Starting phenix.real_space_refine on Sun Jul 5 18:03:39 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7t4x_25691/07_2026/7t4x_25691_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/7t4x_25691/07_2026/7t4x_25691.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7t4x_25691/07_2026/7t4x_25691_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7t4x_25691/07_2026/7t4x_25691_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7t4x_25691/07_2026/7t4x_25691.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7t4x_25691/07_2026/7t4x_25691.map" } resolution = 2.8 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= 0.004 sd= 0.070 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 K 5 8.98 5 P 2 5.49 5 S 82 5.16 5 C 9528 2.51 5 N 2456 2.21 5 O 2547 1.98 5 H 14614 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 29234 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 7197 Number of conformers: 1 Conformer: "" Number of residues, atoms: 439, 7197 Classifications: {'peptide': 439} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 423} Chain breaks: 1 Chain: "B" Number of atoms: 7348 Number of conformers: 1 Conformer: "" Number of residues, atoms: 450, 7348 Classifications: {'peptide': 450} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 434} Chain breaks: 2 Chain: "C" Number of atoms: 7197 Number of conformers: 1 Conformer: "" Number of residues, atoms: 439, 7197 Classifications: {'peptide': 439} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 423} Chain breaks: 1 Chain: "D" Number of atoms: 7348 Number of conformers: 1 Conformer: "" Number of residues, atoms: 450, 7348 Classifications: {'peptide': 450} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 434} Chain breaks: 2 Chain: "A" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 0 Ad-hoc single atom residues: {' K': 5} Chain breaks: 5 Chain: "B" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 50 Unusual residues: {'PTY': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 50 Unusual residues: {'PTY': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 12 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 12 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "C" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 9 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 6 Classifications: {'water': 2} Link IDs: {None: 1} Time building chain proxies: 4.46, per 1000 atoms: 0.15 Number of scatterers: 29234 At special positions: 0 Unit cell: (124.415, 129.425, 118.57, 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) K 5 19.00 S 82 16.00 P 2 15.00 O 2547 8.00 N 2456 7.00 C 9528 6.00 H 14614 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS B 8 " - pdb=" SG CYS B 331 " distance=2.04 Simple disulfide: pdb=" SG CYS D 8 " - pdb=" SG CYS D 331 " distance=2.04 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: 2.00 Conformation dependent library (CDL) restraints added in 856.4 milliseconds 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3400 Finding SS restraints... Secondary structure from input PDB file: 88 helices and 12 sheets defined 70.0% alpha, 6.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.58 Creating SS restraints... Processing helix chain 'A' and resid 54 through 82 removed outlier: 3.879A pdb=" N TRP A 60 " --> pdb=" O LYS A 56 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N VAL A 66 " --> pdb=" O ALA A 62 " (cutoff:3.500A) Proline residue: A 76 - end of helix removed outlier: 3.584A pdb=" N LEU A 82 " --> pdb=" O GLU A 78 " (cutoff:3.500A) Processing helix chain 'A' and resid 88 through 107 removed outlier: 3.564A pdb=" N ILE A 105 " --> pdb=" O ALA A 101 " (cutoff:3.500A) Processing helix chain 'A' and resid 123 through 134 Processing helix chain 'A' and resid 135 through 142 Processing helix chain 'A' and resid 145 through 152 removed outlier: 3.797A pdb=" N ILE A 152 " --> pdb=" O ALA A 148 " (cutoff:3.500A) Processing helix chain 'A' and resid 153 through 155 No H-bonds generated for 'chain 'A' and resid 153 through 155' Processing helix chain 'A' and resid 156 through 164 removed outlier: 3.643A pdb=" N LEU A 163 " --> pdb=" O LEU A 159 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N ARG A 164 " --> pdb=" O PHE A 160 " (cutoff:3.500A) Processing helix chain 'A' and resid 165 through 167 No H-bonds generated for 'chain 'A' and resid 165 through 167' Processing helix chain 'A' and resid 168 through 179 Processing helix chain 'A' and resid 185 through 215 Processing helix chain 'A' and resid 235 through 252 Processing helix chain 'A' and resid 263 through 296 removed outlier: 3.526A pdb=" N GLY A 279 " --> pdb=" O LEU A 275 " (cutoff:3.500A) Processing helix chain 'A' and resid 296 through 317 removed outlier: 3.542A pdb=" N ARG A 300 " --> pdb=" O THR A 296 " (cutoff:3.500A) Processing helix chain 'A' and resid 319 through 336 Processing helix chain 'A' and resid 339 through 348 Processing helix chain 'A' and resid 351 through 368 removed outlier: 5.156A pdb=" N SER A 365 " --> pdb=" O PHE A 361 " (cutoff:3.500A) removed outlier: 5.350A pdb=" N LEU A 366 " --> pdb=" O LEU A 362 " (cutoff:3.500A) Processing helix chain 'A' and resid 369 through 374 removed outlier: 6.144A pdb=" N LEU A 372 " --> pdb=" O LYS A 369 " (cutoff:3.500A) Processing helix chain 'A' and resid 377 through 388 Processing helix chain 'A' and resid 440 through 447 Processing helix chain 'A' and resid 467 through 476 removed outlier: 3.608A pdb=" N ASN A 472 " --> pdb=" O THR A 468 " (cutoff:3.500A) Processing helix chain 'A' and resid 480 through 490 Processing helix chain 'B' and resid 4 through 15 Processing helix chain 'B' and resid 54 through 82 removed outlier: 3.728A pdb=" N VAL B 66 " --> pdb=" O ALA B 62 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LEU B 67 " --> pdb=" O PHE B 63 " (cutoff:3.500A) Proline residue: B 76 - end of helix removed outlier: 3.643A pdb=" N LEU B 82 " --> pdb=" O GLU B 78 " (cutoff:3.500A) Processing helix chain 'B' and resid 88 through 107 Processing helix chain 'B' and resid 123 through 134 Processing helix chain 'B' and resid 135 through 142 Processing helix chain 'B' and resid 145 through 150 Processing helix chain 'B' and resid 151 through 152 No H-bonds generated for 'chain 'B' and resid 151 through 152' Processing helix chain 'B' and resid 153 through 155 No H-bonds generated for 'chain 'B' and resid 153 through 155' Processing helix chain 'B' and resid 156 through 162 Processing helix chain 'B' and resid 163 through 167 Processing helix chain 'B' and resid 168 through 180 removed outlier: 3.779A pdb=" N LYS B 180 " --> pdb=" O ALA B 176 " (cutoff:3.500A) Processing helix chain 'B' and resid 185 through 215 Processing helix chain 'B' and resid 218 through 222 Processing helix chain 'B' and resid 230 through 234 Processing helix chain 'B' and resid 235 through 252 Processing helix chain 'B' and resid 263 through 316 removed outlier: 5.016A pdb=" N ARG B 298 " --> pdb=" O HIS B 294 " (cutoff:3.500A) removed outlier: 5.386A pdb=" N THR B 299 " --> pdb=" O GLY B 295 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N THR B 305 " --> pdb=" O ASN B 301 " (cutoff:3.500A) Processing helix chain 'B' and resid 319 through 348 removed outlier: 4.457A pdb=" N GLN B 325 " --> pdb=" O ARG B 321 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLU B 339 " --> pdb=" O ARG B 335 " (cutoff:3.500A) Processing helix chain 'B' and resid 351 through 367 removed outlier: 3.881A pdb=" N MET B 367 " --> pdb=" O PHE B 363 " (cutoff:3.500A) Processing helix chain 'B' and resid 370 through 374 Processing helix chain 'B' and resid 377 through 386 Processing helix chain 'B' and resid 440 through 445 removed outlier: 3.646A pdb=" N VAL B 444 " --> pdb=" O GLY B 440 " (cutoff:3.500A) Processing helix chain 'B' and resid 467 through 475 Processing helix chain 'B' and resid 477 through 489 removed outlier: 3.765A pdb=" N GLY B 481 " --> pdb=" O ASN B 477 " (cutoff:3.500A) Processing helix chain 'C' and resid 54 through 82 removed outlier: 3.879A pdb=" N TRP C 60 " --> pdb=" O LYS C 56 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N VAL C 66 " --> pdb=" O ALA C 62 " (cutoff:3.500A) Proline residue: C 76 - end of helix removed outlier: 3.584A pdb=" N LEU C 82 " --> pdb=" O GLU C 78 " (cutoff:3.500A) Processing helix chain 'C' and resid 88 through 107 removed outlier: 3.564A pdb=" N ILE C 105 " --> pdb=" O ALA C 101 " (cutoff:3.500A) Processing helix chain 'C' and resid 123 through 134 Processing helix chain 'C' and resid 135 through 142 Processing helix chain 'C' and resid 145 through 152 removed outlier: 3.797A pdb=" N ILE C 152 " --> pdb=" O ALA C 148 " (cutoff:3.500A) Processing helix chain 'C' and resid 153 through 155 No H-bonds generated for 'chain 'C' and resid 153 through 155' Processing helix chain 'C' and resid 156 through 164 removed outlier: 3.642A pdb=" N LEU C 163 " --> pdb=" O LEU C 159 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N ARG C 164 " --> pdb=" O PHE C 160 " (cutoff:3.500A) Processing helix chain 'C' and resid 165 through 167 No H-bonds generated for 'chain 'C' and resid 165 through 167' Processing helix chain 'C' and resid 168 through 179 Processing helix chain 'C' and resid 185 through 215 Processing helix chain 'C' and resid 235 through 252 Processing helix chain 'C' and resid 263 through 296 removed outlier: 3.527A pdb=" N GLY C 279 " --> pdb=" O LEU C 275 " (cutoff:3.500A) Processing helix chain 'C' and resid 296 through 317 removed outlier: 3.542A pdb=" N ARG C 300 " --> pdb=" O THR C 296 " (cutoff:3.500A) Processing helix chain 'C' and resid 319 through 336 Processing helix chain 'C' and resid 339 through 348 Processing helix chain 'C' and resid 351 through 368 removed outlier: 5.156A pdb=" N SER C 365 " --> pdb=" O PHE C 361 " (cutoff:3.500A) removed outlier: 5.351A pdb=" N LEU C 366 " --> pdb=" O LEU C 362 " (cutoff:3.500A) Processing helix chain 'C' and resid 369 through 374 removed outlier: 6.144A pdb=" N LEU C 372 " --> pdb=" O LYS C 369 " (cutoff:3.500A) Processing helix chain 'C' and resid 377 through 388 Processing helix chain 'C' and resid 440 through 447 Processing helix chain 'C' and resid 467 through 476 removed outlier: 3.608A pdb=" N ASN C 472 " --> pdb=" O THR C 468 " (cutoff:3.500A) Processing helix chain 'C' and resid 480 through 490 Processing helix chain 'D' and resid 4 through 15 Processing helix chain 'D' and resid 54 through 82 removed outlier: 3.728A pdb=" N VAL D 66 " --> pdb=" O ALA D 62 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LEU D 67 " --> pdb=" O PHE D 63 " (cutoff:3.500A) Proline residue: D 76 - end of helix removed outlier: 3.643A pdb=" N LEU D 82 " --> pdb=" O GLU D 78 " (cutoff:3.500A) Processing helix chain 'D' and resid 88 through 107 Processing helix chain 'D' and resid 123 through 134 Processing helix chain 'D' and resid 135 through 142 Processing helix chain 'D' and resid 145 through 150 Processing helix chain 'D' and resid 151 through 152 No H-bonds generated for 'chain 'D' and resid 151 through 152' Processing helix chain 'D' and resid 153 through 155 No H-bonds generated for 'chain 'D' and resid 153 through 155' Processing helix chain 'D' and resid 156 through 162 Processing helix chain 'D' and resid 163 through 167 Processing helix chain 'D' and resid 168 through 180 removed outlier: 3.779A pdb=" N LYS D 180 " --> pdb=" O ALA D 176 " (cutoff:3.500A) Processing helix chain 'D' and resid 185 through 215 Processing helix chain 'D' and resid 218 through 222 Processing helix chain 'D' and resid 230 through 234 Processing helix chain 'D' and resid 235 through 252 Processing helix chain 'D' and resid 263 through 316 removed outlier: 5.022A pdb=" N ARG D 298 " --> pdb=" O HIS D 294 " (cutoff:3.500A) removed outlier: 5.390A pdb=" N THR D 299 " --> pdb=" O GLY D 295 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N THR D 305 " --> pdb=" O ASN D 301 " (cutoff:3.500A) Processing helix chain 'D' and resid 319 through 348 removed outlier: 4.457A pdb=" N GLN D 325 " --> pdb=" O ARG D 321 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLU D 339 " --> pdb=" O ARG D 335 " (cutoff:3.500A) Processing helix chain 'D' and resid 351 through 367 removed outlier: 3.881A pdb=" N MET D 367 " --> pdb=" O PHE D 363 " (cutoff:3.500A) Processing helix chain 'D' and resid 370 through 374 Processing helix chain 'D' and resid 377 through 386 Processing helix chain 'D' and resid 440 through 445 removed outlier: 3.646A pdb=" N VAL D 444 " --> pdb=" O GLY D 440 " (cutoff:3.500A) Processing helix chain 'D' and resid 467 through 475 Processing helix chain 'D' and resid 477 through 489 removed outlier: 3.750A pdb=" N GLY D 481 " --> pdb=" O ASN D 477 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 112 through 113 Processing sheet with id=AA2, first strand: chain 'A' and resid 389 through 393 removed outlier: 6.765A pdb=" N GLN A 461 " --> pdb=" O VAL A 413 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ASP A 437 " --> pdb=" O LEU A 412 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 398 through 400 removed outlier: 6.499A pdb=" N ASP A 398 " --> pdb=" O THR A 456 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N THR A 456 " --> pdb=" O ASP A 398 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N ILE A 400 " --> pdb=" O VAL A 454 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ARG A 431 " --> pdb=" O LEU A 419 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 112 through 113 removed outlier: 3.636A pdb=" N TYR B 112 " --> pdb=" O VAL B 121 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 389 through 393 removed outlier: 6.635A pdb=" N GLN B 461 " --> pdb=" O VAL B 413 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N ASP B 437 " --> pdb=" O LEU B 412 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 398 through 400 removed outlier: 6.253A pdb=" N ASP B 398 " --> pdb=" O THR B 456 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N THR B 456 " --> pdb=" O ASP B 398 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N ILE B 400 " --> pdb=" O VAL B 454 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ARG B 431 " --> pdb=" O LEU B 419 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 112 through 113 Processing sheet with id=AA8, first strand: chain 'C' and resid 389 through 393 removed outlier: 6.765A pdb=" N GLN C 461 " --> pdb=" O VAL C 413 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ASP C 437 " --> pdb=" O LEU C 412 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 398 through 400 removed outlier: 6.499A pdb=" N ASP C 398 " --> pdb=" O THR C 456 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N THR C 456 " --> pdb=" O ASP C 398 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N ILE C 400 " --> pdb=" O VAL C 454 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ARG C 431 " --> pdb=" O LEU C 419 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 112 through 113 removed outlier: 3.636A pdb=" N TYR D 112 " --> pdb=" O VAL D 121 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 389 through 393 removed outlier: 6.635A pdb=" N GLN D 461 " --> pdb=" O VAL D 413 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N ASP D 437 " --> pdb=" O LEU D 412 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 398 through 400 removed outlier: 6.253A pdb=" N ASP D 398 " --> pdb=" O THR D 456 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N THR D 456 " --> pdb=" O ASP D 398 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N ILE D 400 " --> pdb=" O VAL D 454 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ARG D 431 " --> pdb=" O LEU D 419 " (cutoff:3.500A) 944 hydrogen bonds defined for protein. 2718 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: 6.79 Time building geometry restraints manager: 2.74 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.83 - 1.03: 14588 1.03 - 1.23: 424 1.23 - 1.43: 6085 1.43 - 1.63: 8335 1.63 - 1.83: 138 Bond restraints: 29570 Sorted by residual: bond pdb=" N SER C 428 " pdb=" H SER C 428 " ideal model delta sigma weight residual 0.860 0.963 -0.103 2.00e-02 2.50e+03 2.64e+01 bond pdb=" N SER A 428 " pdb=" H SER A 428 " ideal model delta sigma weight residual 0.860 0.962 -0.102 2.00e-02 2.50e+03 2.59e+01 bond pdb=" N SER D 428 " pdb=" H SER D 428 " ideal model delta sigma weight residual 0.860 0.962 -0.102 2.00e-02 2.50e+03 2.58e+01 bond pdb=" N SER B 428 " pdb=" H SER B 428 " ideal model delta sigma weight residual 0.860 0.962 -0.102 2.00e-02 2.50e+03 2.58e+01 bond pdb=" N ARG B 47 " pdb=" H ARG B 47 " ideal model delta sigma weight residual 0.860 0.960 -0.100 2.00e-02 2.50e+03 2.51e+01 ... (remaining 29565 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.38: 52429 2.38 - 4.77: 690 4.77 - 7.15: 28 7.15 - 9.53: 6 9.53 - 11.92: 4 Bond angle restraints: 53157 Sorted by residual: angle pdb=" O11 PTY D 901 " pdb=" P1 PTY D 901 " pdb=" O14 PTY D 901 " ideal model delta sigma weight residual 92.90 104.82 -11.92 3.00e+00 1.11e-01 1.58e+01 angle pdb=" O11 PTY B 901 " pdb=" P1 PTY B 901 " pdb=" O14 PTY B 901 " ideal model delta sigma weight residual 92.90 104.79 -11.89 3.00e+00 1.11e-01 1.57e+01 angle pdb=" CA ARG B 374 " pdb=" CB ARG B 374 " pdb=" CG ARG B 374 " ideal model delta sigma weight residual 114.10 121.59 -7.49 2.00e+00 2.50e-01 1.40e+01 angle pdb=" CA ARG D 374 " pdb=" CB ARG D 374 " pdb=" CG ARG D 374 " ideal model delta sigma weight residual 114.10 121.59 -7.49 2.00e+00 2.50e-01 1.40e+01 angle pdb=" N SER D 297 " pdb=" CA SER D 297 " pdb=" C SER D 297 " ideal model delta sigma weight residual 111.11 115.30 -4.19 1.20e+00 6.94e-01 1.22e+01 ... (remaining 53152 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.08: 13348 30.08 - 60.16: 448 60.16 - 90.24: 150 90.24 - 120.32: 0 120.32 - 150.40: 4 Dihedral angle restraints: 13950 sinusoidal: 7448 harmonic: 6502 Sorted by residual: dihedral pdb=" CA THR A 107 " pdb=" C THR A 107 " pdb=" N PHE A 108 " pdb=" CA PHE A 108 " ideal model delta harmonic sigma weight residual 180.00 150.31 29.69 0 5.00e+00 4.00e-02 3.53e+01 dihedral pdb=" CA THR C 107 " pdb=" C THR C 107 " pdb=" N PHE C 108 " pdb=" CA PHE C 108 " ideal model delta harmonic sigma weight residual 180.00 150.35 29.65 0 5.00e+00 4.00e-02 3.52e+01 dihedral pdb=" CA ALA D 349 " pdb=" C ALA D 349 " pdb=" N LEU D 350 " pdb=" CA LEU D 350 " ideal model delta harmonic sigma weight residual -180.00 -151.80 -28.20 0 5.00e+00 4.00e-02 3.18e+01 ... (remaining 13947 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 1463 0.046 - 0.093: 646 0.093 - 0.139: 143 0.139 - 0.185: 26 0.185 - 0.232: 2 Chirality restraints: 2280 Sorted by residual: chirality pdb=" CA TRP A 135 " pdb=" N TRP A 135 " pdb=" C TRP A 135 " pdb=" CB TRP A 135 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.34e+00 chirality pdb=" CA TRP C 135 " pdb=" N TRP C 135 " pdb=" C TRP C 135 " pdb=" CB TRP C 135 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.34e+00 chirality pdb=" CA THR D 253 " pdb=" N THR D 253 " pdb=" C THR D 253 " pdb=" CB THR D 253 " both_signs ideal model delta sigma weight residual False 2.53 2.36 0.16 2.00e-01 2.50e+01 6.59e-01 ... (remaining 2277 not shown) Planarity restraints: 4236 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN B 477 " 0.065 2.00e-02 2.50e+03 7.52e-02 8.48e+01 pdb=" CG ASN B 477 " -0.077 2.00e-02 2.50e+03 pdb=" OD1 ASN B 477 " 0.010 2.00e-02 2.50e+03 pdb=" ND2 ASN B 477 " -0.106 2.00e-02 2.50e+03 pdb="HD21 ASN B 477 " -0.004 2.00e-02 2.50e+03 pdb="HD22 ASN B 477 " 0.111 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN D 477 " -0.065 2.00e-02 2.50e+03 7.51e-02 8.46e+01 pdb=" CG ASN D 477 " 0.077 2.00e-02 2.50e+03 pdb=" OD1 ASN D 477 " -0.010 2.00e-02 2.50e+03 pdb=" ND2 ASN D 477 " 0.105 2.00e-02 2.50e+03 pdb="HD21 ASN D 477 " 0.004 2.00e-02 2.50e+03 pdb="HD22 ASN D 477 " -0.111 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG D 164 " 0.382 9.50e-02 1.11e+02 1.37e-01 7.62e+01 pdb=" NE ARG D 164 " 0.020 2.00e-02 2.50e+03 pdb=" CZ ARG D 164 " -0.017 2.00e-02 2.50e+03 pdb=" NH1 ARG D 164 " 0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG D 164 " -0.104 2.00e-02 2.50e+03 pdb="HH11 ARG D 164 " -0.001 2.00e-02 2.50e+03 pdb="HH12 ARG D 164 " -0.019 2.00e-02 2.50e+03 pdb="HH21 ARG D 164 " -0.008 2.00e-02 2.50e+03 pdb="HH22 ARG D 164 " 0.110 2.00e-02 2.50e+03 ... (remaining 4233 not shown) Histogram of nonbonded interaction distances: 1.61 - 2.32: 6425 2.32 - 3.02: 78447 3.02 - 3.73: 106396 3.73 - 4.43: 156213 4.43 - 5.14: 246691 Nonbonded interactions: 594172 Sorted by model distance: nonbonded pdb=" HG1 THR B 407 " pdb=" OD1 ASP B 408 " model vdw 1.612 2.450 nonbonded pdb=" HG1 THR D 407 " pdb=" OD1 ASP D 408 " model vdw 1.613 2.450 nonbonded pdb=" O GLY D 479 " pdb=" HG1 THR D 482 " model vdw 1.624 2.450 nonbonded pdb=" O GLY B 479 " pdb=" HG1 THR B 482 " model vdw 1.626 2.450 nonbonded pdb=" O GLY C 479 " pdb=" HG1 THR C 482 " model vdw 1.649 2.450 ... (remaining 594167 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 48 through 330 or (resid 331 and (name N or name CA or nam \ e C or name O or name CB or name SG or name H or name HA or name HB2 or name HB3 \ )) or resid 332 through 490)) selection = (chain 'B' and (resid 48 through 179 or (resid 180 and (name N or name CA or nam \ e C or name O or name CB or name CG or name CD or name CE or name NZ or name H o \ r name HA )) or resid 181 through 490)) selection = (chain 'C' and (resid 48 through 330 or (resid 331 and (name N or name CA or nam \ e C or name O or name CB or name SG or name H or name HA or name HB2 or name HB3 \ )) or resid 332 through 490)) selection = (chain 'D' and (resid 48 through 179 or (resid 180 and (name N or name CA or nam \ e C or name O or name CB or name CG or name CD or name CE or name NZ or name H o \ r name HA )) or resid 181 through 490)) } 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: 7.440 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: 0.180 Extract box with map and model: 0.440 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 25.470 Find NCS groups from input model: 0.560 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8307 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 0.079 14958 Z= 0.305 Angle : 0.932 11.917 20276 Z= 0.568 Chirality : 0.051 0.232 2280 Planarity : 0.011 0.111 2528 Dihedral : 13.010 150.403 5444 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 0.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 1.52 % Allowed : 2.41 % Favored : 96.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: -0.26 (0.18), residues: 1758 helix: -0.17 (0.14), residues: 1142 sheet: 1.01 (0.62), residues: 40 loop : 0.09 (0.25), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.002 ARG B 335 TYR 0.044 0.007 TYR C 131 PHE 0.019 0.003 PHE B 109 TRP 0.030 0.006 TRP B 246 HIS 0.011 0.003 HIS B 260 Details of bonding type rmsd/Z covalent geometry : bond 0.00572 / 0.31 (14956) covalent geometry : angle 0.93140 / 0.57 (20272) SS BOND : bond 0.00417 / 0.21 ( 2) SS BOND : angle 2.59962 / 1.60 ( 4) hydrogen bonds : bond 0.12715 / 8.30 ( 944) hydrogen bonds : angle 5.49210 / 4.10 ( 2718) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 180 is missing expected H atoms. Skipping. Residue LYS 180 is missing expected H atoms. Skipping. Evaluate side-chains 293 residues out of total 1578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 269 time to evaluate : 0.544 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: A 312 PHE cc_start: 0.8224 (t80) cc_final: 0.7924 (t80) REVERT: B 264 THR cc_start: 0.8950 (t) cc_final: 0.8705 (m) REVERT: C 312 PHE cc_start: 0.8226 (t80) cc_final: 0.7925 (t80) REVERT: D 264 THR cc_start: 0.8950 (t) cc_final: 0.8706 (m) outliers start: 24 outliers final: 2 residues processed: 287 average time/residue: 1.1782 time to fit residues: 372.3738 Evaluate side-chains 165 residues out of total 1578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 163 time to evaluate : 0.697 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain C residue 370 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 98 optimal weight: 5.9990 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 4.9990 chunk 66 optimal weight: 0.5980 chunk 130 optimal weight: 9.9990 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 0.9990 chunk 77 optimal weight: 9.9990 chunk 122 optimal weight: 4.9990 chunk 91 optimal weight: 0.8980 chunk 149 optimal weight: 0.9980 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 378 ASN B 311 ASN B 475 GLN B 486 ASN D 311 ASN D 325 GLN D 475 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4467 r_free = 0.4467 target = 0.191144 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.118817 restraints weight = 56286.657| |-----------------------------------------------------------------------------| r_work (start): 0.3487 rms_B_bonded: 2.37 r_work: 0.3283 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3168 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.3168 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8529 moved from start: 0.2626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 14958 Z= 0.161 Angle : 0.623 6.216 20276 Z= 0.345 Chirality : 0.040 0.150 2280 Planarity : 0.005 0.059 2528 Dihedral : 9.144 164.506 2056 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 3.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.02 % Favored : 98.98 % Rotamer: Outliers : 1.96 % Allowed : 10.33 % Favored : 87.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.12 (0.20), residues: 1758 helix: 1.08 (0.15), residues: 1148 sheet: 0.23 (0.68), residues: 48 loop : 0.32 (0.28), residues: 562 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 335 TYR 0.018 0.002 TYR C 209 PHE 0.019 0.002 PHE A 452 TRP 0.012 0.002 TRP D 246 HIS 0.004 0.001 HIS A 360 Details of bonding type rmsd/Z covalent geometry : bond 0.00344 / 0.16 (14956) covalent geometry : angle 0.62303 / 0.34 (20272) SS BOND : bond 0.00494 / 0.25 ( 2) SS BOND : angle 1.49108 / 0.90 ( 4) hydrogen bonds : bond 0.06387 / 4.25 ( 944) hydrogen bonds : angle 4.65959 / 3.46 ( 2718) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 180 is missing expected H atoms. Skipping. Residue LYS 180 is missing expected H atoms. Skipping. Evaluate side-chains 185 residues out of total 1578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 154 time to evaluate : 0.810 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: A 129 PHE cc_start: 0.7446 (OUTLIER) cc_final: 0.7069 (m-80) REVERT: A 418 ASP cc_start: 0.7024 (m-30) cc_final: 0.6661 (m-30) REVERT: A 434 LYS cc_start: 0.7451 (mmtp) cc_final: 0.6677 (ttpp) REVERT: A 452 PHE cc_start: 0.8277 (m-80) cc_final: 0.7960 (m-80) REVERT: B 264 THR cc_start: 0.8922 (t) cc_final: 0.8704 (m) REVERT: B 300 ARG cc_start: 0.6564 (tmm160) cc_final: 0.6323 (ttp-170) REVERT: C 129 PHE cc_start: 0.7448 (OUTLIER) cc_final: 0.7068 (m-80) REVERT: C 418 ASP cc_start: 0.7026 (m-30) cc_final: 0.6663 (m-30) REVERT: C 434 LYS cc_start: 0.7447 (mmtp) cc_final: 0.6674 (ttpp) REVERT: C 452 PHE cc_start: 0.8282 (m-80) cc_final: 0.7971 (m-80) REVERT: D 264 THR cc_start: 0.8921 (t) cc_final: 0.8705 (m) outliers start: 31 outliers final: 6 residues processed: 167 average time/residue: 1.0570 time to fit residues: 196.7716 Evaluate side-chains 146 residues out of total 1578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 138 time to evaluate : 0.704 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 PHE Chi-restraints excluded: chain A residue 362 LEU Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain B residue 104 ILE Chi-restraints excluded: chain C residue 129 PHE Chi-restraints excluded: chain C residue 362 LEU Chi-restraints excluded: chain C residue 370 VAL Chi-restraints excluded: chain D residue 104 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 167 optimal weight: 1.9990 chunk 128 optimal weight: 4.9990 chunk 35 optimal weight: 4.9990 chunk 160 optimal weight: 2.9990 chunk 10 optimal weight: 4.9990 chunk 88 optimal weight: 4.9990 chunk 174 optimal weight: 7.9990 chunk 162 optimal weight: 4.9990 chunk 50 optimal weight: 0.7980 chunk 68 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 378 ASN B 311 ASN C 378 ASN D 311 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4444 r_free = 0.4444 target = 0.188779 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.113360 restraints weight = 55982.428| |-----------------------------------------------------------------------------| r_work (start): 0.3416 rms_B_bonded: 1.86 r_work: 0.3258 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.3151 rms_B_bonded: 3.27 restraints_weight: 0.2500 r_work (final): 0.3151 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8585 moved from start: 0.3209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 14958 Z= 0.214 Angle : 0.581 5.207 20276 Z= 0.319 Chirality : 0.040 0.141 2280 Planarity : 0.005 0.042 2528 Dihedral : 8.854 158.802 2056 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 3.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 2.03 % Allowed : 10.84 % Favored : 87.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.18 (0.20), residues: 1758 helix: 1.20 (0.15), residues: 1146 sheet: 0.40 (0.65), residues: 56 loop : 0.15 (0.29), residues: 556 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 170 TYR 0.014 0.002 TYR D 210 PHE 0.014 0.002 PHE A 269 TRP 0.021 0.003 TRP A 246 HIS 0.003 0.001 HIS B 260 Details of bonding type rmsd/Z covalent geometry : bond 0.00504 / 0.21 (14956) covalent geometry : angle 0.58094 / 0.32 (20272) SS BOND : bond 0.00307 / 0.15 ( 2) SS BOND : angle 1.15672 / 0.75 ( 4) hydrogen bonds : bond 0.06266 / 4.15 ( 944) hydrogen bonds : angle 4.38959 / 3.25 ( 2718) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 180 is missing expected H atoms. Skipping. Residue LYS 180 is missing expected H atoms. Skipping. Evaluate side-chains 179 residues out of total 1578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 147 time to evaluate : 0.724 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: A 129 PHE cc_start: 0.7466 (OUTLIER) cc_final: 0.7097 (m-80) REVERT: A 418 ASP cc_start: 0.6952 (m-30) cc_final: 0.6613 (m-30) REVERT: B 300 ARG cc_start: 0.6704 (tmm160) cc_final: 0.6397 (ttp-170) REVERT: C 129 PHE cc_start: 0.7471 (OUTLIER) cc_final: 0.7102 (m-80) REVERT: C 418 ASP cc_start: 0.6966 (m-30) cc_final: 0.6628 (m-30) outliers start: 32 outliers final: 16 residues processed: 165 average time/residue: 0.9511 time to fit residues: 177.0011 Evaluate side-chains 152 residues out of total 1578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 134 time to evaluate : 0.785 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 PHE Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 408 ASP Chi-restraints excluded: chain A residue 454 VAL Chi-restraints excluded: chain B residue 104 ILE Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain B residue 345 GLU Chi-restraints excluded: chain B residue 354 ILE Chi-restraints excluded: chain B residue 360 HIS Chi-restraints excluded: chain C residue 129 PHE Chi-restraints excluded: chain C residue 370 VAL Chi-restraints excluded: chain C residue 408 ASP Chi-restraints excluded: chain C residue 454 VAL Chi-restraints excluded: chain D residue 104 ILE Chi-restraints excluded: chain D residue 228 VAL Chi-restraints excluded: chain D residue 345 GLU Chi-restraints excluded: chain D residue 354 ILE Chi-restraints excluded: chain D residue 360 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 80 optimal weight: 6.9990 chunk 20 optimal weight: 0.1980 chunk 93 optimal weight: 2.9990 chunk 104 optimal weight: 0.9980 chunk 153 optimal weight: 0.9990 chunk 4 optimal weight: 0.0370 chunk 31 optimal weight: 10.0000 chunk 11 optimal weight: 1.9990 chunk 97 optimal weight: 2.9990 chunk 58 optimal weight: 1.9990 chunk 2 optimal weight: 0.7980 overall best weight: 0.6060 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 378 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4461 r_free = 0.4461 target = 0.190107 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.115822 restraints weight = 55725.574| |-----------------------------------------------------------------------------| r_work (start): 0.3463 rms_B_bonded: 1.86 r_work: 0.3313 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.3207 rms_B_bonded: 3.27 restraints_weight: 0.2500 r_work (final): 0.3207 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8508 moved from start: 0.3512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 14958 Z= 0.118 Angle : 0.506 4.747 20276 Z= 0.273 Chirality : 0.037 0.144 2280 Planarity : 0.004 0.046 2528 Dihedral : 8.014 162.971 2056 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 3.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 1.20 % Allowed : 12.23 % Favored : 86.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.58 (0.20), residues: 1758 helix: 1.55 (0.15), residues: 1164 sheet: 0.29 (0.61), residues: 56 loop : 0.17 (0.29), residues: 538 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 298 TYR 0.013 0.001 TYR D 210 PHE 0.009 0.001 PHE C 108 TRP 0.010 0.001 TRP D 73 HIS 0.003 0.001 HIS A 260 Details of bonding type rmsd/Z covalent geometry : bond 0.00255 / 0.12 (14956) covalent geometry : angle 0.50541 / 0.27 (20272) SS BOND : bond 0.00371 / 0.19 ( 2) SS BOND : angle 1.03951 / 0.69 ( 4) hydrogen bonds : bond 0.04999 / 3.34 ( 944) hydrogen bonds : angle 4.13228 / 3.07 ( 2718) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 180 is missing expected H atoms. Skipping. Residue LYS 180 is missing expected H atoms. Skipping. Evaluate side-chains 154 residues out of total 1578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 135 time to evaluate : 0.803 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: A 129 PHE cc_start: 0.7437 (OUTLIER) cc_final: 0.7034 (m-80) REVERT: B 300 ARG cc_start: 0.6687 (tmm160) cc_final: 0.6316 (ttp-170) REVERT: C 129 PHE cc_start: 0.7440 (OUTLIER) cc_final: 0.7037 (m-80) REVERT: C 418 ASP cc_start: 0.6833 (m-30) cc_final: 0.6556 (m-30) outliers start: 19 outliers final: 9 residues processed: 147 average time/residue: 0.9957 time to fit residues: 164.6827 Evaluate side-chains 136 residues out of total 1578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 125 time to evaluate : 0.772 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 PHE Chi-restraints excluded: chain A residue 454 VAL Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain B residue 345 GLU Chi-restraints excluded: chain B residue 360 HIS Chi-restraints excluded: chain C residue 129 PHE Chi-restraints excluded: chain C residue 454 VAL Chi-restraints excluded: chain D residue 228 VAL Chi-restraints excluded: chain D residue 326 MET Chi-restraints excluded: chain D residue 345 GLU Chi-restraints excluded: chain D residue 360 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 158 optimal weight: 0.9980 chunk 71 optimal weight: 8.9990 chunk 5 optimal weight: 0.0770 chunk 162 optimal weight: 0.7980 chunk 95 optimal weight: 8.9990 chunk 23 optimal weight: 1.9990 chunk 103 optimal weight: 1.9990 chunk 76 optimal weight: 9.9990 chunk 82 optimal weight: 5.9990 chunk 63 optimal weight: 0.7980 chunk 69 optimal weight: 2.9990 overall best weight: 0.9340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 287 ASN C 287 ASN C 378 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4389 r_free = 0.4389 target = 0.185090 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.129499 restraints weight = 53528.760| |-----------------------------------------------------------------------------| r_work (start): 0.3713 rms_B_bonded: 1.46 r_work: 0.3287 rms_B_bonded: 1.87 restraints_weight: 0.5000 r_work: 0.3188 rms_B_bonded: 2.92 restraints_weight: 0.2500 r_work (final): 0.3188 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8637 moved from start: 0.3669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 14958 Z= 0.131 Angle : 0.505 5.075 20276 Z= 0.272 Chirality : 0.037 0.142 2280 Planarity : 0.004 0.046 2528 Dihedral : 7.901 165.043 2054 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 3.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 1.20 % Allowed : 12.55 % Favored : 86.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.68 (0.21), residues: 1758 helix: 1.64 (0.15), residues: 1164 sheet: 0.36 (0.57), residues: 60 loop : 0.19 (0.30), residues: 534 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 321 TYR 0.013 0.001 TYR D 210 PHE 0.010 0.001 PHE B 312 TRP 0.012 0.002 TRP C 246 HIS 0.003 0.001 HIS A 491 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.13 (14956) covalent geometry : angle 0.50468 / 0.27 (20272) SS BOND : bond 0.00204 / 0.10 ( 2) SS BOND : angle 1.19651 / 0.76 ( 4) hydrogen bonds : bond 0.05007 / 3.35 ( 944) hydrogen bonds : angle 4.06993 / 3.02 ( 2718) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 180 is missing expected H atoms. Skipping. Residue LYS 180 is missing expected H atoms. Skipping. Evaluate side-chains 155 residues out of total 1578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 136 time to evaluate : 0.744 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: A 129 PHE cc_start: 0.7524 (OUTLIER) cc_final: 0.7108 (m-80) REVERT: B 300 ARG cc_start: 0.6809 (tmm160) cc_final: 0.6457 (ttp-170) REVERT: B 315 ARG cc_start: 0.7743 (tpt90) cc_final: 0.7421 (mmm160) REVERT: B 388 MET cc_start: 0.5216 (ttm) cc_final: 0.4879 (ttm) REVERT: C 129 PHE cc_start: 0.7539 (OUTLIER) cc_final: 0.7116 (m-80) REVERT: C 452 PHE cc_start: 0.8137 (m-10) cc_final: 0.7675 (m-80) REVERT: D 388 MET cc_start: 0.5217 (ttm) cc_final: 0.4884 (ttm) outliers start: 19 outliers final: 13 residues processed: 147 average time/residue: 1.0022 time to fit residues: 164.9164 Evaluate side-chains 142 residues out of total 1578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 127 time to evaluate : 0.735 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 129 PHE Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 454 VAL Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain B residue 345 GLU Chi-restraints excluded: chain B residue 360 HIS Chi-restraints excluded: chain C residue 119 LEU Chi-restraints excluded: chain C residue 129 PHE Chi-restraints excluded: chain C residue 370 VAL Chi-restraints excluded: chain C residue 454 VAL Chi-restraints excluded: chain D residue 228 VAL Chi-restraints excluded: chain D residue 326 MET Chi-restraints excluded: chain D residue 345 GLU Chi-restraints excluded: chain D residue 360 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 38 optimal weight: 9.9990 chunk 100 optimal weight: 1.9990 chunk 72 optimal weight: 4.9990 chunk 76 optimal weight: 9.9990 chunk 143 optimal weight: 2.9990 chunk 117 optimal weight: 1.9990 chunk 61 optimal weight: 0.8980 chunk 140 optimal weight: 2.9990 chunk 32 optimal weight: 5.9990 chunk 88 optimal weight: 0.8980 chunk 139 optimal weight: 0.0060 overall best weight: 1.1600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 378 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4382 r_free = 0.4382 target = 0.184563 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.131320 restraints weight = 53489.616| |-----------------------------------------------------------------------------| r_work (start): 0.3745 rms_B_bonded: 2.06 r_work: 0.3222 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3113 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.3113 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8693 moved from start: 0.3858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 14958 Z= 0.142 Angle : 0.512 7.556 20276 Z= 0.273 Chirality : 0.037 0.143 2280 Planarity : 0.004 0.046 2528 Dihedral : 8.074 165.354 2054 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 1.20 % Allowed : 12.86 % Favored : 85.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.67 (0.21), residues: 1758 helix: 1.67 (0.15), residues: 1162 sheet: 0.13 (0.74), residues: 38 loop : 0.11 (0.30), residues: 558 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 321 TYR 0.014 0.001 TYR D 210 PHE 0.011 0.001 PHE A 452 TRP 0.013 0.002 TRP C 246 HIS 0.003 0.001 HIS A 491 Details of bonding type rmsd/Z covalent geometry : bond 0.00327 / 0.14 (14956) covalent geometry : angle 0.51200 / 0.27 (20272) SS BOND : bond 0.00239 / 0.12 ( 2) SS BOND : angle 0.96661 / 0.63 ( 4) hydrogen bonds : bond 0.05024 / 3.36 ( 944) hydrogen bonds : angle 4.03113 / 2.99 ( 2718) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 180 is missing expected H atoms. Skipping. Residue LYS 180 is missing expected H atoms. Skipping. Evaluate side-chains 156 residues out of total 1578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 137 time to evaluate : 0.699 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: A 129 PHE cc_start: 0.7525 (OUTLIER) cc_final: 0.7097 (m-80) REVERT: B 300 ARG cc_start: 0.6891 (tmm160) cc_final: 0.6598 (ttp-170) REVERT: B 315 ARG cc_start: 0.7764 (tpt90) cc_final: 0.7433 (mmm160) REVERT: B 339 GLU cc_start: 0.7053 (mt-10) cc_final: 0.6668 (mp0) REVERT: B 345 GLU cc_start: 0.7712 (OUTLIER) cc_final: 0.7375 (mp0) REVERT: B 490 GLN cc_start: 0.2683 (OUTLIER) cc_final: 0.0138 (pm20) REVERT: C 129 PHE cc_start: 0.7544 (OUTLIER) cc_final: 0.7111 (m-80) REVERT: D 315 ARG cc_start: 0.7768 (tpt90) cc_final: 0.7430 (mmm160) REVERT: D 339 GLU cc_start: 0.7048 (mt-10) cc_final: 0.6685 (mp0) REVERT: D 345 GLU cc_start: 0.7678 (OUTLIER) cc_final: 0.7337 (mp0) REVERT: D 490 GLN cc_start: 0.2673 (OUTLIER) cc_final: 0.0133 (pm20) outliers start: 19 outliers final: 9 residues processed: 147 average time/residue: 1.0487 time to fit residues: 172.7577 Evaluate side-chains 142 residues out of total 1578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 127 time to evaluate : 0.769 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 PHE Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 454 VAL Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain B residue 345 GLU Chi-restraints excluded: chain B residue 360 HIS Chi-restraints excluded: chain B residue 490 GLN Chi-restraints excluded: chain C residue 129 PHE Chi-restraints excluded: chain C residue 370 VAL Chi-restraints excluded: chain C residue 454 VAL Chi-restraints excluded: chain D residue 228 VAL Chi-restraints excluded: chain D residue 326 MET Chi-restraints excluded: chain D residue 345 GLU Chi-restraints excluded: chain D residue 360 HIS Chi-restraints excluded: chain D residue 490 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 83 optimal weight: 9.9990 chunk 2 optimal weight: 0.6980 chunk 20 optimal weight: 0.3980 chunk 48 optimal weight: 0.3980 chunk 152 optimal weight: 0.9980 chunk 159 optimal weight: 0.0970 chunk 46 optimal weight: 0.9990 chunk 65 optimal weight: 0.8980 chunk 142 optimal weight: 0.7980 chunk 165 optimal weight: 4.9990 chunk 58 optimal weight: 1.9990 overall best weight: 0.4778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 378 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4400 r_free = 0.4400 target = 0.186273 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.129041 restraints weight = 53702.116| |-----------------------------------------------------------------------------| r_work (start): 0.3698 rms_B_bonded: 1.46 r_work: 0.3302 rms_B_bonded: 1.86 restraints_weight: 0.5000 r_work: 0.3205 rms_B_bonded: 2.92 restraints_weight: 0.2500 r_work (final): 0.3205 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8611 moved from start: 0.4049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 14958 Z= 0.103 Angle : 0.476 6.442 20276 Z= 0.253 Chirality : 0.036 0.141 2280 Planarity : 0.004 0.052 2528 Dihedral : 7.630 163.257 2054 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 3.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 1.20 % Allowed : 12.67 % Favored : 86.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.92 (0.21), residues: 1758 helix: 1.89 (0.15), residues: 1164 sheet: 0.05 (0.58), residues: 60 loop : 0.15 (0.30), residues: 534 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 321 TYR 0.013 0.001 TYR B 210 PHE 0.017 0.001 PHE B 312 TRP 0.011 0.001 TRP D 73 HIS 0.002 0.001 HIS C 260 Details of bonding type rmsd/Z covalent geometry : bond 0.00218 / 0.10 (14956) covalent geometry : angle 0.47550 / 0.25 (20272) SS BOND : bond 0.00242 / 0.12 ( 2) SS BOND : angle 0.85344 / 0.54 ( 4) hydrogen bonds : bond 0.04385 / 2.95 ( 944) hydrogen bonds : angle 3.92529 / 2.92 ( 2718) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 180 is missing expected H atoms. Skipping. Residue LYS 180 is missing expected H atoms. Skipping. Evaluate side-chains 153 residues out of total 1578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 134 time to evaluate : 0.509 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: A 129 PHE cc_start: 0.7489 (OUTLIER) cc_final: 0.7104 (m-80) REVERT: B 311 ASN cc_start: 0.8272 (t0) cc_final: 0.7363 (m110) REVERT: B 315 ARG cc_start: 0.7772 (tpt90) cc_final: 0.7466 (mmm160) REVERT: B 339 GLU cc_start: 0.6865 (mt-10) cc_final: 0.6466 (mp0) REVERT: B 345 GLU cc_start: 0.7600 (OUTLIER) cc_final: 0.7342 (mp0) REVERT: C 129 PHE cc_start: 0.7489 (OUTLIER) cc_final: 0.7101 (m-80) REVERT: D 311 ASN cc_start: 0.8262 (t0) cc_final: 0.7375 (m110) REVERT: D 315 ARG cc_start: 0.7772 (tpt90) cc_final: 0.7462 (mmm160) REVERT: D 339 GLU cc_start: 0.6897 (mt-10) cc_final: 0.6541 (mp0) REVERT: D 345 GLU cc_start: 0.7581 (OUTLIER) cc_final: 0.7328 (mp0) outliers start: 19 outliers final: 9 residues processed: 142 average time/residue: 1.0544 time to fit residues: 167.6671 Evaluate side-chains 135 residues out of total 1578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 122 time to evaluate : 0.718 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 PHE Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 454 VAL Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain B residue 345 GLU Chi-restraints excluded: chain B residue 360 HIS Chi-restraints excluded: chain C residue 129 PHE Chi-restraints excluded: chain C residue 370 VAL Chi-restraints excluded: chain C residue 454 VAL Chi-restraints excluded: chain D residue 228 VAL Chi-restraints excluded: chain D residue 326 MET Chi-restraints excluded: chain D residue 345 GLU Chi-restraints excluded: chain D residue 360 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 119 optimal weight: 6.9990 chunk 12 optimal weight: 1.9990 chunk 1 optimal weight: 2.9990 chunk 157 optimal weight: 3.9990 chunk 102 optimal weight: 1.9990 chunk 173 optimal weight: 30.0000 chunk 153 optimal weight: 0.8980 chunk 103 optimal weight: 0.9980 chunk 25 optimal weight: 1.9990 chunk 10 optimal weight: 4.9990 chunk 88 optimal weight: 3.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 378 ASN B 307 GLN D 307 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4376 r_free = 0.4376 target = 0.184087 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.132113 restraints weight = 53860.813| |-----------------------------------------------------------------------------| r_work (start): 0.3752 rms_B_bonded: 2.07 r_work: 0.3211 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3106 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.3106 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8694 moved from start: 0.4119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 14958 Z= 0.174 Angle : 0.516 6.594 20276 Z= 0.277 Chirality : 0.038 0.151 2280 Planarity : 0.004 0.044 2528 Dihedral : 8.183 162.669 2054 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 3.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 1.33 % Allowed : 12.48 % Favored : 86.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.78 (0.21), residues: 1758 helix: 1.77 (0.15), residues: 1160 sheet: 0.13 (0.58), residues: 60 loop : 0.12 (0.30), residues: 538 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 321 TYR 0.015 0.001 TYR D 210 PHE 0.017 0.002 PHE C 109 TRP 0.015 0.002 TRP A 246 HIS 0.003 0.001 HIS A 491 Details of bonding type rmsd/Z covalent geometry : bond 0.00413 / 0.17 (14956) covalent geometry : angle 0.51588 / 0.28 (20272) SS BOND : bond 0.00192 / 0.09 ( 2) SS BOND : angle 0.94975 / 0.61 ( 4) hydrogen bonds : bond 0.05093 / 3.41 ( 944) hydrogen bonds : angle 4.00199 / 2.97 ( 2718) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 180 is missing expected H atoms. Skipping. Residue LYS 180 is missing expected H atoms. Skipping. Evaluate side-chains 146 residues out of total 1578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 125 time to evaluate : 0.858 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: A 129 PHE cc_start: 0.7532 (OUTLIER) cc_final: 0.7141 (m-80) REVERT: B 490 GLN cc_start: 0.2828 (OUTLIER) cc_final: 0.0676 (pm20) REVERT: C 129 PHE cc_start: 0.7524 (OUTLIER) cc_final: 0.7128 (m-80) REVERT: C 452 PHE cc_start: 0.8269 (m-10) cc_final: 0.7837 (m-80) REVERT: D 490 GLN cc_start: 0.2850 (OUTLIER) cc_final: 0.0727 (pm20) outliers start: 21 outliers final: 14 residues processed: 136 average time/residue: 1.1634 time to fit residues: 177.1942 Evaluate side-chains 135 residues out of total 1578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 117 time to evaluate : 0.784 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 129 PHE Chi-restraints excluded: chain A residue 238 MET Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 454 VAL Chi-restraints excluded: chain B residue 345 GLU Chi-restraints excluded: chain B residue 360 HIS Chi-restraints excluded: chain B residue 490 GLN Chi-restraints excluded: chain C residue 119 LEU Chi-restraints excluded: chain C residue 129 PHE Chi-restraints excluded: chain C residue 238 MET Chi-restraints excluded: chain C residue 370 VAL Chi-restraints excluded: chain C residue 388 MET Chi-restraints excluded: chain C residue 454 VAL Chi-restraints excluded: chain D residue 326 MET Chi-restraints excluded: chain D residue 345 GLU Chi-restraints excluded: chain D residue 360 HIS Chi-restraints excluded: chain D residue 490 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 84 optimal weight: 8.9990 chunk 20 optimal weight: 0.2980 chunk 98 optimal weight: 4.9990 chunk 17 optimal weight: 1.9990 chunk 129 optimal weight: 4.9990 chunk 81 optimal weight: 6.9990 chunk 100 optimal weight: 1.9990 chunk 72 optimal weight: 2.9990 chunk 141 optimal weight: 0.6980 chunk 130 optimal weight: 1.9990 chunk 90 optimal weight: 0.2980 overall best weight: 1.0584 ------------------------------------------------------------------------------- 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 = 0.4381 r_free = 0.4381 target = 0.184714 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.128892 restraints weight = 53758.564| |-----------------------------------------------------------------------------| r_work (start): 0.3704 rms_B_bonded: 1.84 r_work: 0.3242 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3149 rms_B_bonded: 3.52 restraints_weight: 0.2500 r_work (final): 0.3149 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8662 moved from start: 0.4228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 14958 Z= 0.131 Angle : 0.495 6.710 20276 Z= 0.263 Chirality : 0.037 0.141 2280 Planarity : 0.004 0.045 2528 Dihedral : 8.087 160.443 2054 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 3.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 1.33 % Allowed : 12.80 % Favored : 85.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.85 (0.21), residues: 1758 helix: 1.81 (0.15), residues: 1162 sheet: 0.26 (0.57), residues: 60 loop : 0.16 (0.30), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 321 TYR 0.013 0.001 TYR D 210 PHE 0.009 0.001 PHE A 269 TRP 0.012 0.002 TRP A 246 HIS 0.001 0.000 HIS A 491 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.13 (14956) covalent geometry : angle 0.49467 / 0.26 (20272) SS BOND : bond 0.00175 / 0.09 ( 2) SS BOND : angle 0.98106 / 0.58 ( 4) hydrogen bonds : bond 0.04761 / 3.20 ( 944) hydrogen bonds : angle 3.95224 / 2.93 ( 2718) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 180 is missing expected H atoms. Skipping. Residue LYS 180 is missing expected H atoms. Skipping. Evaluate side-chains 140 residues out of total 1578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 119 time to evaluate : 0.603 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: A 129 PHE cc_start: 0.7527 (OUTLIER) cc_final: 0.7112 (m-80) REVERT: A 451 LEU cc_start: 0.8076 (mm) cc_final: 0.7822 (mp) REVERT: A 452 PHE cc_start: 0.8211 (m-10) cc_final: 0.7941 (m-80) REVERT: B 315 ARG cc_start: 0.7952 (OUTLIER) cc_final: 0.7592 (mmm160) REVERT: B 339 GLU cc_start: 0.6918 (mt-10) cc_final: 0.6566 (mp0) REVERT: B 490 GLN cc_start: 0.2662 (OUTLIER) cc_final: 0.0621 (pm20) REVERT: C 129 PHE cc_start: 0.7537 (OUTLIER) cc_final: 0.7117 (m-80) REVERT: C 452 PHE cc_start: 0.8202 (m-10) cc_final: 0.7768 (m-80) REVERT: D 339 GLU cc_start: 0.6913 (mt-10) cc_final: 0.6531 (mp0) REVERT: D 490 GLN cc_start: 0.2568 (OUTLIER) cc_final: 0.0518 (pm20) outliers start: 21 outliers final: 9 residues processed: 131 average time/residue: 1.1105 time to fit residues: 163.2045 Evaluate side-chains 131 residues out of total 1578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 117 time to evaluate : 0.816 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 PHE Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 454 VAL Chi-restraints excluded: chain B residue 315 ARG Chi-restraints excluded: chain B residue 345 GLU Chi-restraints excluded: chain B residue 360 HIS Chi-restraints excluded: chain B residue 490 GLN Chi-restraints excluded: chain C residue 129 PHE Chi-restraints excluded: chain C residue 370 VAL Chi-restraints excluded: chain C residue 454 VAL Chi-restraints excluded: chain D residue 315 ARG Chi-restraints excluded: chain D residue 345 GLU Chi-restraints excluded: chain D residue 360 HIS Chi-restraints excluded: chain D residue 490 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 67 optimal weight: 0.9990 chunk 132 optimal weight: 2.9990 chunk 26 optimal weight: 4.9990 chunk 126 optimal weight: 6.9990 chunk 20 optimal weight: 0.2980 chunk 138 optimal weight: 0.5980 chunk 158 optimal weight: 4.9990 chunk 148 optimal weight: 1.9990 chunk 83 optimal weight: 20.0000 chunk 152 optimal weight: 0.9990 chunk 61 optimal weight: 0.5980 overall best weight: 0.6984 ------------------------------------------------------------------------------- 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 = 0.4388 r_free = 0.4388 target = 0.185450 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.132265 restraints weight = 53634.151| |-----------------------------------------------------------------------------| r_work (start): 0.3752 rms_B_bonded: 2.24 r_work: 0.3210 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3104 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.3104 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8667 moved from start: 0.4319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 14958 Z= 0.113 Angle : 0.483 6.840 20276 Z= 0.256 Chirality : 0.036 0.142 2280 Planarity : 0.004 0.045 2528 Dihedral : 7.794 158.711 2054 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 3.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 0.76 % Allowed : 13.24 % Favored : 85.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: 2.02 (0.21), residues: 1758 helix: 1.95 (0.15), residues: 1158 sheet: 0.32 (0.58), residues: 60 loop : 0.22 (0.30), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 321 TYR 0.014 0.001 TYR D 210 PHE 0.017 0.001 PHE A 109 TRP 0.011 0.001 TRP D 73 HIS 0.002 0.000 HIS C 260 Details of bonding type rmsd/Z covalent geometry : bond 0.00253 / 0.11 (14956) covalent geometry : angle 0.48295 / 0.26 (20272) SS BOND : bond 0.00149 / 0.08 ( 2) SS BOND : angle 1.21939 / 0.78 ( 4) hydrogen bonds : bond 0.04466 / 3.01 ( 944) hydrogen bonds : angle 3.89044 / 2.89 ( 2718) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 180 is missing expected H atoms. Skipping. Residue LYS 180 is missing expected H atoms. Skipping. Evaluate side-chains 138 residues out of total 1578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 126 time to evaluate : 0.814 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: A 129 PHE cc_start: 0.7474 (OUTLIER) cc_final: 0.7092 (m-80) REVERT: A 451 LEU cc_start: 0.8035 (mm) cc_final: 0.7832 (mp) REVERT: A 452 PHE cc_start: 0.8271 (m-10) cc_final: 0.7958 (m-80) REVERT: B 339 GLU cc_start: 0.6933 (mt-10) cc_final: 0.6562 (mp0) REVERT: B 490 GLN cc_start: 0.2661 (OUTLIER) cc_final: 0.0610 (pm20) REVERT: C 129 PHE cc_start: 0.7502 (OUTLIER) cc_final: 0.7098 (m-80) REVERT: C 452 PHE cc_start: 0.8263 (m-10) cc_final: 0.7943 (m-80) REVERT: D 339 GLU cc_start: 0.6916 (mt-10) cc_final: 0.6527 (mp0) REVERT: D 490 GLN cc_start: 0.2732 (OUTLIER) cc_final: 0.0661 (pm20) outliers start: 12 outliers final: 8 residues processed: 136 average time/residue: 1.1325 time to fit residues: 173.9742 Evaluate side-chains 129 residues out of total 1578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 117 time to evaluate : 0.797 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 PHE Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 454 VAL Chi-restraints excluded: chain B residue 345 GLU Chi-restraints excluded: chain B residue 360 HIS Chi-restraints excluded: chain B residue 490 GLN Chi-restraints excluded: chain C residue 129 PHE Chi-restraints excluded: chain C residue 370 VAL Chi-restraints excluded: chain C residue 454 VAL Chi-restraints excluded: chain D residue 345 GLU Chi-restraints excluded: chain D residue 360 HIS Chi-restraints excluded: chain D residue 490 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 67 optimal weight: 0.9990 chunk 10 optimal weight: 0.4980 chunk 30 optimal weight: 6.9990 chunk 109 optimal weight: 0.9980 chunk 7 optimal weight: 7.9990 chunk 46 optimal weight: 0.9980 chunk 104 optimal weight: 0.9980 chunk 80 optimal weight: 20.0000 chunk 26 optimal weight: 4.9990 chunk 155 optimal weight: 0.9990 chunk 18 optimal weight: 1.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- 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 = 0.4386 r_free = 0.4386 target = 0.185183 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.130017 restraints weight = 53978.171| |-----------------------------------------------------------------------------| r_work (start): 0.3721 rms_B_bonded: 2.21 r_work: 0.3212 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3108 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.3108 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8681 moved from start: 0.4391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 14958 Z= 0.125 Angle : 0.493 7.348 20276 Z= 0.260 Chirality : 0.037 0.141 2280 Planarity : 0.004 0.044 2528 Dihedral : 7.817 157.286 2054 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 1.08 % Allowed : 13.12 % Favored : 85.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: 2.04 (0.21), residues: 1758 helix: 1.96 (0.15), residues: 1156 sheet: 0.25 (0.58), residues: 60 loop : 0.25 (0.30), residues: 542 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 321 TYR 0.014 0.001 TYR D 210 PHE 0.014 0.001 PHE B 312 TRP 0.011 0.002 TRP C 246 HIS 0.002 0.000 HIS A 491 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.12 (14956) covalent geometry : angle 0.49267 / 0.26 (20272) SS BOND : bond 0.00152 / 0.08 ( 2) SS BOND : angle 1.12019 / 0.74 ( 4) hydrogen bonds : bond 0.04567 / 3.08 ( 944) hydrogen bonds : angle 3.89128 / 2.89 ( 2718) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10056.24 seconds wall clock time: 170 minutes 19.90 seconds (10219.90 seconds total)