Starting phenix.real_space_refine on Wed Jun 25 12:48:55 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7t4x_25691/06_2025/7t4x_25691_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/7t4x_25691/06_2025/7t4x_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_25691/06_2025/7t4x_25691.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7t4x_25691/06_2025/7t4x_25691.map" model { file = "/net/cci-nas-00/data/ceres_data/7t4x_25691/06_2025/7t4x_25691_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7t4x_25691/06_2025/7t4x_25691_trim.cif" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.004 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 16.00, per 1000 atoms: 0.55 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: 7.83 Conformation dependent library (CDL) restraints added in 2.4 seconds 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: 2.51 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: 11.64 Time building geometry restraints manager: 9.49 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: 4.730 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: 0.480 Extract box with map and model: 1.220 Check model and map are aligned: 0.230 Set scattering table: 0.280 Process input model: 65.870 Find NCS groups from input model: 1.410 Set up NCS constraints: 0.130 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: 0.020 Load rotamer database and sin/cos tables:12.550 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 86.920 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.26 (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 TRP 0.030 0.006 TRP B 246 HIS 0.011 0.003 HIS B 260 PHE 0.019 0.003 PHE B 109 TYR 0.044 0.007 TYR C 131 ARG 0.013 0.002 ARG B 335 Details of bonding type rmsd hydrogen bonds : bond 0.12715 ( 944) hydrogen bonds : angle 5.49210 ( 2718) SS BOND : bond 0.00417 ( 2) SS BOND : angle 2.59962 ( 4) covalent geometry : bond 0.00572 (14956) covalent geometry : angle 0.93140 (20272) *********************** 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 : 2.551 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 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: 0.8951 (t) cc_final: 0.8707 (m) outliers start: 24 outliers final: 2 residues processed: 287 average time/residue: 2.8564 time to fit residues: 900.6128 Evaluate side-chains 167 residues out of total 1578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 165 time to evaluate : 2.250 ------------------------------------------------------------------------------- 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 148 optimal weight: 0.9990 chunk 133 optimal weight: 0.0000 chunk 74 optimal weight: 2.9990 chunk 45 optimal weight: 0.8980 chunk 89 optimal weight: 0.7980 chunk 71 optimal weight: 2.9990 chunk 137 optimal weight: 1.9990 chunk 53 optimal weight: 0.8980 chunk 83 optimal weight: 9.9990 chunk 102 optimal weight: 1.9990 chunk 159 optimal weight: 1.9990 overall best weight: 0.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 311 ASN B 475 GLN D 311 ASN D 325 GLN D 475 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4465 r_free = 0.4465 target = 0.190887 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.117749 restraints weight = 55797.133| |-----------------------------------------------------------------------------| r_work (start): 0.3477 rms_B_bonded: 2.29 r_work: 0.3292 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3182 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.3182 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8433 moved from start: 0.2534 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= 0.153 Angle : 0.615 6.014 20276 Z= 0.342 Chirality : 0.039 0.150 2280 Planarity : 0.005 0.059 2528 Dihedral : 9.001 162.798 2056 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 3.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.14 % Favored : 98.86 % Rotamer: Outliers : 1.77 % Allowed : 10.27 % Favored : 87.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.16 (0.20), residues: 1758 helix: 1.09 (0.15), residues: 1150 sheet: 0.31 (0.67), residues: 48 loop : 0.37 (0.27), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP D 246 HIS 0.005 0.001 HIS A 360 PHE 0.013 0.001 PHE A 108 TYR 0.017 0.002 TYR A 209 ARG 0.006 0.000 ARG A 335 Details of bonding type rmsd hydrogen bonds : bond 0.06550 ( 944) hydrogen bonds : angle 4.64879 ( 2718) SS BOND : bond 0.00472 ( 2) SS BOND : angle 1.55442 ( 4) covalent geometry : bond 0.00318 (14956) covalent geometry : angle 0.61456 (20272) *********************** 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 183 residues out of total 1578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 155 time to evaluate : 2.753 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: 0.7492 (OUTLIER) cc_final: 0.7099 (m-80) REVERT: A 418 ASP cc_start: 0.7030 (m-30) cc_final: 0.6681 (m-30) REVERT: A 434 LYS cc_start: 0.7510 (mmtp) cc_final: 0.6732 (ttpp) REVERT: A 452 PHE cc_start: 0.8268 (m-80) cc_final: 0.7976 (m-80) REVERT: B 264 THR cc_start: 0.8964 (t) cc_final: 0.8745 (m) REVERT: C 129 PHE cc_start: 0.7484 (OUTLIER) cc_final: 0.7093 (m-80) REVERT: C 418 ASP cc_start: 0.7039 (m-30) cc_final: 0.6689 (m-30) REVERT: C 434 LYS cc_start: 0.7510 (mmtp) cc_final: 0.6732 (ttpp) REVERT: C 452 PHE cc_start: 0.8280 (m-80) cc_final: 0.7971 (m-80) REVERT: D 264 THR cc_start: 0.8961 (t) cc_final: 0.8745 (m) outliers start: 28 outliers final: 6 residues processed: 169 average time/residue: 2.5739 time to fit residues: 484.0265 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 : 2.428 ------------------------------------------------------------------------------- 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 37 optimal weight: 6.9990 chunk 103 optimal weight: 0.9980 chunk 41 optimal weight: 6.9990 chunk 153 optimal weight: 1.9990 chunk 140 optimal weight: 2.9990 chunk 14 optimal weight: 1.9990 chunk 152 optimal weight: 0.9990 chunk 107 optimal weight: 0.9990 chunk 135 optimal weight: 0.9990 chunk 11 optimal weight: 1.9990 chunk 151 optimal weight: 0.7980 overall best weight: 0.9586 ------------------------------------------------------------------------------- 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 = 0.4461 r_free = 0.4461 target = 0.190586 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.115532 restraints weight = 55957.653| |-----------------------------------------------------------------------------| r_work (start): 0.3442 rms_B_bonded: 1.95 r_work: 0.3298 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3187 rms_B_bonded: 3.33 restraints_weight: 0.2500 r_work (final): 0.3187 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8388 moved from start: 0.3071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 14958 Z= 0.138 Angle : 0.534 4.885 20276 Z= 0.293 Chirality : 0.038 0.143 2280 Planarity : 0.004 0.041 2528 Dihedral : 8.135 158.837 2056 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 3.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 1.58 % Allowed : 11.28 % Favored : 87.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.54 (0.20), residues: 1758 helix: 1.46 (0.15), residues: 1148 sheet: 0.59 (0.66), residues: 56 loop : 0.33 (0.28), residues: 554 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP C 246 HIS 0.002 0.001 HIS A 360 PHE 0.018 0.001 PHE B 312 TYR 0.015 0.001 TYR D 210 ARG 0.002 0.000 ARG A 335 Details of bonding type rmsd hydrogen bonds : bond 0.05622 ( 944) hydrogen bonds : angle 4.30757 ( 2718) SS BOND : bond 0.00318 ( 2) SS BOND : angle 1.14021 ( 4) covalent geometry : bond 0.00303 (14956) covalent geometry : angle 0.53375 (20272) *********************** 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 181 residues out of total 1578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 156 time to evaluate : 2.424 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: 0.7445 (OUTLIER) cc_final: 0.7032 (m-80) REVERT: A 238 MET cc_start: 0.8196 (OUTLIER) cc_final: 0.7972 (mpt) REVERT: A 418 ASP cc_start: 0.6874 (m-30) cc_final: 0.6501 (m-30) REVERT: A 452 PHE cc_start: 0.8256 (m-80) cc_final: 0.8038 (m-80) REVERT: B 298 ARG cc_start: 0.6719 (mpp-170) cc_final: 0.6517 (pmm-80) REVERT: B 345 GLU cc_start: 0.7837 (OUTLIER) cc_final: 0.7498 (mp0) REVERT: C 129 PHE cc_start: 0.7448 (OUTLIER) cc_final: 0.7038 (m-80) REVERT: C 238 MET cc_start: 0.8205 (OUTLIER) cc_final: 0.7982 (mpt) REVERT: C 418 ASP cc_start: 0.6883 (m-30) cc_final: 0.6513 (m-30) REVERT: C 452 PHE cc_start: 0.8244 (m-80) cc_final: 0.8042 (m-80) REVERT: D 298 ARG cc_start: 0.6746 (mpp-170) cc_final: 0.6534 (pmm-80) REVERT: D 345 GLU cc_start: 0.7838 (OUTLIER) cc_final: 0.7501 (mp0) outliers start: 25 outliers final: 9 residues processed: 169 average time/residue: 2.5261 time to fit residues: 474.7974 Evaluate side-chains 152 residues out of total 1578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 137 time to evaluate : 2.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 PHE Chi-restraints excluded: chain A residue 238 MET 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 238 MET Chi-restraints excluded: chain C residue 362 LEU 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 133 optimal weight: 3.9990 chunk 171 optimal weight: 20.0000 chunk 40 optimal weight: 4.9990 chunk 63 optimal weight: 0.8980 chunk 54 optimal weight: 0.9980 chunk 2 optimal weight: 0.9990 chunk 137 optimal weight: 1.9990 chunk 22 optimal weight: 0.9990 chunk 71 optimal weight: 8.9990 chunk 107 optimal weight: 1.9990 chunk 103 optimal weight: 0.9990 overall best weight: 0.9786 ------------------------------------------------------------------------------- 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 = 0.4397 r_free = 0.4397 target = 0.185839 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.134448 restraints weight = 53447.813| |-----------------------------------------------------------------------------| r_work (start): 0.3788 rms_B_bonded: 1.94 r_work: 0.3248 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3142 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.3142 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8524 moved from start: 0.3520 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= 0.133 Angle : 0.519 5.664 20276 Z= 0.280 Chirality : 0.037 0.143 2280 Planarity : 0.004 0.047 2528 Dihedral : 7.933 165.359 2054 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 3.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.61 (0.20), residues: 1758 helix: 1.56 (0.15), residues: 1162 sheet: 0.19 (0.59), residues: 56 loop : 0.23 (0.29), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 246 HIS 0.002 0.001 HIS C 491 PHE 0.010 0.001 PHE A 63 TYR 0.014 0.001 TYR B 210 ARG 0.003 0.000 ARG C 315 Details of bonding type rmsd hydrogen bonds : bond 0.05229 ( 944) hydrogen bonds : angle 4.16709 ( 2718) SS BOND : bond 0.00132 ( 2) SS BOND : angle 1.64024 ( 4) covalent geometry : bond 0.00296 (14956) covalent geometry : angle 0.51817 (20272) *********************** 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 158 residues out of total 1578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 137 time to evaluate : 2.237 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: 0.7560 (OUTLIER) cc_final: 0.7149 (m-80) REVERT: A 418 ASP cc_start: 0.6682 (m-30) cc_final: 0.6457 (m-30) REVERT: B 345 GLU cc_start: 0.7635 (OUTLIER) cc_final: 0.7194 (mp0) REVERT: C 129 PHE cc_start: 0.7559 (OUTLIER) cc_final: 0.7149 (m-80) REVERT: C 418 ASP cc_start: 0.6716 (m-30) cc_final: 0.6493 (m-30) REVERT: D 345 GLU cc_start: 0.7641 (OUTLIER) cc_final: 0.7198 (mp0) outliers start: 21 outliers final: 8 residues processed: 152 average time/residue: 2.4800 time to fit residues: 425.1625 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 : 2.897 ------------------------------------------------------------------------------- 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 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 113 optimal weight: 2.9990 chunk 140 optimal weight: 1.9990 chunk 167 optimal weight: 9.9990 chunk 162 optimal weight: 0.5980 chunk 83 optimal weight: 7.9990 chunk 96 optimal weight: 3.9990 chunk 5 optimal weight: 0.9990 chunk 125 optimal weight: 7.9990 chunk 156 optimal weight: 1.9990 chunk 153 optimal weight: 0.8980 chunk 55 optimal weight: 2.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- 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 = 0.184976 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.136309 restraints weight = 53109.456| |-----------------------------------------------------------------------------| r_work (start): 0.3814 rms_B_bonded: 2.18 r_work: 0.3213 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3101 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.3101 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8562 moved from start: 0.3710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 14958 Z= 0.153 Angle : 0.520 6.005 20276 Z= 0.281 Chirality : 0.037 0.143 2280 Planarity : 0.004 0.047 2528 Dihedral : 8.099 165.854 2054 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 1.52 % Allowed : 12.29 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.65 (0.20), residues: 1758 helix: 1.63 (0.15), residues: 1162 sheet: 0.38 (0.57), residues: 60 loop : 0.13 (0.29), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP C 246 HIS 0.002 0.001 HIS C 491 PHE 0.017 0.001 PHE C 109 TYR 0.014 0.001 TYR D 210 ARG 0.003 0.000 ARG A 315 Details of bonding type rmsd hydrogen bonds : bond 0.05259 ( 944) hydrogen bonds : angle 4.08706 ( 2718) SS BOND : bond 0.00179 ( 2) SS BOND : angle 1.15623 ( 4) covalent geometry : bond 0.00354 (14956) covalent geometry : angle 0.52023 (20272) *********************** 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 164 residues out of total 1578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 140 time to evaluate : 2.584 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 112 TYR cc_start: 0.7190 (p90) cc_final: 0.6932 (p90) REVERT: A 129 PHE cc_start: 0.7546 (OUTLIER) cc_final: 0.7133 (m-80) REVERT: A 452 PHE cc_start: 0.7795 (m-80) cc_final: 0.6945 (m-80) REVERT: B 315 ARG cc_start: 0.7771 (tpt90) cc_final: 0.7423 (mmm160) REVERT: B 345 GLU cc_start: 0.7663 (OUTLIER) cc_final: 0.7327 (mp0) REVERT: C 112 TYR cc_start: 0.7146 (p90) cc_final: 0.6888 (p90) REVERT: C 129 PHE cc_start: 0.7540 (OUTLIER) cc_final: 0.7123 (m-80) REVERT: C 452 PHE cc_start: 0.7832 (m-80) cc_final: 0.6955 (m-80) REVERT: D 345 GLU cc_start: 0.7682 (OUTLIER) cc_final: 0.7342 (mp0) outliers start: 24 outliers final: 8 residues processed: 152 average time/residue: 2.4109 time to fit residues: 413.9403 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 : 2.403 ------------------------------------------------------------------------------- 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 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 44 optimal weight: 4.9990 chunk 7 optimal weight: 0.7980 chunk 112 optimal weight: 1.9990 chunk 32 optimal weight: 8.9990 chunk 6 optimal weight: 1.9990 chunk 61 optimal weight: 0.1980 chunk 27 optimal weight: 0.9980 chunk 70 optimal weight: 7.9990 chunk 2 optimal weight: 0.9980 chunk 173 optimal weight: 20.0000 chunk 35 optimal weight: 9.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- 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 = 0.4387 r_free = 0.4387 target = 0.185200 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.135031 restraints weight = 53525.677| |-----------------------------------------------------------------------------| r_work (start): 0.3797 rms_B_bonded: 2.10 r_work: 0.3229 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3131 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.3131 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8518 moved from start: 0.3932 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= 0.129 Angle : 0.500 4.739 20276 Z= 0.268 Chirality : 0.037 0.142 2280 Planarity : 0.004 0.046 2528 Dihedral : 7.994 164.940 2054 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 3.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 1.27 % Allowed : 13.05 % Favored : 85.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.74 (0.20), residues: 1758 helix: 1.72 (0.15), residues: 1162 sheet: 0.26 (0.56), residues: 60 loop : 0.13 (0.29), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 246 HIS 0.001 0.000 HIS C 260 PHE 0.010 0.001 PHE A 269 TYR 0.014 0.001 TYR D 210 ARG 0.002 0.000 ARG D 300 Details of bonding type rmsd hydrogen bonds : bond 0.04910 ( 944) hydrogen bonds : angle 4.01953 ( 2718) SS BOND : bond 0.00181 ( 2) SS BOND : angle 1.02634 ( 4) covalent geometry : bond 0.00292 (14956) covalent geometry : angle 0.49964 (20272) *********************** 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 150 residues out of total 1578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 130 time to evaluate : 2.211 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 129 PHE cc_start: 0.7500 (OUTLIER) cc_final: 0.7081 (m-80) REVERT: A 452 PHE cc_start: 0.7779 (m-80) cc_final: 0.6898 (m-80) REVERT: B 345 GLU cc_start: 0.7713 (OUTLIER) cc_final: 0.7342 (mp0) REVERT: C 129 PHE cc_start: 0.7505 (OUTLIER) cc_final: 0.7082 (m-80) REVERT: C 452 PHE cc_start: 0.7801 (m-80) cc_final: 0.6894 (m-80) REVERT: D 345 GLU cc_start: 0.7719 (OUTLIER) cc_final: 0.7358 (mp0) outliers start: 20 outliers final: 9 residues processed: 144 average time/residue: 2.3504 time to fit residues: 379.5943 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 : 2.190 ------------------------------------------------------------------------------- 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 412 LEU 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 345 GLU Chi-restraints excluded: chain D residue 360 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 75 optimal weight: 8.9990 chunk 107 optimal weight: 0.9980 chunk 8 optimal weight: 4.9990 chunk 140 optimal weight: 1.9990 chunk 171 optimal weight: 10.0000 chunk 111 optimal weight: 0.7980 chunk 117 optimal weight: 4.9990 chunk 51 optimal weight: 2.9990 chunk 28 optimal weight: 2.9990 chunk 84 optimal weight: 20.0000 chunk 143 optimal weight: 0.1980 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 307 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4376 r_free = 0.4376 target = 0.184208 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.135230 restraints weight = 53377.709| |-----------------------------------------------------------------------------| r_work (start): 0.3800 rms_B_bonded: 2.08 r_work: 0.3220 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3118 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.3118 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8541 moved from start: 0.4028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 14958 Z= 0.157 Angle : 0.518 7.511 20276 Z= 0.277 Chirality : 0.038 0.197 2280 Planarity : 0.004 0.051 2528 Dihedral : 8.289 164.034 2054 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 3.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 1.01 % Allowed : 13.05 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.66 (0.20), residues: 1758 helix: 1.67 (0.15), residues: 1162 sheet: 0.15 (0.58), residues: 58 loop : 0.08 (0.29), residues: 538 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP C 246 HIS 0.002 0.001 HIS A 294 PHE 0.015 0.001 PHE C 109 TYR 0.014 0.001 TYR D 210 ARG 0.003 0.000 ARG D 300 Details of bonding type rmsd hydrogen bonds : bond 0.05132 ( 944) hydrogen bonds : angle 4.02444 ( 2718) SS BOND : bond 0.00172 ( 2) SS BOND : angle 1.03431 ( 4) covalent geometry : bond 0.00371 (14956) covalent geometry : angle 0.51820 (20272) *********************** 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 146 residues out of total 1578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 130 time to evaluate : 3.860 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 129 PHE cc_start: 0.7521 (OUTLIER) cc_final: 0.7109 (m-80) REVERT: A 452 PHE cc_start: 0.7803 (m-80) cc_final: 0.6894 (m-80) REVERT: B 345 GLU cc_start: 0.7674 (OUTLIER) cc_final: 0.7292 (mp0) REVERT: B 490 GLN cc_start: 0.2797 (OUTLIER) cc_final: 0.1416 (mp10) REVERT: C 112 TYR cc_start: 0.7176 (p90) cc_final: 0.6854 (p90) REVERT: C 129 PHE cc_start: 0.7507 (OUTLIER) cc_final: 0.7090 (m-80) REVERT: C 452 PHE cc_start: 0.7825 (m-80) cc_final: 0.6894 (m-80) REVERT: D 345 GLU cc_start: 0.7633 (OUTLIER) cc_final: 0.7256 (mp0) REVERT: D 490 GLN cc_start: 0.2781 (OUTLIER) cc_final: 0.0172 (pm20) outliers start: 16 outliers final: 6 residues processed: 141 average time/residue: 2.8238 time to fit residues: 454.7540 Evaluate side-chains 133 residues out of total 1578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 121 time to evaluate : 4.868 ------------------------------------------------------------------------------- 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 49 optimal weight: 1.9990 chunk 147 optimal weight: 0.9990 chunk 42 optimal weight: 9.9990 chunk 14 optimal weight: 1.9990 chunk 83 optimal weight: 10.0000 chunk 12 optimal weight: 0.9980 chunk 1 optimal weight: 1.9990 chunk 84 optimal weight: 20.0000 chunk 63 optimal weight: 0.0570 chunk 148 optimal weight: 0.9990 chunk 75 optimal weight: 8.9990 overall best weight: 1.0104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 307 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4383 r_free = 0.4383 target = 0.184957 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.133502 restraints weight = 53574.568| |-----------------------------------------------------------------------------| r_work (start): 0.3771 rms_B_bonded: 2.05 r_work: 0.3228 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3122 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.3122 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8540 moved from start: 0.4185 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= 0.129 Angle : 0.499 6.339 20276 Z= 0.266 Chirality : 0.037 0.141 2280 Planarity : 0.004 0.046 2528 Dihedral : 8.141 162.119 2054 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 3.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 1.08 % Allowed : 13.18 % Favored : 85.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.77 (0.20), residues: 1758 helix: 1.75 (0.15), residues: 1162 sheet: 0.24 (0.57), residues: 60 loop : 0.12 (0.29), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 246 HIS 0.003 0.001 HIS A 491 PHE 0.013 0.001 PHE B 312 TYR 0.020 0.001 TYR C 53 ARG 0.004 0.000 ARG D 315 Details of bonding type rmsd hydrogen bonds : bond 0.04820 ( 944) hydrogen bonds : angle 3.95615 ( 2718) SS BOND : bond 0.00188 ( 2) SS BOND : angle 0.95132 ( 4) covalent geometry : bond 0.00296 (14956) covalent geometry : angle 0.49883 (20272) *********************** 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 135 residues out of total 1578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 118 time to evaluate : 2.539 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 129 PHE cc_start: 0.7531 (OUTLIER) cc_final: 0.7141 (m-80) REVERT: A 452 PHE cc_start: 0.7849 (m-80) cc_final: 0.6908 (m-80) REVERT: B 315 ARG cc_start: 0.8088 (OUTLIER) cc_final: 0.7669 (mmm160) REVERT: B 345 GLU cc_start: 0.7660 (OUTLIER) cc_final: 0.7311 (mp0) REVERT: B 490 GLN cc_start: 0.2745 (OUTLIER) cc_final: 0.0683 (pm20) REVERT: C 129 PHE cc_start: 0.7508 (OUTLIER) cc_final: 0.7115 (m-80) REVERT: C 452 PHE cc_start: 0.7846 (m-80) cc_final: 0.6903 (m-80) REVERT: D 345 GLU cc_start: 0.7648 (OUTLIER) cc_final: 0.7295 (mp0) REVERT: D 490 GLN cc_start: 0.2802 (OUTLIER) cc_final: 0.0680 (pm20) outliers start: 17 outliers final: 7 residues processed: 130 average time/residue: 3.0869 time to fit residues: 455.8680 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 : 2.410 ------------------------------------------------------------------------------- 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 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 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 3 optimal weight: 0.3980 chunk 28 optimal weight: 3.9990 chunk 96 optimal weight: 4.9990 chunk 54 optimal weight: 0.9980 chunk 0 optimal weight: 5.9990 chunk 155 optimal weight: 0.9990 chunk 118 optimal weight: 0.2980 chunk 9 optimal weight: 1.9990 chunk 137 optimal weight: 1.9990 chunk 34 optimal weight: 2.9990 chunk 80 optimal weight: 20.0000 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 287 ASN C 287 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4383 r_free = 0.4383 target = 0.185068 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.131707 restraints weight = 53503.825| |-----------------------------------------------------------------------------| r_work (start): 0.3742 rms_B_bonded: 2.65 r_work: 0.3163 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3052 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3052 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8569 moved from start: 0.4270 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= 0.126 Angle : 0.495 6.610 20276 Z= 0.263 Chirality : 0.037 0.142 2280 Planarity : 0.004 0.045 2528 Dihedral : 8.027 160.842 2054 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 3.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 0.95 % Allowed : 13.37 % Favored : 85.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.82 (0.20), residues: 1758 helix: 1.81 (0.15), residues: 1162 sheet: 0.38 (0.57), residues: 60 loop : 0.08 (0.29), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 246 HIS 0.002 0.000 HIS A 491 PHE 0.017 0.001 PHE C 109 TYR 0.014 0.001 TYR B 210 ARG 0.004 0.000 ARG D 315 Details of bonding type rmsd hydrogen bonds : bond 0.04723 ( 944) hydrogen bonds : angle 3.91279 ( 2718) SS BOND : bond 0.00200 ( 2) SS BOND : angle 0.90232 ( 4) covalent geometry : bond 0.00286 (14956) covalent geometry : angle 0.49466 (20272) *********************** 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 133 residues out of total 1578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 118 time to evaluate : 2.515 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 129 PHE cc_start: 0.7546 (OUTLIER) cc_final: 0.7143 (m-80) REVERT: B 345 GLU cc_start: 0.7694 (OUTLIER) cc_final: 0.7330 (mp0) REVERT: B 490 GLN cc_start: 0.2667 (OUTLIER) cc_final: 0.0655 (pm20) REVERT: C 129 PHE cc_start: 0.7520 (OUTLIER) cc_final: 0.7115 (m-80) REVERT: D 345 GLU cc_start: 0.7681 (OUTLIER) cc_final: 0.7312 (mp0) REVERT: D 490 GLN cc_start: 0.2579 (OUTLIER) cc_final: 0.0558 (pm20) outliers start: 15 outliers final: 7 residues processed: 128 average time/residue: 2.1026 time to fit residues: 306.4620 Evaluate side-chains 126 residues out of total 1578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 113 time to evaluate : 2.413 ------------------------------------------------------------------------------- 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 143 optimal weight: 0.9980 chunk 80 optimal weight: 20.0000 chunk 131 optimal weight: 9.9990 chunk 29 optimal weight: 9.9990 chunk 67 optimal weight: 0.9990 chunk 162 optimal weight: 3.9990 chunk 46 optimal weight: 0.9990 chunk 43 optimal weight: 9.9990 chunk 130 optimal weight: 8.9990 chunk 32 optimal weight: 6.9990 chunk 69 optimal weight: 0.9980 overall best weight: 1.5986 ------------------------------------------------------------------------------- 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 = 0.4369 r_free = 0.4369 target = 0.183795 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.134130 restraints weight = 53624.039| |-----------------------------------------------------------------------------| r_work (start): 0.3784 rms_B_bonded: 2.23 r_work: 0.3181 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3077 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.3077 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8579 moved from start: 0.4330 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= 0.174 Angle : 0.521 6.886 20276 Z= 0.280 Chirality : 0.038 0.143 2280 Planarity : 0.004 0.044 2528 Dihedral : 8.467 159.871 2054 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 1.01 % Allowed : 13.31 % Favored : 85.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.66 (0.20), residues: 1758 helix: 1.66 (0.15), residues: 1156 sheet: 0.26 (0.58), residues: 60 loop : 0.10 (0.29), residues: 542 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP C 246 HIS 0.003 0.001 HIS C 294 PHE 0.014 0.002 PHE D 272 TYR 0.020 0.001 TYR C 53 ARG 0.004 0.000 ARG B 300 Details of bonding type rmsd hydrogen bonds : bond 0.05214 ( 944) hydrogen bonds : angle 3.99622 ( 2718) SS BOND : bond 0.00153 ( 2) SS BOND : angle 0.93996 ( 4) covalent geometry : bond 0.00415 (14956) covalent geometry : angle 0.52090 (20272) ********************** 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 132 residues out of total 1578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 116 time to evaluate : 2.258 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 129 PHE cc_start: 0.7591 (OUTLIER) cc_final: 0.7201 (m-80) REVERT: B 345 GLU cc_start: 0.7631 (OUTLIER) cc_final: 0.7255 (mp0) REVERT: B 490 GLN cc_start: 0.2733 (OUTLIER) cc_final: 0.0689 (pm20) REVERT: C 129 PHE cc_start: 0.7586 (OUTLIER) cc_final: 0.7192 (m-80) REVERT: D 345 GLU cc_start: 0.7605 (OUTLIER) cc_final: 0.7210 (mp0) REVERT: D 490 GLN cc_start: 0.2692 (OUTLIER) cc_final: 0.0621 (pm20) outliers start: 16 outliers final: 8 residues processed: 126 average time/residue: 2.1680 time to fit residues: 309.9498 Evaluate side-chains 128 residues out of total 1578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 114 time to evaluate : 2.228 ------------------------------------------------------------------------------- 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 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 37 optimal weight: 6.9990 chunk 153 optimal weight: 0.7980 chunk 7 optimal weight: 8.9990 chunk 89 optimal weight: 0.9980 chunk 124 optimal weight: 3.9990 chunk 98 optimal weight: 5.9990 chunk 120 optimal weight: 9.9990 chunk 94 optimal weight: 5.9990 chunk 33 optimal weight: 5.9990 chunk 157 optimal weight: 4.9990 chunk 11 optimal weight: 1.9990 overall best weight: 2.5586 ------------------------------------------------------------------------------- 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 = 0.4358 r_free = 0.4358 target = 0.182703 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.131725 restraints weight = 53566.500| |-----------------------------------------------------------------------------| r_work (start): 0.3749 rms_B_bonded: 2.45 r_work: 0.3146 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3044 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.3044 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8610 moved from start: 0.4373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.056 14958 Z= 0.249 Angle : 0.576 8.639 20276 Z= 0.310 Chirality : 0.041 0.142 2280 Planarity : 0.004 0.042 2528 Dihedral : 8.950 159.386 2054 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 1.08 % Allowed : 13.43 % Favored : 85.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.31 (0.20), residues: 1758 helix: 1.39 (0.15), residues: 1162 sheet: 0.08 (0.57), residues: 60 loop : -0.03 (0.30), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.003 TRP A 246 HIS 0.003 0.001 HIS D 260 PHE 0.018 0.002 PHE C 109 TYR 0.014 0.002 TYR D 210 ARG 0.003 0.000 ARG D 315 Details of bonding type rmsd hydrogen bonds : bond 0.05845 ( 944) hydrogen bonds : angle 4.12660 ( 2718) SS BOND : bond 0.00131 ( 2) SS BOND : angle 1.02639 ( 4) covalent geometry : bond 0.00600 (14956) covalent geometry : angle 0.57612 (20272) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 23092.84 seconds wall clock time: 399 minutes 6.52 seconds (23946.52 seconds total)