Starting phenix.real_space_refine on Thu Feb 5 11:08:10 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9atr_43834/02_2026/9atr_43834.cif Found real_map, /net/cci-nas-00/data/ceres_data/9atr_43834/02_2026/9atr_43834.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9atr_43834/02_2026/9atr_43834.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9atr_43834/02_2026/9atr_43834.map" model { file = "/net/cci-nas-00/data/ceres_data/9atr_43834/02_2026/9atr_43834.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9atr_43834/02_2026/9atr_43834.cif" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.010 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 66 5.16 5 C 10535 2.51 5 N 2731 2.21 5 O 3131 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 16463 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 4473 Number of conformers: 1 Conformer: "" Number of residues, atoms: 562, 4473 Classifications: {'peptide': 562} Link IDs: {'PTRANS': 32, 'TRANS': 529} Chain breaks: 4 Chain: "B" Number of atoms: 4473 Number of conformers: 1 Conformer: "" Number of residues, atoms: 562, 4473 Classifications: {'peptide': 562} Link IDs: {'PTRANS': 32, 'TRANS': 529} Chain breaks: 4 Chain: "C" Number of atoms: 4473 Number of conformers: 1 Conformer: "" Number of residues, atoms: 562, 4473 Classifications: {'peptide': 562} Link IDs: {'PTRANS': 32, 'TRANS': 529} Chain breaks: 4 Chain: "F" Number of atoms: 968 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 968 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 3, 'TRANS': 125} Chain: "E" Number of atoms: 968 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 968 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 3, 'TRANS': 125} Chain: "H" Number of atoms: 968 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 968 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 3, 'TRANS': 125} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "C" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 3.52, per 1000 atoms: 0.21 Number of scatterers: 16463 At special positions: 0 Unit cell: (156.704, 159.36, 129.259, 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 66 16.00 O 3131 8.00 N 2731 7.00 C 10535 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=24, symmetry=0 Simple disulfide: pdb=" SG CYS A 128 " - pdb=" SG CYS A 162 " distance=2.03 Simple disulfide: pdb=" SG CYS A 287 " - pdb=" SG CYS A 297 " distance=2.03 Simple disulfide: pdb=" SG CYS A 332 " - pdb=" SG CYS A 357 " distance=2.03 Simple disulfide: pdb=" SG CYS A 375 " - pdb=" SG CYS A 428 " distance=2.03 Simple disulfide: pdb=" SG CYS A 387 " - pdb=" SG CYS A 521 " distance=2.03 Simple disulfide: pdb=" SG CYS A 476 " - pdb=" SG CYS A 484 " distance=2.03 Simple disulfide: pdb=" SG CYS A 534 " - pdb=" SG CYS A 586 " distance=2.03 Simple disulfide: pdb=" SG CYS B 128 " - pdb=" SG CYS B 162 " distance=2.03 Simple disulfide: pdb=" SG CYS B 287 " - pdb=" SG CYS B 297 " distance=2.03 Simple disulfide: pdb=" SG CYS B 332 " - pdb=" SG CYS B 357 " distance=2.03 Simple disulfide: pdb=" SG CYS B 375 " - pdb=" SG CYS B 428 " distance=2.03 Simple disulfide: pdb=" SG CYS B 387 " - pdb=" SG CYS B 521 " distance=2.04 Simple disulfide: pdb=" SG CYS B 476 " - pdb=" SG CYS B 484 " distance=2.03 Simple disulfide: pdb=" SG CYS B 534 " - pdb=" SG CYS B 586 " distance=2.03 Simple disulfide: pdb=" SG CYS C 128 " - pdb=" SG CYS C 162 " distance=2.04 Simple disulfide: pdb=" SG CYS C 287 " - pdb=" SG CYS C 297 " distance=2.03 Simple disulfide: pdb=" SG CYS C 332 " - pdb=" SG CYS C 357 " distance=2.03 Simple disulfide: pdb=" SG CYS C 375 " - pdb=" SG CYS C 428 " distance=2.03 Simple disulfide: pdb=" SG CYS C 387 " - pdb=" SG CYS C 521 " distance=2.03 Simple disulfide: pdb=" SG CYS C 476 " - pdb=" SG CYS C 484 " distance=2.03 Simple disulfide: pdb=" SG CYS C 534 " - pdb=" SG CYS C 586 " distance=2.03 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 96 " distance=2.03 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " NAG-ASN " NAG A1300 " - " ASN A 58 " " NAG A1301 " - " ASN A 278 " " NAG B1300 " - " ASN B 58 " " NAG B1301 " - " ASN B 119 " " NAG B1302 " - " ASN B 161 " " NAG B1303 " - " ASN B 278 " " NAG B1304 " - " ASN B 327 " " NAG C1301 " - " ASN C 230 " " NAG D 1 " - " ASN C 58 " Time building additional restraints: 1.18 Conformation dependent library (CDL) restraints added in 681.4 milliseconds 4074 Ramachandran restraints generated. 2037 Oldfield, 0 Emsley, 2037 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: 24 helices and 38 sheets defined 7.5% alpha, 32.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.53 Creating SS restraints... Processing helix chain 'A' and resid 290 through 300 Processing helix chain 'A' and resid 333 through 337 removed outlier: 3.757A pdb=" N GLU A 336 " --> pdb=" O PRO A 333 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N VAL A 337 " --> pdb=" O PHE A 334 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 333 through 337' Processing helix chain 'A' and resid 360 through 367 removed outlier: 3.770A pdb=" N TYR A 365 " --> pdb=" O SER A 362 " (cutoff:3.500A) Processing helix chain 'A' and resid 379 through 383 removed outlier: 3.780A pdb=" N LEU A 383 " --> pdb=" O PRO A 380 " (cutoff:3.500A) Processing helix chain 'A' and resid 400 through 406 removed outlier: 3.811A pdb=" N SER A 404 " --> pdb=" O ASN A 401 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ILE A 406 " --> pdb=" O VAL A 403 " (cutoff:3.500A) Processing helix chain 'A' and resid 412 through 418 removed outlier: 3.510A pdb=" N TYR A 417 " --> pdb=" O ASN A 413 " (cutoff:3.500A) Processing helix chain 'A' and resid 498 through 502 Processing helix chain 'B' and resid 290 through 300 Processing helix chain 'B' and resid 333 through 339 Processing helix chain 'B' and resid 363 through 367 removed outlier: 3.769A pdb=" N ASN B 366 " --> pdb=" O VAL B 363 " (cutoff:3.500A) Processing helix chain 'B' and resid 412 through 418 Processing helix chain 'B' and resid 498 through 501 Processing helix chain 'C' and resid 151 through 155 removed outlier: 4.372A pdb=" N ARG C 154 " --> pdb=" O SER C 151 " (cutoff:3.500A) Processing helix chain 'C' and resid 290 through 300 Processing helix chain 'C' and resid 333 through 339 removed outlier: 4.312A pdb=" N VAL C 337 " --> pdb=" O PRO C 333 " (cutoff:3.500A) Processing helix chain 'C' and resid 360 through 367 removed outlier: 3.576A pdb=" N VAL C 363 " --> pdb=" O ASP C 360 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N TYR C 365 " --> pdb=" O SER C 362 " (cutoff:3.500A) Processing helix chain 'C' and resid 379 through 383 removed outlier: 4.070A pdb=" N LEU C 383 " --> pdb=" O PRO C 380 " (cutoff:3.500A) Processing helix chain 'C' and resid 400 through 406 removed outlier: 3.602A pdb=" N VAL C 403 " --> pdb=" O GLY C 400 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N SER C 404 " --> pdb=" O ASN C 401 " (cutoff:3.500A) Processing helix chain 'C' and resid 412 through 418 Processing helix chain 'C' and resid 498 through 502 Processing helix chain 'F' and resid 87 through 91 Processing helix chain 'E' and resid 87 through 91 Processing helix chain 'H' and resid 62 through 65 removed outlier: 3.643A pdb=" N LYS H 65 " --> pdb=" O ASP H 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 62 through 65' Processing helix chain 'H' and resid 87 through 91 Processing sheet with id=AA1, first strand: chain 'A' and resid 20 through 27 removed outlier: 3.640A pdb=" N THR A 60 " --> pdb=" O VAL A 263 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N VAL A 263 " --> pdb=" O THR A 60 " (cutoff:3.500A) removed outlier: 5.820A pdb=" N SER A 201 " --> pdb=" O PRO A 221 " (cutoff:3.500A) removed outlier: 9.328A pdb=" N HIS A 203 " --> pdb=" O LEU A 219 " (cutoff:3.500A) removed outlier: 9.457A pdb=" N LEU A 219 " --> pdb=" O HIS A 203 " (cutoff:3.500A) removed outlier: 7.079A pdb=" N VAL A 33 " --> pdb=" O LEU A 219 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 45 through 52 removed outlier: 3.959A pdb=" N ASP A 283 " --> pdb=" O LYS A 274 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 81 through 82 removed outlier: 3.826A pdb=" N LEU A 237 " --> pdb=" O GLY A 100 " (cutoff:3.500A) removed outlier: 4.933A pdb=" N GLY A 100 " --> pdb=" O LEU A 237 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N ARG A 99 " --> pdb=" O ASN A 118 " (cutoff:3.500A) removed outlier: 5.268A pdb=" N ASN A 118 " --> pdb=" O ARG A 99 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N CYS A 128 " --> pdb=" O SER A 113 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N LYS A 126 " --> pdb=" O LEU A 115 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N PHE A 164 " --> pdb=" O VAL A 127 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 307 through 315 removed outlier: 5.475A pdb=" N ILE A 308 " --> pdb=" O THR A 595 " (cutoff:3.500A) removed outlier: 7.604A pdb=" N THR A 595 " --> pdb=" O ILE A 308 " (cutoff:3.500A) removed outlier: 5.673A pdb=" N GLN A 310 " --> pdb=" O VAL A 593 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N VAL A 593 " --> pdb=" O GLN A 310 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N SER A 312 " --> pdb=" O VAL A 591 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 352 through 354 Processing sheet with id=AA6, first strand: chain 'A' and resid 448 through 449 Processing sheet with id=AA7, first strand: chain 'A' and resid 469 through 470 Processing sheet with id=AA8, first strand: chain 'A' and resid 534 through 539 removed outlier: 4.210A pdb=" N GLU A 579 " --> pdb=" O ASP A 574 " (cutoff:3.500A) removed outlier: 5.637A pdb=" N ASP A 570 " --> pdb=" O ILE A 583 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N GLY A 562 " --> pdb=" O ASP A 570 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 20 through 27 removed outlier: 7.899A pdb=" N ASN B 58 " --> pdb=" O TYR B 265 " (cutoff:3.500A) removed outlier: 7.079A pdb=" N TYR B 265 " --> pdb=" O ASN B 58 " (cutoff:3.500A) removed outlier: 5.918A pdb=" N SER B 201 " --> pdb=" O PRO B 221 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 45 through 52 removed outlier: 3.750A pdb=" N ASP B 283 " --> pdb=" O LYS B 274 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 81 through 82 removed outlier: 4.400A pdb=" N GLY B 100 " --> pdb=" O LEU B 237 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 113 through 114 removed outlier: 3.506A pdb=" N SER B 113 " --> pdb=" O CYS B 128 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N CYS B 128 " --> pdb=" O SER B 113 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 113 through 114 removed outlier: 3.506A pdb=" N SER B 113 " --> pdb=" O CYS B 128 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N CYS B 128 " --> pdb=" O SER B 113 " (cutoff:3.500A) removed outlier: 11.330A pdb=" N VAL B 123 " --> pdb=" O GLU B 165 " (cutoff:3.500A) removed outlier: 9.954A pdb=" N GLU B 165 " --> pdb=" O VAL B 123 " (cutoff:3.500A) removed outlier: 10.929A pdb=" N ILE B 125 " --> pdb=" O THR B 163 " (cutoff:3.500A) removed outlier: 8.468A pdb=" N THR B 163 " --> pdb=" O ILE B 125 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N VAL B 127 " --> pdb=" O ASN B 161 " (cutoff:3.500A) removed outlier: 7.190A pdb=" N ASN B 161 " --> pdb=" O VAL B 127 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N GLU B 129 " --> pdb=" O ALA B 159 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N ALA B 159 " --> pdb=" O GLU B 129 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N GLN B 131 " --> pdb=" O SER B 157 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 307 through 315 removed outlier: 5.343A pdb=" N ILE B 308 " --> pdb=" O THR B 595 " (cutoff:3.500A) removed outlier: 7.640A pdb=" N THR B 595 " --> pdb=" O ILE B 308 " (cutoff:3.500A) removed outlier: 5.763A pdb=" N GLN B 310 " --> pdb=" O VAL B 593 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N VAL B 593 " --> pdb=" O GLN B 310 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N SER B 312 " --> pdb=" O VAL B 591 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N GLY B 590 " --> pdb=" O GLN B 609 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 321 through 324 Processing sheet with id=AB7, first strand: chain 'B' and resid 352 through 354 Processing sheet with id=AB8, first strand: chain 'B' and resid 357 through 358 removed outlier: 6.516A pdb=" N CYS B 357 " --> pdb=" O CYS B 521 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'B' and resid 448 through 449 Processing sheet with id=AC1, first strand: chain 'B' and resid 469 through 470 Processing sheet with id=AC2, first strand: chain 'C' and resid 20 through 27 removed outlier: 7.389A pdb=" N ASN C 58 " --> pdb=" O TYR C 265 " (cutoff:3.500A) removed outlier: 6.154A pdb=" N TYR C 265 " --> pdb=" O ASN C 58 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N VAL C 263 " --> pdb=" O THR C 60 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N VAL C 223 " --> pdb=" O ILE C 199 " (cutoff:3.500A) removed outlier: 5.984A pdb=" N SER C 201 " --> pdb=" O PRO C 221 " (cutoff:3.500A) removed outlier: 9.276A pdb=" N HIS C 203 " --> pdb=" O LEU C 219 " (cutoff:3.500A) removed outlier: 9.212A pdb=" N LEU C 219 " --> pdb=" O HIS C 203 " (cutoff:3.500A) removed outlier: 7.619A pdb=" N VAL C 33 " --> pdb=" O LEU C 219 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 45 through 52 removed outlier: 3.825A pdb=" N ASP C 283 " --> pdb=" O LYS C 274 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 81 through 82 removed outlier: 3.741A pdb=" N LEU C 237 " --> pdb=" O GLY C 100 " (cutoff:3.500A) removed outlier: 4.756A pdb=" N GLY C 100 " --> pdb=" O LEU C 237 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 123 through 127 removed outlier: 3.570A pdb=" N PHE C 164 " --> pdb=" O VAL C 127 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 307 through 315 removed outlier: 5.383A pdb=" N ILE C 308 " --> pdb=" O THR C 595 " (cutoff:3.500A) removed outlier: 7.400A pdb=" N THR C 595 " --> pdb=" O ILE C 308 " (cutoff:3.500A) removed outlier: 5.546A pdb=" N GLN C 310 " --> pdb=" O VAL C 593 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N VAL C 593 " --> pdb=" O GLN C 310 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N SER C 312 " --> pdb=" O VAL C 591 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 321 through 323 removed outlier: 6.764A pdb=" N ILE C 322 " --> pdb=" O ASN C 538 " (cutoff:3.500A) removed outlier: 5.655A pdb=" N ASP C 570 " --> pdb=" O ILE C 583 " (cutoff:3.500A) removed outlier: 7.301A pdb=" N GLY C 562 " --> pdb=" O ASP C 570 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 350 through 354 Processing sheet with id=AC9, first strand: chain 'C' and resid 448 through 449 Processing sheet with id=AD1, first strand: chain 'C' and resid 469 through 470 Processing sheet with id=AD2, first strand: chain 'F' and resid 3 through 7 removed outlier: 3.592A pdb=" N LEU F 20 " --> pdb=" O LEU F 81 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'F' and resid 10 through 12 removed outlier: 6.320A pdb=" N GLY F 10 " --> pdb=" O THR F 126 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'F' and resid 10 through 12 removed outlier: 6.320A pdb=" N GLY F 10 " --> pdb=" O THR F 126 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'F' and resid 50 through 51 Processing sheet with id=AD6, first strand: chain 'E' and resid 3 through 7 Processing sheet with id=AD7, first strand: chain 'E' and resid 10 through 12 removed outlier: 6.074A pdb=" N GLY E 10 " --> pdb=" O THR E 126 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N TRP E 36 " --> pdb=" O VAL E 48 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'E' and resid 10 through 12 removed outlier: 6.074A pdb=" N GLY E 10 " --> pdb=" O THR E 126 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AE1, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.108A pdb=" N GLY H 10 " --> pdb=" O THR H 126 " (cutoff:3.500A) removed outlier: 7.207A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ARG H 38 " --> pdb=" O GLU H 46 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.108A pdb=" N GLY H 10 " --> pdb=" O THR H 126 " (cutoff:3.500A) 493 hydrogen bonds defined for protein. 1179 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.43 Time building geometry restraints manager: 1.55 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 5185 1.34 - 1.46: 4143 1.46 - 1.58: 7474 1.58 - 1.70: 0 1.70 - 1.83: 72 Bond restraints: 16874 Sorted by residual: bond pdb=" N ASP C 135 " pdb=" CA ASP C 135 " ideal model delta sigma weight residual 1.456 1.489 -0.033 1.13e-02 7.83e+03 8.52e+00 bond pdb=" N PHE C 164 " pdb=" CA PHE C 164 " ideal model delta sigma weight residual 1.455 1.491 -0.036 1.26e-02 6.30e+03 8.14e+00 bond pdb=" N LEU A 529 " pdb=" CA LEU A 529 " ideal model delta sigma weight residual 1.462 1.496 -0.034 1.23e-02 6.61e+03 7.54e+00 bond pdb=" N CYS C 162 " pdb=" CA CYS C 162 " ideal model delta sigma weight residual 1.456 1.490 -0.034 1.27e-02 6.20e+03 7.01e+00 bond pdb=" N ASN C 160 " pdb=" CA ASN C 160 " ideal model delta sigma weight residual 1.456 1.488 -0.033 1.25e-02 6.40e+03 6.87e+00 ... (remaining 16869 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.53: 22689 2.53 - 5.06: 240 5.06 - 7.58: 13 7.58 - 10.11: 2 10.11 - 12.64: 1 Bond angle restraints: 22945 Sorted by residual: angle pdb=" C PHE B 29 " pdb=" CA PHE B 29 " pdb=" CB PHE B 29 " ideal model delta sigma weight residual 116.54 110.61 5.93 1.15e+00 7.56e-01 2.66e+01 angle pdb=" CB MET C 173 " pdb=" CG MET C 173 " pdb=" SD MET C 173 " ideal model delta sigma weight residual 112.70 125.34 -12.64 3.00e+00 1.11e-01 1.77e+01 angle pdb=" CA ASN C 160 " pdb=" C ASN C 160 " pdb=" O ASN C 160 " ideal model delta sigma weight residual 121.55 117.45 4.10 1.06e+00 8.90e-01 1.50e+01 angle pdb=" CA ASN C 230 " pdb=" C ASN C 230 " pdb=" O ASN C 230 " ideal model delta sigma weight residual 120.98 117.14 3.84 1.08e+00 8.57e-01 1.26e+01 angle pdb=" C ASN A 58 " pdb=" N VAL A 59 " pdb=" CA VAL A 59 " ideal model delta sigma weight residual 122.99 118.21 4.78 1.39e+00 5.18e-01 1.18e+01 ... (remaining 22940 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.26: 8952 21.26 - 42.52: 959 42.52 - 63.78: 136 63.78 - 85.04: 19 85.04 - 106.30: 8 Dihedral angle restraints: 10074 sinusoidal: 4062 harmonic: 6012 Sorted by residual: dihedral pdb=" CB CYS C 476 " pdb=" SG CYS C 476 " pdb=" SG CYS C 484 " pdb=" CB CYS C 484 " ideal model delta sinusoidal sigma weight residual -86.00 -135.11 49.11 1 1.00e+01 1.00e-02 3.32e+01 dihedral pdb=" CB CYS E 22 " pdb=" SG CYS E 22 " pdb=" SG CYS E 96 " pdb=" CB CYS E 96 " ideal model delta sinusoidal sigma weight residual -86.00 -41.38 -44.62 1 1.00e+01 1.00e-02 2.77e+01 dihedral pdb=" CB CYS H 22 " pdb=" SG CYS H 22 " pdb=" SG CYS H 96 " pdb=" CB CYS H 96 " ideal model delta sinusoidal sigma weight residual -86.00 -45.56 -40.44 1 1.00e+01 1.00e-02 2.29e+01 ... (remaining 10071 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.073: 2238 0.073 - 0.146: 298 0.146 - 0.220: 14 0.220 - 0.293: 4 0.293 - 0.366: 1 Chirality restraints: 2555 Sorted by residual: chirality pdb=" C1 NAG B1304 " pdb=" ND2 ASN B 327 " pdb=" C2 NAG B1304 " pdb=" O5 NAG B1304 " both_signs ideal model delta sigma weight residual False -2.40 -2.03 -0.37 2.00e-01 2.50e+01 3.35e+00 chirality pdb=" C1 NAG A1300 " pdb=" ND2 ASN A 58 " pdb=" C2 NAG A1300 " pdb=" O5 NAG A1300 " both_signs ideal model delta sigma weight residual False -2.40 -2.66 0.26 2.00e-01 2.50e+01 1.72e+00 chirality pdb=" C1 NAG B1300 " pdb=" ND2 ASN B 58 " pdb=" C2 NAG B1300 " pdb=" O5 NAG B1300 " both_signs ideal model delta sigma weight residual False -2.40 -2.66 0.26 2.00e-01 2.50e+01 1.70e+00 ... (remaining 2552 not shown) Planarity restraints: 2965 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN B 58 " -0.007 2.00e-02 2.50e+03 4.13e-02 2.14e+01 pdb=" CG ASN B 58 " 0.058 2.00e-02 2.50e+03 pdb=" OD1 ASN B 58 " -0.049 2.00e-02 2.50e+03 pdb=" ND2 ASN B 58 " 0.036 2.00e-02 2.50e+03 pdb=" C1 NAG B1300 " -0.038 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE C 229 " 0.020 2.00e-02 2.50e+03 4.13e-02 1.71e+01 pdb=" C ILE C 229 " -0.071 2.00e-02 2.50e+03 pdb=" O ILE C 229 " 0.027 2.00e-02 2.50e+03 pdb=" N ASN C 230 " 0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 58 " 0.036 2.00e-02 2.50e+03 3.47e-02 1.51e+01 pdb=" CG ASN A 58 " -0.032 2.00e-02 2.50e+03 pdb=" OD1 ASN A 58 " 0.003 2.00e-02 2.50e+03 pdb=" ND2 ASN A 58 " -0.046 2.00e-02 2.50e+03 pdb=" C1 NAG A1300 " 0.039 2.00e-02 2.50e+03 ... (remaining 2962 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1227 2.74 - 3.28: 15783 3.28 - 3.82: 26320 3.82 - 4.36: 30569 4.36 - 4.90: 52349 Nonbonded interactions: 126248 Sorted by model distance: nonbonded pdb=" OG1 THR C 106 " pdb=" OD1 ASP C 108 " model vdw 2.196 3.040 nonbonded pdb=" OE1 GLN B 49 " pdb=" OG1 THR B 270 " model vdw 2.207 3.040 nonbonded pdb=" OD2 ASP C 394 " pdb=" OH TYR C 419 " model vdw 2.207 3.040 nonbonded pdb=" O ASP C 290 " pdb=" OG SER C 293 " model vdw 2.217 3.040 nonbonded pdb=" OD1 ASN B 435 " pdb=" OG SER B 439 " model vdw 2.230 3.040 ... (remaining 126243 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: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 16 through 1300) selection = (chain 'B' and resid 16 through 1300) selection = chain 'C' } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'H' } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.450 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: 0.270 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 14.200 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.540 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5718 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 : 0.003 0.047 16908 Z= 0.171 Angle : 0.630 14.352 23023 Z= 0.329 Chirality : 0.048 0.366 2555 Planarity : 0.004 0.060 2956 Dihedral : 16.520 106.303 6162 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 11.39 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.66 % Favored : 95.19 % Rotamer: Outliers : 0.44 % Allowed : 24.83 % Favored : 74.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.79 (0.18), residues: 2037 helix: -1.86 (0.50), residues: 104 sheet: 0.77 (0.20), residues: 647 loop : -1.16 (0.17), residues: 1286 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 353 TYR 0.017 0.001 TYR A 25 PHE 0.029 0.001 PHE C 539 TRP 0.023 0.001 TRP F 36 HIS 0.002 0.001 HIS C 66 Details of bonding type rmsd covalent geometry : bond 0.00332 (16874) covalent geometry : angle 0.60615 (22945) SS BOND : bond 0.00198 ( 24) SS BOND : angle 0.92654 ( 48) hydrogen bonds : bond 0.18012 ( 481) hydrogen bonds : angle 8.24410 ( 1179) link_BETA1-4 : bond 0.00643 ( 1) link_BETA1-4 : angle 3.65129 ( 3) link_NAG-ASN : bond 0.00986 ( 9) link_NAG-ASN : angle 4.86145 ( 27) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4074 Ramachandran restraints generated. 2037 Oldfield, 0 Emsley, 2037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4074 Ramachandran restraints generated. 2037 Oldfield, 0 Emsley, 2037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 66 time to evaluate : 0.638 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 294 GLU cc_start: 0.8750 (tm-30) cc_final: 0.8476 (tm-30) REVERT: C 98 ILE cc_start: 0.8278 (mp) cc_final: 0.7934 (tp) outliers start: 8 outliers final: 4 residues processed: 70 average time/residue: 0.1141 time to fit residues: 13.4379 Evaluate side-chains 67 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 63 time to evaluate : 0.612 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 131 GLN Chi-restraints excluded: chain C residue 196 TYR Chi-restraints excluded: chain F residue 96 CYS Chi-restraints excluded: chain H residue 83 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 98 optimal weight: 0.0970 chunk 194 optimal weight: 50.0000 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 10.0000 chunk 130 optimal weight: 0.0370 chunk 124 optimal weight: 0.9980 chunk 103 optimal weight: 3.9990 chunk 200 optimal weight: 50.0000 chunk 77 optimal weight: 4.9990 chunk 122 optimal weight: 0.9990 overall best weight: 1.2260 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 335 HIS A 446 ASN B 84 ASN ** B 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 576 GLN ** C 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 1 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4735 r_free = 0.4735 target = 0.182852 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4167 r_free = 0.4167 target = 0.142382 restraints weight = 76621.241| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4024 r_free = 0.4024 target = 0.140059 restraints weight = 46389.745| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4087 r_free = 0.4087 target = 0.140640 restraints weight = 45610.732| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.4063 r_free = 0.4063 target = 0.140422 restraints weight = 40334.756| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4063 r_free = 0.4063 target = 0.140408 restraints weight = 38939.994| |-----------------------------------------------------------------------------| r_work (final): 0.3879 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6938 moved from start: 0.0946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 16908 Z= 0.132 Angle : 0.589 13.516 23023 Z= 0.299 Chirality : 0.046 0.236 2555 Planarity : 0.004 0.052 2956 Dihedral : 7.173 84.229 2475 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 9.11 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.71 % Favored : 95.24 % Rotamer: Outliers : 3.39 % Allowed : 23.06 % Favored : 73.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.83 (0.18), residues: 2037 helix: -1.89 (0.47), residues: 105 sheet: 0.66 (0.20), residues: 648 loop : -1.13 (0.17), residues: 1284 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 99 TYR 0.012 0.001 TYR A 200 PHE 0.022 0.001 PHE C 539 TRP 0.007 0.001 TRP H 36 HIS 0.002 0.001 HIS C 203 Details of bonding type rmsd covalent geometry : bond 0.00300 (16874) covalent geometry : angle 0.57560 (22945) SS BOND : bond 0.00225 ( 24) SS BOND : angle 0.67159 ( 48) hydrogen bonds : bond 0.03651 ( 481) hydrogen bonds : angle 6.22470 ( 1179) link_BETA1-4 : bond 0.00754 ( 1) link_BETA1-4 : angle 2.64675 ( 3) link_NAG-ASN : bond 0.00423 ( 9) link_NAG-ASN : angle 3.60215 ( 27) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4074 Ramachandran restraints generated. 2037 Oldfield, 0 Emsley, 2037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4074 Ramachandran restraints generated. 2037 Oldfield, 0 Emsley, 2037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 71 time to evaluate : 0.581 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 116 ILE cc_start: 0.8148 (OUTLIER) cc_final: 0.7664 (mm) REVERT: A 255 THR cc_start: 0.5064 (OUTLIER) cc_final: 0.4807 (p) REVERT: A 271 PHE cc_start: 0.9104 (OUTLIER) cc_final: 0.8707 (m-10) REVERT: A 552 ASN cc_start: 0.1290 (OUTLIER) cc_final: -0.0381 (p0) REVERT: B 116 ILE cc_start: 0.2877 (OUTLIER) cc_final: 0.2199 (mp) REVERT: B 234 PHE cc_start: 0.6439 (p90) cc_final: 0.5865 (p90) REVERT: B 265 TYR cc_start: 0.7177 (m-80) cc_final: 0.6795 (m-80) REVERT: C 98 ILE cc_start: 0.8360 (mp) cc_final: 0.8044 (tp) REVERT: H 96 CYS cc_start: -0.2506 (OUTLIER) cc_final: -0.2747 (m) outliers start: 61 outliers final: 27 residues processed: 125 average time/residue: 0.1009 time to fit residues: 21.2035 Evaluate side-chains 97 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 64 time to evaluate : 0.564 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 VAL Chi-restraints excluded: chain A residue 116 ILE Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain A residue 199 ILE Chi-restraints excluded: chain A residue 204 THR Chi-restraints excluded: chain A residue 255 THR Chi-restraints excluded: chain A residue 271 PHE Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 314 PHE Chi-restraints excluded: chain A residue 542 LEU Chi-restraints excluded: chain A residue 552 ASN Chi-restraints excluded: chain A residue 572 VAL Chi-restraints excluded: chain A residue 577 THR Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 116 ILE Chi-restraints excluded: chain B residue 117 VAL Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 385 ASP Chi-restraints excluded: chain B residue 506 VAL Chi-restraints excluded: chain B residue 521 CYS Chi-restraints excluded: chain B residue 577 THR Chi-restraints excluded: chain C residue 105 THR Chi-restraints excluded: chain C residue 131 GLN Chi-restraints excluded: chain C residue 140 VAL Chi-restraints excluded: chain C residue 193 ILE Chi-restraints excluded: chain C residue 196 TYR Chi-restraints excluded: chain C residue 311 THR Chi-restraints excluded: chain C residue 577 THR Chi-restraints excluded: chain F residue 60 TYR Chi-restraints excluded: chain F residue 71 SER Chi-restraints excluded: chain F residue 96 CYS Chi-restraints excluded: chain H residue 96 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 13 optimal weight: 0.0770 chunk 107 optimal weight: 4.9990 chunk 134 optimal weight: 0.7980 chunk 89 optimal weight: 5.9990 chunk 184 optimal weight: 3.9990 chunk 154 optimal weight: 0.9980 chunk 44 optimal weight: 6.9990 chunk 132 optimal weight: 5.9990 chunk 42 optimal weight: 30.0000 chunk 69 optimal weight: 0.0670 chunk 198 optimal weight: 10.0000 overall best weight: 1.1878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 339 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4724 r_free = 0.4724 target = 0.179990 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4154 r_free = 0.4154 target = 0.145239 restraints weight = 77737.095| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.4084 r_free = 0.4084 target = 0.143637 restraints weight = 52698.142| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4083 r_free = 0.4083 target = 0.143442 restraints weight = 45412.186| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.4090 r_free = 0.4090 target = 0.144023 restraints weight = 44907.451| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4098 r_free = 0.4098 target = 0.144349 restraints weight = 36638.727| |-----------------------------------------------------------------------------| r_work (final): 0.3961 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6476 moved from start: 0.1557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 16908 Z= 0.128 Angle : 0.571 13.993 23023 Z= 0.290 Chirality : 0.045 0.298 2555 Planarity : 0.004 0.062 2956 Dihedral : 6.630 76.092 2472 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 8.74 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.47 % Favored : 95.48 % Rotamer: Outliers : 3.67 % Allowed : 22.67 % Favored : 73.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.78 (0.18), residues: 2037 helix: -1.77 (0.47), residues: 103 sheet: 0.67 (0.20), residues: 644 loop : -1.09 (0.17), residues: 1290 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 210 TYR 0.015 0.001 TYR B 166 PHE 0.017 0.001 PHE A 103 TRP 0.007 0.001 TRP C 432 HIS 0.002 0.001 HIS C 203 Details of bonding type rmsd covalent geometry : bond 0.00287 (16874) covalent geometry : angle 0.55952 (22945) SS BOND : bond 0.00204 ( 24) SS BOND : angle 0.64209 ( 48) hydrogen bonds : bond 0.03560 ( 481) hydrogen bonds : angle 5.88261 ( 1179) link_BETA1-4 : bond 0.01235 ( 1) link_BETA1-4 : angle 2.78046 ( 3) link_NAG-ASN : bond 0.00403 ( 9) link_NAG-ASN : angle 3.20879 ( 27) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4074 Ramachandran restraints generated. 2037 Oldfield, 0 Emsley, 2037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4074 Ramachandran restraints generated. 2037 Oldfield, 0 Emsley, 2037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 69 time to evaluate : 0.592 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 255 THR cc_start: 0.5482 (OUTLIER) cc_final: 0.5199 (p) REVERT: A 271 PHE cc_start: 0.8977 (OUTLIER) cc_final: 0.8616 (m-10) REVERT: A 552 ASN cc_start: 0.0416 (OUTLIER) cc_final: -0.0590 (p0) REVERT: B 116 ILE cc_start: 0.3397 (OUTLIER) cc_final: 0.2839 (mp) REVERT: B 234 PHE cc_start: 0.6682 (p90) cc_final: 0.5184 (p90) REVERT: B 236 THR cc_start: 0.8186 (m) cc_final: 0.7881 (t) REVERT: B 265 TYR cc_start: 0.7125 (m-80) cc_final: 0.6712 (m-80) REVERT: C 98 ILE cc_start: 0.8413 (mp) cc_final: 0.8112 (tp) REVERT: C 555 PHE cc_start: 0.4054 (OUTLIER) cc_final: 0.2722 (m-10) outliers start: 66 outliers final: 37 residues processed: 130 average time/residue: 0.0982 time to fit residues: 22.1250 Evaluate side-chains 106 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 64 time to evaluate : 0.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 VAL Chi-restraints excluded: chain A residue 199 ILE Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 255 THR Chi-restraints excluded: chain A residue 271 PHE Chi-restraints excluded: chain A residue 314 PHE Chi-restraints excluded: chain A residue 529 LEU Chi-restraints excluded: chain A residue 542 LEU Chi-restraints excluded: chain A residue 543 THR Chi-restraints excluded: chain A residue 552 ASN Chi-restraints excluded: chain A residue 572 VAL Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 116 ILE Chi-restraints excluded: chain B residue 117 VAL Chi-restraints excluded: chain B residue 199 ILE Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 227 ILE Chi-restraints excluded: chain B residue 385 ASP Chi-restraints excluded: chain B residue 521 CYS Chi-restraints excluded: chain B residue 577 THR Chi-restraints excluded: chain B residue 580 ILE Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain C residue 38 LYS Chi-restraints excluded: chain C residue 39 VAL Chi-restraints excluded: chain C residue 122 ASN Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 140 VAL Chi-restraints excluded: chain C residue 193 ILE Chi-restraints excluded: chain C residue 196 TYR Chi-restraints excluded: chain C residue 311 THR Chi-restraints excluded: chain C residue 346 VAL Chi-restraints excluded: chain C residue 521 CYS Chi-restraints excluded: chain C residue 555 PHE Chi-restraints excluded: chain C residue 577 THR Chi-restraints excluded: chain F residue 60 TYR Chi-restraints excluded: chain F residue 96 CYS Chi-restraints excluded: chain H residue 39 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 185 optimal weight: 50.0000 chunk 43 optimal weight: 0.0770 chunk 100 optimal weight: 10.0000 chunk 45 optimal weight: 1.9990 chunk 13 optimal weight: 0.3980 chunk 188 optimal weight: 40.0000 chunk 122 optimal weight: 0.9980 chunk 127 optimal weight: 0.7980 chunk 111 optimal weight: 20.0000 chunk 63 optimal weight: 0.6980 chunk 84 optimal weight: 5.9990 overall best weight: 0.5938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 405 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 = 0.4734 r_free = 0.4734 target = 0.182519 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4155 r_free = 0.4155 target = 0.142164 restraints weight = 76644.903| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4030 r_free = 0.4030 target = 0.139901 restraints weight = 44054.098| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4068 r_free = 0.4068 target = 0.140359 restraints weight = 41667.139| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.4067 r_free = 0.4067 target = 0.140406 restraints weight = 35342.017| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4066 r_free = 0.4066 target = 0.140392 restraints weight = 33447.646| |-----------------------------------------------------------------------------| r_work (final): 0.3877 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6899 moved from start: 0.1863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 16908 Z= 0.097 Angle : 0.544 13.653 23023 Z= 0.270 Chirality : 0.044 0.186 2555 Planarity : 0.004 0.062 2956 Dihedral : 6.067 70.159 2469 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.17 % Favored : 95.78 % Rotamer: Outliers : 3.06 % Allowed : 23.22 % Favored : 73.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.68 (0.18), residues: 2037 helix: -1.63 (0.48), residues: 103 sheet: 0.79 (0.20), residues: 637 loop : -1.04 (0.17), residues: 1297 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 353 TYR 0.017 0.001 TYR B 376 PHE 0.020 0.001 PHE B 103 TRP 0.012 0.001 TRP B 101 HIS 0.002 0.000 HIS C 203 Details of bonding type rmsd covalent geometry : bond 0.00220 (16874) covalent geometry : angle 0.53371 (22945) SS BOND : bond 0.00170 ( 24) SS BOND : angle 0.53604 ( 48) hydrogen bonds : bond 0.03099 ( 481) hydrogen bonds : angle 5.50513 ( 1179) link_BETA1-4 : bond 0.01256 ( 1) link_BETA1-4 : angle 2.74501 ( 3) link_NAG-ASN : bond 0.00433 ( 9) link_NAG-ASN : angle 3.06280 ( 27) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4074 Ramachandran restraints generated. 2037 Oldfield, 0 Emsley, 2037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4074 Ramachandran restraints generated. 2037 Oldfield, 0 Emsley, 2037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 69 time to evaluate : 0.519 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 116 ILE cc_start: 0.8072 (OUTLIER) cc_final: 0.7849 (mm) REVERT: A 255 THR cc_start: 0.5195 (OUTLIER) cc_final: 0.4954 (p) REVERT: B 116 ILE cc_start: 0.3367 (OUTLIER) cc_final: 0.2904 (mp) REVERT: B 234 PHE cc_start: 0.6735 (p90) cc_final: 0.5350 (p90) REVERT: B 236 THR cc_start: 0.8089 (m) cc_final: 0.7832 (t) REVERT: B 265 TYR cc_start: 0.7283 (m-80) cc_final: 0.6820 (m-80) REVERT: B 374 LYS cc_start: 0.8649 (tptp) cc_final: 0.8219 (ttpt) REVERT: C 98 ILE cc_start: 0.8410 (mp) cc_final: 0.8086 (tp) REVERT: C 555 PHE cc_start: 0.4157 (OUTLIER) cc_final: 0.2920 (m-80) outliers start: 55 outliers final: 34 residues processed: 119 average time/residue: 0.0875 time to fit residues: 18.1468 Evaluate side-chains 103 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 65 time to evaluate : 0.506 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 VAL Chi-restraints excluded: chain A residue 58 ASN Chi-restraints excluded: chain A residue 116 ILE Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain A residue 199 ILE Chi-restraints excluded: chain A residue 204 THR Chi-restraints excluded: chain A residue 255 THR Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 314 PHE Chi-restraints excluded: chain A residue 521 CYS Chi-restraints excluded: chain A residue 542 LEU Chi-restraints excluded: chain A residue 572 VAL Chi-restraints excluded: chain A residue 577 THR Chi-restraints excluded: chain A residue 598 THR Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 116 ILE Chi-restraints excluded: chain B residue 117 VAL Chi-restraints excluded: chain B residue 227 ILE Chi-restraints excluded: chain B residue 388 PHE Chi-restraints excluded: chain B residue 521 CYS Chi-restraints excluded: chain B residue 577 THR Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 38 LYS Chi-restraints excluded: chain C residue 105 THR Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 140 VAL Chi-restraints excluded: chain C residue 193 ILE Chi-restraints excluded: chain C residue 196 TYR Chi-restraints excluded: chain C residue 199 ILE Chi-restraints excluded: chain C residue 311 THR Chi-restraints excluded: chain C residue 346 VAL Chi-restraints excluded: chain C residue 521 CYS Chi-restraints excluded: chain C residue 555 PHE Chi-restraints excluded: chain C residue 556 LEU Chi-restraints excluded: chain F residue 60 TYR Chi-restraints excluded: chain F residue 96 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 54 optimal weight: 20.0000 chunk 140 optimal weight: 6.9990 chunk 68 optimal weight: 7.9990 chunk 22 optimal weight: 0.7980 chunk 61 optimal weight: 7.9990 chunk 60 optimal weight: 4.9990 chunk 24 optimal weight: 0.9990 chunk 9 optimal weight: 8.9990 chunk 97 optimal weight: 10.0000 chunk 72 optimal weight: 2.9990 chunk 101 optimal weight: 5.9990 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 214 GLN ** A 405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 552 ASN ** A 560 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 84 ASN ** B 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 435 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 502 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4649 r_free = 0.4649 target = 0.175981 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.131619 restraints weight = 75078.660| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.129650 restraints weight = 48544.532| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.129384 restraints weight = 47576.553| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.129853 restraints weight = 38517.144| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.129767 restraints weight = 35419.683| |-----------------------------------------------------------------------------| r_work (final): 0.3680 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7239 moved from start: 0.3103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.093 16908 Z= 0.274 Angle : 0.738 16.248 23023 Z= 0.375 Chirality : 0.049 0.281 2555 Planarity : 0.005 0.072 2956 Dihedral : 7.012 72.416 2469 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 13.93 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.77 % Favored : 93.13 % Rotamer: Outliers : 4.94 % Allowed : 22.39 % Favored : 72.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.98 (0.18), residues: 2037 helix: -1.79 (0.47), residues: 97 sheet: 0.58 (0.20), residues: 603 loop : -1.22 (0.17), residues: 1337 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 353 TYR 0.028 0.002 TYR A 88 PHE 0.032 0.002 PHE B 103 TRP 0.011 0.001 TRP B 432 HIS 0.005 0.001 HIS B 335 Details of bonding type rmsd covalent geometry : bond 0.00607 (16874) covalent geometry : angle 0.72642 (22945) SS BOND : bond 0.00264 ( 24) SS BOND : angle 0.79410 ( 48) hydrogen bonds : bond 0.04247 ( 481) hydrogen bonds : angle 6.38129 ( 1179) link_BETA1-4 : bond 0.00602 ( 1) link_BETA1-4 : angle 3.56376 ( 3) link_NAG-ASN : bond 0.00992 ( 9) link_NAG-ASN : angle 3.73028 ( 27) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4074 Ramachandran restraints generated. 2037 Oldfield, 0 Emsley, 2037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4074 Ramachandran restraints generated. 2037 Oldfield, 0 Emsley, 2037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 60 time to evaluate : 0.370 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 255 THR cc_start: 0.5236 (OUTLIER) cc_final: 0.5005 (p) REVERT: A 271 PHE cc_start: 0.9206 (OUTLIER) cc_final: 0.8802 (m-10) REVERT: A 568 THR cc_start: 0.7702 (t) cc_final: 0.7493 (p) REVERT: B 116 ILE cc_start: 0.4246 (OUTLIER) cc_final: 0.3801 (mp) REVERT: B 234 PHE cc_start: 0.6967 (p90) cc_final: 0.5641 (p90) REVERT: B 265 TYR cc_start: 0.7399 (m-80) cc_final: 0.6972 (m-80) REVERT: B 374 LYS cc_start: 0.8894 (OUTLIER) cc_final: 0.8107 (pttt) REVERT: C 97 ILE cc_start: 0.8937 (tp) cc_final: 0.8626 (tp) REVERT: C 98 ILE cc_start: 0.8947 (mp) cc_final: 0.8664 (tp) REVERT: C 325 PHE cc_start: 0.4567 (OUTLIER) cc_final: 0.4340 (m-10) REVERT: C 555 PHE cc_start: 0.5464 (OUTLIER) cc_final: 0.4187 (m-80) outliers start: 89 outliers final: 57 residues processed: 141 average time/residue: 0.0921 time to fit residues: 21.6289 Evaluate side-chains 116 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 53 time to evaluate : 0.473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 33 VAL Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 199 ILE Chi-restraints excluded: chain A residue 204 THR Chi-restraints excluded: chain A residue 210 ARG Chi-restraints excluded: chain A residue 255 THR Chi-restraints excluded: chain A residue 271 PHE Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 301 SER Chi-restraints excluded: chain A residue 314 PHE Chi-restraints excluded: chain A residue 521 CYS Chi-restraints excluded: chain A residue 525 LYS Chi-restraints excluded: chain A residue 529 LEU Chi-restraints excluded: chain A residue 540 ASN Chi-restraints excluded: chain A residue 542 LEU Chi-restraints excluded: chain A residue 572 VAL Chi-restraints excluded: chain A residue 577 THR Chi-restraints excluded: chain A residue 578 LEU Chi-restraints excluded: chain A residue 598 THR Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 65 ILE Chi-restraints excluded: chain B residue 93 GLU Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain B residue 116 ILE Chi-restraints excluded: chain B residue 117 VAL Chi-restraints excluded: chain B residue 199 ILE Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 227 ILE Chi-restraints excluded: chain B residue 314 PHE Chi-restraints excluded: chain B residue 337 VAL Chi-restraints excluded: chain B residue 347 TYR Chi-restraints excluded: chain B residue 374 LYS Chi-restraints excluded: chain B residue 385 ASP Chi-restraints excluded: chain B residue 388 PHE Chi-restraints excluded: chain B residue 506 VAL Chi-restraints excluded: chain B residue 521 CYS Chi-restraints excluded: chain B residue 577 THR Chi-restraints excluded: chain B residue 580 ILE Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain C residue 39 VAL Chi-restraints excluded: chain C residue 87 VAL Chi-restraints excluded: chain C residue 105 THR Chi-restraints excluded: chain C residue 122 ASN Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 140 VAL Chi-restraints excluded: chain C residue 193 ILE Chi-restraints excluded: chain C residue 196 TYR Chi-restraints excluded: chain C residue 199 ILE Chi-restraints excluded: chain C residue 311 THR Chi-restraints excluded: chain C residue 325 PHE Chi-restraints excluded: chain C residue 346 VAL Chi-restraints excluded: chain C residue 397 VAL Chi-restraints excluded: chain C residue 521 CYS Chi-restraints excluded: chain C residue 542 LEU Chi-restraints excluded: chain C residue 555 PHE Chi-restraints excluded: chain F residue 60 TYR Chi-restraints excluded: chain F residue 71 SER Chi-restraints excluded: chain F residue 96 CYS Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain H residue 39 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 129 optimal weight: 0.7980 chunk 6 optimal weight: 0.9990 chunk 10 optimal weight: 7.9990 chunk 47 optimal weight: 1.9990 chunk 105 optimal weight: 1.9990 chunk 141 optimal weight: 7.9990 chunk 172 optimal weight: 50.0000 chunk 35 optimal weight: 0.0870 chunk 44 optimal weight: 4.9990 chunk 81 optimal weight: 9.9990 chunk 149 optimal weight: 30.0000 overall best weight: 1.1764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 214 GLN ** B 435 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 502 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4679 r_free = 0.4679 target = 0.178025 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4026 r_free = 0.4026 target = 0.134779 restraints weight = 75318.511| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.132506 restraints weight = 45060.509| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.132742 restraints weight = 42834.945| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.132814 restraints weight = 36289.780| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.132769 restraints weight = 34344.829| |-----------------------------------------------------------------------------| r_work (final): 0.3737 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7169 moved from start: 0.3287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 16908 Z= 0.125 Angle : 0.579 13.505 23023 Z= 0.292 Chirality : 0.046 0.312 2555 Planarity : 0.004 0.071 2956 Dihedral : 6.316 68.103 2469 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.66 % Favored : 95.29 % Rotamer: Outliers : 3.56 % Allowed : 23.33 % Favored : 73.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.81 (0.18), residues: 2037 helix: -1.79 (0.46), residues: 103 sheet: 0.67 (0.20), residues: 638 loop : -1.11 (0.17), residues: 1296 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 353 TYR 0.014 0.001 TYR A 200 PHE 0.026 0.001 PHE B 103 TRP 0.014 0.001 TRP B 101 HIS 0.002 0.000 HIS C 203 Details of bonding type rmsd covalent geometry : bond 0.00284 (16874) covalent geometry : angle 0.56805 (22945) SS BOND : bond 0.00175 ( 24) SS BOND : angle 0.56813 ( 48) hydrogen bonds : bond 0.03287 ( 481) hydrogen bonds : angle 5.75244 ( 1179) link_BETA1-4 : bond 0.01018 ( 1) link_BETA1-4 : angle 2.95858 ( 3) link_NAG-ASN : bond 0.00661 ( 9) link_NAG-ASN : angle 3.10621 ( 27) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4074 Ramachandran restraints generated. 2037 Oldfield, 0 Emsley, 2037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4074 Ramachandran restraints generated. 2037 Oldfield, 0 Emsley, 2037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 60 time to evaluate : 0.518 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 255 THR cc_start: 0.5258 (OUTLIER) cc_final: 0.5022 (p) REVERT: A 271 PHE cc_start: 0.9090 (OUTLIER) cc_final: 0.8755 (m-10) REVERT: A 463 ASP cc_start: 0.4409 (OUTLIER) cc_final: 0.3996 (m-30) REVERT: B 234 PHE cc_start: 0.7007 (p90) cc_final: 0.5764 (p90) REVERT: B 237 LEU cc_start: 0.9179 (mt) cc_final: 0.8890 (mm) REVERT: B 265 TYR cc_start: 0.7331 (m-80) cc_final: 0.7023 (m-80) REVERT: B 374 LYS cc_start: 0.8876 (OUTLIER) cc_final: 0.8203 (pttt) REVERT: C 97 ILE cc_start: 0.8834 (tp) cc_final: 0.8521 (tp) REVERT: C 98 ILE cc_start: 0.8818 (mp) cc_final: 0.8577 (tp) REVERT: C 325 PHE cc_start: 0.4830 (OUTLIER) cc_final: 0.4544 (m-10) REVERT: C 536 ASN cc_start: 0.8170 (OUTLIER) cc_final: 0.7917 (t0) REVERT: C 555 PHE cc_start: 0.5509 (OUTLIER) cc_final: 0.4138 (m-80) outliers start: 64 outliers final: 42 residues processed: 119 average time/residue: 0.0988 time to fit residues: 19.7691 Evaluate side-chains 105 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 56 time to evaluate : 0.594 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 VAL Chi-restraints excluded: chain A residue 65 ILE Chi-restraints excluded: chain A residue 199 ILE Chi-restraints excluded: chain A residue 204 THR Chi-restraints excluded: chain A residue 210 ARG Chi-restraints excluded: chain A residue 255 THR Chi-restraints excluded: chain A residue 271 PHE Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 314 PHE Chi-restraints excluded: chain A residue 463 ASP Chi-restraints excluded: chain A residue 521 CYS Chi-restraints excluded: chain A residue 525 LYS Chi-restraints excluded: chain A residue 542 LEU Chi-restraints excluded: chain A residue 572 VAL Chi-restraints excluded: chain A residue 577 THR Chi-restraints excluded: chain A residue 584 THR Chi-restraints excluded: chain A residue 598 THR Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain B residue 117 VAL Chi-restraints excluded: chain B residue 199 ILE Chi-restraints excluded: chain B residue 204 THR Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 374 LYS Chi-restraints excluded: chain B residue 388 PHE Chi-restraints excluded: chain B residue 521 CYS Chi-restraints excluded: chain B residue 577 THR Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain C residue 38 LYS Chi-restraints excluded: chain C residue 105 THR Chi-restraints excluded: chain C residue 111 THR Chi-restraints excluded: chain C residue 122 ASN Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 193 ILE Chi-restraints excluded: chain C residue 196 TYR Chi-restraints excluded: chain C residue 199 ILE Chi-restraints excluded: chain C residue 311 THR Chi-restraints excluded: chain C residue 323 VAL Chi-restraints excluded: chain C residue 325 PHE Chi-restraints excluded: chain C residue 346 VAL Chi-restraints excluded: chain C residue 521 CYS Chi-restraints excluded: chain C residue 536 ASN Chi-restraints excluded: chain C residue 555 PHE Chi-restraints excluded: chain C residue 556 LEU Chi-restraints excluded: chain F residue 60 TYR Chi-restraints excluded: chain F residue 96 CYS Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain H residue 39 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 76 optimal weight: 5.9990 chunk 148 optimal weight: 20.0000 chunk 181 optimal weight: 50.0000 chunk 7 optimal weight: 9.9990 chunk 62 optimal weight: 0.7980 chunk 22 optimal weight: 2.9990 chunk 9 optimal weight: 6.9990 chunk 70 optimal weight: 1.9990 chunk 53 optimal weight: 8.9990 chunk 176 optimal weight: 5.9990 chunk 97 optimal weight: 9.9990 overall best weight: 3.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 435 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 502 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 241 HIS C 327 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4599 r_free = 0.4599 target = 0.175032 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.133771 restraints weight = 69819.507| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.131444 restraints weight = 49254.752| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.131600 restraints weight = 44982.075| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.132015 restraints weight = 40534.988| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.132925 restraints weight = 34496.362| |-----------------------------------------------------------------------------| r_work (final): 0.3717 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6864 moved from start: 0.4634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.069 16908 Z= 0.305 Angle : 0.767 13.185 23023 Z= 0.397 Chirality : 0.050 0.302 2555 Planarity : 0.006 0.079 2956 Dihedral : 7.232 71.276 2469 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 15.65 Ramachandran Plot: Outliers : 0.15 % Allowed : 7.22 % Favored : 92.64 % Rotamer: Outliers : 4.33 % Allowed : 22.83 % Favored : 72.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.17 (0.18), residues: 2037 helix: -2.42 (0.41), residues: 103 sheet: 0.50 (0.21), residues: 608 loop : -1.33 (0.17), residues: 1326 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 353 TYR 0.033 0.002 TYR B 447 PHE 0.034 0.003 PHE B 103 TRP 0.015 0.001 TRP B 432 HIS 0.006 0.001 HIS B 335 Details of bonding type rmsd covalent geometry : bond 0.00676 (16874) covalent geometry : angle 0.75758 (22945) SS BOND : bond 0.00250 ( 24) SS BOND : angle 0.85775 ( 48) hydrogen bonds : bond 0.04404 ( 481) hydrogen bonds : angle 6.55840 ( 1179) link_BETA1-4 : bond 0.00063 ( 1) link_BETA1-4 : angle 3.82292 ( 3) link_NAG-ASN : bond 0.00519 ( 9) link_NAG-ASN : angle 3.40617 ( 27) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4074 Ramachandran restraints generated. 2037 Oldfield, 0 Emsley, 2037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4074 Ramachandran restraints generated. 2037 Oldfield, 0 Emsley, 2037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 63 time to evaluate : 0.636 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 255 THR cc_start: 0.5895 (OUTLIER) cc_final: 0.5656 (p) REVERT: A 271 PHE cc_start: 0.9243 (OUTLIER) cc_final: 0.8847 (m-10) REVERT: A 423 ASP cc_start: 0.5387 (OUTLIER) cc_final: 0.5178 (t0) REVERT: A 463 ASP cc_start: 0.3809 (OUTLIER) cc_final: 0.3602 (m-30) REVERT: B 121 THR cc_start: 0.6004 (OUTLIER) cc_final: 0.5625 (p) REVERT: B 234 PHE cc_start: 0.7157 (p90) cc_final: 0.6931 (p90) REVERT: B 347 TYR cc_start: 0.7631 (OUTLIER) cc_final: 0.7338 (p90) REVERT: B 374 LYS cc_start: 0.9017 (OUTLIER) cc_final: 0.8427 (ttpt) REVERT: B 464 ILE cc_start: 0.8995 (mt) cc_final: 0.8404 (tp) REVERT: C 97 ILE cc_start: 0.9074 (tp) cc_final: 0.8723 (tp) REVERT: C 325 PHE cc_start: 0.5105 (OUTLIER) cc_final: 0.4827 (m-10) REVERT: C 327 ASN cc_start: 0.5041 (OUTLIER) cc_final: 0.4794 (t0) REVERT: C 555 PHE cc_start: 0.6645 (OUTLIER) cc_final: 0.5902 (m-80) REVERT: C 558 PHE cc_start: 0.6699 (p90) cc_final: 0.6210 (p90) outliers start: 78 outliers final: 50 residues processed: 136 average time/residue: 0.0917 time to fit residues: 21.2163 Evaluate side-chains 113 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 53 time to evaluate : 0.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 VAL Chi-restraints excluded: chain A residue 65 ILE Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 199 ILE Chi-restraints excluded: chain A residue 204 THR Chi-restraints excluded: chain A residue 210 ARG Chi-restraints excluded: chain A residue 216 PHE Chi-restraints excluded: chain A residue 255 THR Chi-restraints excluded: chain A residue 271 PHE Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 314 PHE Chi-restraints excluded: chain A residue 423 ASP Chi-restraints excluded: chain A residue 463 ASP Chi-restraints excluded: chain A residue 521 CYS Chi-restraints excluded: chain A residue 542 LEU Chi-restraints excluded: chain A residue 572 VAL Chi-restraints excluded: chain A residue 577 THR Chi-restraints excluded: chain A residue 578 LEU Chi-restraints excluded: chain A residue 584 THR Chi-restraints excluded: chain A residue 598 THR Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain B residue 117 VAL Chi-restraints excluded: chain B residue 121 THR Chi-restraints excluded: chain B residue 196 TYR Chi-restraints excluded: chain B residue 199 ILE Chi-restraints excluded: chain B residue 204 THR Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 311 THR Chi-restraints excluded: chain B residue 328 ILE Chi-restraints excluded: chain B residue 347 TYR Chi-restraints excluded: chain B residue 374 LYS Chi-restraints excluded: chain B residue 376 TYR Chi-restraints excluded: chain B residue 388 PHE Chi-restraints excluded: chain B residue 521 CYS Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain C residue 39 VAL Chi-restraints excluded: chain C residue 87 VAL Chi-restraints excluded: chain C residue 111 THR Chi-restraints excluded: chain C residue 122 ASN Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 193 ILE Chi-restraints excluded: chain C residue 196 TYR Chi-restraints excluded: chain C residue 199 ILE Chi-restraints excluded: chain C residue 204 THR Chi-restraints excluded: chain C residue 311 THR Chi-restraints excluded: chain C residue 325 PHE Chi-restraints excluded: chain C residue 327 ASN Chi-restraints excluded: chain C residue 346 VAL Chi-restraints excluded: chain C residue 397 VAL Chi-restraints excluded: chain C residue 521 CYS Chi-restraints excluded: chain C residue 542 LEU Chi-restraints excluded: chain C residue 555 PHE Chi-restraints excluded: chain F residue 60 TYR Chi-restraints excluded: chain F residue 71 SER Chi-restraints excluded: chain F residue 96 CYS Chi-restraints excluded: chain E residue 79 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 196 optimal weight: 5.9990 chunk 180 optimal weight: 5.9990 chunk 136 optimal weight: 0.6980 chunk 20 optimal weight: 2.9990 chunk 16 optimal weight: 2.9990 chunk 158 optimal weight: 1.9990 chunk 123 optimal weight: 6.9990 chunk 7 optimal weight: 2.9990 chunk 18 optimal weight: 0.0770 chunk 91 optimal weight: 0.0060 chunk 64 optimal weight: 8.9990 overall best weight: 1.1558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 435 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 502 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 327 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4631 r_free = 0.4631 target = 0.178761 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.135030 restraints weight = 66300.212| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.136010 restraints weight = 42015.245| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.136133 restraints weight = 29505.899| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.136148 restraints weight = 29487.008| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.136216 restraints weight = 25866.586| |-----------------------------------------------------------------------------| r_work (final): 0.3748 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6542 moved from start: 0.4693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 16908 Z= 0.130 Angle : 0.611 13.447 23023 Z= 0.308 Chirality : 0.046 0.325 2555 Planarity : 0.004 0.074 2956 Dihedral : 6.473 69.448 2469 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 9.97 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.76 % Favored : 95.19 % Rotamer: Outliers : 3.28 % Allowed : 24.28 % Favored : 72.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.98 (0.18), residues: 2037 helix: -2.00 (0.46), residues: 97 sheet: 0.61 (0.21), residues: 624 loop : -1.24 (0.17), residues: 1316 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 353 TYR 0.016 0.001 TYR B 166 PHE 0.018 0.001 PHE B 103 TRP 0.014 0.001 TRP B 101 HIS 0.002 0.001 HIS C 203 Details of bonding type rmsd covalent geometry : bond 0.00297 (16874) covalent geometry : angle 0.60111 (22945) SS BOND : bond 0.00198 ( 24) SS BOND : angle 0.54148 ( 48) hydrogen bonds : bond 0.03294 ( 481) hydrogen bonds : angle 5.86960 ( 1179) link_BETA1-4 : bond 0.00944 ( 1) link_BETA1-4 : angle 3.17787 ( 3) link_NAG-ASN : bond 0.00396 ( 9) link_NAG-ASN : angle 3.10166 ( 27) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4074 Ramachandran restraints generated. 2037 Oldfield, 0 Emsley, 2037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4074 Ramachandran restraints generated. 2037 Oldfield, 0 Emsley, 2037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 57 time to evaluate : 0.641 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 255 THR cc_start: 0.5516 (OUTLIER) cc_final: 0.5313 (p) REVERT: A 271 PHE cc_start: 0.9333 (OUTLIER) cc_final: 0.8937 (m-10) REVERT: A 423 ASP cc_start: 0.5692 (OUTLIER) cc_final: 0.5491 (t0) REVERT: A 463 ASP cc_start: 0.4031 (OUTLIER) cc_final: 0.3657 (m-30) REVERT: B 234 PHE cc_start: 0.7372 (p90) cc_final: 0.6061 (p90) REVERT: B 237 LEU cc_start: 0.9211 (mt) cc_final: 0.8961 (mm) REVERT: B 265 TYR cc_start: 0.7809 (m-80) cc_final: 0.7385 (m-80) REVERT: B 347 TYR cc_start: 0.6938 (OUTLIER) cc_final: 0.6627 (p90) REVERT: B 374 LYS cc_start: 0.8849 (OUTLIER) cc_final: 0.8350 (ttpt) REVERT: B 464 ILE cc_start: 0.8916 (mt) cc_final: 0.8388 (tp) REVERT: C 97 ILE cc_start: 0.9042 (tp) cc_final: 0.8757 (tp) REVERT: C 325 PHE cc_start: 0.5770 (OUTLIER) cc_final: 0.5488 (m-10) REVERT: C 555 PHE cc_start: 0.6799 (OUTLIER) cc_final: 0.6095 (m-10) REVERT: C 558 PHE cc_start: 0.7348 (p90) cc_final: 0.6736 (p90) outliers start: 59 outliers final: 45 residues processed: 112 average time/residue: 0.0972 time to fit residues: 18.4929 Evaluate side-chains 106 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 53 time to evaluate : 0.586 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 VAL Chi-restraints excluded: chain A residue 65 ILE Chi-restraints excluded: chain A residue 199 ILE Chi-restraints excluded: chain A residue 204 THR Chi-restraints excluded: chain A residue 210 ARG Chi-restraints excluded: chain A residue 216 PHE Chi-restraints excluded: chain A residue 255 THR Chi-restraints excluded: chain A residue 271 PHE Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 314 PHE Chi-restraints excluded: chain A residue 423 ASP Chi-restraints excluded: chain A residue 463 ASP Chi-restraints excluded: chain A residue 521 CYS Chi-restraints excluded: chain A residue 525 LYS Chi-restraints excluded: chain A residue 542 LEU Chi-restraints excluded: chain A residue 572 VAL Chi-restraints excluded: chain A residue 577 THR Chi-restraints excluded: chain A residue 584 THR Chi-restraints excluded: chain A residue 598 THR Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain B residue 117 VAL Chi-restraints excluded: chain B residue 199 ILE Chi-restraints excluded: chain B residue 204 THR Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 285 VAL Chi-restraints excluded: chain B residue 311 THR Chi-restraints excluded: chain B residue 347 TYR Chi-restraints excluded: chain B residue 374 LYS Chi-restraints excluded: chain B residue 376 TYR Chi-restraints excluded: chain B residue 388 PHE Chi-restraints excluded: chain B residue 521 CYS Chi-restraints excluded: chain B residue 580 ILE Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain C residue 122 ASN Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 125 ILE Chi-restraints excluded: chain C residue 193 ILE Chi-restraints excluded: chain C residue 196 TYR Chi-restraints excluded: chain C residue 199 ILE Chi-restraints excluded: chain C residue 204 THR Chi-restraints excluded: chain C residue 235 GLN Chi-restraints excluded: chain C residue 311 THR Chi-restraints excluded: chain C residue 325 PHE Chi-restraints excluded: chain C residue 346 VAL Chi-restraints excluded: chain C residue 397 VAL Chi-restraints excluded: chain C residue 521 CYS Chi-restraints excluded: chain C residue 555 PHE Chi-restraints excluded: chain F residue 60 TYR Chi-restraints excluded: chain F residue 96 CYS Chi-restraints excluded: chain E residue 27 PHE Chi-restraints excluded: chain E residue 79 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 183 optimal weight: 30.0000 chunk 10 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 170 optimal weight: 7.9990 chunk 182 optimal weight: 6.9990 chunk 194 optimal weight: 50.0000 chunk 49 optimal weight: 0.0270 chunk 153 optimal weight: 30.0000 chunk 192 optimal weight: 8.9990 chunk 4 optimal weight: 5.9990 chunk 1 optimal weight: 0.9990 overall best weight: 2.2046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 540 ASN ** B 435 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 502 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4596 r_free = 0.4596 target = 0.177512 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.133225 restraints weight = 64277.711| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.134145 restraints weight = 38114.079| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.133768 restraints weight = 28899.576| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.133980 restraints weight = 27726.000| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.134256 restraints weight = 26092.606| |-----------------------------------------------------------------------------| r_work (final): 0.3681 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6655 moved from start: 0.5475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 16908 Z= 0.202 Angle : 0.667 13.223 23023 Z= 0.336 Chirality : 0.047 0.261 2555 Planarity : 0.005 0.075 2956 Dihedral : 6.536 69.457 2469 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 12.20 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.97 % Favored : 92.93 % Rotamer: Outliers : 3.06 % Allowed : 24.67 % Favored : 72.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.03 (0.18), residues: 2037 helix: -2.16 (0.45), residues: 103 sheet: 0.61 (0.21), residues: 625 loop : -1.29 (0.17), residues: 1309 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 99 TYR 0.025 0.001 TYR B 447 PHE 0.029 0.002 PHE B 103 TRP 0.009 0.001 TRP B 432 HIS 0.007 0.001 HIS C 203 Details of bonding type rmsd covalent geometry : bond 0.00458 (16874) covalent geometry : angle 0.65628 (22945) SS BOND : bond 0.00189 ( 24) SS BOND : angle 0.64287 ( 48) hydrogen bonds : bond 0.03644 ( 481) hydrogen bonds : angle 5.97621 ( 1179) link_BETA1-4 : bond 0.00178 ( 1) link_BETA1-4 : angle 3.75844 ( 3) link_NAG-ASN : bond 0.00418 ( 9) link_NAG-ASN : angle 3.23634 ( 27) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4074 Ramachandran restraints generated. 2037 Oldfield, 0 Emsley, 2037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4074 Ramachandran restraints generated. 2037 Oldfield, 0 Emsley, 2037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 55 time to evaluate : 0.408 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 255 THR cc_start: 0.5712 (OUTLIER) cc_final: 0.5497 (p) REVERT: A 271 PHE cc_start: 0.9410 (OUTLIER) cc_final: 0.8967 (m-10) REVERT: A 463 ASP cc_start: 0.3930 (OUTLIER) cc_final: 0.3521 (m-30) REVERT: B 234 PHE cc_start: 0.7408 (p90) cc_final: 0.5961 (p90) REVERT: B 265 TYR cc_start: 0.7771 (m-80) cc_final: 0.7291 (m-80) REVERT: B 347 TYR cc_start: 0.7481 (OUTLIER) cc_final: 0.7063 (p90) REVERT: B 374 LYS cc_start: 0.8905 (OUTLIER) cc_final: 0.8379 (ttpt) REVERT: C 97 ILE cc_start: 0.9094 (tp) cc_final: 0.8814 (tp) REVERT: C 235 GLN cc_start: 0.8483 (OUTLIER) cc_final: 0.7719 (tp40) REVERT: C 325 PHE cc_start: 0.5723 (OUTLIER) cc_final: 0.5335 (m-10) REVERT: C 558 PHE cc_start: 0.7554 (p90) cc_final: 0.7059 (p90) outliers start: 55 outliers final: 42 residues processed: 108 average time/residue: 0.0902 time to fit residues: 16.6804 Evaluate side-chains 97 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 48 time to evaluate : 0.506 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 VAL Chi-restraints excluded: chain A residue 65 ILE Chi-restraints excluded: chain A residue 199 ILE Chi-restraints excluded: chain A residue 210 ARG Chi-restraints excluded: chain A residue 216 PHE Chi-restraints excluded: chain A residue 255 THR Chi-restraints excluded: chain A residue 271 PHE Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 314 PHE Chi-restraints excluded: chain A residue 463 ASP Chi-restraints excluded: chain A residue 521 CYS Chi-restraints excluded: chain A residue 525 LYS Chi-restraints excluded: chain A residue 540 ASN Chi-restraints excluded: chain A residue 542 LEU Chi-restraints excluded: chain A residue 572 VAL Chi-restraints excluded: chain A residue 577 THR Chi-restraints excluded: chain A residue 578 LEU Chi-restraints excluded: chain A residue 584 THR Chi-restraints excluded: chain A residue 598 THR Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 117 VAL Chi-restraints excluded: chain B residue 199 ILE Chi-restraints excluded: chain B residue 204 THR Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 347 TYR Chi-restraints excluded: chain B residue 374 LYS Chi-restraints excluded: chain B residue 388 PHE Chi-restraints excluded: chain B residue 521 CYS Chi-restraints excluded: chain B residue 580 ILE Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain C residue 39 VAL Chi-restraints excluded: chain C residue 87 VAL Chi-restraints excluded: chain C residue 111 THR Chi-restraints excluded: chain C residue 122 ASN Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 125 ILE Chi-restraints excluded: chain C residue 193 ILE Chi-restraints excluded: chain C residue 196 TYR Chi-restraints excluded: chain C residue 199 ILE Chi-restraints excluded: chain C residue 204 THR Chi-restraints excluded: chain C residue 235 GLN Chi-restraints excluded: chain C residue 311 THR Chi-restraints excluded: chain C residue 325 PHE Chi-restraints excluded: chain C residue 346 VAL Chi-restraints excluded: chain C residue 397 VAL Chi-restraints excluded: chain F residue 60 TYR Chi-restraints excluded: chain F residue 96 CYS Chi-restraints excluded: chain E residue 79 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 74 optimal weight: 0.8980 chunk 27 optimal weight: 8.9990 chunk 141 optimal weight: 20.0000 chunk 119 optimal weight: 0.9990 chunk 47 optimal weight: 2.9990 chunk 197 optimal weight: 50.0000 chunk 159 optimal weight: 4.9990 chunk 12 optimal weight: 0.0570 chunk 98 optimal weight: 2.9990 chunk 177 optimal weight: 20.0000 chunk 184 optimal weight: 9.9990 overall best weight: 1.5904 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 435 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 502 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 = 0.4603 r_free = 0.4603 target = 0.172459 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.130166 restraints weight = 71899.249| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.126219 restraints weight = 45124.589| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.127211 restraints weight = 36417.958| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.127033 restraints weight = 32465.334| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.127117 restraints weight = 28245.740| |-----------------------------------------------------------------------------| r_work (final): 0.3645 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6910 moved from start: 0.5648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 16908 Z= 0.149 Angle : 0.607 13.027 23023 Z= 0.305 Chirality : 0.046 0.240 2555 Planarity : 0.005 0.087 2956 Dihedral : 6.261 68.395 2469 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 10.37 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.20 % Favored : 94.75 % Rotamer: Outliers : 2.83 % Allowed : 24.94 % Favored : 72.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.04 (0.18), residues: 2037 helix: -2.08 (0.45), residues: 103 sheet: 0.54 (0.21), residues: 640 loop : -1.27 (0.17), residues: 1294 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 353 TYR 0.015 0.001 TYR B 156 PHE 0.020 0.002 PHE B 103 TRP 0.013 0.001 TRP B 101 HIS 0.003 0.001 HIS C 203 Details of bonding type rmsd covalent geometry : bond 0.00343 (16874) covalent geometry : angle 0.59724 (22945) SS BOND : bond 0.00184 ( 24) SS BOND : angle 0.56700 ( 48) hydrogen bonds : bond 0.03297 ( 481) hydrogen bonds : angle 5.74148 ( 1179) link_BETA1-4 : bond 0.00973 ( 1) link_BETA1-4 : angle 3.23892 ( 3) link_NAG-ASN : bond 0.00395 ( 9) link_NAG-ASN : angle 3.05354 ( 27) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4074 Ramachandran restraints generated. 2037 Oldfield, 0 Emsley, 2037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4074 Ramachandran restraints generated. 2037 Oldfield, 0 Emsley, 2037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 51 time to evaluate : 0.538 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 255 THR cc_start: 0.5502 (OUTLIER) cc_final: 0.5286 (p) REVERT: A 463 ASP cc_start: 0.3905 (OUTLIER) cc_final: 0.3496 (m-30) REVERT: B 234 PHE cc_start: 0.7049 (p90) cc_final: 0.5689 (p90) REVERT: B 237 LEU cc_start: 0.9233 (mt) cc_final: 0.9008 (mm) REVERT: B 265 TYR cc_start: 0.7733 (m-80) cc_final: 0.7444 (m-80) REVERT: B 347 TYR cc_start: 0.7240 (OUTLIER) cc_final: 0.6788 (p90) REVERT: B 374 LYS cc_start: 0.8908 (OUTLIER) cc_final: 0.8432 (ttpt) REVERT: C 233 ARG cc_start: 0.8905 (OUTLIER) cc_final: 0.7848 (ptm-80) REVERT: C 325 PHE cc_start: 0.5826 (OUTLIER) cc_final: 0.5408 (m-10) REVERT: C 558 PHE cc_start: 0.7442 (p90) cc_final: 0.7037 (p90) outliers start: 51 outliers final: 40 residues processed: 100 average time/residue: 0.1088 time to fit residues: 17.6855 Evaluate side-chains 92 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 46 time to evaluate : 0.682 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 VAL Chi-restraints excluded: chain A residue 65 ILE Chi-restraints excluded: chain A residue 199 ILE Chi-restraints excluded: chain A residue 210 ARG Chi-restraints excluded: chain A residue 216 PHE Chi-restraints excluded: chain A residue 255 THR Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 314 PHE Chi-restraints excluded: chain A residue 463 ASP Chi-restraints excluded: chain A residue 521 CYS Chi-restraints excluded: chain A residue 525 LYS Chi-restraints excluded: chain A residue 542 LEU Chi-restraints excluded: chain A residue 572 VAL Chi-restraints excluded: chain A residue 577 THR Chi-restraints excluded: chain A residue 584 THR Chi-restraints excluded: chain A residue 598 THR Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 117 VAL Chi-restraints excluded: chain B residue 199 ILE Chi-restraints excluded: chain B residue 204 THR Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 347 TYR Chi-restraints excluded: chain B residue 374 LYS Chi-restraints excluded: chain B residue 388 PHE Chi-restraints excluded: chain B residue 426 THR Chi-restraints excluded: chain B residue 521 CYS Chi-restraints excluded: chain B residue 580 ILE Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain C residue 39 VAL Chi-restraints excluded: chain C residue 111 THR Chi-restraints excluded: chain C residue 122 ASN Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 125 ILE Chi-restraints excluded: chain C residue 193 ILE Chi-restraints excluded: chain C residue 196 TYR Chi-restraints excluded: chain C residue 199 ILE Chi-restraints excluded: chain C residue 204 THR Chi-restraints excluded: chain C residue 233 ARG Chi-restraints excluded: chain C residue 235 GLN Chi-restraints excluded: chain C residue 325 PHE Chi-restraints excluded: chain C residue 346 VAL Chi-restraints excluded: chain C residue 397 VAL Chi-restraints excluded: chain C residue 521 CYS Chi-restraints excluded: chain F residue 60 TYR Chi-restraints excluded: chain F residue 96 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 153 optimal weight: 20.0000 chunk 24 optimal weight: 1.9990 chunk 81 optimal weight: 0.6980 chunk 33 optimal weight: 20.0000 chunk 201 optimal weight: 40.0000 chunk 53 optimal weight: 0.3980 chunk 107 optimal weight: 0.8980 chunk 103 optimal weight: 4.9990 chunk 110 optimal weight: 8.9990 chunk 154 optimal weight: 8.9990 chunk 143 optimal weight: 6.9990 overall best weight: 1.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 540 ASN ** B 435 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 502 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4587 r_free = 0.4587 target = 0.171156 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.130519 restraints weight = 71434.007| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.126944 restraints weight = 44536.431| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.127962 restraints weight = 36080.623| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.128159 restraints weight = 30394.907| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.128288 restraints weight = 26389.463| |-----------------------------------------------------------------------------| r_work (final): 0.3663 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6787 moved from start: 0.6133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 16908 Z= 0.169 Angle : 0.632 12.600 23023 Z= 0.316 Chirality : 0.046 0.239 2555 Planarity : 0.005 0.076 2956 Dihedral : 6.251 67.930 2469 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 11.46 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.58 % Favored : 93.37 % Rotamer: Outliers : 2.78 % Allowed : 25.00 % Favored : 72.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.00 (0.19), residues: 2037 helix: -2.17 (0.44), residues: 109 sheet: 0.73 (0.21), residues: 633 loop : -1.32 (0.17), residues: 1295 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 353 TYR 0.022 0.001 TYR B 196 PHE 0.027 0.002 PHE B 103 TRP 0.009 0.001 TRP B 101 HIS 0.003 0.001 HIS C 203 Details of bonding type rmsd covalent geometry : bond 0.00385 (16874) covalent geometry : angle 0.62259 (22945) SS BOND : bond 0.00177 ( 24) SS BOND : angle 0.61257 ( 48) hydrogen bonds : bond 0.03427 ( 481) hydrogen bonds : angle 5.73588 ( 1179) link_BETA1-4 : bond 0.00803 ( 1) link_BETA1-4 : angle 3.42433 ( 3) link_NAG-ASN : bond 0.00359 ( 9) link_NAG-ASN : angle 3.00752 ( 27) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3270.73 seconds wall clock time: 57 minutes 4.00 seconds (3424.00 seconds total)