Starting phenix.real_space_refine on Wed Jun 11 17:48:51 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8yx7_39649/06_2025/8yx7_39649.cif Found real_map, /net/cci-nas-00/data/ceres_data/8yx7_39649/06_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_39649/06_2025/8yx7_39649.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8yx7_39649/06_2025/8yx7_39649.map" model { file = "/net/cci-nas-00/data/ceres_data/8yx7_39649/06_2025/8yx7_39649.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8yx7_39649/06_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-5710/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: 5.78, per 1000 atoms: 0.44 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=10, 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 Simple disulfide: pdb=" SG CYS C 157 " - pdb=" SG CYS C 171 " distance=2.03 Simple disulfide: pdb=" SG CYS B 157 " - pdb=" SG CYS B 171 " distance=2.03 Simple disulfide: pdb=" SG CYS E 157 " - pdb=" SG CYS E 171 " distance=2.03 Simple disulfide: pdb=" SG CYS D 157 " - pdb=" SG CYS D 171 " distance=2.03 Simple disulfide: pdb=" SG CYS C 289 " - pdb=" SG CYS C 394 " distance=2.03 Simple disulfide: pdb=" SG CYS B 289 " - pdb=" SG CYS B 394 " distance=2.03 Simple disulfide: pdb=" SG CYS E 289 " - pdb=" SG CYS E 394 " distance=2.03 Simple disulfide: pdb=" SG CYS D 289 " - pdb=" SG CYS D 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: 3.18 Conformation dependent library (CDL) restraints added in 1.7 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: 1.38 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: 4.13 Time building geometry restraints manager: 3.77 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: 7030 11.22 - 22.45: 795 22.45 - 33.67: 270 33.67 - 44.90: 65 44.90 - 56.12: 20 Dihedral angle restraints: 8180 sinusoidal: 3385 harmonic: 4795 Sorted by residual: dihedral pdb=" CB CYS D 289 " pdb=" SG CYS D 289 " pdb=" SG CYS D 394 " pdb=" CB CYS D 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=" 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=" CB CYS C 289 " pdb=" SG CYS C 289 " pdb=" SG CYS C 394 " pdb=" CB CYS C 394 " ideal model delta sinusoidal sigma weight residual -86.00 -117.08 31.08 1 1.00e+01 1.00e-02 1.38e+01 ... (remaining 8177 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: 2.23 - 2.76: 1814 2.76 - 3.30: 12090 3.30 - 3.83: 22021 3.83 - 4.37: 25754 4.37 - 4.90: 45159 Nonbonded interactions: 106838 Sorted by model distance: nonbonded pdb=" O ALA B 247 " pdb=" OH TYR B 264 " model vdw 2.227 3.040 nonbonded pdb=" O ALA C 247 " pdb=" OH TYR C 264 " model vdw 2.227 3.040 nonbonded pdb=" O ALA D 247 " pdb=" OH TYR D 264 " model vdw 2.227 3.040 nonbonded pdb=" O ALA A 247 " pdb=" OH TYR A 264 " model vdw 2.227 3.040 nonbonded pdb=" O ALA E 247 " pdb=" OH TYR E 264 " model vdw 2.227 3.040 ... (remaining 106833 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: 0.10 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: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 17.750 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.490 Check model and map are aligned: 0.080 Set scattering table: 0.140 Process input model: 28.840 Find NCS groups from input model: 0.250 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: 0.000 Load rotamer database and sin/cos tables:14.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 61.700 ------------------------------------------------------------------------------- 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 13410 Z= 0.346 Angle : 0.581 5.926 18370 Z= 0.264 Chirality : 0.041 0.147 2235 Planarity : 0.003 0.024 2250 Dihedral : 10.872 56.122 5010 Min Nonbonded Distance : 2.227 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 Details of bonding type rmsd link_NAG-ASN : bond 0.00101 ( 10) link_NAG-ASN : angle 1.01321 ( 30) link_BETA1-4 : bond 0.00084 ( 5) link_BETA1-4 : angle 0.47366 ( 15) hydrogen bonds : bond 0.11820 ( 680) hydrogen bonds : angle 4.49157 ( 2100) SS BOND : bond 0.00077 ( 10) SS BOND : angle 1.05905 ( 20) covalent geometry : bond 0.00701 (13385) covalent geometry : angle 0.57898 (18305) *********************** 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 : 1.467 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: 1.1188 time to fit residues: 525.8452 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 : 1.410 ------------------------------------------------------------------------------- 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: 3.9990 chunk 93 optimal weight: 4.9990 chunk 145 optimal weight: 0.0470 overall best weight: 1.7082 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 GLN B 188 GLN C 156 ASN C 382 GLN D 188 GLN E 188 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.095689 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2967 r_free = 0.2967 target = 0.079191 restraints weight = 20701.630| |-----------------------------------------------------------------------------| r_work (start): 0.2963 rms_B_bonded: 3.04 r_work: 0.2800 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.2800 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2784 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2784 r_free = 0.2784 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.80 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2784 r_free = 0.2784 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.85 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2784 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7691 moved from start: 0.1939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 13410 Z= 0.206 Angle : 0.599 6.591 18370 Z= 0.292 Chirality : 0.042 0.147 2235 Planarity : 0.004 0.048 2250 Dihedral : 4.433 30.450 2062 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 3.64 % Allowed : 10.70 % Favored : 85.66 % 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: 2.34 (0.21), residues: 1600 helix: 3.55 (0.20), residues: 515 sheet: 1.26 (0.24), residues: 430 loop : 0.13 (0.25), residues: 655 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 112 HIS 0.002 0.001 HIS B 276 PHE 0.021 0.002 PHE C 72 TYR 0.015 0.002 TYR D 176 ARG 0.007 0.001 ARG B 257 Details of bonding type rmsd link_NAG-ASN : bond 0.00421 ( 10) link_NAG-ASN : angle 1.86240 ( 30) link_BETA1-4 : bond 0.00391 ( 5) link_BETA1-4 : angle 0.81250 ( 15) hydrogen bonds : bond 0.04142 ( 680) hydrogen bonds : angle 3.93203 ( 2100) SS BOND : bond 0.00807 ( 10) SS BOND : angle 1.53255 ( 20) covalent geometry : bond 0.00473 (13385) covalent geometry : angle 0.59254 (18305) *********************** 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 346 residues out of total 1430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 294 time to evaluate : 1.427 Fit side-chains REVERT: A 75 ASP cc_start: 0.7818 (t0) cc_final: 0.7473 (t0) REVERT: A 201 GLU cc_start: 0.8560 (mt-10) cc_final: 0.7951 (mp0) REVERT: A 260 GLU cc_start: 0.8762 (OUTLIER) cc_final: 0.8394 (pm20) REVERT: A 391 TRP cc_start: 0.8068 (m-90) cc_final: 0.7846 (m-90) REVERT: B 48 GLU cc_start: 0.7851 (tp30) cc_final: 0.7561 (tp30) REVERT: B 112 TRP cc_start: 0.8044 (OUTLIER) cc_final: 0.7543 (t-100) REVERT: B 124 GLU cc_start: 0.8475 (mp0) cc_final: 0.8134 (mp0) REVERT: B 154 GLU cc_start: 0.8743 (tt0) cc_final: 0.8539 (tt0) REVERT: B 201 GLU cc_start: 0.8495 (mt-10) cc_final: 0.8005 (mp0) REVERT: B 391 TRP cc_start: 0.8152 (m-90) cc_final: 0.7836 (m-90) REVERT: C 124 GLU cc_start: 0.8429 (mp0) cc_final: 0.8121 (mp0) REVERT: C 154 GLU cc_start: 0.8804 (tt0) cc_final: 0.8592 (tt0) REVERT: C 201 GLU cc_start: 0.8597 (mt-10) cc_final: 0.8057 (mp0) REVERT: C 221 GLN cc_start: 0.8497 (pt0) cc_final: 0.7878 (pt0) REVERT: D 78 ARG cc_start: 0.8557 (OUTLIER) cc_final: 0.8264 (mtp85) REVERT: D 113 GLU cc_start: 0.8549 (mp0) cc_final: 0.8223 (mp0) REVERT: D 124 GLU cc_start: 0.8362 (mp0) cc_final: 0.7980 (mp0) REVERT: D 160 GLU cc_start: 0.8206 (OUTLIER) cc_final: 0.8000 (mt-10) REVERT: D 364 GLU cc_start: 0.7851 (mt-10) cc_final: 0.7432 (mt-10) REVERT: D 372 LEU cc_start: 0.8091 (OUTLIER) cc_final: 0.7862 (tt) REVERT: D 391 TRP cc_start: 0.8207 (m-90) cc_final: 0.7914 (m-10) REVERT: E 113 GLU cc_start: 0.8567 (mp0) cc_final: 0.8337 (mp0) REVERT: E 124 GLU cc_start: 0.8366 (mp0) cc_final: 0.8073 (mp0) REVERT: E 214 GLN cc_start: 0.8104 (mm-40) cc_final: 0.7840 (pt0) REVERT: E 221 GLN cc_start: 0.8498 (pt0) cc_final: 0.8094 (pt0) REVERT: E 257 ARG cc_start: 0.8933 (ptp90) cc_final: 0.8281 (ptp-110) REVERT: E 391 TRP cc_start: 0.8147 (m-90) cc_final: 0.7865 (m-10) outliers start: 52 outliers final: 22 residues processed: 325 average time/residue: 1.4471 time to fit residues: 514.7045 Evaluate side-chains 285 residues out of total 1430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 258 time to evaluate : 1.492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain A residue 260 GLU 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 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 160 GLU Chi-restraints excluded: chain D residue 191 VAL Chi-restraints excluded: chain D residue 198 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: 1.9990 chunk 88 optimal weight: 3.9990 chunk 65 optimal weight: 2.9990 chunk 98 optimal weight: 0.9980 chunk 63 optimal weight: 0.7980 chunk 114 optimal weight: 2.9990 chunk 42 optimal weight: 3.9990 chunk 53 optimal weight: 0.9980 chunk 105 optimal weight: 3.9990 chunk 92 optimal weight: 4.9990 chunk 102 optimal weight: 0.7980 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 188 GLN D 188 GLN E 382 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.096021 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2979 r_free = 0.2979 target = 0.079755 restraints weight = 20766.718| |-----------------------------------------------------------------------------| r_work (start): 0.2963 rms_B_bonded: 3.00 r_work: 0.2800 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.2800 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2786 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2786 r_free = 0.2786 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 = 0.2786 r_free = 0.2786 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.87 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2786 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7682 moved from start: 0.2128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 13410 Z= 0.150 Angle : 0.547 6.914 18370 Z= 0.265 Chirality : 0.040 0.146 2235 Planarity : 0.004 0.031 2250 Dihedral : 4.154 29.776 2062 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 3.36 % Allowed : 13.57 % Favored : 83.08 % 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: 1.12 (0.24), residues: 420 loop : 0.06 (0.25), residues: 665 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 112 HIS 0.002 0.000 HIS D 276 PHE 0.018 0.001 PHE E 72 TYR 0.015 0.002 TYR D 176 ARG 0.006 0.000 ARG E 78 Details of bonding type rmsd link_NAG-ASN : bond 0.00201 ( 10) link_NAG-ASN : angle 1.31892 ( 30) link_BETA1-4 : bond 0.00064 ( 5) link_BETA1-4 : angle 0.83297 ( 15) hydrogen bonds : bond 0.03962 ( 680) hydrogen bonds : angle 3.84498 ( 2100) SS BOND : bond 0.00569 ( 10) SS BOND : angle 1.35039 ( 20) covalent geometry : bond 0.00343 (13385) covalent geometry : angle 0.54342 (18305) *********************** 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 339 residues out of total 1430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 291 time to evaluate : 1.549 Fit side-chains REVERT: A 75 ASP cc_start: 0.7791 (t0) cc_final: 0.7420 (t0) REVERT: A 124 GLU cc_start: 0.8346 (mp0) cc_final: 0.7963 (mp0) REVERT: A 184 GLU cc_start: 0.8279 (pt0) cc_final: 0.8036 (pt0) REVERT: A 201 GLU cc_start: 0.8577 (mt-10) cc_final: 0.7943 (mp0) REVERT: A 221 GLN cc_start: 0.8577 (pt0) cc_final: 0.8078 (pt0) REVERT: A 260 GLU cc_start: 0.8727 (pt0) cc_final: 0.8415 (pm20) REVERT: B 48 GLU cc_start: 0.7871 (tp30) cc_final: 0.7517 (tp30) REVERT: B 75 ASP cc_start: 0.7587 (t0) cc_final: 0.7205 (t0) REVERT: B 113 GLU cc_start: 0.8798 (mp0) cc_final: 0.8456 (mp0) REVERT: B 124 GLU cc_start: 0.8425 (mp0) cc_final: 0.8019 (mp0) REVERT: B 201 GLU cc_start: 0.8522 (mt-10) cc_final: 0.8026 (mp0) REVERT: B 260 GLU cc_start: 0.8595 (pm20) cc_final: 0.8338 (pm20) REVERT: B 391 TRP cc_start: 0.8111 (m-90) cc_final: 0.7816 (m-90) REVERT: C 112 TRP cc_start: 0.8089 (OUTLIER) cc_final: 0.7238 (t-100) REVERT: C 132 ASP cc_start: 0.8055 (p0) cc_final: 0.7619 (t0) REVERT: C 176 TYR cc_start: 0.8419 (m-80) cc_final: 0.8102 (m-80) REVERT: C 188 GLN cc_start: 0.8089 (tt0) cc_final: 0.7517 (tt0) REVERT: C 201 GLU cc_start: 0.8615 (mt-10) cc_final: 0.8049 (mp0) REVERT: D 75 ASP cc_start: 0.7656 (t0) cc_final: 0.7415 (t0) REVERT: D 78 ARG cc_start: 0.8547 (OUTLIER) cc_final: 0.8259 (mtp85) REVERT: D 113 GLU cc_start: 0.8515 (mp0) cc_final: 0.8282 (mp0) REVERT: D 160 GLU cc_start: 0.8217 (OUTLIER) cc_final: 0.7933 (mt-10) REVERT: D 364 GLU cc_start: 0.7845 (mt-10) cc_final: 0.7624 (mt-10) REVERT: D 372 LEU cc_start: 0.8061 (OUTLIER) cc_final: 0.7842 (tt) REVERT: D 391 TRP cc_start: 0.8188 (m-90) cc_final: 0.7900 (m-90) REVERT: E 132 ASP cc_start: 0.8003 (OUTLIER) cc_final: 0.7601 (t0) REVERT: E 214 GLN cc_start: 0.8104 (mm-40) cc_final: 0.7874 (pt0) REVERT: E 221 GLN cc_start: 0.8451 (pt0) cc_final: 0.8072 (pt0) REVERT: E 257 ARG cc_start: 0.8935 (ptp90) cc_final: 0.8270 (ptp-110) REVERT: E 259 ILE cc_start: 0.9404 (pt) cc_final: 0.9194 (mp) REVERT: E 260 GLU cc_start: 0.8847 (pm20) cc_final: 0.8301 (pm20) REVERT: E 382 GLN cc_start: 0.8404 (mm110) cc_final: 0.8136 (mm-40) REVERT: E 391 TRP cc_start: 0.8128 (m-90) cc_final: 0.7817 (m-10) outliers start: 48 outliers final: 19 residues processed: 322 average time/residue: 1.1391 time to fit residues: 401.8617 Evaluate side-chains 296 residues out of total 1430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 272 time to evaluate : 1.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain A residue 275 LEU Chi-restraints excluded: chain B residue 210 GLN 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 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 160 GLU 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 299 ILE Chi-restraints excluded: chain E residue 372 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 88 optimal weight: 0.9980 chunk 83 optimal weight: 0.0670 chunk 135 optimal weight: 1.9990 chunk 5 optimal weight: 7.9990 chunk 138 optimal weight: 0.9980 chunk 15 optimal weight: 5.9990 chunk 106 optimal weight: 3.9990 chunk 113 optimal weight: 3.9990 chunk 46 optimal weight: 0.9980 chunk 148 optimal weight: 4.9990 chunk 98 optimal weight: 1.9990 overall best weight: 1.0120 ------------------------------------------------------------------------------- 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 = 0.3226 r_free = 0.3226 target = 0.096133 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.079944 restraints weight = 20547.771| |-----------------------------------------------------------------------------| r_work (start): 0.2998 rms_B_bonded: 2.99 r_work: 0.2835 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.2835 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2814 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2814 r_free = 0.2814 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.87 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2814 r_free = 0.2814 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.87 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2814 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7717 moved from start: 0.2345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 13410 Z= 0.139 Angle : 0.531 6.963 18370 Z= 0.259 Chirality : 0.040 0.144 2235 Planarity : 0.004 0.037 2250 Dihedral : 3.982 30.801 2062 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 3.57 % Allowed : 14.41 % Favored : 82.03 % 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: 2.12 (0.21), residues: 1600 helix: 3.43 (0.20), residues: 515 sheet: 0.96 (0.24), residues: 420 loop : 0.10 (0.25), residues: 665 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 112 HIS 0.002 0.000 HIS D 276 PHE 0.018 0.001 PHE E 72 TYR 0.013 0.002 TYR B 176 ARG 0.007 0.000 ARG D 257 Details of bonding type rmsd link_NAG-ASN : bond 0.00104 ( 10) link_NAG-ASN : angle 1.24945 ( 30) link_BETA1-4 : bond 0.00067 ( 5) link_BETA1-4 : angle 0.88571 ( 15) hydrogen bonds : bond 0.03831 ( 680) hydrogen bonds : angle 3.78643 ( 2100) SS BOND : bond 0.00409 ( 10) SS BOND : angle 1.00084 ( 20) covalent geometry : bond 0.00317 (13385) covalent geometry : angle 0.52824 (18305) *********************** 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 332 residues out of total 1430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 281 time to evaluate : 1.464 Fit side-chains REVERT: A 75 ASP cc_start: 0.7866 (t0) cc_final: 0.7488 (t0) REVERT: A 81 MET cc_start: 0.8708 (ttp) cc_final: 0.8464 (ptm) REVERT: A 112 TRP cc_start: 0.8118 (OUTLIER) cc_final: 0.7427 (t-100) REVERT: A 124 GLU cc_start: 0.8390 (mp0) cc_final: 0.7968 (mp0) REVERT: A 132 ASP cc_start: 0.7404 (t0) cc_final: 0.7171 (p0) REVERT: A 201 GLU cc_start: 0.8618 (mt-10) cc_final: 0.7987 (mp0) REVERT: A 214 GLN cc_start: 0.8182 (mm-40) cc_final: 0.7880 (pt0) REVERT: A 221 GLN cc_start: 0.8633 (pt0) cc_final: 0.8138 (pt0) REVERT: A 260 GLU cc_start: 0.8725 (pt0) cc_final: 0.8422 (pm20) REVERT: A 402 GLU cc_start: 0.7577 (mt-10) cc_final: 0.7321 (pt0) REVERT: B 48 GLU cc_start: 0.7921 (tp30) cc_final: 0.7564 (tp30) REVERT: B 75 ASP cc_start: 0.7684 (t0) cc_final: 0.7286 (t0) REVERT: B 113 GLU cc_start: 0.8788 (mp0) cc_final: 0.8385 (mp0) REVERT: B 124 GLU cc_start: 0.8472 (mp0) cc_final: 0.7981 (mp0) REVERT: B 132 ASP cc_start: 0.7426 (t0) cc_final: 0.7189 (p0) REVERT: B 201 GLU cc_start: 0.8557 (mt-10) cc_final: 0.8069 (mp0) REVERT: B 214 GLN cc_start: 0.8284 (mm-40) cc_final: 0.8073 (pt0) REVERT: B 260 GLU cc_start: 0.8635 (pm20) cc_final: 0.8325 (pm20) REVERT: B 391 TRP cc_start: 0.8095 (m-90) cc_final: 0.7794 (m-90) REVERT: C 112 TRP cc_start: 0.8064 (OUTLIER) cc_final: 0.7271 (t-100) REVERT: C 132 ASP cc_start: 0.7968 (OUTLIER) cc_final: 0.7588 (t0) REVERT: C 176 TYR cc_start: 0.8380 (m-80) cc_final: 0.8080 (m-80) REVERT: C 188 GLN cc_start: 0.8167 (tt0) cc_final: 0.7585 (tt0) REVERT: C 201 GLU cc_start: 0.8627 (mt-10) cc_final: 0.8061 (mp0) REVERT: D 63 ASP cc_start: 0.8353 (t70) cc_final: 0.8066 (t0) REVERT: D 112 TRP cc_start: 0.8124 (OUTLIER) cc_final: 0.7371 (t-100) REVERT: D 364 GLU cc_start: 0.7842 (mt-10) cc_final: 0.7443 (mt-10) REVERT: D 372 LEU cc_start: 0.8076 (OUTLIER) cc_final: 0.7861 (tt) REVERT: D 391 TRP cc_start: 0.8187 (m-90) cc_final: 0.7901 (m-90) REVERT: E 132 ASP cc_start: 0.8032 (OUTLIER) cc_final: 0.7610 (t0) REVERT: E 214 GLN cc_start: 0.8153 (mm-40) cc_final: 0.7904 (pt0) REVERT: E 221 GLN cc_start: 0.8479 (pt0) cc_final: 0.8104 (pt0) REVERT: E 257 ARG cc_start: 0.8916 (ptp90) cc_final: 0.8264 (ptp-110) REVERT: E 260 GLU cc_start: 0.8868 (pm20) cc_final: 0.8344 (pm20) REVERT: E 391 TRP cc_start: 0.8140 (m-90) cc_final: 0.7871 (m-10) outliers start: 51 outliers final: 20 residues processed: 311 average time/residue: 1.1106 time to fit residues: 379.5912 Evaluate side-chains 291 residues out of total 1430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 265 time to evaluate : 1.588 ------------------------------------------------------------------------------- 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 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 132 ASP Chi-restraints excluded: chain C residue 198 VAL Chi-restraints excluded: chain C residue 259 ILE Chi-restraints excluded: chain C residue 306 LEU Chi-restraints excluded: chain C residue 373 VAL Chi-restraints excluded: chain D residue 112 TRP Chi-restraints excluded: chain D residue 146 LYS Chi-restraints excluded: chain D residue 198 VAL Chi-restraints excluded: chain D residue 299 ILE Chi-restraints excluded: chain D residue 372 LEU Chi-restraints excluded: chain E residue 132 ASP Chi-restraints excluded: chain E residue 198 VAL Chi-restraints excluded: chain E residue 237 LEU Chi-restraints excluded: chain E residue 275 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 124 optimal weight: 4.9990 chunk 0 optimal weight: 6.9990 chunk 98 optimal weight: 0.9980 chunk 151 optimal weight: 5.9990 chunk 114 optimal weight: 4.9990 chunk 122 optimal weight: 1.9990 chunk 34 optimal weight: 2.9990 chunk 111 optimal weight: 1.9990 chunk 35 optimal weight: 3.9990 chunk 102 optimal weight: 5.9990 chunk 127 optimal weight: 4.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 276 HIS B 276 HIS C 276 HIS D 276 HIS E 73 ASN E 382 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.091517 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2903 r_free = 0.2903 target = 0.075260 restraints weight = 21193.859| |-----------------------------------------------------------------------------| r_work (start): 0.2923 rms_B_bonded: 3.01 r_work: 0.2758 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.2758 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2741 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2741 r_free = 0.2741 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.87 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2741 r_free = 0.2741 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.87 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2741 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7755 moved from start: 0.2741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.042 13410 Z= 0.267 Angle : 0.617 6.512 18370 Z= 0.303 Chirality : 0.043 0.156 2235 Planarity : 0.004 0.031 2250 Dihedral : 4.256 31.624 2062 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 4.48 % Allowed : 14.13 % Favored : 81.40 % 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: 1.83 (0.21), residues: 1600 helix: 2.89 (0.20), residues: 545 sheet: 0.65 (0.23), residues: 420 loop : 0.18 (0.25), residues: 635 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP D 112 HIS 0.004 0.001 HIS A 276 PHE 0.028 0.002 PHE C 72 TYR 0.012 0.002 TYR B 264 ARG 0.009 0.001 ARG D 257 Details of bonding type rmsd link_NAG-ASN : bond 0.00466 ( 10) link_NAG-ASN : angle 1.56090 ( 30) link_BETA1-4 : bond 0.00234 ( 5) link_BETA1-4 : angle 0.97993 ( 15) hydrogen bonds : bond 0.04219 ( 680) hydrogen bonds : angle 3.96100 ( 2100) SS BOND : bond 0.00698 ( 10) SS BOND : angle 1.40209 ( 20) covalent geometry : bond 0.00620 (13385) covalent geometry : angle 0.61224 (18305) *********************** 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 325 residues out of total 1430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 261 time to evaluate : 1.516 Fit side-chains REVERT: A 81 MET cc_start: 0.8689 (ttp) cc_final: 0.8477 (ptm) REVERT: A 124 GLU cc_start: 0.8375 (mp0) cc_final: 0.8101 (mp0) REVERT: A 132 ASP cc_start: 0.7482 (t0) cc_final: 0.7101 (t0) REVERT: A 201 GLU cc_start: 0.8644 (mt-10) cc_final: 0.8040 (mp0) REVERT: A 214 GLN cc_start: 0.8255 (mm-40) cc_final: 0.7906 (pt0) REVERT: A 260 GLU cc_start: 0.8715 (pt0) cc_final: 0.8398 (pm20) REVERT: A 364 GLU cc_start: 0.8104 (mt-10) cc_final: 0.7691 (mt-10) REVERT: B 48 GLU cc_start: 0.8014 (tp30) cc_final: 0.7780 (tp30) REVERT: B 75 ASP cc_start: 0.7756 (t0) cc_final: 0.7452 (t0) REVERT: B 112 TRP cc_start: 0.8287 (OUTLIER) cc_final: 0.7532 (t-100) REVERT: B 124 GLU cc_start: 0.8444 (mp0) cc_final: 0.7982 (mp0) REVERT: B 146 LYS cc_start: 0.8329 (mtmm) cc_final: 0.8031 (mtpp) REVERT: B 201 GLU cc_start: 0.8539 (mt-10) cc_final: 0.8003 (mp0) REVERT: B 214 GLN cc_start: 0.8295 (mm-40) cc_final: 0.7978 (pt0) REVERT: B 260 GLU cc_start: 0.8677 (pm20) cc_final: 0.8327 (pm20) REVERT: B 391 TRP cc_start: 0.8289 (m-90) cc_final: 0.8026 (m-90) REVERT: C 112 TRP cc_start: 0.8416 (OUTLIER) cc_final: 0.8089 (t-100) REVERT: C 132 ASP cc_start: 0.7912 (OUTLIER) cc_final: 0.7584 (t0) REVERT: C 146 LYS cc_start: 0.8167 (OUTLIER) cc_final: 0.7713 (mtpp) REVERT: C 201 GLU cc_start: 0.8678 (mt-10) cc_final: 0.8042 (mp0) REVERT: D 124 GLU cc_start: 0.8372 (mp0) cc_final: 0.8143 (mp0) REVERT: D 132 ASP cc_start: 0.7178 (t0) cc_final: 0.6849 (p0) REVERT: D 160 GLU cc_start: 0.8399 (mt-10) cc_final: 0.8049 (mt-10) REVERT: D 364 GLU cc_start: 0.7922 (mt-10) cc_final: 0.7507 (mt-10) REVERT: D 372 LEU cc_start: 0.8113 (OUTLIER) cc_final: 0.7866 (tt) REVERT: D 391 TRP cc_start: 0.8151 (m-90) cc_final: 0.7912 (m-90) REVERT: E 81 MET cc_start: 0.8749 (ttp) cc_final: 0.8494 (ptt) REVERT: E 112 TRP cc_start: 0.8387 (OUTLIER) cc_final: 0.7321 (t-100) REVERT: E 132 ASP cc_start: 0.8037 (OUTLIER) cc_final: 0.7763 (t0) REVERT: E 214 GLN cc_start: 0.8172 (mm-40) cc_final: 0.7932 (pt0) REVERT: E 221 GLN cc_start: 0.8579 (pt0) cc_final: 0.8076 (pt0) REVERT: E 257 ARG cc_start: 0.8899 (ptp90) cc_final: 0.8286 (ptp-110) REVERT: E 260 GLU cc_start: 0.8920 (pm20) cc_final: 0.8427 (pm20) REVERT: E 382 GLN cc_start: 0.8424 (mm110) cc_final: 0.8149 (mm-40) REVERT: E 391 TRP cc_start: 0.8204 (m-90) cc_final: 0.7983 (m-10) outliers start: 64 outliers final: 27 residues processed: 294 average time/residue: 1.2535 time to fit residues: 403.9995 Evaluate side-chains 282 residues out of total 1430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 248 time to evaluate : 2.270 ------------------------------------------------------------------------------- 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 373 VAL Chi-restraints excluded: chain B residue 112 TRP Chi-restraints excluded: chain B residue 210 GLN 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 B residue 394 CYS 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 198 VAL Chi-restraints excluded: chain C residue 259 ILE Chi-restraints excluded: chain C residue 372 LEU Chi-restraints excluded: chain C residue 373 VAL Chi-restraints excluded: chain D residue 50 ILE Chi-restraints excluded: chain D residue 198 VAL Chi-restraints excluded: chain D residue 237 LEU Chi-restraints excluded: chain D residue 260 GLU 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 107 optimal weight: 0.9980 chunk 72 optimal weight: 0.8980 chunk 125 optimal weight: 0.6980 chunk 39 optimal weight: 0.5980 chunk 151 optimal weight: 0.7980 chunk 101 optimal weight: 7.9990 chunk 89 optimal weight: 2.9990 chunk 124 optimal weight: 4.9990 chunk 20 optimal weight: 1.9990 chunk 155 optimal weight: 0.6980 chunk 75 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 = 0.3209 r_free = 0.3209 target = 0.094878 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 22)----------------| | r_work = 0.2965 r_free = 0.2965 target = 0.078691 restraints weight = 20890.213| |-----------------------------------------------------------------------------| r_work (start): 0.2972 rms_B_bonded: 3.03 r_work: 0.2809 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.2809 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2795 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2795 r_free = 0.2795 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.87 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2795 r_free = 0.2795 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.86 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2795 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7707 moved from start: 0.2741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 13410 Z= 0.121 Angle : 0.543 7.765 18370 Z= 0.263 Chirality : 0.039 0.145 2235 Planarity : 0.003 0.029 2250 Dihedral : 4.039 31.490 2062 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 2.59 % Allowed : 16.29 % Favored : 81.12 % 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: 1.90 (0.21), residues: 1600 helix: 2.99 (0.20), residues: 545 sheet: 0.68 (0.23), residues: 420 loop : 0.19 (0.26), residues: 635 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP D 112 HIS 0.001 0.000 HIS E 276 PHE 0.031 0.002 PHE D 385 TYR 0.017 0.002 TYR A 272 ARG 0.007 0.000 ARG A 78 Details of bonding type rmsd link_NAG-ASN : bond 0.00139 ( 10) link_NAG-ASN : angle 1.22569 ( 30) link_BETA1-4 : bond 0.00067 ( 5) link_BETA1-4 : angle 0.88931 ( 15) hydrogen bonds : bond 0.03866 ( 680) hydrogen bonds : angle 3.76863 ( 2100) SS BOND : bond 0.00393 ( 10) SS BOND : angle 0.96272 ( 20) covalent geometry : bond 0.00272 (13385) covalent geometry : angle 0.53978 (18305) *********************** 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 306 residues out of total 1430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 269 time to evaluate : 1.554 Fit side-chains REVERT: A 75 ASP cc_start: 0.7824 (t0) cc_final: 0.7442 (t0) REVERT: A 124 GLU cc_start: 0.8383 (mp0) cc_final: 0.7981 (mp0) REVERT: A 132 ASP cc_start: 0.7488 (t0) cc_final: 0.7057 (t0) REVERT: A 154 GLU cc_start: 0.8676 (tt0) cc_final: 0.8181 (tt0) REVERT: A 201 GLU cc_start: 0.8591 (mt-10) cc_final: 0.7993 (mp0) REVERT: A 214 GLN cc_start: 0.8227 (mm-40) cc_final: 0.7923 (pt0) REVERT: A 260 GLU cc_start: 0.8730 (pt0) cc_final: 0.8410 (pm20) REVERT: A 364 GLU cc_start: 0.8087 (mt-10) cc_final: 0.7669 (mt-10) REVERT: B 48 GLU cc_start: 0.8016 (tp30) cc_final: 0.7756 (tp30) REVERT: B 75 ASP cc_start: 0.7628 (t0) cc_final: 0.7332 (t0) REVERT: B 124 GLU cc_start: 0.8423 (mp0) cc_final: 0.7950 (mp0) REVERT: B 132 ASP cc_start: 0.7446 (t0) cc_final: 0.7167 (p0) REVERT: B 146 LYS cc_start: 0.8291 (mtmm) cc_final: 0.8008 (mtpp) REVERT: B 201 GLU cc_start: 0.8518 (mt-10) cc_final: 0.7992 (mp0) REVERT: B 214 GLN cc_start: 0.8303 (mm-40) cc_final: 0.8030 (pt0) REVERT: B 260 GLU cc_start: 0.8711 (pm20) cc_final: 0.8349 (pm20) REVERT: B 272 TYR cc_start: 0.8611 (t80) cc_final: 0.8352 (t80) REVERT: B 391 TRP cc_start: 0.8137 (m-90) cc_final: 0.7882 (m-90) REVERT: C 112 TRP cc_start: 0.8203 (OUTLIER) cc_final: 0.7832 (t-100) REVERT: C 129 ASP cc_start: 0.8391 (t0) cc_final: 0.8188 (t0) REVERT: C 132 ASP cc_start: 0.7847 (OUTLIER) cc_final: 0.7545 (t0) REVERT: C 201 GLU cc_start: 0.8677 (mt-10) cc_final: 0.8070 (mp0) REVERT: D 63 ASP cc_start: 0.8354 (t70) cc_final: 0.8042 (t0) REVERT: D 75 ASP cc_start: 0.7677 (t0) cc_final: 0.7398 (t0) REVERT: D 78 ARG cc_start: 0.8532 (mmm-85) cc_final: 0.8259 (mtp85) REVERT: D 132 ASP cc_start: 0.7132 (t0) cc_final: 0.6787 (p0) REVERT: D 160 GLU cc_start: 0.8362 (mt-10) cc_final: 0.8059 (mt-10) REVERT: D 364 GLU cc_start: 0.7918 (mt-10) cc_final: 0.7488 (mt-10) REVERT: D 372 LEU cc_start: 0.8038 (OUTLIER) cc_final: 0.7678 (tp) REVERT: D 391 TRP cc_start: 0.8100 (m-90) cc_final: 0.7820 (m-90) REVERT: E 112 TRP cc_start: 0.8112 (OUTLIER) cc_final: 0.6894 (t-100) REVERT: E 221 GLN cc_start: 0.8473 (pt0) cc_final: 0.8157 (pt0) REVERT: E 257 ARG cc_start: 0.8886 (ptp90) cc_final: 0.8259 (ptp-110) REVERT: E 260 GLU cc_start: 0.8933 (pm20) cc_final: 0.8439 (pm20) REVERT: E 391 TRP cc_start: 0.8031 (m-90) cc_final: 0.7812 (m-10) outliers start: 37 outliers final: 15 residues processed: 288 average time/residue: 1.1994 time to fit residues: 378.1645 Evaluate side-chains 280 residues out of total 1430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 261 time to evaluate : 1.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 LEU 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 B residue 394 CYS Chi-restraints excluded: chain C residue 81 MET Chi-restraints excluded: chain C residue 112 TRP Chi-restraints excluded: chain C residue 132 ASP Chi-restraints excluded: chain C residue 179 SER Chi-restraints excluded: chain C residue 198 VAL Chi-restraints excluded: chain D residue 237 LEU Chi-restraints excluded: chain D residue 372 LEU Chi-restraints excluded: chain E residue 112 TRP Chi-restraints excluded: chain E residue 198 VAL Chi-restraints excluded: chain E residue 237 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 95 optimal weight: 0.4980 chunk 28 optimal weight: 3.9990 chunk 122 optimal weight: 5.9990 chunk 136 optimal weight: 3.9990 chunk 157 optimal weight: 0.8980 chunk 135 optimal weight: 1.9990 chunk 3 optimal weight: 5.9990 chunk 71 optimal weight: 2.9990 chunk 100 optimal weight: 2.9990 chunk 105 optimal weight: 4.9990 chunk 108 optimal weight: 6.9990 overall best weight: 1.8786 ------------------------------------------------------------------------------- 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 = 0.3177 r_free = 0.3177 target = 0.092784 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2932 r_free = 0.2932 target = 0.076698 restraints weight = 20917.512| |-----------------------------------------------------------------------------| r_work (start): 0.2913 rms_B_bonded: 2.99 r_work: 0.2751 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.2751 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2751 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2751 r_free = 0.2751 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.86 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2751 r_free = 0.2751 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.86 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2751 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7773 moved from start: 0.2886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 13410 Z= 0.217 Angle : 0.585 9.077 18370 Z= 0.284 Chirality : 0.041 0.153 2235 Planarity : 0.004 0.026 2250 Dihedral : 4.043 17.200 2060 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 3.43 % Allowed : 15.94 % Favored : 80.63 % 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: 1.86 (0.21), residues: 1600 helix: 2.92 (0.20), residues: 545 sheet: 0.59 (0.23), residues: 440 loop : 0.25 (0.26), residues: 615 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP B 112 HIS 0.003 0.000 HIS E 276 PHE 0.030 0.002 PHE D 385 TYR 0.014 0.002 TYR A 272 ARG 0.007 0.000 ARG D 257 Details of bonding type rmsd link_NAG-ASN : bond 0.00301 ( 10) link_NAG-ASN : angle 1.42876 ( 30) link_BETA1-4 : bond 0.00083 ( 5) link_BETA1-4 : angle 0.92894 ( 15) hydrogen bonds : bond 0.04047 ( 680) hydrogen bonds : angle 3.83325 ( 2100) SS BOND : bond 0.00796 ( 10) SS BOND : angle 1.11162 ( 20) covalent geometry : bond 0.00502 (13385) covalent geometry : angle 0.58178 (18305) *********************** 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 298 residues out of total 1430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 249 time to evaluate : 1.378 Fit side-chains REVERT: A 81 MET cc_start: 0.8736 (ttp) cc_final: 0.8524 (ptm) REVERT: A 112 TRP cc_start: 0.8145 (OUTLIER) cc_final: 0.7870 (t-100) REVERT: A 201 GLU cc_start: 0.8668 (mt-10) cc_final: 0.8088 (mp0) REVERT: A 214 GLN cc_start: 0.8241 (mm-40) cc_final: 0.7949 (pt0) REVERT: A 402 GLU cc_start: 0.7622 (mt-10) cc_final: 0.7417 (mt-10) REVERT: B 48 GLU cc_start: 0.8051 (tp30) cc_final: 0.7824 (tp30) REVERT: B 112 TRP cc_start: 0.8042 (OUTLIER) cc_final: 0.7725 (t-100) REVERT: B 124 GLU cc_start: 0.8462 (mp0) cc_final: 0.7949 (mp0) REVERT: B 146 LYS cc_start: 0.8354 (mtmm) cc_final: 0.8085 (mtpp) REVERT: B 201 GLU cc_start: 0.8569 (mt-10) cc_final: 0.8034 (mp0) REVERT: B 214 GLN cc_start: 0.8306 (mm-40) cc_final: 0.8047 (pt0) REVERT: B 260 GLU cc_start: 0.8739 (pm20) cc_final: 0.8358 (pm20) REVERT: B 272 TYR cc_start: 0.8597 (t80) cc_final: 0.8311 (t80) REVERT: B 391 TRP cc_start: 0.8266 (m-90) cc_final: 0.8039 (m-90) REVERT: C 75 ASP cc_start: 0.7620 (t0) cc_final: 0.7070 (t0) REVERT: C 112 TRP cc_start: 0.8387 (OUTLIER) cc_final: 0.8080 (t-100) REVERT: C 129 ASP cc_start: 0.8471 (t0) cc_final: 0.8210 (t0) REVERT: C 132 ASP cc_start: 0.7836 (OUTLIER) cc_final: 0.7530 (t0) REVERT: C 146 LYS cc_start: 0.8193 (OUTLIER) cc_final: 0.7735 (mtpp) REVERT: C 201 GLU cc_start: 0.8697 (mt-10) cc_final: 0.8071 (mp0) REVERT: D 63 ASP cc_start: 0.8423 (t70) cc_final: 0.8138 (t0) REVERT: D 129 ASP cc_start: 0.8392 (t0) cc_final: 0.8191 (t0) REVERT: D 132 ASP cc_start: 0.7347 (t0) cc_final: 0.6875 (t0) REVERT: D 160 GLU cc_start: 0.8411 (mt-10) cc_final: 0.8112 (mt-10) REVERT: D 364 GLU cc_start: 0.7983 (mt-10) cc_final: 0.7573 (mt-10) REVERT: D 372 LEU cc_start: 0.8099 (OUTLIER) cc_final: 0.7863 (tt) REVERT: D 391 TRP cc_start: 0.8190 (m-90) cc_final: 0.7951 (m-90) REVERT: D 402 GLU cc_start: 0.8379 (mt-10) cc_final: 0.8120 (mm-30) REVERT: E 81 MET cc_start: 0.8790 (ttp) cc_final: 0.8497 (ptt) REVERT: E 112 TRP cc_start: 0.8313 (OUTLIER) cc_final: 0.7196 (t-100) REVERT: E 132 ASP cc_start: 0.7937 (OUTLIER) cc_final: 0.7673 (t0) REVERT: E 221 GLN cc_start: 0.8575 (pt0) cc_final: 0.8030 (pt0) REVERT: E 257 ARG cc_start: 0.8908 (ptp90) cc_final: 0.8282 (ptp-110) REVERT: E 260 GLU cc_start: 0.8945 (pm20) cc_final: 0.8501 (pm20) outliers start: 49 outliers final: 28 residues processed: 273 average time/residue: 1.1705 time to fit residues: 350.1406 Evaluate side-chains 281 residues out of total 1430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 245 time to evaluate : 1.554 ------------------------------------------------------------------------------- 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 285 SER 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 112 TRP 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 B residue 373 VAL Chi-restraints excluded: chain B residue 394 CYS 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 179 SER Chi-restraints excluded: chain C residue 198 VAL Chi-restraints excluded: chain C residue 210 GLN Chi-restraints excluded: chain C residue 372 LEU Chi-restraints excluded: chain C residue 373 VAL Chi-restraints excluded: chain C residue 394 CYS Chi-restraints excluded: chain D residue 112 TRP Chi-restraints excluded: chain D residue 153 THR Chi-restraints excluded: chain D residue 372 LEU Chi-restraints excluded: chain D residue 373 VAL Chi-restraints excluded: chain D residue 394 CYS 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 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 Chi-restraints excluded: chain E residue 394 CYS 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: 0.9990 chunk 153 optimal weight: 1.9990 chunk 89 optimal weight: 2.9990 chunk 101 optimal weight: 0.9980 chunk 27 optimal weight: 0.9980 chunk 28 optimal weight: 3.9990 chunk 8 optimal weight: 0.9990 chunk 116 optimal weight: 4.9990 chunk 50 optimal weight: 3.9990 chunk 71 optimal weight: 0.0980 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 382 GLN E 382 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.095210 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.079191 restraints weight = 20879.558| |-----------------------------------------------------------------------------| r_work (start): 0.2980 rms_B_bonded: 3.01 r_work: 0.2818 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.2818 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2803 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2803 r_free = 0.2803 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 = 0.2803 r_free = 0.2803 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.86 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2803 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7702 moved from start: 0.2852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 13410 Z= 0.128 Angle : 0.549 9.938 18370 Z= 0.263 Chirality : 0.039 0.142 2235 Planarity : 0.003 0.030 2250 Dihedral : 3.893 15.881 2060 Min Nonbonded Distance : 2.625 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 2.24 % Allowed : 18.04 % 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: 1.92 (0.21), residues: 1600 helix: 3.03 (0.20), residues: 545 sheet: 0.61 (0.23), residues: 440 loop : 0.23 (0.27), residues: 615 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 0.021 0.001 PHE D 385 TYR 0.020 0.002 TYR B 176 ARG 0.007 0.000 ARG A 78 Details of bonding type rmsd link_NAG-ASN : bond 0.00138 ( 10) link_NAG-ASN : angle 1.19355 ( 30) link_BETA1-4 : bond 0.00148 ( 5) link_BETA1-4 : angle 0.91303 ( 15) hydrogen bonds : bond 0.03802 ( 680) hydrogen bonds : angle 3.71100 ( 2100) SS BOND : bond 0.00341 ( 10) SS BOND : angle 0.85901 ( 20) covalent geometry : bond 0.00292 (13385) covalent geometry : angle 0.54696 (18305) *********************** 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 297 residues out of total 1430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 265 time to evaluate : 1.420 Fit side-chains REVERT: A 75 ASP cc_start: 0.7830 (t0) cc_final: 0.7484 (t0) REVERT: A 124 GLU cc_start: 0.8398 (mp0) cc_final: 0.7805 (mp0) REVERT: A 132 ASP cc_start: 0.7412 (t0) cc_final: 0.6945 (t0) REVERT: A 201 GLU cc_start: 0.8602 (mt-10) cc_final: 0.7957 (mp0) REVERT: A 214 GLN cc_start: 0.8218 (mm-40) cc_final: 0.7981 (pt0) REVERT: A 260 GLU cc_start: 0.8722 (pm20) cc_final: 0.8192 (pm20) REVERT: A 364 GLU cc_start: 0.8075 (mt-10) cc_final: 0.7654 (mt-10) REVERT: B 48 GLU cc_start: 0.8050 (tp30) cc_final: 0.7814 (tp30) REVERT: B 75 ASP cc_start: 0.7529 (t0) cc_final: 0.7236 (t0) REVERT: B 124 GLU cc_start: 0.8369 (mp0) cc_final: 0.7853 (mp0) REVERT: B 146 LYS cc_start: 0.8283 (mtmm) cc_final: 0.8019 (mtpp) REVERT: B 154 GLU cc_start: 0.8807 (tt0) cc_final: 0.8587 (tt0) REVERT: B 201 GLU cc_start: 0.8540 (mt-10) cc_final: 0.8007 (mp0) REVERT: B 214 GLN cc_start: 0.8307 (mm-40) cc_final: 0.8038 (pt0) REVERT: B 260 GLU cc_start: 0.8757 (pm20) cc_final: 0.8377 (pm20) REVERT: B 272 TYR cc_start: 0.8586 (t80) cc_final: 0.8345 (t80) REVERT: B 364 GLU cc_start: 0.7664 (OUTLIER) cc_final: 0.6749 (mp0) REVERT: B 391 TRP cc_start: 0.8111 (m-90) cc_final: 0.7868 (m-90) REVERT: C 75 ASP cc_start: 0.7554 (t0) cc_final: 0.7140 (t0) REVERT: C 112 TRP cc_start: 0.8149 (OUTLIER) cc_final: 0.7859 (t-100) REVERT: C 129 ASP cc_start: 0.8454 (t0) cc_final: 0.8127 (OUTLIER) REVERT: C 201 GLU cc_start: 0.8680 (mt-10) cc_final: 0.8055 (mp0) REVERT: D 132 ASP cc_start: 0.7340 (t0) cc_final: 0.6861 (t0) REVERT: D 364 GLU cc_start: 0.7925 (mt-10) cc_final: 0.7502 (mt-10) REVERT: D 372 LEU cc_start: 0.8028 (OUTLIER) cc_final: 0.7682 (tp) REVERT: D 391 TRP cc_start: 0.8100 (m-90) cc_final: 0.7849 (m-90) REVERT: D 402 GLU cc_start: 0.8352 (mt-10) cc_final: 0.8101 (mm-30) REVERT: E 81 MET cc_start: 0.8746 (ttp) cc_final: 0.8444 (ptt) REVERT: E 112 TRP cc_start: 0.8071 (OUTLIER) cc_final: 0.7059 (t-100) REVERT: E 124 GLU cc_start: 0.8328 (mp0) cc_final: 0.8058 (mp0) REVERT: E 221 GLN cc_start: 0.8454 (pt0) cc_final: 0.7967 (pt0) REVERT: E 257 ARG cc_start: 0.8901 (ptp90) cc_final: 0.8270 (ptp-110) REVERT: E 260 GLU cc_start: 0.8896 (pm20) cc_final: 0.8483 (pm20) REVERT: E 285 SER cc_start: 0.8703 (t) cc_final: 0.8354 (t) outliers start: 32 outliers final: 15 residues processed: 278 average time/residue: 1.2817 time to fit residues: 388.2989 Evaluate side-chains 280 residues out of total 1430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 262 time to evaluate : 1.584 ------------------------------------------------------------------------------- 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 364 GLU Chi-restraints excluded: chain B residue 394 CYS Chi-restraints excluded: chain C residue 81 MET Chi-restraints excluded: chain C residue 112 TRP Chi-restraints excluded: chain C residue 179 SER Chi-restraints excluded: chain C residue 198 VAL Chi-restraints excluded: chain C residue 210 GLN Chi-restraints excluded: chain C residue 259 ILE Chi-restraints excluded: chain C residue 394 CYS Chi-restraints excluded: chain D residue 153 THR Chi-restraints excluded: chain D residue 372 LEU Chi-restraints excluded: chain E residue 112 TRP Chi-restraints excluded: chain E residue 198 VAL Chi-restraints excluded: chain E residue 372 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 92 optimal weight: 3.9990 chunk 23 optimal weight: 5.9990 chunk 128 optimal weight: 5.9990 chunk 81 optimal weight: 3.9990 chunk 25 optimal weight: 3.9990 chunk 43 optimal weight: 2.9990 chunk 106 optimal weight: 6.9990 chunk 112 optimal weight: 0.9980 chunk 75 optimal weight: 0.6980 chunk 137 optimal weight: 6.9990 chunk 13 optimal weight: 3.9990 overall best weight: 2.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 382 GLN E 73 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.091422 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.2905 r_free = 0.2905 target = 0.075253 restraints weight = 21028.883| |-----------------------------------------------------------------------------| r_work (start): 0.2898 rms_B_bonded: 2.98 r_work: 0.2735 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.2735 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2735 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2735 r_free = 0.2735 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.86 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2735 r_free = 0.2735 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.86 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2735 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7787 moved from start: 0.3013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.094 13410 Z= 0.278 Angle : 0.633 10.515 18370 Z= 0.306 Chirality : 0.043 0.158 2235 Planarity : 0.004 0.031 2250 Dihedral : 4.143 17.366 2060 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 3.15 % Allowed : 17.48 % Favored : 79.37 % 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: 1.73 (0.21), residues: 1600 helix: 2.86 (0.20), residues: 545 sheet: 0.48 (0.23), residues: 450 loop : 0.15 (0.26), residues: 605 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP B 112 HIS 0.002 0.000 HIS A 144 PHE 0.029 0.002 PHE D 385 TYR 0.032 0.002 TYR C 176 ARG 0.009 0.001 ARG D 257 Details of bonding type rmsd link_NAG-ASN : bond 0.00426 ( 10) link_NAG-ASN : angle 1.50187 ( 30) link_BETA1-4 : bond 0.00159 ( 5) link_BETA1-4 : angle 0.93480 ( 15) hydrogen bonds : bond 0.04145 ( 680) hydrogen bonds : angle 3.87935 ( 2100) SS BOND : bond 0.00792 ( 10) SS BOND : angle 1.24307 ( 20) covalent geometry : bond 0.00646 (13385) covalent geometry : angle 0.62941 (18305) *********************** 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 314 residues out of total 1430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 269 time to evaluate : 1.447 Fit side-chains REVERT: A 75 ASP cc_start: 0.7910 (t0) cc_final: 0.7530 (t0) REVERT: A 81 MET cc_start: 0.8747 (ttp) cc_final: 0.8507 (ptm) REVERT: A 113 GLU cc_start: 0.8668 (mm-30) cc_final: 0.8459 (mm-30) REVERT: A 124 GLU cc_start: 0.8411 (mp0) cc_final: 0.7907 (mp0) REVERT: A 201 GLU cc_start: 0.8661 (mt-10) cc_final: 0.8077 (mp0) REVERT: A 260 GLU cc_start: 0.8790 (pm20) cc_final: 0.8252 (pm20) REVERT: A 364 GLU cc_start: 0.8131 (mt-10) cc_final: 0.7715 (mt-10) REVERT: B 48 GLU cc_start: 0.8126 (tp30) cc_final: 0.7888 (tp30) REVERT: B 75 ASP cc_start: 0.7645 (t0) cc_final: 0.7322 (t0) REVERT: B 112 TRP cc_start: 0.8151 (OUTLIER) cc_final: 0.7824 (t-100) REVERT: B 124 GLU cc_start: 0.8417 (mp0) cc_final: 0.7911 (mp0) REVERT: B 146 LYS cc_start: 0.8346 (mtmm) cc_final: 0.8085 (mtpp) REVERT: B 214 GLN cc_start: 0.8309 (mm-40) cc_final: 0.8037 (pt0) REVERT: B 272 TYR cc_start: 0.8608 (t80) cc_final: 0.8302 (t80) REVERT: B 364 GLU cc_start: 0.7712 (mp0) cc_final: 0.6763 (mp0) REVERT: B 391 TRP cc_start: 0.8294 (m-90) cc_final: 0.8068 (m-10) REVERT: C 75 ASP cc_start: 0.7676 (t0) cc_final: 0.7212 (t0) REVERT: C 112 TRP cc_start: 0.8439 (OUTLIER) cc_final: 0.7972 (t-100) REVERT: C 129 ASP cc_start: 0.8459 (t0) cc_final: 0.8149 (t0) REVERT: C 132 ASP cc_start: 0.7810 (p0) cc_final: 0.7469 (t0) REVERT: C 201 GLU cc_start: 0.8675 (mt-10) cc_final: 0.8048 (mp0) REVERT: C 260 GLU cc_start: 0.8924 (pm20) cc_final: 0.8528 (pm20) REVERT: D 63 ASP cc_start: 0.8441 (t70) cc_final: 0.8153 (t0) REVERT: D 129 ASP cc_start: 0.8418 (t0) cc_final: 0.8132 (t0) REVERT: D 132 ASP cc_start: 0.7408 (t0) cc_final: 0.6911 (t0) REVERT: D 364 GLU cc_start: 0.8047 (mt-10) cc_final: 0.7636 (mt-10) REVERT: D 372 LEU cc_start: 0.8109 (OUTLIER) cc_final: 0.7863 (tt) REVERT: D 391 TRP cc_start: 0.8156 (m-90) cc_final: 0.7913 (m-90) REVERT: D 402 GLU cc_start: 0.8333 (mt-10) cc_final: 0.8093 (mm-30) REVERT: E 81 MET cc_start: 0.8771 (ttp) cc_final: 0.8491 (ptt) REVERT: E 132 ASP cc_start: 0.7885 (OUTLIER) cc_final: 0.7579 (t0) REVERT: E 221 GLN cc_start: 0.8582 (pt0) cc_final: 0.8135 (pt0) REVERT: E 257 ARG cc_start: 0.8906 (ptp90) cc_final: 0.8285 (ptp-110) REVERT: E 260 GLU cc_start: 0.8929 (pm20) cc_final: 0.8483 (pm20) REVERT: E 285 SER cc_start: 0.8806 (t) cc_final: 0.8452 (t) outliers start: 45 outliers final: 28 residues processed: 288 average time/residue: 1.3785 time to fit residues: 438.9629 Evaluate side-chains 280 residues out of total 1430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 248 time to evaluate : 1.846 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 MET Chi-restraints excluded: chain A residue 123 LEU Chi-restraints excluded: chain A residue 233 SER 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 112 TRP Chi-restraints excluded: chain B residue 210 GLN Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain B residue 279 LEU Chi-restraints excluded: chain B residue 372 LEU Chi-restraints excluded: chain B residue 373 VAL Chi-restraints excluded: chain B residue 394 CYS Chi-restraints excluded: chain C residue 112 TRP Chi-restraints excluded: chain C residue 179 SER Chi-restraints excluded: chain C residue 198 VAL Chi-restraints excluded: chain C residue 210 GLN Chi-restraints excluded: chain C residue 259 ILE Chi-restraints excluded: chain C residue 373 VAL Chi-restraints excluded: chain C residue 394 CYS Chi-restraints excluded: chain D residue 50 ILE Chi-restraints excluded: chain D residue 123 LEU Chi-restraints excluded: chain D residue 153 THR Chi-restraints excluded: chain D residue 260 GLU Chi-restraints excluded: chain D residue 372 LEU Chi-restraints excluded: chain D residue 373 VAL Chi-restraints excluded: chain D residue 394 CYS Chi-restraints excluded: chain E residue 132 ASP Chi-restraints excluded: chain E residue 198 VAL Chi-restraints excluded: chain E residue 372 LEU Chi-restraints excluded: chain E residue 373 VAL Chi-restraints excluded: chain E residue 394 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 49 optimal weight: 2.9990 chunk 23 optimal weight: 0.7980 chunk 85 optimal weight: 0.9980 chunk 1 optimal weight: 0.6980 chunk 127 optimal weight: 0.0470 chunk 73 optimal weight: 4.9990 chunk 106 optimal weight: 0.4980 chunk 136 optimal weight: 0.9990 chunk 81 optimal weight: 0.6980 chunk 22 optimal weight: 0.7980 chunk 8 optimal weight: 0.9980 overall best weight: 0.5478 ------------------------------------------------------------------------------- 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 = 0.3197 r_free = 0.3197 target = 0.094402 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2953 r_free = 0.2953 target = 0.078287 restraints weight = 20613.060| |-----------------------------------------------------------------------------| r_work (start): 0.2952 rms_B_bonded: 3.02 r_work: 0.2791 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.2791 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2795 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2795 r_free = 0.2795 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.86 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2795 r_free = 0.2795 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.85 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2795 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7736 moved from start: 0.2973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 13410 Z= 0.115 Angle : 0.566 9.954 18370 Z= 0.269 Chirality : 0.039 0.143 2235 Planarity : 0.003 0.037 2250 Dihedral : 3.965 15.789 2060 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 1.68 % Allowed : 19.37 % Favored : 78.95 % 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: 1.85 (0.21), residues: 1600 helix: 2.99 (0.20), residues: 545 sheet: 0.55 (0.23), residues: 440 loop : 0.20 (0.26), residues: 615 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP D 362 HIS 0.001 0.000 HIS D 190 PHE 0.020 0.002 PHE D 385 TYR 0.027 0.002 TYR E 176 ARG 0.009 0.000 ARG D 257 Details of bonding type rmsd link_NAG-ASN : bond 0.00115 ( 10) link_NAG-ASN : angle 1.20186 ( 30) link_BETA1-4 : bond 0.00102 ( 5) link_BETA1-4 : angle 0.89824 ( 15) hydrogen bonds : bond 0.03850 ( 680) hydrogen bonds : angle 3.73428 ( 2100) SS BOND : bond 0.00306 ( 10) SS BOND : angle 0.90112 ( 20) covalent geometry : bond 0.00257 (13385) covalent geometry : angle 0.56389 (18305) ********************** 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 287 residues out of total 1430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 263 time to evaluate : 1.634 Fit side-chains REVERT: A 75 ASP cc_start: 0.7861 (t0) cc_final: 0.7504 (t0) REVERT: A 124 GLU cc_start: 0.8432 (mp0) cc_final: 0.7823 (mp0) REVERT: A 201 GLU cc_start: 0.8642 (mt-10) cc_final: 0.8012 (mp0) REVERT: A 260 GLU cc_start: 0.8793 (pm20) cc_final: 0.8256 (pm20) REVERT: A 364 GLU cc_start: 0.8093 (mt-10) cc_final: 0.7671 (mt-10) REVERT: B 48 GLU cc_start: 0.8113 (tp30) cc_final: 0.7831 (tp30) REVERT: B 75 ASP cc_start: 0.7604 (t0) cc_final: 0.7300 (t0) REVERT: B 124 GLU cc_start: 0.8363 (mp0) cc_final: 0.7839 (mp0) REVERT: B 146 LYS cc_start: 0.8320 (mtmm) cc_final: 0.8063 (mtpp) REVERT: B 201 GLU cc_start: 0.8561 (mt-10) cc_final: 0.8033 (mp0) REVERT: B 214 GLN cc_start: 0.8326 (mm-40) cc_final: 0.8053 (pt0) REVERT: B 260 GLU cc_start: 0.8796 (pm20) cc_final: 0.8412 (pm20) REVERT: B 272 TYR cc_start: 0.8548 (t80) cc_final: 0.8311 (t80) REVERT: B 364 GLU cc_start: 0.7690 (mp0) cc_final: 0.6742 (mp0) REVERT: B 391 TRP cc_start: 0.8141 (m-90) cc_final: 0.7904 (m-90) REVERT: B 402 GLU cc_start: 0.8321 (mm-30) cc_final: 0.8013 (mm-30) REVERT: C 112 TRP cc_start: 0.8198 (OUTLIER) cc_final: 0.7947 (t-100) REVERT: C 201 GLU cc_start: 0.8675 (mt-10) cc_final: 0.8038 (mp0) REVERT: C 260 GLU cc_start: 0.8916 (pm20) cc_final: 0.8514 (pm20) REVERT: D 124 GLU cc_start: 0.8335 (mp0) cc_final: 0.8074 (mp0) REVERT: D 364 GLU cc_start: 0.8006 (mt-10) cc_final: 0.7572 (mt-10) REVERT: D 372 LEU cc_start: 0.8057 (OUTLIER) cc_final: 0.7695 (tp) REVERT: D 402 GLU cc_start: 0.8313 (mt-10) cc_final: 0.8058 (mm-30) REVERT: E 113 GLU cc_start: 0.8614 (mp0) cc_final: 0.8376 (mm-30) REVERT: E 124 GLU cc_start: 0.8321 (mp0) cc_final: 0.8105 (mp0) REVERT: E 221 GLN cc_start: 0.8526 (pt0) cc_final: 0.8005 (pt0) REVERT: E 257 ARG cc_start: 0.8915 (ptp90) cc_final: 0.8278 (ptp-110) REVERT: E 260 GLU cc_start: 0.8911 (pm20) cc_final: 0.8507 (pm20) REVERT: E 285 SER cc_start: 0.8669 (t) cc_final: 0.8371 (t) outliers start: 24 outliers final: 17 residues processed: 273 average time/residue: 1.4799 time to fit residues: 439.2992 Evaluate side-chains 284 residues out of total 1430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 265 time to evaluate : 1.536 ------------------------------------------------------------------------------- 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 285 SER Chi-restraints excluded: chain A residue 394 CYS Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain B residue 279 LEU Chi-restraints excluded: chain B residue 378 VAL Chi-restraints excluded: chain B residue 394 CYS Chi-restraints excluded: chain C residue 112 TRP Chi-restraints excluded: chain C residue 179 SER Chi-restraints excluded: chain C residue 198 VAL Chi-restraints excluded: chain C residue 210 GLN Chi-restraints excluded: chain C residue 259 ILE Chi-restraints excluded: chain C residue 394 CYS Chi-restraints excluded: chain D residue 153 THR Chi-restraints excluded: chain D residue 372 LEU Chi-restraints excluded: chain D residue 394 CYS Chi-restraints excluded: chain E residue 198 VAL Chi-restraints excluded: chain E residue 394 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 74 optimal weight: 4.9990 chunk 1 optimal weight: 5.9990 chunk 88 optimal weight: 3.9990 chunk 126 optimal weight: 0.0050 chunk 111 optimal weight: 4.9990 chunk 10 optimal weight: 5.9990 chunk 56 optimal weight: 0.6980 chunk 154 optimal weight: 4.9990 chunk 36 optimal weight: 0.8980 chunk 83 optimal weight: 0.4980 chunk 127 optimal weight: 0.0040 overall best weight: 0.4206 ------------------------------------------------------------------------------- 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 = 0.3345 r_free = 0.3345 target = 0.103328 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.087076 restraints weight = 20449.070| |-----------------------------------------------------------------------------| r_work (start): 0.3032 rms_B_bonded: 3.04 r_work: 0.2847 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.2847 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2861 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2861 r_free = 0.2861 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.85 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2861 r_free = 0.2861 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.87 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2861 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8036 moved from start: 0.2980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 13410 Z= 0.107 Angle : 0.554 10.633 18370 Z= 0.262 Chirality : 0.039 0.144 2235 Planarity : 0.003 0.035 2250 Dihedral : 3.797 15.283 2060 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 1.54 % Allowed : 19.65 % Favored : 78.81 % 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: 3.12 (0.20), residues: 545 sheet: 0.63 (0.24), residues: 440 loop : 0.23 (0.27), residues: 615 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP D 362 HIS 0.001 0.000 HIS A 276 PHE 0.018 0.001 PHE A 72 TYR 0.028 0.002 TYR E 176 ARG 0.009 0.000 ARG D 257 Details of bonding type rmsd link_NAG-ASN : bond 0.00150 ( 10) link_NAG-ASN : angle 1.10957 ( 30) link_BETA1-4 : bond 0.00151 ( 5) link_BETA1-4 : angle 0.89664 ( 15) hydrogen bonds : bond 0.03749 ( 680) hydrogen bonds : angle 3.66201 ( 2100) SS BOND : bond 0.00309 ( 10) SS BOND : angle 0.77585 ( 20) covalent geometry : bond 0.00238 (13385) covalent geometry : angle 0.55154 (18305) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9211.29 seconds wall clock time: 161 minutes 49.89 seconds (9709.89 seconds total)