Starting phenix.real_space_refine on Sun May 18 07:27:50 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8fsb_29418/05_2025/8fsb_29418.cif Found real_map, /net/cci-nas-00/data/ceres_data/8fsb_29418/05_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_29418/05_2025/8fsb_29418.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8fsb_29418/05_2025/8fsb_29418.map" model { file = "/net/cci-nas-00/data/ceres_data/8fsb_29418/05_2025/8fsb_29418.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8fsb_29418/05_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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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: 9.30, per 1000 atoms: 0.56 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 2.1 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: 1.50 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: 5.04 Time building geometry restraints manager: 5.12 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: 1.110 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: 0.570 Check model and map are aligned: 0.110 Set scattering table: 0.140 Process input model: 36.830 Find NCS groups from input model: 0.970 Set up NCS constraints: 0.060 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:13.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 53.500 ------------------------------------------------------------------------------- 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 : 1.763 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: 1.2624 time to fit residues: 299.1855 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 : 1.752 ------------------------------------------------------------------------------- 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 = 56)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.074627 restraints weight = 31845.624| |-----------------------------------------------------------------------------| r_work (start): 0.3056 rms_B_bonded: 2.45 r_work: 0.2929 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.2810 rms_B_bonded: 4.68 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 : 7.167 58.264 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 5.14288 ( 45) hydrogen bonds : bond 0.04196 ( 765) hydrogen bonds : angle 4.68613 ( 2190) SS BOND : bond 0.00148 ( 5) SS BOND : angle 0.24839 ( 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 : 1.733 Fit side-chains REVERT: A 145 ASP cc_start: 0.8139 (m-30) cc_final: 0.7913 (m-30) REVERT: A 410 ARG cc_start: 0.7643 (ttp-170) cc_final: 0.7202 (tpm-80) REVERT: A 411 HIS cc_start: 0.8089 (m90) cc_final: 0.7815 (m-70) REVERT: A 433 LEU cc_start: 0.9062 (mp) cc_final: 0.8837 (mm) REVERT: B 410 ARG cc_start: 0.7645 (ttp-170) cc_final: 0.7289 (tpt90) REVERT: B 411 HIS cc_start: 0.8047 (m90) cc_final: 0.7695 (m-70) REVERT: C 419 MET cc_start: 0.5195 (mmt) cc_final: 0.4952 (tmm) REVERT: D 410 ARG cc_start: 0.7793 (ttp-170) cc_final: 0.7363 (tpt90) REVERT: D 411 HIS cc_start: 0.7809 (m90) cc_final: 0.7350 (m90) REVERT: E 197 LYS cc_start: 0.8579 (OUTLIER) cc_final: 0.8345 (mmtp) REVERT: E 232 ILE cc_start: 0.7989 (mm) cc_final: 0.7722 (mm) REVERT: E 416 ARG cc_start: 0.6461 (ttt180) cc_final: 0.5980 (tpm170) REVERT: E 419 MET cc_start: 0.5361 (mmt) cc_final: 0.5097 (tmm) outliers start: 35 outliers final: 12 residues processed: 123 average time/residue: 0.9352 time to fit residues: 134.0595 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 : 1.745 ------------------------------------------------------------------------------- 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: 0.0970 chunk 93 optimal weight: 0.9980 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: 0.0000 chunk 57 optimal weight: 3.9990 chunk 123 optimal weight: 1.9990 chunk 101 optimal weight: 2.9990 chunk 110 optimal weight: 8.9990 overall best weight: 1.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 22 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.117445 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.071012 restraints weight = 31842.049| |-----------------------------------------------------------------------------| r_work (start): 0.2984 rms_B_bonded: 2.46 r_work: 0.2853 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2733 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.2733 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8403 moved from start: 0.2303 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= 0.141 Angle : 0.605 8.200 23410 Z= 0.305 Chirality : 0.043 0.150 2740 Planarity : 0.004 0.028 2845 Dihedral : 6.950 58.195 2505 Min Nonbonded Distance : 2.300 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 2.06 % Allowed : 11.71 % Favored : 86.23 % 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: 0.74 (0.19), residues: 815 sheet: -0.60 (0.25), residues: 395 loop : -1.69 (0.21), residues: 745 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 156 HIS 0.004 0.001 HIS E 411 PHE 0.014 0.001 PHE A 142 TYR 0.014 0.001 TYR A 61 ARG 0.003 0.000 ARG B 416 Details of bonding type rmsd link_NAG-ASN : bond 0.00635 ( 15) link_NAG-ASN : angle 4.31888 ( 45) hydrogen bonds : bond 0.04201 ( 765) hydrogen bonds : angle 4.49500 ( 2190) SS BOND : bond 0.00029 ( 5) SS BOND : angle 0.30812 ( 10) covalent geometry : bond 0.00325 (17095) covalent geometry : angle 0.57511 (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 122 residues out of total 1845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 84 time to evaluate : 1.921 Fit side-chains REVERT: A 410 ARG cc_start: 0.7603 (ttp-170) cc_final: 0.7194 (tpm-80) REVERT: A 411 HIS cc_start: 0.7992 (m90) cc_final: 0.7684 (m90) REVERT: B 419 MET cc_start: 0.5448 (tmm) cc_final: 0.5232 (tmm) REVERT: D 410 ARG cc_start: 0.7718 (ttp-170) cc_final: 0.7310 (tpt90) REVERT: D 411 HIS cc_start: 0.7742 (m90) cc_final: 0.7282 (m90) REVERT: D 419 MET cc_start: 0.5765 (tmm) cc_final: 0.5565 (tmm) REVERT: E 197 LYS cc_start: 0.8530 (OUTLIER) cc_final: 0.8323 (mmtp) REVERT: E 411 HIS cc_start: 0.7603 (m-70) cc_final: 0.7364 (m90) REVERT: E 416 ARG cc_start: 0.6545 (ttt180) cc_final: 0.6015 (tpm170) outliers start: 38 outliers final: 12 residues processed: 110 average time/residue: 0.9263 time to fit residues: 119.0986 Evaluate side-chains 92 residues out of total 1845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 79 time to evaluate : 1.895 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 280 THR 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: 2.9990 chunk 27 optimal weight: 6.9990 chunk 171 optimal weight: 3.9990 chunk 131 optimal weight: 3.9990 chunk 126 optimal weight: 0.0870 chunk 188 optimal weight: 20.0000 chunk 36 optimal weight: 8.9990 chunk 177 optimal weight: 2.9990 chunk 100 optimal weight: 0.9980 chunk 59 optimal weight: 3.9990 overall best weight: 1.8164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 147 GLN D 161 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.114659 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2971 r_free = 0.2971 target = 0.067983 restraints weight = 31778.561| |-----------------------------------------------------------------------------| r_work (start): 0.2921 rms_B_bonded: 2.43 r_work: 0.2784 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.2665 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.2665 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8478 moved from start: 0.2816 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= 0.201 Angle : 0.668 9.193 23410 Z= 0.336 Chirality : 0.045 0.155 2740 Planarity : 0.004 0.034 2845 Dihedral : 7.318 59.964 2505 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 2.11 % Allowed : 14.04 % Favored : 83.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.82 (0.19), residues: 1955 helix: 0.72 (0.19), residues: 820 sheet: -0.93 (0.25), residues: 375 loop : -1.71 (0.21), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 156 HIS 0.003 0.001 HIS A 119 PHE 0.015 0.002 PHE A 142 TYR 0.018 0.002 TYR C 61 ARG 0.003 0.000 ARG E 28 Details of bonding type rmsd link_NAG-ASN : bond 0.00576 ( 15) link_NAG-ASN : angle 4.48958 ( 45) hydrogen bonds : bond 0.04761 ( 765) hydrogen bonds : angle 4.61244 ( 2190) SS BOND : bond 0.00034 ( 5) SS BOND : angle 0.33951 ( 10) covalent geometry : bond 0.00481 (17095) covalent geometry : angle 0.63862 (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 124 residues out of total 1845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 85 time to evaluate : 2.074 Fit side-chains REVERT: A 410 ARG cc_start: 0.7669 (ttp-170) cc_final: 0.7219 (tpm-80) REVERT: A 411 HIS cc_start: 0.7952 (m90) cc_final: 0.7638 (m90) REVERT: B 419 MET cc_start: 0.5709 (tmm) cc_final: 0.5386 (tmm) REVERT: B 441 TYR cc_start: 0.7555 (OUTLIER) cc_final: 0.7352 (m-80) REVERT: D 410 ARG cc_start: 0.7664 (ttp-170) cc_final: 0.7279 (tpt90) REVERT: D 411 HIS cc_start: 0.7827 (m90) cc_final: 0.7370 (m90) REVERT: D 419 MET cc_start: 0.5934 (tmm) cc_final: 0.5623 (tmm) REVERT: E 416 ARG cc_start: 0.6633 (ttt180) cc_final: 0.5842 (tpm170) outliers start: 39 outliers final: 17 residues processed: 106 average time/residue: 0.9234 time to fit residues: 114.7554 Evaluate side-chains 100 residues out of total 1845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 82 time to evaluate : 1.875 ------------------------------------------------------------------------------- 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 232 ILE Chi-restraints excluded: chain A residue 303 PHE Chi-restraints excluded: chain A residue 441 TYR Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 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 303 PHE Chi-restraints excluded: chain C residue 442 LEU Chi-restraints excluded: chain D residue 441 TYR Chi-restraints excluded: chain E residue 45 MET Chi-restraints excluded: chain E residue 197 LYS Chi-restraints excluded: chain E residue 225 VAL Chi-restraints excluded: chain E residue 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: 4.9990 chunk 158 optimal weight: 1.9990 chunk 48 optimal weight: 1.9990 chunk 150 optimal weight: 5.9990 chunk 58 optimal weight: 1.9990 chunk 164 optimal weight: 0.0070 chunk 5 optimal weight: 2.9990 chunk 136 optimal weight: 0.9980 chunk 60 optimal weight: 4.9990 chunk 189 optimal weight: 4.9990 chunk 130 optimal weight: 0.9980 overall best weight: 1.2002 ------------------------------------------------------------------------------- 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 = 0.3805 r_free = 0.3805 target = 0.115345 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.068896 restraints weight = 32191.571| |-----------------------------------------------------------------------------| r_work (start): 0.2943 rms_B_bonded: 2.43 r_work: 0.2809 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.2690 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.2690 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8433 moved from start: 0.2882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 17115 Z= 0.147 Angle : 0.601 9.475 23410 Z= 0.302 Chirality : 0.043 0.151 2740 Planarity : 0.004 0.033 2845 Dihedral : 7.062 58.360 2505 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 2.82 % Allowed : 14.74 % Favored : 82.44 % 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: -0.71 (0.19), residues: 1955 helix: 0.84 (0.19), residues: 820 sheet: -0.92 (0.25), residues: 375 loop : -1.66 (0.21), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 156 HIS 0.003 0.001 HIS A 18 PHE 0.012 0.001 PHE A 142 TYR 0.014 0.001 TYR E 67 ARG 0.002 0.000 ARG B 416 Details of bonding type rmsd link_NAG-ASN : bond 0.00612 ( 15) link_NAG-ASN : angle 4.24503 ( 45) hydrogen bonds : bond 0.04147 ( 765) hydrogen bonds : angle 4.51022 ( 2190) SS BOND : bond 0.00028 ( 5) SS BOND : angle 0.27956 ( 10) covalent geometry : bond 0.00345 (17095) covalent geometry : angle 0.57204 (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 133 residues out of total 1845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 81 time to evaluate : 2.014 Fit side-chains REVERT: A 291 MET cc_start: 0.7634 (tpp) cc_final: 0.7356 (tpp) REVERT: A 410 ARG cc_start: 0.7617 (ttp-170) cc_final: 0.7172 (tpm-80) REVERT: A 411 HIS cc_start: 0.7751 (m90) cc_final: 0.7422 (m90) REVERT: B 419 MET cc_start: 0.5672 (tmm) cc_final: 0.5288 (tmm) REVERT: C 235 MET cc_start: 0.7440 (pp-130) cc_final: 0.7157 (pp-130) REVERT: C 419 MET cc_start: 0.5315 (mpt) cc_final: 0.4324 (tmm) REVERT: D 116 TYR cc_start: 0.9368 (OUTLIER) cc_final: 0.8591 (m-10) REVERT: D 410 ARG cc_start: 0.7676 (ttp-170) cc_final: 0.7302 (tpt90) REVERT: D 411 HIS cc_start: 0.7806 (m90) cc_final: 0.7360 (m90) REVERT: D 419 MET cc_start: 0.6004 (tmm) cc_final: 0.5730 (tmm) REVERT: E 120 ARG cc_start: 0.7656 (OUTLIER) cc_final: 0.7240 (mtp85) REVERT: E 411 HIS cc_start: 0.7696 (m90) cc_final: 0.7488 (m90) REVERT: E 416 ARG cc_start: 0.6634 (ttt180) cc_final: 0.5771 (tpm170) outliers start: 52 outliers final: 22 residues processed: 112 average time/residue: 1.0397 time to fit residues: 135.9085 Evaluate side-chains 101 residues out of total 1845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 77 time to evaluate : 1.737 ------------------------------------------------------------------------------- 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 303 PHE Chi-restraints excluded: chain A residue 441 TYR Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 303 PHE Chi-restraints excluded: chain B residue 442 LEU Chi-restraints excluded: chain C residue 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 C residue 442 LEU Chi-restraints excluded: chain D residue 53 GLU Chi-restraints excluded: chain D residue 116 TYR Chi-restraints excluded: chain D residue 232 ILE Chi-restraints excluded: chain D residue 317 VAL Chi-restraints excluded: chain D residue 441 TYR Chi-restraints excluded: chain E residue 45 MET Chi-restraints excluded: chain E residue 120 ARG Chi-restraints excluded: chain E residue 225 VAL Chi-restraints excluded: chain E residue 232 ILE Chi-restraints excluded: chain E residue 269 VAL Chi-restraints excluded: chain E residue 441 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 50 optimal weight: 3.9990 chunk 92 optimal weight: 3.9990 chunk 21 optimal weight: 1.9990 chunk 99 optimal weight: 0.8980 chunk 82 optimal weight: 3.9990 chunk 133 optimal weight: 0.5980 chunk 0 optimal weight: 4.9990 chunk 189 optimal weight: 0.5980 chunk 77 optimal weight: 0.9990 chunk 185 optimal weight: 0.8980 chunk 98 optimal weight: 0.6980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 = 0.3819 r_free = 0.3819 target = 0.116378 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.070052 restraints weight = 32118.774| |-----------------------------------------------------------------------------| r_work (start): 0.2967 rms_B_bonded: 2.45 r_work: 0.2834 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.2715 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.2715 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8409 moved from start: 0.2963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 17115 Z= 0.118 Angle : 0.571 10.410 23410 Z= 0.287 Chirality : 0.043 0.150 2740 Planarity : 0.004 0.031 2845 Dihedral : 6.843 56.783 2505 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 1.79 % Allowed : 16.31 % Favored : 81.90 % 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: -0.52 (0.19), residues: 1955 helix: 0.99 (0.19), residues: 825 sheet: -0.77 (0.25), residues: 395 loop : -1.61 (0.22), residues: 735 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 68 HIS 0.002 0.000 HIS A 18 PHE 0.011 0.001 PHE A 142 TYR 0.014 0.001 TYR E 67 ARG 0.002 0.000 ARG B 416 Details of bonding type rmsd link_NAG-ASN : bond 0.00644 ( 15) link_NAG-ASN : angle 3.96170 ( 45) hydrogen bonds : bond 0.03706 ( 765) hydrogen bonds : angle 4.39613 ( 2190) SS BOND : bond 0.00037 ( 5) SS BOND : angle 0.26459 ( 10) covalent geometry : bond 0.00263 (17095) covalent geometry : angle 0.54427 (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: 33 poor density : 79 time to evaluate : 2.003 Fit side-chains REVERT: A 410 ARG cc_start: 0.7536 (ttp-170) cc_final: 0.7146 (tpm-80) REVERT: A 411 HIS cc_start: 0.7741 (m90) cc_final: 0.7413 (m90) REVERT: B 419 MET cc_start: 0.5679 (tmm) cc_final: 0.5287 (tmm) REVERT: C 235 MET cc_start: 0.7298 (pp-130) cc_final: 0.7031 (pp-130) REVERT: C 419 MET cc_start: 0.5231 (mpt) cc_final: 0.4253 (tmm) REVERT: D 116 TYR cc_start: 0.9321 (OUTLIER) cc_final: 0.8499 (m-10) REVERT: D 410 ARG cc_start: 0.7664 (ttp-170) cc_final: 0.7303 (tpt90) REVERT: D 411 HIS cc_start: 0.7786 (m90) cc_final: 0.7343 (m90) REVERT: D 419 MET cc_start: 0.5994 (tmm) cc_final: 0.5719 (tmm) REVERT: E 120 ARG cc_start: 0.7557 (OUTLIER) cc_final: 0.7116 (mtp85) REVERT: E 411 HIS cc_start: 0.7777 (m90) cc_final: 0.7533 (m90) REVERT: E 416 ARG cc_start: 0.6613 (ttt180) cc_final: 0.5765 (tpm170) outliers start: 33 outliers final: 16 residues processed: 94 average time/residue: 0.9968 time to fit residues: 109.1200 Evaluate side-chains 96 residues out of total 1845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 78 time to evaluate : 1.797 ------------------------------------------------------------------------------- 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 232 ILE Chi-restraints excluded: chain B residue 280 THR Chi-restraints excluded: chain B residue 303 PHE 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 53 GLU Chi-restraints excluded: chain D residue 116 TYR 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 197 LYS Chi-restraints excluded: chain E residue 225 VAL Chi-restraints excluded: chain E residue 232 ILE Chi-restraints excluded: chain E residue 269 VAL Chi-restraints excluded: chain E residue 441 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 33 optimal weight: 6.9990 chunk 106 optimal weight: 0.9990 chunk 193 optimal weight: 0.9980 chunk 12 optimal weight: 2.9990 chunk 171 optimal weight: 3.9990 chunk 109 optimal weight: 7.9990 chunk 115 optimal weight: 6.9990 chunk 186 optimal weight: 0.0170 chunk 62 optimal weight: 0.0970 chunk 150 optimal weight: 0.9990 chunk 108 optimal weight: 10.0000 overall best weight: 0.6220 ------------------------------------------------------------------------------- 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 = 0.3827 r_free = 0.3827 target = 0.116868 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.070670 restraints weight = 31975.693| |-----------------------------------------------------------------------------| r_work (start): 0.2981 rms_B_bonded: 2.46 r_work: 0.2852 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2733 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.2733 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8390 moved from start: 0.3041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 17115 Z= 0.110 Angle : 0.556 11.374 23410 Z= 0.279 Chirality : 0.042 0.150 2740 Planarity : 0.003 0.030 2845 Dihedral : 6.723 56.567 2505 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 1.79 % Allowed : 17.02 % Favored : 81.19 % 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: -0.41 (0.19), residues: 1955 helix: 1.09 (0.19), residues: 825 sheet: -0.70 (0.25), residues: 395 loop : -1.55 (0.22), residues: 735 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 156 HIS 0.002 0.000 HIS A 18 PHE 0.009 0.001 PHE A 142 TYR 0.014 0.001 TYR A 67 ARG 0.002 0.000 ARG B 416 Details of bonding type rmsd link_NAG-ASN : bond 0.00644 ( 15) link_NAG-ASN : angle 3.76338 ( 45) hydrogen bonds : bond 0.03479 ( 765) hydrogen bonds : angle 4.31457 ( 2190) SS BOND : bond 0.00028 ( 5) SS BOND : angle 0.23794 ( 10) covalent geometry : bond 0.00245 (17095) covalent geometry : angle 0.53201 (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 115 residues out of total 1845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 82 time to evaluate : 1.664 Fit side-chains REVERT: A 291 MET cc_start: 0.7768 (tpp) cc_final: 0.7506 (tpp) REVERT: A 410 ARG cc_start: 0.7478 (ttp-170) cc_final: 0.7152 (tpm-80) REVERT: A 411 HIS cc_start: 0.7723 (m90) cc_final: 0.7392 (m90) REVERT: B 419 MET cc_start: 0.5844 (tmm) cc_final: 0.5448 (tmm) REVERT: B 441 TYR cc_start: 0.7372 (OUTLIER) cc_final: 0.7153 (m-80) REVERT: C 235 MET cc_start: 0.7184 (OUTLIER) cc_final: 0.6930 (pp-130) REVERT: D 116 TYR cc_start: 0.9301 (OUTLIER) cc_final: 0.8477 (m-10) REVERT: D 410 ARG cc_start: 0.7699 (ttp-170) cc_final: 0.7366 (tpm170) REVERT: D 411 HIS cc_start: 0.7871 (m90) cc_final: 0.7548 (m90) REVERT: D 419 MET cc_start: 0.6041 (tmm) cc_final: 0.5781 (tmm) REVERT: E 411 HIS cc_start: 0.7806 (m90) cc_final: 0.7532 (m90) REVERT: E 416 ARG cc_start: 0.6669 (ttt180) cc_final: 0.5787 (tpm170) outliers start: 33 outliers final: 15 residues processed: 100 average time/residue: 0.9068 time to fit residues: 105.9531 Evaluate side-chains 96 residues out of total 1845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 78 time to evaluate : 1.694 ------------------------------------------------------------------------------- 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 441 TYR Chi-restraints excluded: chain C residue 232 ILE Chi-restraints excluded: chain C residue 235 MET 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 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=2.00 ------------------------------------------------------------------------------- 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: 0.8980 chunk 168 optimal weight: 0.8980 chunk 179 optimal weight: 0.9980 chunk 2 optimal weight: 0.9990 chunk 66 optimal weight: 0.0770 chunk 10 optimal weight: 2.9990 chunk 33 optimal weight: 5.9990 chunk 136 optimal weight: 2.9990 chunk 164 optimal weight: 2.9990 overall best weight: 0.7740 ------------------------------------------------------------------------------- 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 = 0.3822 r_free = 0.3822 target = 0.116483 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.070238 restraints weight = 31887.250| |-----------------------------------------------------------------------------| r_work (start): 0.2971 rms_B_bonded: 2.45 r_work: 0.2839 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2721 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.2721 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8401 moved from start: 0.3106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 17115 Z= 0.118 Angle : 0.574 11.624 23410 Z= 0.286 Chirality : 0.042 0.149 2740 Planarity : 0.004 0.031 2845 Dihedral : 6.767 56.959 2505 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 1.95 % Allowed : 17.07 % Favored : 80.98 % 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: -0.37 (0.19), residues: 1955 helix: 1.11 (0.19), residues: 825 sheet: -0.69 (0.25), residues: 395 loop : -1.52 (0.22), residues: 735 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 156 HIS 0.002 0.000 HIS A 18 PHE 0.008 0.001 PHE A 142 TYR 0.014 0.001 TYR E 67 ARG 0.002 0.000 ARG B 416 Details of bonding type rmsd link_NAG-ASN : bond 0.00622 ( 15) link_NAG-ASN : angle 3.76151 ( 45) hydrogen bonds : bond 0.03585 ( 765) hydrogen bonds : angle 4.31158 ( 2190) SS BOND : bond 0.00017 ( 5) SS BOND : angle 0.21414 ( 10) covalent geometry : bond 0.00268 (17095) covalent geometry : angle 0.55048 (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 117 residues out of total 1845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 81 time to evaluate : 1.785 Fit side-chains REVERT: A 410 ARG cc_start: 0.7495 (ttp-170) cc_final: 0.7159 (tpm-80) REVERT: A 411 HIS cc_start: 0.7740 (m90) cc_final: 0.7422 (m90) REVERT: B 419 MET cc_start: 0.5712 (tmm) cc_final: 0.5340 (tmm) REVERT: C 203 ILE cc_start: 0.9323 (OUTLIER) cc_final: 0.9111 (pp) REVERT: C 235 MET cc_start: 0.7189 (OUTLIER) cc_final: 0.6936 (pp-130) REVERT: D 116 TYR cc_start: 0.9309 (OUTLIER) cc_final: 0.8489 (m-10) REVERT: D 410 ARG cc_start: 0.7695 (ttp-170) cc_final: 0.7333 (tpt90) REVERT: D 411 HIS cc_start: 0.7872 (m90) cc_final: 0.7403 (m90) REVERT: D 419 MET cc_start: 0.6096 (tmm) cc_final: 0.5831 (tmm) REVERT: E 120 ARG cc_start: 0.7557 (OUTLIER) cc_final: 0.6987 (mmp80) REVERT: E 411 HIS cc_start: 0.7835 (m90) cc_final: 0.7543 (m90) REVERT: E 416 ARG cc_start: 0.6707 (ttt180) cc_final: 0.5781 (tpm170) outliers start: 36 outliers final: 16 residues processed: 101 average time/residue: 0.8588 time to fit residues: 102.1794 Evaluate side-chains 98 residues out of total 1845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 78 time to evaluate : 1.704 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 303 PHE Chi-restraints excluded: chain A residue 441 TYR Chi-restraints excluded: chain B residue 58 LEU Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 280 THR Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 232 ILE Chi-restraints excluded: chain C residue 235 MET Chi-restraints excluded: chain C residue 303 PHE Chi-restraints excluded: chain C residue 441 TYR 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 120 ARG 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 188 optimal weight: 0.9980 chunk 133 optimal weight: 0.9990 chunk 191 optimal weight: 7.9990 chunk 28 optimal weight: 6.9990 chunk 38 optimal weight: 1.9990 chunk 174 optimal weight: 0.8980 chunk 48 optimal weight: 3.9990 chunk 76 optimal weight: 5.9990 chunk 98 optimal weight: 2.9990 chunk 176 optimal weight: 0.9980 chunk 141 optimal weight: 5.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- 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 = 0.3805 r_free = 0.3805 target = 0.115361 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2992 r_free = 0.2992 target = 0.068859 restraints weight = 32083.215| |-----------------------------------------------------------------------------| r_work (start): 0.2944 rms_B_bonded: 2.44 r_work: 0.2810 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2691 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.2691 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8426 moved from start: 0.3195 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= 0.146 Angle : 0.616 12.124 23410 Z= 0.304 Chirality : 0.043 0.158 2740 Planarity : 0.004 0.034 2845 Dihedral : 6.948 58.726 2505 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 1.46 % Allowed : 17.94 % Favored : 80.60 % 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: -0.42 (0.19), residues: 1955 helix: 1.08 (0.19), residues: 825 sheet: -0.77 (0.24), residues: 395 loop : -1.53 (0.22), residues: 735 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 156 HIS 0.002 0.000 HIS B 18 PHE 0.009 0.001 PHE A 199 TYR 0.013 0.001 TYR D 67 ARG 0.002 0.000 ARG C 306 Details of bonding type rmsd link_NAG-ASN : bond 0.00589 ( 15) link_NAG-ASN : angle 3.92783 ( 45) hydrogen bonds : bond 0.03990 ( 765) hydrogen bonds : angle 4.37282 ( 2190) SS BOND : bond 0.00023 ( 5) SS BOND : angle 0.22773 ( 10) covalent geometry : bond 0.00340 (17095) covalent geometry : angle 0.59179 (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 106 residues out of total 1845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 79 time to evaluate : 1.736 Fit side-chains REVERT: A 410 ARG cc_start: 0.7500 (ttp-170) cc_final: 0.7162 (tpm-80) REVERT: A 411 HIS cc_start: 0.7708 (m90) cc_final: 0.7397 (m90) REVERT: B 419 MET cc_start: 0.5649 (tmm) cc_final: 0.5353 (tmm) REVERT: C 203 ILE cc_start: 0.9339 (OUTLIER) cc_final: 0.9128 (pp) REVERT: C 235 MET cc_start: 0.7268 (OUTLIER) cc_final: 0.7012 (pp-130) REVERT: D 116 TYR cc_start: 0.9347 (OUTLIER) cc_final: 0.8583 (m-10) REVERT: D 410 ARG cc_start: 0.7704 (ttp-170) cc_final: 0.7333 (tpt90) REVERT: D 411 HIS cc_start: 0.7974 (m90) cc_final: 0.7490 (m90) REVERT: E 120 ARG cc_start: 0.7592 (OUTLIER) cc_final: 0.7033 (mmp80) REVERT: E 411 HIS cc_start: 0.7676 (m90) cc_final: 0.7447 (m90) REVERT: E 416 ARG cc_start: 0.6701 (ttt180) cc_final: 0.5836 (tpm170) outliers start: 27 outliers final: 15 residues processed: 93 average time/residue: 0.9756 time to fit residues: 105.9319 Evaluate side-chains 96 residues out of total 1845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 77 time to evaluate : 1.977 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 232 ILE 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 203 ILE Chi-restraints excluded: chain C residue 232 ILE Chi-restraints excluded: chain C residue 235 MET Chi-restraints excluded: chain C residue 303 PHE Chi-restraints excluded: chain C residue 441 TYR Chi-restraints excluded: chain D residue 53 GLU Chi-restraints excluded: chain D residue 116 TYR 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 110 optimal weight: 7.9990 chunk 65 optimal weight: 10.0000 chunk 107 optimal weight: 6.9990 chunk 36 optimal weight: 3.9990 chunk 44 optimal weight: 0.9990 chunk 111 optimal weight: 5.9990 chunk 136 optimal weight: 0.9990 chunk 140 optimal weight: 6.9990 chunk 101 optimal weight: 2.9990 chunk 162 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- 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 = 0.3783 r_free = 0.3783 target = 0.113908 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.2963 r_free = 0.2963 target = 0.067488 restraints weight = 32209.760| |-----------------------------------------------------------------------------| r_work (start): 0.2913 rms_B_bonded: 2.43 r_work: 0.2778 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2658 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.2658 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8476 moved from start: 0.3326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 17115 Z= 0.196 Angle : 0.666 12.772 23410 Z= 0.330 Chirality : 0.045 0.154 2740 Planarity : 0.004 0.038 2845 Dihedral : 7.243 59.328 2505 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer: Outliers : 1.73 % Allowed : 17.89 % Favored : 80.38 % 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: 0.93 (0.19), residues: 825 sheet: -0.97 (0.24), residues: 375 loop : -1.56 (0.21), residues: 755 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 156 HIS 0.003 0.001 HIS B 18 PHE 0.011 0.001 PHE C 80 TYR 0.014 0.002 TYR C 61 ARG 0.002 0.000 ARG A 28 Details of bonding type rmsd link_NAG-ASN : bond 0.00560 ( 15) link_NAG-ASN : angle 4.24893 ( 45) hydrogen bonds : bond 0.04565 ( 765) hydrogen bonds : angle 4.48765 ( 2190) SS BOND : bond 0.00040 ( 5) SS BOND : angle 0.24314 ( 10) covalent geometry : bond 0.00469 (17095) covalent geometry : angle 0.64012 (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 114 residues out of total 1845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 82 time to evaluate : 1.998 Fit side-chains REVERT: B 419 MET cc_start: 0.5851 (tmm) cc_final: 0.5598 (tmm) REVERT: C 235 MET cc_start: 0.7446 (OUTLIER) cc_final: 0.7236 (pp-130) REVERT: D 410 ARG cc_start: 0.7730 (ttp-170) cc_final: 0.7318 (tpt90) REVERT: D 411 HIS cc_start: 0.7889 (m90) cc_final: 0.7425 (m90) REVERT: E 120 ARG cc_start: 0.7741 (OUTLIER) cc_final: 0.7248 (mtp85) REVERT: E 411 HIS cc_start: 0.7598 (m90) cc_final: 0.7365 (m90) REVERT: E 416 ARG cc_start: 0.6673 (ttt180) cc_final: 0.5732 (tpm170) outliers start: 32 outliers final: 15 residues processed: 100 average time/residue: 0.9227 time to fit residues: 108.0359 Evaluate side-chains 98 residues out of total 1845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 81 time to evaluate : 1.732 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 269 VAL Chi-restraints excluded: chain B residue 280 THR Chi-restraints excluded: chain B residue 303 PHE Chi-restraints excluded: chain C residue 232 ILE Chi-restraints excluded: chain C residue 235 MET Chi-restraints excluded: chain C residue 441 TYR Chi-restraints excluded: chain D residue 53 GLU 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 197 LYS 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: 8.9990 chunk 35 optimal weight: 0.9990 chunk 131 optimal weight: 3.9990 chunk 147 optimal weight: 0.5980 chunk 97 optimal weight: 5.9990 chunk 94 optimal weight: 0.9990 chunk 114 optimal weight: 3.9990 chunk 40 optimal weight: 0.0270 chunk 151 optimal weight: 0.7980 chunk 120 optimal weight: 0.9980 chunk 10 optimal weight: 0.2980 overall best weight: 0.5438 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.116506 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.070493 restraints weight = 32170.931| |-----------------------------------------------------------------------------| r_work (start): 0.2977 rms_B_bonded: 2.45 r_work: 0.2846 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2727 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.2727 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8393 moved from start: 0.3308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 17115 Z= 0.112 Angle : 0.591 12.478 23410 Z= 0.291 Chirality : 0.043 0.149 2740 Planarity : 0.004 0.031 2845 Dihedral : 6.834 56.742 2505 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 0.98 % Allowed : 19.08 % Favored : 79.95 % 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: -0.47 (0.19), residues: 1955 helix: 1.03 (0.19), residues: 825 sheet: -0.85 (0.24), residues: 395 loop : -1.51 (0.22), residues: 735 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 68 HIS 0.002 0.000 HIS A 18 PHE 0.008 0.001 PHE A 153 TYR 0.014 0.001 TYR D 67 ARG 0.002 0.000 ARG A 306 Details of bonding type rmsd link_NAG-ASN : bond 0.00642 ( 15) link_NAG-ASN : angle 3.77871 ( 45) hydrogen bonds : bond 0.03529 ( 765) hydrogen bonds : angle 4.34070 ( 2190) SS BOND : bond 0.00024 ( 5) SS BOND : angle 0.34599 ( 10) covalent geometry : bond 0.00248 (17095) covalent geometry : angle 0.56831 (23355) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12101.89 seconds wall clock time: 208 minutes 24.42 seconds (12504.42 seconds total)