Starting phenix.real_space_refine on Wed Sep 17 07:22:10 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9dk8_46946/09_2025/9dk8_46946.cif Found real_map, /net/cci-nas-00/data/ceres_data/9dk8_46946/09_2025/9dk8_46946.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9dk8_46946/09_2025/9dk8_46946.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9dk8_46946/09_2025/9dk8_46946.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9dk8_46946/09_2025/9dk8_46946.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9dk8_46946/09_2025/9dk8_46946.map" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.025 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 36 5.16 5 C 4206 2.51 5 N 1194 2.21 5 O 1242 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 6678 Number of models: 1 Model: "" Number of chains: 6 Chain: "E" Number of atoms: 1113 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 1113 Classifications: {'peptide': 143} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 7, 'TRANS': 135} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 1113 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 1113 Classifications: {'peptide': 143} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 7, 'TRANS': 135} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "F" Number of atoms: 1113 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 1113 Classifications: {'peptide': 143} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 7, 'TRANS': 135} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 1113 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 1113 Classifications: {'peptide': 143} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 7, 'TRANS': 135} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "A" Number of atoms: 1113 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 1113 Classifications: {'peptide': 143} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 7, 'TRANS': 135} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 1113 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 1113 Classifications: {'peptide': 143} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 7, 'TRANS': 135} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 1.61, per 1000 atoms: 0.24 Number of scatterers: 6678 At special positions: 0 Unit cell: (66.825, 62.7, 137.775, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 36 16.00 O 1242 8.00 N 1194 7.00 C 4206 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.57 Conformation dependent library (CDL) restraints added in 357.1 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1644 Finding SS restraints... Secondary structure from input PDB file: 44 helices and 6 sheets defined 49.4% alpha, 11.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.23 Creating SS restraints... Processing helix chain 'E' and resid 405 through 420 removed outlier: 3.954A pdb=" N ALA E 409 " --> pdb=" O ASP E 405 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N GLY E 420 " --> pdb=" O LEU E 416 " (cutoff:3.500A) Processing helix chain 'E' and resid 439 through 448 Processing helix chain 'E' and resid 457 through 461 removed outlier: 3.985A pdb=" N ASP E 461 " --> pdb=" O SER E 458 " (cutoff:3.500A) Processing helix chain 'E' and resid 462 through 479 Processing helix chain 'E' and resid 495 through 499 removed outlier: 3.803A pdb=" N LEU E 499 " --> pdb=" O PRO E 496 " (cutoff:3.500A) Processing helix chain 'E' and resid 503 through 508 Processing helix chain 'E' and resid 519 through 528 Processing helix chain 'B' and resid 405 through 419 removed outlier: 3.990A pdb=" N ALA B 418 " --> pdb=" O GLU B 414 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N LEU B 419 " --> pdb=" O LYS B 415 " (cutoff:3.500A) Processing helix chain 'B' and resid 426 through 431 removed outlier: 4.044A pdb=" N PHE B 431 " --> pdb=" O CYS B 428 " (cutoff:3.500A) Processing helix chain 'B' and resid 438 through 448 Processing helix chain 'B' and resid 462 through 479 Processing helix chain 'B' and resid 495 through 499 removed outlier: 3.604A pdb=" N LEU B 499 " --> pdb=" O PRO B 496 " (cutoff:3.500A) Processing helix chain 'B' and resid 500 through 507 removed outlier: 4.067A pdb=" N LEU B 506 " --> pdb=" O ASP B 502 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N LEU B 507 " --> pdb=" O THR B 503 " (cutoff:3.500A) Processing helix chain 'B' and resid 519 through 528 Processing helix chain 'F' and resid 405 through 419 removed outlier: 3.852A pdb=" N ALA F 409 " --> pdb=" O ASP F 405 " (cutoff:3.500A) Processing helix chain 'F' and resid 442 through 448 removed outlier: 3.595A pdb=" N ILE F 446 " --> pdb=" O LEU F 442 " (cutoff:3.500A) Processing helix chain 'F' and resid 457 through 461 removed outlier: 3.905A pdb=" N ASP F 461 " --> pdb=" O SER F 458 " (cutoff:3.500A) Processing helix chain 'F' and resid 462 through 479 removed outlier: 3.507A pdb=" N HIS F 467 " --> pdb=" O ARG F 463 " (cutoff:3.500A) Processing helix chain 'F' and resid 495 through 499 Processing helix chain 'F' and resid 500 through 505 Processing helix chain 'F' and resid 506 through 508 No H-bonds generated for 'chain 'F' and resid 506 through 508' Processing helix chain 'F' and resid 519 through 528 Processing helix chain 'D' and resid 405 through 419 removed outlier: 3.542A pdb=" N ALA D 409 " --> pdb=" O ASP D 405 " (cutoff:3.500A) Processing helix chain 'D' and resid 426 through 430 Processing helix chain 'D' and resid 440 through 448 Processing helix chain 'D' and resid 457 through 461 removed outlier: 4.081A pdb=" N ASP D 461 " --> pdb=" O SER D 458 " (cutoff:3.500A) Processing helix chain 'D' and resid 462 through 479 Processing helix chain 'D' and resid 495 through 499 removed outlier: 3.982A pdb=" N LEU D 499 " --> pdb=" O PRO D 496 " (cutoff:3.500A) Processing helix chain 'D' and resid 500 through 505 removed outlier: 3.569A pdb=" N SER D 505 " --> pdb=" O SER D 501 " (cutoff:3.500A) Processing helix chain 'D' and resid 506 through 510 removed outlier: 4.381A pdb=" N GLY D 509 " --> pdb=" O LEU D 506 " (cutoff:3.500A) Processing helix chain 'D' and resid 519 through 528 Processing helix chain 'A' and resid 405 through 420 removed outlier: 3.819A pdb=" N ALA A 409 " --> pdb=" O ASP A 405 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N GLY A 420 " --> pdb=" O LEU A 416 " (cutoff:3.500A) Processing helix chain 'A' and resid 426 through 430 removed outlier: 3.505A pdb=" N ASP A 430 " --> pdb=" O PHE A 427 " (cutoff:3.500A) Processing helix chain 'A' and resid 437 through 448 Processing helix chain 'A' and resid 462 through 479 Processing helix chain 'A' and resid 500 through 505 Processing helix chain 'A' and resid 519 through 528 Processing helix chain 'C' and resid 405 through 419 Processing helix chain 'C' and resid 441 through 448 Processing helix chain 'C' and resid 457 through 461 removed outlier: 3.954A pdb=" N ASP C 461 " --> pdb=" O SER C 458 " (cutoff:3.500A) Processing helix chain 'C' and resid 462 through 479 Processing helix chain 'C' and resid 495 through 499 removed outlier: 4.153A pdb=" N LEU C 499 " --> pdb=" O PRO C 496 " (cutoff:3.500A) Processing helix chain 'C' and resid 500 through 505 Processing helix chain 'C' and resid 519 through 528 Processing sheet with id=AA1, first strand: chain 'E' and resid 395 through 400 removed outlier: 6.618A pdb=" N ASN E 396 " --> pdb=" O PHE E 451 " (cutoff:3.500A) removed outlier: 7.509A pdb=" N ILE E 453 " --> pdb=" O ASN E 396 " (cutoff:3.500A) removed outlier: 6.171A pdb=" N VAL E 398 " --> pdb=" O ILE E 453 " (cutoff:3.500A) removed outlier: 7.071A pdb=" N LEU E 455 " --> pdb=" O VAL E 398 " (cutoff:3.500A) removed outlier: 7.092A pdb=" N LEU E 400 " --> pdb=" O LEU E 455 " (cutoff:3.500A) removed outlier: 8.208A pdb=" N ILE E 487 " --> pdb=" O ALA E 450 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N ILE E 452 " --> pdb=" O ILE E 487 " (cutoff:3.500A) removed outlier: 7.196A pdb=" N PHE E 489 " --> pdb=" O ILE E 452 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N LEU E 454 " --> pdb=" O PHE E 489 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 395 through 400 removed outlier: 6.435A pdb=" N ASN B 396 " --> pdb=" O PHE B 451 " (cutoff:3.500A) removed outlier: 7.660A pdb=" N ILE B 453 " --> pdb=" O ASN B 396 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N VAL B 398 " --> pdb=" O ILE B 453 " (cutoff:3.500A) removed outlier: 7.212A pdb=" N LEU B 455 " --> pdb=" O VAL B 398 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N LEU B 400 " --> pdb=" O LEU B 455 " (cutoff:3.500A) removed outlier: 8.701A pdb=" N ILE B 487 " --> pdb=" O ALA B 450 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N ILE B 452 " --> pdb=" O ILE B 487 " (cutoff:3.500A) removed outlier: 7.481A pdb=" N PHE B 489 " --> pdb=" O ILE B 452 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N LEU B 454 " --> pdb=" O PHE B 489 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'F' and resid 395 through 400 removed outlier: 6.922A pdb=" N ASN F 396 " --> pdb=" O SER F 449 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 395 through 400 removed outlier: 6.594A pdb=" N ASN D 396 " --> pdb=" O PHE D 451 " (cutoff:3.500A) removed outlier: 7.901A pdb=" N ILE D 453 " --> pdb=" O ASN D 396 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N VAL D 398 " --> pdb=" O ILE D 453 " (cutoff:3.500A) removed outlier: 7.180A pdb=" N LEU D 455 " --> pdb=" O VAL D 398 " (cutoff:3.500A) removed outlier: 7.025A pdb=" N LEU D 400 " --> pdb=" O LEU D 455 " (cutoff:3.500A) removed outlier: 8.520A pdb=" N ILE D 487 " --> pdb=" O ALA D 450 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N ILE D 452 " --> pdb=" O ILE D 487 " (cutoff:3.500A) removed outlier: 7.288A pdb=" N PHE D 489 " --> pdb=" O ILE D 452 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N LEU D 454 " --> pdb=" O PHE D 489 " (cutoff:3.500A) removed outlier: 8.093A pdb=" N LEU D 513 " --> pdb=" O VAL D 486 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 395 through 400 removed outlier: 6.927A pdb=" N ASN A 396 " --> pdb=" O SER A 449 " (cutoff:3.500A) removed outlier: 8.622A pdb=" N ILE A 487 " --> pdb=" O ALA A 450 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N ILE A 452 " --> pdb=" O ILE A 487 " (cutoff:3.500A) removed outlier: 7.335A pdb=" N PHE A 489 " --> pdb=" O ILE A 452 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N LEU A 454 " --> pdb=" O PHE A 489 " (cutoff:3.500A) removed outlier: 8.182A pdb=" N LEU A 513 " --> pdb=" O VAL A 486 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 395 through 400 removed outlier: 7.008A pdb=" N ASN C 396 " --> pdb=" O PHE C 451 " (cutoff:3.500A) removed outlier: 7.705A pdb=" N ILE C 453 " --> pdb=" O ASN C 396 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N VAL C 398 " --> pdb=" O ILE C 453 " (cutoff:3.500A) removed outlier: 7.087A pdb=" N LEU C 455 " --> pdb=" O VAL C 398 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N LEU C 400 " --> pdb=" O LEU C 455 " (cutoff:3.500A) removed outlier: 7.992A pdb=" N ILE C 487 " --> pdb=" O ALA C 450 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N ILE C 452 " --> pdb=" O ILE C 487 " (cutoff:3.500A) removed outlier: 7.267A pdb=" N PHE C 489 " --> pdb=" O ILE C 452 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N LEU C 454 " --> pdb=" O PHE C 489 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 258 hydrogen bonds defined for protein. 708 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: 0.93 Time building geometry restraints manager: 0.78 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2290 1.34 - 1.46: 1183 1.46 - 1.57: 3289 1.57 - 1.69: 0 1.69 - 1.81: 48 Bond restraints: 6810 Sorted by residual: bond pdb=" C VAL C 433 " pdb=" N PRO C 434 " ideal model delta sigma weight residual 1.334 1.358 -0.024 2.34e-02 1.83e+03 1.04e+00 bond pdb=" C LEU A 490 " pdb=" O LEU A 490 " ideal model delta sigma weight residual 1.246 1.237 0.009 9.20e-03 1.18e+04 9.04e-01 bond pdb=" CD GLU B 417 " pdb=" OE1 GLU B 417 " ideal model delta sigma weight residual 1.249 1.232 0.017 1.90e-02 2.77e+03 8.13e-01 bond pdb=" C SER A 495 " pdb=" N PRO A 496 " ideal model delta sigma weight residual 1.334 1.341 -0.007 8.40e-03 1.42e+04 7.41e-01 bond pdb=" C VAL E 433 " pdb=" N PRO E 434 " ideal model delta sigma weight residual 1.334 1.353 -0.019 2.34e-02 1.83e+03 6.66e-01 ... (remaining 6805 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.99: 9096 1.99 - 3.98: 108 3.98 - 5.97: 16 5.97 - 7.95: 0 7.95 - 9.94: 2 Bond angle restraints: 9222 Sorted by residual: angle pdb=" N VAL A 433 " pdb=" CA VAL A 433 " pdb=" C VAL A 433 " ideal model delta sigma weight residual 112.35 108.85 3.50 1.20e+00 6.94e-01 8.51e+00 angle pdb=" CA LEU B 513 " pdb=" CB LEU B 513 " pdb=" CG LEU B 513 " ideal model delta sigma weight residual 116.30 126.24 -9.94 3.50e+00 8.16e-02 8.07e+00 angle pdb=" C PHE A 489 " pdb=" N LEU A 490 " pdb=" CA LEU A 490 " ideal model delta sigma weight residual 122.42 118.39 4.03 1.52e+00 4.33e-01 7.03e+00 angle pdb=" C LEU B 416 " pdb=" N GLU B 417 " pdb=" CA GLU B 417 " ideal model delta sigma weight residual 120.72 116.44 4.28 1.67e+00 3.59e-01 6.56e+00 angle pdb=" N VAL E 433 " pdb=" CA VAL E 433 " pdb=" C VAL E 433 " ideal model delta sigma weight residual 108.88 114.39 -5.51 2.16e+00 2.14e-01 6.51e+00 ... (remaining 9217 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.66: 3713 17.66 - 35.31: 369 35.31 - 52.96: 52 52.96 - 70.62: 8 70.62 - 88.27: 10 Dihedral angle restraints: 4152 sinusoidal: 1650 harmonic: 2502 Sorted by residual: dihedral pdb=" CA ARG B 512 " pdb=" C ARG B 512 " pdb=" N LEU B 513 " pdb=" CA LEU B 513 " ideal model delta harmonic sigma weight residual 180.00 161.83 18.17 0 5.00e+00 4.00e-02 1.32e+01 dihedral pdb=" CA ARG F 436 " pdb=" C ARG F 436 " pdb=" N GLY F 437 " pdb=" CA GLY F 437 " ideal model delta harmonic sigma weight residual 180.00 162.27 17.73 0 5.00e+00 4.00e-02 1.26e+01 dihedral pdb=" CA PRO D 434 " pdb=" C PRO D 434 " pdb=" N GLY D 435 " pdb=" CA GLY D 435 " ideal model delta harmonic sigma weight residual 180.00 162.72 17.28 0 5.00e+00 4.00e-02 1.19e+01 ... (remaining 4149 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 671 0.028 - 0.056: 247 0.056 - 0.084: 73 0.084 - 0.113: 44 0.113 - 0.141: 21 Chirality restraints: 1056 Sorted by residual: chirality pdb=" CB ILE D 519 " pdb=" CA ILE D 519 " pdb=" CG1 ILE D 519 " pdb=" CG2 ILE D 519 " both_signs ideal model delta sigma weight residual False 2.64 2.50 0.14 2.00e-01 2.50e+01 4.95e-01 chirality pdb=" CB ILE E 519 " pdb=" CA ILE E 519 " pdb=" CG1 ILE E 519 " pdb=" CG2 ILE E 519 " both_signs ideal model delta sigma weight residual False 2.64 2.50 0.14 2.00e-01 2.50e+01 4.90e-01 chirality pdb=" CB ILE F 519 " pdb=" CA ILE F 519 " pdb=" CG1 ILE F 519 " pdb=" CG2 ILE F 519 " both_signs ideal model delta sigma weight residual False 2.64 2.51 0.13 2.00e-01 2.50e+01 4.54e-01 ... (remaining 1053 not shown) Planarity restraints: 1218 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS F 529 " -0.034 5.00e-02 4.00e+02 5.11e-02 4.18e+00 pdb=" N PRO F 530 " 0.088 5.00e-02 4.00e+02 pdb=" CA PRO F 530 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO F 530 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS D 529 " -0.031 5.00e-02 4.00e+02 4.70e-02 3.54e+00 pdb=" N PRO D 530 " 0.081 5.00e-02 4.00e+02 pdb=" CA PRO D 530 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO D 530 " -0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS E 529 " 0.029 5.00e-02 4.00e+02 4.50e-02 3.24e+00 pdb=" N PRO E 530 " -0.078 5.00e-02 4.00e+02 pdb=" CA PRO E 530 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO E 530 " 0.025 5.00e-02 4.00e+02 ... (remaining 1215 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 714 2.75 - 3.28: 7002 3.28 - 3.82: 10709 3.82 - 4.36: 12153 4.36 - 4.90: 21247 Nonbonded interactions: 51825 Sorted by model distance: nonbonded pdb=" O SER F 501 " pdb=" OG SER F 505 " model vdw 2.207 3.040 nonbonded pdb=" NZ LYS D 415 " pdb=" OE2 GLU D 515 " model vdw 2.239 3.120 nonbonded pdb=" NH2 ARG E 463 " pdb=" O ARG F 479 " model vdw 2.244 3.120 nonbonded pdb=" NH2 ARG F 463 " pdb=" O SER C 482 " model vdw 2.248 3.120 nonbonded pdb=" O ARG B 479 " pdb=" NH2 ARG A 463 " model vdw 2.272 3.120 ... (remaining 51820 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' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } 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: 1.010 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: 0.000 Extract box with map and model: 0.100 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 7.540 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.010 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: 0.010 Load rotamer database and sin/cos tables:1.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.080 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8056 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6810 Z= 0.129 Angle : 0.559 9.942 9222 Z= 0.295 Chirality : 0.039 0.141 1056 Planarity : 0.004 0.051 1218 Dihedral : 14.361 88.273 2508 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.38 % Favored : 93.62 % Rotamer: Outliers : 0.00 % Allowed : 0.41 % Favored : 99.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.16 (0.30), residues: 846 helix: 1.58 (0.28), residues: 348 sheet: -1.21 (0.49), residues: 120 loop : -1.35 (0.32), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 532 TYR 0.009 0.002 TYR D 395 PHE 0.018 0.002 PHE D 431 HIS 0.005 0.001 HIS F 401 Details of bonding type rmsd covalent geometry : bond 0.00289 ( 6810) covalent geometry : angle 0.55916 ( 9222) hydrogen bonds : bond 0.14106 ( 258) hydrogen bonds : angle 5.85060 ( 708) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 225 time to evaluate : 0.171 Fit side-chains revert: symmetry clash REVERT: E 406 GLU cc_start: 0.8561 (mm-30) cc_final: 0.8238 (mm-30) REVERT: E 423 ASP cc_start: 0.8473 (m-30) cc_final: 0.8248 (m-30) REVERT: E 461 ASP cc_start: 0.8094 (t0) cc_final: 0.7892 (t0) REVERT: E 526 ASN cc_start: 0.8244 (m110) cc_final: 0.7811 (m-40) REVERT: B 395 TYR cc_start: 0.8598 (m-80) cc_final: 0.8279 (m-10) REVERT: F 429 GLU cc_start: 0.7654 (tp30) cc_final: 0.7414 (tp30) REVERT: D 423 ASP cc_start: 0.8785 (m-30) cc_final: 0.8569 (m-30) REVERT: A 461 ASP cc_start: 0.8528 (t0) cc_final: 0.8315 (t0) REVERT: C 406 GLU cc_start: 0.8610 (mp0) cc_final: 0.8102 (mp0) REVERT: C 431 PHE cc_start: 0.8489 (t80) cc_final: 0.8276 (t80) REVERT: C 484 ASP cc_start: 0.8233 (t0) cc_final: 0.7936 (t0) REVERT: C 526 ASN cc_start: 0.8644 (t0) cc_final: 0.8381 (t0) outliers start: 0 outliers final: 0 residues processed: 225 average time/residue: 0.1205 time to fit residues: 32.9378 Evaluate side-chains 191 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 191 time to evaluate : 0.181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 49 optimal weight: 0.9980 chunk 53 optimal weight: 3.9990 chunk 5 optimal weight: 3.9990 chunk 33 optimal weight: 5.9990 chunk 65 optimal weight: 0.9980 chunk 62 optimal weight: 0.8980 chunk 51 optimal weight: 5.9990 chunk 38 optimal weight: 0.8980 chunk 61 optimal weight: 0.9980 chunk 45 optimal weight: 5.9990 chunk 74 optimal weight: 1.9990 overall best weight: 0.9580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 459 ASN E 471 GLN E 476 ASN B 407 HIS ** B 470 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 459 ASN C 470 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.138722 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.108513 restraints weight = 9911.038| |-----------------------------------------------------------------------------| r_work (start): 0.3542 rms_B_bonded: 3.84 r_work: 0.3364 rms_B_bonded: 4.69 restraints_weight: 0.5000 r_work (final): 0.3364 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8067 moved from start: 0.1347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 6810 Z= 0.124 Angle : 0.556 7.310 9222 Z= 0.292 Chirality : 0.041 0.287 1056 Planarity : 0.005 0.051 1218 Dihedral : 4.431 17.720 912 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer: Outliers : 1.63 % Allowed : 9.76 % Favored : 88.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.13 (0.31), residues: 846 helix: 2.07 (0.29), residues: 312 sheet: -1.19 (0.50), residues: 120 loop : -1.09 (0.32), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 403 TYR 0.014 0.002 TYR F 395 PHE 0.025 0.002 PHE A 431 HIS 0.004 0.001 HIS F 401 Details of bonding type rmsd covalent geometry : bond 0.00291 ( 6810) covalent geometry : angle 0.55644 ( 9222) hydrogen bonds : bond 0.03258 ( 258) hydrogen bonds : angle 4.75860 ( 708) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 205 time to evaluate : 0.281 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 406 GLU cc_start: 0.8627 (mm-30) cc_final: 0.8323 (mm-30) REVERT: E 429 GLU cc_start: 0.8045 (tm-30) cc_final: 0.7741 (tm-30) REVERT: E 461 ASP cc_start: 0.8198 (t0) cc_final: 0.7994 (t0) REVERT: E 526 ASN cc_start: 0.8240 (m110) cc_final: 0.7797 (m-40) REVERT: B 395 TYR cc_start: 0.8645 (m-80) cc_final: 0.8416 (m-10) REVERT: B 406 GLU cc_start: 0.8400 (mp0) cc_final: 0.8174 (mp0) REVERT: B 447 ASP cc_start: 0.8945 (m-30) cc_final: 0.8631 (m-30) REVERT: B 473 MET cc_start: 0.8553 (mmm) cc_final: 0.7727 (mmm) REVERT: B 478 THR cc_start: 0.8888 (m) cc_final: 0.8652 (m) REVERT: F 520 PHE cc_start: 0.7474 (t80) cc_final: 0.7233 (t80) REVERT: D 423 ASP cc_start: 0.8930 (m-30) cc_final: 0.8695 (m-30) REVERT: D 512 ARG cc_start: 0.8709 (ptp90) cc_final: 0.8490 (ptp-170) REVERT: D 526 ASN cc_start: 0.8785 (t0) cc_final: 0.8582 (m-40) REVERT: C 406 GLU cc_start: 0.8785 (mp0) cc_final: 0.8281 (mp0) REVERT: C 431 PHE cc_start: 0.8536 (t80) cc_final: 0.8317 (t80) REVERT: C 484 ASP cc_start: 0.8401 (t0) cc_final: 0.7715 (t0) outliers start: 12 outliers final: 8 residues processed: 208 average time/residue: 0.1232 time to fit residues: 31.0737 Evaluate side-chains 200 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 192 time to evaluate : 0.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 410 LEU Chi-restraints excluded: chain B residue 417 GLU Chi-restraints excluded: chain F residue 416 LEU Chi-restraints excluded: chain F residue 462 CYS Chi-restraints excluded: chain F residue 510 LEU Chi-restraints excluded: chain A residue 416 LEU Chi-restraints excluded: chain A residue 532 ARG Chi-restraints excluded: chain C residue 416 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 34 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 64 optimal weight: 5.9990 chunk 45 optimal weight: 0.4980 chunk 72 optimal weight: 7.9990 chunk 19 optimal weight: 3.9990 chunk 11 optimal weight: 4.9990 chunk 41 optimal weight: 8.9990 chunk 27 optimal weight: 0.9990 chunk 5 optimal weight: 10.0000 chunk 50 optimal weight: 0.8980 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 471 GLN ** B 470 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 459 ASN ** F 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.135704 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.106606 restraints weight = 9793.709| |-----------------------------------------------------------------------------| r_work (start): 0.3541 rms_B_bonded: 3.69 r_work: 0.3364 rms_B_bonded: 4.55 restraints_weight: 0.5000 r_work (final): 0.3364 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8076 moved from start: 0.1612 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 6810 Z= 0.135 Angle : 0.546 7.261 9222 Z= 0.289 Chirality : 0.040 0.156 1056 Planarity : 0.005 0.051 1218 Dihedral : 4.453 17.452 912 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.38 % Favored : 93.62 % Rotamer: Outliers : 2.71 % Allowed : 12.87 % Favored : 84.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.14 (0.31), residues: 846 helix: 2.13 (0.30), residues: 312 sheet: -1.28 (0.50), residues: 120 loop : -1.10 (0.32), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 436 TYR 0.008 0.001 TYR C 395 PHE 0.024 0.002 PHE A 431 HIS 0.004 0.001 HIS F 401 Details of bonding type rmsd covalent geometry : bond 0.00323 ( 6810) covalent geometry : angle 0.54574 ( 9222) hydrogen bonds : bond 0.02802 ( 258) hydrogen bonds : angle 4.62862 ( 708) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 202 time to evaluate : 0.279 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 406 GLU cc_start: 0.8601 (mm-30) cc_final: 0.8272 (mm-30) REVERT: E 423 ASP cc_start: 0.8656 (m-30) cc_final: 0.8421 (m-30) REVERT: E 526 ASN cc_start: 0.8240 (m110) cc_final: 0.7791 (m-40) REVERT: B 447 ASP cc_start: 0.8984 (m-30) cc_final: 0.8665 (m-30) REVERT: B 473 MET cc_start: 0.8612 (mmm) cc_final: 0.7747 (mmm) REVERT: B 478 THR cc_start: 0.8914 (m) cc_final: 0.8697 (m) REVERT: F 520 PHE cc_start: 0.7630 (t80) cc_final: 0.7335 (t80) REVERT: D 423 ASP cc_start: 0.8917 (m-30) cc_final: 0.8669 (m-30) REVERT: D 512 ARG cc_start: 0.8522 (ptp90) cc_final: 0.8292 (ptp-170) REVERT: C 406 GLU cc_start: 0.8817 (mp0) cc_final: 0.8255 (mp0) REVERT: C 431 PHE cc_start: 0.8587 (t80) cc_final: 0.8322 (t80) REVERT: C 484 ASP cc_start: 0.8356 (t0) cc_final: 0.7836 (t0) outliers start: 20 outliers final: 10 residues processed: 208 average time/residue: 0.1167 time to fit residues: 29.8168 Evaluate side-chains 205 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 195 time to evaluate : 0.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 410 LEU Chi-restraints excluded: chain B residue 417 GLU Chi-restraints excluded: chain B residue 469 VAL Chi-restraints excluded: chain B residue 510 LEU Chi-restraints excluded: chain F residue 416 LEU Chi-restraints excluded: chain F residue 436 ARG Chi-restraints excluded: chain F residue 462 CYS Chi-restraints excluded: chain F residue 510 LEU Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain A residue 416 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 63 optimal weight: 3.9990 chunk 61 optimal weight: 1.9990 chunk 24 optimal weight: 8.9990 chunk 9 optimal weight: 6.9990 chunk 81 optimal weight: 2.9990 chunk 22 optimal weight: 5.9990 chunk 74 optimal weight: 0.0060 chunk 28 optimal weight: 7.9990 chunk 53 optimal weight: 3.9990 chunk 82 optimal weight: 2.9990 chunk 19 optimal weight: 5.9990 overall best weight: 2.4004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 470 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 476 ASN A 476 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.131392 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.102551 restraints weight = 10083.531| |-----------------------------------------------------------------------------| r_work (start): 0.3509 rms_B_bonded: 3.71 r_work: 0.3390 rms_B_bonded: 4.18 restraints_weight: 0.5000 r_work (final): 0.3390 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8148 moved from start: 0.1935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 6810 Z= 0.207 Angle : 0.597 7.484 9222 Z= 0.318 Chirality : 0.042 0.160 1056 Planarity : 0.005 0.051 1218 Dihedral : 4.716 21.805 912 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.45 % Favored : 92.55 % Rotamer: Outliers : 2.85 % Allowed : 14.50 % Favored : 82.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.14 (0.31), residues: 846 helix: 1.77 (0.28), residues: 342 sheet: -1.50 (0.49), residues: 120 loop : -1.36 (0.34), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 403 TYR 0.009 0.002 TYR F 395 PHE 0.034 0.002 PHE A 431 HIS 0.004 0.001 HIS F 401 Details of bonding type rmsd covalent geometry : bond 0.00490 ( 6810) covalent geometry : angle 0.59744 ( 9222) hydrogen bonds : bond 0.03048 ( 258) hydrogen bonds : angle 4.68012 ( 708) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 193 time to evaluate : 0.197 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 406 GLU cc_start: 0.8541 (mm-30) cc_final: 0.8210 (mm-30) REVERT: E 429 GLU cc_start: 0.7903 (tm-30) cc_final: 0.7564 (tm-30) REVERT: E 526 ASN cc_start: 0.8240 (m110) cc_final: 0.7785 (m-40) REVERT: B 406 GLU cc_start: 0.8445 (mp0) cc_final: 0.8176 (mp0) REVERT: B 414 GLU cc_start: 0.8830 (mt-10) cc_final: 0.8383 (mt-10) REVERT: B 417 GLU cc_start: 0.7978 (OUTLIER) cc_final: 0.7596 (pt0) REVERT: B 447 ASP cc_start: 0.9032 (m-30) cc_final: 0.8688 (m-30) REVERT: F 410 LEU cc_start: 0.8760 (OUTLIER) cc_final: 0.8510 (pp) REVERT: F 462 CYS cc_start: 0.8331 (OUTLIER) cc_final: 0.8038 (m) REVERT: D 423 ASP cc_start: 0.8874 (m-30) cc_final: 0.8624 (m-30) REVERT: D 512 ARG cc_start: 0.8567 (ptp90) cc_final: 0.8274 (ptp-170) REVERT: C 403 ARG cc_start: 0.8401 (tpp80) cc_final: 0.8109 (tpp80) REVERT: C 406 GLU cc_start: 0.8738 (mp0) cc_final: 0.8186 (mp0) REVERT: C 484 ASP cc_start: 0.8305 (t0) cc_final: 0.7833 (t0) outliers start: 21 outliers final: 10 residues processed: 199 average time/residue: 0.1258 time to fit residues: 30.6720 Evaluate side-chains 201 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 188 time to evaluate : 0.195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 410 LEU Chi-restraints excluded: chain E residue 490 LEU Chi-restraints excluded: chain B residue 417 GLU Chi-restraints excluded: chain B residue 469 VAL Chi-restraints excluded: chain B residue 510 LEU Chi-restraints excluded: chain F residue 410 LEU Chi-restraints excluded: chain F residue 416 LEU Chi-restraints excluded: chain F residue 436 ARG Chi-restraints excluded: chain F residue 462 CYS Chi-restraints excluded: chain F residue 510 LEU Chi-restraints excluded: chain D residue 527 THR Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain C residue 478 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 70 optimal weight: 5.9990 chunk 63 optimal weight: 0.8980 chunk 73 optimal weight: 0.8980 chunk 39 optimal weight: 0.0970 chunk 11 optimal weight: 2.9990 chunk 23 optimal weight: 2.9990 chunk 30 optimal weight: 6.9990 chunk 40 optimal weight: 2.9990 chunk 28 optimal weight: 5.9990 chunk 1 optimal weight: 5.9990 chunk 66 optimal weight: 0.0470 overall best weight: 0.9878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 470 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 443 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 476 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.134425 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.105350 restraints weight = 10034.485| |-----------------------------------------------------------------------------| r_work (start): 0.3524 rms_B_bonded: 3.76 r_work: 0.3350 rms_B_bonded: 4.56 restraints_weight: 0.5000 r_work (final): 0.3350 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8081 moved from start: 0.2016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6810 Z= 0.122 Angle : 0.559 7.033 9222 Z= 0.295 Chirality : 0.039 0.156 1056 Planarity : 0.004 0.050 1218 Dihedral : 4.508 19.173 912 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.03 % Favored : 93.97 % Rotamer: Outliers : 1.90 % Allowed : 17.75 % Favored : 80.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.05 (0.31), residues: 846 helix: 1.91 (0.28), residues: 342 sheet: -1.57 (0.49), residues: 120 loop : -1.33 (0.33), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E 403 TYR 0.008 0.002 TYR B 395 PHE 0.026 0.001 PHE A 431 HIS 0.004 0.001 HIS F 401 Details of bonding type rmsd covalent geometry : bond 0.00290 ( 6810) covalent geometry : angle 0.55926 ( 9222) hydrogen bonds : bond 0.02632 ( 258) hydrogen bonds : angle 4.64159 ( 708) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 196 time to evaluate : 0.272 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 423 ASP cc_start: 0.8611 (m-30) cc_final: 0.8391 (m-30) REVERT: E 429 GLU cc_start: 0.7929 (tm-30) cc_final: 0.7599 (tm-30) REVERT: E 526 ASN cc_start: 0.8239 (m110) cc_final: 0.7786 (m-40) REVERT: B 414 GLU cc_start: 0.8810 (mt-10) cc_final: 0.8384 (mt-10) REVERT: B 417 GLU cc_start: 0.8026 (OUTLIER) cc_final: 0.7625 (pt0) REVERT: B 447 ASP cc_start: 0.9084 (m-30) cc_final: 0.8812 (m-30) REVERT: F 429 GLU cc_start: 0.7548 (tp30) cc_final: 0.7316 (tp30) REVERT: F 462 CYS cc_start: 0.8365 (OUTLIER) cc_final: 0.8064 (m) REVERT: D 512 ARG cc_start: 0.8381 (ptp90) cc_final: 0.8083 (ptp-170) REVERT: A 417 GLU cc_start: 0.8423 (tm-30) cc_final: 0.8211 (pt0) REVERT: A 493 GLU cc_start: 0.8784 (mp0) cc_final: 0.8576 (mp0) REVERT: C 406 GLU cc_start: 0.8778 (mp0) cc_final: 0.8256 (mp0) REVERT: C 431 PHE cc_start: 0.8593 (t80) cc_final: 0.8368 (t80) REVERT: C 484 ASP cc_start: 0.8190 (t0) cc_final: 0.7752 (t0) outliers start: 14 outliers final: 9 residues processed: 200 average time/residue: 0.1233 time to fit residues: 30.4475 Evaluate side-chains 199 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 188 time to evaluate : 0.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 416 LEU Chi-restraints excluded: chain B residue 417 GLU Chi-restraints excluded: chain B residue 469 VAL Chi-restraints excluded: chain B residue 510 LEU Chi-restraints excluded: chain F residue 416 LEU Chi-restraints excluded: chain F residue 436 ARG Chi-restraints excluded: chain F residue 462 CYS Chi-restraints excluded: chain F residue 510 LEU Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain A residue 416 LEU Chi-restraints excluded: chain C residue 416 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 76 optimal weight: 0.8980 chunk 11 optimal weight: 7.9990 chunk 49 optimal weight: 2.9990 chunk 16 optimal weight: 4.9990 chunk 46 optimal weight: 5.9990 chunk 38 optimal weight: 5.9990 chunk 35 optimal weight: 0.9990 chunk 24 optimal weight: 0.4980 chunk 22 optimal weight: 5.9990 chunk 78 optimal weight: 2.9990 chunk 23 optimal weight: 2.9990 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 470 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 443 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.132572 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.103359 restraints weight = 10031.245| |-----------------------------------------------------------------------------| r_work (start): 0.3496 rms_B_bonded: 3.75 r_work: 0.3329 rms_B_bonded: 4.53 restraints_weight: 0.5000 r_work (final): 0.3329 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8118 moved from start: 0.2177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 6810 Z= 0.161 Angle : 0.586 7.312 9222 Z= 0.311 Chirality : 0.040 0.169 1056 Planarity : 0.005 0.051 1218 Dihedral : 4.588 19.496 912 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.09 % Favored : 92.91 % Rotamer: Outliers : 2.30 % Allowed : 18.56 % Favored : 79.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.10 (0.31), residues: 846 helix: 1.91 (0.28), residues: 342 sheet: -1.69 (0.48), residues: 120 loop : -1.38 (0.34), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG E 403 TYR 0.010 0.002 TYR F 395 PHE 0.027 0.002 PHE A 431 HIS 0.004 0.001 HIS F 401 Details of bonding type rmsd covalent geometry : bond 0.00384 ( 6810) covalent geometry : angle 0.58614 ( 9222) hydrogen bonds : bond 0.02764 ( 258) hydrogen bonds : angle 4.61442 ( 708) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 188 time to evaluate : 0.290 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 406 GLU cc_start: 0.8603 (mm-30) cc_final: 0.8138 (mm-30) REVERT: E 413 ARG cc_start: 0.8108 (tmm-80) cc_final: 0.7799 (ptm160) REVERT: E 423 ASP cc_start: 0.8592 (m-30) cc_final: 0.8377 (m-30) REVERT: E 429 GLU cc_start: 0.7928 (tm-30) cc_final: 0.7576 (tm-30) REVERT: E 526 ASN cc_start: 0.8221 (m110) cc_final: 0.7735 (m-40) REVERT: B 406 GLU cc_start: 0.8421 (mp0) cc_final: 0.8160 (mp0) REVERT: B 414 GLU cc_start: 0.8843 (mt-10) cc_final: 0.8432 (mt-10) REVERT: B 417 GLU cc_start: 0.8056 (OUTLIER) cc_final: 0.7637 (pt0) REVERT: B 447 ASP cc_start: 0.9073 (m-30) cc_final: 0.8752 (m-30) REVERT: F 410 LEU cc_start: 0.8761 (mt) cc_final: 0.8509 (pp) REVERT: F 462 CYS cc_start: 0.8441 (OUTLIER) cc_final: 0.8145 (m) REVERT: D 462 CYS cc_start: 0.8597 (p) cc_final: 0.8245 (p) REVERT: D 512 ARG cc_start: 0.8387 (ptp90) cc_final: 0.8037 (ptp-170) REVERT: A 417 GLU cc_start: 0.8429 (tm-30) cc_final: 0.8222 (pt0) REVERT: A 493 GLU cc_start: 0.8699 (mp0) cc_final: 0.8493 (mp0) REVERT: C 403 ARG cc_start: 0.8421 (tpp80) cc_final: 0.8137 (tpp80) REVERT: C 406 GLU cc_start: 0.8776 (mp0) cc_final: 0.8230 (mp0) REVERT: C 484 ASP cc_start: 0.8184 (t0) cc_final: 0.7752 (t0) outliers start: 17 outliers final: 8 residues processed: 191 average time/residue: 0.1170 time to fit residues: 27.5934 Evaluate side-chains 192 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 182 time to evaluate : 0.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 416 LEU Chi-restraints excluded: chain B residue 417 GLU Chi-restraints excluded: chain B residue 469 VAL Chi-restraints excluded: chain B residue 510 LEU Chi-restraints excluded: chain F residue 436 ARG Chi-restraints excluded: chain F residue 462 CYS Chi-restraints excluded: chain F residue 510 LEU Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain A residue 416 LEU Chi-restraints excluded: chain A residue 502 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 55 optimal weight: 3.9990 chunk 33 optimal weight: 4.9990 chunk 24 optimal weight: 0.9990 chunk 61 optimal weight: 1.9990 chunk 8 optimal weight: 8.9990 chunk 12 optimal weight: 2.9990 chunk 58 optimal weight: 6.9990 chunk 53 optimal weight: 0.3980 chunk 0 optimal weight: 8.9990 chunk 48 optimal weight: 0.9990 chunk 70 optimal weight: 5.9990 overall best weight: 1.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 476 ASN ** B 470 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 443 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.133711 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.104440 restraints weight = 10053.082| |-----------------------------------------------------------------------------| r_work (start): 0.3538 rms_B_bonded: 3.75 r_work: 0.3425 rms_B_bonded: 4.21 restraints_weight: 0.5000 r_work (final): 0.3425 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8146 moved from start: 0.2322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 6810 Z= 0.148 Angle : 0.580 7.212 9222 Z= 0.307 Chirality : 0.040 0.159 1056 Planarity : 0.005 0.050 1218 Dihedral : 4.560 19.337 912 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.62 % Favored : 93.38 % Rotamer: Outliers : 2.17 % Allowed : 19.65 % Favored : 78.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.07 (0.31), residues: 846 helix: 1.96 (0.28), residues: 342 sheet: -1.68 (0.49), residues: 120 loop : -1.39 (0.33), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG E 403 TYR 0.009 0.002 TYR F 395 PHE 0.027 0.001 PHE A 431 HIS 0.004 0.001 HIS F 401 Details of bonding type rmsd covalent geometry : bond 0.00354 ( 6810) covalent geometry : angle 0.58027 ( 9222) hydrogen bonds : bond 0.02657 ( 258) hydrogen bonds : angle 4.59653 ( 708) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 182 time to evaluate : 0.261 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 406 GLU cc_start: 0.8558 (mm-30) cc_final: 0.8121 (mm-30) REVERT: E 413 ARG cc_start: 0.8104 (tmm-80) cc_final: 0.7831 (ptm160) REVERT: E 414 GLU cc_start: 0.7931 (mt-10) cc_final: 0.7712 (mt-10) REVERT: E 423 ASP cc_start: 0.8560 (m-30) cc_final: 0.8358 (m-30) REVERT: E 429 GLU cc_start: 0.7985 (tm-30) cc_final: 0.7646 (tm-30) REVERT: E 493 GLU cc_start: 0.8168 (mp0) cc_final: 0.7664 (mp0) REVERT: E 526 ASN cc_start: 0.8242 (m110) cc_final: 0.7750 (m-40) REVERT: B 406 GLU cc_start: 0.8322 (mp0) cc_final: 0.8060 (mp0) REVERT: B 414 GLU cc_start: 0.8828 (mt-10) cc_final: 0.8448 (mt-10) REVERT: B 417 GLU cc_start: 0.8035 (OUTLIER) cc_final: 0.7622 (pt0) REVERT: B 447 ASP cc_start: 0.9054 (m-30) cc_final: 0.8766 (m-30) REVERT: F 462 CYS cc_start: 0.8496 (OUTLIER) cc_final: 0.8206 (m) REVERT: D 462 CYS cc_start: 0.8592 (p) cc_final: 0.8251 (p) REVERT: D 512 ARG cc_start: 0.8380 (ptp90) cc_final: 0.8076 (ptp-170) REVERT: C 403 ARG cc_start: 0.8412 (tpp80) cc_final: 0.8127 (tpp80) REVERT: C 406 GLU cc_start: 0.8731 (mp0) cc_final: 0.8216 (mp0) REVERT: C 484 ASP cc_start: 0.8069 (t0) cc_final: 0.7681 (t0) outliers start: 16 outliers final: 8 residues processed: 188 average time/residue: 0.1080 time to fit residues: 25.3353 Evaluate side-chains 190 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 180 time to evaluate : 0.197 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 510 LEU Chi-restraints excluded: chain B residue 417 GLU Chi-restraints excluded: chain B residue 469 VAL Chi-restraints excluded: chain B residue 510 LEU Chi-restraints excluded: chain F residue 436 ARG Chi-restraints excluded: chain F residue 462 CYS Chi-restraints excluded: chain F residue 510 LEU Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain A residue 416 LEU Chi-restraints excluded: chain C residue 416 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 42 optimal weight: 5.9990 chunk 45 optimal weight: 0.7980 chunk 33 optimal weight: 4.9990 chunk 62 optimal weight: 2.9990 chunk 68 optimal weight: 0.0670 chunk 20 optimal weight: 1.9990 chunk 50 optimal weight: 1.9990 chunk 28 optimal weight: 5.9990 chunk 31 optimal weight: 5.9990 chunk 29 optimal weight: 10.0000 chunk 41 optimal weight: 6.9990 overall best weight: 1.5724 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 476 ASN ** B 470 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 443 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 476 ASN C 476 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.135504 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.105813 restraints weight = 10040.074| |-----------------------------------------------------------------------------| r_work (start): 0.3495 rms_B_bonded: 3.82 r_work: 0.3323 rms_B_bonded: 4.59 restraints_weight: 0.5000 r_work (final): 0.3323 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8129 moved from start: 0.2411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 6810 Z= 0.156 Angle : 0.596 7.416 9222 Z= 0.318 Chirality : 0.040 0.168 1056 Planarity : 0.005 0.050 1218 Dihedral : 4.592 20.006 912 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.97 % Favored : 93.03 % Rotamer: Outliers : 2.03 % Allowed : 21.14 % Favored : 76.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.08 (0.31), residues: 846 helix: 1.94 (0.28), residues: 342 sheet: -1.71 (0.49), residues: 120 loop : -1.37 (0.34), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG E 403 TYR 0.007 0.001 TYR A 395 PHE 0.026 0.001 PHE A 431 HIS 0.004 0.001 HIS F 401 Details of bonding type rmsd covalent geometry : bond 0.00373 ( 6810) covalent geometry : angle 0.59615 ( 9222) hydrogen bonds : bond 0.02736 ( 258) hydrogen bonds : angle 4.60185 ( 708) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 181 time to evaluate : 0.250 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 406 GLU cc_start: 0.8558 (mm-30) cc_final: 0.8136 (mm-30) REVERT: E 413 ARG cc_start: 0.8092 (tmm-80) cc_final: 0.7811 (ptm160) REVERT: E 414 GLU cc_start: 0.7936 (mt-10) cc_final: 0.7704 (mt-10) REVERT: E 429 GLU cc_start: 0.7965 (tm-30) cc_final: 0.7611 (tm-30) REVERT: E 526 ASN cc_start: 0.8236 (m110) cc_final: 0.7746 (m-40) REVERT: B 406 GLU cc_start: 0.8372 (mp0) cc_final: 0.8078 (mp0) REVERT: B 414 GLU cc_start: 0.8848 (mt-10) cc_final: 0.8456 (mt-10) REVERT: B 417 GLU cc_start: 0.8060 (OUTLIER) cc_final: 0.7641 (pt0) REVERT: B 447 ASP cc_start: 0.9093 (m-30) cc_final: 0.8783 (m-30) REVERT: F 462 CYS cc_start: 0.8447 (t) cc_final: 0.8120 (m) REVERT: D 462 CYS cc_start: 0.8629 (p) cc_final: 0.8300 (p) REVERT: D 512 ARG cc_start: 0.8324 (ptp90) cc_final: 0.8025 (ptp-170) REVERT: C 403 ARG cc_start: 0.8437 (tpp80) cc_final: 0.8160 (tpp80) REVERT: C 406 GLU cc_start: 0.8749 (mp0) cc_final: 0.8219 (mp0) REVERT: C 484 ASP cc_start: 0.8055 (t0) cc_final: 0.7597 (t0) outliers start: 15 outliers final: 9 residues processed: 186 average time/residue: 0.1076 time to fit residues: 24.9594 Evaluate side-chains 188 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 178 time to evaluate : 0.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 510 LEU Chi-restraints excluded: chain B residue 417 GLU Chi-restraints excluded: chain B residue 469 VAL Chi-restraints excluded: chain B residue 510 LEU Chi-restraints excluded: chain F residue 436 ARG Chi-restraints excluded: chain F residue 510 LEU Chi-restraints excluded: chain D residue 416 LEU Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain A residue 416 LEU Chi-restraints excluded: chain A residue 532 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 40 optimal weight: 3.9990 chunk 30 optimal weight: 2.9990 chunk 54 optimal weight: 1.9990 chunk 82 optimal weight: 1.9990 chunk 50 optimal weight: 0.6980 chunk 27 optimal weight: 3.9990 chunk 47 optimal weight: 1.9990 chunk 51 optimal weight: 3.9990 chunk 72 optimal weight: 3.9990 chunk 18 optimal weight: 2.9990 chunk 7 optimal weight: 0.9980 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 476 ASN ** F 443 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 476 ASN D 526 ASN ** A 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 476 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.135427 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.105719 restraints weight = 10043.991| |-----------------------------------------------------------------------------| r_work (start): 0.3495 rms_B_bonded: 3.81 r_work: 0.3326 rms_B_bonded: 4.58 restraints_weight: 0.5000 r_work (final): 0.3326 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8117 moved from start: 0.2474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 6810 Z= 0.157 Angle : 0.607 7.333 9222 Z= 0.323 Chirality : 0.040 0.174 1056 Planarity : 0.005 0.052 1218 Dihedral : 4.603 20.542 912 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.97 % Favored : 93.03 % Rotamer: Outliers : 2.17 % Allowed : 21.41 % Favored : 76.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.11 (0.31), residues: 846 helix: 1.96 (0.28), residues: 342 sheet: -1.77 (0.48), residues: 120 loop : -1.42 (0.34), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG E 403 TYR 0.007 0.001 TYR A 395 PHE 0.027 0.001 PHE A 431 HIS 0.004 0.001 HIS F 401 Details of bonding type rmsd covalent geometry : bond 0.00377 ( 6810) covalent geometry : angle 0.60705 ( 9222) hydrogen bonds : bond 0.02688 ( 258) hydrogen bonds : angle 4.59567 ( 708) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 182 time to evaluate : 0.210 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 406 GLU cc_start: 0.8586 (mm-30) cc_final: 0.8227 (mm-30) REVERT: E 413 ARG cc_start: 0.8059 (tmm-80) cc_final: 0.7777 (ptm160) REVERT: E 414 GLU cc_start: 0.7934 (mt-10) cc_final: 0.7668 (mt-10) REVERT: E 429 GLU cc_start: 0.7953 (tm-30) cc_final: 0.7590 (tm-30) REVERT: E 526 ASN cc_start: 0.8217 (m110) cc_final: 0.7730 (m-40) REVERT: B 414 GLU cc_start: 0.8857 (mt-10) cc_final: 0.8461 (mt-10) REVERT: B 417 GLU cc_start: 0.8065 (OUTLIER) cc_final: 0.7640 (pt0) REVERT: B 447 ASP cc_start: 0.9091 (m-30) cc_final: 0.8771 (m-30) REVERT: B 522 ARG cc_start: 0.8688 (ttt-90) cc_final: 0.8426 (ttt-90) REVERT: F 462 CYS cc_start: 0.8516 (t) cc_final: 0.8179 (m) REVERT: D 462 CYS cc_start: 0.8617 (p) cc_final: 0.8345 (p) REVERT: D 512 ARG cc_start: 0.8283 (ptp90) cc_final: 0.7969 (ptp-170) REVERT: C 403 ARG cc_start: 0.8449 (tpp80) cc_final: 0.8127 (tpp80) REVERT: C 406 GLU cc_start: 0.8884 (mp0) cc_final: 0.8432 (mp0) REVERT: C 484 ASP cc_start: 0.8008 (t0) cc_final: 0.7552 (t0) outliers start: 16 outliers final: 12 residues processed: 187 average time/residue: 0.1150 time to fit residues: 26.4397 Evaluate side-chains 192 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 179 time to evaluate : 0.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 490 LEU Chi-restraints excluded: chain E residue 510 LEU Chi-restraints excluded: chain B residue 417 GLU Chi-restraints excluded: chain B residue 469 VAL Chi-restraints excluded: chain B residue 510 LEU Chi-restraints excluded: chain F residue 436 ARG Chi-restraints excluded: chain F residue 510 LEU Chi-restraints excluded: chain D residue 416 LEU Chi-restraints excluded: chain D residue 526 ASN Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain A residue 416 LEU Chi-restraints excluded: chain A residue 532 ARG Chi-restraints excluded: chain C residue 416 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 52 optimal weight: 0.0370 chunk 29 optimal weight: 9.9990 chunk 64 optimal weight: 0.9990 chunk 39 optimal weight: 0.4980 chunk 54 optimal weight: 0.7980 chunk 58 optimal weight: 0.0070 chunk 57 optimal weight: 5.9990 chunk 26 optimal weight: 2.9990 chunk 27 optimal weight: 0.9990 chunk 60 optimal weight: 0.7980 chunk 42 optimal weight: 5.9990 overall best weight: 0.4276 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 476 ASN ** B 470 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 443 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 476 ASN D 526 ASN ** A 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 476 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.136917 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.107470 restraints weight = 9932.906| |-----------------------------------------------------------------------------| r_work (start): 0.3545 rms_B_bonded: 3.76 r_work: 0.3383 rms_B_bonded: 4.56 restraints_weight: 0.5000 r_work (final): 0.3383 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8054 moved from start: 0.2531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 6810 Z= 0.121 Angle : 0.625 15.293 9222 Z= 0.324 Chirality : 0.039 0.187 1056 Planarity : 0.005 0.054 1218 Dihedral : 4.447 20.063 912 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.15 % Favored : 93.85 % Rotamer: Outliers : 1.76 % Allowed : 21.68 % Favored : 76.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.10 (0.30), residues: 846 helix: 2.01 (0.28), residues: 342 sheet: -1.73 (0.49), residues: 120 loop : -1.46 (0.33), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG E 403 TYR 0.005 0.001 TYR A 395 PHE 0.023 0.001 PHE A 431 HIS 0.004 0.001 HIS F 401 Details of bonding type rmsd covalent geometry : bond 0.00284 ( 6810) covalent geometry : angle 0.62513 ( 9222) hydrogen bonds : bond 0.02574 ( 258) hydrogen bonds : angle 4.61795 ( 708) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 191 time to evaluate : 0.285 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 406 GLU cc_start: 0.8591 (mm-30) cc_final: 0.8167 (mm-30) REVERT: E 413 ARG cc_start: 0.8017 (tmm-80) cc_final: 0.7753 (ptm160) REVERT: E 429 GLU cc_start: 0.7905 (tm-30) cc_final: 0.7575 (tm-30) REVERT: E 526 ASN cc_start: 0.8244 (m110) cc_final: 0.7793 (m-40) REVERT: B 414 GLU cc_start: 0.8803 (mt-10) cc_final: 0.8461 (mt-10) REVERT: B 417 GLU cc_start: 0.8058 (OUTLIER) cc_final: 0.7639 (pt0) REVERT: B 447 ASP cc_start: 0.9089 (m-30) cc_final: 0.8796 (m-30) REVERT: F 462 CYS cc_start: 0.8494 (t) cc_final: 0.8177 (m) REVERT: D 462 CYS cc_start: 0.8584 (p) cc_final: 0.8310 (p) REVERT: D 512 ARG cc_start: 0.8161 (ptp90) cc_final: 0.7853 (ptp-170) REVERT: A 417 GLU cc_start: 0.8381 (tm-30) cc_final: 0.8179 (pt0) REVERT: C 403 ARG cc_start: 0.8365 (tpp80) cc_final: 0.8034 (tpp80) REVERT: C 406 GLU cc_start: 0.8874 (mp0) cc_final: 0.8430 (mp0) REVERT: C 484 ASP cc_start: 0.7875 (t0) cc_final: 0.7519 (t0) outliers start: 13 outliers final: 7 residues processed: 195 average time/residue: 0.1254 time to fit residues: 29.9996 Evaluate side-chains 193 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 185 time to evaluate : 0.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 490 LEU Chi-restraints excluded: chain E residue 510 LEU Chi-restraints excluded: chain B residue 417 GLU Chi-restraints excluded: chain B residue 469 VAL Chi-restraints excluded: chain B residue 510 LEU Chi-restraints excluded: chain F residue 436 ARG Chi-restraints excluded: chain F residue 510 LEU Chi-restraints excluded: chain A residue 416 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 16 optimal weight: 5.9990 chunk 1 optimal weight: 2.9990 chunk 12 optimal weight: 7.9990 chunk 58 optimal weight: 6.9990 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 1.9990 chunk 26 optimal weight: 0.9990 chunk 52 optimal weight: 10.0000 chunk 37 optimal weight: 0.7980 chunk 55 optimal weight: 0.0170 chunk 72 optimal weight: 7.9990 overall best weight: 1.3624 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 468 GLN E 476 ASN ** B 470 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 459 ASN C 476 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.134746 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.105450 restraints weight = 9967.466| |-----------------------------------------------------------------------------| r_work (start): 0.3519 rms_B_bonded: 3.73 r_work: 0.3348 rms_B_bonded: 4.53 restraints_weight: 0.5000 r_work (final): 0.3348 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8115 moved from start: 0.2556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 6810 Z= 0.151 Angle : 0.643 13.222 9222 Z= 0.336 Chirality : 0.040 0.179 1056 Planarity : 0.005 0.050 1218 Dihedral : 4.520 19.265 912 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.50 % Favored : 93.50 % Rotamer: Outliers : 1.36 % Allowed : 21.82 % Favored : 76.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.15 (0.30), residues: 846 helix: 1.82 (0.28), residues: 348 sheet: -1.72 (0.48), residues: 120 loop : -1.40 (0.33), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG E 403 TYR 0.007 0.001 TYR A 395 PHE 0.025 0.001 PHE A 431 HIS 0.004 0.001 HIS F 401 Details of bonding type rmsd covalent geometry : bond 0.00362 ( 6810) covalent geometry : angle 0.64280 ( 9222) hydrogen bonds : bond 0.02629 ( 258) hydrogen bonds : angle 4.60246 ( 708) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1589.37 seconds wall clock time: 28 minutes 0.94 seconds (1680.94 seconds total)