Starting phenix.real_space_refine on Sat Feb 7 01:08:07 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7t4x_25691/02_2026/7t4x_25691_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/7t4x_25691/02_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7t4x_25691/02_2026/7t4x_25691.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7t4x_25691/02_2026/7t4x_25691.map" model { file = "/net/cci-nas-00/data/ceres_data/7t4x_25691/02_2026/7t4x_25691_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7t4x_25691/02_2026/7t4x_25691_trim.cif" } 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-2.0-5952/lib/python3.9/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, 5 Unusual residues: {' K': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} 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: 4.90, per 1000 atoms: 0.17 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: 2.52 Conformation dependent library (CDL) restraints added in 655.1 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: 0.86 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: 6.71 Time building geometry restraints manager: 3.45 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: 6.360 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.150 Extract box with map and model: 0.410 Check model and map are aligned: 0.090 Set scattering table: 0.070 Process input model: 26.420 Find NCS groups from input model: 0.490 Set up NCS constraints: 0.030 Set refine NCS operators: 0.010 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:8.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.440 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8125 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 covalent geometry : bond 0.00572 (14956) covalent geometry : angle 0.93140 (20272) SS BOND : bond 0.00417 ( 2) SS BOND : angle 2.59962 ( 4) hydrogen bonds : bond 0.12715 ( 944) hydrogen bonds : angle 5.49210 ( 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 : 0.762 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: 1.3786 time to fit residues: 430.6332 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 : 0.758 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: A 378 ASN B 311 ASN B 475 GLN B 486 ASN C 378 ASN D 311 ASN D 325 GLN D 475 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4468 r_free = 0.4468 target = 0.191158 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.116143 restraints weight = 56127.208| |-----------------------------------------------------------------------------| r_work (start): 0.3452 rms_B_bonded: 1.98 r_work: 0.3309 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3196 rms_B_bonded: 3.37 restraints_weight: 0.2500 r_work (final): 0.3196 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8364 moved from start: 0.2718 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= 0.161 Angle : 0.614 6.000 20276 Z= 0.339 Chirality : 0.039 0.148 2280 Planarity : 0.005 0.055 2528 Dihedral : 9.074 164.851 2056 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 3.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Rotamer: Outliers : 1.90 % Allowed : 10.65 % Favored : 87.45 % 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: 1.20 (0.20), residues: 1758 helix: 1.12 (0.15), residues: 1148 sheet: 0.19 (0.67), residues: 48 loop : 0.41 (0.28), residues: 562 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 164 TYR 0.017 0.002 TYR A 209 PHE 0.017 0.002 PHE A 452 TRP 0.014 0.002 TRP C 246 HIS 0.005 0.001 HIS A 360 Details of bonding type rmsd covalent geometry : bond 0.00344 (14956) covalent geometry : angle 0.61368 (20272) SS BOND : bond 0.00504 ( 2) SS BOND : angle 1.50829 ( 4) hydrogen bonds : bond 0.06192 ( 944) hydrogen bonds : angle 4.60458 ( 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: 30 poor density : 155 time to evaluate : 0.771 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: 0.7455 (OUTLIER) cc_final: 0.7060 (m-80) REVERT: A 418 ASP cc_start: 0.6995 (m-30) cc_final: 0.6617 (m-30) REVERT: A 434 LYS cc_start: 0.7502 (mmtp) cc_final: 0.6729 (ttpp) REVERT: B 300 ARG cc_start: 0.6533 (tmm160) cc_final: 0.6226 (ttp-170) REVERT: C 129 PHE cc_start: 0.7447 (OUTLIER) cc_final: 0.7053 (m-80) REVERT: C 418 ASP cc_start: 0.7004 (m-30) cc_final: 0.6629 (m-30) REVERT: C 434 LYS cc_start: 0.7510 (mmtp) cc_final: 0.6734 (ttpp) REVERT: D 315 ARG cc_start: 0.8027 (tpt90) cc_final: 0.7523 (tpm170) REVERT: D 388 MET cc_start: 0.5467 (ttm) cc_final: 0.5238 (ttm) outliers start: 30 outliers final: 6 residues processed: 169 average time/residue: 1.1716 time to fit residues: 218.5802 Evaluate side-chains 145 residues out of total 1578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 137 time to evaluate : 0.725 ------------------------------------------------------------------------------- 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: 3.9990 chunk 128 optimal weight: 1.9990 chunk 35 optimal weight: 0.4980 chunk 160 optimal weight: 0.9990 chunk 10 optimal weight: 6.9990 chunk 88 optimal weight: 4.9990 chunk 174 optimal weight: 20.0000 chunk 162 optimal weight: 3.9990 chunk 50 optimal weight: 0.9990 chunk 68 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 overall best weight: 1.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4454 r_free = 0.4454 target = 0.189883 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.117981 restraints weight = 55680.222| |-----------------------------------------------------------------------------| r_work (start): 0.3482 rms_B_bonded: 2.33 r_work: 0.3251 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3143 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.3143 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8524 moved from start: 0.3272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 14958 Z= 0.156 Angle : 0.546 5.657 20276 Z= 0.298 Chirality : 0.038 0.143 2280 Planarity : 0.004 0.042 2528 Dihedral : 8.234 157.333 2056 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 3.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 1.52 % Allowed : 11.15 % Favored : 87.33 % 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: 1.42 (0.20), residues: 1758 helix: 1.36 (0.15), residues: 1160 sheet: 0.39 (0.62), residues: 56 loop : 0.27 (0.29), residues: 542 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 86 TYR 0.014 0.001 TYR D 210 PHE 0.012 0.002 PHE A 269 TRP 0.016 0.002 TRP C 246 HIS 0.002 0.001 HIS A 491 Details of bonding type rmsd covalent geometry : bond 0.00356 (14956) covalent geometry : angle 0.54590 (20272) SS BOND : bond 0.00342 ( 2) SS BOND : angle 1.07407 ( 4) hydrogen bonds : bond 0.05767 ( 944) hydrogen bonds : angle 4.30289 ( 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 167 residues out of total 1578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 143 time to evaluate : 0.835 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: A 129 PHE cc_start: 0.7514 (OUTLIER) cc_final: 0.7102 (m-80) REVERT: A 418 ASP cc_start: 0.6949 (m-30) cc_final: 0.6624 (m-30) REVERT: A 452 PHE cc_start: 0.8238 (m-80) cc_final: 0.7921 (m-80) REVERT: B 300 ARG cc_start: 0.6715 (tmm160) cc_final: 0.6440 (ttp-170) REVERT: C 129 PHE cc_start: 0.7515 (OUTLIER) cc_final: 0.7103 (m-80) REVERT: C 339 GLU cc_start: 0.6265 (OUTLIER) cc_final: 0.6052 (mt-10) REVERT: C 418 ASP cc_start: 0.6962 (m-30) cc_final: 0.6646 (m-30) REVERT: C 452 PHE cc_start: 0.8234 (m-80) cc_final: 0.7919 (m-80) outliers start: 24 outliers final: 12 residues processed: 157 average time/residue: 1.0189 time to fit residues: 178.8080 Evaluate side-chains 146 residues out of total 1578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 131 time to evaluate : 0.776 ------------------------------------------------------------------------------- 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 326 MET 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 339 GLU 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 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: 9.9990 chunk 20 optimal weight: 0.6980 chunk 93 optimal weight: 0.9990 chunk 104 optimal weight: 1.9990 chunk 153 optimal weight: 1.9990 chunk 4 optimal weight: 0.8980 chunk 31 optimal weight: 8.9990 chunk 11 optimal weight: 1.9990 chunk 97 optimal weight: 1.9990 chunk 58 optimal weight: 1.9990 chunk 2 optimal weight: 0.9980 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 378 ASN C 378 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4462 r_free = 0.4462 target = 0.190288 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.115176 restraints weight = 55391.479| |-----------------------------------------------------------------------------| r_work (start): 0.3428 rms_B_bonded: 1.94 r_work: 0.3282 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.3173 rms_B_bonded: 3.26 restraints_weight: 0.2500 r_work (final): 0.3173 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8380 moved from start: 0.3536 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= 0.140 Angle : 0.515 5.571 20276 Z= 0.279 Chirality : 0.037 0.140 2280 Planarity : 0.004 0.043 2528 Dihedral : 8.083 165.495 2054 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 3.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % 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: 1.59 (0.20), residues: 1758 helix: 1.55 (0.15), residues: 1162 sheet: 0.37 (0.59), residues: 58 loop : 0.21 (0.29), residues: 538 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 321 TYR 0.013 0.001 TYR B 210 PHE 0.010 0.001 PHE C 269 TRP 0.013 0.002 TRP A 246 HIS 0.002 0.001 HIS C 491 Details of bonding type rmsd covalent geometry : bond 0.00319 (14956) covalent geometry : angle 0.51434 (20272) SS BOND : bond 0.00336 ( 2) SS BOND : angle 1.10379 ( 4) hydrogen bonds : bond 0.05253 ( 944) hydrogen bonds : angle 4.14091 ( 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 155 residues out of total 1578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 136 time to evaluate : 0.763 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: A 129 PHE cc_start: 0.7427 (OUTLIER) cc_final: 0.7027 (m-80) REVERT: A 388 MET cc_start: 0.7707 (mmt) cc_final: 0.7414 (mtp) REVERT: B 300 ARG cc_start: 0.6733 (tmm160) cc_final: 0.6361 (ttp-170) REVERT: C 129 PHE cc_start: 0.7427 (OUTLIER) cc_final: 0.7004 (m-80) REVERT: C 388 MET cc_start: 0.7721 (mmt) cc_final: 0.7426 (mtp) REVERT: D 298 ARG cc_start: 0.6622 (mtm-85) cc_final: 0.6358 (pmm-80) REVERT: D 345 GLU cc_start: 0.7677 (OUTLIER) cc_final: 0.7216 (mp0) outliers start: 19 outliers final: 12 residues processed: 151 average time/residue: 1.0780 time to fit residues: 181.6922 Evaluate side-chains 139 residues out of total 1578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 124 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 326 MET 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 408 ASP 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: 0.4980 chunk 71 optimal weight: 10.0000 chunk 5 optimal weight: 1.9990 chunk 162 optimal weight: 1.9990 chunk 95 optimal weight: 0.0370 chunk 23 optimal weight: 1.9990 chunk 103 optimal weight: 1.9990 chunk 76 optimal weight: 10.0000 chunk 82 optimal weight: 5.9990 chunk 63 optimal weight: 0.0070 chunk 69 optimal weight: 2.9990 overall best weight: 0.9080 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 287 ASN A 378 ASN C 287 ASN C 378 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4392 r_free = 0.4392 target = 0.185435 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.132555 restraints weight = 53194.134| |-----------------------------------------------------------------------------| r_work (start): 0.3761 rms_B_bonded: 1.84 r_work: 0.3249 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.3148 rms_B_bonded: 3.52 restraints_weight: 0.2500 r_work (final): 0.3148 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8518 moved from start: 0.3738 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= 0.126 Angle : 0.491 4.914 20276 Z= 0.266 Chirality : 0.037 0.143 2280 Planarity : 0.004 0.043 2528 Dihedral : 7.904 164.869 2054 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 3.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 1.33 % Allowed : 12.29 % Favored : 86.38 % 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: 1.69 (0.20), residues: 1758 helix: 1.67 (0.15), residues: 1164 sheet: 0.05 (0.73), residues: 38 loop : 0.16 (0.29), residues: 556 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 170 TYR 0.014 0.001 TYR D 210 PHE 0.012 0.001 PHE D 312 TRP 0.012 0.002 TRP A 246 HIS 0.002 0.000 HIS A 260 Details of bonding type rmsd covalent geometry : bond 0.00281 (14956) covalent geometry : angle 0.49086 (20272) SS BOND : bond 0.00293 ( 2) SS BOND : angle 0.92832 ( 4) hydrogen bonds : bond 0.04965 ( 944) hydrogen bonds : angle 4.05112 ( 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 157 residues out of total 1578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 136 time to evaluate : 0.750 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: 0.7547 (OUTLIER) cc_final: 0.7116 (m-80) REVERT: A 465 MET cc_start: 0.6724 (mmm) cc_final: 0.6495 (mmm) REVERT: B 300 ARG cc_start: 0.6869 (tmm160) cc_final: 0.6561 (ttp-170) REVERT: B 315 ARG cc_start: 0.7763 (tpt90) cc_final: 0.7424 (mmm160) REVERT: B 339 GLU cc_start: 0.6934 (mt-10) cc_final: 0.6592 (mp0) REVERT: B 345 GLU cc_start: 0.7650 (OUTLIER) cc_final: 0.7287 (mp0) REVERT: C 129 PHE cc_start: 0.7549 (OUTLIER) cc_final: 0.7118 (m-80) REVERT: C 465 MET cc_start: 0.6705 (mmm) cc_final: 0.6482 (mmm) REVERT: D 315 ARG cc_start: 0.7719 (tpt90) cc_final: 0.7483 (mmm160) REVERT: D 339 GLU cc_start: 0.6905 (mt-10) cc_final: 0.6566 (mp0) REVERT: D 345 GLU cc_start: 0.7643 (OUTLIER) cc_final: 0.7276 (mp0) outliers start: 21 outliers final: 10 residues processed: 146 average time/residue: 1.1735 time to fit residues: 190.6104 Evaluate side-chains 140 residues out of total 1578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 126 time to evaluate : 0.646 ------------------------------------------------------------------------------- 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 Chi-restraints excluded: chain D residue 465 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 38 optimal weight: 4.9990 chunk 100 optimal weight: 1.9990 chunk 72 optimal weight: 4.9990 chunk 76 optimal weight: 10.0000 chunk 143 optimal weight: 2.9990 chunk 117 optimal weight: 10.0000 chunk 61 optimal weight: 0.5980 chunk 140 optimal weight: 1.9990 chunk 32 optimal weight: 3.9990 chunk 88 optimal weight: 3.9990 chunk 139 optimal weight: 0.9990 overall best weight: 1.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 378 ASN B 477 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4447 r_free = 0.4447 target = 0.189073 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.116543 restraints weight = 55742.667| |-----------------------------------------------------------------------------| r_work (start): 0.3464 rms_B_bonded: 2.31 r_work: 0.3232 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3124 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.3124 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8502 moved from start: 0.3883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 14958 Z= 0.178 Angle : 0.522 5.690 20276 Z= 0.282 Chirality : 0.038 0.142 2280 Planarity : 0.004 0.043 2528 Dihedral : 8.455 165.234 2054 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 3.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 1.01 % Allowed : 12.93 % Favored : 86.06 % 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: 1.61 (0.20), residues: 1758 helix: 1.60 (0.15), residues: 1162 sheet: 0.05 (0.57), residues: 60 loop : 0.17 (0.30), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 321 TYR 0.014 0.001 TYR D 210 PHE 0.014 0.002 PHE B 272 TRP 0.016 0.002 TRP A 246 HIS 0.002 0.001 HIS C 491 Details of bonding type rmsd covalent geometry : bond 0.00420 (14956) covalent geometry : angle 0.52185 (20272) SS BOND : bond 0.00258 ( 2) SS BOND : angle 0.99268 ( 4) hydrogen bonds : bond 0.05378 ( 944) hydrogen bonds : angle 4.07990 ( 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 148 residues out of total 1578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 132 time to evaluate : 0.719 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: A 129 PHE cc_start: 0.7444 (OUTLIER) cc_final: 0.7009 (m-80) REVERT: B 345 GLU cc_start: 0.7697 (OUTLIER) cc_final: 0.7273 (mp0) REVERT: B 490 GLN cc_start: 0.2940 (OUTLIER) cc_final: 0.0498 (pm20) REVERT: C 129 PHE cc_start: 0.7460 (OUTLIER) cc_final: 0.7026 (m-80) REVERT: D 315 ARG cc_start: 0.7816 (tpt90) cc_final: 0.7536 (mmm160) REVERT: D 345 GLU cc_start: 0.7669 (OUTLIER) cc_final: 0.7237 (mp0) REVERT: D 490 GLN cc_start: 0.2944 (OUTLIER) cc_final: 0.0514 (pm20) outliers start: 16 outliers final: 6 residues processed: 142 average time/residue: 1.2249 time to fit residues: 192.5998 Evaluate side-chains 139 residues out of total 1578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 127 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 83 optimal weight: 20.0000 chunk 2 optimal weight: 0.9980 chunk 20 optimal weight: 0.0980 chunk 48 optimal weight: 0.0470 chunk 152 optimal weight: 0.9990 chunk 159 optimal weight: 0.4980 chunk 46 optimal weight: 0.9980 chunk 65 optimal weight: 0.9990 chunk 142 optimal weight: 0.3980 chunk 165 optimal weight: 9.9990 chunk 58 optimal weight: 1.9990 overall best weight: 0.4078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 378 ASN B 307 GLN C 378 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4400 r_free = 0.4400 target = 0.186469 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 104)---------------| | r_work = 0.3755 r_free = 0.3755 target = 0.128186 restraints weight = 53444.243| |-----------------------------------------------------------------------------| r_work (start): 0.3682 rms_B_bonded: 1.39 r_work: 0.3293 rms_B_bonded: 1.78 restraints_weight: 0.5000 r_work: 0.3199 rms_B_bonded: 2.69 restraints_weight: 0.2500 r_work (final): 0.3199 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8446 moved from start: 0.4039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 14958 Z= 0.101 Angle : 0.475 6.377 20276 Z= 0.253 Chirality : 0.036 0.141 2280 Planarity : 0.004 0.044 2528 Dihedral : 7.763 162.067 2054 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 3.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 1.01 % Allowed : 12.61 % Favored : 86.38 % 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: 1.94 (0.20), residues: 1758 helix: 1.90 (0.15), residues: 1162 sheet: -0.04 (0.56), residues: 60 loop : 0.19 (0.30), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 321 TYR 0.013 0.001 TYR D 210 PHE 0.007 0.001 PHE A 409 TRP 0.012 0.001 TRP D 73 HIS 0.003 0.001 HIS D 260 Details of bonding type rmsd covalent geometry : bond 0.00214 (14956) covalent geometry : angle 0.47527 (20272) SS BOND : bond 0.00321 ( 2) SS BOND : angle 0.78821 ( 4) hydrogen bonds : bond 0.04437 ( 944) hydrogen bonds : angle 3.92198 ( 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 151 residues out of total 1578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 135 time to evaluate : 0.797 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: 0.7491 (OUTLIER) cc_final: 0.7099 (m-80) REVERT: B 311 ASN cc_start: 0.8288 (t0) cc_final: 0.7382 (m110) REVERT: B 315 ARG cc_start: 0.7778 (tpt90) cc_final: 0.7455 (mmm160) REVERT: B 339 GLU cc_start: 0.6819 (mt-10) cc_final: 0.6498 (mp0) REVERT: B 345 GLU cc_start: 0.7612 (OUTLIER) cc_final: 0.7252 (mp0) REVERT: B 490 GLN cc_start: 0.2833 (OUTLIER) cc_final: 0.0794 (pm20) REVERT: C 129 PHE cc_start: 0.7486 (OUTLIER) cc_final: 0.7095 (m-80) REVERT: C 452 PHE cc_start: 0.8194 (m-10) cc_final: 0.7772 (m-80) REVERT: D 311 ASN cc_start: 0.8283 (t0) cc_final: 0.7379 (m110) REVERT: D 339 GLU cc_start: 0.6796 (mt-10) cc_final: 0.6481 (mp0) REVERT: D 345 GLU cc_start: 0.7603 (OUTLIER) cc_final: 0.7278 (mp0) REVERT: D 490 GLN cc_start: 0.2832 (OUTLIER) cc_final: 0.0791 (pm20) outliers start: 16 outliers final: 7 residues processed: 147 average time/residue: 1.2174 time to fit residues: 197.9513 Evaluate side-chains 136 residues out of total 1578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 123 time to evaluate : 0.736 ------------------------------------------------------------------------------- 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 345 GLU Chi-restraints excluded: chain D residue 360 HIS Chi-restraints excluded: chain D residue 490 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 119 optimal weight: 10.0000 chunk 12 optimal weight: 1.9990 chunk 1 optimal weight: 1.9990 chunk 157 optimal weight: 1.9990 chunk 102 optimal weight: 1.9990 chunk 173 optimal weight: 9.9990 chunk 153 optimal weight: 0.9990 chunk 103 optimal weight: 0.9980 chunk 25 optimal weight: 1.9990 chunk 10 optimal weight: 3.9990 chunk 88 optimal weight: 3.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 378 ASN D 307 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4373 r_free = 0.4373 target = 0.184100 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 106)---------------| | r_work = 0.3454 r_free = 0.3454 target = 0.111178 restraints weight = 53597.756| |-----------------------------------------------------------------------------| r_work (start): 0.3363 rms_B_bonded: 2.07 r_work: 0.3130 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3026 rms_B_bonded: 3.35 restraints_weight: 0.2500 r_work (final): 0.3026 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8529 moved from start: 0.4131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 14958 Z= 0.173 Angle : 0.519 7.003 20276 Z= 0.280 Chirality : 0.038 0.143 2280 Planarity : 0.004 0.052 2528 Dihedral : 8.313 162.237 2054 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 0.89 % Allowed : 12.93 % 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: 1.74 (0.20), residues: 1758 helix: 1.75 (0.15), residues: 1160 sheet: 0.04 (0.57), residues: 60 loop : 0.10 (0.30), residues: 538 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 321 TYR 0.015 0.001 TYR D 210 PHE 0.017 0.002 PHE C 109 TRP 0.016 0.002 TRP A 246 HIS 0.002 0.001 HIS D 260 Details of bonding type rmsd covalent geometry : bond 0.00413 (14956) covalent geometry : angle 0.51933 (20272) SS BOND : bond 0.00225 ( 2) SS BOND : angle 0.91843 ( 4) hydrogen bonds : bond 0.05156 ( 944) hydrogen bonds : angle 4.01422 ( 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 138 residues out of total 1578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 124 time to evaluate : 0.796 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: 0.7463 (OUTLIER) cc_final: 0.7083 (m-80) REVERT: B 345 GLU cc_start: 0.7624 (OUTLIER) cc_final: 0.7159 (mp0) REVERT: B 490 GLN cc_start: 0.2710 (OUTLIER) cc_final: 0.0767 (pm20) REVERT: C 129 PHE cc_start: 0.7458 (OUTLIER) cc_final: 0.7074 (m-80) REVERT: C 452 PHE cc_start: 0.8363 (m-10) cc_final: 0.7918 (m-80) REVERT: D 345 GLU cc_start: 0.7601 (OUTLIER) cc_final: 0.7129 (mp0) REVERT: D 490 GLN cc_start: 0.2749 (OUTLIER) cc_final: 0.0824 (pm20) outliers start: 14 outliers final: 7 residues processed: 134 average time/residue: 1.1299 time to fit residues: 169.0995 Evaluate side-chains 133 residues out of total 1578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 120 time to evaluate : 0.523 ------------------------------------------------------------------------------- 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 150 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: 10.0000 chunk 20 optimal weight: 0.4980 chunk 98 optimal weight: 4.9990 chunk 17 optimal weight: 0.4980 chunk 129 optimal weight: 5.9990 chunk 81 optimal weight: 4.9990 chunk 100 optimal weight: 1.9990 chunk 72 optimal weight: 0.5980 chunk 141 optimal weight: 0.8980 chunk 130 optimal weight: 0.9990 chunk 90 optimal weight: 0.8980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4387 r_free = 0.4387 target = 0.185397 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.130215 restraints weight = 53553.938| |-----------------------------------------------------------------------------| r_work (start): 0.3722 rms_B_bonded: 2.10 r_work: 0.3219 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3115 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.3115 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8535 moved from start: 0.4220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 14958 Z= 0.112 Angle : 0.483 7.078 20276 Z= 0.258 Chirality : 0.037 0.141 2280 Planarity : 0.004 0.044 2528 Dihedral : 7.937 160.014 2054 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 3.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 0.89 % Allowed : 12.99 % 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: 1.90 (0.20), residues: 1758 helix: 1.88 (0.15), residues: 1162 sheet: 0.14 (0.57), residues: 60 loop : 0.11 (0.29), 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 0.008 0.001 PHE C 269 TRP 0.011 0.001 TRP D 73 HIS 0.002 0.000 HIS B 260 Details of bonding type rmsd covalent geometry : bond 0.00249 (14956) covalent geometry : angle 0.48269 (20272) SS BOND : bond 0.00241 ( 2) SS BOND : angle 0.87196 ( 4) hydrogen bonds : bond 0.04596 ( 944) hydrogen bonds : angle 3.91782 ( 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 135 residues out of total 1578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 121 time to evaluate : 0.816 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: 0.7550 (OUTLIER) cc_final: 0.7148 (m-80) REVERT: B 339 GLU cc_start: 0.6904 (mt-10) cc_final: 0.6539 (mp0) REVERT: B 345 GLU cc_start: 0.7610 (OUTLIER) cc_final: 0.7188 (mp0) REVERT: B 490 GLN cc_start: 0.2686 (OUTLIER) cc_final: 0.0679 (pm20) REVERT: C 129 PHE cc_start: 0.7528 (OUTLIER) cc_final: 0.7128 (m-80) REVERT: C 451 LEU cc_start: 0.8289 (mp) cc_final: 0.8087 (mp) REVERT: C 452 PHE cc_start: 0.8198 (m-10) cc_final: 0.7877 (m-80) REVERT: D 339 GLU cc_start: 0.6897 (mt-10) cc_final: 0.6542 (mp0) REVERT: D 345 GLU cc_start: 0.7602 (OUTLIER) cc_final: 0.7178 (mp0) REVERT: D 490 GLN cc_start: 0.2581 (OUTLIER) cc_final: 0.0558 (pm20) outliers start: 14 outliers final: 7 residues processed: 131 average time/residue: 1.1722 time to fit residues: 171.2259 Evaluate side-chains 132 residues out of total 1578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 119 time to evaluate : 0.821 ------------------------------------------------------------------------------- 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 150 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 67 optimal weight: 0.9980 chunk 132 optimal weight: 0.8980 chunk 26 optimal weight: 4.9990 chunk 126 optimal weight: 7.9990 chunk 20 optimal weight: 0.9990 chunk 138 optimal weight: 0.9990 chunk 158 optimal weight: 5.9990 chunk 148 optimal weight: 1.9990 chunk 83 optimal weight: 20.0000 chunk 152 optimal weight: 0.4980 chunk 61 optimal weight: 0.5980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4392 r_free = 0.4392 target = 0.185484 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.128928 restraints weight = 53212.135| |-----------------------------------------------------------------------------| r_work (start): 0.3698 rms_B_bonded: 1.52 r_work: 0.3276 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.3181 rms_B_bonded: 3.01 restraints_weight: 0.2500 r_work (final): 0.3181 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8493 moved from start: 0.4294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 14958 Z= 0.118 Angle : 0.485 7.123 20276 Z= 0.258 Chirality : 0.037 0.143 2280 Planarity : 0.004 0.044 2528 Dihedral : 7.839 159.019 2054 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 3.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 0.82 % Allowed : 12.99 % 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: 1.95 (0.20), residues: 1758 helix: 1.92 (0.15), residues: 1162 sheet: 0.18 (0.58), residues: 60 loop : 0.11 (0.29), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 321 TYR 0.014 0.001 TYR D 210 PHE 0.017 0.001 PHE C 109 TRP 0.011 0.001 TRP A 246 HIS 0.002 0.000 HIS C 260 Details of bonding type rmsd covalent geometry : bond 0.00268 (14956) covalent geometry : angle 0.48516 (20272) SS BOND : bond 0.00182 ( 2) SS BOND : angle 1.17582 ( 4) hydrogen bonds : bond 0.04572 ( 944) hydrogen bonds : angle 3.89438 ( 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: 13 poor density : 125 time to evaluate : 0.536 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: 0.7527 (OUTLIER) cc_final: 0.7144 (m-80) REVERT: B 339 GLU cc_start: 0.6858 (mt-10) cc_final: 0.6450 (mp0) REVERT: B 345 GLU cc_start: 0.7574 (OUTLIER) cc_final: 0.7155 (mp0) REVERT: B 490 GLN cc_start: 0.2741 (OUTLIER) cc_final: 0.0694 (pm20) REVERT: C 129 PHE cc_start: 0.7529 (OUTLIER) cc_final: 0.7146 (m-80) REVERT: C 451 LEU cc_start: 0.8280 (mp) cc_final: 0.8057 (mp) REVERT: C 452 PHE cc_start: 0.8187 (m-10) cc_final: 0.7901 (m-80) REVERT: D 339 GLU cc_start: 0.6882 (mt-10) cc_final: 0.6467 (mp0) REVERT: D 345 GLU cc_start: 0.7524 (OUTLIER) cc_final: 0.7104 (mp0) REVERT: D 465 MET cc_start: 0.3832 (ttt) cc_final: 0.3524 (mtt) REVERT: D 490 GLN cc_start: 0.2588 (OUTLIER) cc_final: 0.0558 (pm20) outliers start: 13 outliers final: 6 residues processed: 135 average time/residue: 1.1375 time to fit residues: 171.7581 Evaluate side-chains 135 residues out of total 1578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 123 time to evaluate : 0.825 ------------------------------------------------------------------------------- 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: 0.9980 chunk 10 optimal weight: 5.9990 chunk 30 optimal weight: 6.9990 chunk 109 optimal weight: 0.7980 chunk 7 optimal weight: 5.9990 chunk 46 optimal weight: 0.9990 chunk 104 optimal weight: 0.5980 chunk 80 optimal weight: 6.9990 chunk 26 optimal weight: 4.9990 chunk 155 optimal weight: 0.9990 chunk 18 optimal weight: 1.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4392 r_free = 0.4392 target = 0.185512 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.130136 restraints weight = 53480.806| |-----------------------------------------------------------------------------| r_work (start): 0.3719 rms_B_bonded: 1.94 r_work: 0.3235 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3130 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.3130 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8529 moved from start: 0.4363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 14958 Z= 0.121 Angle : 0.498 10.525 20276 Z= 0.261 Chirality : 0.037 0.141 2280 Planarity : 0.004 0.043 2528 Dihedral : 7.819 157.772 2054 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 3.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 0.95 % Allowed : 13.05 % 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: 1.95 (0.20), residues: 1758 helix: 1.93 (0.15), residues: 1162 sheet: 0.19 (0.57), residues: 60 loop : 0.11 (0.29), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 321 TYR 0.014 0.001 TYR D 210 PHE 0.012 0.001 PHE B 312 TRP 0.011 0.002 TRP A 246 HIS 0.001 0.000 HIS A 260 Details of bonding type rmsd covalent geometry : bond 0.00277 (14956) covalent geometry : angle 0.49753 (20272) SS BOND : bond 0.00138 ( 2) SS BOND : angle 1.12699 ( 4) hydrogen bonds : bond 0.04571 ( 944) hydrogen bonds : angle 3.89260 ( 2718) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10792.06 seconds wall clock time: 182 minutes 42.03 seconds (10962.03 seconds total)