Starting phenix.real_space_refine on Sun Aug 9 13:19:23 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8t0e_40941/08_2026/8t0e_40941_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8t0e_40941/08_2026/8t0e_40941.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8t0e_40941/08_2026/8t0e_40941_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8t0e_40941/08_2026/8t0e_40941_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8t0e_40941/08_2026/8t0e_40941.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8t0e_40941/08_2026/8t0e_40941.map" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 1.000 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: 7 Type Number sf(0) Gaussians P 4 5.49 5 S 100 5.16 5 Na 1 4.78 5 C 11428 2.51 5 N 2796 2.21 5 O 3104 1.98 5 H 17436 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 32 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 34869 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 8669 Number of conformers: 1 Conformer: "" Number of residues, atoms: 531, 8669 Classifications: {'peptide': 531} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 516} Chain: "D" Number of atoms: 8669 Number of conformers: 1 Conformer: "" Number of residues, atoms: 531, 8669 Classifications: {'peptide': 531} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 516} Chain: "B" Number of atoms: 8669 Number of conformers: 1 Conformer: "" Number of residues, atoms: 531, 8669 Classifications: {'peptide': 531} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 516} Chain: "C" Number of atoms: 8669 Number of conformers: 1 Conformer: "" Number of residues, atoms: 531, 8669 Classifications: {'peptide': 531} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 516} Chain: "A" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 46 Unusual residues: {' NA': 1, '8IJ': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 14 Chain: "D" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 45 Unusual residues: {'8IJ': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 14 Chain: "B" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 45 Unusual residues: {'8IJ': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 14 Chain: "C" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 45 Unusual residues: {'8IJ': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 14 Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 3 Classifications: {'water': 1} Chain: "D" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 3 Classifications: {'water': 1} Chain: "B" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 3 Classifications: {'water': 1} Chain: "C" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 3 Classifications: {'water': 1} Time building chain proxies: 5.78, per 1000 atoms: 0.17 Number of scatterers: 34869 At special positions: 0 Unit cell: (119.405, 119.405, 111.055, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) S 100 16.00 P 4 15.00 Na 1 11.00 O 3104 8.00 N 2796 7.00 C 11428 6.00 H 17436 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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 Time building additional restraints: 3.37 Conformation dependent library (CDL) restraints added in 1.1 seconds 4232 Ramachandran restraints generated. 2116 Oldfield, 0 Emsley, 2116 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4016 Finding SS restraints... Secondary structure from input PDB file: 96 helices and 4 sheets defined 64.8% alpha, 3.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.68 Creating SS restraints... Processing helix chain 'A' and resid 203 through 212 Processing helix chain 'A' and resid 213 through 222 removed outlier: 3.792A pdb=" N VAL A 217 " --> pdb=" O ASN A 213 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N THR A 218 " --> pdb=" O MET A 214 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 237 Processing helix chain 'A' and resid 250 through 258 Processing helix chain 'A' and resid 286 through 295 Processing helix chain 'A' and resid 298 through 320 Processing helix chain 'A' and resid 335 through 344 Processing helix chain 'A' and resid 345 through 354 Processing helix chain 'A' and resid 362 through 366 removed outlier: 3.803A pdb=" N LEU A 365 " --> pdb=" O CYS A 362 " (cutoff:3.500A) Processing helix chain 'A' and resid 394 through 401 Processing helix chain 'A' and resid 408 through 413 removed outlier: 4.515A pdb=" N LEU A 413 " --> pdb=" O ARG A 409 " (cutoff:3.500A) Processing helix chain 'A' and resid 415 through 429 Processing helix chain 'A' and resid 429 through 454 Processing helix chain 'A' and resid 468 through 500 Processing helix chain 'A' and resid 504 through 508 removed outlier: 3.733A pdb=" N PHE A 507 " --> pdb=" O LYS A 504 " (cutoff:3.500A) Processing helix chain 'A' and resid 510 through 531 removed outlier: 3.538A pdb=" N ILE A 514 " --> pdb=" O SER A 510 " (cutoff:3.500A) Processing helix chain 'A' and resid 532 through 534 No H-bonds generated for 'chain 'A' and resid 532 through 534' Processing helix chain 'A' and resid 535 through 551 removed outlier: 4.331A pdb=" N ALA A 539 " --> pdb=" O LYS A 535 " (cutoff:3.500A) Processing helix chain 'A' and resid 552 through 557 Processing helix chain 'A' and resid 559 through 599 removed outlier: 4.348A pdb=" N LEU A 577 " --> pdb=" O ILE A 573 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N CYS A 578 " --> pdb=" O LEU A 574 " (cutoff:3.500A) Processing helix chain 'A' and resid 629 through 642 removed outlier: 3.876A pdb=" N PHE A 640 " --> pdb=" O GLU A 636 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N THR A 641 " --> pdb=" O LEU A 637 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N ILE A 642 " --> pdb=" O PHE A 638 " (cutoff:3.500A) Processing helix chain 'A' and resid 655 through 670 Processing helix chain 'A' and resid 673 through 689 Processing helix chain 'A' and resid 689 through 711 Processing helix chain 'D' and resid 203 through 212 Processing helix chain 'D' and resid 213 through 222 removed outlier: 3.791A pdb=" N VAL D 217 " --> pdb=" O ASN D 213 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N THR D 218 " --> pdb=" O MET D 214 " (cutoff:3.500A) Processing helix chain 'D' and resid 233 through 237 Processing helix chain 'D' and resid 250 through 258 Processing helix chain 'D' and resid 286 through 295 Processing helix chain 'D' and resid 298 through 320 Processing helix chain 'D' and resid 335 through 344 Processing helix chain 'D' and resid 345 through 354 Processing helix chain 'D' and resid 362 through 366 removed outlier: 3.803A pdb=" N LEU D 365 " --> pdb=" O CYS D 362 " (cutoff:3.500A) Processing helix chain 'D' and resid 394 through 401 Processing helix chain 'D' and resid 408 through 413 removed outlier: 4.515A pdb=" N LEU D 413 " --> pdb=" O ARG D 409 " (cutoff:3.500A) Processing helix chain 'D' and resid 415 through 429 Processing helix chain 'D' and resid 429 through 454 Processing helix chain 'D' and resid 468 through 500 Processing helix chain 'D' and resid 504 through 508 removed outlier: 3.732A pdb=" N PHE D 507 " --> pdb=" O LYS D 504 " (cutoff:3.500A) Processing helix chain 'D' and resid 510 through 531 removed outlier: 3.538A pdb=" N ILE D 514 " --> pdb=" O SER D 510 " (cutoff:3.500A) Processing helix chain 'D' and resid 532 through 534 No H-bonds generated for 'chain 'D' and resid 532 through 534' Processing helix chain 'D' and resid 535 through 551 removed outlier: 4.331A pdb=" N ALA D 539 " --> pdb=" O LYS D 535 " (cutoff:3.500A) Processing helix chain 'D' and resid 552 through 557 Processing helix chain 'D' and resid 559 through 599 removed outlier: 4.348A pdb=" N LEU D 577 " --> pdb=" O ILE D 573 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N CYS D 578 " --> pdb=" O LEU D 574 " (cutoff:3.500A) Processing helix chain 'D' and resid 629 through 642 removed outlier: 3.876A pdb=" N PHE D 640 " --> pdb=" O GLU D 636 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N THR D 641 " --> pdb=" O LEU D 637 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N ILE D 642 " --> pdb=" O PHE D 638 " (cutoff:3.500A) Processing helix chain 'D' and resid 655 through 670 Processing helix chain 'D' and resid 673 through 689 Processing helix chain 'D' and resid 689 through 711 Processing helix chain 'B' and resid 203 through 212 Processing helix chain 'B' and resid 213 through 222 removed outlier: 3.792A pdb=" N VAL B 217 " --> pdb=" O ASN B 213 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N THR B 218 " --> pdb=" O MET B 214 " (cutoff:3.500A) Processing helix chain 'B' and resid 233 through 237 Processing helix chain 'B' and resid 250 through 258 Processing helix chain 'B' and resid 286 through 295 Processing helix chain 'B' and resid 298 through 320 Processing helix chain 'B' and resid 335 through 344 Processing helix chain 'B' and resid 345 through 354 Processing helix chain 'B' and resid 362 through 366 removed outlier: 3.803A pdb=" N LEU B 365 " --> pdb=" O CYS B 362 " (cutoff:3.500A) Processing helix chain 'B' and resid 394 through 401 Processing helix chain 'B' and resid 408 through 413 removed outlier: 4.515A pdb=" N LEU B 413 " --> pdb=" O ARG B 409 " (cutoff:3.500A) Processing helix chain 'B' and resid 415 through 429 Processing helix chain 'B' and resid 429 through 454 Processing helix chain 'B' and resid 468 through 500 Processing helix chain 'B' and resid 504 through 508 removed outlier: 3.732A pdb=" N PHE B 507 " --> pdb=" O LYS B 504 " (cutoff:3.500A) Processing helix chain 'B' and resid 510 through 531 removed outlier: 3.538A pdb=" N ILE B 514 " --> pdb=" O SER B 510 " (cutoff:3.500A) Processing helix chain 'B' and resid 532 through 534 No H-bonds generated for 'chain 'B' and resid 532 through 534' Processing helix chain 'B' and resid 535 through 551 removed outlier: 4.331A pdb=" N ALA B 539 " --> pdb=" O LYS B 535 " (cutoff:3.500A) Processing helix chain 'B' and resid 552 through 557 Processing helix chain 'B' and resid 559 through 599 removed outlier: 4.348A pdb=" N LEU B 577 " --> pdb=" O ILE B 573 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N CYS B 578 " --> pdb=" O LEU B 574 " (cutoff:3.500A) Processing helix chain 'B' and resid 629 through 642 removed outlier: 3.876A pdb=" N PHE B 640 " --> pdb=" O GLU B 636 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N THR B 641 " --> pdb=" O LEU B 637 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N ILE B 642 " --> pdb=" O PHE B 638 " (cutoff:3.500A) Processing helix chain 'B' and resid 655 through 670 Processing helix chain 'B' and resid 673 through 689 Processing helix chain 'B' and resid 689 through 711 Processing helix chain 'C' and resid 203 through 212 Processing helix chain 'C' and resid 213 through 222 removed outlier: 3.792A pdb=" N VAL C 217 " --> pdb=" O ASN C 213 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N THR C 218 " --> pdb=" O MET C 214 " (cutoff:3.500A) Processing helix chain 'C' and resid 233 through 237 Processing helix chain 'C' and resid 250 through 258 Processing helix chain 'C' and resid 286 through 295 Processing helix chain 'C' and resid 298 through 320 Processing helix chain 'C' and resid 335 through 344 Processing helix chain 'C' and resid 345 through 354 Processing helix chain 'C' and resid 362 through 366 removed outlier: 3.803A pdb=" N LEU C 365 " --> pdb=" O CYS C 362 " (cutoff:3.500A) Processing helix chain 'C' and resid 394 through 401 Processing helix chain 'C' and resid 408 through 413 removed outlier: 4.515A pdb=" N LEU C 413 " --> pdb=" O ARG C 409 " (cutoff:3.500A) Processing helix chain 'C' and resid 415 through 429 Processing helix chain 'C' and resid 429 through 454 Processing helix chain 'C' and resid 468 through 500 Processing helix chain 'C' and resid 504 through 508 removed outlier: 3.733A pdb=" N PHE C 507 " --> pdb=" O LYS C 504 " (cutoff:3.500A) Processing helix chain 'C' and resid 510 through 531 removed outlier: 3.538A pdb=" N ILE C 514 " --> pdb=" O SER C 510 " (cutoff:3.500A) Processing helix chain 'C' and resid 532 through 534 No H-bonds generated for 'chain 'C' and resid 532 through 534' Processing helix chain 'C' and resid 535 through 551 removed outlier: 4.331A pdb=" N ALA C 539 " --> pdb=" O LYS C 535 " (cutoff:3.500A) Processing helix chain 'C' and resid 552 through 557 Processing helix chain 'C' and resid 559 through 599 removed outlier: 4.348A pdb=" N LEU C 577 " --> pdb=" O ILE C 573 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N CYS C 578 " --> pdb=" O LEU C 574 " (cutoff:3.500A) Processing helix chain 'C' and resid 629 through 642 removed outlier: 3.876A pdb=" N PHE C 640 " --> pdb=" O GLU C 636 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N THR C 641 " --> pdb=" O LEU C 637 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N ILE C 642 " --> pdb=" O PHE C 638 " (cutoff:3.500A) Processing helix chain 'C' and resid 655 through 670 Processing helix chain 'C' and resid 673 through 689 Processing helix chain 'C' and resid 689 through 711 Processing sheet with id=AA1, first strand: chain 'A' and resid 368 through 373 removed outlier: 6.729A pdb=" N SER A 379 " --> pdb=" O GLU A 371 " (cutoff:3.500A) removed outlier: 4.761A pdb=" N ALA A 373 " --> pdb=" O VAL A 377 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N VAL A 377 " --> pdb=" O ALA A 373 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N SER A 380 " --> pdb=" O VAL A 744 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 368 through 373 removed outlier: 6.729A pdb=" N SER D 379 " --> pdb=" O GLU D 371 " (cutoff:3.500A) removed outlier: 4.761A pdb=" N ALA D 373 " --> pdb=" O VAL D 377 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N VAL D 377 " --> pdb=" O ALA D 373 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N SER D 380 " --> pdb=" O VAL D 744 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 368 through 373 removed outlier: 6.730A pdb=" N SER B 379 " --> pdb=" O GLU B 371 " (cutoff:3.500A) removed outlier: 4.761A pdb=" N ALA B 373 " --> pdb=" O VAL B 377 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N VAL B 377 " --> pdb=" O ALA B 373 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N SER B 380 " --> pdb=" O VAL B 744 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 368 through 373 removed outlier: 6.729A pdb=" N SER C 379 " --> pdb=" O GLU C 371 " (cutoff:3.500A) removed outlier: 4.761A pdb=" N ALA C 373 " --> pdb=" O VAL C 377 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N VAL C 377 " --> pdb=" O ALA C 373 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N SER C 380 " --> pdb=" O VAL C 744 " (cutoff:3.500A) 996 hydrogen bonds defined for protein. 2904 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: 8.54 Time building geometry restraints manager: 4.69 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 16313 1.03 - 1.23: 1268 1.23 - 1.42: 7471 1.42 - 1.62: 10056 1.62 - 1.81: 172 Bond restraints: 35280 Sorted by residual: bond pdb=" N THR C 302 " pdb=" H THR C 302 " ideal model delta sigma weight residual 0.860 1.038 -0.178 2.00e-02 2.50e+03 7.90e+01 bond pdb=" N THR D 302 " pdb=" H THR D 302 " ideal model delta sigma weight residual 0.860 1.038 -0.178 2.00e-02 2.50e+03 7.90e+01 bond pdb=" N THR B 302 " pdb=" H THR B 302 " ideal model delta sigma weight residual 0.860 1.038 -0.178 2.00e-02 2.50e+03 7.90e+01 bond pdb=" N THR A 302 " pdb=" H THR A 302 " ideal model delta sigma weight residual 0.860 1.038 -0.178 2.00e-02 2.50e+03 7.90e+01 bond pdb=" N ASP A 281 " pdb=" H ASP A 281 " ideal model delta sigma weight residual 0.860 1.038 -0.178 2.00e-02 2.50e+03 7.89e+01 ... (remaining 35275 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.42: 63316 4.42 - 8.84: 212 8.84 - 13.26: 12 13.26 - 17.68: 4 17.68 - 22.10: 4 Bond angle restraints: 63548 Sorted by residual: angle pdb=" CB GLU C 249 " pdb=" CG GLU C 249 " pdb=" CD GLU C 249 " ideal model delta sigma weight residual 112.60 98.56 14.04 1.70e+00 3.46e-01 6.82e+01 angle pdb=" CB GLU D 249 " pdb=" CG GLU D 249 " pdb=" CD GLU D 249 " ideal model delta sigma weight residual 112.60 98.56 14.04 1.70e+00 3.46e-01 6.82e+01 angle pdb=" CB GLU A 249 " pdb=" CG GLU A 249 " pdb=" CD GLU A 249 " ideal model delta sigma weight residual 112.60 98.56 14.04 1.70e+00 3.46e-01 6.82e+01 angle pdb=" CB GLU B 249 " pdb=" CG GLU B 249 " pdb=" CD GLU B 249 " ideal model delta sigma weight residual 112.60 98.56 14.04 1.70e+00 3.46e-01 6.82e+01 angle pdb=" O1 8IJ D 901 " pdb=" P2 8IJ D 901 " pdb=" O3 8IJ D 901 " ideal model delta sigma weight residual 121.24 99.14 22.10 3.00e+00 1.11e-01 5.43e+01 ... (remaining 63543 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.04: 15707 27.04 - 54.08: 821 54.08 - 81.12: 184 81.12 - 108.16: 32 108.16 - 135.20: 4 Dihedral angle restraints: 16748 sinusoidal: 8976 harmonic: 7772 Sorted by residual: dihedral pdb=" C50 8IJ C 901 " pdb=" C51 8IJ C 901 " pdb=" C52 8IJ C 901 " pdb=" C53 8IJ C 901 " ideal model delta sinusoidal sigma weight residual 60.97 -163.83 -135.20 1 3.00e+01 1.11e-03 1.82e+01 dihedral pdb=" C50 8IJ A 901 " pdb=" C51 8IJ A 901 " pdb=" C52 8IJ A 901 " pdb=" C53 8IJ A 901 " ideal model delta sinusoidal sigma weight residual 60.97 -163.85 -135.18 1 3.00e+01 1.11e-03 1.82e+01 dihedral pdb=" C50 8IJ B 901 " pdb=" C51 8IJ B 901 " pdb=" C52 8IJ B 901 " pdb=" C53 8IJ B 901 " ideal model delta sinusoidal sigma weight residual 60.97 -163.86 -135.17 1 3.00e+01 1.11e-03 1.82e+01 ... (remaining 16745 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 1853 0.034 - 0.068: 583 0.068 - 0.101: 208 0.101 - 0.135: 59 0.135 - 0.169: 17 Chirality restraints: 2720 Sorted by residual: chirality pdb=" CA THR A 302 " pdb=" N THR A 302 " pdb=" C THR A 302 " pdb=" CB THR A 302 " both_signs ideal model delta sigma weight residual False 2.53 2.70 -0.17 2.00e-01 2.50e+01 7.15e-01 chirality pdb=" CA THR C 302 " pdb=" N THR C 302 " pdb=" C THR C 302 " pdb=" CB THR C 302 " both_signs ideal model delta sigma weight residual False 2.53 2.70 -0.17 2.00e-01 2.50e+01 7.15e-01 chirality pdb=" CA THR D 302 " pdb=" N THR D 302 " pdb=" C THR D 302 " pdb=" CB THR D 302 " both_signs ideal model delta sigma weight residual False 2.53 2.70 -0.17 2.00e-01 2.50e+01 7.15e-01 ... (remaining 2717 not shown) Planarity restraints: 5036 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN B 232 " -0.263 2.00e-02 2.50e+03 2.66e-01 1.06e+03 pdb=" CG ASN B 232 " 0.015 2.00e-02 2.50e+03 pdb=" OD1 ASN B 232 " 0.255 2.00e-02 2.50e+03 pdb=" ND2 ASN B 232 " -0.000 2.00e-02 2.50e+03 pdb="HD21 ASN B 232 " -0.384 2.00e-02 2.50e+03 pdb="HD22 ASN B 232 " 0.378 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 232 " 0.263 2.00e-02 2.50e+03 2.66e-01 1.06e+03 pdb=" CG ASN C 232 " -0.015 2.00e-02 2.50e+03 pdb=" OD1 ASN C 232 " -0.255 2.00e-02 2.50e+03 pdb=" ND2 ASN C 232 " 0.000 2.00e-02 2.50e+03 pdb="HD21 ASN C 232 " 0.384 2.00e-02 2.50e+03 pdb="HD22 ASN C 232 " -0.378 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 232 " -0.263 2.00e-02 2.50e+03 2.66e-01 1.06e+03 pdb=" CG ASN A 232 " 0.015 2.00e-02 2.50e+03 pdb=" OD1 ASN A 232 " 0.255 2.00e-02 2.50e+03 pdb=" ND2 ASN A 232 " -0.000 2.00e-02 2.50e+03 pdb="HD21 ASN A 232 " -0.384 2.00e-02 2.50e+03 pdb="HD22 ASN A 232 " 0.378 2.00e-02 2.50e+03 ... (remaining 5033 not shown) Histogram of nonbonded interaction distances: 1.62 - 2.21: 2856 2.21 - 2.81: 72996 2.81 - 3.41: 94969 3.41 - 4.00: 120912 4.00 - 4.60: 187480 Nonbonded interactions: 479213 Sorted by model distance: nonbonded pdb=" OE1 GLU A 359 " pdb=" H CYS A 362 " model vdw 1.617 2.450 nonbonded pdb=" OE1 GLU C 359 " pdb=" H CYS C 362 " model vdw 1.617 2.450 nonbonded pdb=" OE1 GLU B 359 " pdb=" H CYS B 362 " model vdw 1.617 2.450 nonbonded pdb=" OE1 GLU D 359 " pdb=" H CYS D 362 " model vdw 1.617 2.450 nonbonded pdb=" HA GLU A 536 " pdb=" HE2 PHE D 655 " model vdw 1.648 2.270 ... (remaining 479208 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 199 through 901) selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.670 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.220 Extract box with map and model: 0.630 Check model and map are aligned: 0.110 Set scattering table: 0.090 Process input model: 32.910 Find NCS groups from input model: 0.640 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.680 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8263 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 : 0.006 0.072 17844 Z= 0.398 Angle : 0.976 22.103 24144 Z= 0.599 Chirality : 0.041 0.169 2720 Planarity : 0.005 0.053 2972 Dihedral : 18.263 135.196 6640 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.40 % Favored : 89.60 % Rotamer: Outliers : 2.13 % Allowed : 1.07 % Favored : 96.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: -0.04 (0.19), residues: 2116 helix: 1.41 (0.15), residues: 1264 sheet: -0.14 (0.58), residues: 84 loop : -2.61 (0.21), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 701 TYR 0.010 0.001 TYR B 351 PHE 0.022 0.001 PHE B 655 TRP 0.039 0.002 TRP B 272 HIS 0.001 0.000 HIS D 364 Details of bonding type rmsd/Z covalent geometry : bond 0.00619 / 0.40 (17844) covalent geometry : angle 0.97611 / 0.60 (24144) hydrogen bonds : bond 0.12685 / 8.67 ( 996) hydrogen bonds : angle 5.81500 / 4.09 ( 2904) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4232 Ramachandran restraints generated. 2116 Oldfield, 0 Emsley, 2116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4232 Ramachandran restraints generated. 2116 Oldfield, 0 Emsley, 2116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 650 residues out of total 1876 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 610 time to evaluate : 0.883 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 300 ASP cc_start: 0.8509 (p0) cc_final: 0.8291 (p0) REVERT: A 351 TYR cc_start: 0.8775 (t80) cc_final: 0.8346 (t80) REVERT: A 397 GLU cc_start: 0.8481 (tm-30) cc_final: 0.8157 (tm-30) REVERT: A 442 CYS cc_start: 0.8383 (m) cc_final: 0.8127 (m) REVERT: A 481 SER cc_start: 0.9378 (p) cc_final: 0.9121 (p) REVERT: D 300 ASP cc_start: 0.8510 (p0) cc_final: 0.8293 (p0) REVERT: D 351 TYR cc_start: 0.8773 (t80) cc_final: 0.8345 (t80) REVERT: D 397 GLU cc_start: 0.8479 (tm-30) cc_final: 0.8157 (tm-30) REVERT: D 442 CYS cc_start: 0.8383 (m) cc_final: 0.8125 (m) REVERT: D 481 SER cc_start: 0.9376 (p) cc_final: 0.9119 (p) REVERT: B 300 ASP cc_start: 0.8511 (p0) cc_final: 0.8293 (p0) REVERT: B 351 TYR cc_start: 0.8776 (t80) cc_final: 0.8347 (t80) REVERT: B 397 GLU cc_start: 0.8482 (tm-30) cc_final: 0.8161 (tm-30) REVERT: B 442 CYS cc_start: 0.8383 (m) cc_final: 0.8125 (m) REVERT: B 481 SER cc_start: 0.9377 (p) cc_final: 0.9120 (p) REVERT: C 300 ASP cc_start: 0.8511 (p0) cc_final: 0.8293 (p0) REVERT: C 351 TYR cc_start: 0.8775 (t80) cc_final: 0.8346 (t80) REVERT: C 397 GLU cc_start: 0.8480 (tm-30) cc_final: 0.8157 (tm-30) REVERT: C 442 CYS cc_start: 0.8382 (m) cc_final: 0.8125 (m) REVERT: C 481 SER cc_start: 0.9371 (p) cc_final: 0.9117 (p) outliers start: 40 outliers final: 10 residues processed: 618 average time/residue: 0.2847 time to fit residues: 274.4895 Evaluate side-chains 492 residues out of total 1876 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 482 time to evaluate : 0.914 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 304 PHE Chi-restraints excluded: chain A residue 352 ILE Chi-restraints excluded: chain A residue 536 GLU Chi-restraints excluded: chain D residue 304 PHE Chi-restraints excluded: chain D residue 352 ILE Chi-restraints excluded: chain D residue 536 GLU Chi-restraints excluded: chain B residue 304 PHE Chi-restraints excluded: chain B residue 352 ILE Chi-restraints excluded: chain C residue 304 PHE Chi-restraints excluded: chain C residue 352 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 98 optimal weight: 0.5980 chunk 194 optimal weight: 0.9980 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 0.7980 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 0.6980 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 1.9990 chunk 200 optimal weight: 2.9990 chunk 77 optimal weight: 0.5980 chunk 122 optimal weight: 3.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.139382 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.101598 restraints weight = 90201.079| |-----------------------------------------------------------------------------| r_work (start): 0.3175 rms_B_bonded: 3.17 r_work: 0.3040 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3040 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8329 moved from start: 0.1510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 17844 Z= 0.124 Angle : 0.521 5.496 24144 Z= 0.282 Chirality : 0.035 0.122 2720 Planarity : 0.004 0.051 2972 Dihedral : 10.920 77.470 2618 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.84 % Favored : 92.16 % Rotamer: Outliers : 1.49 % Allowed : 11.83 % Favored : 86.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: 0.48 (0.19), residues: 2116 helix: 1.93 (0.15), residues: 1288 sheet: -0.27 (0.56), residues: 84 loop : -2.72 (0.21), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D 211 TYR 0.014 0.001 TYR D 309 PHE 0.014 0.001 PHE A 304 TRP 0.006 0.001 TRP D 272 HIS 0.002 0.000 HIS B 289 Details of bonding type rmsd/Z covalent geometry : bond 0.00257 / 0.12 (17844) covalent geometry : angle 0.52076 / 0.28 (24144) hydrogen bonds : bond 0.04853 / 3.23 ( 996) hydrogen bonds : angle 4.29430 / 3.07 ( 2904) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4232 Ramachandran restraints generated. 2116 Oldfield, 0 Emsley, 2116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4232 Ramachandran restraints generated. 2116 Oldfield, 0 Emsley, 2116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 553 residues out of total 1876 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 525 time to evaluate : 0.950 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 304 PHE cc_start: 0.9230 (OUTLIER) cc_final: 0.8919 (p90) REVERT: A 351 TYR cc_start: 0.8803 (t80) cc_final: 0.8432 (t80) REVERT: A 397 GLU cc_start: 0.8717 (tm-30) cc_final: 0.8344 (tm-30) REVERT: A 442 CYS cc_start: 0.9098 (m) cc_final: 0.8847 (m) REVERT: D 304 PHE cc_start: 0.9227 (OUTLIER) cc_final: 0.8915 (p90) REVERT: D 351 TYR cc_start: 0.8799 (t80) cc_final: 0.8432 (t80) REVERT: D 397 GLU cc_start: 0.8718 (tm-30) cc_final: 0.8347 (tm-30) REVERT: D 442 CYS cc_start: 0.9088 (m) cc_final: 0.8837 (m) REVERT: B 304 PHE cc_start: 0.9236 (OUTLIER) cc_final: 0.8930 (p90) REVERT: B 351 TYR cc_start: 0.8795 (t80) cc_final: 0.8426 (t80) REVERT: B 397 GLU cc_start: 0.8699 (tm-30) cc_final: 0.8326 (tm-30) REVERT: B 442 CYS cc_start: 0.9068 (m) cc_final: 0.8813 (m) REVERT: C 304 PHE cc_start: 0.9231 (OUTLIER) cc_final: 0.8919 (p90) REVERT: C 351 TYR cc_start: 0.8800 (t80) cc_final: 0.8430 (t80) REVERT: C 397 GLU cc_start: 0.8716 (tm-30) cc_final: 0.8346 (tm-30) REVERT: C 442 CYS cc_start: 0.9067 (m) cc_final: 0.8813 (m) outliers start: 28 outliers final: 16 residues processed: 531 average time/residue: 0.2800 time to fit residues: 235.1457 Evaluate side-chains 526 residues out of total 1876 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 506 time to evaluate : 0.920 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 267 LEU Chi-restraints excluded: chain A residue 304 PHE Chi-restraints excluded: chain A residue 352 ILE Chi-restraints excluded: chain A residue 388 ASP Chi-restraints excluded: chain A residue 514 ILE Chi-restraints excluded: chain D residue 267 LEU Chi-restraints excluded: chain D residue 304 PHE Chi-restraints excluded: chain D residue 352 ILE Chi-restraints excluded: chain D residue 388 ASP Chi-restraints excluded: chain D residue 514 ILE Chi-restraints excluded: chain B residue 267 LEU Chi-restraints excluded: chain B residue 304 PHE Chi-restraints excluded: chain B residue 352 ILE Chi-restraints excluded: chain B residue 388 ASP Chi-restraints excluded: chain B residue 514 ILE Chi-restraints excluded: chain C residue 267 LEU Chi-restraints excluded: chain C residue 304 PHE Chi-restraints excluded: chain C residue 352 ILE Chi-restraints excluded: chain C residue 388 ASP Chi-restraints excluded: chain C residue 514 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 162 optimal weight: 7.9990 chunk 66 optimal weight: 1.9990 chunk 191 optimal weight: 3.9990 chunk 131 optimal weight: 0.0010 chunk 1 optimal weight: 0.7980 chunk 113 optimal weight: 5.9990 chunk 177 optimal weight: 5.9990 chunk 42 optimal weight: 2.9990 chunk 197 optimal weight: 2.9990 chunk 147 optimal weight: 2.9990 chunk 61 optimal weight: 2.9990 overall best weight: 1.7592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.137582 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.099099 restraints weight = 90804.096| |-----------------------------------------------------------------------------| r_work (start): 0.3143 rms_B_bonded: 3.22 r_work: 0.3014 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3014 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8362 moved from start: 0.1801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 17844 Z= 0.173 Angle : 0.518 5.069 24144 Z= 0.288 Chirality : 0.035 0.120 2720 Planarity : 0.003 0.043 2972 Dihedral : 10.213 89.170 2612 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.88 % Favored : 91.12 % Rotamer: Outliers : 2.13 % Allowed : 14.93 % Favored : 82.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: 0.52 (0.19), residues: 2116 helix: 2.02 (0.15), residues: 1288 sheet: -0.28 (0.57), residues: 84 loop : -2.81 (0.20), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 701 TYR 0.016 0.001 TYR B 309 PHE 0.011 0.001 PHE D 304 TRP 0.006 0.001 TRP B 272 HIS 0.001 0.000 HIS A 206 Details of bonding type rmsd/Z covalent geometry : bond 0.00371 / 0.17 (17844) covalent geometry : angle 0.51849 / 0.29 (24144) hydrogen bonds : bond 0.04904 / 3.25 ( 996) hydrogen bonds : angle 4.20879 / 3.02 ( 2904) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4232 Ramachandran restraints generated. 2116 Oldfield, 0 Emsley, 2116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4232 Ramachandran restraints generated. 2116 Oldfield, 0 Emsley, 2116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 562 residues out of total 1876 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 522 time to evaluate : 0.924 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 304 PHE cc_start: 0.9243 (OUTLIER) cc_final: 0.8931 (p90) REVERT: A 397 GLU cc_start: 0.8763 (tm-30) cc_final: 0.8327 (tm-30) REVERT: A 442 CYS cc_start: 0.9141 (m) cc_final: 0.8901 (m) REVERT: D 304 PHE cc_start: 0.9235 (OUTLIER) cc_final: 0.8927 (p90) REVERT: D 397 GLU cc_start: 0.8766 (tm-30) cc_final: 0.8335 (tm-30) REVERT: D 442 CYS cc_start: 0.9136 (m) cc_final: 0.8894 (m) REVERT: B 304 PHE cc_start: 0.9239 (OUTLIER) cc_final: 0.8936 (p90) REVERT: B 397 GLU cc_start: 0.8759 (tm-30) cc_final: 0.8325 (tm-30) REVERT: B 442 CYS cc_start: 0.9127 (m) cc_final: 0.8882 (m) REVERT: C 304 PHE cc_start: 0.9246 (OUTLIER) cc_final: 0.8941 (p90) REVERT: C 397 GLU cc_start: 0.8773 (tm-30) cc_final: 0.8342 (tm-30) REVERT: C 442 CYS cc_start: 0.9135 (m) cc_final: 0.8892 (m) outliers start: 40 outliers final: 28 residues processed: 534 average time/residue: 0.2753 time to fit residues: 232.7968 Evaluate side-chains 502 residues out of total 1876 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 470 time to evaluate : 0.910 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 267 LEU Chi-restraints excluded: chain A residue 304 PHE Chi-restraints excluded: chain A residue 352 ILE Chi-restraints excluded: chain A residue 388 ASP Chi-restraints excluded: chain A residue 493 ILE Chi-restraints excluded: chain A residue 514 ILE Chi-restraints excluded: chain A residue 520 SER Chi-restraints excluded: chain A residue 686 VAL Chi-restraints excluded: chain D residue 267 LEU Chi-restraints excluded: chain D residue 304 PHE Chi-restraints excluded: chain D residue 352 ILE Chi-restraints excluded: chain D residue 388 ASP Chi-restraints excluded: chain D residue 493 ILE Chi-restraints excluded: chain D residue 514 ILE Chi-restraints excluded: chain D residue 520 SER Chi-restraints excluded: chain D residue 686 VAL Chi-restraints excluded: chain B residue 267 LEU Chi-restraints excluded: chain B residue 304 PHE Chi-restraints excluded: chain B residue 352 ILE Chi-restraints excluded: chain B residue 388 ASP Chi-restraints excluded: chain B residue 493 ILE Chi-restraints excluded: chain B residue 514 ILE Chi-restraints excluded: chain B residue 520 SER Chi-restraints excluded: chain B residue 686 VAL Chi-restraints excluded: chain C residue 267 LEU Chi-restraints excluded: chain C residue 304 PHE Chi-restraints excluded: chain C residue 352 ILE Chi-restraints excluded: chain C residue 388 ASP Chi-restraints excluded: chain C residue 493 ILE Chi-restraints excluded: chain C residue 514 ILE Chi-restraints excluded: chain C residue 520 SER Chi-restraints excluded: chain C residue 686 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 71 optimal weight: 6.9990 chunk 90 optimal weight: 0.6980 chunk 122 optimal weight: 6.9990 chunk 118 optimal weight: 5.9990 chunk 40 optimal weight: 4.9990 chunk 96 optimal weight: 1.9990 chunk 120 optimal weight: 4.9990 chunk 186 optimal weight: 1.9990 chunk 42 optimal weight: 2.9990 chunk 107 optimal weight: 0.7980 chunk 155 optimal weight: 1.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.138167 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.099225 restraints weight = 90765.514| |-----------------------------------------------------------------------------| r_work (start): 0.3147 rms_B_bonded: 3.27 r_work: 0.3017 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3017 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8355 moved from start: 0.2000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 17844 Z= 0.153 Angle : 0.510 5.231 24144 Z= 0.279 Chirality : 0.034 0.118 2720 Planarity : 0.004 0.060 2972 Dihedral : 9.842 81.754 2612 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.47 % Favored : 92.53 % Rotamer: Outliers : 2.24 % Allowed : 15.30 % Favored : 82.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: 0.66 (0.19), residues: 2116 helix: 2.13 (0.15), residues: 1288 sheet: -0.33 (0.57), residues: 84 loop : -2.73 (0.20), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 499 TYR 0.012 0.001 TYR C 309 PHE 0.010 0.001 PHE A 304 TRP 0.006 0.001 TRP C 272 HIS 0.001 0.000 HIS A 289 Details of bonding type rmsd/Z covalent geometry : bond 0.00327 / 0.15 (17844) covalent geometry : angle 0.51047 / 0.28 (24144) hydrogen bonds : bond 0.04701 / 3.11 ( 996) hydrogen bonds : angle 4.02793 / 2.89 ( 2904) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4232 Ramachandran restraints generated. 2116 Oldfield, 0 Emsley, 2116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4232 Ramachandran restraints generated. 2116 Oldfield, 0 Emsley, 2116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 553 residues out of total 1876 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 511 time to evaluate : 0.859 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 267 LEU cc_start: 0.8499 (OUTLIER) cc_final: 0.8224 (tt) REVERT: A 309 TYR cc_start: 0.9005 (t80) cc_final: 0.8795 (t80) REVERT: A 397 GLU cc_start: 0.8749 (tm-30) cc_final: 0.8278 (tm-30) REVERT: A 442 CYS cc_start: 0.9126 (m) cc_final: 0.8870 (m) REVERT: D 267 LEU cc_start: 0.8496 (OUTLIER) cc_final: 0.8210 (tt) REVERT: D 304 PHE cc_start: 0.9235 (OUTLIER) cc_final: 0.8905 (p90) REVERT: D 397 GLU cc_start: 0.8765 (tm-30) cc_final: 0.8300 (tm-30) REVERT: D 442 CYS cc_start: 0.9149 (m) cc_final: 0.8894 (m) REVERT: B 267 LEU cc_start: 0.8500 (OUTLIER) cc_final: 0.8217 (tt) REVERT: B 304 PHE cc_start: 0.9238 (OUTLIER) cc_final: 0.8917 (p90) REVERT: B 397 GLU cc_start: 0.8761 (tm-30) cc_final: 0.8294 (tm-30) REVERT: B 442 CYS cc_start: 0.9135 (m) cc_final: 0.8881 (m) REVERT: C 267 LEU cc_start: 0.8497 (OUTLIER) cc_final: 0.8220 (tt) REVERT: C 309 TYR cc_start: 0.9028 (t80) cc_final: 0.8827 (t80) REVERT: C 397 GLU cc_start: 0.8773 (tm-30) cc_final: 0.8309 (tm-30) REVERT: C 442 CYS cc_start: 0.9137 (m) cc_final: 0.8880 (m) outliers start: 42 outliers final: 28 residues processed: 519 average time/residue: 0.2750 time to fit residues: 226.1940 Evaluate side-chains 502 residues out of total 1876 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 468 time to evaluate : 1.002 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 267 LEU Chi-restraints excluded: chain A residue 352 ILE Chi-restraints excluded: chain A residue 388 ASP Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain A residue 493 ILE Chi-restraints excluded: chain A residue 514 ILE Chi-restraints excluded: chain A residue 520 SER Chi-restraints excluded: chain A residue 686 VAL Chi-restraints excluded: chain D residue 267 LEU Chi-restraints excluded: chain D residue 304 PHE Chi-restraints excluded: chain D residue 352 ILE Chi-restraints excluded: chain D residue 388 ASP Chi-restraints excluded: chain D residue 440 VAL Chi-restraints excluded: chain D residue 493 ILE Chi-restraints excluded: chain D residue 514 ILE Chi-restraints excluded: chain D residue 520 SER Chi-restraints excluded: chain D residue 686 VAL Chi-restraints excluded: chain B residue 267 LEU Chi-restraints excluded: chain B residue 304 PHE Chi-restraints excluded: chain B residue 352 ILE Chi-restraints excluded: chain B residue 388 ASP Chi-restraints excluded: chain B residue 440 VAL Chi-restraints excluded: chain B residue 493 ILE Chi-restraints excluded: chain B residue 514 ILE Chi-restraints excluded: chain B residue 520 SER Chi-restraints excluded: chain B residue 686 VAL Chi-restraints excluded: chain C residue 267 LEU Chi-restraints excluded: chain C residue 352 ILE Chi-restraints excluded: chain C residue 388 ASP Chi-restraints excluded: chain C residue 440 VAL Chi-restraints excluded: chain C residue 493 ILE Chi-restraints excluded: chain C residue 514 ILE Chi-restraints excluded: chain C residue 520 SER Chi-restraints excluded: chain C residue 686 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 141 optimal weight: 1.9990 chunk 63 optimal weight: 1.9990 chunk 138 optimal weight: 2.9990 chunk 58 optimal weight: 4.9990 chunk 108 optimal weight: 7.9990 chunk 186 optimal weight: 2.9990 chunk 15 optimal weight: 3.9990 chunk 56 optimal weight: 5.9990 chunk 91 optimal weight: 1.9990 chunk 179 optimal weight: 3.9990 chunk 166 optimal weight: 5.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 228 GLN D 228 GLN B 228 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.136180 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.097783 restraints weight = 91475.662| |-----------------------------------------------------------------------------| r_work (start): 0.3118 rms_B_bonded: 3.20 r_work: 0.2985 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.2985 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8395 moved from start: 0.2164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 17844 Z= 0.220 Angle : 0.548 5.085 24144 Z= 0.304 Chirality : 0.036 0.123 2720 Planarity : 0.004 0.050 2972 Dihedral : 9.728 72.440 2608 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.65 % Favored : 91.35 % Rotamer: Outliers : 2.67 % Allowed : 15.57 % Favored : 81.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: 0.47 (0.19), residues: 2116 helix: 2.00 (0.15), residues: 1292 sheet: -0.41 (0.57), residues: 84 loop : -2.88 (0.20), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 701 TYR 0.011 0.001 TYR C 309 PHE 0.018 0.001 PHE A 304 TRP 0.008 0.001 TRP B 740 HIS 0.003 0.001 HIS B 364 Details of bonding type rmsd/Z covalent geometry : bond 0.00472 / 0.22 (17844) covalent geometry : angle 0.54764 / 0.30 (24144) hydrogen bonds : bond 0.05072 / 3.35 ( 996) hydrogen bonds : angle 4.22013 / 3.03 ( 2904) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4232 Ramachandran restraints generated. 2116 Oldfield, 0 Emsley, 2116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4232 Ramachandran restraints generated. 2116 Oldfield, 0 Emsley, 2116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 545 residues out of total 1876 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 495 time to evaluate : 0.850 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 397 GLU cc_start: 0.8755 (tm-30) cc_final: 0.8253 (tm-30) REVERT: A 442 CYS cc_start: 0.9149 (m) cc_final: 0.8904 (m) REVERT: A 551 ASN cc_start: 0.9547 (m-40) cc_final: 0.9309 (m110) REVERT: D 304 PHE cc_start: 0.9250 (OUTLIER) cc_final: 0.8931 (p90) REVERT: D 397 GLU cc_start: 0.8754 (tm-30) cc_final: 0.8255 (tm-30) REVERT: D 442 CYS cc_start: 0.9169 (m) cc_final: 0.8927 (m) REVERT: D 551 ASN cc_start: 0.9560 (m-40) cc_final: 0.9327 (m110) REVERT: B 304 PHE cc_start: 0.9256 (OUTLIER) cc_final: 0.8939 (p90) REVERT: B 397 GLU cc_start: 0.8752 (tm-30) cc_final: 0.8254 (tm-30) REVERT: B 442 CYS cc_start: 0.9180 (m) cc_final: 0.8935 (m) REVERT: B 551 ASN cc_start: 0.9553 (m-40) cc_final: 0.9318 (m110) REVERT: C 397 GLU cc_start: 0.8763 (tm-30) cc_final: 0.8265 (tm-30) REVERT: C 442 CYS cc_start: 0.9154 (m) cc_final: 0.8914 (m) REVERT: C 551 ASN cc_start: 0.9553 (m-40) cc_final: 0.9320 (m110) outliers start: 50 outliers final: 44 residues processed: 503 average time/residue: 0.2649 time to fit residues: 212.3291 Evaluate side-chains 510 residues out of total 1876 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 464 time to evaluate : 0.885 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 267 LEU Chi-restraints excluded: chain A residue 352 ILE Chi-restraints excluded: chain A residue 388 ASP Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain A residue 473 PHE Chi-restraints excluded: chain A residue 493 ILE Chi-restraints excluded: chain A residue 514 ILE Chi-restraints excluded: chain A residue 520 SER Chi-restraints excluded: chain A residue 586 VAL Chi-restraints excluded: chain A residue 592 SER Chi-restraints excluded: chain A residue 686 VAL Chi-restraints excluded: chain D residue 267 LEU Chi-restraints excluded: chain D residue 304 PHE Chi-restraints excluded: chain D residue 352 ILE Chi-restraints excluded: chain D residue 388 ASP Chi-restraints excluded: chain D residue 440 VAL Chi-restraints excluded: chain D residue 473 PHE Chi-restraints excluded: chain D residue 493 ILE Chi-restraints excluded: chain D residue 514 ILE Chi-restraints excluded: chain D residue 520 SER Chi-restraints excluded: chain D residue 586 VAL Chi-restraints excluded: chain D residue 592 SER Chi-restraints excluded: chain D residue 686 VAL Chi-restraints excluded: chain B residue 267 LEU Chi-restraints excluded: chain B residue 304 PHE Chi-restraints excluded: chain B residue 352 ILE Chi-restraints excluded: chain B residue 388 ASP Chi-restraints excluded: chain B residue 440 VAL Chi-restraints excluded: chain B residue 473 PHE Chi-restraints excluded: chain B residue 493 ILE Chi-restraints excluded: chain B residue 514 ILE Chi-restraints excluded: chain B residue 520 SER Chi-restraints excluded: chain B residue 586 VAL Chi-restraints excluded: chain B residue 592 SER Chi-restraints excluded: chain B residue 686 VAL Chi-restraints excluded: chain C residue 267 LEU Chi-restraints excluded: chain C residue 352 ILE Chi-restraints excluded: chain C residue 388 ASP Chi-restraints excluded: chain C residue 440 VAL Chi-restraints excluded: chain C residue 473 PHE Chi-restraints excluded: chain C residue 493 ILE Chi-restraints excluded: chain C residue 514 ILE Chi-restraints excluded: chain C residue 520 SER Chi-restraints excluded: chain C residue 586 VAL Chi-restraints excluded: chain C residue 592 SER Chi-restraints excluded: chain C residue 686 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 128 optimal weight: 3.9990 chunk 85 optimal weight: 3.9990 chunk 34 optimal weight: 1.9990 chunk 175 optimal weight: 5.9990 chunk 151 optimal weight: 0.9990 chunk 59 optimal weight: 7.9990 chunk 154 optimal weight: 0.8980 chunk 199 optimal weight: 2.9990 chunk 153 optimal weight: 2.9990 chunk 93 optimal weight: 0.1980 chunk 19 optimal weight: 5.9990 overall best weight: 1.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.137604 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.099711 restraints weight = 90394.005| |-----------------------------------------------------------------------------| r_work (start): 0.3149 rms_B_bonded: 3.22 r_work: 0.3014 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3014 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8358 moved from start: 0.2247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 17844 Z= 0.147 Angle : 0.508 5.550 24144 Z= 0.277 Chirality : 0.034 0.116 2720 Planarity : 0.005 0.076 2972 Dihedral : 9.342 71.303 2608 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.37 % Favored : 92.63 % Rotamer: Outliers : 2.72 % Allowed : 16.36 % Favored : 80.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: 0.64 (0.19), residues: 2116 helix: 2.18 (0.15), residues: 1292 sheet: -0.44 (0.56), residues: 84 loop : -2.89 (0.20), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG D 211 TYR 0.013 0.001 TYR C 309 PHE 0.018 0.001 PHE C 304 TRP 0.007 0.001 TRP A 740 HIS 0.001 0.000 HIS D 289 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.15 (17844) covalent geometry : angle 0.50842 / 0.28 (24144) hydrogen bonds : bond 0.04721 / 3.13 ( 996) hydrogen bonds : angle 3.96781 / 2.85 ( 2904) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4232 Ramachandran restraints generated. 2116 Oldfield, 0 Emsley, 2116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4232 Ramachandran restraints generated. 2116 Oldfield, 0 Emsley, 2116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 563 residues out of total 1876 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 512 time to evaluate : 0.722 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 397 GLU cc_start: 0.8717 (tm-30) cc_final: 0.8208 (tm-30) REVERT: A 428 ARG cc_start: 0.8685 (mmt90) cc_final: 0.8417 (mmt90) REVERT: A 442 CYS cc_start: 0.9141 (m) cc_final: 0.8876 (m) REVERT: D 304 PHE cc_start: 0.9250 (OUTLIER) cc_final: 0.8895 (p90) REVERT: D 397 GLU cc_start: 0.8731 (tm-30) cc_final: 0.8228 (tm-30) REVERT: D 428 ARG cc_start: 0.8679 (mmt90) cc_final: 0.8409 (mmt90) REVERT: D 442 CYS cc_start: 0.9144 (m) cc_final: 0.8878 (m) REVERT: B 304 PHE cc_start: 0.9253 (OUTLIER) cc_final: 0.8908 (p90) REVERT: B 397 GLU cc_start: 0.8722 (tm-30) cc_final: 0.8216 (tm-30) REVERT: B 428 ARG cc_start: 0.8684 (mmt90) cc_final: 0.8418 (mmt90) REVERT: B 442 CYS cc_start: 0.9147 (m) cc_final: 0.8881 (m) REVERT: C 397 GLU cc_start: 0.8738 (tm-30) cc_final: 0.8235 (tm-30) REVERT: C 428 ARG cc_start: 0.8674 (mmt90) cc_final: 0.8407 (mmt90) REVERT: C 442 CYS cc_start: 0.9145 (m) cc_final: 0.8878 (m) outliers start: 51 outliers final: 44 residues processed: 524 average time/residue: 0.2618 time to fit residues: 219.3270 Evaluate side-chains 512 residues out of total 1876 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 466 time to evaluate : 0.841 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 267 LEU Chi-restraints excluded: chain A residue 352 ILE Chi-restraints excluded: chain A residue 388 ASP Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain A residue 493 ILE Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 514 ILE Chi-restraints excluded: chain A residue 520 SER Chi-restraints excluded: chain A residue 578 CYS Chi-restraints excluded: chain A residue 586 VAL Chi-restraints excluded: chain A residue 686 VAL Chi-restraints excluded: chain D residue 267 LEU Chi-restraints excluded: chain D residue 304 PHE Chi-restraints excluded: chain D residue 352 ILE Chi-restraints excluded: chain D residue 388 ASP Chi-restraints excluded: chain D residue 440 VAL Chi-restraints excluded: chain D residue 493 ILE Chi-restraints excluded: chain D residue 503 LEU Chi-restraints excluded: chain D residue 514 ILE Chi-restraints excluded: chain D residue 520 SER Chi-restraints excluded: chain D residue 578 CYS Chi-restraints excluded: chain D residue 586 VAL Chi-restraints excluded: chain D residue 686 VAL Chi-restraints excluded: chain B residue 267 LEU Chi-restraints excluded: chain B residue 304 PHE Chi-restraints excluded: chain B residue 352 ILE Chi-restraints excluded: chain B residue 388 ASP Chi-restraints excluded: chain B residue 440 VAL Chi-restraints excluded: chain B residue 493 ILE Chi-restraints excluded: chain B residue 503 LEU Chi-restraints excluded: chain B residue 514 ILE Chi-restraints excluded: chain B residue 520 SER Chi-restraints excluded: chain B residue 578 CYS Chi-restraints excluded: chain B residue 586 VAL Chi-restraints excluded: chain B residue 686 VAL Chi-restraints excluded: chain C residue 267 LEU Chi-restraints excluded: chain C residue 352 ILE Chi-restraints excluded: chain C residue 388 ASP Chi-restraints excluded: chain C residue 440 VAL Chi-restraints excluded: chain C residue 493 ILE Chi-restraints excluded: chain C residue 503 LEU Chi-restraints excluded: chain C residue 514 ILE Chi-restraints excluded: chain C residue 520 SER Chi-restraints excluded: chain C residue 578 CYS Chi-restraints excluded: chain C residue 586 VAL Chi-restraints excluded: chain C residue 686 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 14 optimal weight: 6.9990 chunk 62 optimal weight: 3.9990 chunk 9 optimal weight: 0.8980 chunk 112 optimal weight: 2.9990 chunk 97 optimal weight: 2.9990 chunk 209 optimal weight: 8.9990 chunk 63 optimal weight: 0.7980 chunk 42 optimal weight: 0.9980 chunk 156 optimal weight: 7.9990 chunk 20 optimal weight: 2.9990 chunk 13 optimal weight: 1.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.137319 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.099153 restraints weight = 90489.723| |-----------------------------------------------------------------------------| r_work (start): 0.3139 rms_B_bonded: 3.23 r_work: 0.3008 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3008 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8361 moved from start: 0.2350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 17844 Z= 0.157 Angle : 0.525 6.642 24144 Z= 0.286 Chirality : 0.035 0.115 2720 Planarity : 0.004 0.054 2972 Dihedral : 9.268 73.889 2608 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.65 % Favored : 91.35 % Rotamer: Outliers : 3.30 % Allowed : 16.90 % Favored : 79.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: 0.64 (0.19), residues: 2116 helix: 2.20 (0.15), residues: 1292 sheet: -0.33 (0.56), residues: 84 loop : -2.96 (0.20), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 701 TYR 0.009 0.001 TYR C 309 PHE 0.018 0.001 PHE A 304 TRP 0.007 0.001 TRP A 740 HIS 0.003 0.000 HIS A 364 Details of bonding type rmsd/Z covalent geometry : bond 0.00341 / 0.16 (17844) covalent geometry : angle 0.52537 / 0.29 (24144) hydrogen bonds : bond 0.04712 / 3.12 ( 996) hydrogen bonds : angle 3.96563 / 2.84 ( 2904) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4232 Ramachandran restraints generated. 2116 Oldfield, 0 Emsley, 2116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4232 Ramachandran restraints generated. 2116 Oldfield, 0 Emsley, 2116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 547 residues out of total 1876 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 485 time to evaluate : 0.945 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 397 GLU cc_start: 0.8728 (tm-30) cc_final: 0.8220 (tm-30) REVERT: A 442 CYS cc_start: 0.9164 (m) cc_final: 0.8897 (m) REVERT: D 304 PHE cc_start: 0.9246 (OUTLIER) cc_final: 0.8867 (p90) REVERT: D 397 GLU cc_start: 0.8738 (tm-30) cc_final: 0.8234 (tm-30) REVERT: D 442 CYS cc_start: 0.9142 (m) cc_final: 0.8872 (m) REVERT: B 304 PHE cc_start: 0.9249 (OUTLIER) cc_final: 0.8877 (p90) REVERT: B 397 GLU cc_start: 0.8730 (tm-30) cc_final: 0.8226 (tm-30) REVERT: B 442 CYS cc_start: 0.9148 (m) cc_final: 0.8882 (m) REVERT: C 397 GLU cc_start: 0.8741 (tm-30) cc_final: 0.8238 (tm-30) REVERT: C 442 CYS cc_start: 0.9153 (m) cc_final: 0.8885 (m) outliers start: 62 outliers final: 54 residues processed: 498 average time/residue: 0.2698 time to fit residues: 213.8537 Evaluate side-chains 529 residues out of total 1876 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 473 time to evaluate : 0.864 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 267 LEU Chi-restraints excluded: chain A residue 352 ILE Chi-restraints excluded: chain A residue 365 LEU Chi-restraints excluded: chain A residue 388 ASP Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain A residue 473 PHE Chi-restraints excluded: chain A residue 493 ILE Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 514 ILE Chi-restraints excluded: chain A residue 520 SER Chi-restraints excluded: chain A residue 578 CYS Chi-restraints excluded: chain A residue 586 VAL Chi-restraints excluded: chain A residue 592 SER Chi-restraints excluded: chain A residue 686 VAL Chi-restraints excluded: chain D residue 267 LEU Chi-restraints excluded: chain D residue 304 PHE Chi-restraints excluded: chain D residue 352 ILE Chi-restraints excluded: chain D residue 388 ASP Chi-restraints excluded: chain D residue 440 VAL Chi-restraints excluded: chain D residue 473 PHE Chi-restraints excluded: chain D residue 493 ILE Chi-restraints excluded: chain D residue 503 LEU Chi-restraints excluded: chain D residue 514 ILE Chi-restraints excluded: chain D residue 520 SER Chi-restraints excluded: chain D residue 578 CYS Chi-restraints excluded: chain D residue 586 VAL Chi-restraints excluded: chain D residue 592 SER Chi-restraints excluded: chain D residue 686 VAL Chi-restraints excluded: chain B residue 267 LEU Chi-restraints excluded: chain B residue 304 PHE Chi-restraints excluded: chain B residue 352 ILE Chi-restraints excluded: chain B residue 388 ASP Chi-restraints excluded: chain B residue 440 VAL Chi-restraints excluded: chain B residue 473 PHE Chi-restraints excluded: chain B residue 493 ILE Chi-restraints excluded: chain B residue 503 LEU Chi-restraints excluded: chain B residue 514 ILE Chi-restraints excluded: chain B residue 520 SER Chi-restraints excluded: chain B residue 578 CYS Chi-restraints excluded: chain B residue 586 VAL Chi-restraints excluded: chain B residue 592 SER Chi-restraints excluded: chain B residue 686 VAL Chi-restraints excluded: chain C residue 267 LEU Chi-restraints excluded: chain C residue 308 MET Chi-restraints excluded: chain C residue 352 ILE Chi-restraints excluded: chain C residue 365 LEU Chi-restraints excluded: chain C residue 388 ASP Chi-restraints excluded: chain C residue 440 VAL Chi-restraints excluded: chain C residue 493 ILE Chi-restraints excluded: chain C residue 503 LEU Chi-restraints excluded: chain C residue 514 ILE Chi-restraints excluded: chain C residue 520 SER Chi-restraints excluded: chain C residue 578 CYS Chi-restraints excluded: chain C residue 586 VAL Chi-restraints excluded: chain C residue 592 SER Chi-restraints excluded: chain C residue 686 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 95 optimal weight: 2.9990 chunk 28 optimal weight: 0.9980 chunk 62 optimal weight: 1.9990 chunk 148 optimal weight: 2.9990 chunk 209 optimal weight: 8.9990 chunk 39 optimal weight: 1.9990 chunk 203 optimal weight: 1.9990 chunk 189 optimal weight: 0.0970 chunk 34 optimal weight: 2.9990 chunk 140 optimal weight: 0.8980 chunk 207 optimal weight: 2.9990 overall best weight: 1.1982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.138385 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.100066 restraints weight = 90098.418| |-----------------------------------------------------------------------------| r_work (start): 0.3158 rms_B_bonded: 3.26 r_work: 0.3027 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3027 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8344 moved from start: 0.2420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 17844 Z= 0.136 Angle : 0.520 7.490 24144 Z= 0.280 Chirality : 0.034 0.116 2720 Planarity : 0.005 0.080 2972 Dihedral : 9.165 79.279 2608 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.66 % Favored : 92.34 % Rotamer: Outliers : 2.40 % Allowed : 18.28 % Favored : 79.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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 (0.19), residues: 2116 helix: 2.34 (0.15), residues: 1292 sheet: -0.31 (0.54), residues: 84 loop : -2.94 (0.20), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 211 TYR 0.013 0.001 TYR A 309 PHE 0.017 0.001 PHE C 304 TRP 0.007 0.001 TRP C 426 HIS 0.001 0.000 HIS A 364 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.14 (17844) covalent geometry : angle 0.51967 / 0.28 (24144) hydrogen bonds : bond 0.04575 / 3.02 ( 996) hydrogen bonds : angle 3.86381 / 2.77 ( 2904) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4232 Ramachandran restraints generated. 2116 Oldfield, 0 Emsley, 2116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4232 Ramachandran restraints generated. 2116 Oldfield, 0 Emsley, 2116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 554 residues out of total 1876 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 509 time to evaluate : 1.000 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 397 GLU cc_start: 0.8721 (tm-30) cc_final: 0.8211 (tm-30) REVERT: A 442 CYS cc_start: 0.9161 (m) cc_final: 0.8894 (m) REVERT: A 458 GLU cc_start: 0.7727 (mm-30) cc_final: 0.7485 (mm-30) REVERT: D 301 ASN cc_start: 0.8627 (t0) cc_final: 0.8218 (t0) REVERT: D 304 PHE cc_start: 0.9240 (OUTLIER) cc_final: 0.8939 (p90) REVERT: D 397 GLU cc_start: 0.8724 (tm-30) cc_final: 0.8218 (tm-30) REVERT: D 442 CYS cc_start: 0.9148 (m) cc_final: 0.8881 (m) REVERT: D 458 GLU cc_start: 0.7741 (mm-30) cc_final: 0.7539 (mm-30) REVERT: B 301 ASN cc_start: 0.8625 (t0) cc_final: 0.8228 (t0) REVERT: B 304 PHE cc_start: 0.9244 (OUTLIER) cc_final: 0.8951 (p90) REVERT: B 397 GLU cc_start: 0.8716 (tm-30) cc_final: 0.8209 (tm-30) REVERT: B 442 CYS cc_start: 0.9158 (m) cc_final: 0.8892 (m) REVERT: B 458 GLU cc_start: 0.7777 (mm-30) cc_final: 0.7570 (mm-30) REVERT: C 397 GLU cc_start: 0.8731 (tm-30) cc_final: 0.8227 (tm-30) REVERT: C 442 CYS cc_start: 0.9143 (m) cc_final: 0.8876 (m) outliers start: 45 outliers final: 34 residues processed: 522 average time/residue: 0.2626 time to fit residues: 218.5555 Evaluate side-chains 523 residues out of total 1876 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 487 time to evaluate : 0.922 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 267 LEU Chi-restraints excluded: chain A residue 352 ILE Chi-restraints excluded: chain A residue 388 ASP Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 514 ILE Chi-restraints excluded: chain A residue 520 SER Chi-restraints excluded: chain A residue 578 CYS Chi-restraints excluded: chain A residue 686 VAL Chi-restraints excluded: chain D residue 267 LEU Chi-restraints excluded: chain D residue 304 PHE Chi-restraints excluded: chain D residue 352 ILE Chi-restraints excluded: chain D residue 388 ASP Chi-restraints excluded: chain D residue 503 LEU Chi-restraints excluded: chain D residue 514 ILE Chi-restraints excluded: chain D residue 520 SER Chi-restraints excluded: chain D residue 578 CYS Chi-restraints excluded: chain D residue 686 VAL Chi-restraints excluded: chain B residue 267 LEU Chi-restraints excluded: chain B residue 304 PHE Chi-restraints excluded: chain B residue 352 ILE Chi-restraints excluded: chain B residue 388 ASP Chi-restraints excluded: chain B residue 503 LEU Chi-restraints excluded: chain B residue 514 ILE Chi-restraints excluded: chain B residue 520 SER Chi-restraints excluded: chain B residue 578 CYS Chi-restraints excluded: chain B residue 686 VAL Chi-restraints excluded: chain C residue 267 LEU Chi-restraints excluded: chain C residue 308 MET Chi-restraints excluded: chain C residue 313 LEU Chi-restraints excluded: chain C residue 352 ILE Chi-restraints excluded: chain C residue 388 ASP Chi-restraints excluded: chain C residue 503 LEU Chi-restraints excluded: chain C residue 514 ILE Chi-restraints excluded: chain C residue 520 SER Chi-restraints excluded: chain C residue 578 CYS Chi-restraints excluded: chain C residue 686 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 14 optimal weight: 6.9990 chunk 108 optimal weight: 8.9990 chunk 18 optimal weight: 5.9990 chunk 57 optimal weight: 7.9990 chunk 206 optimal weight: 1.9990 chunk 111 optimal weight: 3.9990 chunk 3 optimal weight: 0.7980 chunk 200 optimal weight: 1.9990 chunk 63 optimal weight: 0.6980 chunk 201 optimal weight: 0.8980 chunk 88 optimal weight: 2.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.138562 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.100494 restraints weight = 90287.879| |-----------------------------------------------------------------------------| r_work (start): 0.3158 rms_B_bonded: 3.27 r_work: 0.3025 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3025 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8349 moved from start: 0.2485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 17844 Z= 0.142 Angle : 0.530 8.529 24144 Z= 0.285 Chirality : 0.034 0.117 2720 Planarity : 0.004 0.057 2972 Dihedral : 9.156 83.976 2608 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.36 % Favored : 91.64 % Rotamer: Outliers : 2.35 % Allowed : 18.50 % Favored : 79.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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 (0.19), residues: 2116 helix: 2.36 (0.15), residues: 1292 sheet: -0.25 (0.54), residues: 84 loop : -2.95 (0.20), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 701 TYR 0.012 0.001 TYR A 309 PHE 0.018 0.001 PHE A 304 TRP 0.006 0.001 TRP B 426 HIS 0.001 0.000 HIS A 364 Details of bonding type rmsd/Z covalent geometry : bond 0.00309 / 0.14 (17844) covalent geometry : angle 0.52974 / 0.28 (24144) hydrogen bonds : bond 0.04571 / 3.01 ( 996) hydrogen bonds : angle 3.87523 / 2.78 ( 2904) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4232 Ramachandran restraints generated. 2116 Oldfield, 0 Emsley, 2116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4232 Ramachandran restraints generated. 2116 Oldfield, 0 Emsley, 2116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 536 residues out of total 1876 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 492 time to evaluate : 0.842 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 397 GLU cc_start: 0.8733 (tm-30) cc_final: 0.8226 (tm-30) REVERT: A 442 CYS cc_start: 0.9153 (m) cc_final: 0.8889 (m) REVERT: A 458 GLU cc_start: 0.7796 (mm-30) cc_final: 0.7530 (mm-30) REVERT: D 301 ASN cc_start: 0.8656 (t0) cc_final: 0.8205 (t0) REVERT: D 304 PHE cc_start: 0.9259 (OUTLIER) cc_final: 0.8980 (p90) REVERT: D 397 GLU cc_start: 0.8737 (tm-30) cc_final: 0.8233 (tm-30) REVERT: D 442 CYS cc_start: 0.9157 (m) cc_final: 0.8890 (m) REVERT: D 458 GLU cc_start: 0.7716 (mm-30) cc_final: 0.7470 (mm-30) REVERT: B 301 ASN cc_start: 0.8649 (t0) cc_final: 0.8202 (t0) REVERT: B 304 PHE cc_start: 0.9258 (OUTLIER) cc_final: 0.8982 (p90) REVERT: B 397 GLU cc_start: 0.8724 (tm-30) cc_final: 0.8219 (tm-30) REVERT: B 442 CYS cc_start: 0.9176 (m) cc_final: 0.8910 (m) REVERT: B 458 GLU cc_start: 0.7759 (mm-30) cc_final: 0.7501 (mm-30) REVERT: C 397 GLU cc_start: 0.8725 (tm-30) cc_final: 0.8218 (tm-30) REVERT: C 442 CYS cc_start: 0.9160 (m) cc_final: 0.8896 (m) REVERT: C 458 GLU cc_start: 0.7737 (mm-30) cc_final: 0.7462 (mm-30) outliers start: 44 outliers final: 37 residues processed: 502 average time/residue: 0.2431 time to fit residues: 194.8085 Evaluate side-chains 512 residues out of total 1876 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 473 time to evaluate : 0.897 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 267 LEU Chi-restraints excluded: chain A residue 272 TRP Chi-restraints excluded: chain A residue 352 ILE Chi-restraints excluded: chain A residue 493 ILE Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 514 ILE Chi-restraints excluded: chain A residue 520 SER Chi-restraints excluded: chain A residue 578 CYS Chi-restraints excluded: chain A residue 686 VAL Chi-restraints excluded: chain D residue 267 LEU Chi-restraints excluded: chain D residue 272 TRP Chi-restraints excluded: chain D residue 304 PHE Chi-restraints excluded: chain D residue 352 ILE Chi-restraints excluded: chain D residue 493 ILE Chi-restraints excluded: chain D residue 503 LEU Chi-restraints excluded: chain D residue 520 SER Chi-restraints excluded: chain D residue 578 CYS Chi-restraints excluded: chain D residue 686 VAL Chi-restraints excluded: chain B residue 267 LEU Chi-restraints excluded: chain B residue 272 TRP Chi-restraints excluded: chain B residue 304 PHE Chi-restraints excluded: chain B residue 352 ILE Chi-restraints excluded: chain B residue 473 PHE Chi-restraints excluded: chain B residue 493 ILE Chi-restraints excluded: chain B residue 503 LEU Chi-restraints excluded: chain B residue 520 SER Chi-restraints excluded: chain B residue 578 CYS Chi-restraints excluded: chain B residue 686 VAL Chi-restraints excluded: chain C residue 267 LEU Chi-restraints excluded: chain C residue 272 TRP Chi-restraints excluded: chain C residue 308 MET Chi-restraints excluded: chain C residue 313 LEU Chi-restraints excluded: chain C residue 352 ILE Chi-restraints excluded: chain C residue 388 ASP Chi-restraints excluded: chain C residue 493 ILE Chi-restraints excluded: chain C residue 503 LEU Chi-restraints excluded: chain C residue 520 SER Chi-restraints excluded: chain C residue 578 CYS Chi-restraints excluded: chain C residue 686 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 23 optimal weight: 0.9980 chunk 63 optimal weight: 0.8980 chunk 11 optimal weight: 4.9990 chunk 134 optimal weight: 2.9990 chunk 151 optimal weight: 0.9990 chunk 8 optimal weight: 0.6980 chunk 149 optimal weight: 0.9990 chunk 156 optimal weight: 2.9990 chunk 182 optimal weight: 0.9990 chunk 152 optimal weight: 0.9990 chunk 48 optimal weight: 1.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 223 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.139203 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.101232 restraints weight = 90371.871| |-----------------------------------------------------------------------------| r_work (start): 0.3170 rms_B_bonded: 3.28 r_work: 0.3040 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3040 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8333 moved from start: 0.2593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 17844 Z= 0.126 Angle : 0.541 10.197 24144 Z= 0.287 Chirality : 0.034 0.117 2720 Planarity : 0.005 0.110 2972 Dihedral : 9.117 87.261 2608 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.61 % Favored : 92.39 % Rotamer: Outliers : 1.81 % Allowed : 18.92 % Favored : 79.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: 0.89 (0.19), residues: 2116 helix: 2.43 (0.15), residues: 1292 sheet: -0.23 (0.54), residues: 84 loop : -2.94 (0.20), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG A 211 TYR 0.011 0.001 TYR A 309 PHE 0.022 0.001 PHE C 245 TRP 0.007 0.001 TRP C 426 HIS 0.002 0.000 HIS B 289 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.13 (17844) covalent geometry : angle 0.54111 / 0.29 (24144) hydrogen bonds : bond 0.04470 / 2.95 ( 996) hydrogen bonds : angle 3.77604 / 2.71 ( 2904) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4232 Ramachandran restraints generated. 2116 Oldfield, 0 Emsley, 2116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4232 Ramachandran restraints generated. 2116 Oldfield, 0 Emsley, 2116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 522 residues out of total 1876 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 488 time to evaluate : 0.920 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 397 GLU cc_start: 0.8715 (tm-30) cc_final: 0.8206 (tm-30) REVERT: A 442 CYS cc_start: 0.9153 (m) cc_final: 0.8883 (m) REVERT: A 458 GLU cc_start: 0.7699 (mm-30) cc_final: 0.7412 (mm-30) REVERT: A 664 LEU cc_start: 0.9467 (mt) cc_final: 0.9256 (mm) REVERT: A 716 MET cc_start: 0.5837 (mmm) cc_final: 0.5122 (mmm) REVERT: D 301 ASN cc_start: 0.8660 (t0) cc_final: 0.8244 (t0) REVERT: D 304 PHE cc_start: 0.9240 (OUTLIER) cc_final: 0.8965 (p90) REVERT: D 397 GLU cc_start: 0.8715 (tm-30) cc_final: 0.8208 (tm-30) REVERT: D 442 CYS cc_start: 0.9154 (m) cc_final: 0.8883 (m) REVERT: D 458 GLU cc_start: 0.7677 (mm-30) cc_final: 0.7430 (mm-30) REVERT: D 664 LEU cc_start: 0.9468 (mt) cc_final: 0.9253 (mm) REVERT: D 716 MET cc_start: 0.5843 (mmm) cc_final: 0.5118 (mmm) REVERT: B 301 ASN cc_start: 0.8654 (t0) cc_final: 0.8239 (t0) REVERT: B 304 PHE cc_start: 0.9244 (OUTLIER) cc_final: 0.8971 (p90) REVERT: B 397 GLU cc_start: 0.8716 (tm-30) cc_final: 0.8211 (tm-30) REVERT: B 442 CYS cc_start: 0.9169 (m) cc_final: 0.8897 (m) REVERT: B 458 GLU cc_start: 0.7693 (mm-30) cc_final: 0.7442 (mm-30) REVERT: B 664 LEU cc_start: 0.9462 (mt) cc_final: 0.9249 (mm) REVERT: B 716 MET cc_start: 0.5822 (mmm) cc_final: 0.5117 (mmm) REVERT: C 397 GLU cc_start: 0.8710 (tm-30) cc_final: 0.8203 (tm-30) REVERT: C 442 CYS cc_start: 0.9170 (m) cc_final: 0.8901 (m) REVERT: C 458 GLU cc_start: 0.7659 (mm-30) cc_final: 0.7398 (mm-30) REVERT: C 664 LEU cc_start: 0.9470 (mt) cc_final: 0.9255 (mm) REVERT: C 716 MET cc_start: 0.5851 (mmm) cc_final: 0.5126 (mmm) outliers start: 34 outliers final: 32 residues processed: 499 average time/residue: 0.2560 time to fit residues: 202.7000 Evaluate side-chains 501 residues out of total 1876 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 467 time to evaluate : 0.778 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 267 LEU Chi-restraints excluded: chain A residue 272 TRP Chi-restraints excluded: chain A residue 352 ILE Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 520 SER Chi-restraints excluded: chain A residue 578 CYS Chi-restraints excluded: chain A residue 686 VAL Chi-restraints excluded: chain D residue 267 LEU Chi-restraints excluded: chain D residue 272 TRP Chi-restraints excluded: chain D residue 304 PHE Chi-restraints excluded: chain D residue 352 ILE Chi-restraints excluded: chain D residue 503 LEU Chi-restraints excluded: chain D residue 520 SER Chi-restraints excluded: chain D residue 578 CYS Chi-restraints excluded: chain D residue 686 VAL Chi-restraints excluded: chain B residue 223 ASN Chi-restraints excluded: chain B residue 267 LEU Chi-restraints excluded: chain B residue 272 TRP Chi-restraints excluded: chain B residue 304 PHE Chi-restraints excluded: chain B residue 352 ILE Chi-restraints excluded: chain B residue 503 LEU Chi-restraints excluded: chain B residue 520 SER Chi-restraints excluded: chain B residue 578 CYS Chi-restraints excluded: chain B residue 686 VAL Chi-restraints excluded: chain C residue 267 LEU Chi-restraints excluded: chain C residue 272 TRP Chi-restraints excluded: chain C residue 308 MET Chi-restraints excluded: chain C residue 313 LEU Chi-restraints excluded: chain C residue 352 ILE Chi-restraints excluded: chain C residue 388 ASP Chi-restraints excluded: chain C residue 503 LEU Chi-restraints excluded: chain C residue 520 SER Chi-restraints excluded: chain C residue 578 CYS Chi-restraints excluded: chain C residue 686 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 20 optimal weight: 2.9990 chunk 21 optimal weight: 0.7980 chunk 1 optimal weight: 1.9990 chunk 164 optimal weight: 6.9990 chunk 74 optimal weight: 4.9990 chunk 211 optimal weight: 0.8980 chunk 61 optimal weight: 4.9990 chunk 90 optimal weight: 1.9990 chunk 50 optimal weight: 0.8980 chunk 118 optimal weight: 0.0570 chunk 75 optimal weight: 1.9990 overall best weight: 0.9300 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.139205 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.100885 restraints weight = 90255.762| |-----------------------------------------------------------------------------| r_work (start): 0.3166 rms_B_bonded: 3.32 r_work: 0.3040 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3040 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8335 moved from start: 0.2672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.192 17844 Z= 0.165 Angle : 0.720 58.828 24144 Z= 0.418 Chirality : 0.036 0.679 2720 Planarity : 0.005 0.110 2972 Dihedral : 9.113 87.272 2608 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.42 % Favored : 92.58 % Rotamer: Outliers : 1.97 % Allowed : 18.71 % Favored : 79.32 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 7.14 % 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: 0.89 (0.19), residues: 2116 helix: 2.44 (0.15), residues: 1292 sheet: -0.23 (0.54), residues: 84 loop : -2.95 (0.20), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 211 TYR 0.010 0.001 TYR A 309 PHE 0.017 0.001 PHE C 304 TRP 0.005 0.001 TRP B 697 HIS 0.002 0.000 HIS B 289 Details of bonding type rmsd/Z covalent geometry : bond 0.00348 / 0.17 (17844) covalent geometry : angle 0.72025 / 0.42 (24144) hydrogen bonds : bond 0.04470 / 2.95 ( 996) hydrogen bonds : angle 3.77565 / 2.71 ( 2904) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8392.86 seconds wall clock time: 143 minutes 11.61 seconds (8591.61 seconds total)