Starting phenix.real_space_refine on Sat Jun 14 23:51:41 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8fsb_29418/06_2025/8fsb_29418.cif Found real_map, /net/cci-nas-00/data/ceres_data/8fsb_29418/06_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8fsb_29418/06_2025/8fsb_29418.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8fsb_29418/06_2025/8fsb_29418.map" model { file = "/net/cci-nas-00/data/ceres_data/8fsb_29418/06_2025/8fsb_29418.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8fsb_29418/06_2025/8fsb_29418.cif" } resolution = 2.75 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 9.96, per 1000 atoms: 0.60 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: 4.47 Conformation dependent library (CDL) restraints added in 2.2 seconds 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: 1.74 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: 4.78 Time building geometry restraints manager: 5.29 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: 0.03 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: 3.210 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.690 Check model and map are aligned: 0.130 Set scattering table: 0.160 Process input model: 38.220 Find NCS groups from input model: 0.880 Set up NCS constraints: 0.050 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:13.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 56.440 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.019 0.001 TRP E 168 HIS 0.002 0.001 HIS C 18 PHE 0.021 0.002 PHE E 303 TYR 0.015 0.002 TYR D 61 ARG 0.007 0.000 ARG B 31 Details of bonding type rmsd link_NAG-ASN : bond 0.01362 ( 15) link_NAG-ASN : angle 6.74761 ( 45) hydrogen bonds : bond 0.17697 ( 765) hydrogen bonds : angle 5.96769 ( 2190) SS BOND : bond 0.00026 ( 5) SS BOND : angle 0.02350 ( 10) covalent geometry : bond 0.00388 (17095) covalent geometry : angle 0.71411 (23355) *********************** 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 : 2.062 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: 1.3353 time to fit residues: 316.1896 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 : 1.930 ------------------------------------------------------------------------------- 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 164 optimal weight: 2.9990 chunk 147 optimal weight: 3.9990 chunk 82 optimal weight: 0.4980 chunk 50 optimal weight: 0.4980 chunk 99 optimal weight: 0.9990 chunk 78 optimal weight: 4.9990 chunk 152 optimal weight: 3.9990 chunk 59 optimal weight: 0.4980 chunk 92 optimal weight: 2.9990 chunk 113 optimal weight: 0.9990 chunk 177 optimal weight: 0.7980 overall best weight: 0.6582 ------------------------------------------------------------------------------- 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 = 0.3875 r_free = 0.3875 target = 0.120000 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.074622 restraints weight = 31845.687| |-----------------------------------------------------------------------------| r_work (start): 0.3056 rms_B_bonded: 2.45 r_work: 0.2928 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.2810 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.2810 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8348 moved from start: 0.1726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 17115 Z= 0.127 Angle : 0.619 9.102 23410 Z= 0.308 Chirality : 0.043 0.163 2740 Planarity : 0.004 0.032 2845 Dihedral : 7.166 58.263 2507 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 1.90 % Allowed : 9.27 % Favored : 88.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.66 (0.19), residues: 1955 helix: 0.80 (0.19), residues: 790 sheet: -0.50 (0.26), residues: 395 loop : -1.68 (0.21), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 168 HIS 0.002 0.000 HIS A 18 PHE 0.012 0.001 PHE A 142 TYR 0.012 0.001 TYR B 61 ARG 0.006 0.000 ARG A 306 Details of bonding type rmsd link_NAG-ASN : bond 0.00928 ( 15) link_NAG-ASN : angle 5.14282 ( 45) hydrogen bonds : bond 0.04196 ( 765) hydrogen bonds : angle 4.68611 ( 2190) SS BOND : bond 0.00148 ( 5) SS BOND : angle 0.24845 ( 10) covalent geometry : bond 0.00286 (17095) covalent geometry : angle 0.57685 (23355) *********************** 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: 35 poor density : 94 time to evaluate : 1.854 Fit side-chains REVERT: A 145 ASP cc_start: 0.8141 (m-30) cc_final: 0.7916 (m-30) REVERT: A 410 ARG cc_start: 0.7640 (ttp-170) cc_final: 0.7200 (tpm-80) REVERT: A 411 HIS cc_start: 0.8092 (m90) cc_final: 0.7817 (m-70) REVERT: A 433 LEU cc_start: 0.9059 (mp) cc_final: 0.8835 (mm) REVERT: B 410 ARG cc_start: 0.7642 (ttp-170) cc_final: 0.7286 (tpt90) REVERT: B 411 HIS cc_start: 0.8050 (m90) cc_final: 0.7698 (m-70) REVERT: C 419 MET cc_start: 0.5196 (mmt) cc_final: 0.4951 (tmm) REVERT: D 410 ARG cc_start: 0.7791 (ttp-170) cc_final: 0.7361 (tpt90) REVERT: D 411 HIS cc_start: 0.7812 (m90) cc_final: 0.7353 (m90) REVERT: E 197 LYS cc_start: 0.8580 (OUTLIER) cc_final: 0.8346 (mmtp) REVERT: E 232 ILE cc_start: 0.7990 (mm) cc_final: 0.7723 (mm) REVERT: E 416 ARG cc_start: 0.6464 (ttt180) cc_final: 0.5983 (tpm170) REVERT: E 419 MET cc_start: 0.5361 (mmt) cc_final: 0.5095 (tmm) outliers start: 35 outliers final: 12 residues processed: 123 average time/residue: 0.9704 time to fit residues: 138.7537 Evaluate side-chains 96 residues out of total 1845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 83 time to evaluate : 1.888 ------------------------------------------------------------------------------- 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 225 VAL Chi-restraints excluded: chain B residue 232 ILE 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 442 LEU 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 8 optimal weight: 3.9990 chunk 93 optimal weight: 1.9990 chunk 20 optimal weight: 2.9990 chunk 96 optimal weight: 4.9990 chunk 181 optimal weight: 6.9990 chunk 127 optimal weight: 1.9990 chunk 113 optimal weight: 0.8980 chunk 57 optimal weight: 3.9990 chunk 123 optimal weight: 0.9990 chunk 101 optimal weight: 10.0000 chunk 110 optimal weight: 6.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 22 ASN D 161 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.115456 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2992 r_free = 0.2992 target = 0.068973 restraints weight = 31766.424| |-----------------------------------------------------------------------------| r_work (start): 0.2943 rms_B_bonded: 2.42 r_work: 0.2806 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.2687 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.2687 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8460 moved from start: 0.2426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 17115 Z= 0.203 Angle : 0.663 8.927 23410 Z= 0.335 Chirality : 0.045 0.155 2740 Planarity : 0.004 0.031 2845 Dihedral : 7.238 59.911 2505 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 2.01 % Allowed : 11.98 % Favored : 86.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.83 (0.19), residues: 1955 helix: 0.64 (0.19), residues: 815 sheet: -0.87 (0.25), residues: 375 loop : -1.64 (0.21), residues: 765 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 156 HIS 0.003 0.001 HIS C 119 PHE 0.016 0.001 PHE A 142 TYR 0.019 0.002 TYR C 61 ARG 0.003 0.000 ARG E 28 Details of bonding type rmsd link_NAG-ASN : bond 0.00555 ( 15) link_NAG-ASN : angle 4.61477 ( 45) hydrogen bonds : bond 0.04775 ( 765) hydrogen bonds : angle 4.62703 ( 2190) SS BOND : bond 0.00029 ( 5) SS BOND : angle 0.34539 ( 10) covalent geometry : bond 0.00486 (17095) covalent geometry : angle 0.63232 (23355) *********************** 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 123 residues out of total 1845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 86 time to evaluate : 1.866 Fit side-chains REVERT: A 410 ARG cc_start: 0.7626 (ttp-170) cc_final: 0.7189 (tpm-80) REVERT: A 411 HIS cc_start: 0.8027 (m90) cc_final: 0.7721 (m90) REVERT: B 410 ARG cc_start: 0.7635 (ttp-170) cc_final: 0.7279 (tpt90) REVERT: B 411 HIS cc_start: 0.7933 (m90) cc_final: 0.7501 (m-70) REVERT: C 235 MET cc_start: 0.7477 (pp-130) cc_final: 0.7217 (pp-130) REVERT: C 419 MET cc_start: 0.5313 (mmt) cc_final: 0.5014 (tmm) REVERT: D 410 ARG cc_start: 0.7744 (ttp-170) cc_final: 0.7344 (tpt90) REVERT: D 411 HIS cc_start: 0.7781 (m90) cc_final: 0.7344 (m90) REVERT: E 411 HIS cc_start: 0.7548 (m-70) cc_final: 0.7320 (m90) REVERT: E 416 ARG cc_start: 0.6611 (ttt180) cc_final: 0.5947 (tpm170) outliers start: 37 outliers final: 15 residues processed: 110 average time/residue: 1.0743 time to fit residues: 138.5650 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 : 2.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 303 PHE 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 225 VAL Chi-restraints excluded: chain C residue 232 ILE Chi-restraints excluded: chain C residue 303 PHE Chi-restraints excluded: chain C residue 442 LEU 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 45 optimal weight: 1.9990 chunk 38 optimal weight: 3.9990 chunk 27 optimal weight: 4.9990 chunk 171 optimal weight: 2.9990 chunk 131 optimal weight: 1.9990 chunk 126 optimal weight: 0.6980 chunk 188 optimal weight: 20.0000 chunk 36 optimal weight: 5.9990 chunk 177 optimal weight: 0.9990 chunk 100 optimal weight: 4.9990 chunk 59 optimal weight: 2.9990 overall best weight: 1.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 147 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.114684 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.2971 r_free = 0.2971 target = 0.067948 restraints weight = 31869.389| |-----------------------------------------------------------------------------| r_work (start): 0.2923 rms_B_bonded: 2.42 r_work: 0.2791 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2673 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.2673 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8444 moved from start: 0.2825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 17115 Z= 0.191 Angle : 0.649 9.262 23410 Z= 0.326 Chirality : 0.045 0.151 2740 Planarity : 0.004 0.034 2845 Dihedral : 7.221 58.919 2505 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 2.28 % Allowed : 14.31 % Favored : 83.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.83 (0.19), residues: 1955 helix: 0.73 (0.19), residues: 820 sheet: -0.95 (0.25), residues: 375 loop : -1.72 (0.21), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 156 HIS 0.002 0.001 HIS C 118 PHE 0.014 0.001 PHE A 142 TYR 0.015 0.002 TYR C 61 ARG 0.002 0.000 ARG A 28 Details of bonding type rmsd link_NAG-ASN : bond 0.00573 ( 15) link_NAG-ASN : angle 4.51247 ( 45) hydrogen bonds : bond 0.04588 ( 765) hydrogen bonds : angle 4.64070 ( 2190) SS BOND : bond 0.00015 ( 5) SS BOND : angle 0.31032 ( 10) covalent geometry : bond 0.00457 (17095) covalent geometry : angle 0.61871 (23355) *********************** 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 125 residues out of total 1845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 83 time to evaluate : 1.980 Fit side-chains REVERT: A 410 ARG cc_start: 0.7664 (ttp-170) cc_final: 0.7194 (tpm-80) REVERT: A 411 HIS cc_start: 0.7874 (m90) cc_final: 0.7512 (m90) REVERT: C 235 MET cc_start: 0.7457 (pp-130) cc_final: 0.7207 (pp-130) REVERT: C 419 MET cc_start: 0.5363 (mmt) cc_final: 0.5030 (tmm) REVERT: D 91 ASP cc_start: 0.8909 (p0) cc_final: 0.8652 (p0) REVERT: D 410 ARG cc_start: 0.7693 (ttp-170) cc_final: 0.7300 (tpt90) REVERT: D 411 HIS cc_start: 0.7796 (m90) cc_final: 0.7342 (m90) REVERT: E 120 ARG cc_start: 0.7612 (OUTLIER) cc_final: 0.7225 (mtp85) REVERT: E 416 ARG cc_start: 0.6644 (ttt180) cc_final: 0.5877 (tpm170) outliers start: 42 outliers final: 14 residues processed: 108 average time/residue: 1.0398 time to fit residues: 129.9669 Evaluate side-chains 92 residues out of total 1845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 77 time to evaluate : 2.040 ------------------------------------------------------------------------------- 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 A residue 442 LEU Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 442 LEU 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 441 TYR Chi-restraints excluded: chain E residue 120 ARG 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 111 optimal weight: 8.9990 chunk 158 optimal weight: 1.9990 chunk 48 optimal weight: 0.9990 chunk 150 optimal weight: 0.9990 chunk 58 optimal weight: 2.9990 chunk 164 optimal weight: 0.0070 chunk 5 optimal weight: 2.9990 chunk 136 optimal weight: 0.9990 chunk 60 optimal weight: 4.9990 chunk 189 optimal weight: 6.9990 chunk 130 optimal weight: 1.9990 overall best weight: 1.0006 ------------------------------------------------------------------------------- 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 = 0.3809 r_free = 0.3809 target = 0.115722 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.069239 restraints weight = 32170.566| |-----------------------------------------------------------------------------| r_work (start): 0.2949 rms_B_bonded: 2.44 r_work: 0.2815 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2696 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.2696 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8426 moved from start: 0.2901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 17115 Z= 0.134 Angle : 0.592 10.035 23410 Z= 0.297 Chirality : 0.043 0.151 2740 Planarity : 0.004 0.033 2845 Dihedral : 6.978 57.671 2505 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 2.11 % Allowed : 15.56 % Favored : 82.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.69 (0.19), residues: 1955 helix: 0.88 (0.19), residues: 820 sheet: -0.92 (0.25), residues: 375 loop : -1.67 (0.21), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 156 HIS 0.002 0.001 HIS E 119 PHE 0.011 0.001 PHE A 142 TYR 0.014 0.001 TYR E 67 ARG 0.002 0.000 ARG E 306 Details of bonding type rmsd link_NAG-ASN : bond 0.00624 ( 15) link_NAG-ASN : angle 4.13591 ( 45) hydrogen bonds : bond 0.03959 ( 765) hydrogen bonds : angle 4.49962 ( 2190) SS BOND : bond 0.00045 ( 5) SS BOND : angle 0.27580 ( 10) covalent geometry : bond 0.00309 (17095) covalent geometry : angle 0.56444 (23355) *********************** 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 120 residues out of total 1845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 81 time to evaluate : 1.830 Fit side-chains REVERT: A 410 ARG cc_start: 0.7555 (ttp-170) cc_final: 0.7178 (tpm-80) REVERT: A 411 HIS cc_start: 0.7748 (m90) cc_final: 0.7420 (m90) REVERT: C 235 MET cc_start: 0.7411 (pp-130) cc_final: 0.7162 (pp-130) REVERT: C 419 MET cc_start: 0.5393 (mmt) cc_final: 0.5016 (tmm) REVERT: D 91 ASP cc_start: 0.8870 (p0) cc_final: 0.8624 (p0) REVERT: D 116 TYR cc_start: 0.9354 (OUTLIER) cc_final: 0.8569 (m-10) REVERT: D 410 ARG cc_start: 0.7681 (ttp-170) cc_final: 0.7308 (tpt90) REVERT: D 411 HIS cc_start: 0.7800 (m90) cc_final: 0.7353 (m90) REVERT: E 411 HIS cc_start: 0.7809 (m90) cc_final: 0.7595 (m90) REVERT: E 416 ARG cc_start: 0.6673 (ttt180) cc_final: 0.5801 (tpm170) outliers start: 39 outliers final: 16 residues processed: 103 average time/residue: 0.9766 time to fit residues: 118.0592 Evaluate side-chains 96 residues out of total 1845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 79 time to evaluate : 1.797 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 441 TYR Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 303 PHE Chi-restraints excluded: chain B residue 441 TYR Chi-restraints excluded: chain B residue 442 LEU 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 441 TYR 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 197 LYS 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 50 optimal weight: 3.9990 chunk 92 optimal weight: 2.9990 chunk 21 optimal weight: 0.8980 chunk 99 optimal weight: 0.9980 chunk 82 optimal weight: 0.3980 chunk 133 optimal weight: 0.1980 chunk 0 optimal weight: 4.9990 chunk 189 optimal weight: 0.9990 chunk 77 optimal weight: 1.9990 chunk 185 optimal weight: 0.9980 chunk 98 optimal weight: 0.6980 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 = 0.3820 r_free = 0.3820 target = 0.116472 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.070197 restraints weight = 32189.789| |-----------------------------------------------------------------------------| r_work (start): 0.2970 rms_B_bonded: 2.46 r_work: 0.2838 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2719 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.2719 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8404 moved from start: 0.2991 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= 0.114 Angle : 0.573 10.695 23410 Z= 0.287 Chirality : 0.042 0.147 2740 Planarity : 0.004 0.032 2845 Dihedral : 6.813 56.546 2505 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 1.57 % Allowed : 16.75 % Favored : 81.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.53 (0.19), residues: 1955 helix: 1.01 (0.19), residues: 825 sheet: -0.78 (0.24), residues: 395 loop : -1.63 (0.22), residues: 735 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 68 HIS 0.002 0.000 HIS C 119 PHE 0.012 0.001 PHE A 438 TYR 0.020 0.001 TYR B 441 ARG 0.002 0.000 ARG B 416 Details of bonding type rmsd link_NAG-ASN : bond 0.00638 ( 15) link_NAG-ASN : angle 3.87549 ( 45) hydrogen bonds : bond 0.03639 ( 765) hydrogen bonds : angle 4.40732 ( 2190) SS BOND : bond 0.00049 ( 5) SS BOND : angle 0.26131 ( 10) covalent geometry : bond 0.00254 (17095) covalent geometry : angle 0.54762 (23355) *********************** 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 112 residues out of total 1845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 83 time to evaluate : 4.716 Fit side-chains REVERT: A 410 ARG cc_start: 0.7545 (ttp-170) cc_final: 0.7171 (tpm-80) REVERT: A 411 HIS cc_start: 0.7743 (m90) cc_final: 0.7418 (m90) REVERT: C 235 MET cc_start: 0.7343 (pp-130) cc_final: 0.7074 (pp-130) REVERT: C 419 MET cc_start: 0.5397 (mmt) cc_final: 0.5142 (tmm) REVERT: D 53 GLU cc_start: 0.8445 (OUTLIER) cc_final: 0.8073 (pt0) REVERT: D 116 TYR cc_start: 0.9306 (OUTLIER) cc_final: 0.8446 (m-10) REVERT: D 410 ARG cc_start: 0.7708 (ttp-170) cc_final: 0.7338 (tpt90) REVERT: D 411 HIS cc_start: 0.7820 (m90) cc_final: 0.7378 (m90) REVERT: E 411 HIS cc_start: 0.7810 (m90) cc_final: 0.7565 (m90) REVERT: E 416 ARG cc_start: 0.6629 (ttt180) cc_final: 0.5770 (tpm170) outliers start: 29 outliers final: 17 residues processed: 97 average time/residue: 1.3005 time to fit residues: 151.0024 Evaluate side-chains 99 residues out of total 1845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 80 time to evaluate : 2.211 ------------------------------------------------------------------------------- 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 280 THR Chi-restraints excluded: chain B residue 303 PHE Chi-restraints excluded: chain B residue 442 LEU 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 232 ILE 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 33 optimal weight: 0.7980 chunk 106 optimal weight: 0.9990 chunk 193 optimal weight: 8.9990 chunk 12 optimal weight: 1.9990 chunk 171 optimal weight: 3.9990 chunk 109 optimal weight: 9.9990 chunk 115 optimal weight: 6.9990 chunk 186 optimal weight: 8.9990 chunk 62 optimal weight: 5.9990 chunk 150 optimal weight: 5.9990 chunk 108 optimal weight: 10.0000 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 125 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.112693 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.2924 r_free = 0.2924 target = 0.065827 restraints weight = 32339.325| |-----------------------------------------------------------------------------| r_work (start): 0.2877 rms_B_bonded: 2.43 r_work: 0.2742 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2623 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.2623 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8504 moved from start: 0.3311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.055 17115 Z= 0.278 Angle : 0.717 11.449 23410 Z= 0.359 Chirality : 0.047 0.221 2740 Planarity : 0.005 0.039 2845 Dihedral : 7.506 59.878 2505 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.37 % Favored : 94.63 % Rotamer: Outliers : 2.71 % Allowed : 16.64 % Favored : 80.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.73 (0.19), residues: 1955 helix: 0.95 (0.19), residues: 795 sheet: -1.03 (0.24), residues: 375 loop : -1.68 (0.21), residues: 785 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 156 HIS 0.004 0.001 HIS C 118 PHE 0.014 0.002 PHE D 80 TYR 0.017 0.002 TYR C 61 ARG 0.004 0.000 ARG A 28 Details of bonding type rmsd link_NAG-ASN : bond 0.00503 ( 15) link_NAG-ASN : angle 4.66635 ( 45) hydrogen bonds : bond 0.05198 ( 765) hydrogen bonds : angle 4.71672 ( 2190) SS BOND : bond 0.00079 ( 5) SS BOND : angle 0.28413 ( 10) covalent geometry : bond 0.00676 (17095) covalent geometry : angle 0.68813 (23355) *********************** 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 135 residues out of total 1845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 85 time to evaluate : 1.796 Fit side-chains REVERT: A 433 LEU cc_start: 0.9143 (mp) cc_final: 0.8939 (mm) REVERT: C 419 MET cc_start: 0.5432 (mmt) cc_final: 0.4964 (tmm) REVERT: D 410 ARG cc_start: 0.7732 (ttp-170) cc_final: 0.7347 (tpt90) REVERT: D 411 HIS cc_start: 0.7851 (m90) cc_final: 0.7383 (m90) REVERT: E 416 ARG cc_start: 0.6747 (ttt180) cc_final: 0.5899 (tpm170) outliers start: 50 outliers final: 22 residues processed: 120 average time/residue: 0.7857 time to fit residues: 113.3334 Evaluate side-chains 105 residues out of total 1845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 83 time to evaluate : 1.783 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 288 VAL Chi-restraints excluded: chain A residue 441 TYR Chi-restraints excluded: chain B residue 58 LEU Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 269 VAL Chi-restraints excluded: chain B residue 280 THR Chi-restraints excluded: chain B residue 288 VAL Chi-restraints excluded: chain B residue 442 LEU 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 440 ILE Chi-restraints excluded: chain C residue 441 TYR Chi-restraints excluded: chain C residue 442 LEU 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 225 VAL 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 63 optimal weight: 5.9990 chunk 184 optimal weight: 1.9990 chunk 119 optimal weight: 0.6980 chunk 168 optimal weight: 0.3980 chunk 179 optimal weight: 10.0000 chunk 2 optimal weight: 0.9990 chunk 66 optimal weight: 0.0980 chunk 10 optimal weight: 0.6980 chunk 33 optimal weight: 6.9990 chunk 136 optimal weight: 0.9980 chunk 164 optimal weight: 0.8980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 125 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.115777 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.069722 restraints weight = 31962.458| |-----------------------------------------------------------------------------| r_work (start): 0.2960 rms_B_bonded: 2.44 r_work: 0.2829 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2710 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.2710 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8406 moved from start: 0.3241 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= 0.115 Angle : 0.589 11.783 23410 Z= 0.292 Chirality : 0.043 0.145 2740 Planarity : 0.004 0.031 2845 Dihedral : 6.896 56.966 2505 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 2.01 % Allowed : 17.67 % Favored : 80.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.57 (0.19), residues: 1955 helix: 0.99 (0.19), residues: 825 sheet: -0.97 (0.24), residues: 375 loop : -1.57 (0.21), residues: 755 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 68 HIS 0.003 0.000 HIS E 411 PHE 0.009 0.001 PHE A 142 TYR 0.015 0.001 TYR D 67 ARG 0.002 0.000 ARG A 306 Details of bonding type rmsd link_NAG-ASN : bond 0.00615 ( 15) link_NAG-ASN : angle 3.95666 ( 45) hydrogen bonds : bond 0.03698 ( 765) hydrogen bonds : angle 4.47278 ( 2190) SS BOND : bond 0.00016 ( 5) SS BOND : angle 0.36810 ( 10) covalent geometry : bond 0.00256 (17095) covalent geometry : angle 0.56301 (23355) *********************** 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 122 residues out of total 1845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 85 time to evaluate : 2.024 Fit side-chains REVERT: A 291 MET cc_start: 0.7741 (tpp) cc_final: 0.7453 (tpp) REVERT: A 433 LEU cc_start: 0.9086 (mp) cc_final: 0.8886 (mm) REVERT: B 441 TYR cc_start: 0.7385 (OUTLIER) cc_final: 0.7168 (m-10) REVERT: C 419 MET cc_start: 0.5491 (mmt) cc_final: 0.5011 (tmm) REVERT: D 53 GLU cc_start: 0.8457 (OUTLIER) cc_final: 0.8106 (pt0) REVERT: D 91 ASP cc_start: 0.8917 (p0) cc_final: 0.8706 (p0) REVERT: D 116 TYR cc_start: 0.9293 (OUTLIER) cc_final: 0.8525 (m-10) REVERT: D 410 ARG cc_start: 0.7742 (ttp-170) cc_final: 0.7345 (tpt90) REVERT: D 411 HIS cc_start: 0.7935 (m90) cc_final: 0.7452 (m90) REVERT: E 120 ARG cc_start: 0.7559 (OUTLIER) cc_final: 0.7090 (mtp85) REVERT: E 416 ARG cc_start: 0.6722 (ttt180) cc_final: 0.5740 (tpm170) outliers start: 37 outliers final: 19 residues processed: 109 average time/residue: 0.8102 time to fit residues: 105.6350 Evaluate side-chains 105 residues out of total 1845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 82 time to evaluate : 1.784 ------------------------------------------------------------------------------- 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 280 THR Chi-restraints excluded: chain B residue 303 PHE Chi-restraints excluded: chain B residue 441 TYR Chi-restraints excluded: chain B residue 442 LEU 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 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 269 VAL 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 441 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 188 optimal weight: 8.9990 chunk 133 optimal weight: 0.8980 chunk 191 optimal weight: 1.9990 chunk 28 optimal weight: 0.9990 chunk 38 optimal weight: 4.9990 chunk 174 optimal weight: 2.9990 chunk 48 optimal weight: 2.9990 chunk 76 optimal weight: 8.9990 chunk 98 optimal weight: 3.9990 chunk 176 optimal weight: 1.9990 chunk 141 optimal weight: 5.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- 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 = 0.3777 r_free = 0.3777 target = 0.113543 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.2957 r_free = 0.2957 target = 0.067219 restraints weight = 32194.335| |-----------------------------------------------------------------------------| r_work (start): 0.2908 rms_B_bonded: 2.43 r_work: 0.2771 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.2651 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.2651 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8485 moved from start: 0.3365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 17115 Z= 0.191 Angle : 0.657 12.545 23410 Z= 0.325 Chirality : 0.045 0.171 2740 Planarity : 0.004 0.037 2845 Dihedral : 7.196 59.317 2505 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.37 % Favored : 94.63 % Rotamer: Outliers : 1.84 % Allowed : 18.32 % Favored : 79.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.61 (0.19), residues: 1955 helix: 1.07 (0.19), residues: 795 sheet: -1.02 (0.24), residues: 375 loop : -1.62 (0.21), residues: 785 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 156 HIS 0.003 0.001 HIS B 18 PHE 0.012 0.001 PHE C 254 TYR 0.014 0.002 TYR D 67 ARG 0.003 0.000 ARG A 28 Details of bonding type rmsd link_NAG-ASN : bond 0.00529 ( 15) link_NAG-ASN : angle 4.25309 ( 45) hydrogen bonds : bond 0.04482 ( 765) hydrogen bonds : angle 4.55598 ( 2190) SS BOND : bond 0.00035 ( 5) SS BOND : angle 0.21440 ( 10) covalent geometry : bond 0.00458 (17095) covalent geometry : angle 0.63068 (23355) *********************** 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 119 residues out of total 1845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 85 time to evaluate : 1.967 Fit side-chains REVERT: C 419 MET cc_start: 0.5463 (mmt) cc_final: 0.4967 (tmm) REVERT: D 53 GLU cc_start: 0.8638 (OUTLIER) cc_final: 0.8273 (pt0) REVERT: D 91 ASP cc_start: 0.8974 (p0) cc_final: 0.8732 (p0) REVERT: D 410 ARG cc_start: 0.7747 (ttp-170) cc_final: 0.7344 (tpt90) REVERT: D 411 HIS cc_start: 0.7882 (m90) cc_final: 0.7416 (m90) REVERT: E 120 ARG cc_start: 0.7683 (OUTLIER) cc_final: 0.7252 (mtp85) REVERT: E 416 ARG cc_start: 0.6743 (ttt180) cc_final: 0.5803 (tpm170) outliers start: 34 outliers final: 21 residues processed: 104 average time/residue: 0.9525 time to fit residues: 116.4297 Evaluate side-chains 106 residues out of total 1845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 83 time to evaluate : 1.973 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 MET 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 280 THR Chi-restraints excluded: chain B residue 411 HIS Chi-restraints excluded: chain B residue 442 LEU Chi-restraints excluded: chain C residue 232 ILE Chi-restraints excluded: chain C residue 269 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 D residue 53 GLU Chi-restraints excluded: chain D residue 58 LEU Chi-restraints excluded: chain D residue 269 VAL 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 441 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 110 optimal weight: 0.9980 chunk 65 optimal weight: 9.9990 chunk 107 optimal weight: 9.9990 chunk 36 optimal weight: 9.9990 chunk 44 optimal weight: 0.7980 chunk 111 optimal weight: 5.9990 chunk 136 optimal weight: 6.9990 chunk 140 optimal weight: 2.9990 chunk 101 optimal weight: 2.9990 chunk 162 optimal weight: 0.9990 chunk 19 optimal weight: 1.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- 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 = 0.3780 r_free = 0.3780 target = 0.113761 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2961 r_free = 0.2961 target = 0.067433 restraints weight = 32328.677| |-----------------------------------------------------------------------------| r_work (start): 0.2914 rms_B_bonded: 2.43 r_work: 0.2780 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2660 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.2660 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8455 moved from start: 0.3417 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 17115 Z= 0.175 Angle : 0.656 12.671 23410 Z= 0.322 Chirality : 0.044 0.182 2740 Planarity : 0.004 0.035 2845 Dihedral : 7.159 59.432 2505 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.81 % Favored : 95.19 % Rotamer: Outliers : 1.57 % Allowed : 18.70 % Favored : 79.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.64 (0.19), residues: 1955 helix: 1.05 (0.19), residues: 795 sheet: -1.05 (0.24), residues: 375 loop : -1.62 (0.21), residues: 785 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 156 HIS 0.003 0.001 HIS A 18 PHE 0.013 0.001 PHE C 254 TYR 0.015 0.002 TYR D 67 ARG 0.002 0.000 ARG D 28 Details of bonding type rmsd link_NAG-ASN : bond 0.00535 ( 15) link_NAG-ASN : angle 4.21748 ( 45) hydrogen bonds : bond 0.04355 ( 765) hydrogen bonds : angle 4.55043 ( 2190) SS BOND : bond 0.00041 ( 5) SS BOND : angle 0.27159 ( 10) covalent geometry : bond 0.00417 (17095) covalent geometry : angle 0.62986 (23355) ********************** 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 112 residues out of total 1845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 83 time to evaluate : 1.779 Fit side-chains REVERT: C 419 MET cc_start: 0.5428 (mmt) cc_final: 0.4944 (tmm) REVERT: D 53 GLU cc_start: 0.8561 (OUTLIER) cc_final: 0.8260 (pt0) REVERT: D 91 ASP cc_start: 0.8969 (p0) cc_final: 0.8712 (p0) REVERT: D 410 ARG cc_start: 0.7742 (ttp-170) cc_final: 0.7339 (tpt90) REVERT: D 411 HIS cc_start: 0.7914 (m90) cc_final: 0.7462 (m90) REVERT: E 120 ARG cc_start: 0.7597 (OUTLIER) cc_final: 0.7158 (mtp85) REVERT: E 416 ARG cc_start: 0.6737 (ttt180) cc_final: 0.5740 (tpm170) outliers start: 29 outliers final: 19 residues processed: 100 average time/residue: 0.8179 time to fit residues: 97.2323 Evaluate side-chains 102 residues out of total 1845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 81 time to evaluate : 1.776 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 MET 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 280 THR 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 D residue 53 GLU Chi-restraints excluded: chain D residue 58 LEU Chi-restraints excluded: chain D residue 269 VAL 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 236 VAL Chi-restraints excluded: chain E residue 269 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 110 optimal weight: 9.9990 chunk 35 optimal weight: 20.0000 chunk 131 optimal weight: 2.9990 chunk 147 optimal weight: 20.0000 chunk 97 optimal weight: 2.9990 chunk 94 optimal weight: 1.9990 chunk 114 optimal weight: 5.9990 chunk 40 optimal weight: 4.9990 chunk 151 optimal weight: 5.9990 chunk 120 optimal weight: 1.9990 chunk 10 optimal weight: 0.5980 overall best weight: 2.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 125 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.112589 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2937 r_free = 0.2937 target = 0.066276 restraints weight = 32330.920| |-----------------------------------------------------------------------------| r_work (start): 0.2888 rms_B_bonded: 2.43 r_work: 0.2752 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2634 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.2634 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8495 moved from start: 0.3551 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= 0.222 Angle : 0.698 13.054 23410 Z= 0.344 Chirality : 0.046 0.187 2740 Planarity : 0.004 0.038 2845 Dihedral : 7.387 59.237 2505 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.88 % Favored : 94.12 % Rotamer: Outliers : 1.68 % Allowed : 18.92 % Favored : 79.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.75 (0.19), residues: 1955 helix: 0.96 (0.19), residues: 795 sheet: -1.12 (0.24), residues: 375 loop : -1.66 (0.21), residues: 785 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 156 HIS 0.003 0.001 HIS B 18 PHE 0.016 0.002 PHE C 254 TYR 0.014 0.002 TYR C 61 ARG 0.003 0.000 ARG E 28 Details of bonding type rmsd link_NAG-ASN : bond 0.00496 ( 15) link_NAG-ASN : angle 4.47434 ( 45) hydrogen bonds : bond 0.04854 ( 765) hydrogen bonds : angle 4.64935 ( 2190) SS BOND : bond 0.00058 ( 5) SS BOND : angle 0.25474 ( 10) covalent geometry : bond 0.00535 (17095) covalent geometry : angle 0.67105 (23355) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13663.03 seconds wall clock time: 237 minutes 1.95 seconds (14221.95 seconds total)