Starting phenix.real_space_refine on Tue Nov 18 09:48:51 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8yx7_39649/11_2025/8yx7_39649.cif Found real_map, /net/cci-nas-00/data/ceres_data/8yx7_39649/11_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_39649/11_2025/8yx7_39649.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8yx7_39649/11_2025/8yx7_39649.map" model { file = "/net/cci-nas-00/data/ceres_data/8yx7_39649/11_2025/8yx7_39649.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8yx7_39649/11_2025/8yx7_39649.cif" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/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: "F" 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: B, C, D, E, G, H, I, 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: 2.51, per 1000 atoms: 0.19 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 B 157 " - pdb=" SG CYS B 171 " distance=2.03 Simple disulfide: pdb=" SG CYS C 157 " - pdb=" SG CYS C 171 " distance=2.03 Simple disulfide: pdb=" SG CYS D 157 " - pdb=" SG CYS D 171 " distance=2.03 Simple disulfide: pdb=" SG CYS E 157 " - pdb=" SG CYS E 171 " distance=2.03 Simple disulfide: pdb=" SG CYS B 289 " - pdb=" SG CYS B 394 " distance=2.03 Simple disulfide: pdb=" SG CYS C 289 " - pdb=" SG CYS C 394 " distance=2.03 Simple disulfide: pdb=" SG CYS D 289 " - pdb=" SG CYS D 394 " distance=2.03 Simple disulfide: pdb=" SG CYS E 289 " - pdb=" SG CYS E 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: 1.14 Conformation dependent library (CDL) restraints added in 568.1 milliseconds 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: 0.45 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: 2.15 Time building geometry restraints manager: 1.47 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: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' } ncs_group { reference = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' 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: 1.420 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.200 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 12.440 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.020 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:6.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.410 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 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 ARG 0.002 0.000 ARG A 138 TYR 0.013 0.001 TYR E 264 PHE 0.016 0.001 PHE A 72 TRP 0.005 0.001 TRP A 116 HIS 0.001 0.000 HIS A 276 Details of bonding type rmsd covalent geometry : bond 0.00701 (13385) covalent geometry : angle 0.57898 (18305) SS BOND : bond 0.00077 ( 10) SS BOND : angle 1.05905 ( 20) hydrogen bonds : bond 0.11820 ( 680) hydrogen bonds : angle 4.49157 ( 2100) link_BETA1-4 : bond 0.00084 ( 5) link_BETA1-4 : angle 0.47366 ( 15) link_NAG-ASN : bond 0.00101 ( 10) link_NAG-ASN : angle 1.01321 ( 30) *********************** 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 : 0.599 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: 0.8188 (pt0) REVERT: A 259 ILE cc_start: 0.9352 (pt) cc_final: 0.9138 (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: 0.7986 (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: 0.5523 time to fit residues: 259.0908 Evaluate side-chains 289 residues out of total 1430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 288 time to evaluate : 0.503 ------------------------------------------------------------------------------- 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 98 optimal weight: 3.9990 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 0.8980 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 3.9990 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 0.9980 chunk 91 optimal weight: 6.9990 chunk 149 optimal weight: 0.6980 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 GLN A 382 GLN B 188 GLN B 382 GLN C 156 ASN C 382 GLN D 188 GLN E 188 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.097634 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.081150 restraints weight = 20638.893| |-----------------------------------------------------------------------------| r_work (start): 0.2943 rms_B_bonded: 3.04 r_work: 0.2778 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.2778 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2805 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2805 r_free = 0.2805 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.80 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2805 r_free = 0.2805 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.85 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2805 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7653 moved from start: 0.1807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 13410 Z= 0.174 Angle : 0.571 6.380 18370 Z= 0.280 Chirality : 0.041 0.146 2235 Planarity : 0.004 0.043 2250 Dihedral : 4.329 28.755 2062 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 3.36 % Allowed : 11.19 % Favored : 85.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.51 (0.21), residues: 1600 helix: 3.64 (0.20), residues: 515 sheet: 1.49 (0.24), residues: 405 loop : 0.22 (0.25), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 257 TYR 0.014 0.002 TYR D 176 PHE 0.020 0.002 PHE C 72 TRP 0.013 0.001 TRP A 112 HIS 0.002 0.000 HIS B 276 Details of bonding type rmsd covalent geometry : bond 0.00403 (13385) covalent geometry : angle 0.56524 (18305) SS BOND : bond 0.00574 ( 10) SS BOND : angle 1.62789 ( 20) hydrogen bonds : bond 0.04264 ( 680) hydrogen bonds : angle 3.91927 ( 2100) link_BETA1-4 : bond 0.00132 ( 5) link_BETA1-4 : angle 0.96810 ( 15) link_NAG-ASN : bond 0.00298 ( 10) link_NAG-ASN : angle 1.59242 ( 30) *********************** 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 341 residues out of total 1430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 293 time to evaluate : 0.520 Fit side-chains REVERT: A 75 ASP cc_start: 0.7800 (t0) cc_final: 0.7448 (t0) REVERT: A 201 GLU cc_start: 0.8542 (mt-10) cc_final: 0.7945 (mp0) REVERT: A 210 GLN cc_start: 0.7952 (pt0) cc_final: 0.7689 (pt0) REVERT: A 221 GLN cc_start: 0.8453 (pt0) cc_final: 0.7797 (pt0) REVERT: A 391 TRP cc_start: 0.8056 (m-90) cc_final: 0.7845 (m-90) REVERT: A 402 GLU cc_start: 0.8188 (OUTLIER) cc_final: 0.7978 (mt-10) REVERT: B 48 GLU cc_start: 0.7811 (tp30) cc_final: 0.7518 (tp30) REVERT: B 124 GLU cc_start: 0.8435 (mp0) cc_final: 0.8104 (mp0) REVERT: B 154 GLU cc_start: 0.8748 (tt0) cc_final: 0.8541 (tt0) REVERT: B 184 GLU cc_start: 0.8117 (pt0) cc_final: 0.7898 (pt0) REVERT: B 201 GLU cc_start: 0.8459 (mt-10) cc_final: 0.7982 (mp0) REVERT: B 391 TRP cc_start: 0.8116 (m-90) cc_final: 0.7804 (m-90) REVERT: C 124 GLU cc_start: 0.8376 (mp0) cc_final: 0.8139 (mp0) REVERT: C 154 GLU cc_start: 0.8735 (tt0) cc_final: 0.8415 (tt0) REVERT: C 188 GLN cc_start: 0.8078 (tt0) cc_final: 0.7430 (tt0) REVERT: C 201 GLU cc_start: 0.8571 (mt-10) cc_final: 0.8043 (mp0) REVERT: C 210 GLN cc_start: 0.8091 (pt0) cc_final: 0.7876 (pt0) REVERT: C 214 GLN cc_start: 0.8099 (mm-40) cc_final: 0.7823 (pt0) REVERT: C 221 GLN cc_start: 0.8431 (pt0) cc_final: 0.7766 (pt0) REVERT: D 124 GLU cc_start: 0.8336 (mp0) cc_final: 0.8000 (mp0) REVERT: D 142 ASP cc_start: 0.9161 (m-30) cc_final: 0.8452 (p0) REVERT: D 160 GLU cc_start: 0.8237 (OUTLIER) cc_final: 0.7965 (mt-10) REVERT: D 364 GLU cc_start: 0.7832 (mt-10) cc_final: 0.7430 (mt-10) REVERT: D 372 LEU cc_start: 0.8057 (OUTLIER) cc_final: 0.7839 (tt) REVERT: D 391 TRP cc_start: 0.8185 (m-90) cc_final: 0.7895 (m-90) REVERT: E 113 GLU cc_start: 0.8494 (mp0) cc_final: 0.8250 (mp0) REVERT: E 124 GLU cc_start: 0.8327 (mp0) cc_final: 0.7973 (mp0) REVERT: E 129 ASP cc_start: 0.8321 (t0) cc_final: 0.8120 (t0) REVERT: E 142 ASP cc_start: 0.9123 (m-30) cc_final: 0.8536 (p0) REVERT: E 221 GLN cc_start: 0.8459 (pt0) cc_final: 0.8003 (pt0) REVERT: E 257 ARG cc_start: 0.8933 (ptp90) cc_final: 0.8271 (ptp-110) REVERT: E 260 GLU cc_start: 0.8815 (pt0) cc_final: 0.8441 (pm20) REVERT: E 368 ARG cc_start: 0.7482 (mtp180) cc_final: 0.7179 (mtm-85) REVERT: E 391 TRP cc_start: 0.8117 (m-90) cc_final: 0.7782 (m-10) outliers start: 48 outliers final: 22 residues processed: 323 average time/residue: 0.6136 time to fit residues: 216.0386 Evaluate side-chains 293 residues out of total 1430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 268 time to evaluate : 0.485 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain A residue 275 LEU Chi-restraints excluded: chain A residue 373 VAL Chi-restraints excluded: chain A residue 402 GLU Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain B residue 372 LEU Chi-restraints excluded: chain B residue 373 VAL 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 275 LEU Chi-restraints excluded: chain C residue 373 VAL Chi-restraints excluded: chain D residue 146 LYS Chi-restraints excluded: chain D residue 160 GLU Chi-restraints excluded: chain D residue 191 VAL Chi-restraints excluded: chain D residue 275 LEU Chi-restraints excluded: chain D residue 372 LEU Chi-restraints excluded: chain D residue 373 VAL Chi-restraints excluded: chain E residue 198 VAL Chi-restraints excluded: chain E residue 210 GLN Chi-restraints excluded: chain E residue 293 LEU Chi-restraints excluded: chain E residue 299 ILE Chi-restraints excluded: chain E residue 372 LEU Chi-restraints excluded: chain E residue 373 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 12 optimal weight: 0.8980 chunk 139 optimal weight: 3.9990 chunk 84 optimal weight: 0.5980 chunk 129 optimal weight: 1.9990 chunk 106 optimal weight: 3.9990 chunk 10 optimal weight: 5.9990 chunk 130 optimal weight: 2.9990 chunk 72 optimal weight: 0.9990 chunk 145 optimal weight: 4.9990 chunk 70 optimal weight: 4.9990 chunk 2 optimal weight: 2.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 214 GLN B 188 GLN D 188 GLN E 382 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.095502 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2970 r_free = 0.2970 target = 0.079141 restraints weight = 20966.614| |-----------------------------------------------------------------------------| r_work (start): 0.2953 rms_B_bonded: 3.02 r_work: 0.2789 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.2789 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2773 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2773 r_free = 0.2773 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 = 0.2773 r_free = 0.2773 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.87 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2773 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7688 moved from start: 0.2127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 13410 Z= 0.185 Angle : 0.560 8.054 18370 Z= 0.273 Chirality : 0.040 0.150 2235 Planarity : 0.004 0.025 2250 Dihedral : 4.156 30.366 2062 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 3.64 % Allowed : 12.87 % Favored : 83.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.20 (0.21), residues: 1600 helix: 3.46 (0.20), residues: 515 sheet: 1.18 (0.24), residues: 420 loop : 0.03 (0.25), residues: 665 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 78 TYR 0.016 0.002 TYR A 176 PHE 0.020 0.002 PHE E 72 TRP 0.016 0.001 TRP C 112 HIS 0.002 0.000 HIS D 276 Details of bonding type rmsd covalent geometry : bond 0.00429 (13385) covalent geometry : angle 0.55594 (18305) SS BOND : bond 0.00347 ( 10) SS BOND : angle 1.20879 ( 20) hydrogen bonds : bond 0.04027 ( 680) hydrogen bonds : angle 3.87010 ( 2100) link_BETA1-4 : bond 0.00122 ( 5) link_BETA1-4 : angle 0.85235 ( 15) link_NAG-ASN : bond 0.00233 ( 10) link_NAG-ASN : angle 1.37364 ( 30) *********************** 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 338 residues out of total 1430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 286 time to evaluate : 0.333 Fit side-chains REVERT: A 75 ASP cc_start: 0.7817 (t0) cc_final: 0.7458 (t0) REVERT: A 201 GLU cc_start: 0.8568 (mt-10) cc_final: 0.7920 (mp0) REVERT: A 260 GLU cc_start: 0.8774 (pm20) cc_final: 0.8104 (pm20) REVERT: A 391 TRP cc_start: 0.8050 (m-90) cc_final: 0.7848 (m-90) REVERT: B 48 GLU cc_start: 0.7866 (tp30) cc_final: 0.7585 (tp30) REVERT: B 75 ASP cc_start: 0.7654 (t0) cc_final: 0.7248 (t0) REVERT: B 112 TRP cc_start: 0.8100 (OUTLIER) cc_final: 0.7301 (t-100) REVERT: B 124 GLU cc_start: 0.8422 (mp0) cc_final: 0.8009 (mp0) REVERT: B 154 GLU cc_start: 0.8782 (tt0) cc_final: 0.8529 (tt0) REVERT: B 201 GLU cc_start: 0.8532 (mt-10) cc_final: 0.8020 (mp0) REVERT: B 260 GLU cc_start: 0.8642 (pm20) cc_final: 0.8336 (pm20) REVERT: B 391 TRP cc_start: 0.8145 (m-90) cc_final: 0.7851 (m-90) REVERT: C 142 ASP cc_start: 0.9103 (m-30) cc_final: 0.8335 (p0) REVERT: C 176 TYR cc_start: 0.8421 (m-80) cc_final: 0.8160 (m-80) REVERT: C 188 GLN cc_start: 0.8079 (tt0) cc_final: 0.7497 (tt0) REVERT: C 201 GLU cc_start: 0.8617 (mt-10) cc_final: 0.8046 (mp0) REVERT: C 210 GLN cc_start: 0.8073 (pt0) cc_final: 0.7859 (pt0) REVERT: C 214 GLN cc_start: 0.8234 (mm-40) cc_final: 0.7946 (pt0) REVERT: C 221 GLN cc_start: 0.8454 (pt0) cc_final: 0.7752 (pt0) REVERT: D 63 ASP cc_start: 0.8416 (t70) cc_final: 0.8068 (t0) REVERT: D 78 ARG cc_start: 0.8496 (mmm-85) cc_final: 0.8238 (mtp85) REVERT: D 113 GLU cc_start: 0.8515 (mp0) cc_final: 0.8232 (mp0) REVERT: D 142 ASP cc_start: 0.9186 (m-30) cc_final: 0.8476 (p0) REVERT: D 160 GLU cc_start: 0.8226 (OUTLIER) cc_final: 0.7942 (mt-10) REVERT: D 364 GLU cc_start: 0.7850 (mt-10) cc_final: 0.7457 (mt-10) REVERT: D 372 LEU cc_start: 0.8071 (OUTLIER) cc_final: 0.7851 (tt) REVERT: D 391 TRP cc_start: 0.8210 (m-90) cc_final: 0.7916 (m-90) REVERT: E 124 GLU cc_start: 0.8348 (mp0) cc_final: 0.8118 (mp0) REVERT: E 132 ASP cc_start: 0.8031 (OUTLIER) cc_final: 0.7621 (t0) REVERT: E 142 ASP cc_start: 0.9149 (m-30) cc_final: 0.8530 (p0) REVERT: E 221 GLN cc_start: 0.8470 (pt0) cc_final: 0.8088 (pt0) REVERT: E 257 ARG cc_start: 0.8937 (ptp90) cc_final: 0.8285 (ptp-110) REVERT: E 382 GLN cc_start: 0.8363 (mm110) cc_final: 0.8107 (mm-40) REVERT: E 391 TRP cc_start: 0.8134 (m-90) cc_final: 0.7867 (m-10) outliers start: 52 outliers final: 22 residues processed: 320 average time/residue: 0.5699 time to fit residues: 199.4699 Evaluate side-chains 289 residues out of total 1430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 263 time to evaluate : 0.503 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain A residue 275 LEU Chi-restraints excluded: chain A residue 373 VAL Chi-restraints excluded: chain B residue 112 TRP Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain B residue 364 GLU Chi-restraints excluded: chain B residue 372 LEU Chi-restraints excluded: chain B residue 373 VAL Chi-restraints excluded: chain C residue 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 146 LYS Chi-restraints excluded: chain D residue 160 GLU Chi-restraints excluded: chain D residue 299 ILE Chi-restraints excluded: chain D residue 372 LEU Chi-restraints excluded: chain D residue 373 VAL Chi-restraints excluded: chain E residue 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 Chi-restraints excluded: chain E residue 373 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 27 optimal weight: 5.9990 chunk 148 optimal weight: 0.8980 chunk 77 optimal weight: 3.9990 chunk 43 optimal weight: 2.9990 chunk 127 optimal weight: 0.9990 chunk 102 optimal weight: 4.9990 chunk 32 optimal weight: 5.9990 chunk 19 optimal weight: 4.9990 chunk 31 optimal weight: 0.0020 chunk 113 optimal weight: 3.9990 chunk 62 optimal weight: 0.9980 overall best weight: 1.1792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 276 HIS C 276 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.095799 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2972 r_free = 0.2972 target = 0.079415 restraints weight = 20779.449| |-----------------------------------------------------------------------------| r_work (start): 0.2956 rms_B_bonded: 3.05 r_work: 0.2794 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.2794 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2776 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2776 r_free = 0.2776 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 = 0.2776 r_free = 0.2776 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.88 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2776 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7690 moved from start: 0.2356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 13410 Z= 0.154 Angle : 0.543 6.262 18370 Z= 0.265 Chirality : 0.040 0.145 2235 Planarity : 0.003 0.027 2250 Dihedral : 4.031 30.053 2062 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 3.57 % Allowed : 14.62 % Favored : 81.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.13 (0.21), residues: 1600 helix: 3.42 (0.20), residues: 515 sheet: 0.99 (0.24), residues: 420 loop : 0.10 (0.25), residues: 665 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 78 TYR 0.013 0.002 TYR B 176 PHE 0.019 0.001 PHE E 72 TRP 0.022 0.001 TRP B 112 HIS 0.002 0.000 HIS D 276 Details of bonding type rmsd covalent geometry : bond 0.00352 (13385) covalent geometry : angle 0.53923 (18305) SS BOND : bond 0.00520 ( 10) SS BOND : angle 1.16861 ( 20) hydrogen bonds : bond 0.03891 ( 680) hydrogen bonds : angle 3.80507 ( 2100) link_BETA1-4 : bond 0.00099 ( 5) link_BETA1-4 : angle 0.91445 ( 15) link_NAG-ASN : bond 0.00142 ( 10) link_NAG-ASN : angle 1.26331 ( 30) *********************** 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 325 residues out of total 1430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 274 time to evaluate : 0.500 Fit side-chains REVERT: A 75 ASP cc_start: 0.7820 (t0) cc_final: 0.7425 (t0) REVERT: A 112 TRP cc_start: 0.8190 (OUTLIER) cc_final: 0.7464 (t-100) REVERT: A 124 GLU cc_start: 0.8337 (mp0) cc_final: 0.7940 (mp0) REVERT: A 184 GLU cc_start: 0.8340 (pt0) cc_final: 0.8131 (pt0) REVERT: A 201 GLU cc_start: 0.8592 (mt-10) cc_final: 0.7959 (mp0) REVERT: A 214 GLN cc_start: 0.8196 (mm-40) cc_final: 0.7969 (pt0) REVERT: A 260 GLU cc_start: 0.8743 (pm20) cc_final: 0.8213 (pm20) REVERT: A 391 TRP cc_start: 0.8031 (m-90) cc_final: 0.7777 (m-90) REVERT: B 48 GLU cc_start: 0.7930 (tp30) cc_final: 0.7571 (tp30) REVERT: B 75 ASP cc_start: 0.7626 (t0) cc_final: 0.7216 (t0) REVERT: B 124 GLU cc_start: 0.8435 (mp0) cc_final: 0.7985 (mp0) REVERT: B 132 ASP cc_start: 0.7371 (t0) cc_final: 0.7166 (p0) REVERT: B 146 LYS cc_start: 0.8253 (mtmm) cc_final: 0.7954 (mtpp) REVERT: B 154 GLU cc_start: 0.8782 (tt0) cc_final: 0.8563 (tt0) REVERT: B 201 GLU cc_start: 0.8550 (mt-10) cc_final: 0.8040 (mp0) REVERT: B 214 GLN cc_start: 0.8280 (mm-40) cc_final: 0.8055 (pt0) REVERT: B 260 GLU cc_start: 0.8594 (pm20) cc_final: 0.8302 (pm20) REVERT: B 391 TRP cc_start: 0.8143 (m-90) cc_final: 0.7821 (m-90) REVERT: C 112 TRP cc_start: 0.8081 (OUTLIER) cc_final: 0.7266 (t-100) REVERT: C 136 GLN cc_start: 0.9032 (mt0) cc_final: 0.8781 (mt0) REVERT: C 176 TYR cc_start: 0.8374 (m-80) cc_final: 0.7987 (m-80) REVERT: C 188 GLN cc_start: 0.8103 (tt0) cc_final: 0.7517 (tt0) REVERT: C 201 GLU cc_start: 0.8620 (mt-10) cc_final: 0.8048 (mp0) REVERT: C 214 GLN cc_start: 0.8266 (mm-40) cc_final: 0.7996 (pt0) REVERT: D 63 ASP cc_start: 0.8391 (t70) cc_final: 0.8048 (t0) REVERT: D 78 ARG cc_start: 0.8531 (mmm-85) cc_final: 0.8320 (mtp85) REVERT: D 112 TRP cc_start: 0.8145 (OUTLIER) cc_final: 0.7513 (t-100) REVERT: D 142 ASP cc_start: 0.9168 (m-30) cc_final: 0.8462 (p0) REVERT: D 364 GLU cc_start: 0.7839 (mt-10) cc_final: 0.7444 (mt-10) REVERT: D 372 LEU cc_start: 0.8052 (OUTLIER) cc_final: 0.7840 (tt) REVERT: D 391 TRP cc_start: 0.8181 (m-90) cc_final: 0.7894 (m-90) REVERT: E 112 TRP cc_start: 0.8005 (OUTLIER) cc_final: 0.7124 (t-100) REVERT: E 124 GLU cc_start: 0.8362 (mp0) cc_final: 0.8110 (mp0) REVERT: E 132 ASP cc_start: 0.8042 (OUTLIER) cc_final: 0.7621 (t0) REVERT: E 221 GLN cc_start: 0.8444 (pt0) cc_final: 0.8095 (pt0) REVERT: E 391 TRP cc_start: 0.8146 (m-90) cc_final: 0.7885 (m-10) outliers start: 51 outliers final: 22 residues processed: 302 average time/residue: 0.6104 time to fit residues: 200.6381 Evaluate side-chains 293 residues out of total 1430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 265 time to evaluate : 0.524 ------------------------------------------------------------------------------- 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 210 GLN Chi-restraints excluded: chain A residue 275 LEU Chi-restraints excluded: chain A residue 373 VAL Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain B residue 372 LEU Chi-restraints excluded: chain B residue 373 VAL Chi-restraints excluded: chain C residue 112 TRP Chi-restraints excluded: chain C residue 179 SER 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 372 LEU Chi-restraints excluded: chain C residue 373 VAL Chi-restraints excluded: chain D residue 112 TRP Chi-restraints excluded: chain D residue 299 ILE Chi-restraints excluded: chain D residue 372 LEU Chi-restraints excluded: chain D residue 373 VAL Chi-restraints excluded: chain E residue 112 TRP Chi-restraints excluded: chain E residue 132 ASP Chi-restraints excluded: chain E residue 198 VAL Chi-restraints excluded: chain E residue 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 148 optimal weight: 3.9990 chunk 81 optimal weight: 0.7980 chunk 10 optimal weight: 4.9990 chunk 33 optimal weight: 0.8980 chunk 40 optimal weight: 1.9990 chunk 140 optimal weight: 3.9990 chunk 92 optimal weight: 4.9990 chunk 51 optimal weight: 0.6980 chunk 125 optimal weight: 4.9990 chunk 98 optimal weight: 1.9990 chunk 118 optimal weight: 2.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 276 HIS E 73 ASN E 382 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.095154 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2966 r_free = 0.2966 target = 0.078881 restraints weight = 20978.351| |-----------------------------------------------------------------------------| r_work (start): 0.2970 rms_B_bonded: 3.05 r_work: 0.2808 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.2808 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2796 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2796 r_free = 0.2796 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.88 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2796 r_free = 0.2796 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.87 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2796 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7713 moved from start: 0.2528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 13410 Z= 0.163 Angle : 0.552 6.961 18370 Z= 0.269 Chirality : 0.040 0.148 2235 Planarity : 0.004 0.040 2250 Dihedral : 3.991 30.879 2062 Min Nonbonded Distance : 2.612 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 3.22 % Allowed : 14.76 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.03 (0.21), residues: 1600 helix: 3.38 (0.20), residues: 515 sheet: 0.86 (0.23), residues: 420 loop : 0.06 (0.24), residues: 665 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 257 TYR 0.015 0.002 TYR B 176 PHE 0.019 0.002 PHE E 72 TRP 0.022 0.001 TRP D 112 HIS 0.002 0.000 HIS D 276 Details of bonding type rmsd covalent geometry : bond 0.00376 (13385) covalent geometry : angle 0.54920 (18305) SS BOND : bond 0.00604 ( 10) SS BOND : angle 1.00914 ( 20) hydrogen bonds : bond 0.03879 ( 680) hydrogen bonds : angle 3.79015 ( 2100) link_BETA1-4 : bond 0.00040 ( 5) link_BETA1-4 : angle 0.91425 ( 15) link_NAG-ASN : bond 0.00157 ( 10) link_NAG-ASN : angle 1.31539 ( 30) *********************** 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 320 residues out of total 1430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 274 time to evaluate : 0.523 Fit side-chains REVERT: A 75 ASP cc_start: 0.7799 (t0) cc_final: 0.7430 (t0) REVERT: A 124 GLU cc_start: 0.8359 (mp0) cc_final: 0.7897 (mp0) REVERT: A 184 GLU cc_start: 0.8347 (pt0) cc_final: 0.8138 (pt0) REVERT: A 201 GLU cc_start: 0.8625 (mt-10) cc_final: 0.7995 (mp0) REVERT: A 214 GLN cc_start: 0.8254 (mm-40) cc_final: 0.7987 (pt0) REVERT: A 260 GLU cc_start: 0.8788 (pm20) cc_final: 0.8239 (pm20) REVERT: A 391 TRP cc_start: 0.8066 (m-90) cc_final: 0.7803 (m-90) REVERT: B 48 GLU cc_start: 0.7959 (tp30) cc_final: 0.7601 (tp30) REVERT: B 75 ASP cc_start: 0.7646 (t0) cc_final: 0.7354 (t0) REVERT: B 124 GLU cc_start: 0.8454 (mp0) cc_final: 0.7946 (mp0) REVERT: B 132 ASP cc_start: 0.7504 (t0) cc_final: 0.7081 (p0) REVERT: B 146 LYS cc_start: 0.8307 (mtmm) cc_final: 0.8002 (mtpp) REVERT: B 201 GLU cc_start: 0.8545 (mt-10) cc_final: 0.8026 (mp0) REVERT: B 214 GLN cc_start: 0.8292 (mm-40) cc_final: 0.8074 (pt0) REVERT: B 260 GLU cc_start: 0.8654 (pm20) cc_final: 0.8318 (pm20) REVERT: B 364 GLU cc_start: 0.7721 (mp0) cc_final: 0.6762 (mp0) REVERT: B 391 TRP cc_start: 0.8130 (m-90) cc_final: 0.7812 (m-90) REVERT: C 112 TRP cc_start: 0.8107 (OUTLIER) cc_final: 0.7271 (t-100) REVERT: C 129 ASP cc_start: 0.8385 (t0) cc_final: 0.8125 (t0) REVERT: C 136 GLN cc_start: 0.9061 (mt0) cc_final: 0.8830 (mt0) REVERT: C 188 GLN cc_start: 0.8120 (tt0) cc_final: 0.7553 (tt0) REVERT: C 201 GLU cc_start: 0.8618 (mt-10) cc_final: 0.8041 (mp0) REVERT: C 214 GLN cc_start: 0.8289 (mm-40) cc_final: 0.8031 (pt0) REVERT: D 63 ASP cc_start: 0.8428 (t70) cc_final: 0.8073 (t0) REVERT: D 75 ASP cc_start: 0.7646 (t0) cc_final: 0.7405 (t0) REVERT: D 78 ARG cc_start: 0.8490 (mmm-85) cc_final: 0.8205 (mtp85) REVERT: D 132 ASP cc_start: 0.7307 (t0) cc_final: 0.7093 (p0) REVERT: D 142 ASP cc_start: 0.9156 (m-30) cc_final: 0.8468 (p0) REVERT: D 160 GLU cc_start: 0.8437 (mt-10) cc_final: 0.8079 (mt-10) REVERT: D 364 GLU cc_start: 0.7871 (mt-10) cc_final: 0.7458 (mt-10) REVERT: D 372 LEU cc_start: 0.8077 (OUTLIER) cc_final: 0.7859 (tt) REVERT: D 391 TRP cc_start: 0.8169 (m-90) cc_final: 0.7889 (m-90) REVERT: E 124 GLU cc_start: 0.8369 (mp0) cc_final: 0.8154 (mp0) REVERT: E 132 ASP cc_start: 0.8006 (OUTLIER) cc_final: 0.7634 (t0) REVERT: E 221 GLN cc_start: 0.8493 (pt0) cc_final: 0.8146 (pt0) REVERT: E 257 ARG cc_start: 0.8878 (ptp90) cc_final: 0.8265 (ptp-110) REVERT: E 391 TRP cc_start: 0.8154 (m-90) cc_final: 0.7890 (m-10) outliers start: 46 outliers final: 23 residues processed: 303 average time/residue: 0.6026 time to fit residues: 198.9077 Evaluate side-chains 287 residues out of total 1430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 261 time to evaluate : 0.544 ------------------------------------------------------------------------------- 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 210 GLN Chi-restraints excluded: chain A residue 275 LEU Chi-restraints excluded: chain A residue 373 VAL 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 372 LEU Chi-restraints excluded: chain B residue 373 VAL 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 306 LEU Chi-restraints excluded: chain C residue 372 LEU Chi-restraints excluded: chain C residue 373 VAL Chi-restraints excluded: chain D residue 237 LEU 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 110 optimal weight: 4.9990 chunk 89 optimal weight: 4.9990 chunk 133 optimal weight: 7.9990 chunk 44 optimal weight: 1.9990 chunk 47 optimal weight: 5.9990 chunk 10 optimal weight: 5.9990 chunk 98 optimal weight: 0.6980 chunk 119 optimal weight: 4.9990 chunk 6 optimal weight: 0.9990 chunk 141 optimal weight: 4.9990 chunk 83 optimal weight: 0.9980 overall best weight: 1.9386 ------------------------------------------------------------------------------- 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 = 0.3180 r_free = 0.3180 target = 0.093024 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2931 r_free = 0.2931 target = 0.076785 restraints weight = 20884.837| |-----------------------------------------------------------------------------| r_work (start): 0.2886 rms_B_bonded: 3.01 r_work: 0.2720 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.2720 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2747 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2747 r_free = 0.2747 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.87 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2747 r_free = 0.2747 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.86 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2747 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7696 moved from start: 0.2733 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= 0.225 Angle : 0.581 7.955 18370 Z= 0.284 Chirality : 0.041 0.152 2235 Planarity : 0.004 0.036 2250 Dihedral : 4.025 16.175 2060 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 4.27 % Allowed : 15.03 % Favored : 80.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.91 (0.21), residues: 1600 helix: 2.94 (0.20), residues: 545 sheet: 0.73 (0.23), residues: 420 loop : 0.21 (0.26), residues: 635 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG D 257 TYR 0.012 0.002 TYR B 176 PHE 0.031 0.002 PHE D 385 TRP 0.026 0.001 TRP B 112 HIS 0.003 0.000 HIS A 276 Details of bonding type rmsd covalent geometry : bond 0.00523 (13385) covalent geometry : angle 0.57766 (18305) SS BOND : bond 0.00584 ( 10) SS BOND : angle 1.13736 ( 20) hydrogen bonds : bond 0.04039 ( 680) hydrogen bonds : angle 3.84819 ( 2100) link_BETA1-4 : bond 0.00101 ( 5) link_BETA1-4 : angle 0.93528 ( 15) link_NAG-ASN : bond 0.00306 ( 10) link_NAG-ASN : angle 1.40672 ( 30) *********************** 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 323 residues out of total 1430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 262 time to evaluate : 0.548 Fit side-chains REVERT: A 112 TRP cc_start: 0.8080 (OUTLIER) cc_final: 0.7718 (t-100) REVERT: A 124 GLU cc_start: 0.8325 (mp0) cc_final: 0.7928 (mp0) REVERT: A 154 GLU cc_start: 0.8641 (tt0) cc_final: 0.8092 (tt0) REVERT: A 184 GLU cc_start: 0.8336 (pt0) cc_final: 0.8124 (pt0) REVERT: A 201 GLU cc_start: 0.8576 (mt-10) cc_final: 0.7976 (mp0) REVERT: A 214 GLN cc_start: 0.8270 (mm-40) cc_final: 0.7939 (pt0) REVERT: A 260 GLU cc_start: 0.8786 (pm20) cc_final: 0.8320 (pm20) REVERT: A 364 GLU cc_start: 0.8086 (mt-10) cc_final: 0.7687 (mt-10) REVERT: A 391 TRP cc_start: 0.8112 (m-90) cc_final: 0.7876 (m-90) REVERT: B 48 GLU cc_start: 0.8015 (tp30) cc_final: 0.7785 (tp30) REVERT: B 112 TRP cc_start: 0.8038 (OUTLIER) cc_final: 0.7522 (t-100) REVERT: B 124 GLU cc_start: 0.8420 (mp0) cc_final: 0.7981 (mp0) REVERT: B 132 ASP cc_start: 0.7254 (t0) cc_final: 0.7005 (t0) REVERT: B 146 LYS cc_start: 0.8288 (mtmm) cc_final: 0.8008 (mtpp) REVERT: B 201 GLU cc_start: 0.8520 (mt-10) cc_final: 0.7982 (mp0) REVERT: B 214 GLN cc_start: 0.8310 (mm-40) cc_final: 0.8035 (pt0) REVERT: B 260 GLU cc_start: 0.8671 (pm20) cc_final: 0.8316 (pm20) REVERT: B 391 TRP cc_start: 0.8172 (m-90) cc_final: 0.7905 (m-90) REVERT: C 112 TRP cc_start: 0.8235 (OUTLIER) cc_final: 0.7830 (t-100) REVERT: C 129 ASP cc_start: 0.8385 (t0) cc_final: 0.8018 (t0) REVERT: C 146 LYS cc_start: 0.8072 (OUTLIER) cc_final: 0.7635 (mtpp) REVERT: C 176 TYR cc_start: 0.8376 (m-80) cc_final: 0.8102 (m-80) REVERT: C 188 GLN cc_start: 0.8025 (tt0) cc_final: 0.7381 (tt0) REVERT: C 201 GLU cc_start: 0.8664 (mt-10) cc_final: 0.8040 (mp0) REVERT: C 214 GLN cc_start: 0.8251 (mm-40) cc_final: 0.7976 (pt0) REVERT: D 63 ASP cc_start: 0.8455 (t70) cc_final: 0.8106 (t0) REVERT: D 75 ASP cc_start: 0.7620 (t0) cc_final: 0.7411 (t0) REVERT: D 129 ASP cc_start: 0.8375 (t0) cc_final: 0.8123 (OUTLIER) REVERT: D 132 ASP cc_start: 0.7121 (t0) cc_final: 0.6744 (p0) REVERT: D 160 GLU cc_start: 0.8380 (mt-10) cc_final: 0.8059 (mt-10) REVERT: D 364 GLU cc_start: 0.7885 (mt-10) cc_final: 0.7468 (mt-10) REVERT: D 372 LEU cc_start: 0.8060 (OUTLIER) cc_final: 0.7840 (tt) REVERT: D 391 TRP cc_start: 0.8163 (m-90) cc_final: 0.7925 (m-90) REVERT: E 112 TRP cc_start: 0.8082 (OUTLIER) cc_final: 0.7120 (t-100) REVERT: E 124 GLU cc_start: 0.8314 (mp0) cc_final: 0.8020 (mp0) REVERT: E 132 ASP cc_start: 0.8003 (OUTLIER) cc_final: 0.7749 (t0) REVERT: E 221 GLN cc_start: 0.8480 (pt0) cc_final: 0.8116 (pt0) REVERT: E 257 ARG cc_start: 0.8885 (ptp90) cc_final: 0.8250 (ptp-110) REVERT: E 391 TRP cc_start: 0.8188 (m-90) cc_final: 0.7965 (m-10) outliers start: 61 outliers final: 27 residues processed: 293 average time/residue: 0.6239 time to fit residues: 198.5770 Evaluate side-chains 277 residues out of total 1430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 244 time to evaluate : 0.549 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 TRP Chi-restraints excluded: chain A residue 123 LEU Chi-restraints excluded: chain A residue 210 GLN Chi-restraints excluded: chain A residue 275 LEU Chi-restraints excluded: chain A residue 373 VAL Chi-restraints excluded: chain B residue 112 TRP Chi-restraints excluded: chain B residue 210 GLN Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain B residue 372 LEU Chi-restraints excluded: chain B residue 373 VAL Chi-restraints excluded: chain C residue 112 TRP Chi-restraints excluded: chain C residue 146 LYS Chi-restraints excluded: chain C residue 179 SER Chi-restraints excluded: chain C residue 198 VAL 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 50 ILE Chi-restraints excluded: chain D residue 146 LYS Chi-restraints excluded: chain D residue 198 VAL Chi-restraints excluded: chain D residue 237 LEU Chi-restraints excluded: chain D residue 275 LEU Chi-restraints excluded: chain D residue 299 ILE Chi-restraints excluded: chain D residue 372 LEU Chi-restraints excluded: chain 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 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 112 optimal weight: 4.9990 chunk 155 optimal weight: 0.5980 chunk 2 optimal weight: 0.7980 chunk 10 optimal weight: 2.9990 chunk 136 optimal weight: 0.7980 chunk 73 optimal weight: 5.9990 chunk 17 optimal weight: 2.9990 chunk 145 optimal weight: 0.8980 chunk 36 optimal weight: 0.8980 chunk 18 optimal weight: 0.9990 chunk 123 optimal weight: 0.6980 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 = 0.3217 r_free = 0.3217 target = 0.095425 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.2972 r_free = 0.2972 target = 0.079195 restraints weight = 20770.841| |-----------------------------------------------------------------------------| r_work (start): 0.2952 rms_B_bonded: 3.03 r_work: 0.2792 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.2792 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2797 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2797 r_free = 0.2797 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.86 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2797 r_free = 0.2797 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.86 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2797 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7735 moved from start: 0.2761 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= 0.124 Angle : 0.547 9.041 18370 Z= 0.262 Chirality : 0.039 0.143 2235 Planarity : 0.003 0.030 2250 Dihedral : 3.885 15.268 2060 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 2.38 % Allowed : 17.27 % Favored : 80.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.97 (0.21), residues: 1600 helix: 3.03 (0.20), residues: 545 sheet: 0.78 (0.24), residues: 420 loop : 0.21 (0.26), residues: 635 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 78 TYR 0.017 0.002 TYR E 272 PHE 0.023 0.001 PHE D 385 TRP 0.024 0.001 TRP E 112 HIS 0.002 0.000 HIS A 276 Details of bonding type rmsd covalent geometry : bond 0.00279 (13385) covalent geometry : angle 0.54400 (18305) SS BOND : bond 0.00447 ( 10) SS BOND : angle 0.89124 ( 20) hydrogen bonds : bond 0.03821 ( 680) hydrogen bonds : angle 3.73585 ( 2100) link_BETA1-4 : bond 0.00110 ( 5) link_BETA1-4 : angle 0.90288 ( 15) link_NAG-ASN : bond 0.00122 ( 10) link_NAG-ASN : angle 1.21245 ( 30) *********************** 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 290 residues out of total 1430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 256 time to evaluate : 0.597 Fit side-chains REVERT: A 75 ASP cc_start: 0.7832 (t0) cc_final: 0.7468 (t0) REVERT: A 124 GLU cc_start: 0.8401 (mp0) cc_final: 0.7859 (mp0) REVERT: A 154 GLU cc_start: 0.8708 (tt0) cc_final: 0.8213 (tt0) REVERT: A 184 GLU cc_start: 0.8425 (pt0) cc_final: 0.8217 (pt0) REVERT: A 201 GLU cc_start: 0.8638 (mt-10) cc_final: 0.7998 (mp0) REVERT: A 214 GLN cc_start: 0.8253 (mm-40) cc_final: 0.8004 (pt0) REVERT: A 260 GLU cc_start: 0.8819 (pm20) cc_final: 0.8364 (pm20) REVERT: A 364 GLU cc_start: 0.8096 (mt-10) cc_final: 0.7687 (mt-10) REVERT: A 391 TRP cc_start: 0.8075 (m-90) cc_final: 0.7824 (m-90) REVERT: B 48 GLU cc_start: 0.8032 (tp30) cc_final: 0.7770 (tp30) REVERT: B 124 GLU cc_start: 0.8455 (mp0) cc_final: 0.7899 (mp0) REVERT: B 132 ASP cc_start: 0.7401 (t0) cc_final: 0.7129 (t0) REVERT: B 146 LYS cc_start: 0.8313 (mtmm) cc_final: 0.8014 (mtpp) REVERT: B 201 GLU cc_start: 0.8552 (mt-10) cc_final: 0.8026 (mp0) REVERT: B 214 GLN cc_start: 0.8302 (mm-40) cc_final: 0.8050 (pt0) REVERT: B 260 GLU cc_start: 0.8759 (pm20) cc_final: 0.8401 (pm20) REVERT: B 272 TYR cc_start: 0.8612 (t80) cc_final: 0.8379 (t80) REVERT: B 391 TRP cc_start: 0.8166 (m-90) cc_final: 0.7914 (m-10) REVERT: C 75 ASP cc_start: 0.7630 (t0) cc_final: 0.7035 (t0) REVERT: C 112 TRP cc_start: 0.8078 (OUTLIER) cc_final: 0.7524 (t-100) REVERT: C 129 ASP cc_start: 0.8465 (t0) cc_final: 0.8042 (t0) REVERT: C 132 ASP cc_start: 0.7401 (t0) cc_final: 0.7088 (p0) REVERT: C 188 GLN cc_start: 0.8140 (tt0) cc_final: 0.7530 (tt0) REVERT: C 201 GLU cc_start: 0.8711 (mt-10) cc_final: 0.8091 (mp0) REVERT: C 214 GLN cc_start: 0.8259 (mm-40) cc_final: 0.8012 (pt0) REVERT: C 260 GLU cc_start: 0.8962 (pm20) cc_final: 0.8551 (pm20) REVERT: D 78 ARG cc_start: 0.8522 (mmm-85) cc_final: 0.8317 (mtm110) REVERT: D 132 ASP cc_start: 0.7085 (t0) cc_final: 0.6749 (p0) REVERT: D 364 GLU cc_start: 0.7925 (mt-10) cc_final: 0.7530 (mt-10) REVERT: D 372 LEU cc_start: 0.8065 (OUTLIER) cc_final: 0.7707 (tp) REVERT: D 391 TRP cc_start: 0.8097 (m-90) cc_final: 0.7857 (m-90) REVERT: E 113 GLU cc_start: 0.8696 (mp0) cc_final: 0.8457 (mm-30) REVERT: E 124 GLU cc_start: 0.8355 (mp0) cc_final: 0.8149 (mp0) REVERT: E 132 ASP cc_start: 0.7922 (OUTLIER) cc_final: 0.7630 (t0) REVERT: E 221 GLN cc_start: 0.8495 (pt0) cc_final: 0.8163 (pt0) REVERT: E 257 ARG cc_start: 0.8895 (ptp90) cc_final: 0.8270 (ptp-110) REVERT: E 260 GLU cc_start: 0.8780 (pt0) cc_final: 0.8568 (pm20) REVERT: E 285 SER cc_start: 0.8752 (t) cc_final: 0.8392 (t) REVERT: E 391 TRP cc_start: 0.8057 (m-90) cc_final: 0.7831 (m-10) outliers start: 34 outliers final: 15 residues processed: 274 average time/residue: 0.6463 time to fit residues: 192.1336 Evaluate side-chains 276 residues out of total 1430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 258 time to evaluate : 0.506 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 LEU Chi-restraints excluded: chain A residue 275 LEU Chi-restraints excluded: chain A residue 394 CYS Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain B residue 372 LEU Chi-restraints excluded: chain B residue 378 VAL 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 372 LEU 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 372 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 67 optimal weight: 4.9990 chunk 118 optimal weight: 0.7980 chunk 21 optimal weight: 0.7980 chunk 20 optimal weight: 0.9990 chunk 79 optimal weight: 5.9990 chunk 116 optimal weight: 0.9990 chunk 52 optimal weight: 5.9990 chunk 66 optimal weight: 0.9980 chunk 56 optimal weight: 0.9980 chunk 4 optimal weight: 3.9990 chunk 131 optimal weight: 5.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 276 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.095498 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.2976 r_free = 0.2976 target = 0.079448 restraints weight = 20616.265| |-----------------------------------------------------------------------------| r_work (start): 0.2955 rms_B_bonded: 3.01 r_work: 0.2795 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.2795 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2807 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2807 r_free = 0.2807 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 = 0.2807 r_free = 0.2807 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.86 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2807 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7674 moved from start: 0.2807 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= 0.135 Angle : 0.545 9.910 18370 Z= 0.261 Chirality : 0.040 0.158 2235 Planarity : 0.003 0.029 2250 Dihedral : 3.839 16.003 2060 Min Nonbonded Distance : 2.619 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 2.31 % Allowed : 17.90 % Favored : 79.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.98 (0.21), residues: 1600 helix: 3.04 (0.20), residues: 545 sheet: 0.78 (0.24), residues: 420 loop : 0.20 (0.26), residues: 635 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 257 TYR 0.025 0.002 TYR E 176 PHE 0.022 0.001 PHE D 385 TRP 0.024 0.001 TRP B 112 HIS 0.002 0.000 HIS A 276 Details of bonding type rmsd covalent geometry : bond 0.00309 (13385) covalent geometry : angle 0.54215 (18305) SS BOND : bond 0.00471 ( 10) SS BOND : angle 0.86282 ( 20) hydrogen bonds : bond 0.03808 ( 680) hydrogen bonds : angle 3.72427 ( 2100) link_BETA1-4 : bond 0.00107 ( 5) link_BETA1-4 : angle 0.92131 ( 15) link_NAG-ASN : bond 0.00099 ( 10) link_NAG-ASN : angle 1.21908 ( 30) *********************** 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 295 residues out of total 1430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 262 time to evaluate : 0.467 Fit side-chains REVERT: A 81 MET cc_start: 0.8692 (ttp) cc_final: 0.8343 (ptt) REVERT: A 124 GLU cc_start: 0.8379 (mp0) cc_final: 0.7812 (mp0) REVERT: A 184 GLU cc_start: 0.8380 (pt0) cc_final: 0.8177 (pt0) REVERT: A 201 GLU cc_start: 0.8590 (mt-10) cc_final: 0.7964 (mp0) REVERT: A 214 GLN cc_start: 0.8245 (mm-40) cc_final: 0.8007 (pt0) REVERT: A 260 GLU cc_start: 0.8787 (pm20) cc_final: 0.8351 (pm20) REVERT: A 364 GLU cc_start: 0.8053 (mt-10) cc_final: 0.7590 (mt-10) REVERT: A 391 TRP cc_start: 0.8054 (m-90) cc_final: 0.7802 (m-90) REVERT: B 48 GLU cc_start: 0.7981 (tp30) cc_final: 0.7744 (tp30) REVERT: B 124 GLU cc_start: 0.8432 (mp0) cc_final: 0.7857 (mp0) REVERT: B 132 ASP cc_start: 0.7412 (t0) cc_final: 0.7121 (t0) REVERT: B 146 LYS cc_start: 0.8234 (mtmm) cc_final: 0.7947 (mtpp) REVERT: B 201 GLU cc_start: 0.8528 (mt-10) cc_final: 0.8006 (mp0) REVERT: B 214 GLN cc_start: 0.8328 (mm-40) cc_final: 0.8046 (pt0) REVERT: B 260 GLU cc_start: 0.8751 (pm20) cc_final: 0.8391 (pm20) REVERT: B 272 TYR cc_start: 0.8544 (t80) cc_final: 0.8294 (t80) REVERT: B 391 TRP cc_start: 0.8145 (m-90) cc_final: 0.7900 (m-90) REVERT: C 75 ASP cc_start: 0.7551 (t0) cc_final: 0.7121 (t0) REVERT: C 112 TRP cc_start: 0.8040 (OUTLIER) cc_final: 0.7547 (t-100) REVERT: C 129 ASP cc_start: 0.8426 (t0) cc_final: 0.7977 (t0) REVERT: C 132 ASP cc_start: 0.7463 (t0) cc_final: 0.7135 (p0) REVERT: C 146 LYS cc_start: 0.8059 (OUTLIER) cc_final: 0.7618 (mtpp) REVERT: C 188 GLN cc_start: 0.8065 (tt0) cc_final: 0.7440 (tt0) REVERT: C 201 GLU cc_start: 0.8675 (mt-10) cc_final: 0.8074 (mp0) REVERT: C 214 GLN cc_start: 0.8274 (mm-40) cc_final: 0.8036 (pt0) REVERT: C 260 GLU cc_start: 0.8926 (pm20) cc_final: 0.8630 (pm20) REVERT: D 63 ASP cc_start: 0.8409 (t70) cc_final: 0.8081 (t0) REVERT: D 75 ASP cc_start: 0.7620 (t0) cc_final: 0.7389 (t0) REVERT: D 129 ASP cc_start: 0.8346 (t0) cc_final: 0.7963 (OUTLIER) REVERT: D 132 ASP cc_start: 0.7076 (t0) cc_final: 0.6621 (t0) REVERT: D 160 GLU cc_start: 0.8425 (mt-10) cc_final: 0.8027 (mt-10) REVERT: D 364 GLU cc_start: 0.7906 (mt-10) cc_final: 0.7502 (mt-10) REVERT: D 391 TRP cc_start: 0.8075 (m-90) cc_final: 0.7830 (m-90) REVERT: D 402 GLU cc_start: 0.8302 (mm-30) cc_final: 0.8085 (mm-30) REVERT: E 132 ASP cc_start: 0.7895 (OUTLIER) cc_final: 0.7611 (t0) REVERT: E 221 GLN cc_start: 0.8421 (pt0) cc_final: 0.8096 (pt0) REVERT: E 257 ARG cc_start: 0.8891 (ptp90) cc_final: 0.8251 (ptp-110) REVERT: E 260 GLU cc_start: 0.8746 (pt0) cc_final: 0.8538 (pm20) outliers start: 33 outliers final: 19 residues processed: 278 average time/residue: 0.6203 time to fit residues: 187.5604 Evaluate side-chains 277 residues out of total 1430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 256 time to evaluate : 0.509 ------------------------------------------------------------------------------- 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 394 CYS Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain B residue 372 LEU Chi-restraints excluded: chain B residue 378 VAL 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 146 LYS Chi-restraints excluded: chain C residue 179 SER Chi-restraints excluded: chain C residue 198 VAL Chi-restraints excluded: chain C residue 372 LEU Chi-restraints excluded: chain D residue 146 LYS Chi-restraints excluded: chain D residue 153 THR Chi-restraints excluded: chain D residue 299 ILE Chi-restraints excluded: chain E residue 132 ASP Chi-restraints excluded: chain E residue 198 VAL Chi-restraints excluded: chain E residue 275 LEU Chi-restraints excluded: chain E residue 372 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 25 optimal weight: 3.9990 chunk 14 optimal weight: 0.0770 chunk 88 optimal weight: 4.9990 chunk 149 optimal weight: 0.4980 chunk 147 optimal weight: 0.3980 chunk 84 optimal weight: 3.9990 chunk 113 optimal weight: 2.9990 chunk 158 optimal weight: 2.9990 chunk 17 optimal weight: 1.9990 chunk 131 optimal weight: 5.9990 chunk 144 optimal weight: 0.9990 overall best weight: 0.7942 ------------------------------------------------------------------------------- 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 = 0.3226 r_free = 0.3226 target = 0.096070 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.080009 restraints weight = 20720.293| |-----------------------------------------------------------------------------| r_work (start): 0.2920 rms_B_bonded: 3.02 r_work: 0.2758 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.2758 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2793 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2793 r_free = 0.2793 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 = 0.2793 r_free = 0.2793 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.86 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2793 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7648 moved from start: 0.2845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 13410 Z= 0.127 Angle : 0.556 10.573 18370 Z= 0.264 Chirality : 0.040 0.142 2235 Planarity : 0.003 0.035 2250 Dihedral : 3.799 15.305 2060 Min Nonbonded Distance : 2.618 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 1.68 % Allowed : 18.74 % Favored : 79.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.03 (0.21), residues: 1600 helix: 3.09 (0.20), residues: 545 sheet: 0.80 (0.24), residues: 420 loop : 0.21 (0.26), residues: 635 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 257 TYR 0.031 0.002 TYR E 176 PHE 0.024 0.002 PHE A 385 TRP 0.023 0.001 TRP B 112 HIS 0.002 0.000 HIS A 276 Details of bonding type rmsd covalent geometry : bond 0.00291 (13385) covalent geometry : angle 0.55396 (18305) SS BOND : bond 0.00428 ( 10) SS BOND : angle 0.80802 ( 20) hydrogen bonds : bond 0.03770 ( 680) hydrogen bonds : angle 3.68100 ( 2100) link_BETA1-4 : bond 0.00132 ( 5) link_BETA1-4 : angle 0.92915 ( 15) link_NAG-ASN : bond 0.00056 ( 10) link_NAG-ASN : angle 1.19855 ( 30) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3200 Ramachandran restraints generated. 1600 Oldfield, 0 Emsley, 1600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3200 Ramachandran restraints generated. 1600 Oldfield, 0 Emsley, 1600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 1430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 267 time to evaluate : 0.514 Fit side-chains REVERT: A 75 ASP cc_start: 0.7751 (t0) cc_final: 0.7427 (t0) REVERT: A 81 MET cc_start: 0.8676 (ttp) cc_final: 0.8322 (ptt) REVERT: A 124 GLU cc_start: 0.8363 (mp0) cc_final: 0.7803 (mp0) REVERT: A 201 GLU cc_start: 0.8582 (mt-10) cc_final: 0.7955 (mp0) REVERT: A 214 GLN cc_start: 0.8222 (mm-40) cc_final: 0.7984 (pt0) REVERT: A 260 GLU cc_start: 0.8783 (pm20) cc_final: 0.8309 (pm20) REVERT: A 364 GLU cc_start: 0.8042 (mt-10) cc_final: 0.7585 (mt-10) REVERT: A 391 TRP cc_start: 0.8053 (m-90) cc_final: 0.7804 (m-90) REVERT: B 48 GLU cc_start: 0.7983 (tp30) cc_final: 0.7732 (tp30) REVERT: B 124 GLU cc_start: 0.8383 (mp0) cc_final: 0.7808 (mp0) REVERT: B 132 ASP cc_start: 0.7323 (t0) cc_final: 0.7013 (t0) REVERT: B 146 LYS cc_start: 0.8224 (mtmm) cc_final: 0.7940 (mtpp) REVERT: B 201 GLU cc_start: 0.8510 (mt-10) cc_final: 0.7990 (mp0) REVERT: B 214 GLN cc_start: 0.8322 (mm-40) cc_final: 0.8046 (pt0) REVERT: B 260 GLU cc_start: 0.8751 (pm20) cc_final: 0.8389 (pm20) REVERT: B 272 TYR cc_start: 0.8500 (t80) cc_final: 0.8257 (t80) REVERT: B 391 TRP cc_start: 0.8117 (m-90) cc_final: 0.7870 (m-90) REVERT: C 75 ASP cc_start: 0.7536 (t0) cc_final: 0.7098 (t0) REVERT: C 112 TRP cc_start: 0.7992 (OUTLIER) cc_final: 0.7615 (t-100) REVERT: C 124 GLU cc_start: 0.8134 (mp0) cc_final: 0.7706 (mp0) REVERT: C 129 ASP cc_start: 0.8307 (t0) cc_final: 0.7869 (t0) REVERT: C 132 ASP cc_start: 0.7505 (t0) cc_final: 0.7143 (p0) REVERT: C 154 GLU cc_start: 0.8683 (tt0) cc_final: 0.8399 (tt0) REVERT: C 188 GLN cc_start: 0.8037 (tt0) cc_final: 0.7473 (tt0) REVERT: C 201 GLU cc_start: 0.8636 (mt-10) cc_final: 0.8057 (mp0) REVERT: C 214 GLN cc_start: 0.8267 (mm-40) cc_final: 0.8037 (pt0) REVERT: C 260 GLU cc_start: 0.8934 (pm20) cc_final: 0.8655 (pm20) REVERT: C 364 GLU cc_start: 0.8008 (mt-10) cc_final: 0.7609 (mt-10) REVERT: D 124 GLU cc_start: 0.8265 (mp0) cc_final: 0.8005 (mp0) REVERT: D 132 ASP cc_start: 0.7196 (t0) cc_final: 0.6745 (t0) REVERT: D 160 GLU cc_start: 0.8411 (mt-10) cc_final: 0.8013 (mt-10) REVERT: D 201 GLU cc_start: 0.8677 (mt-10) cc_final: 0.8020 (mp0) REVERT: D 364 GLU cc_start: 0.7885 (mt-10) cc_final: 0.7475 (mt-10) REVERT: D 391 TRP cc_start: 0.8150 (m-90) cc_final: 0.7912 (m-90) REVERT: D 402 GLU cc_start: 0.8295 (mm-30) cc_final: 0.8060 (mm-30) REVERT: E 132 ASP cc_start: 0.7852 (OUTLIER) cc_final: 0.7603 (t0) REVERT: E 221 GLN cc_start: 0.8373 (pt0) cc_final: 0.7989 (pt0) REVERT: E 257 ARG cc_start: 0.8888 (ptp90) cc_final: 0.8251 (ptp-110) REVERT: E 260 GLU cc_start: 0.8741 (pt0) cc_final: 0.8518 (pm20) outliers start: 24 outliers final: 16 residues processed: 278 average time/residue: 0.6437 time to fit residues: 193.6799 Evaluate side-chains 294 residues out of total 1430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 276 time to evaluate : 0.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 LEU Chi-restraints excluded: chain A residue 275 LEU Chi-restraints excluded: chain A residue 394 CYS Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain B residue 372 LEU Chi-restraints excluded: chain B residue 378 VAL 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 372 LEU Chi-restraints excluded: chain D residue 146 LYS Chi-restraints excluded: chain D residue 153 THR Chi-restraints excluded: chain D residue 299 ILE Chi-restraints excluded: chain E residue 132 ASP Chi-restraints excluded: chain E residue 198 VAL Chi-restraints excluded: chain E residue 372 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 16 optimal weight: 5.9990 chunk 8 optimal weight: 3.9990 chunk 23 optimal weight: 0.9980 chunk 24 optimal weight: 1.9990 chunk 1 optimal weight: 5.9990 chunk 79 optimal weight: 2.9990 chunk 74 optimal weight: 5.9990 chunk 81 optimal weight: 2.9990 chunk 14 optimal weight: 0.7980 chunk 152 optimal weight: 1.9990 chunk 38 optimal weight: 0.7980 overall best weight: 1.3184 ------------------------------------------------------------------------------- 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 = 0.3214 r_free = 0.3214 target = 0.095550 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2977 r_free = 0.2977 target = 0.079457 restraints weight = 20794.634| |-----------------------------------------------------------------------------| r_work (start): 0.2897 rms_B_bonded: 3.00 r_work: 0.2734 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.2734 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2767 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2767 r_free = 0.2767 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.86 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2767 r_free = 0.2767 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.88 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2767 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7665 moved from start: 0.2901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 13410 Z= 0.166 Angle : 0.574 10.915 18370 Z= 0.273 Chirality : 0.040 0.154 2235 Planarity : 0.003 0.036 2250 Dihedral : 3.863 15.694 2060 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 2.24 % Allowed : 18.46 % Favored : 79.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.02 (0.21), residues: 1600 helix: 3.08 (0.20), residues: 545 sheet: 0.77 (0.24), residues: 420 loop : 0.23 (0.26), residues: 635 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 257 TYR 0.032 0.002 TYR E 176 PHE 0.023 0.002 PHE A 385 TRP 0.024 0.001 TRP B 112 HIS 0.001 0.000 HIS E 276 Details of bonding type rmsd covalent geometry : bond 0.00382 (13385) covalent geometry : angle 0.57170 (18305) SS BOND : bond 0.00525 ( 10) SS BOND : angle 0.93974 ( 20) hydrogen bonds : bond 0.03857 ( 680) hydrogen bonds : angle 3.71773 ( 2100) link_BETA1-4 : bond 0.00035 ( 5) link_BETA1-4 : angle 0.92349 ( 15) link_NAG-ASN : bond 0.00161 ( 10) link_NAG-ASN : angle 1.27707 ( 30) ********************** 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 312 residues out of total 1430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 280 time to evaluate : 0.520 Fit side-chains REVERT: A 75 ASP cc_start: 0.7779 (t0) cc_final: 0.7422 (t0) REVERT: A 81 MET cc_start: 0.8733 (ttp) cc_final: 0.8418 (ptt) REVERT: A 124 GLU cc_start: 0.8341 (mp0) cc_final: 0.7753 (mp0) REVERT: A 201 GLU cc_start: 0.8588 (mt-10) cc_final: 0.7963 (mp0) REVERT: A 260 GLU cc_start: 0.8787 (pm20) cc_final: 0.8350 (pm20) REVERT: A 364 GLU cc_start: 0.8066 (mt-10) cc_final: 0.7633 (mt-10) REVERT: A 391 TRP cc_start: 0.8036 (m-90) cc_final: 0.7799 (m-90) REVERT: B 48 GLU cc_start: 0.8024 (tp30) cc_final: 0.7766 (tp30) REVERT: B 124 GLU cc_start: 0.8360 (mp0) cc_final: 0.7762 (mp0) REVERT: B 132 ASP cc_start: 0.7449 (t0) cc_final: 0.7134 (t0) REVERT: B 146 LYS cc_start: 0.8251 (mtmm) cc_final: 0.7966 (mtpp) REVERT: B 201 GLU cc_start: 0.8515 (mt-10) cc_final: 0.7992 (mp0) REVERT: B 214 GLN cc_start: 0.8364 (mm-40) cc_final: 0.8095 (pt0) REVERT: B 260 GLU cc_start: 0.8747 (pm20) cc_final: 0.8389 (pm20) REVERT: B 272 TYR cc_start: 0.8517 (t80) cc_final: 0.8251 (t80) REVERT: B 364 GLU cc_start: 0.7667 (mp0) cc_final: 0.6650 (mp0) REVERT: B 391 TRP cc_start: 0.8168 (m-90) cc_final: 0.7930 (m-90) REVERT: C 75 ASP cc_start: 0.7558 (t0) cc_final: 0.7102 (t0) REVERT: C 112 TRP cc_start: 0.7953 (OUTLIER) cc_final: 0.7270 (t-100) REVERT: C 124 GLU cc_start: 0.8215 (mp0) cc_final: 0.7692 (mp0) REVERT: C 129 ASP cc_start: 0.8402 (t0) cc_final: 0.7943 (t0) REVERT: C 132 ASP cc_start: 0.7534 (t0) cc_final: 0.7192 (p0) REVERT: C 146 LYS cc_start: 0.8047 (OUTLIER) cc_final: 0.7602 (mtpp) REVERT: C 154 GLU cc_start: 0.8701 (tt0) cc_final: 0.8377 (tt0) REVERT: C 188 GLN cc_start: 0.8023 (tt0) cc_final: 0.7470 (tt0) REVERT: C 201 GLU cc_start: 0.8638 (mt-10) cc_final: 0.8036 (mp0) REVERT: C 214 GLN cc_start: 0.8257 (mm-40) cc_final: 0.8027 (pt0) REVERT: C 260 GLU cc_start: 0.8930 (pm20) cc_final: 0.8621 (pm20) REVERT: C 364 GLU cc_start: 0.8082 (mt-10) cc_final: 0.7703 (mt-10) REVERT: D 63 ASP cc_start: 0.8412 (t70) cc_final: 0.8055 (t0) REVERT: D 75 ASP cc_start: 0.7639 (t0) cc_final: 0.7407 (t0) REVERT: D 129 ASP cc_start: 0.8317 (t0) cc_final: 0.7926 (t0) REVERT: D 132 ASP cc_start: 0.7286 (t0) cc_final: 0.6813 (t0) REVERT: D 160 GLU cc_start: 0.8421 (mt-10) cc_final: 0.8034 (mt-10) REVERT: D 201 GLU cc_start: 0.8681 (mt-10) cc_final: 0.8049 (mp0) REVERT: D 364 GLU cc_start: 0.7903 (mt-10) cc_final: 0.7493 (mt-10) REVERT: D 391 TRP cc_start: 0.8079 (m-90) cc_final: 0.7835 (m-90) REVERT: D 402 GLU cc_start: 0.8275 (mm-30) cc_final: 0.8045 (mm-30) REVERT: E 112 TRP cc_start: 0.7944 (OUTLIER) cc_final: 0.6762 (t-100) REVERT: E 132 ASP cc_start: 0.7878 (OUTLIER) cc_final: 0.7576 (t0) REVERT: E 221 GLN cc_start: 0.8414 (pt0) cc_final: 0.8055 (pt0) REVERT: E 257 ARG cc_start: 0.8889 (ptp90) cc_final: 0.8250 (ptp-110) REVERT: E 260 GLU cc_start: 0.8775 (pt0) cc_final: 0.8533 (pm20) outliers start: 32 outliers final: 17 residues processed: 293 average time/residue: 0.6343 time to fit residues: 202.1618 Evaluate side-chains 278 residues out of total 1430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 257 time to evaluate : 0.450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 LEU Chi-restraints excluded: chain A residue 275 LEU Chi-restraints excluded: chain A residue 394 CYS Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain B residue 372 LEU Chi-restraints excluded: chain 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 146 LYS Chi-restraints excluded: chain C residue 179 SER Chi-restraints excluded: chain C residue 198 VAL 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 146 LYS Chi-restraints excluded: chain D residue 153 THR Chi-restraints excluded: chain D residue 299 ILE 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 372 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 116 optimal weight: 1.9990 chunk 135 optimal weight: 2.9990 chunk 42 optimal weight: 1.9990 chunk 26 optimal weight: 5.9990 chunk 155 optimal weight: 0.0270 chunk 136 optimal weight: 2.9990 chunk 145 optimal weight: 3.9990 chunk 27 optimal weight: 0.0870 chunk 45 optimal weight: 2.9990 chunk 76 optimal weight: 4.9990 chunk 99 optimal weight: 4.9990 overall best weight: 1.4222 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 382 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.094308 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2955 r_free = 0.2955 target = 0.078263 restraints weight = 20789.895| |-----------------------------------------------------------------------------| r_work (start): 0.2940 rms_B_bonded: 3.02 r_work: 0.2778 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.2778 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2766 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2766 r_free = 0.2766 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.88 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2766 r_free = 0.2766 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.88 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2766 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7757 moved from start: 0.2899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 13410 Z= 0.176 Angle : 0.580 9.927 18370 Z= 0.278 Chirality : 0.040 0.146 2235 Planarity : 0.004 0.036 2250 Dihedral : 3.916 15.901 2060 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 1.96 % Allowed : 19.16 % Favored : 78.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.02 (0.21), residues: 1600 helix: 3.05 (0.20), residues: 545 sheet: 0.75 (0.23), residues: 440 loop : 0.27 (0.27), residues: 615 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 257 TYR 0.033 0.002 TYR E 176 PHE 0.023 0.002 PHE A 385 TRP 0.023 0.001 TRP B 112 HIS 0.002 0.000 HIS A 276 Details of bonding type rmsd covalent geometry : bond 0.00404 (13385) covalent geometry : angle 0.57683 (18305) SS BOND : bond 0.00538 ( 10) SS BOND : angle 0.93664 ( 20) hydrogen bonds : bond 0.03901 ( 680) hydrogen bonds : angle 3.74932 ( 2100) link_BETA1-4 : bond 0.00028 ( 5) link_BETA1-4 : angle 0.91666 ( 15) link_NAG-ASN : bond 0.00164 ( 10) link_NAG-ASN : angle 1.29380 ( 30) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4361.63 seconds wall clock time: 75 minutes 14.04 seconds (4514.04 seconds total)