Starting phenix.real_space_refine on Sun Aug 24 03:35:10 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8fsb_29418/08_2025/8fsb_29418.cif Found real_map, /net/cci-nas-00/data/ceres_data/8fsb_29418/08_2025/8fsb_29418.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.75 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8fsb_29418/08_2025/8fsb_29418.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8fsb_29418/08_2025/8fsb_29418.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8fsb_29418/08_2025/8fsb_29418.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8fsb_29418/08_2025/8fsb_29418.map" } resolution = 2.75 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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 45 5.16 5 C 10950 2.51 5 N 2700 2.21 5 O 2945 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 15 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 16640 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 3273 Number of conformers: 1 Conformer: "" Number of residues, atoms: 395, 3273 Classifications: {'peptide': 395} Link IDs: {'PTRANS': 20, 'TRANS': 374} Chain breaks: 1 Chain: "B" Number of atoms: 3273 Number of conformers: 1 Conformer: "" Number of residues, atoms: 395, 3273 Classifications: {'peptide': 395} Link IDs: {'PTRANS': 20, 'TRANS': 374} Chain breaks: 1 Chain: "A" Number of atoms: 55 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 55 Unusual residues: {'NAG': 3, 'SRO': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "B" Number of atoms: 55 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 55 Unusual residues: {'NAG': 3, 'SRO': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Restraints were copied for chains: C, D, E Time building chain proxies: 3.35, per 1000 atoms: 0.20 Number of scatterers: 16640 At special positions: 0 Unit cell: (97.9, 97.9, 171.6, 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 45 16.00 O 2945 8.00 N 2700 7.00 C 10950 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS A 135 " - pdb=" SG CYS A 149 " distance=2.03 Simple disulfide: pdb=" SG CYS B 135 " - pdb=" SG CYS B 149 " distance=2.03 Simple disulfide: pdb=" SG CYS C 135 " - pdb=" SG CYS C 149 " distance=2.03 Simple disulfide: pdb=" SG CYS D 135 " - pdb=" SG CYS D 149 " distance=2.03 Simple disulfide: pdb=" SG CYS E 135 " - pdb=" SG CYS E 149 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A 501 " - " ASN A 82 " " NAG A 502 " - " ASN A 148 " " NAG A 503 " - " ASN A 164 " " NAG B 502 " - " ASN B 82 " " NAG B 503 " - " ASN B 148 " " NAG B 504 " - " ASN B 164 " " NAG C 502 " - " ASN C 82 " " NAG C 503 " - " ASN C 148 " " NAG C 504 " - " ASN C 164 " " NAG D 502 " - " ASN D 82 " " NAG D 503 " - " ASN D 148 " " NAG D 504 " - " ASN D 164 " " NAG E 502 " - " ASN E 82 " " NAG E 503 " - " ASN E 148 " " NAG E 504 " - " ASN E 164 " Time building additional restraints: 1.11 Conformation dependent library (CDL) restraints added in 694.7 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3840 Finding SS restraints... Secondary structure from input PDB file: 80 helices and 10 sheets defined 48.1% alpha, 20.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.48 Creating SS restraints... Processing helix chain 'A' and resid 10 through 21 Processing helix chain 'A' and resid 76 through 81 removed outlier: 3.906A pdb=" N ASP A 81 " --> pdb=" O GLU A 78 " (cutoff:3.500A) Processing helix chain 'A' and resid 89 through 93 Processing helix chain 'A' and resid 141 through 144 Processing helix chain 'A' and resid 170 through 176 removed outlier: 3.532A pdb=" N VAL A 174 " --> pdb=" O SER A 170 " (cutoff:3.500A) Processing helix chain 'A' and resid 220 through 233 removed outlier: 4.978A pdb=" N LEU A 229 " --> pdb=" O VAL A 225 " (cutoff:3.500A) Proline residue: A 230 - end of helix Processing helix chain 'A' and resid 233 through 243 removed outlier: 3.984A pdb=" N CYS A 243 " --> pdb=" O ILE A 239 " (cutoff:3.500A) Processing helix chain 'A' and resid 250 through 270 removed outlier: 3.655A pdb=" N LEU A 266 " --> pdb=" O TYR A 262 " (cutoff:3.500A) Processing helix chain 'A' and resid 281 through 308 removed outlier: 3.508A pdb=" N VAL A 285 " --> pdb=" O PRO A 281 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N VAL A 308 " --> pdb=" O ILE A 304 " (cutoff:3.500A) Processing helix chain 'A' and resid 319 through 327 removed outlier: 4.548A pdb=" N HIS A 323 " --> pdb=" O ASP A 319 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N ASP A 327 " --> pdb=" O HIS A 323 " (cutoff:3.500A) Processing helix chain 'A' and resid 327 through 332 Processing helix chain 'A' and resid 398 through 410 Processing helix chain 'A' and resid 411 through 418 Processing helix chain 'A' and resid 419 through 424 Processing helix chain 'A' and resid 426 through 461 removed outlier: 4.280A pdb=" N VAL A 432 " --> pdb=" O ARG A 428 " (cutoff:3.500A) removed outlier: 4.684A pdb=" N LEU A 433 " --> pdb=" O VAL A 429 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N ASP A 434 " --> pdb=" O GLY A 430 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N LEU A 436 " --> pdb=" O VAL A 432 " (cutoff:3.500A) Processing helix chain 'A' and resid 462 through 465 removed outlier: 3.906A pdb=" N LEU A 465 " --> pdb=" O SER A 462 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 462 through 465' Processing helix chain 'B' and resid 10 through 21 Processing helix chain 'B' and resid 76 through 81 removed outlier: 3.906A pdb=" N ASP B 81 " --> pdb=" O GLU B 78 " (cutoff:3.500A) Processing helix chain 'B' and resid 89 through 93 Processing helix chain 'B' and resid 141 through 144 Processing helix chain 'B' and resid 170 through 176 removed outlier: 3.533A pdb=" N VAL B 174 " --> pdb=" O SER B 170 " (cutoff:3.500A) Processing helix chain 'B' and resid 220 through 233 removed outlier: 4.978A pdb=" N LEU B 229 " --> pdb=" O VAL B 225 " (cutoff:3.500A) Proline residue: B 230 - end of helix Processing helix chain 'B' and resid 233 through 243 removed outlier: 3.985A pdb=" N CYS B 243 " --> pdb=" O ILE B 239 " (cutoff:3.500A) Processing helix chain 'B' and resid 250 through 270 removed outlier: 3.655A pdb=" N LEU B 266 " --> pdb=" O TYR B 262 " (cutoff:3.500A) Processing helix chain 'B' and resid 281 through 308 removed outlier: 3.509A pdb=" N VAL B 285 " --> pdb=" O PRO B 281 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N VAL B 308 " --> pdb=" O ILE B 304 " (cutoff:3.500A) Processing helix chain 'B' and resid 319 through 327 removed outlier: 4.548A pdb=" N HIS B 323 " --> pdb=" O ASP B 319 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N ASP B 327 " --> pdb=" O HIS B 323 " (cutoff:3.500A) Processing helix chain 'B' and resid 327 through 332 Processing helix chain 'B' and resid 398 through 410 Processing helix chain 'B' and resid 411 through 418 Processing helix chain 'B' and resid 419 through 424 Processing helix chain 'B' and resid 426 through 461 removed outlier: 4.280A pdb=" N VAL B 432 " --> pdb=" O ARG B 428 " (cutoff:3.500A) removed outlier: 4.684A pdb=" N LEU B 433 " --> pdb=" O VAL B 429 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N ASP B 434 " --> pdb=" O GLY B 430 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N LEU B 436 " --> pdb=" O VAL B 432 " (cutoff:3.500A) Processing helix chain 'B' and resid 462 through 465 removed outlier: 3.906A pdb=" N LEU B 465 " --> pdb=" O SER B 462 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 462 through 465' Processing helix chain 'C' and resid 10 through 21 Processing helix chain 'C' and resid 76 through 81 removed outlier: 3.906A pdb=" N ASP C 81 " --> pdb=" O GLU C 78 " (cutoff:3.500A) Processing helix chain 'C' and resid 89 through 93 Processing helix chain 'C' and resid 141 through 144 Processing helix chain 'C' and resid 170 through 176 removed outlier: 3.532A pdb=" N VAL C 174 " --> pdb=" O SER C 170 " (cutoff:3.500A) Processing helix chain 'C' and resid 220 through 233 removed outlier: 4.978A pdb=" N LEU C 229 " --> pdb=" O VAL C 225 " (cutoff:3.500A) Proline residue: C 230 - end of helix Processing helix chain 'C' and resid 233 through 243 removed outlier: 3.984A pdb=" N CYS C 243 " --> pdb=" O ILE C 239 " (cutoff:3.500A) Processing helix chain 'C' and resid 250 through 270 removed outlier: 3.655A pdb=" N LEU C 266 " --> pdb=" O TYR C 262 " (cutoff:3.500A) Processing helix chain 'C' and resid 281 through 308 removed outlier: 3.509A pdb=" N VAL C 285 " --> pdb=" O PRO C 281 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N VAL C 308 " --> pdb=" O ILE C 304 " (cutoff:3.500A) Processing helix chain 'C' and resid 319 through 327 removed outlier: 4.548A pdb=" N HIS C 323 " --> pdb=" O ASP C 319 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N ASP C 327 " --> pdb=" O HIS C 323 " (cutoff:3.500A) Processing helix chain 'C' and resid 327 through 332 Processing helix chain 'C' and resid 398 through 410 Processing helix chain 'C' and resid 411 through 418 Processing helix chain 'C' and resid 419 through 424 Processing helix chain 'C' and resid 426 through 461 removed outlier: 4.280A pdb=" N VAL C 432 " --> pdb=" O ARG C 428 " (cutoff:3.500A) removed outlier: 4.684A pdb=" N LEU C 433 " --> pdb=" O VAL C 429 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N ASP C 434 " --> pdb=" O GLY C 430 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N LEU C 436 " --> pdb=" O VAL C 432 " (cutoff:3.500A) Processing helix chain 'C' and resid 462 through 465 removed outlier: 3.906A pdb=" N LEU C 465 " --> pdb=" O SER C 462 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 462 through 465' Processing helix chain 'D' and resid 10 through 21 Processing helix chain 'D' and resid 76 through 81 removed outlier: 3.906A pdb=" N ASP D 81 " --> pdb=" O GLU D 78 " (cutoff:3.500A) Processing helix chain 'D' and resid 89 through 93 Processing helix chain 'D' and resid 141 through 144 Processing helix chain 'D' and resid 170 through 176 removed outlier: 3.533A pdb=" N VAL D 174 " --> pdb=" O SER D 170 " (cutoff:3.500A) Processing helix chain 'D' and resid 220 through 233 removed outlier: 4.977A pdb=" N LEU D 229 " --> pdb=" O VAL D 225 " (cutoff:3.500A) Proline residue: D 230 - end of helix Processing helix chain 'D' and resid 233 through 243 removed outlier: 3.984A pdb=" N CYS D 243 " --> pdb=" O ILE D 239 " (cutoff:3.500A) Processing helix chain 'D' and resid 250 through 270 removed outlier: 3.654A pdb=" N LEU D 266 " --> pdb=" O TYR D 262 " (cutoff:3.500A) Processing helix chain 'D' and resid 281 through 308 removed outlier: 3.508A pdb=" N VAL D 285 " --> pdb=" O PRO D 281 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N VAL D 308 " --> pdb=" O ILE D 304 " (cutoff:3.500A) Processing helix chain 'D' and resid 319 through 327 removed outlier: 4.549A pdb=" N HIS D 323 " --> pdb=" O ASP D 319 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N ASP D 327 " --> pdb=" O HIS D 323 " (cutoff:3.500A) Processing helix chain 'D' and resid 327 through 332 Processing helix chain 'D' and resid 398 through 410 Processing helix chain 'D' and resid 411 through 418 Processing helix chain 'D' and resid 419 through 424 Processing helix chain 'D' and resid 426 through 461 removed outlier: 4.280A pdb=" N VAL D 432 " --> pdb=" O ARG D 428 " (cutoff:3.500A) removed outlier: 4.684A pdb=" N LEU D 433 " --> pdb=" O VAL D 429 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N ASP D 434 " --> pdb=" O GLY D 430 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N LEU D 436 " --> pdb=" O VAL D 432 " (cutoff:3.500A) Processing helix chain 'D' and resid 462 through 465 removed outlier: 3.906A pdb=" N LEU D 465 " --> pdb=" O SER D 462 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 462 through 465' Processing helix chain 'E' and resid 10 through 21 Processing helix chain 'E' and resid 76 through 81 removed outlier: 3.905A pdb=" N ASP E 81 " --> pdb=" O GLU E 78 " (cutoff:3.500A) Processing helix chain 'E' and resid 89 through 93 Processing helix chain 'E' and resid 141 through 144 Processing helix chain 'E' and resid 170 through 176 removed outlier: 3.532A pdb=" N VAL E 174 " --> pdb=" O SER E 170 " (cutoff:3.500A) Processing helix chain 'E' and resid 220 through 233 removed outlier: 4.977A pdb=" N LEU E 229 " --> pdb=" O VAL E 225 " (cutoff:3.500A) Proline residue: E 230 - end of helix Processing helix chain 'E' and resid 233 through 243 removed outlier: 3.984A pdb=" N CYS E 243 " --> pdb=" O ILE E 239 " (cutoff:3.500A) Processing helix chain 'E' and resid 250 through 270 removed outlier: 3.655A pdb=" N LEU E 266 " --> pdb=" O TYR E 262 " (cutoff:3.500A) Processing helix chain 'E' and resid 281 through 308 removed outlier: 3.507A pdb=" N VAL E 285 " --> pdb=" O PRO E 281 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N VAL E 308 " --> pdb=" O ILE E 304 " (cutoff:3.500A) Processing helix chain 'E' and resid 319 through 327 removed outlier: 4.548A pdb=" N HIS E 323 " --> pdb=" O ASP E 319 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N ASP E 327 " --> pdb=" O HIS E 323 " (cutoff:3.500A) Processing helix chain 'E' and resid 327 through 332 Processing helix chain 'E' and resid 398 through 410 Processing helix chain 'E' and resid 411 through 418 Processing helix chain 'E' and resid 419 through 424 Processing helix chain 'E' and resid 426 through 461 removed outlier: 4.280A pdb=" N VAL E 432 " --> pdb=" O ARG E 428 " (cutoff:3.500A) removed outlier: 4.685A pdb=" N LEU E 433 " --> pdb=" O VAL E 429 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N ASP E 434 " --> pdb=" O GLY E 430 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N LEU E 436 " --> pdb=" O VAL E 432 " (cutoff:3.500A) Processing helix chain 'E' and resid 462 through 465 removed outlier: 3.906A pdb=" N LEU E 465 " --> pdb=" O SER E 462 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 462 through 465' Processing sheet with id=AA1, first strand: chain 'A' and resid 87 through 88 removed outlier: 7.149A pdb=" N TYR A 61 " --> pdb=" O ILE A 48 " (cutoff:3.500A) removed outlier: 5.814A pdb=" N ILE A 48 " --> pdb=" O TYR A 61 " (cutoff:3.500A) removed outlier: 8.133A pdb=" N TRP A 63 " --> pdb=" O TYR A 46 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N TYR A 46 " --> pdb=" O TRP A 63 " (cutoff:3.500A) removed outlier: 7.928A pdb=" N ARG A 65 " --> pdb=" O ILE A 44 " (cutoff:3.500A) removed outlier: 7.678A pdb=" N ILE A 44 " --> pdb=" O ARG A 65 " (cutoff:3.500A) removed outlier: 8.447A pdb=" N TYR A 67 " --> pdb=" O ASP A 42 " (cutoff:3.500A) removed outlier: 8.282A pdb=" N ASP A 42 " --> pdb=" O TYR A 67 " (cutoff:3.500A) removed outlier: 9.109A pdb=" N THR A 69 " --> pdb=" O SER A 40 " (cutoff:3.500A) removed outlier: 9.910A pdb=" N SER A 40 " --> pdb=" O THR A 69 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 98 through 100 removed outlier: 3.551A pdb=" N ILE A 216 " --> pdb=" O GLN A 147 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N SER A 155 " --> pdb=" O ALA A 208 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N ALA A 208 " --> pdb=" O SER A 155 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N GLU A 191 " --> pdb=" O ILE A 215 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N ARG A 217 " --> pdb=" O LEU A 189 " (cutoff:3.500A) removed outlier: 5.531A pdb=" N LEU A 189 " --> pdb=" O ARG A 217 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 87 through 88 removed outlier: 7.149A pdb=" N TYR B 61 " --> pdb=" O ILE B 48 " (cutoff:3.500A) removed outlier: 5.814A pdb=" N ILE B 48 " --> pdb=" O TYR B 61 " (cutoff:3.500A) removed outlier: 8.133A pdb=" N TRP B 63 " --> pdb=" O TYR B 46 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N TYR B 46 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 7.928A pdb=" N ARG B 65 " --> pdb=" O ILE B 44 " (cutoff:3.500A) removed outlier: 7.678A pdb=" N ILE B 44 " --> pdb=" O ARG B 65 " (cutoff:3.500A) removed outlier: 8.447A pdb=" N TYR B 67 " --> pdb=" O ASP B 42 " (cutoff:3.500A) removed outlier: 8.282A pdb=" N ASP B 42 " --> pdb=" O TYR B 67 " (cutoff:3.500A) removed outlier: 9.109A pdb=" N THR B 69 " --> pdb=" O SER B 40 " (cutoff:3.500A) removed outlier: 9.910A pdb=" N SER B 40 " --> pdb=" O THR B 69 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 98 through 100 removed outlier: 3.551A pdb=" N ILE B 216 " --> pdb=" O GLN B 147 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N SER B 155 " --> pdb=" O ALA B 208 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N ALA B 208 " --> pdb=" O SER B 155 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N GLU B 191 " --> pdb=" O ILE B 215 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N ARG B 217 " --> pdb=" O LEU B 189 " (cutoff:3.500A) removed outlier: 5.531A pdb=" N LEU B 189 " --> pdb=" O ARG B 217 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 87 through 88 removed outlier: 7.150A pdb=" N TYR C 61 " --> pdb=" O ILE C 48 " (cutoff:3.500A) removed outlier: 5.815A pdb=" N ILE C 48 " --> pdb=" O TYR C 61 " (cutoff:3.500A) removed outlier: 8.133A pdb=" N TRP C 63 " --> pdb=" O TYR C 46 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N TYR C 46 " --> pdb=" O TRP C 63 " (cutoff:3.500A) removed outlier: 7.928A pdb=" N ARG C 65 " --> pdb=" O ILE C 44 " (cutoff:3.500A) removed outlier: 7.679A pdb=" N ILE C 44 " --> pdb=" O ARG C 65 " (cutoff:3.500A) removed outlier: 8.448A pdb=" N TYR C 67 " --> pdb=" O ASP C 42 " (cutoff:3.500A) removed outlier: 8.283A pdb=" N ASP C 42 " --> pdb=" O TYR C 67 " (cutoff:3.500A) removed outlier: 9.109A pdb=" N THR C 69 " --> pdb=" O SER C 40 " (cutoff:3.500A) removed outlier: 9.911A pdb=" N SER C 40 " --> pdb=" O THR C 69 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 98 through 100 removed outlier: 3.550A pdb=" N ILE C 216 " --> pdb=" O GLN C 147 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N SER C 155 " --> pdb=" O ALA C 208 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N ALA C 208 " --> pdb=" O SER C 155 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N GLU C 191 " --> pdb=" O ILE C 215 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N ARG C 217 " --> pdb=" O LEU C 189 " (cutoff:3.500A) removed outlier: 5.531A pdb=" N LEU C 189 " --> pdb=" O ARG C 217 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 87 through 88 removed outlier: 7.150A pdb=" N TYR D 61 " --> pdb=" O ILE D 48 " (cutoff:3.500A) removed outlier: 5.814A pdb=" N ILE D 48 " --> pdb=" O TYR D 61 " (cutoff:3.500A) removed outlier: 8.132A pdb=" N TRP D 63 " --> pdb=" O TYR D 46 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N TYR D 46 " --> pdb=" O TRP D 63 " (cutoff:3.500A) removed outlier: 7.928A pdb=" N ARG D 65 " --> pdb=" O ILE D 44 " (cutoff:3.500A) removed outlier: 7.678A pdb=" N ILE D 44 " --> pdb=" O ARG D 65 " (cutoff:3.500A) removed outlier: 8.447A pdb=" N TYR D 67 " --> pdb=" O ASP D 42 " (cutoff:3.500A) removed outlier: 8.283A pdb=" N ASP D 42 " --> pdb=" O TYR D 67 " (cutoff:3.500A) removed outlier: 9.109A pdb=" N THR D 69 " --> pdb=" O SER D 40 " (cutoff:3.500A) removed outlier: 9.911A pdb=" N SER D 40 " --> pdb=" O THR D 69 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 98 through 100 removed outlier: 3.552A pdb=" N ILE D 216 " --> pdb=" O GLN D 147 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N SER D 155 " --> pdb=" O ALA D 208 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N ALA D 208 " --> pdb=" O SER D 155 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N GLU D 191 " --> pdb=" O ILE D 215 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N ARG D 217 " --> pdb=" O LEU D 189 " (cutoff:3.500A) removed outlier: 5.530A pdb=" N LEU D 189 " --> pdb=" O ARG D 217 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 87 through 88 removed outlier: 7.149A pdb=" N TYR E 61 " --> pdb=" O ILE E 48 " (cutoff:3.500A) removed outlier: 5.814A pdb=" N ILE E 48 " --> pdb=" O TYR E 61 " (cutoff:3.500A) removed outlier: 8.132A pdb=" N TRP E 63 " --> pdb=" O TYR E 46 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N TYR E 46 " --> pdb=" O TRP E 63 " (cutoff:3.500A) removed outlier: 7.928A pdb=" N ARG E 65 " --> pdb=" O ILE E 44 " (cutoff:3.500A) removed outlier: 7.677A pdb=" N ILE E 44 " --> pdb=" O ARG E 65 " (cutoff:3.500A) removed outlier: 8.447A pdb=" N TYR E 67 " --> pdb=" O ASP E 42 " (cutoff:3.500A) removed outlier: 8.282A pdb=" N ASP E 42 " --> pdb=" O TYR E 67 " (cutoff:3.500A) removed outlier: 9.110A pdb=" N THR E 69 " --> pdb=" O SER E 40 " (cutoff:3.500A) removed outlier: 9.910A pdb=" N SER E 40 " --> pdb=" O THR E 69 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 98 through 100 removed outlier: 3.551A pdb=" N ILE E 216 " --> pdb=" O GLN E 147 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N SER E 155 " --> pdb=" O ALA E 208 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N ALA E 208 " --> pdb=" O SER E 155 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N GLU E 191 " --> pdb=" O ILE E 215 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N ARG E 217 " --> pdb=" O LEU E 189 " (cutoff:3.500A) removed outlier: 5.530A pdb=" N LEU E 189 " --> pdb=" O ARG E 217 " (cutoff:3.500A) 765 hydrogen bonds defined for protein. 2190 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: 2.66 Time building geometry restraints manager: 1.54 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4698 1.34 - 1.45: 2904 1.45 - 1.57: 9423 1.57 - 1.69: 0 1.69 - 1.81: 70 Bond restraints: 17095 Sorted by residual: bond pdb=" C LEU D 244 " pdb=" N PRO D 245 " ideal model delta sigma weight residual 1.329 1.371 -0.042 1.18e-02 7.18e+03 1.28e+01 bond pdb=" C LEU E 244 " pdb=" N PRO E 245 " ideal model delta sigma weight residual 1.329 1.371 -0.042 1.18e-02 7.18e+03 1.27e+01 bond pdb=" C LEU A 244 " pdb=" N PRO A 245 " ideal model delta sigma weight residual 1.329 1.371 -0.042 1.18e-02 7.18e+03 1.27e+01 bond pdb=" C LEU B 244 " pdb=" N PRO B 245 " ideal model delta sigma weight residual 1.329 1.371 -0.042 1.18e-02 7.18e+03 1.26e+01 bond pdb=" C LEU C 244 " pdb=" N PRO C 245 " ideal model delta sigma weight residual 1.329 1.370 -0.041 1.18e-02 7.18e+03 1.21e+01 ... (remaining 17090 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.69: 22534 1.69 - 3.38: 692 3.38 - 5.07: 99 5.07 - 6.76: 10 6.76 - 8.45: 20 Bond angle restraints: 23355 Sorted by residual: angle pdb=" N MET B 419 " pdb=" CA MET B 419 " pdb=" C MET B 419 " ideal model delta sigma weight residual 113.18 107.52 5.66 1.33e+00 5.65e-01 1.81e+01 angle pdb=" N MET A 419 " pdb=" CA MET A 419 " pdb=" C MET A 419 " ideal model delta sigma weight residual 113.18 107.56 5.62 1.33e+00 5.65e-01 1.79e+01 angle pdb=" N MET D 419 " pdb=" CA MET D 419 " pdb=" C MET D 419 " ideal model delta sigma weight residual 113.18 107.57 5.61 1.33e+00 5.65e-01 1.78e+01 angle pdb=" N MET E 419 " pdb=" CA MET E 419 " pdb=" C MET E 419 " ideal model delta sigma weight residual 113.18 107.58 5.60 1.33e+00 5.65e-01 1.77e+01 angle pdb=" N MET C 419 " pdb=" CA MET C 419 " pdb=" C MET C 419 " ideal model delta sigma weight residual 113.18 107.60 5.58 1.33e+00 5.65e-01 1.76e+01 ... (remaining 23350 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.06: 9005 15.06 - 30.12: 910 30.12 - 45.18: 250 45.18 - 60.24: 50 60.24 - 75.30: 35 Dihedral angle restraints: 10250 sinusoidal: 4355 harmonic: 5895 Sorted by residual: dihedral pdb=" CA ASP E 425 " pdb=" C ASP E 425 " pdb=" N TRP E 426 " pdb=" CA TRP E 426 " ideal model delta harmonic sigma weight residual -180.00 -151.88 -28.12 0 5.00e+00 4.00e-02 3.16e+01 dihedral pdb=" CA ASP D 425 " pdb=" C ASP D 425 " pdb=" N TRP D 426 " pdb=" CA TRP D 426 " ideal model delta harmonic sigma weight residual -180.00 -151.89 -28.11 0 5.00e+00 4.00e-02 3.16e+01 dihedral pdb=" CA ASP A 425 " pdb=" C ASP A 425 " pdb=" N TRP A 426 " pdb=" CA TRP A 426 " ideal model delta harmonic sigma weight residual 180.00 -151.90 -28.10 0 5.00e+00 4.00e-02 3.16e+01 ... (remaining 10247 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 1889 0.044 - 0.088: 623 0.088 - 0.132: 203 0.132 - 0.176: 15 0.176 - 0.220: 10 Chirality restraints: 2740 Sorted by residual: chirality pdb=" CA PHE E 142 " pdb=" N PHE E 142 " pdb=" C PHE E 142 " pdb=" CB PHE E 142 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.21e+00 chirality pdb=" CA PHE A 142 " pdb=" N PHE A 142 " pdb=" C PHE A 142 " pdb=" CB PHE A 142 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.21e+00 chirality pdb=" CA PHE B 142 " pdb=" N PHE B 142 " pdb=" C PHE B 142 " pdb=" CB PHE B 142 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.20e+00 ... (remaining 2737 not shown) Planarity restraints: 2860 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP A 81 " -0.010 2.00e-02 2.50e+03 2.03e-02 4.13e+00 pdb=" C ASP A 81 " 0.035 2.00e-02 2.50e+03 pdb=" O ASP A 81 " -0.013 2.00e-02 2.50e+03 pdb=" N ASN A 82 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP D 81 " 0.010 2.00e-02 2.50e+03 2.03e-02 4.11e+00 pdb=" C ASP D 81 " -0.035 2.00e-02 2.50e+03 pdb=" O ASP D 81 " 0.013 2.00e-02 2.50e+03 pdb=" N ASN D 82 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP E 81 " 0.010 2.00e-02 2.50e+03 2.03e-02 4.10e+00 pdb=" C ASP E 81 " -0.035 2.00e-02 2.50e+03 pdb=" O ASP E 81 " 0.013 2.00e-02 2.50e+03 pdb=" N ASN E 82 " 0.012 2.00e-02 2.50e+03 ... (remaining 2857 not shown) Histogram of nonbonded interaction distances: 2.38 - 2.88: 5880 2.88 - 3.39: 15218 3.39 - 3.89: 26649 3.89 - 4.40: 28941 4.40 - 4.90: 49993 Nonbonded interactions: 126681 Sorted by model distance: nonbonded pdb=" OD1 ASN E 148 " pdb=" N2 NAG E 503 " model vdw 2.376 3.120 nonbonded pdb=" OD1 ASN C 148 " pdb=" N2 NAG C 503 " model vdw 2.376 3.120 nonbonded pdb=" OD1 ASN A 148 " pdb=" N2 NAG A 502 " model vdw 2.376 3.120 nonbonded pdb=" OD1 ASN B 148 " pdb=" N2 NAG B 503 " model vdw 2.376 3.120 nonbonded pdb=" OD1 ASN D 148 " pdb=" N2 NAG D 503 " model vdw 2.377 3.120 ... (remaining 126676 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: 0.01 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 7 through 465 or resid 502 through 503)) selection = (chain 'B' and (resid 7 through 465 or resid 502 through 503)) selection = (chain 'C' and (resid 7 through 465 or resid 502 through 503)) selection = (chain 'D' and (resid 7 through 465 or resid 502 through 503)) selection = (chain 'E' and (resid 7 through 465 or resid 502 through 503)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 1.710 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: 0.000 Extract box with map and model: 0.240 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 14.100 Find NCS groups from input model: 0.410 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: 0.010 Load rotamer database and sin/cos tables:6.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.970 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8010 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 : 0.004 0.054 17115 Z= 0.212 Angle : 0.772 10.108 23410 Z= 0.394 Chirality : 0.048 0.220 2740 Planarity : 0.004 0.031 2845 Dihedral : 14.088 75.300 6395 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 4.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.32 % Favored : 94.68 % Rotamer: Outliers : 0.00 % Allowed : 0.81 % Favored : 99.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.81 (0.19), residues: 1955 helix: 0.60 (0.19), residues: 745 sheet: -0.43 (0.26), residues: 395 loop : -1.65 (0.21), residues: 815 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 31 TYR 0.015 0.002 TYR D 61 PHE 0.021 0.002 PHE E 303 TRP 0.019 0.001 TRP E 168 HIS 0.002 0.001 HIS C 18 Details of bonding type rmsd covalent geometry : bond 0.00388 (17095) covalent geometry : angle 0.71411 (23355) SS BOND : bond 0.00026 ( 5) SS BOND : angle 0.02350 ( 10) hydrogen bonds : bond 0.17697 ( 765) hydrogen bonds : angle 5.96769 ( 2190) link_NAG-ASN : bond 0.01362 ( 15) link_NAG-ASN : angle 6.74761 ( 45) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 1845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 213 time to evaluate : 0.689 Fit side-chains revert: symmetry clash REVERT: A 410 ARG cc_start: 0.7560 (ttp-170) cc_final: 0.7237 (tpm-80) REVERT: A 411 HIS cc_start: 0.7745 (m90) cc_final: 0.7528 (m-70) REVERT: B 410 ARG cc_start: 0.7780 (ttp-170) cc_final: 0.7425 (tpt90) REVERT: B 411 HIS cc_start: 0.7759 (m90) cc_final: 0.7485 (m-70) REVERT: C 411 HIS cc_start: 0.7722 (m90) cc_final: 0.7504 (m-70) REVERT: C 419 MET cc_start: 0.5392 (mmt) cc_final: 0.5163 (tmm) REVERT: D 410 ARG cc_start: 0.7845 (ttp-170) cc_final: 0.7533 (tpt90) REVERT: D 411 HIS cc_start: 0.7490 (m90) cc_final: 0.7156 (m90) REVERT: E 416 ARG cc_start: 0.6574 (ttt180) cc_final: 0.5786 (tpm170) REVERT: E 419 MET cc_start: 0.5515 (mmt) cc_final: 0.5246 (tmm) outliers start: 0 outliers final: 1 residues processed: 213 average time/residue: 0.6519 time to fit residues: 153.6184 Evaluate side-chains 90 residues out of total 1845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 89 time to evaluate : 0.615 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 442 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 98 optimal weight: 1.9990 chunk 194 optimal weight: 1.9990 chunk 107 optimal weight: 7.9990 chunk 10 optimal weight: 0.5980 chunk 66 optimal weight: 0.6980 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 0.7980 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 0.7980 chunk 122 optimal weight: 3.9990 chunk 91 optimal weight: 1.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 22 ASN B 161 GLN C 9 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.118735 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.072433 restraints weight = 31680.780| |-----------------------------------------------------------------------------| r_work (start): 0.3016 rms_B_bonded: 2.47 r_work: 0.2889 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.2770 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.2770 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8375 moved from start: 0.1922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 17115 Z= 0.146 Angle : 0.636 9.407 23410 Z= 0.318 Chirality : 0.044 0.170 2740 Planarity : 0.004 0.028 2845 Dihedral : 7.142 58.310 2507 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 1.95 % Allowed : 8.89 % Favored : 89.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.72 (0.19), residues: 1955 helix: 0.65 (0.19), residues: 815 sheet: -0.58 (0.26), residues: 395 loop : -1.64 (0.22), residues: 745 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 306 TYR 0.016 0.002 TYR B 61 PHE 0.012 0.001 PHE A 142 TRP 0.012 0.001 TRP C 168 HIS 0.002 0.001 HIS C 119 Details of bonding type rmsd covalent geometry : bond 0.00340 (17095) covalent geometry : angle 0.59697 (23355) SS BOND : bond 0.00113 ( 5) SS BOND : angle 0.28839 ( 10) hydrogen bonds : bond 0.04294 ( 765) hydrogen bonds : angle 4.66964 ( 2190) link_NAG-ASN : bond 0.00866 ( 15) link_NAG-ASN : angle 5.04631 ( 45) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 1845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 93 time to evaluate : 0.711 Fit side-chains REVERT: A 145 ASP cc_start: 0.8095 (m-30) cc_final: 0.7852 (m-30) REVERT: A 410 ARG cc_start: 0.7667 (ttp-170) cc_final: 0.7198 (tpm-80) REVERT: A 411 HIS cc_start: 0.8090 (m90) cc_final: 0.7818 (m-70) REVERT: A 433 LEU cc_start: 0.9074 (mp) cc_final: 0.8850 (mm) REVERT: B 410 ARG cc_start: 0.7643 (ttp-170) cc_final: 0.7285 (tpt90) REVERT: B 411 HIS cc_start: 0.8058 (m90) cc_final: 0.7700 (m-70) REVERT: C 419 MET cc_start: 0.5194 (mmt) cc_final: 0.4949 (tmm) REVERT: D 410 ARG cc_start: 0.7793 (ttp-170) cc_final: 0.7364 (tpt90) REVERT: D 411 HIS cc_start: 0.7758 (m90) cc_final: 0.7295 (m90) REVERT: E 197 LYS cc_start: 0.8556 (OUTLIER) cc_final: 0.8325 (mmtp) REVERT: E 232 ILE cc_start: 0.8127 (mm) cc_final: 0.7814 (mm) REVERT: E 416 ARG cc_start: 0.6441 (ttt180) cc_final: 0.5937 (tpm170) REVERT: E 419 MET cc_start: 0.5212 (mmt) cc_final: 0.4963 (tmm) outliers start: 36 outliers final: 14 residues processed: 123 average time/residue: 0.4983 time to fit residues: 70.8580 Evaluate side-chains 98 residues out of total 1845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 83 time to evaluate : 0.699 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 303 PHE Chi-restraints excluded: chain A residue 440 ILE Chi-restraints excluded: chain B residue 22 ASN Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 280 THR Chi-restraints excluded: chain B residue 440 ILE Chi-restraints excluded: chain C residue 225 VAL Chi-restraints excluded: chain C residue 232 ILE Chi-restraints excluded: chain C residue 442 LEU Chi-restraints excluded: chain D residue 225 VAL Chi-restraints excluded: chain E residue 197 LYS Chi-restraints excluded: chain E residue 225 VAL Chi-restraints excluded: chain E residue 269 VAL Chi-restraints excluded: chain E residue 440 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 182 optimal weight: 0.4980 chunk 0 optimal weight: 4.9990 chunk 52 optimal weight: 0.1980 chunk 12 optimal weight: 0.9980 chunk 121 optimal weight: 0.4980 chunk 86 optimal weight: 0.9980 chunk 78 optimal weight: 4.9990 chunk 88 optimal weight: 0.9990 chunk 160 optimal weight: 4.9990 chunk 38 optimal weight: 3.9990 chunk 110 optimal weight: 8.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 22 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.118810 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.072631 restraints weight = 32246.094| |-----------------------------------------------------------------------------| r_work (start): 0.3020 rms_B_bonded: 2.50 r_work: 0.2888 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.2768 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.2768 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8378 moved from start: 0.2172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 17115 Z= 0.117 Angle : 0.576 8.335 23410 Z= 0.290 Chirality : 0.043 0.162 2740 Planarity : 0.004 0.026 2845 Dihedral : 6.869 57.825 2505 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer: Outliers : 1.95 % Allowed : 12.20 % Favored : 85.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.68 (0.19), residues: 1955 helix: 0.80 (0.19), residues: 815 sheet: -0.58 (0.25), residues: 395 loop : -1.75 (0.21), residues: 745 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 416 TYR 0.010 0.001 TYR E 67 PHE 0.013 0.001 PHE A 142 TRP 0.008 0.001 TRP D 168 HIS 0.002 0.000 HIS A 18 Details of bonding type rmsd covalent geometry : bond 0.00258 (17095) covalent geometry : angle 0.54567 (23355) SS BOND : bond 0.00082 ( 5) SS BOND : angle 0.23322 ( 10) hydrogen bonds : bond 0.03867 ( 765) hydrogen bonds : angle 4.48219 ( 2190) link_NAG-ASN : bond 0.00700 ( 15) link_NAG-ASN : angle 4.27584 ( 45) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 1845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 84 time to evaluate : 0.690 Fit side-chains REVERT: A 145 ASP cc_start: 0.8208 (m-30) cc_final: 0.7967 (m-30) REVERT: A 410 ARG cc_start: 0.7592 (ttp-170) cc_final: 0.7190 (tpm-80) REVERT: A 411 HIS cc_start: 0.7978 (m90) cc_final: 0.7678 (m-70) REVERT: B 410 ARG cc_start: 0.7567 (ttp-170) cc_final: 0.7160 (tpt90) REVERT: B 411 HIS cc_start: 0.8039 (m90) cc_final: 0.7689 (m-70) REVERT: D 410 ARG cc_start: 0.7743 (ttp-170) cc_final: 0.7337 (tpt90) REVERT: D 411 HIS cc_start: 0.7757 (m90) cc_final: 0.7315 (m90) REVERT: D 419 MET cc_start: 0.5706 (tmm) cc_final: 0.5483 (tmm) REVERT: E 197 LYS cc_start: 0.8529 (OUTLIER) cc_final: 0.8308 (mmtp) REVERT: E 416 ARG cc_start: 0.6470 (ttt180) cc_final: 0.5988 (tpm170) outliers start: 36 outliers final: 10 residues processed: 109 average time/residue: 0.4675 time to fit residues: 58.7520 Evaluate side-chains 93 residues out of total 1845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 82 time to evaluate : 0.727 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 280 THR Chi-restraints excluded: chain C residue 225 VAL Chi-restraints excluded: chain C residue 303 PHE Chi-restraints excluded: chain D residue 53 GLU Chi-restraints excluded: chain D residue 225 VAL Chi-restraints excluded: chain D residue 232 ILE Chi-restraints excluded: chain E residue 197 LYS Chi-restraints excluded: chain E residue 225 VAL Chi-restraints excluded: chain E residue 269 VAL Chi-restraints excluded: chain E residue 441 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 114 optimal weight: 10.0000 chunk 185 optimal weight: 4.9990 chunk 146 optimal weight: 0.8980 chunk 161 optimal weight: 3.9990 chunk 112 optimal weight: 0.9980 chunk 194 optimal weight: 0.6980 chunk 34 optimal weight: 0.2980 chunk 95 optimal weight: 3.9990 chunk 174 optimal weight: 4.9990 chunk 60 optimal weight: 1.9990 chunk 82 optimal weight: 1.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 22 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.117096 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.070489 restraints weight = 32029.076| |-----------------------------------------------------------------------------| r_work (start): 0.2974 rms_B_bonded: 2.46 r_work: 0.2842 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.2723 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.2723 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8408 moved from start: 0.2537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 17115 Z= 0.133 Angle : 0.594 9.468 23410 Z= 0.297 Chirality : 0.043 0.154 2740 Planarity : 0.004 0.030 2845 Dihedral : 6.908 57.905 2505 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.81 % Favored : 95.19 % Rotamer: Outliers : 1.90 % Allowed : 13.55 % Favored : 84.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.63 (0.19), residues: 1955 helix: 0.87 (0.19), residues: 815 sheet: -0.65 (0.25), residues: 395 loop : -1.71 (0.22), residues: 745 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 416 TYR 0.012 0.001 TYR A 61 PHE 0.013 0.001 PHE A 142 TRP 0.010 0.001 TRP C 156 HIS 0.002 0.000 HIS A 18 Details of bonding type rmsd covalent geometry : bond 0.00308 (17095) covalent geometry : angle 0.56626 (23355) SS BOND : bond 0.00037 ( 5) SS BOND : angle 0.29926 ( 10) hydrogen bonds : bond 0.03982 ( 765) hydrogen bonds : angle 4.41637 ( 2190) link_NAG-ASN : bond 0.00650 ( 15) link_NAG-ASN : angle 4.11521 ( 45) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 1845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 85 time to evaluate : 0.654 Fit side-chains REVERT: A 410 ARG cc_start: 0.7595 (ttp-170) cc_final: 0.7195 (tpm-80) REVERT: A 411 HIS cc_start: 0.7991 (m90) cc_final: 0.7685 (m90) REVERT: B 410 ARG cc_start: 0.7565 (ttp-170) cc_final: 0.7167 (tpt90) REVERT: B 411 HIS cc_start: 0.7920 (m90) cc_final: 0.7475 (m-70) REVERT: C 53 GLU cc_start: 0.8516 (OUTLIER) cc_final: 0.8287 (pt0) REVERT: D 410 ARG cc_start: 0.7719 (ttp-170) cc_final: 0.7308 (tpt90) REVERT: D 411 HIS cc_start: 0.7757 (m90) cc_final: 0.7319 (m90) REVERT: D 419 MET cc_start: 0.5997 (tmm) cc_final: 0.5753 (tmm) REVERT: E 197 LYS cc_start: 0.8525 (OUTLIER) cc_final: 0.8314 (mmtp) REVERT: E 416 ARG cc_start: 0.6546 (ttt180) cc_final: 0.5926 (tpm170) outliers start: 35 outliers final: 19 residues processed: 106 average time/residue: 0.4460 time to fit residues: 54.7865 Evaluate side-chains 100 residues out of total 1845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 79 time to evaluate : 0.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 303 PHE Chi-restraints excluded: chain A residue 441 TYR Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 280 THR Chi-restraints excluded: chain B residue 303 PHE Chi-restraints excluded: chain B residue 442 LEU Chi-restraints excluded: chain C residue 53 GLU Chi-restraints excluded: chain C residue 225 VAL Chi-restraints excluded: chain C residue 303 PHE Chi-restraints excluded: chain C residue 442 LEU Chi-restraints excluded: chain D residue 53 GLU Chi-restraints excluded: chain D residue 225 VAL Chi-restraints excluded: chain D residue 232 ILE Chi-restraints excluded: chain D residue 441 TYR Chi-restraints excluded: chain E residue 45 MET Chi-restraints excluded: chain E residue 197 LYS Chi-restraints excluded: chain E residue 225 VAL Chi-restraints excluded: chain E residue 232 ILE Chi-restraints excluded: chain E residue 269 VAL Chi-restraints excluded: chain E residue 441 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 27 optimal weight: 4.9990 chunk 167 optimal weight: 3.9990 chunk 38 optimal weight: 3.9990 chunk 132 optimal weight: 3.9990 chunk 177 optimal weight: 2.9990 chunk 176 optimal weight: 0.8980 chunk 21 optimal weight: 0.9990 chunk 148 optimal weight: 4.9990 chunk 153 optimal weight: 9.9990 chunk 166 optimal weight: 0.9990 chunk 112 optimal weight: 20.0000 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 147 GLN D 161 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.114521 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2969 r_free = 0.2969 target = 0.067861 restraints weight = 32006.724| |-----------------------------------------------------------------------------| r_work (start): 0.2919 rms_B_bonded: 2.43 r_work: 0.2784 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2665 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.2665 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8468 moved from start: 0.2875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 17115 Z= 0.211 Angle : 0.662 9.429 23410 Z= 0.332 Chirality : 0.045 0.157 2740 Planarity : 0.004 0.034 2845 Dihedral : 7.259 59.892 2505 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 2.44 % Allowed : 14.63 % Favored : 82.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.72 (0.19), residues: 1955 helix: 0.81 (0.18), residues: 825 sheet: -0.91 (0.25), residues: 375 loop : -1.66 (0.21), residues: 755 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 28 TYR 0.017 0.002 TYR C 61 PHE 0.013 0.001 PHE A 142 TRP 0.014 0.002 TRP B 156 HIS 0.003 0.001 HIS A 119 Details of bonding type rmsd covalent geometry : bond 0.00509 (17095) covalent geometry : angle 0.63286 (23355) SS BOND : bond 0.00025 ( 5) SS BOND : angle 0.31170 ( 10) hydrogen bonds : bond 0.04735 ( 765) hydrogen bonds : angle 4.57726 ( 2190) link_NAG-ASN : bond 0.00541 ( 15) link_NAG-ASN : angle 4.46720 ( 45) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 1845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 82 time to evaluate : 0.556 Fit side-chains REVERT: A 410 ARG cc_start: 0.7654 (ttp-170) cc_final: 0.7192 (tpm-80) REVERT: A 411 HIS cc_start: 0.7740 (m90) cc_final: 0.7406 (m90) REVERT: C 53 GLU cc_start: 0.8644 (OUTLIER) cc_final: 0.8033 (pt0) REVERT: D 91 ASP cc_start: 0.8904 (p0) cc_final: 0.8649 (p0) REVERT: D 410 ARG cc_start: 0.7716 (ttp-170) cc_final: 0.7303 (tpt90) REVERT: D 411 HIS cc_start: 0.7777 (m90) cc_final: 0.7324 (m90) REVERT: E 416 ARG cc_start: 0.6609 (ttt180) cc_final: 0.5834 (tpm170) outliers start: 45 outliers final: 21 residues processed: 109 average time/residue: 0.3974 time to fit residues: 50.8628 Evaluate side-chains 100 residues out of total 1845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 78 time to evaluate : 0.458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 303 PHE Chi-restraints excluded: chain A residue 441 TYR Chi-restraints excluded: chain B residue 45 MET Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 303 PHE Chi-restraints excluded: chain B residue 442 LEU Chi-restraints excluded: chain C residue 53 GLU Chi-restraints excluded: chain C residue 225 VAL Chi-restraints excluded: chain C residue 303 PHE Chi-restraints excluded: chain C residue 441 TYR Chi-restraints excluded: chain C residue 442 LEU Chi-restraints excluded: chain D residue 53 GLU Chi-restraints excluded: chain D residue 225 VAL Chi-restraints excluded: chain D residue 232 ILE Chi-restraints excluded: chain D residue 317 VAL Chi-restraints excluded: chain D residue 441 TYR Chi-restraints excluded: chain E residue 197 LYS Chi-restraints excluded: chain E residue 225 VAL Chi-restraints excluded: chain E residue 269 VAL Chi-restraints excluded: chain E residue 441 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 54 optimal weight: 2.9990 chunk 91 optimal weight: 3.9990 chunk 89 optimal weight: 2.9990 chunk 67 optimal weight: 0.8980 chunk 87 optimal weight: 1.9990 chunk 119 optimal weight: 2.9990 chunk 20 optimal weight: 2.9990 chunk 145 optimal weight: 0.8980 chunk 182 optimal weight: 8.9990 chunk 52 optimal weight: 2.9990 chunk 180 optimal weight: 6.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 147 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.113848 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2958 r_free = 0.2958 target = 0.067445 restraints weight = 32042.094| |-----------------------------------------------------------------------------| r_work (start): 0.2908 rms_B_bonded: 2.42 r_work: 0.2772 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2654 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.2654 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8484 moved from start: 0.3129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 17115 Z= 0.209 Angle : 0.667 10.229 23410 Z= 0.335 Chirality : 0.046 0.186 2740 Planarity : 0.004 0.037 2845 Dihedral : 7.273 59.022 2505 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 2.44 % Allowed : 15.99 % Favored : 81.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.77 (0.19), residues: 1955 helix: 0.79 (0.18), residues: 825 sheet: -0.98 (0.25), residues: 375 loop : -1.68 (0.21), residues: 755 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 28 TYR 0.014 0.002 TYR C 61 PHE 0.012 0.001 PHE C 80 TRP 0.014 0.002 TRP C 156 HIS 0.003 0.001 HIS A 18 Details of bonding type rmsd covalent geometry : bond 0.00502 (17095) covalent geometry : angle 0.63722 (23355) SS BOND : bond 0.00028 ( 5) SS BOND : angle 0.27990 ( 10) hydrogen bonds : bond 0.04745 ( 765) hydrogen bonds : angle 4.60842 ( 2190) link_NAG-ASN : bond 0.00553 ( 15) link_NAG-ASN : angle 4.57439 ( 45) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 1845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 81 time to evaluate : 0.526 Fit side-chains REVERT: A 235 MET cc_start: 0.7498 (pp-130) cc_final: 0.7280 (pp-130) REVERT: A 291 MET cc_start: 0.7606 (tpp) cc_final: 0.7331 (tpp) REVERT: B 441 TYR cc_start: 0.7530 (OUTLIER) cc_final: 0.7327 (m-80) REVERT: C 53 GLU cc_start: 0.8747 (OUTLIER) cc_final: 0.8119 (pt0) REVERT: D 91 ASP cc_start: 0.8899 (p0) cc_final: 0.8654 (p0) REVERT: D 410 ARG cc_start: 0.7752 (ttp-170) cc_final: 0.7370 (tpt90) REVERT: D 411 HIS cc_start: 0.7884 (m90) cc_final: 0.7419 (m90) REVERT: E 120 ARG cc_start: 0.7624 (OUTLIER) cc_final: 0.7203 (mtp85) REVERT: E 416 ARG cc_start: 0.6684 (ttt180) cc_final: 0.5914 (tpm170) outliers start: 45 outliers final: 24 residues processed: 108 average time/residue: 0.4090 time to fit residues: 50.9860 Evaluate side-chains 106 residues out of total 1845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 79 time to evaluate : 0.604 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 303 PHE Chi-restraints excluded: chain A residue 441 TYR Chi-restraints excluded: chain B residue 45 MET Chi-restraints excluded: chain B residue 166 THR Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 303 PHE Chi-restraints excluded: chain B residue 411 HIS Chi-restraints excluded: chain B residue 441 TYR Chi-restraints excluded: chain C residue 53 GLU Chi-restraints excluded: chain C residue 225 VAL Chi-restraints excluded: chain C residue 232 ILE Chi-restraints excluded: chain C residue 288 VAL Chi-restraints excluded: chain C residue 303 PHE Chi-restraints excluded: chain C residue 441 TYR Chi-restraints excluded: chain C residue 442 LEU Chi-restraints excluded: chain D residue 53 GLU Chi-restraints excluded: chain D residue 225 VAL Chi-restraints excluded: chain D residue 288 VAL Chi-restraints excluded: chain D residue 317 VAL Chi-restraints excluded: chain D residue 441 TYR Chi-restraints excluded: chain E residue 45 MET Chi-restraints excluded: chain E residue 120 ARG Chi-restraints excluded: chain E residue 197 LYS Chi-restraints excluded: chain E residue 225 VAL Chi-restraints excluded: chain E residue 269 VAL Chi-restraints excluded: chain E residue 441 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 13 optimal weight: 3.9990 chunk 51 optimal weight: 0.8980 chunk 115 optimal weight: 5.9990 chunk 68 optimal weight: 9.9990 chunk 123 optimal weight: 0.9980 chunk 12 optimal weight: 0.7980 chunk 42 optimal weight: 1.9990 chunk 31 optimal weight: 0.8980 chunk 78 optimal weight: 4.9990 chunk 113 optimal weight: 7.9990 chunk 66 optimal weight: 6.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- 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 = 0.3797 r_free = 0.3797 target = 0.115009 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.068738 restraints weight = 31977.717| |-----------------------------------------------------------------------------| r_work (start): 0.2938 rms_B_bonded: 2.43 r_work: 0.2805 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2685 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.2685 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8434 moved from start: 0.3157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 17115 Z= 0.144 Angle : 0.617 10.772 23410 Z= 0.306 Chirality : 0.043 0.153 2740 Planarity : 0.004 0.034 2845 Dihedral : 7.040 58.160 2505 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 2.01 % Allowed : 17.29 % Favored : 80.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.64 (0.19), residues: 1955 helix: 0.93 (0.19), residues: 825 sheet: -0.96 (0.25), residues: 375 loop : -1.63 (0.21), residues: 755 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 416 TYR 0.015 0.001 TYR E 67 PHE 0.011 0.001 PHE A 142 TRP 0.010 0.001 TRP E 156 HIS 0.003 0.000 HIS A 18 Details of bonding type rmsd covalent geometry : bond 0.00336 (17095) covalent geometry : angle 0.58868 (23355) SS BOND : bond 0.00021 ( 5) SS BOND : angle 0.26129 ( 10) hydrogen bonds : bond 0.04103 ( 765) hydrogen bonds : angle 4.51423 ( 2190) link_NAG-ASN : bond 0.00623 ( 15) link_NAG-ASN : angle 4.22704 ( 45) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 1845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 82 time to evaluate : 0.526 Fit side-chains REVERT: C 53 GLU cc_start: 0.8558 (OUTLIER) cc_final: 0.8299 (pt0) REVERT: D 91 ASP cc_start: 0.8874 (p0) cc_final: 0.8634 (p0) REVERT: D 116 TYR cc_start: 0.9356 (OUTLIER) cc_final: 0.8581 (m-10) REVERT: D 410 ARG cc_start: 0.7727 (ttp-170) cc_final: 0.7338 (tpt90) REVERT: D 411 HIS cc_start: 0.7986 (m90) cc_final: 0.7502 (m90) REVERT: E 120 ARG cc_start: 0.7692 (OUTLIER) cc_final: 0.7226 (mtp85) REVERT: E 416 ARG cc_start: 0.6659 (ttt180) cc_final: 0.5853 (tpm170) outliers start: 37 outliers final: 20 residues processed: 102 average time/residue: 0.4674 time to fit residues: 55.5613 Evaluate side-chains 101 residues out of total 1845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 78 time to evaluate : 0.628 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 303 PHE Chi-restraints excluded: chain A residue 441 TYR Chi-restraints excluded: chain B residue 58 LEU Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 280 THR Chi-restraints excluded: chain B residue 303 PHE Chi-restraints excluded: chain C residue 53 GLU Chi-restraints excluded: chain C residue 225 VAL Chi-restraints excluded: chain C residue 232 ILE Chi-restraints excluded: chain C residue 303 PHE Chi-restraints excluded: chain C residue 440 ILE Chi-restraints excluded: chain C residue 441 TYR Chi-restraints excluded: chain C residue 442 LEU Chi-restraints excluded: chain D residue 53 GLU Chi-restraints excluded: chain D residue 116 TYR Chi-restraints excluded: chain D residue 232 ILE Chi-restraints excluded: chain D residue 317 VAL Chi-restraints excluded: chain D residue 441 TYR Chi-restraints excluded: chain E residue 45 MET Chi-restraints excluded: chain E residue 120 ARG Chi-restraints excluded: chain E residue 232 ILE Chi-restraints excluded: chain E residue 269 VAL Chi-restraints excluded: chain E residue 441 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 22 optimal weight: 0.6980 chunk 29 optimal weight: 0.9990 chunk 183 optimal weight: 6.9990 chunk 145 optimal weight: 0.9980 chunk 65 optimal weight: 5.9990 chunk 165 optimal weight: 0.6980 chunk 184 optimal weight: 2.9990 chunk 74 optimal weight: 7.9990 chunk 52 optimal weight: 2.9990 chunk 2 optimal weight: 0.7980 chunk 82 optimal weight: 5.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- 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 = 0.3806 r_free = 0.3806 target = 0.115663 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.069595 restraints weight = 32177.896| |-----------------------------------------------------------------------------| r_work (start): 0.2957 rms_B_bonded: 2.43 r_work: 0.2824 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2705 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.2705 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8413 moved from start: 0.3197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 17115 Z= 0.125 Angle : 0.598 11.580 23410 Z= 0.296 Chirality : 0.043 0.153 2740 Planarity : 0.004 0.033 2845 Dihedral : 6.896 57.183 2505 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer: Outliers : 2.01 % Allowed : 17.51 % Favored : 80.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.54 (0.19), residues: 1955 helix: 1.01 (0.19), residues: 825 sheet: -0.86 (0.24), residues: 395 loop : -1.60 (0.22), residues: 735 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 416 TYR 0.015 0.001 TYR A 67 PHE 0.009 0.001 PHE A 142 TRP 0.010 0.001 TRP A 68 HIS 0.002 0.000 HIS A 18 Details of bonding type rmsd covalent geometry : bond 0.00284 (17095) covalent geometry : angle 0.57188 (23355) SS BOND : bond 0.00020 ( 5) SS BOND : angle 0.26988 ( 10) hydrogen bonds : bond 0.03792 ( 765) hydrogen bonds : angle 4.42546 ( 2190) link_NAG-ASN : bond 0.00639 ( 15) link_NAG-ASN : angle 3.99914 ( 45) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 1845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 80 time to evaluate : 0.679 Fit side-chains REVERT: A 291 MET cc_start: 0.7803 (tpp) cc_final: 0.7478 (tpp) REVERT: C 53 GLU cc_start: 0.8533 (OUTLIER) cc_final: 0.8265 (pt0) REVERT: D 116 TYR cc_start: 0.9306 (OUTLIER) cc_final: 0.8446 (m-10) REVERT: D 410 ARG cc_start: 0.7704 (ttp-170) cc_final: 0.7331 (tpt90) REVERT: D 411 HIS cc_start: 0.7942 (m90) cc_final: 0.7464 (m90) REVERT: E 416 ARG cc_start: 0.6629 (ttt180) cc_final: 0.5877 (tpm170) outliers start: 37 outliers final: 20 residues processed: 104 average time/residue: 0.4130 time to fit residues: 50.8960 Evaluate side-chains 99 residues out of total 1845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 77 time to evaluate : 0.467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 303 PHE Chi-restraints excluded: chain A residue 441 TYR Chi-restraints excluded: chain B residue 58 LEU Chi-restraints excluded: chain B residue 240 VAL Chi-restraints excluded: chain B residue 280 THR Chi-restraints excluded: chain B residue 303 PHE Chi-restraints excluded: chain C residue 53 GLU Chi-restraints excluded: chain C residue 232 ILE Chi-restraints excluded: chain C residue 240 VAL Chi-restraints excluded: chain C residue 303 PHE Chi-restraints excluded: chain C residue 440 ILE Chi-restraints excluded: chain C residue 441 TYR Chi-restraints excluded: chain C residue 442 LEU Chi-restraints excluded: chain D residue 53 GLU Chi-restraints excluded: chain D residue 116 TYR Chi-restraints excluded: chain D residue 232 ILE Chi-restraints excluded: chain D residue 317 VAL Chi-restraints excluded: chain D residue 441 TYR Chi-restraints excluded: chain E residue 232 ILE Chi-restraints excluded: chain E residue 269 VAL Chi-restraints excluded: chain E residue 288 VAL Chi-restraints excluded: chain E residue 441 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 62 optimal weight: 3.9990 chunk 90 optimal weight: 0.7980 chunk 186 optimal weight: 3.9990 chunk 33 optimal weight: 4.9990 chunk 29 optimal weight: 9.9990 chunk 1 optimal weight: 2.9990 chunk 181 optimal weight: 7.9990 chunk 4 optimal weight: 0.8980 chunk 155 optimal weight: 0.9980 chunk 58 optimal weight: 0.9990 chunk 42 optimal weight: 0.7980 overall best weight: 0.8982 ------------------------------------------------------------------------------- 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 = 0.3806 r_free = 0.3806 target = 0.115541 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.069253 restraints weight = 32141.707| |-----------------------------------------------------------------------------| r_work (start): 0.2953 rms_B_bonded: 2.46 r_work: 0.2820 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2701 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.2701 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8417 moved from start: 0.3268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 17115 Z= 0.129 Angle : 0.612 12.194 23410 Z= 0.301 Chirality : 0.043 0.153 2740 Planarity : 0.004 0.033 2845 Dihedral : 6.900 57.433 2505 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 1.73 % Allowed : 18.16 % Favored : 80.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.52 (0.19), residues: 1955 helix: 1.00 (0.19), residues: 825 sheet: -0.84 (0.24), residues: 395 loop : -1.57 (0.22), residues: 735 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 306 TYR 0.015 0.001 TYR D 67 PHE 0.009 0.001 PHE C 254 TRP 0.009 0.001 TRP E 156 HIS 0.002 0.000 HIS A 18 Details of bonding type rmsd covalent geometry : bond 0.00295 (17095) covalent geometry : angle 0.58729 (23355) SS BOND : bond 0.00016 ( 5) SS BOND : angle 0.24410 ( 10) hydrogen bonds : bond 0.03883 ( 765) hydrogen bonds : angle 4.40090 ( 2190) link_NAG-ASN : bond 0.00626 ( 15) link_NAG-ASN : angle 3.95655 ( 45) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 1845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 81 time to evaluate : 0.692 Fit side-chains REVERT: B 441 TYR cc_start: 0.7393 (OUTLIER) cc_final: 0.7178 (m-10) REVERT: C 53 GLU cc_start: 0.8531 (OUTLIER) cc_final: 0.8263 (pt0) REVERT: D 116 TYR cc_start: 0.9321 (OUTLIER) cc_final: 0.8515 (m-10) REVERT: D 410 ARG cc_start: 0.7704 (ttp-170) cc_final: 0.7331 (tpt90) REVERT: D 411 HIS cc_start: 0.7945 (m90) cc_final: 0.7480 (m90) REVERT: E 120 ARG cc_start: 0.7591 (OUTLIER) cc_final: 0.7131 (mtp85) REVERT: E 416 ARG cc_start: 0.6621 (ttt180) cc_final: 0.5821 (tpm170) outliers start: 32 outliers final: 19 residues processed: 100 average time/residue: 0.4430 time to fit residues: 51.6966 Evaluate side-chains 102 residues out of total 1845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 79 time to evaluate : 0.674 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 303 PHE Chi-restraints excluded: chain A residue 441 TYR Chi-restraints excluded: chain B residue 58 LEU Chi-restraints excluded: chain B residue 240 VAL Chi-restraints excluded: chain B residue 280 THR Chi-restraints excluded: chain B residue 441 TYR Chi-restraints excluded: chain C residue 53 GLU Chi-restraints excluded: chain C residue 240 VAL Chi-restraints excluded: chain C residue 303 PHE Chi-restraints excluded: chain C residue 440 ILE Chi-restraints excluded: chain C residue 441 TYR Chi-restraints excluded: chain C residue 442 LEU Chi-restraints excluded: chain D residue 53 GLU Chi-restraints excluded: chain D residue 58 LEU Chi-restraints excluded: chain D residue 116 TYR Chi-restraints excluded: chain D residue 232 ILE Chi-restraints excluded: chain D residue 317 VAL Chi-restraints excluded: chain D residue 441 TYR Chi-restraints excluded: chain E residue 120 ARG Chi-restraints excluded: chain E residue 232 ILE Chi-restraints excluded: chain E residue 269 VAL Chi-restraints excluded: chain E residue 288 VAL Chi-restraints excluded: chain E residue 441 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 36 optimal weight: 8.9990 chunk 76 optimal weight: 2.9990 chunk 87 optimal weight: 3.9990 chunk 160 optimal weight: 1.9990 chunk 33 optimal weight: 6.9990 chunk 151 optimal weight: 6.9990 chunk 124 optimal weight: 0.5980 chunk 170 optimal weight: 2.9990 chunk 183 optimal weight: 0.2980 chunk 181 optimal weight: 1.9990 chunk 149 optimal weight: 8.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- 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 = 0.3784 r_free = 0.3784 target = 0.114036 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.067713 restraints weight = 31940.180| |-----------------------------------------------------------------------------| r_work (start): 0.2919 rms_B_bonded: 2.43 r_work: 0.2783 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.2664 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.2664 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8474 moved from start: 0.3363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 17115 Z= 0.178 Angle : 0.660 12.917 23410 Z= 0.325 Chirality : 0.044 0.166 2740 Planarity : 0.004 0.037 2845 Dihedral : 7.166 58.873 2505 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.47 % Favored : 94.53 % Rotamer: Outliers : 1.52 % Allowed : 18.48 % Favored : 80.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.62 (0.19), residues: 1955 helix: 1.03 (0.19), residues: 795 sheet: -0.98 (0.24), residues: 375 loop : -1.59 (0.21), residues: 785 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 306 TYR 0.013 0.002 TYR D 67 PHE 0.012 0.001 PHE C 254 TRP 0.013 0.001 TRP B 156 HIS 0.003 0.001 HIS B 18 Details of bonding type rmsd covalent geometry : bond 0.00422 (17095) covalent geometry : angle 0.63482 (23355) SS BOND : bond 0.00033 ( 5) SS BOND : angle 0.24952 ( 10) hydrogen bonds : bond 0.04413 ( 765) hydrogen bonds : angle 4.49438 ( 2190) link_NAG-ASN : bond 0.00575 ( 15) link_NAG-ASN : angle 4.20722 ( 45) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 1845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 82 time to evaluate : 0.692 Fit side-chains REVERT: C 53 GLU cc_start: 0.8618 (OUTLIER) cc_final: 0.8363 (pt0) REVERT: D 91 ASP cc_start: 0.8891 (p0) cc_final: 0.8642 (p0) REVERT: D 410 ARG cc_start: 0.7709 (ttp-170) cc_final: 0.7330 (tpt90) REVERT: D 411 HIS cc_start: 0.7918 (m90) cc_final: 0.7475 (m90) REVERT: E 120 ARG cc_start: 0.7639 (OUTLIER) cc_final: 0.7201 (mtp85) REVERT: E 416 ARG cc_start: 0.6685 (ttt180) cc_final: 0.5884 (tpm170) outliers start: 28 outliers final: 22 residues processed: 100 average time/residue: 0.4196 time to fit residues: 49.5229 Evaluate side-chains 105 residues out of total 1845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 81 time to evaluate : 0.646 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 269 VAL Chi-restraints excluded: chain A residue 303 PHE Chi-restraints excluded: chain A residue 441 TYR Chi-restraints excluded: chain B residue 58 LEU Chi-restraints excluded: chain B residue 240 VAL Chi-restraints excluded: chain B residue 269 VAL Chi-restraints excluded: chain B residue 280 THR Chi-restraints excluded: chain B residue 303 PHE Chi-restraints excluded: chain C residue 53 GLU Chi-restraints excluded: chain C residue 240 VAL Chi-restraints excluded: chain C residue 303 PHE Chi-restraints excluded: chain C residue 440 ILE Chi-restraints excluded: chain C residue 441 TYR Chi-restraints excluded: chain C residue 442 LEU Chi-restraints excluded: chain D residue 53 GLU Chi-restraints excluded: chain D residue 58 LEU Chi-restraints excluded: chain D residue 317 VAL Chi-restraints excluded: chain D residue 441 TYR Chi-restraints excluded: chain E residue 120 ARG Chi-restraints excluded: chain E residue 232 ILE Chi-restraints excluded: chain E residue 269 VAL Chi-restraints excluded: chain E residue 288 VAL Chi-restraints excluded: chain E residue 441 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 23 optimal weight: 7.9990 chunk 162 optimal weight: 1.9990 chunk 94 optimal weight: 1.9990 chunk 172 optimal weight: 1.9990 chunk 114 optimal weight: 5.9990 chunk 147 optimal weight: 20.0000 chunk 30 optimal weight: 3.9990 chunk 123 optimal weight: 1.9990 chunk 121 optimal weight: 3.9990 chunk 100 optimal weight: 3.9990 chunk 70 optimal weight: 0.7980 overall best weight: 1.7588 ------------------------------------------------------------------------------- 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 = 0.3778 r_free = 0.3778 target = 0.113614 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2961 r_free = 0.2961 target = 0.067370 restraints weight = 32150.174| |-----------------------------------------------------------------------------| r_work (start): 0.2911 rms_B_bonded: 2.42 r_work: 0.2777 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2657 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.2657 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8474 moved from start: 0.3441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 17115 Z= 0.192 Angle : 0.671 13.109 23410 Z= 0.331 Chirality : 0.045 0.169 2740 Planarity : 0.004 0.037 2845 Dihedral : 7.246 59.001 2505 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer: Outliers : 1.57 % Allowed : 18.43 % Favored : 80.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.72 (0.19), residues: 1955 helix: 0.82 (0.19), residues: 825 sheet: -1.02 (0.24), residues: 375 loop : -1.61 (0.21), residues: 755 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 28 TYR 0.014 0.002 TYR D 67 PHE 0.013 0.001 PHE C 254 TRP 0.013 0.001 TRP C 156 HIS 0.003 0.001 HIS A 18 Details of bonding type rmsd covalent geometry : bond 0.00459 (17095) covalent geometry : angle 0.64460 (23355) SS BOND : bond 0.00033 ( 5) SS BOND : angle 0.24132 ( 10) hydrogen bonds : bond 0.04564 ( 765) hydrogen bonds : angle 4.53270 ( 2190) link_NAG-ASN : bond 0.00565 ( 15) link_NAG-ASN : angle 4.32289 ( 45) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6073.63 seconds wall clock time: 104 minutes 7.57 seconds (6247.57 seconds total)