D' and resid 361 through 391 Processing helix chain 'D' and resid 399 through 404 Processing helix chain 'E' and resid 94 through 97 Processing helix chain 'E' and resid 113 through 115 No H-bonds generated for 'chain 'E' and resid 113 through 115' Processing helix chain 'E' and resid 160 through 164 removed outlier: 4.224A pdb=" N HIS E 163 " --> pdb=" O GLU E 160 " (cutoff:3.500A) Processing helix chain 'E' and resid 231 through 252 removed outlier: 4.692A pdb=" N VAL E 239 " --> pdb=" O ILE E 235 " (cutoff:3.500A) Proline residue: E 240 - end of helix Processing helix chain 'E' and resid 258 through 283 removed outlier: 4.400A pdb=" N ILE E 262 " --> pdb=" O ALA E 258 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N GLY E 263 " --> pdb=" O ILE E 259 " (cutoff:3.500A) Processing helix chain 'E' and resid 291 through 320 removed outlier: 3.859A pdb=" N TYR E 295 " --> pdb=" O PRO E 291 " (cutoff:3.500A) Processing helix chain 'E' and resid 361 through 391 Processing helix chain 'E' and resid 399 through 404 Processing sheet with id=AA1, first strand: chain 'A' and resid 107 through 111 removed outlier: 5.773A pdb=" N GLN A 136 " --> pdb=" O ASN A 148 " (cutoff:3.500A) removed outlier: 4.999A pdb=" N ASN A 148 " --> pdb=" O GLN A 136 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N HIS A 144 " --> pdb=" O ASP A 140 " (cutoff:3.500A) removed outlier: 7.217A pdb=" N ALA A 150 " --> pdb=" O TRP A 130 " (cutoff:3.500A) removed outlier: 4.785A pdb=" N TRP A 130 " --> pdb=" O ALA A 150 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N ALA A 152 " --> pdb=" O VAL A 128 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N VAL A 128 " --> pdb=" O ALA A 152 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N GLU A 154 " --> pdb=" O LEU A 126 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 107 through 111 removed outlier: 5.773A pdb=" N GLN A 136 " --> pdb=" O ASN A 148 " (cutoff:3.500A) removed outlier: 4.999A pdb=" N ASN A 148 " --> pdb=" O GLN A 136 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N HIS A 144 " --> pdb=" O ASP A 140 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ASN A 73 " --> pdb=" O SER A 82 " (cutoff:3.500A) removed outlier: 7.366A pdb=" N MET A 84 " --> pdb=" O VAL A 71 " (cutoff:3.500A) removed outlier: 5.890A pdb=" N VAL A 71 " --> pdb=" O MET A 84 " (cutoff:3.500A) removed outlier: 8.601A pdb=" N LEU A 86 " --> pdb=" O SER A 69 " (cutoff:3.500A) removed outlier: 7.122A pdb=" N SER A 69 " --> pdb=" O LEU A 86 " (cutoff:3.500A) removed outlier: 7.855A pdb=" N ARG A 88 " --> pdb=" O PHE A 67 " (cutoff:3.500A) removed outlier: 7.893A pdb=" N PHE A 67 " --> pdb=" O ARG A 88 " (cutoff:3.500A) removed outlier: 7.859A pdb=" N SER A 90 " --> pdb=" O ARG A 65 " (cutoff:3.500A) removed outlier: 7.797A pdb=" N ARG A 65 " --> pdb=" O SER A 90 " (cutoff:3.500A) removed outlier: 8.760A pdb=" N LEU A 92 " --> pdb=" O ASP A 63 " (cutoff:3.500A) removed outlier: 9.665A pdb=" N ASP A 63 " --> pdb=" O LEU A 92 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 120 through 122 removed outlier: 4.072A pdb=" N ASP A 206 " --> pdb=" O ARG A 225 " (cutoff:3.500A) removed outlier: 7.102A pdb=" N LYS A 227 " --> pdb=" O VAL A 204 " (cutoff:3.500A) removed outlier: 5.500A pdb=" N VAL A 204 " --> pdb=" O LYS A 227 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 107 through 111 removed outlier: 5.773A pdb=" N GLN B 136 " --> pdb=" O ASN B 148 " (cutoff:3.500A) removed outlier: 4.998A pdb=" N ASN B 148 " --> pdb=" O GLN B 136 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N HIS B 144 " --> pdb=" O ASP B 140 " (cutoff:3.500A) removed outlier: 7.217A pdb=" N ALA B 150 " --> pdb=" O TRP B 130 " (cutoff:3.500A) removed outlier: 4.786A pdb=" N TRP B 130 " --> pdb=" O ALA B 150 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N ALA B 152 " --> pdb=" O VAL B 128 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N VAL B 128 " --> pdb=" O ALA B 152 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N GLU B 154 " --> pdb=" O LEU B 126 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 107 through 111 removed outlier: 5.773A pdb=" N GLN B 136 " --> pdb=" O ASN B 148 " (cutoff:3.500A) removed outlier: 4.998A pdb=" N ASN B 148 " --> pdb=" O GLN B 136 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N HIS B 144 " --> pdb=" O ASP B 140 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N ASN B 73 " --> pdb=" O SER B 82 " (cutoff:3.500A) removed outlier: 7.366A pdb=" N MET B 84 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 5.890A pdb=" N VAL B 71 " --> pdb=" O MET B 84 " (cutoff:3.500A) removed outlier: 8.601A pdb=" N LEU B 86 " --> pdb=" O SER B 69 " (cutoff:3.500A) removed outlier: 7.123A pdb=" N SER B 69 " --> pdb=" O LEU B 86 " (cutoff:3.500A) removed outlier: 7.855A pdb=" N ARG B 88 " --> pdb=" O PHE B 67 " (cutoff:3.500A) removed outlier: 7.893A pdb=" N PHE B 67 " --> pdb=" O ARG B 88 " (cutoff:3.500A) removed outlier: 7.859A pdb=" N SER B 90 " --> pdb=" O ARG B 65 " (cutoff:3.500A) removed outlier: 7.797A pdb=" N ARG B 65 " --> pdb=" O SER B 90 " (cutoff:3.500A) removed outlier: 8.759A pdb=" N LEU B 92 " --> pdb=" O ASP B 63 " (cutoff:3.500A) removed outlier: 9.665A pdb=" N ASP B 63 " --> pdb=" O LEU B 92 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 120 through 122 removed outlier: 4.073A pdb=" N ASP B 206 " --> pdb=" O ARG B 225 " (cutoff:3.500A) removed outlier: 7.102A pdb=" N LYS B 227 " --> pdb=" O VAL B 204 " (cutoff:3.500A) removed outlier: 5.500A pdb=" N VAL B 204 " --> pdb=" O LYS B 227 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 107 through 111 removed outlier: 5.772A pdb=" N GLN C 136 " --> pdb=" O ASN C 148 " (cutoff:3.500A) removed outlier: 4.999A pdb=" N ASN C 148 " --> pdb=" O GLN C 136 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N HIS C 144 " --> pdb=" O ASP C 140 " (cutoff:3.500A) removed outlier: 7.217A pdb=" N ALA C 150 " --> pdb=" O TRP C 130 " (cutoff:3.500A) removed outlier: 4.786A pdb=" N TRP C 130 " --> pdb=" O ALA C 150 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N ALA C 152 " --> pdb=" O VAL C 128 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N VAL C 128 " --> pdb=" O ALA C 152 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N GLU C 154 " --> pdb=" O LEU C 126 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 107 through 111 removed outlier: 5.772A pdb=" N GLN C 136 " --> pdb=" O ASN C 148 " (cutoff:3.500A) removed outlier: 4.999A pdb=" N ASN C 148 " --> pdb=" O GLN C 136 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N HIS C 144 " --> pdb=" O ASP C 140 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ASN C 73 " --> pdb=" O SER C 82 " (cutoff:3.500A) removed outlier: 7.366A pdb=" N MET C 84 " --> pdb=" O VAL C 71 " (cutoff:3.500A) removed outlier: 5.890A pdb=" N VAL C 71 " --> pdb=" O MET C 84 " (cutoff:3.500A) removed outlier: 8.601A pdb=" N LEU C 86 " --> pdb=" O SER C 69 " (cutoff:3.500A) removed outlier: 7.122A pdb=" N SER C 69 " --> pdb=" O LEU C 86 " (cutoff:3.500A) removed outlier: 7.854A pdb=" N ARG C 88 " --> pdb=" O PHE C 67 " (cutoff:3.500A) removed outlier: 7.893A pdb=" N PHE C 67 " --> pdb=" O ARG C 88 " (cutoff:3.500A) removed outlier: 7.859A pdb=" N SER C 90 " --> pdb=" O ARG C 65 " (cutoff:3.500A) removed outlier: 7.796A pdb=" N ARG C 65 " --> pdb=" O SER C 90 " (cutoff:3.500A) removed outlier: 8.760A pdb=" N LEU C 92 " --> pdb=" O ASP C 63 " (cutoff:3.500A) removed outlier: 9.665A pdb=" N ASP C 63 " --> pdb=" O LEU C 92 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 120 through 122 removed outlier: 4.072A pdb=" N ASP C 206 " --> pdb=" O ARG C 225 " (cutoff:3.500A) removed outlier: 7.103A pdb=" N LYS C 227 " --> pdb=" O VAL C 204 " (cutoff:3.500A) removed outlier: 5.500A pdb=" N VAL C 204 " --> pdb=" O LYS C 227 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 107 through 111 removed outlier: 5.773A pdb=" N GLN D 136 " --> pdb=" O ASN D 148 " (cutoff:3.500A) removed outlier: 4.999A pdb=" N ASN D 148 " --> pdb=" O GLN D 136 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N HIS D 144 " --> pdb=" O ASP D 140 " (cutoff:3.500A) removed outlier: 7.217A pdb=" N ALA D 150 " --> pdb=" O TRP D 130 " (cutoff:3.500A) removed outlier: 4.786A pdb=" N TRP D 130 " --> pdb=" O ALA D 150 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N ALA D 152 " --> pdb=" O VAL D 128 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N VAL D 128 " --> pdb=" O ALA D 152 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N GLU D 154 " --> pdb=" O LEU D 126 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 107 through 111 removed outlier: 5.773A pdb=" N GLN D 136 " --> pdb=" O ASN D 148 " (cutoff:3.500A) removed outlier: 4.999A pdb=" N ASN D 148 " --> pdb=" O GLN D 136 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N HIS D 144 " --> pdb=" O ASP D 140 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ASN D 73 " --> pdb=" O SER D 82 " (cutoff:3.500A) removed outlier: 7.366A pdb=" N MET D 84 " --> pdb=" O VAL D 71 " (cutoff:3.500A) removed outlier: 5.890A pdb=" N VAL D 71 " --> pdb=" O MET D 84 " (cutoff:3.500A) removed outlier: 8.601A pdb=" N LEU D 86 " --> pdb=" O SER D 69 " (cutoff:3.500A) removed outlier: 7.123A pdb=" N SER D 69 " --> pdb=" O LEU D 86 " (cutoff:3.500A) removed outlier: 7.855A pdb=" N ARG D 88 " --> pdb=" O PHE D 67 " (cutoff:3.500A) removed outlier: 7.893A pdb=" N PHE D 67 " --> pdb=" O ARG D 88 " (cutoff:3.500A) removed outlier: 7.859A pdb=" N SER D 90 " --> pdb=" O ARG D 65 " (cutoff:3.500A) removed outlier: 7.796A pdb=" N ARG D 65 " --> pdb=" O SER D 90 " (cutoff:3.500A) removed outlier: 8.760A pdb=" N LEU D 92 " --> pdb=" O ASP D 63 " (cutoff:3.500A) removed outlier: 9.664A pdb=" N ASP D 63 " --> pdb=" O LEU D 92 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 120 through 122 removed outlier: 4.073A pdb=" N ASP D 206 " --> pdb=" O ARG D 225 " (cutoff:3.500A) removed outlier: 7.102A pdb=" N LYS D 227 " --> pdb=" O VAL D 204 " (cutoff:3.500A) removed outlier: 5.500A pdb=" N VAL D 204 " --> pdb=" O LYS D 227 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 107 through 111 removed outlier: 5.772A pdb=" N GLN E 136 " --> pdb=" O ASN E 148 " (cutoff:3.500A) removed outlier: 4.998A pdb=" N ASN E 148 " --> pdb=" O GLN E 136 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N HIS E 144 " --> pdb=" O ASP E 140 " (cutoff:3.500A) removed outlier: 7.217A pdb=" N ALA E 150 " --> pdb=" O TRP E 130 " (cutoff:3.500A) removed outlier: 4.785A pdb=" N TRP E 130 " --> pdb=" O ALA E 150 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N ALA E 152 " --> pdb=" O VAL E 128 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N VAL E 128 " --> pdb=" O ALA E 152 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N GLU E 154 " --> pdb=" O LEU E 126 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 107 through 111 removed outlier: 5.772A pdb=" N GLN E 136 " --> pdb=" O ASN E 148 " (cutoff:3.500A) removed outlier: 4.998A pdb=" N ASN E 148 " --> pdb=" O GLN E 136 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N HIS E 144 " --> pdb=" O ASP E 140 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N ASN E 73 " --> pdb=" O SER E 82 " (cutoff:3.500A) removed outlier: 7.366A pdb=" N MET E 84 " --> pdb=" O VAL E 71 " (cutoff:3.500A) removed outlier: 5.890A pdb=" N VAL E 71 " --> pdb=" O MET E 84 " (cutoff:3.500A) removed outlier: 8.601A pdb=" N LEU E 86 " --> pdb=" O SER E 69 " (cutoff:3.500A) removed outlier: 7.123A pdb=" N SER E 69 " --> pdb=" O LEU E 86 " (cutoff:3.500A) removed outlier: 7.855A pdb=" N ARG E 88 " --> pdb=" O PHE E 67 " (cutoff:3.500A) removed outlier: 7.893A pdb=" N PHE E 67 " --> pdb=" O ARG E 88 " (cutoff:3.500A) removed outlier: 7.859A pdb=" N SER E 90 " --> pdb=" O ARG E 65 " (cutoff:3.500A) removed outlier: 7.797A pdb=" N ARG E 65 " --> pdb=" O SER E 90 " (cutoff:3.500A) removed outlier: 8.760A pdb=" N LEU E 92 " --> pdb=" O ASP E 63 " (cutoff:3.500A) removed outlier: 9.665A pdb=" N ASP E 63 " --> pdb=" O LEU E 92 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 120 through 122 removed outlier: 4.073A pdb=" N ASP E 206 " --> pdb=" O ARG E 225 " (cutoff:3.500A) removed outlier: 7.102A pdb=" N LYS E 227 " --> pdb=" O VAL E 204 " (cutoff:3.500A) removed outlier: 5.500A pdb=" N VAL E 204 " --> pdb=" O LYS E 227 " (cutoff:3.500A) 715 hydrogen bonds defined for protein. 2100 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: 4.36 Time building geometry restraints manager: 4.15 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 2020 1.31 - 1.43: 3605 1.43 - 1.56: 7685 1.56 - 1.68: 0 1.68 - 1.81: 75 Bond restraints: 13385 Sorted by residual: bond pdb=" C7 NAG I 2 " pdb=" N2 NAG I 2 " ideal model delta sigma weight residual 1.346 1.463 -0.117 2.00e-02 2.50e+03 3.40e+01 bond pdb=" C7 NAG G 2 " pdb=" N2 NAG G 2 " ideal model delta sigma weight residual 1.346 1.463 -0.117 2.00e-02 2.50e+03 3.40e+01 bond pdb=" C7 NAG H 2 " pdb=" N2 NAG H 2 " ideal model delta sigma weight residual 1.346 1.463 -0.117 2.00e-02 2.50e+03 3.40e+01 bond pdb=" C7 NAG F 2 " pdb=" N2 NAG F 2 " ideal model delta sigma weight residual 1.346 1.462 -0.116 2.00e-02 2.50e+03 3.39e+01 bond pdb=" C7 NAG J 2 " pdb=" N2 NAG J 2 " ideal model delta sigma weight residual 1.346 1.462 -0.116 2.00e-02 2.50e+03 3.39e+01 ... (remaining 13380 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.19: 17651 1.19 - 2.37: 391 2.37 - 3.56: 178 3.56 - 4.74: 38 4.74 - 5.93: 47 Bond angle restraints: 18305 Sorted by residual: angle pdb=" N LEU B 237 " pdb=" CA LEU B 237 " pdb=" C LEU B 237 " ideal model delta sigma weight residual 113.18 115.61 -2.43 1.33e+00 5.65e-01 3.35e+00 angle pdb=" N LEU D 237 " pdb=" CA LEU D 237 " pdb=" C LEU D 237 " ideal model delta sigma weight residual 113.18 115.61 -2.43 1.33e+00 5.65e-01 3.34e+00 angle pdb=" N LEU C 237 " pdb=" CA LEU C 237 " pdb=" C LEU C 237 " ideal model delta sigma weight residual 113.18 115.60 -2.42 1.33e+00 5.65e-01 3.31e+00 angle pdb=" N LEU E 237 " pdb=" CA LEU E 237 " pdb=" C LEU E 237 " ideal model delta sigma weight residual 113.18 115.58 -2.40 1.33e+00 5.65e-01 3.25e+00 angle pdb=" N LEU A 237 " pdb=" CA LEU A 237 " pdb=" C LEU A 237 " ideal model delta sigma weight residual 113.18 115.57 -2.39 1.33e+00 5.65e-01 3.24e+00 ... (remaining 18300 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 11.22: 7026 11.22 - 22.45: 795 22.45 - 33.67: 258 33.67 - 44.90: 57 44.90 - 56.12: 20 Dihedral angle restraints: 8156 sinusoidal: 3361 harmonic: 4795 Sorted by residual: dihedral pdb=" CB CYS A 289 " pdb=" SG CYS A 289 " pdb=" SG CYS A 394 " pdb=" CB CYS A 394 " ideal model delta sinusoidal sigma weight residual -86.00 -117.09 31.09 1 1.00e+01 1.00e-02 1.38e+01 dihedral pdb=" CA VAL A 71 " pdb=" C VAL A 71 " pdb=" N PHE A 72 " pdb=" CA PHE A 72 " ideal model delta harmonic sigma weight residual -180.00 -164.59 -15.41 0 5.00e+00 4.00e-02 9.49e+00 dihedral pdb=" CA VAL C 71 " pdb=" C VAL C 71 " pdb=" N PHE C 72 " pdb=" CA PHE C 72 " ideal model delta harmonic sigma weight residual 180.00 -164.60 -15.40 0 5.00e+00 4.00e-02 9.49e+00 ... (remaining 8153 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 1432 0.030 - 0.059: 544 0.059 - 0.088: 124 0.088 - 0.118: 76 0.118 - 0.147: 59 Chirality restraints: 2235 Sorted by residual: chirality pdb=" C5 NAG B 501 " pdb=" C4 NAG B 501 " pdb=" C6 NAG B 501 " pdb=" O5 NAG B 501 " both_signs ideal model delta sigma weight residual False -2.41 -2.56 0.15 2.00e-01 2.50e+01 5.44e-01 chirality pdb=" C5 NAG E 501 " pdb=" C4 NAG E 501 " pdb=" C6 NAG E 501 " pdb=" O5 NAG E 501 " both_signs ideal model delta sigma weight residual False -2.41 -2.56 0.15 2.00e-01 2.50e+01 5.29e-01 chirality pdb=" CA TRP E 362 " pdb=" N TRP E 362 " pdb=" C TRP E 362 " pdb=" CB TRP E 362 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 5.19e-01 ... (remaining 2232 not shown) Planarity restraints: 2260 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE B 234 " 0.005 2.00e-02 2.50e+03 1.08e-02 1.17e+00 pdb=" C ILE B 234 " -0.019 2.00e-02 2.50e+03 pdb=" O ILE B 234 " 0.007 2.00e-02 2.50e+03 pdb=" N ILE B 235 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE C 234 " 0.005 2.00e-02 2.50e+03 1.08e-02 1.16e+00 pdb=" C ILE C 234 " -0.019 2.00e-02 2.50e+03 pdb=" O ILE C 234 " 0.007 2.00e-02 2.50e+03 pdb=" N ILE C 235 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE D 234 " 0.005 2.00e-02 2.50e+03 1.07e-02 1.15e+00 pdb=" C ILE D 234 " -0.019 2.00e-02 2.50e+03 pdb=" O ILE D 234 " 0.007 2.00e-02 2.50e+03 pdb=" N ILE D 235 " 0.006 2.00e-02 2.50e+03 ... (remaining 2257 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.60: 58 2.60 - 3.18: 10619 3.18 - 3.75: 20083 3.75 - 4.33: 28687 4.33 - 4.90: 47415 Nonbonded interactions: 106862 Sorted by model distance: nonbonded pdb=" SG CYS C 157 " pdb=" SG CYS C 171 " model vdw 2.030 3.760 nonbonded pdb=" SG CYS E 157 " pdb=" SG CYS E 171 " model vdw 2.030 3.760 nonbonded pdb=" SG CYS B 157 " pdb=" SG CYS B 171 " model vdw 2.030 3.760 nonbonded pdb=" SG CYS C 289 " pdb=" SG CYS C 394 " model vdw 2.030 3.760 nonbonded pdb=" SG CYS E 289 " pdb=" SG CYS E 394 " model vdw 2.031 3.760 ... (remaining 106857 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: 0.14 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'E' selection = chain 'D' } ncs_group { reference = chain 'G' selection = chain 'F' selection = chain 'I' selection = chain 'H' selection = chain 'J' } 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=0.80 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.470 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: 0.530 Check model and map are aligned: 0.090 Set scattering table: 0.110 Process input model: 30.150 Find NCS groups from input model: 0.350 Set up NCS constraints: 0.040 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:12.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.100 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8031 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 : 0.007 0.117 13385 Z= 0.439 Angle : 0.579 5.926 18305 Z= 0.263 Chirality : 0.041 0.147 2235 Planarity : 0.003 0.024 2250 Dihedral : 10.872 56.122 5010 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.94 % Favored : 99.06 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.69 (0.21), residues: 1600 helix: 3.39 (0.20), residues: 545 sheet: 1.80 (0.24), residues: 405 loop : 0.38 (0.26), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 116 HIS 0.001 0.000 HIS A 276 PHE 0.016 0.001 PHE A 72 TYR 0.013 0.001 TYR E 264 ARG 0.002 0.000 ARG A 138 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3200 Ramachandran restraints generated. 1600 Oldfield, 0 Emsley, 1600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3200 Ramachandran restraints generated. 1600 Oldfield, 0 Emsley, 1600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 428 residues out of total 1430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 428 time to evaluate : 1.515 Fit side-chains REVERT: A 75 ASP cc_start: 0.8373 (t0) cc_final: 0.7986 (t0) REVERT: A 124 GLU cc_start: 0.8208 (mp0) cc_final: 0.7921 (pm20) REVERT: A 221 GLN cc_start: 0.8634 (pt0) cc_final: 0.8187 (pt0) REVERT: A 259 ILE cc_start: 0.9352 (pt) cc_final: 0.9139 (pt) REVERT: A 391 TRP cc_start: 0.8159 (m-90) cc_final: 0.7825 (m-90) REVERT: B 124 GLU cc_start: 0.8189 (mp0) cc_final: 0.7985 (mp0) REVERT: B 259 ILE cc_start: 0.9409 (pt) cc_final: 0.9192 (pt) REVERT: B 391 TRP cc_start: 0.8253 (m-90) cc_final: 0.7967 (m-90) REVERT: C 124 GLU cc_start: 0.8134 (mp0) cc_final: 0.7791 (pm20) REVERT: C 210 GLN cc_start: 0.8137 (pt0) cc_final: 0.7922 (pt0) REVERT: C 221 GLN cc_start: 0.8665 (pt0) cc_final: 0.8148 (pt0) REVERT: C 364 GLU cc_start: 0.7627 (mt-10) cc_final: 0.7405 (mt-10) REVERT: D 124 GLU cc_start: 0.8114 (mp0) cc_final: 0.7801 (pm20) REVERT: D 364 GLU cc_start: 0.7805 (mt-10) cc_final: 0.7501 (mt-10) REVERT: D 391 TRP cc_start: 0.8195 (m-90) cc_final: 0.7946 (m-90) REVERT: E 221 GLN cc_start: 0.8614 (pt0) cc_final: 0.8293 (pt0) REVERT: E 391 TRP cc_start: 0.8111 (m-90) cc_final: 0.7818 (m-10) outliers start: 0 outliers final: 1 residues processed: 428 average time/residue: 1.1831 time to fit residues: 554.9373 Evaluate side-chains 290 residues out of total 1430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 289 time to evaluate : 1.638 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 259 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 135 optimal weight: 4.9990 chunk 121 optimal weight: 4.9990 chunk 67 optimal weight: 2.9990 chunk 41 optimal weight: 6.9990 chunk 81 optimal weight: 0.7980 chunk 64 optimal weight: 0.6980 chunk 125 optimal weight: 3.9990 chunk 48 optimal weight: 5.9990 chunk 76 optimal weight: 0.8980 chunk 93 optimal weight: 4.9990 chunk 145 optimal weight: 0.0470 overall best weight: 1.0880 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 GLN A 382 GLN B 188 GLN C 156 ASN C 382 GLN D 188 GLN E 188 GLN E 382 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.098233 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.081934 restraints weight = 20743.486| |-----------------------------------------------------------------------------| r_work (start): 0.3013 rms_B_bonded: 3.02 r_work: 0.2852 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.2852 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2852 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2852 r_free = 0.2852 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.80 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2852 r_free = 0.2852 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.82 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2852 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7684 moved from start: 0.1861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 13385 Z= 0.233 Angle : 0.571 6.632 18305 Z= 0.280 Chirality : 0.041 0.143 2235 Planarity : 0.004 0.049 2250 Dihedral : 4.358 29.543 2062 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 3.29 % Allowed : 11.26 % Favored : 85.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.48 (0.21), residues: 1600 helix: 3.65 (0.20), residues: 515 sheet: 1.47 (0.24), residues: 405 loop : 0.18 (0.24), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 112 HIS 0.002 0.000 HIS B 276 PHE 0.020 0.002 PHE E 72 TYR 0.014 0.002 TYR D 176 ARG 0.006 0.001 ARG B 257 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3200 Ramachandran restraints generated. 1600 Oldfield, 0 Emsley, 1600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3200 Ramachandran restraints generated. 1600 Oldfield, 0 Emsley, 1600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 353 residues out of total 1430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 306 time to evaluate : 1.462 Fit side-chains REVERT: A 75 ASP cc_start: 0.7839 (t0) cc_final: 0.7497 (t0) REVERT: A 201 GLU cc_start: 0.8544 (mt-10) cc_final: 0.7937 (mp0) REVERT: A 210 GLN cc_start: 0.7970 (pt0) cc_final: 0.7696 (pt0) REVERT: A 221 GLN cc_start: 0.8462 (pt0) cc_final: 0.7824 (pt0) REVERT: A 260 GLU cc_start: 0.8775 (pt0) cc_final: 0.8404 (pm20) REVERT: A 391 TRP cc_start: 0.8064 (m-90) cc_final: 0.7856 (m-90) REVERT: A 402 GLU cc_start: 0.8209 (OUTLIER) cc_final: 0.8009 (mt-10) REVERT: B 48 GLU cc_start: 0.7841 (tp30) cc_final: 0.7547 (tp30) REVERT: B 124 GLU cc_start: 0.8467 (mp0) cc_final: 0.8154 (mp0) REVERT: B 154 GLU cc_start: 0.8748 (tt0) cc_final: 0.8547 (tt0) REVERT: B 201 GLU cc_start: 0.8496 (mt-10) cc_final: 0.8033 (mp0) REVERT: B 391 TRP cc_start: 0.8136 (m-90) cc_final: 0.7812 (m-90) REVERT: C 124 GLU cc_start: 0.8402 (mp0) cc_final: 0.8183 (mp0) REVERT: C 141 GLN cc_start: 0.8905 (pt0) cc_final: 0.8124 (pm20) REVERT: C 154 GLU cc_start: 0.8788 (tt0) cc_final: 0.8476 (tt0) REVERT: C 176 TYR cc_start: 0.8316 (m-80) cc_final: 0.7912 (m-80) REVERT: C 188 GLN cc_start: 0.8142 (tt0) cc_final: 0.7490 (tt0) REVERT: C 201 GLU cc_start: 0.8590 (mt-10) cc_final: 0.8074 (mp0) REVERT: C 221 GLN cc_start: 0.8486 (pt0) cc_final: 0.7781 (pt0) REVERT: D 75 ASP cc_start: 0.7683 (t0) cc_final: 0.7479 (t0) REVERT: D 78 ARG cc_start: 0.8574 (OUTLIER) cc_final: 0.8234 (mtp85) REVERT: D 113 GLU cc_start: 0.8515 (mp0) cc_final: 0.8213 (mp0) REVERT: D 188 GLN cc_start: 0.8051 (tt0) cc_final: 0.7725 (tt0) REVERT: D 364 GLU cc_start: 0.7839 (mt-10) cc_final: 0.7440 (mt-10) REVERT: D 372 LEU cc_start: 0.8092 (OUTLIER) cc_final: 0.7869 (tt) REVERT: D 391 TRP cc_start: 0.8193 (m-90) cc_final: 0.7898 (m-90) REVERT: E 113 GLU cc_start: 0.8526 (mp0) cc_final: 0.8276 (mp0) REVERT: E 124 GLU cc_start: 0.8387 (mp0) cc_final: 0.8047 (mp0) REVERT: E 221 GLN cc_start: 0.8518 (pt0) cc_final: 0.8064 (pt0) REVERT: E 257 ARG cc_start: 0.8932 (ptp90) cc_final: 0.8281 (ptp-110) REVERT: E 391 TRP cc_start: 0.8137 (m-90) cc_final: 0.7801 (m-10) outliers start: 47 outliers final: 19 residues processed: 337 average time/residue: 1.1812 time to fit residues: 435.8881 Evaluate side-chains 281 residues out of total 1430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 259 time to evaluate : 1.607 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain A residue 275 LEU Chi-restraints excluded: chain A residue 373 VAL Chi-restraints excluded: chain A residue 402 GLU Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain B residue 372 LEU Chi-restraints excluded: chain B residue 373 VAL Chi-restraints excluded: chain C residue 198 VAL Chi-restraints excluded: chain C residue 259 ILE Chi-restraints excluded: chain C residue 275 LEU Chi-restraints excluded: chain C residue 373 VAL Chi-restraints excluded: chain D residue 78 ARG Chi-restraints excluded: chain D residue 191 VAL Chi-restraints excluded: chain D residue 275 LEU Chi-restraints excluded: chain D residue 372 LEU Chi-restraints excluded: chain D residue 373 VAL Chi-restraints excluded: chain E residue 198 VAL Chi-restraints excluded: chain E residue 210 GLN Chi-restraints excluded: chain E residue 293 LEU Chi-restraints excluded: chain E residue 299 ILE Chi-restraints excluded: chain E residue 372 LEU Chi-restraints excluded: chain E residue 373 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 107 optimal weight: 0.9980 chunk 88 optimal weight: 0.0570 chunk 65 optimal weight: 3.9990 chunk 98 optimal weight: 3.9990 chunk 63 optimal weight: 10.0000 chunk 114 optimal weight: 0.5980 chunk 42 optimal weight: 5.9990 chunk 53 optimal weight: 2.9990 chunk 105 optimal weight: 3.9990 chunk 92 optimal weight: 3.9990 chunk 102 optimal weight: 2.9990 overall best weight: 1.5302 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 382 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.095017 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2964 r_free = 0.2964 target = 0.078908 restraints weight = 21078.373| |-----------------------------------------------------------------------------| r_work (start): 0.2981 rms_B_bonded: 3.01 r_work: 0.2820 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.2820 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2805 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2805 r_free = 0.2805 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.82 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2805 r_free = 0.2805 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.84 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2805 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7711 moved from start: 0.2121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 13385 Z= 0.283 Angle : 0.572 8.645 18305 Z= 0.278 Chirality : 0.041 0.150 2235 Planarity : 0.004 0.025 2250 Dihedral : 4.175 29.642 2062 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 3.92 % Allowed : 13.08 % Favored : 83.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.20 (0.21), residues: 1600 helix: 3.48 (0.20), residues: 515 sheet: 1.16 (0.24), residues: 420 loop : 0.03 (0.24), residues: 665 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 112 HIS 0.002 0.000 HIS D 276 PHE 0.020 0.002 PHE E 72 TYR 0.018 0.002 TYR A 176 ARG 0.006 0.000 ARG E 78 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3200 Ramachandran restraints generated. 1600 Oldfield, 0 Emsley, 1600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3200 Ramachandran restraints generated. 1600 Oldfield, 0 Emsley, 1600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 330 residues out of total 1430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 274 time to evaluate : 1.509 Fit side-chains REVERT: A 75 ASP cc_start: 0.7832 (t0) cc_final: 0.7470 (t0) REVERT: A 201 GLU cc_start: 0.8587 (mt-10) cc_final: 0.7953 (mp0) REVERT: A 391 TRP cc_start: 0.8047 (m-90) cc_final: 0.7842 (m-90) REVERT: B 48 GLU cc_start: 0.7839 (tp30) cc_final: 0.7558 (tp30) REVERT: B 75 ASP cc_start: 0.7670 (t0) cc_final: 0.7274 (t0) REVERT: B 112 TRP cc_start: 0.8107 (OUTLIER) cc_final: 0.7331 (t-100) REVERT: B 124 GLU cc_start: 0.8448 (mp0) cc_final: 0.8052 (mp0) REVERT: B 154 GLU cc_start: 0.8812 (tt0) cc_final: 0.8528 (tt0) REVERT: B 201 GLU cc_start: 0.8540 (mt-10) cc_final: 0.8048 (mp0) REVERT: B 260 GLU cc_start: 0.8623 (pm20) cc_final: 0.8374 (pm20) REVERT: B 391 TRP cc_start: 0.8163 (m-90) cc_final: 0.7841 (m-90) REVERT: C 112 TRP cc_start: 0.8067 (OUTLIER) cc_final: 0.7319 (t-100) REVERT: C 129 ASP cc_start: 0.8441 (t0) cc_final: 0.8090 (t0) REVERT: C 132 ASP cc_start: 0.8067 (p0) cc_final: 0.7656 (t0) REVERT: C 176 TYR cc_start: 0.8409 (m-80) cc_final: 0.7955 (m-80) REVERT: C 188 GLN cc_start: 0.8125 (tt0) cc_final: 0.7563 (tt0) REVERT: C 201 GLU cc_start: 0.8622 (mt-10) cc_final: 0.8056 (mp0) REVERT: C 221 GLN cc_start: 0.8550 (pt0) cc_final: 0.8169 (pt0) REVERT: D 63 ASP cc_start: 0.8428 (t70) cc_final: 0.8102 (t0) REVERT: D 78 ARG cc_start: 0.8540 (OUTLIER) cc_final: 0.8259 (mtp85) REVERT: D 113 GLU cc_start: 0.8536 (mp0) cc_final: 0.8325 (mp0) REVERT: D 364 GLU cc_start: 0.7843 (mt-10) cc_final: 0.7448 (mt-10) REVERT: D 372 LEU cc_start: 0.8095 (OUTLIER) cc_final: 0.7870 (tt) REVERT: D 391 TRP cc_start: 0.8223 (m-90) cc_final: 0.7919 (m-10) REVERT: E 81 MET cc_start: 0.8624 (ttp) cc_final: 0.8406 (ptm) REVERT: E 132 ASP cc_start: 0.8039 (OUTLIER) cc_final: 0.7658 (t0) REVERT: E 221 GLN cc_start: 0.8554 (pt0) cc_final: 0.8184 (pt0) REVERT: E 257 ARG cc_start: 0.8926 (ptp90) cc_final: 0.8293 (ptp-110) REVERT: E 260 GLU cc_start: 0.8885 (pm20) cc_final: 0.8289 (pm20) REVERT: E 382 GLN cc_start: 0.8368 (mm110) cc_final: 0.8104 (mm-40) REVERT: E 391 TRP cc_start: 0.8137 (m-90) cc_final: 0.7837 (m-10) outliers start: 56 outliers final: 22 residues processed: 311 average time/residue: 1.1387 time to fit residues: 390.1902 Evaluate side-chains 288 residues out of total 1430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 261 time to evaluate : 1.434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain A residue 275 LEU Chi-restraints excluded: chain A residue 373 VAL Chi-restraints excluded: chain B residue 112 TRP Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain B residue 364 GLU Chi-restraints excluded: chain B residue 372 LEU Chi-restraints excluded: chain B residue 373 VAL Chi-restraints excluded: chain C residue 112 TRP Chi-restraints excluded: chain C residue 172 SER Chi-restraints excluded: chain C residue 179 SER Chi-restraints excluded: chain C residue 198 VAL Chi-restraints excluded: chain C residue 259 ILE Chi-restraints excluded: chain C residue 275 LEU Chi-restraints excluded: chain C residue 372 LEU Chi-restraints excluded: chain C residue 373 VAL Chi-restraints excluded: chain D residue 78 ARG Chi-restraints excluded: chain D residue 146 LYS Chi-restraints excluded: chain D residue 372 LEU Chi-restraints excluded: chain D residue 373 VAL Chi-restraints excluded: chain E residue 132 ASP Chi-restraints excluded: chain E residue 198 VAL Chi-restraints excluded: chain E residue 210 GLN Chi-restraints excluded: chain E residue 275 LEU Chi-restraints excluded: chain E residue 372 LEU Chi-restraints excluded: chain E residue 373 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 88 optimal weight: 3.9990 chunk 83 optimal weight: 0.9980 chunk 135 optimal weight: 4.9990 chunk 5 optimal weight: 0.4980 chunk 138 optimal weight: 3.9990 chunk 15 optimal weight: 4.9990 chunk 106 optimal weight: 3.9990 chunk 113 optimal weight: 3.9990 chunk 46 optimal weight: 1.9990 chunk 148 optimal weight: 2.9990 chunk 98 optimal weight: 1.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 276 HIS B 276 HIS C 276 HIS D 276 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.093793 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2946 r_free = 0.2946 target = 0.077842 restraints weight = 20924.186| |-----------------------------------------------------------------------------| r_work (start): 0.2902 rms_B_bonded: 2.98 r_work: 0.2740 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.2740 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2777 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2777 r_free = 0.2777 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.84 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2777 r_free = 0.2777 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.85 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2777 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7711 moved from start: 0.2450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 13385 Z= 0.305 Angle : 0.567 6.598 18305 Z= 0.278 Chirality : 0.041 0.149 2235 Planarity : 0.004 0.029 2250 Dihedral : 4.105 30.488 2062 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 3.78 % Allowed : 14.62 % Favored : 81.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.08 (0.21), residues: 1600 helix: 3.36 (0.20), residues: 515 sheet: 0.94 (0.24), residues: 420 loop : 0.10 (0.25), residues: 665 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 112 HIS 0.003 0.000 HIS D 276 PHE 0.021 0.002 PHE E 72 TYR 0.011 0.002 TYR A 272 ARG 0.006 0.000 ARG B 78 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3200 Ramachandran restraints generated. 1600 Oldfield, 0 Emsley, 1600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3200 Ramachandran restraints generated. 1600 Oldfield, 0 Emsley, 1600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 1430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 256 time to evaluate : 1.449 Fit side-chains REVERT: A 75 ASP cc_start: 0.7865 (t0) cc_final: 0.7493 (t0) REVERT: A 112 TRP cc_start: 0.8269 (OUTLIER) cc_final: 0.7583 (t-100) REVERT: A 124 GLU cc_start: 0.8375 (mp0) cc_final: 0.8056 (mp0) REVERT: A 154 GLU cc_start: 0.8718 (tt0) cc_final: 0.8496 (tt0) REVERT: A 184 GLU cc_start: 0.8349 (pt0) cc_final: 0.8135 (pt0) REVERT: A 201 GLU cc_start: 0.8585 (mt-10) cc_final: 0.7977 (mp0) REVERT: A 214 GLN cc_start: 0.8145 (mm-40) cc_final: 0.7813 (pt0) REVERT: A 260 GLU cc_start: 0.8779 (pm20) cc_final: 0.8217 (pm20) REVERT: A 391 TRP cc_start: 0.8053 (m-90) cc_final: 0.7841 (m-90) REVERT: B 48 GLU cc_start: 0.7925 (tp30) cc_final: 0.7670 (tp30) REVERT: B 75 ASP cc_start: 0.7701 (t0) cc_final: 0.7274 (t0) REVERT: B 124 GLU cc_start: 0.8453 (mp0) cc_final: 0.7993 (mp0) REVERT: B 132 ASP cc_start: 0.7347 (t0) cc_final: 0.7115 (p0) REVERT: B 146 LYS cc_start: 0.8266 (mtmm) cc_final: 0.7966 (mtpp) REVERT: B 154 GLU cc_start: 0.8817 (tt0) cc_final: 0.8567 (tt0) REVERT: B 201 GLU cc_start: 0.8574 (mt-10) cc_final: 0.8049 (mp0) REVERT: B 214 GLN cc_start: 0.8260 (mm-40) cc_final: 0.8024 (pt0) REVERT: B 260 GLU cc_start: 0.8666 (pm20) cc_final: 0.8362 (pm20) REVERT: B 391 TRP cc_start: 0.8176 (m-90) cc_final: 0.7905 (m-90) REVERT: C 112 TRP cc_start: 0.8218 (OUTLIER) cc_final: 0.7459 (t-100) REVERT: C 129 ASP cc_start: 0.8522 (t0) cc_final: 0.8108 (t0) REVERT: C 146 LYS cc_start: 0.8103 (OUTLIER) cc_final: 0.7684 (mtpp) REVERT: C 188 GLN cc_start: 0.8127 (tt0) cc_final: 0.7565 (tt0) REVERT: C 201 GLU cc_start: 0.8639 (mt-10) cc_final: 0.8055 (mp0) REVERT: D 63 ASP cc_start: 0.8455 (t70) cc_final: 0.8141 (t0) REVERT: D 78 ARG cc_start: 0.8586 (OUTLIER) cc_final: 0.8135 (mtm-85) REVERT: D 112 TRP cc_start: 0.8244 (OUTLIER) cc_final: 0.7509 (t-100) REVERT: D 160 GLU cc_start: 0.8466 (mt-10) cc_final: 0.8109 (mt-10) REVERT: D 364 GLU cc_start: 0.7836 (mt-10) cc_final: 0.7450 (mt-10) REVERT: D 372 LEU cc_start: 0.8079 (OUTLIER) cc_final: 0.7850 (tt) REVERT: D 391 TRP cc_start: 0.8226 (m-90) cc_final: 0.7949 (m-90) REVERT: E 112 TRP cc_start: 0.8095 (OUTLIER) cc_final: 0.7058 (t-100) REVERT: E 132 ASP cc_start: 0.8056 (OUTLIER) cc_final: 0.7639 (t0) REVERT: E 221 GLN cc_start: 0.8512 (pt0) cc_final: 0.8159 (pt0) REVERT: E 257 ARG cc_start: 0.8941 (ptp90) cc_final: 0.8286 (ptp-110) REVERT: E 260 GLU cc_start: 0.8885 (pm20) cc_final: 0.8397 (pm20) REVERT: E 391 TRP cc_start: 0.8191 (m-90) cc_final: 0.7927 (m-10) outliers start: 54 outliers final: 23 residues processed: 283 average time/residue: 1.3100 time to fit residues: 409.2516 Evaluate side-chains 268 residues out of total 1430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 237 time to evaluate : 1.587 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 MET Chi-restraints excluded: chain A residue 112 TRP Chi-restraints excluded: chain A residue 123 LEU Chi-restraints excluded: chain A residue 210 GLN Chi-restraints excluded: chain A residue 275 LEU Chi-restraints excluded: chain A residue 373 VAL Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain B residue 372 LEU Chi-restraints excluded: chain B residue 373 VAL Chi-restraints excluded: chain C residue 112 TRP Chi-restraints excluded: chain C residue 146 LYS Chi-restraints excluded: chain C residue 172 SER Chi-restraints excluded: chain C residue 198 VAL Chi-restraints excluded: chain C residue 259 ILE Chi-restraints excluded: chain C residue 275 LEU Chi-restraints excluded: chain C residue 372 LEU Chi-restraints excluded: chain C residue 373 VAL Chi-restraints excluded: chain D residue 78 ARG Chi-restraints excluded: chain D residue 112 TRP Chi-restraints excluded: chain D residue 299 ILE Chi-restraints excluded: chain D residue 372 LEU Chi-restraints excluded: chain D residue 373 VAL Chi-restraints excluded: chain E residue 112 TRP Chi-restraints excluded: chain E residue 132 ASP Chi-restraints excluded: chain E residue 198 VAL Chi-restraints excluded: chain E residue 210 GLN Chi-restraints excluded: chain E residue 237 LEU Chi-restraints excluded: chain E residue 275 LEU Chi-restraints excluded: chain E residue 372 LEU Chi-restraints excluded: chain E residue 373 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 124 optimal weight: 4.9990 chunk 0 optimal weight: 5.9990 chunk 98 optimal weight: 0.9990 chunk 151 optimal weight: 8.9990 chunk 114 optimal weight: 3.9990 chunk 122 optimal weight: 3.9990 chunk 34 optimal weight: 0.9990 chunk 111 optimal weight: 0.8980 chunk 35 optimal weight: 2.9990 chunk 102 optimal weight: 0.0970 chunk 127 optimal weight: 1.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 382 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.094349 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.2952 r_free = 0.2952 target = 0.078375 restraints weight = 21147.769| |-----------------------------------------------------------------------------| r_work (start): 0.2923 rms_B_bonded: 3.01 r_work: 0.2762 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.2762 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2790 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2790 r_free = 0.2790 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.85 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2790 r_free = 0.2790 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.85 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2790 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7661 moved from start: 0.2573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 13385 Z= 0.212 Angle : 0.540 7.066 18305 Z= 0.263 Chirality : 0.040 0.146 2235 Planarity : 0.004 0.031 2250 Dihedral : 3.980 30.498 2062 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 3.36 % Allowed : 14.48 % Favored : 82.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.05 (0.21), residues: 1600 helix: 3.38 (0.20), residues: 515 sheet: 0.84 (0.24), residues: 420 loop : 0.11 (0.25), residues: 665 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 112 HIS 0.002 0.000 HIS E 276 PHE 0.019 0.002 PHE D 72 TYR 0.014 0.002 TYR B 176 ARG 0.006 0.000 ARG C 78 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3200 Ramachandran restraints generated. 1600 Oldfield, 0 Emsley, 1600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3200 Ramachandran restraints generated. 1600 Oldfield, 0 Emsley, 1600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 1430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 259 time to evaluate : 1.457 Fit side-chains REVERT: A 75 ASP cc_start: 0.7763 (t0) cc_final: 0.7414 (t0) REVERT: A 124 GLU cc_start: 0.8335 (mp0) cc_final: 0.7900 (mp0) REVERT: A 154 GLU cc_start: 0.8670 (tt0) cc_final: 0.8464 (tt0) REVERT: A 184 GLU cc_start: 0.8317 (pt0) cc_final: 0.8110 (pt0) REVERT: A 201 GLU cc_start: 0.8581 (mt-10) cc_final: 0.7971 (mp0) REVERT: A 214 GLN cc_start: 0.8202 (mm-40) cc_final: 0.7854 (pt0) REVERT: A 260 GLU cc_start: 0.8776 (pm20) cc_final: 0.8282 (pm20) REVERT: A 391 TRP cc_start: 0.8031 (m-90) cc_final: 0.7783 (m-90) REVERT: B 48 GLU cc_start: 0.7921 (tp30) cc_final: 0.7570 (tp30) REVERT: B 75 ASP cc_start: 0.7574 (t0) cc_final: 0.7288 (t0) REVERT: B 124 GLU cc_start: 0.8425 (mp0) cc_final: 0.7940 (mp0) REVERT: B 132 ASP cc_start: 0.7483 (t0) cc_final: 0.7031 (p0) REVERT: B 146 LYS cc_start: 0.8256 (mtmm) cc_final: 0.7962 (mtpp) REVERT: B 154 GLU cc_start: 0.8733 (tt0) cc_final: 0.8509 (tt0) REVERT: B 201 GLU cc_start: 0.8538 (mt-10) cc_final: 0.8040 (mp0) REVERT: B 214 GLN cc_start: 0.8255 (mm-40) cc_final: 0.8023 (pt0) REVERT: B 260 GLU cc_start: 0.8653 (pm20) cc_final: 0.8317 (pm20) REVERT: B 364 GLU cc_start: 0.7636 (mp0) cc_final: 0.6729 (mp0) REVERT: B 391 TRP cc_start: 0.8148 (m-90) cc_final: 0.7910 (m-90) REVERT: C 112 TRP cc_start: 0.8112 (OUTLIER) cc_final: 0.7336 (t-100) REVERT: C 129 ASP cc_start: 0.8503 (t0) cc_final: 0.8065 (t0) REVERT: C 188 GLN cc_start: 0.8054 (tt0) cc_final: 0.7471 (tt0) REVERT: C 201 GLU cc_start: 0.8624 (mt-10) cc_final: 0.8043 (mp0) REVERT: D 63 ASP cc_start: 0.8378 (t70) cc_final: 0.8076 (t0) REVERT: D 75 ASP cc_start: 0.7623 (t0) cc_final: 0.7411 (t0) REVERT: D 113 GLU cc_start: 0.8772 (mp0) cc_final: 0.8259 (mp0) REVERT: D 129 ASP cc_start: 0.8288 (t0) cc_final: 0.7940 (t0) REVERT: D 364 GLU cc_start: 0.7850 (mt-10) cc_final: 0.7459 (mt-10) REVERT: D 372 LEU cc_start: 0.8035 (OUTLIER) cc_final: 0.7821 (tt) REVERT: D 391 TRP cc_start: 0.8170 (m-90) cc_final: 0.7889 (m-90) REVERT: E 81 MET cc_start: 0.8638 (ttp) cc_final: 0.8388 (ptt) REVERT: E 221 GLN cc_start: 0.8424 (pt0) cc_final: 0.8067 (pt0) REVERT: E 260 GLU cc_start: 0.8895 (pm20) cc_final: 0.8430 (pm20) REVERT: E 391 TRP cc_start: 0.8122 (m-90) cc_final: 0.7867 (m-10) outliers start: 48 outliers final: 19 residues processed: 287 average time/residue: 1.1945 time to fit residues: 375.2687 Evaluate side-chains 278 residues out of total 1430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 257 time to evaluate : 1.473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 MET Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 275 LEU Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain B residue 372 LEU Chi-restraints excluded: chain C residue 112 TRP Chi-restraints excluded: chain C residue 172 SER Chi-restraints excluded: chain C residue 198 VAL Chi-restraints excluded: chain C residue 275 LEU Chi-restraints excluded: chain C residue 306 LEU Chi-restraints excluded: chain C residue 372 LEU Chi-restraints excluded: chain C residue 373 VAL Chi-restraints excluded: chain D residue 146 LYS Chi-restraints excluded: chain D residue 198 VAL Chi-restraints excluded: chain D residue 237 LEU Chi-restraints excluded: chain D residue 275 LEU Chi-restraints excluded: chain D residue 299 ILE Chi-restraints excluded: chain D residue 372 LEU Chi-restraints excluded: chain E residue 198 VAL Chi-restraints excluded: chain E residue 372 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 107 optimal weight: 2.9990 chunk 72 optimal weight: 1.9990 chunk 125 optimal weight: 4.9990 chunk 39 optimal weight: 2.9990 chunk 151 optimal weight: 0.9980 chunk 101 optimal weight: 7.9990 chunk 89 optimal weight: 4.9990 chunk 124 optimal weight: 4.9990 chunk 20 optimal weight: 3.9990 chunk 155 optimal weight: 0.8980 chunk 75 optimal weight: 0.7980 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.093362 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2932 r_free = 0.2932 target = 0.077188 restraints weight = 21284.494| |-----------------------------------------------------------------------------| r_work (start): 0.2928 rms_B_bonded: 3.03 r_work: 0.2767 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.2767 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2748 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2748 r_free = 0.2748 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.85 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2747 r_free = 0.2747 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.88 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2747 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7698 moved from start: 0.2670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 13385 Z= 0.285 Angle : 0.564 8.632 18305 Z= 0.273 Chirality : 0.040 0.150 2235 Planarity : 0.004 0.047 2250 Dihedral : 3.933 16.331 2060 Min Nonbonded Distance : 2.613 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 3.71 % Allowed : 14.76 % Favored : 81.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.99 (0.21), residues: 1600 helix: 3.03 (0.20), residues: 545 sheet: 0.78 (0.24), residues: 420 loop : 0.23 (0.26), residues: 635 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP B 112 HIS 0.002 0.000 HIS E 276 PHE 0.021 0.002 PHE C 72 TYR 0.016 0.002 TYR A 272 ARG 0.011 0.000 ARG D 257 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3200 Ramachandran restraints generated. 1600 Oldfield, 0 Emsley, 1600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3200 Ramachandran restraints generated. 1600 Oldfield, 0 Emsley, 1600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 1430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 256 time to evaluate : 1.482 Fit side-chains REVERT: A 81 MET cc_start: 0.8745 (ttp) cc_final: 0.8443 (ptm) REVERT: A 112 TRP cc_start: 0.8049 (OUTLIER) cc_final: 0.7596 (t-100) REVERT: A 124 GLU cc_start: 0.8358 (mp0) cc_final: 0.7983 (mp0) REVERT: A 154 GLU cc_start: 0.8669 (tt0) cc_final: 0.8455 (tt0) REVERT: A 184 GLU cc_start: 0.8340 (pt0) cc_final: 0.8138 (pt0) REVERT: A 201 GLU cc_start: 0.8588 (mt-10) cc_final: 0.7963 (mp0) REVERT: A 214 GLN cc_start: 0.8213 (mm-40) cc_final: 0.7856 (pt0) REVERT: A 260 GLU cc_start: 0.8777 (pm20) cc_final: 0.8232 (pm20) REVERT: A 364 GLU cc_start: 0.8083 (mt-10) cc_final: 0.7669 (mt-10) REVERT: A 391 TRP cc_start: 0.8062 (m-90) cc_final: 0.7820 (m-90) REVERT: B 48 GLU cc_start: 0.7988 (tp30) cc_final: 0.7744 (tp30) REVERT: B 112 TRP cc_start: 0.7897 (OUTLIER) cc_final: 0.6943 (t-100) REVERT: B 124 GLU cc_start: 0.8437 (mp0) cc_final: 0.7989 (mp0) REVERT: B 132 ASP cc_start: 0.7321 (t0) cc_final: 0.6801 (p0) REVERT: B 146 LYS cc_start: 0.8282 (mtmm) cc_final: 0.7989 (mtpp) REVERT: B 154 GLU cc_start: 0.8797 (tt0) cc_final: 0.8559 (tt0) REVERT: B 201 GLU cc_start: 0.8561 (mt-10) cc_final: 0.8020 (mp0) REVERT: B 214 GLN cc_start: 0.8291 (mm-40) cc_final: 0.8015 (pt0) REVERT: B 260 GLU cc_start: 0.8684 (pm20) cc_final: 0.8319 (pm20) REVERT: B 364 GLU cc_start: 0.7603 (mt-10) cc_final: 0.6670 (mp0) REVERT: B 391 TRP cc_start: 0.8214 (m-90) cc_final: 0.7965 (m-90) REVERT: C 112 TRP cc_start: 0.8233 (OUTLIER) cc_final: 0.7830 (t-100) REVERT: C 129 ASP cc_start: 0.8530 (t0) cc_final: 0.8057 (t0) REVERT: C 132 ASP cc_start: 0.7871 (OUTLIER) cc_final: 0.7571 (t0) REVERT: C 146 LYS cc_start: 0.8132 (OUTLIER) cc_final: 0.7699 (mtpp) REVERT: C 188 GLN cc_start: 0.8069 (tt0) cc_final: 0.7485 (tt0) REVERT: C 201 GLU cc_start: 0.8647 (mt-10) cc_final: 0.8053 (mp0) REVERT: D 63 ASP cc_start: 0.8401 (t70) cc_final: 0.8110 (t0) REVERT: D 75 ASP cc_start: 0.7683 (t0) cc_final: 0.7475 (t0) REVERT: D 113 GLU cc_start: 0.8737 (mp0) cc_final: 0.8336 (mp0) REVERT: D 129 ASP cc_start: 0.8380 (t0) cc_final: 0.8032 (t0) REVERT: D 132 ASP cc_start: 0.7929 (p0) cc_final: 0.7544 (t0) REVERT: D 160 GLU cc_start: 0.8453 (mt-10) cc_final: 0.8083 (mt-10) REVERT: D 364 GLU cc_start: 0.7852 (mt-10) cc_final: 0.7482 (mt-10) REVERT: D 372 LEU cc_start: 0.8045 (OUTLIER) cc_final: 0.7826 (tt) REVERT: D 391 TRP cc_start: 0.8184 (m-90) cc_final: 0.7951 (m-90) REVERT: E 81 MET cc_start: 0.8642 (ttp) cc_final: 0.8387 (ptt) REVERT: E 112 TRP cc_start: 0.8164 (OUTLIER) cc_final: 0.6967 (t-100) REVERT: E 132 ASP cc_start: 0.7945 (OUTLIER) cc_final: 0.7588 (t0) REVERT: E 221 GLN cc_start: 0.8487 (pt0) cc_final: 0.8175 (pt0) REVERT: E 257 ARG cc_start: 0.8902 (ptp90) cc_final: 0.8279 (ptp-110) REVERT: E 260 GLU cc_start: 0.8929 (pm20) cc_final: 0.8479 (pm20) REVERT: E 285 SER cc_start: 0.8762 (t) cc_final: 0.8369 (t) REVERT: E 391 TRP cc_start: 0.8176 (m-90) cc_final: 0.7957 (m-10) outliers start: 53 outliers final: 25 residues processed: 288 average time/residue: 1.2289 time to fit residues: 386.9104 Evaluate side-chains 265 residues out of total 1430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 232 time to evaluate : 1.514 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 TRP Chi-restraints excluded: chain A residue 123 LEU Chi-restraints excluded: chain A residue 210 GLN Chi-restraints excluded: chain A residue 275 LEU Chi-restraints excluded: chain A residue 373 VAL Chi-restraints excluded: chain B residue 112 TRP Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain B residue 372 LEU Chi-restraints excluded: chain B residue 373 VAL Chi-restraints excluded: chain C residue 112 TRP Chi-restraints excluded: chain C residue 132 ASP Chi-restraints excluded: chain C residue 146 LYS Chi-restraints excluded: chain C residue 172 SER Chi-restraints excluded: chain C residue 198 VAL Chi-restraints excluded: chain C residue 210 GLN Chi-restraints excluded: chain C residue 275 LEU Chi-restraints excluded: chain C residue 306 LEU Chi-restraints excluded: chain C residue 372 LEU Chi-restraints excluded: chain C residue 373 VAL Chi-restraints excluded: chain D residue 146 LYS Chi-restraints excluded: chain D residue 153 THR Chi-restraints excluded: chain D residue 198 VAL Chi-restraints excluded: chain D residue 237 LEU Chi-restraints excluded: chain D residue 275 LEU Chi-restraints excluded: chain D residue 372 LEU Chi-restraints excluded: chain D residue 373 VAL Chi-restraints excluded: chain E residue 112 TRP Chi-restraints excluded: chain E residue 132 ASP Chi-restraints excluded: chain E residue 198 VAL Chi-restraints excluded: chain E residue 275 LEU Chi-restraints excluded: chain E residue 372 LEU Chi-restraints excluded: chain E residue 373 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 95 optimal weight: 0.1980 chunk 28 optimal weight: 4.9990 chunk 122 optimal weight: 2.9990 chunk 136 optimal weight: 2.9990 chunk 157 optimal weight: 4.9990 chunk 135 optimal weight: 1.9990 chunk 3 optimal weight: 2.9990 chunk 71 optimal weight: 2.9990 chunk 100 optimal weight: 2.9990 chunk 105 optimal weight: 0.7980 chunk 108 optimal weight: 0.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 276 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.094700 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.078472 restraints weight = 20870.103| |-----------------------------------------------------------------------------| r_work (start): 0.2905 rms_B_bonded: 3.03 r_work: 0.2742 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.2742 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2780 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2780 r_free = 0.2780 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.88 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2780 r_free = 0.2780 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.86 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2780 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7703 moved from start: 0.2774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 13385 Z= 0.264 Angle : 0.560 9.134 18305 Z= 0.271 Chirality : 0.040 0.148 2235 Planarity : 0.004 0.048 2250 Dihedral : 3.916 15.367 2060 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 3.22 % Allowed : 15.94 % Favored : 80.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.96 (0.21), residues: 1600 helix: 3.00 (0.20), residues: 545 sheet: 0.78 (0.24), residues: 420 loop : 0.20 (0.26), residues: 635 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP B 112 HIS 0.002 0.000 HIS E 276 PHE 0.033 0.002 PHE D 385 TYR 0.016 0.002 TYR A 272 ARG 0.012 0.000 ARG D 257 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3200 Ramachandran restraints generated. 1600 Oldfield, 0 Emsley, 1600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3200 Ramachandran restraints generated. 1600 Oldfield, 0 Emsley, 1600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 1430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 246 time to evaluate : 1.613 Fit side-chains REVERT: A 75 ASP cc_start: 0.7826 (t0) cc_final: 0.7447 (t0) REVERT: A 81 MET cc_start: 0.8750 (ttp) cc_final: 0.8528 (ptm) REVERT: A 124 GLU cc_start: 0.8357 (mp0) cc_final: 0.7958 (mp0) REVERT: A 154 GLU cc_start: 0.8728 (tt0) cc_final: 0.8512 (tt0) REVERT: A 184 GLU cc_start: 0.8371 (pt0) cc_final: 0.8158 (pt0) REVERT: A 201 GLU cc_start: 0.8594 (mt-10) cc_final: 0.7971 (mp0) REVERT: A 214 GLN cc_start: 0.8216 (mm-40) cc_final: 0.7899 (pt0) REVERT: A 260 GLU cc_start: 0.8793 (pm20) cc_final: 0.8283 (pm20) REVERT: A 364 GLU cc_start: 0.8081 (mt-10) cc_final: 0.7608 (mt-10) REVERT: A 391 TRP cc_start: 0.8078 (m-90) cc_final: 0.7838 (m-90) REVERT: B 48 GLU cc_start: 0.8007 (tp30) cc_final: 0.7759 (tp30) REVERT: B 124 GLU cc_start: 0.8430 (mp0) cc_final: 0.7946 (mp0) REVERT: B 132 ASP cc_start: 0.7323 (t0) cc_final: 0.7020 (t0) REVERT: B 146 LYS cc_start: 0.8291 (mtmm) cc_final: 0.8003 (mtpp) REVERT: B 154 GLU cc_start: 0.8820 (tt0) cc_final: 0.8565 (tt0) REVERT: B 201 GLU cc_start: 0.8530 (mt-10) cc_final: 0.7992 (mp0) REVERT: B 214 GLN cc_start: 0.8319 (mm-40) cc_final: 0.8051 (pt0) REVERT: B 260 GLU cc_start: 0.8738 (pm20) cc_final: 0.8370 (pm20) REVERT: B 272 TYR cc_start: 0.8605 (t80) cc_final: 0.8339 (t80) REVERT: B 364 GLU cc_start: 0.7612 (mt-10) cc_final: 0.6665 (mp0) REVERT: B 391 TRP cc_start: 0.8191 (m-90) cc_final: 0.7937 (m-90) REVERT: C 112 TRP cc_start: 0.8242 (OUTLIER) cc_final: 0.7930 (t-100) REVERT: C 132 ASP cc_start: 0.7814 (OUTLIER) cc_final: 0.7507 (t0) REVERT: C 188 GLN cc_start: 0.8077 (tt0) cc_final: 0.7475 (tt0) REVERT: C 201 GLU cc_start: 0.8636 (mt-10) cc_final: 0.8032 (mp0) REVERT: C 260 GLU cc_start: 0.8924 (pm20) cc_final: 0.8552 (pm20) REVERT: D 113 GLU cc_start: 0.8730 (mp0) cc_final: 0.8115 (mp0) REVERT: D 364 GLU cc_start: 0.7932 (mt-10) cc_final: 0.7561 (mt-10) REVERT: D 372 LEU cc_start: 0.8044 (OUTLIER) cc_final: 0.7825 (tt) REVERT: D 391 TRP cc_start: 0.8183 (m-90) cc_final: 0.7951 (m-90) REVERT: E 112 TRP cc_start: 0.8170 (OUTLIER) cc_final: 0.7011 (t-100) REVERT: E 132 ASP cc_start: 0.7931 (OUTLIER) cc_final: 0.7630 (t0) REVERT: E 221 GLN cc_start: 0.8498 (pt0) cc_final: 0.8186 (pt0) REVERT: E 257 ARG cc_start: 0.8897 (ptp90) cc_final: 0.8274 (ptp-110) REVERT: E 260 GLU cc_start: 0.8925 (pm20) cc_final: 0.8497 (pm20) REVERT: E 285 SER cc_start: 0.8767 (t) cc_final: 0.8396 (t) REVERT: E 391 TRP cc_start: 0.8145 (m-90) cc_final: 0.7922 (m-10) outliers start: 46 outliers final: 24 residues processed: 272 average time/residue: 1.2543 time to fit residues: 371.9652 Evaluate side-chains 278 residues out of total 1430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 249 time to evaluate : 1.440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 LEU Chi-restraints excluded: chain A residue 210 GLN Chi-restraints excluded: chain A residue 275 LEU Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 373 VAL Chi-restraints excluded: chain A residue 394 CYS Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain B residue 372 LEU Chi-restraints excluded: chain B residue 373 VAL Chi-restraints excluded: chain C residue 112 TRP Chi-restraints excluded: chain C residue 132 ASP Chi-restraints excluded: chain C residue 172 SER Chi-restraints excluded: chain C residue 198 VAL Chi-restraints excluded: chain C residue 210 GLN Chi-restraints excluded: chain C residue 275 LEU Chi-restraints excluded: chain C residue 306 LEU Chi-restraints excluded: chain C residue 372 LEU Chi-restraints excluded: chain C residue 373 VAL Chi-restraints excluded: chain D residue 153 THR Chi-restraints excluded: chain D residue 299 ILE Chi-restraints excluded: chain D residue 372 LEU Chi-restraints excluded: chain D residue 373 VAL Chi-restraints excluded: chain E residue 112 TRP Chi-restraints excluded: chain E residue 132 ASP Chi-restraints excluded: chain E residue 198 VAL Chi-restraints excluded: chain E residue 275 LEU Chi-restraints excluded: chain E residue 372 LEU Chi-restraints excluded: chain E residue 373 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 32 optimal weight: 5.9990 chunk 10 optimal weight: 0.8980 chunk 153 optimal weight: 1.9990 chunk 89 optimal weight: 0.7980 chunk 101 optimal weight: 0.9990 chunk 27 optimal weight: 3.9990 chunk 28 optimal weight: 4.9990 chunk 8 optimal weight: 0.7980 chunk 116 optimal weight: 3.9990 chunk 50 optimal weight: 1.9990 chunk 71 optimal weight: 0.7980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 382 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.094573 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2958 r_free = 0.2958 target = 0.078530 restraints weight = 21141.009| |-----------------------------------------------------------------------------| r_work (start): 0.2929 rms_B_bonded: 3.00 r_work: 0.2766 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.2766 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2804 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2804 r_free = 0.2804 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.86 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2804 r_free = 0.2804 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.85 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2804 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7703 moved from start: 0.2797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 13385 Z= 0.197 Angle : 0.545 9.928 18305 Z= 0.261 Chirality : 0.040 0.146 2235 Planarity : 0.003 0.048 2250 Dihedral : 3.892 16.293 2060 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 2.17 % Allowed : 17.13 % Favored : 80.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.99 (0.21), residues: 1600 helix: 3.09 (0.20), residues: 545 sheet: 0.73 (0.23), residues: 440 loop : 0.19 (0.27), residues: 615 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP B 112 HIS 0.001 0.000 HIS D 163 PHE 0.025 0.001 PHE D 385 TYR 0.022 0.002 TYR B 176 ARG 0.010 0.000 ARG D 257 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3200 Ramachandran restraints generated. 1600 Oldfield, 0 Emsley, 1600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3200 Ramachandran restraints generated. 1600 Oldfield, 0 Emsley, 1600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 1430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 268 time to evaluate : 1.615 Fit side-chains REVERT: A 75 ASP cc_start: 0.7814 (t0) cc_final: 0.7433 (t0) REVERT: A 81 MET cc_start: 0.8733 (ttp) cc_final: 0.8514 (ptm) REVERT: A 124 GLU cc_start: 0.8384 (mp0) cc_final: 0.7833 (mp0) REVERT: A 184 GLU cc_start: 0.8368 (pt0) cc_final: 0.8159 (pt0) REVERT: A 201 GLU cc_start: 0.8595 (mt-10) cc_final: 0.7977 (mp0) REVERT: A 214 GLN cc_start: 0.8204 (mm-40) cc_final: 0.7941 (pt0) REVERT: A 260 GLU cc_start: 0.8810 (pm20) cc_final: 0.8333 (pm20) REVERT: A 364 GLU cc_start: 0.8058 (mt-10) cc_final: 0.7587 (mt-10) REVERT: A 391 TRP cc_start: 0.8053 (m-90) cc_final: 0.7813 (m-90) REVERT: B 48 GLU cc_start: 0.8010 (tp30) cc_final: 0.7750 (tp30) REVERT: B 124 GLU cc_start: 0.8431 (mp0) cc_final: 0.7986 (mp0) REVERT: B 132 ASP cc_start: 0.7331 (t0) cc_final: 0.7006 (t0) REVERT: B 146 LYS cc_start: 0.8287 (mtmm) cc_final: 0.8006 (mtpp) REVERT: B 154 GLU cc_start: 0.8817 (tt0) cc_final: 0.8589 (tt0) REVERT: B 201 GLU cc_start: 0.8553 (mt-10) cc_final: 0.8022 (mp0) REVERT: B 214 GLN cc_start: 0.8316 (mm-40) cc_final: 0.8048 (pt0) REVERT: B 260 GLU cc_start: 0.8771 (pm20) cc_final: 0.8403 (pm20) REVERT: B 272 TYR cc_start: 0.8544 (t80) cc_final: 0.8293 (t80) REVERT: B 364 GLU cc_start: 0.7534 (mt-10) cc_final: 0.6555 (mp0) REVERT: B 391 TRP cc_start: 0.8188 (m-90) cc_final: 0.7943 (m-90) REVERT: C 112 TRP cc_start: 0.8157 (OUTLIER) cc_final: 0.7841 (t-100) REVERT: C 129 ASP cc_start: 0.8600 (t0) cc_final: 0.8072 (t0) REVERT: C 132 ASP cc_start: 0.7792 (p0) cc_final: 0.7466 (t0) REVERT: C 154 GLU cc_start: 0.8707 (tt0) cc_final: 0.8342 (tt0) REVERT: C 188 GLN cc_start: 0.8103 (tt0) cc_final: 0.7484 (tt0) REVERT: C 201 GLU cc_start: 0.8679 (mt-10) cc_final: 0.8036 (mp0) REVERT: C 260 GLU cc_start: 0.8922 (pm20) cc_final: 0.8649 (pm20) REVERT: C 364 GLU cc_start: 0.8042 (mt-10) cc_final: 0.7638 (mt-10) REVERT: D 113 GLU cc_start: 0.8747 (mp0) cc_final: 0.8213 (mp0) REVERT: D 364 GLU cc_start: 0.7926 (mt-10) cc_final: 0.7550 (mt-10) REVERT: D 372 LEU cc_start: 0.8039 (OUTLIER) cc_final: 0.7692 (tp) REVERT: D 391 TRP cc_start: 0.8192 (m-90) cc_final: 0.7957 (m-90) REVERT: D 402 GLU cc_start: 0.8343 (mt-10) cc_final: 0.8091 (mm-30) REVERT: E 81 MET cc_start: 0.8678 (ttp) cc_final: 0.8397 (ptt) REVERT: E 112 TRP cc_start: 0.8075 (OUTLIER) cc_final: 0.6859 (t-100) REVERT: E 132 ASP cc_start: 0.7883 (OUTLIER) cc_final: 0.7610 (t0) REVERT: E 221 GLN cc_start: 0.8505 (pt0) cc_final: 0.8158 (pt0) REVERT: E 257 ARG cc_start: 0.8906 (ptp90) cc_final: 0.8268 (ptp-110) REVERT: E 260 GLU cc_start: 0.8939 (pm20) cc_final: 0.8551 (pm20) REVERT: E 285 SER cc_start: 0.8712 (t) cc_final: 0.8347 (t) outliers start: 31 outliers final: 14 residues processed: 286 average time/residue: 1.2865 time to fit residues: 400.2945 Evaluate side-chains 261 residues out of total 1430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 243 time to evaluate : 1.547 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 LEU Chi-restraints excluded: chain A residue 275 LEU Chi-restraints excluded: chain A residue 394 CYS Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain B residue 372 LEU Chi-restraints excluded: chain C residue 112 TRP Chi-restraints excluded: chain C residue 172 SER Chi-restraints excluded: chain C residue 210 GLN Chi-restraints excluded: chain C residue 275 LEU Chi-restraints excluded: chain C residue 306 LEU Chi-restraints excluded: chain C residue 372 LEU Chi-restraints excluded: chain D residue 153 THR Chi-restraints excluded: chain D residue 299 ILE Chi-restraints excluded: chain D residue 372 LEU Chi-restraints excluded: chain E residue 112 TRP Chi-restraints excluded: chain E residue 132 ASP Chi-restraints excluded: chain E residue 372 LEU Chi-restraints excluded: chain E residue 373 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 92 optimal weight: 4.9990 chunk 23 optimal weight: 0.9990 chunk 128 optimal weight: 5.9990 chunk 81 optimal weight: 4.9990 chunk 25 optimal weight: 0.9980 chunk 43 optimal weight: 0.9990 chunk 106 optimal weight: 4.9990 chunk 112 optimal weight: 2.9990 chunk 75 optimal weight: 0.7980 chunk 137 optimal weight: 6.9990 chunk 13 optimal weight: 3.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.094259 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 22)----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.078375 restraints weight = 20970.186| |-----------------------------------------------------------------------------| r_work (start): 0.2943 rms_B_bonded: 3.00 r_work: 0.2784 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.2784 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2791 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2791 r_free = 0.2791 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.85 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2791 r_free = 0.2791 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.85 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2791 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7693 moved from start: 0.2832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 13385 Z= 0.258 Angle : 0.579 10.472 18305 Z= 0.277 Chirality : 0.040 0.159 2235 Planarity : 0.003 0.043 2250 Dihedral : 3.893 14.419 2060 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 2.94 % Allowed : 16.99 % Favored : 80.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.96 (0.21), residues: 1600 helix: 3.07 (0.20), residues: 545 sheet: 0.71 (0.24), residues: 440 loop : 0.18 (0.27), residues: 615 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP B 112 HIS 0.002 0.000 HIS A 276 PHE 0.026 0.002 PHE D 385 TYR 0.030 0.002 TYR C 176 ARG 0.010 0.000 ARG D 257 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3200 Ramachandran restraints generated. 1600 Oldfield, 0 Emsley, 1600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3200 Ramachandran restraints generated. 1600 Oldfield, 0 Emsley, 1600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 1430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 249 time to evaluate : 1.603 Fit side-chains REVERT: A 75 ASP cc_start: 0.7791 (t0) cc_final: 0.7422 (t0) REVERT: A 112 TRP cc_start: 0.7986 (OUTLIER) cc_final: 0.7745 (t-100) REVERT: A 124 GLU cc_start: 0.8390 (mp0) cc_final: 0.7818 (mp0) REVERT: A 154 GLU cc_start: 0.8675 (tt0) cc_final: 0.8177 (tt0) REVERT: A 184 GLU cc_start: 0.8377 (pt0) cc_final: 0.8177 (pt0) REVERT: A 201 GLU cc_start: 0.8591 (mt-10) cc_final: 0.7969 (mp0) REVERT: A 214 GLN cc_start: 0.8167 (mm-40) cc_final: 0.7934 (pt0) REVERT: A 260 GLU cc_start: 0.8786 (pm20) cc_final: 0.8302 (pm20) REVERT: A 364 GLU cc_start: 0.8067 (mt-10) cc_final: 0.7626 (mt-10) REVERT: A 391 TRP cc_start: 0.8044 (m-90) cc_final: 0.7818 (m-90) REVERT: B 48 GLU cc_start: 0.8028 (tp30) cc_final: 0.7762 (tp30) REVERT: B 124 GLU cc_start: 0.8401 (mp0) cc_final: 0.7920 (mp0) REVERT: B 132 ASP cc_start: 0.7433 (t0) cc_final: 0.7111 (t0) REVERT: B 146 LYS cc_start: 0.8267 (mtmm) cc_final: 0.7985 (mtpp) REVERT: B 154 GLU cc_start: 0.8791 (tt0) cc_final: 0.8531 (tt0) REVERT: B 201 GLU cc_start: 0.8553 (mt-10) cc_final: 0.8000 (mp0) REVERT: B 214 GLN cc_start: 0.8304 (mm-40) cc_final: 0.8032 (pt0) REVERT: B 260 GLU cc_start: 0.8782 (pm20) cc_final: 0.8415 (pm20) REVERT: B 272 TYR cc_start: 0.8562 (t80) cc_final: 0.8285 (t80) REVERT: B 364 GLU cc_start: 0.7486 (OUTLIER) cc_final: 0.6518 (mp0) REVERT: B 391 TRP cc_start: 0.8215 (m-90) cc_final: 0.7962 (m-90) REVERT: C 75 ASP cc_start: 0.7533 (t0) cc_final: 0.6941 (t0) REVERT: C 112 TRP cc_start: 0.8084 (OUTLIER) cc_final: 0.7420 (t-100) REVERT: C 124 GLU cc_start: 0.8238 (mp0) cc_final: 0.7977 (mp0) REVERT: C 132 ASP cc_start: 0.7811 (OUTLIER) cc_final: 0.7455 (t0) REVERT: C 146 LYS cc_start: 0.8135 (OUTLIER) cc_final: 0.7683 (mtpp) REVERT: C 154 GLU cc_start: 0.8663 (tt0) cc_final: 0.8300 (tt0) REVERT: C 188 GLN cc_start: 0.8049 (tt0) cc_final: 0.7435 (tt0) REVERT: C 201 GLU cc_start: 0.8667 (mt-10) cc_final: 0.8035 (mp0) REVERT: C 260 GLU cc_start: 0.8931 (pm20) cc_final: 0.8599 (pm20) REVERT: C 364 GLU cc_start: 0.8060 (mt-10) cc_final: 0.7688 (mt-10) REVERT: D 113 GLU cc_start: 0.8740 (mp0) cc_final: 0.8431 (mp0) REVERT: D 364 GLU cc_start: 0.7938 (mt-10) cc_final: 0.7559 (mt-10) REVERT: D 372 LEU cc_start: 0.8030 (OUTLIER) cc_final: 0.7818 (tt) REVERT: D 402 GLU cc_start: 0.8339 (mt-10) cc_final: 0.8087 (mm-30) REVERT: E 81 MET cc_start: 0.8634 (ttp) cc_final: 0.8378 (ptt) REVERT: E 112 TRP cc_start: 0.8163 (OUTLIER) cc_final: 0.6962 (t-100) REVERT: E 132 ASP cc_start: 0.7897 (OUTLIER) cc_final: 0.7591 (t0) REVERT: E 221 GLN cc_start: 0.8521 (pt0) cc_final: 0.8138 (pt0) REVERT: E 257 ARG cc_start: 0.8896 (ptp90) cc_final: 0.8246 (ptp-110) REVERT: E 260 GLU cc_start: 0.8928 (pm20) cc_final: 0.8530 (pm20) REVERT: E 285 SER cc_start: 0.8710 (t) cc_final: 0.8366 (t) outliers start: 42 outliers final: 21 residues processed: 269 average time/residue: 1.3519 time to fit residues: 395.0844 Evaluate side-chains 276 residues out of total 1430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 247 time to evaluate : 1.651 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 TRP Chi-restraints excluded: chain A residue 123 LEU Chi-restraints excluded: chain A residue 275 LEU Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 373 VAL Chi-restraints excluded: chain A residue 394 CYS Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain B residue 364 GLU Chi-restraints excluded: chain B residue 372 LEU Chi-restraints excluded: chain C residue 112 TRP Chi-restraints excluded: chain C residue 132 ASP Chi-restraints excluded: chain C residue 146 LYS Chi-restraints excluded: chain C residue 172 SER Chi-restraints excluded: chain C residue 179 SER Chi-restraints excluded: chain C residue 210 GLN Chi-restraints excluded: chain C residue 275 LEU Chi-restraints excluded: chain C residue 306 LEU Chi-restraints excluded: chain C residue 372 LEU Chi-restraints excluded: chain C residue 373 VAL Chi-restraints excluded: chain D residue 123 LEU Chi-restraints excluded: chain D residue 153 THR Chi-restraints excluded: chain D residue 172 SER Chi-restraints excluded: chain D residue 299 ILE Chi-restraints excluded: chain D residue 372 LEU Chi-restraints excluded: chain D residue 373 VAL Chi-restraints excluded: chain E residue 112 TRP Chi-restraints excluded: chain E residue 132 ASP Chi-restraints excluded: chain E residue 372 LEU Chi-restraints excluded: chain E residue 373 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 49 optimal weight: 3.9990 chunk 23 optimal weight: 0.9980 chunk 85 optimal weight: 2.9990 chunk 1 optimal weight: 5.9990 chunk 127 optimal weight: 0.0980 chunk 73 optimal weight: 5.9990 chunk 106 optimal weight: 4.9990 chunk 136 optimal weight: 3.9990 chunk 81 optimal weight: 0.9990 chunk 22 optimal weight: 0.6980 chunk 8 optimal weight: 3.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 382 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.094007 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2949 r_free = 0.2949 target = 0.078013 restraints weight = 20908.525| |-----------------------------------------------------------------------------| r_work (start): 0.2946 rms_B_bonded: 3.00 r_work: 0.2788 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.2788 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2797 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2797 r_free = 0.2797 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.85 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2797 r_free = 0.2797 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.85 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2797 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7687 moved from start: 0.2862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 13385 Z= 0.234 Angle : 0.583 10.938 18305 Z= 0.277 Chirality : 0.040 0.145 2235 Planarity : 0.004 0.041 2250 Dihedral : 3.887 14.349 2060 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 2.17 % Allowed : 18.11 % Favored : 79.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.95 (0.21), residues: 1600 helix: 3.09 (0.20), residues: 545 sheet: 0.73 (0.24), residues: 420 loop : 0.12 (0.26), residues: 635 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP B 112 HIS 0.001 0.000 HIS A 276 PHE 0.024 0.002 PHE D 385 TYR 0.034 0.002 TYR E 176 ARG 0.010 0.000 ARG D 257 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3200 Ramachandran restraints generated. 1600 Oldfield, 0 Emsley, 1600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3200 Ramachandran restraints generated. 1600 Oldfield, 0 Emsley, 1600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 1430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 251 time to evaluate : 1.456 Fit side-chains REVERT: A 75 ASP cc_start: 0.7784 (t0) cc_final: 0.7415 (t0) REVERT: A 81 MET cc_start: 0.8736 (ttp) cc_final: 0.8387 (ptt) REVERT: A 124 GLU cc_start: 0.8387 (mp0) cc_final: 0.7816 (mp0) REVERT: A 184 GLU cc_start: 0.8377 (pt0) cc_final: 0.8167 (pt0) REVERT: A 201 GLU cc_start: 0.8592 (mt-10) cc_final: 0.7964 (mp0) REVERT: A 260 GLU cc_start: 0.8792 (pm20) cc_final: 0.8309 (pm20) REVERT: A 364 GLU cc_start: 0.8057 (mt-10) cc_final: 0.7612 (mt-10) REVERT: A 391 TRP cc_start: 0.8020 (m-90) cc_final: 0.7792 (m-90) REVERT: B 48 GLU cc_start: 0.8041 (tp30) cc_final: 0.7768 (tp30) REVERT: B 124 GLU cc_start: 0.8388 (mp0) cc_final: 0.7905 (mp0) REVERT: B 146 LYS cc_start: 0.8267 (mtmm) cc_final: 0.7985 (mtpp) REVERT: B 154 GLU cc_start: 0.8797 (tt0) cc_final: 0.8540 (tt0) REVERT: B 201 GLU cc_start: 0.8550 (mt-10) cc_final: 0.8000 (mp0) REVERT: B 214 GLN cc_start: 0.8300 (mm-40) cc_final: 0.8031 (pt0) REVERT: B 260 GLU cc_start: 0.8778 (pm20) cc_final: 0.8409 (pm20) REVERT: B 272 TYR cc_start: 0.8577 (t80) cc_final: 0.8289 (t80) REVERT: B 364 GLU cc_start: 0.7478 (mt-10) cc_final: 0.6506 (mp0) REVERT: B 391 TRP cc_start: 0.8187 (m-90) cc_final: 0.7927 (m-90) REVERT: C 75 ASP cc_start: 0.7547 (t0) cc_final: 0.7150 (t0) REVERT: C 123 LEU cc_start: 0.8731 (mt) cc_final: 0.8453 (mt) REVERT: C 124 GLU cc_start: 0.8338 (mp0) cc_final: 0.8044 (mp0) REVERT: C 132 ASP cc_start: 0.7765 (OUTLIER) cc_final: 0.7430 (t0) REVERT: C 154 GLU cc_start: 0.8683 (tt0) cc_final: 0.8297 (tt0) REVERT: C 188 GLN cc_start: 0.8052 (tt0) cc_final: 0.7440 (tt0) REVERT: C 201 GLU cc_start: 0.8670 (mt-10) cc_final: 0.8035 (mp0) REVERT: C 260 GLU cc_start: 0.8932 (pm20) cc_final: 0.8634 (pm20) REVERT: C 364 GLU cc_start: 0.8069 (mt-10) cc_final: 0.7670 (mt-10) REVERT: D 81 MET cc_start: 0.8276 (ttp) cc_final: 0.8052 (ttm) REVERT: D 112 TRP cc_start: 0.8033 (t-100) cc_final: 0.7788 (t-100) REVERT: D 113 GLU cc_start: 0.8711 (mp0) cc_final: 0.8111 (mp0) REVERT: D 364 GLU cc_start: 0.7934 (mt-10) cc_final: 0.7550 (mt-10) REVERT: D 372 LEU cc_start: 0.8021 (OUTLIER) cc_final: 0.7667 (tp) REVERT: D 402 GLU cc_start: 0.8304 (mt-10) cc_final: 0.8065 (mm-30) REVERT: E 81 MET cc_start: 0.8627 (ttp) cc_final: 0.8378 (ptt) REVERT: E 112 TRP cc_start: 0.8141 (OUTLIER) cc_final: 0.6946 (t-100) REVERT: E 132 ASP cc_start: 0.7855 (OUTLIER) cc_final: 0.7583 (t0) REVERT: E 221 GLN cc_start: 0.8503 (pt0) cc_final: 0.8162 (pt0) REVERT: E 257 ARG cc_start: 0.8887 (ptp90) cc_final: 0.8243 (ptp-110) REVERT: E 260 GLU cc_start: 0.8921 (pm20) cc_final: 0.8518 (pm20) REVERT: E 285 SER cc_start: 0.8687 (t) cc_final: 0.8348 (t) outliers start: 31 outliers final: 18 residues processed: 266 average time/residue: 1.3797 time to fit residues: 398.5641 Evaluate side-chains 270 residues out of total 1430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 248 time to evaluate : 1.673 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 LEU Chi-restraints excluded: chain A residue 275 LEU Chi-restraints excluded: chain A residue 373 VAL Chi-restraints excluded: chain A residue 394 CYS Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain B residue 372 LEU Chi-restraints excluded: chain C residue 132 ASP Chi-restraints excluded: chain C residue 172 SER Chi-restraints excluded: chain C residue 210 GLN Chi-restraints excluded: chain C residue 275 LEU Chi-restraints excluded: chain C residue 306 LEU Chi-restraints excluded: chain C residue 372 LEU Chi-restraints excluded: chain C residue 373 VAL Chi-restraints excluded: chain D residue 123 LEU Chi-restraints excluded: chain D residue 153 THR Chi-restraints excluded: chain D residue 299 ILE Chi-restraints excluded: chain D residue 372 LEU Chi-restraints excluded: chain D residue 373 VAL Chi-restraints excluded: chain E residue 112 TRP Chi-restraints excluded: chain E residue 132 ASP Chi-restraints excluded: chain E residue 372 LEU Chi-restraints excluded: chain E residue 373 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 74 optimal weight: 1.9990 chunk 1 optimal weight: 2.9990 chunk 88 optimal weight: 0.0670 chunk 126 optimal weight: 3.9990 chunk 111 optimal weight: 0.8980 chunk 10 optimal weight: 3.9990 chunk 56 optimal weight: 2.9990 chunk 154 optimal weight: 1.9990 chunk 36 optimal weight: 0.7980 chunk 83 optimal weight: 0.9980 chunk 127 optimal weight: 0.0040 overall best weight: 0.5530 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.096289 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.080338 restraints weight = 20776.476| |-----------------------------------------------------------------------------| r_work (start): 0.2977 rms_B_bonded: 3.02 r_work: 0.2819 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.2819 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2831 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2831 r_free = 0.2831 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.85 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2831 r_free = 0.2831 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.85 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2831 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7665 moved from start: 0.2880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 13385 Z= 0.167 Angle : 0.563 10.471 18305 Z= 0.266 Chirality : 0.039 0.147 2235 Planarity : 0.003 0.038 2250 Dihedral : 3.782 14.958 2060 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 1.12 % Allowed : 19.58 % Favored : 79.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.02 (0.21), residues: 1600 helix: 3.27 (0.20), residues: 540 sheet: 0.75 (0.24), residues: 420 loop : 0.09 (0.26), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP C 112 HIS 0.001 0.000 HIS A 276 PHE 0.020 0.001 PHE A 385 TYR 0.030 0.002 TYR E 176 ARG 0.010 0.000 ARG D 257 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8390.04 seconds wall clock time: 149 minutes 32.37 seconds (8972.37 seconds total)