Starting phenix.real_space_refine on Thu May 1 07:18:48 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8shc_40483/05_2025/8shc_40483.cif Found real_map, /net/cci-nas-00/data/ceres_data/8shc_40483/05_2025/8shc_40483.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8shc_40483/05_2025/8shc_40483.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8shc_40483/05_2025/8shc_40483.map" model { file = "/net/cci-nas-00/data/ceres_data/8shc_40483/05_2025/8shc_40483.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8shc_40483/05_2025/8shc_40483.cif" } resolution = 3.0 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= 0.041 sd= 0.266 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians P 6 5.49 5 S 36 5.16 5 Cl 2 4.86 5 C 7056 2.51 5 N 1550 2.21 5 O 1802 1.98 5 F 12 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/chem_data/mon_lib" Total number of atoms: 10464 Number of models: 1 Model: "" Number of chains: 4 Chain: "D" Number of atoms: 4755 Number of conformers: 1 Conformer: "" Number of residues, atoms: 613, 4755 Classifications: {'peptide': 613} Link IDs: {'PTRANS': 24, 'TRANS': 588} Chain breaks: 3 Chain: "C" Number of atoms: 4755 Number of conformers: 1 Conformer: "" Number of residues, atoms: 613, 4755 Classifications: {'peptide': 613} Link IDs: {'PTRANS': 24, 'TRANS': 588} Chain breaks: 3 Chain: "D" Number of atoms: 477 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 477 Unusual residues: {' CL': 1, 'AV0': 2, 'CLR': 6, 'LBN': 9, 'NFL': 2} Classifications: {'undetermined': 20} Link IDs: {None: 19} Unresolved non-hydrogen bonds: 340 Unresolved non-hydrogen angles: 420 Unresolved non-hydrogen dihedrals: 351 Unresolved non-hydrogen chiralities: 17 Planarities with less than four sites: {'LBN:plan-2': 6, 'LBN:plan-3': 7, 'LBN:plan-1': 7} Unresolved non-hydrogen planarities: 72 Chain: "C" Number of atoms: 477 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 477 Unusual residues: {' CL': 1, 'AV0': 2, 'CLR': 6, 'LBN': 9, 'NFL': 2} Classifications: {'undetermined': 20} Link IDs: {None: 19} Unresolved non-hydrogen bonds: 340 Unresolved non-hydrogen angles: 420 Unresolved non-hydrogen dihedrals: 351 Unresolved non-hydrogen chiralities: 17 Planarities with less than four sites: {'LBN:plan-2': 6, 'LBN:plan-3': 7, 'LBN:plan-1': 7} Unresolved non-hydrogen planarities: 72 Time building chain proxies: 7.44, per 1000 atoms: 0.71 Number of scatterers: 10464 At special positions: 0 Unit cell: (122.1, 73.7, 107.8, 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) Cl 2 17.00 S 36 16.00 P 6 15.00 F 12 9.00 O 1802 8.00 N 1550 7.00 C 7056 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.42 Conformation dependent library (CDL) restraints added in 1.7 seconds 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2288 Finding SS restraints... Secondary structure from input PDB file: 62 helices and 3 sheets defined 71.5% alpha, 4.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.18 Creating SS restraints... Processing helix chain 'D' and resid 28 through 36 Processing helix chain 'D' and resid 70 through 74 removed outlier: 3.724A pdb=" N ASP D 73 " --> pdb=" O PRO D 70 " (cutoff:3.500A) Processing helix chain 'D' and resid 79 through 106 removed outlier: 4.183A pdb=" N LEU D 84 " --> pdb=" O ILE D 80 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N LEU D 85 " --> pdb=" O LYS D 81 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N SER D 86 " --> pdb=" O GLU D 82 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N LEU D 100 " --> pdb=" O LEU D 96 " (cutoff:3.500A) Processing helix chain 'D' and resid 114 through 131 removed outlier: 3.916A pdb=" N TYR D 118 " --> pdb=" O GLY D 114 " (cutoff:3.500A) Proline residue: D 123 - end of helix removed outlier: 4.543A pdb=" N ILE D 129 " --> pdb=" O LEU D 125 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N PHE D 130 " --> pdb=" O THR D 126 " (cutoff:3.500A) Processing helix chain 'D' and resid 141 through 156 removed outlier: 3.841A pdb=" N SER D 145 " --> pdb=" O PHE D 141 " (cutoff:3.500A) Processing helix chain 'D' and resid 157 through 162 Processing helix chain 'D' and resid 177 through 206 Processing helix chain 'D' and resid 209 through 215 removed outlier: 4.077A pdb=" N VAL D 212 " --> pdb=" O GLY D 209 " (cutoff:3.500A) Processing helix chain 'D' and resid 216 through 241 removed outlier: 3.505A pdb=" N ASN D 241 " --> pdb=" O LYS D 237 " (cutoff:3.500A) Processing helix chain 'D' and resid 251 through 264 Processing helix chain 'D' and resid 265 through 267 No H-bonds generated for 'chain 'D' and resid 265 through 267' Processing helix chain 'D' and resid 268 through 292 Processing helix chain 'D' and resid 301 through 318 Processing helix chain 'D' and resid 318 through 323 removed outlier: 3.531A pdb=" N ASN D 322 " --> pdb=" O ASN D 318 " (cutoff:3.500A) Processing helix chain 'D' and resid 342 through 348 removed outlier: 3.897A pdb=" N LEU D 345 " --> pdb=" O PRO D 342 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N SER D 347 " --> pdb=" O SER D 344 " (cutoff:3.500A) Processing helix chain 'D' and resid 349 through 376 removed outlier: 4.006A pdb=" N SER D 355 " --> pdb=" O THR D 351 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LYS D 374 " --> pdb=" O VAL D 370 " (cutoff:3.500A) Processing helix chain 'D' and resid 380 through 397 Processing helix chain 'D' and resid 406 through 416 removed outlier: 3.696A pdb=" N THR D 416 " --> pdb=" O VAL D 412 " (cutoff:3.500A) Processing helix chain 'D' and resid 421 through 437 Processing helix chain 'D' and resid 439 through 443 removed outlier: 3.636A pdb=" N LEU D 442 " --> pdb=" O GLY D 439 " (cutoff:3.500A) Processing helix chain 'D' and resid 446 through 457 removed outlier: 3.952A pdb=" N LEU D 450 " --> pdb=" O GLN D 446 " (cutoff:3.500A) Processing helix chain 'D' and resid 458 through 463 Processing helix chain 'D' and resid 466 through 475 removed outlier: 4.560A pdb=" N ARG D 470 " --> pdb=" O CYS D 466 " (cutoff:3.500A) Processing helix chain 'D' and resid 475 through 491 removed outlier: 3.513A pdb=" N ALA D 479 " --> pdb=" O ASN D 475 " (cutoff:3.500A) Processing helix chain 'D' and resid 493 through 515 Processing helix chain 'D' and resid 533 through 537 removed outlier: 4.201A pdb=" N LYS D 537 " --> pdb=" O THR D 533 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 533 through 537' Processing helix chain 'D' and resid 555 through 571 Processing helix chain 'D' and resid 573 through 585 removed outlier: 3.697A pdb=" N VAL D 577 " --> pdb=" O ASP D 573 " (cutoff:3.500A) Processing helix chain 'D' and resid 669 through 686 removed outlier: 3.839A pdb=" N ILE D 686 " --> pdb=" O GLU D 682 " (cutoff:3.500A) Processing helix chain 'D' and resid 696 through 706 Processing helix chain 'D' and resid 723 through 731 Processing helix chain 'C' and resid 28 through 36 Processing helix chain 'C' and resid 70 through 74 removed outlier: 3.721A pdb=" N ASP C 73 " --> pdb=" O PRO C 70 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 106 removed outlier: 4.183A pdb=" N LEU C 84 " --> pdb=" O ILE C 80 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N LEU C 85 " --> pdb=" O LYS C 81 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N SER C 86 " --> pdb=" O GLU C 82 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N LEU C 100 " --> pdb=" O LEU C 96 " (cutoff:3.500A) Processing helix chain 'C' and resid 114 through 131 removed outlier: 3.917A pdb=" N TYR C 118 " --> pdb=" O GLY C 114 " (cutoff:3.500A) Proline residue: C 123 - end of helix removed outlier: 4.542A pdb=" N ILE C 129 " --> pdb=" O LEU C 125 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N PHE C 130 " --> pdb=" O THR C 126 " (cutoff:3.500A) Processing helix chain 'C' and resid 141 through 156 removed outlier: 3.843A pdb=" N SER C 145 " --> pdb=" O PHE C 141 " (cutoff:3.500A) Processing helix chain 'C' and resid 157 through 162 Processing helix chain 'C' and resid 177 through 206 Processing helix chain 'C' and resid 209 through 215 removed outlier: 4.076A pdb=" N VAL C 212 " --> pdb=" O GLY C 209 " (cutoff:3.500A) Processing helix chain 'C' and resid 216 through 241 removed outlier: 3.504A pdb=" N ASN C 241 " --> pdb=" O LYS C 237 " (cutoff:3.500A) Processing helix chain 'C' and resid 251 through 264 Processing helix chain 'C' and resid 265 through 267 No H-bonds generated for 'chain 'C' and resid 265 through 267' Processing helix chain 'C' and resid 268 through 292 Processing helix chain 'C' and resid 301 through 318 Processing helix chain 'C' and resid 318 through 323 removed outlier: 3.531A pdb=" N ASN C 322 " --> pdb=" O ASN C 318 " (cutoff:3.500A) Processing helix chain 'C' and resid 342 through 348 removed outlier: 3.897A pdb=" N LEU C 345 " --> pdb=" O PRO C 342 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N SER C 347 " --> pdb=" O SER C 344 " (cutoff:3.500A) Processing helix chain 'C' and resid 349 through 376 removed outlier: 4.010A pdb=" N SER C 355 " --> pdb=" O THR C 351 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LYS C 374 " --> pdb=" O VAL C 370 " (cutoff:3.500A) Processing helix chain 'C' and resid 380 through 397 Processing helix chain 'C' and resid 406 through 416 removed outlier: 3.696A pdb=" N THR C 416 " --> pdb=" O VAL C 412 " (cutoff:3.500A) Processing helix chain 'C' and resid 421 through 437 Processing helix chain 'C' and resid 439 through 443 removed outlier: 3.636A pdb=" N LEU C 442 " --> pdb=" O GLY C 439 " (cutoff:3.500A) Processing helix chain 'C' and resid 446 through 457 removed outlier: 3.952A pdb=" N LEU C 450 " --> pdb=" O GLN C 446 " (cutoff:3.500A) Processing helix chain 'C' and resid 458 through 463 Processing helix chain 'C' and resid 466 through 475 removed outlier: 4.560A pdb=" N ARG C 470 " --> pdb=" O CYS C 466 " (cutoff:3.500A) Processing helix chain 'C' and resid 475 through 491 removed outlier: 3.514A pdb=" N ALA C 479 " --> pdb=" O ASN C 475 " (cutoff:3.500A) Processing helix chain 'C' and resid 493 through 515 Processing helix chain 'C' and resid 533 through 537 removed outlier: 4.197A pdb=" N LYS C 537 " --> pdb=" O THR C 533 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 533 through 537' Processing helix chain 'C' and resid 555 through 571 Processing helix chain 'C' and resid 573 through 585 removed outlier: 3.697A pdb=" N VAL C 577 " --> pdb=" O ASP C 573 " (cutoff:3.500A) Processing helix chain 'C' and resid 669 through 686 removed outlier: 3.838A pdb=" N ILE C 686 " --> pdb=" O GLU C 682 " (cutoff:3.500A) Processing helix chain 'C' and resid 696 through 706 Processing helix chain 'C' and resid 723 through 731 Processing sheet with id=AA1, first strand: chain 'D' and resid 19 through 25 removed outlier: 3.718A pdb=" N VAL D 22 " --> pdb=" O VAL C 22 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N VAL C 22 " --> pdb=" O VAL D 22 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 530 through 532 removed outlier: 4.399A pdb=" N SER D 517 " --> pdb=" O SER D 551 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N ILE D 547 " --> pdb=" O LEU D 521 " (cutoff:3.500A) removed outlier: 9.072A pdb=" N SER D 523 " --> pdb=" O VAL D 545 " (cutoff:3.500A) removed outlier: 12.888A pdb=" N VAL D 545 " --> pdb=" O SER D 523 " (cutoff:3.500A) removed outlier: 6.195A pdb=" N LYS D 546 " --> pdb=" O VAL D 659 " (cutoff:3.500A) removed outlier: 7.385A pdb=" N ASP D 661 " --> pdb=" O LYS D 546 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N LEU D 548 " --> pdb=" O ASP D 661 " (cutoff:3.500A) removed outlier: 8.789A pdb=" N PHE D 719 " --> pdb=" O VAL D 690 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N PHE D 692 " --> pdb=" O PHE D 719 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 530 through 532 removed outlier: 4.399A pdb=" N SER C 517 " --> pdb=" O SER C 551 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N ILE C 547 " --> pdb=" O LEU C 521 " (cutoff:3.500A) removed outlier: 9.073A pdb=" N SER C 523 " --> pdb=" O VAL C 545 " (cutoff:3.500A) removed outlier: 12.888A pdb=" N VAL C 545 " --> pdb=" O SER C 523 " (cutoff:3.500A) removed outlier: 6.195A pdb=" N LYS C 546 " --> pdb=" O VAL C 659 " (cutoff:3.500A) removed outlier: 7.384A pdb=" N ASP C 661 " --> pdb=" O LYS C 546 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N LEU C 548 " --> pdb=" O ASP C 661 " (cutoff:3.500A) removed outlier: 8.789A pdb=" N PHE C 719 " --> pdb=" O VAL C 690 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N PHE C 692 " --> pdb=" O PHE C 719 " (cutoff:3.500A) 608 hydrogen bonds defined for protein. 1782 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: 3.54 Time building geometry restraints manager: 3.50 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 1496 1.32 - 1.44: 2733 1.44 - 1.56: 6393 1.56 - 1.68: 12 1.68 - 1.81: 56 Bond restraints: 10690 Sorted by residual: bond pdb=" C10 LBN D 817 " pdb=" C7 LBN D 817 " ideal model delta sigma weight residual 1.523 1.455 0.068 2.00e-02 2.50e+03 1.17e+01 bond pdb=" C10 LBN D 820 " pdb=" C7 LBN D 820 " ideal model delta sigma weight residual 1.523 1.455 0.068 2.00e-02 2.50e+03 1.15e+01 bond pdb=" C10 LBN C 811 " pdb=" C7 LBN C 811 " ideal model delta sigma weight residual 1.523 1.456 0.067 2.00e-02 2.50e+03 1.13e+01 bond pdb=" C36 LBN D 813 " pdb=" C37 LBN D 813 " ideal model delta sigma weight residual 1.524 1.462 0.062 2.00e-02 2.50e+03 9.62e+00 bond pdb=" O2 LBN D 813 " pdb=" P1 LBN D 813 " ideal model delta sigma weight residual 1.650 1.588 0.062 2.00e-02 2.50e+03 9.51e+00 ... (remaining 10685 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.12: 14201 2.12 - 4.24: 253 4.24 - 6.36: 31 6.36 - 8.48: 11 8.48 - 10.60: 6 Bond angle restraints: 14502 Sorted by residual: angle pdb=" O1 LBN C 816 " pdb=" P1 LBN C 816 " pdb=" O2 LBN C 816 " ideal model delta sigma weight residual 93.45 104.05 -10.60 3.00e+00 1.11e-01 1.25e+01 angle pdb=" O1 LBN D 802 " pdb=" P1 LBN D 802 " pdb=" O2 LBN D 802 " ideal model delta sigma weight residual 93.45 104.04 -10.59 3.00e+00 1.11e-01 1.25e+01 angle pdb=" O1 LBN D 812 " pdb=" P1 LBN D 812 " pdb=" O2 LBN D 812 " ideal model delta sigma weight residual 93.45 103.84 -10.39 3.00e+00 1.11e-01 1.20e+01 angle pdb=" O1 LBN C 806 " pdb=" P1 LBN C 806 " pdb=" O2 LBN C 806 " ideal model delta sigma weight residual 93.45 103.80 -10.35 3.00e+00 1.11e-01 1.19e+01 angle pdb=" C ILE C 491 " pdb=" N LEU C 492 " pdb=" CA LEU C 492 " ideal model delta sigma weight residual 121.54 127.38 -5.84 1.91e+00 2.74e-01 9.35e+00 ... (remaining 14497 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.83: 6808 33.83 - 67.66: 236 67.66 - 101.49: 58 101.49 - 135.32: 58 135.32 - 169.15: 6 Dihedral angle restraints: 7166 sinusoidal: 3616 harmonic: 3550 Sorted by residual: dihedral pdb=" CA VAL C 722 " pdb=" C VAL C 722 " pdb=" N HIS C 723 " pdb=" CA HIS C 723 " ideal model delta harmonic sigma weight residual 180.00 151.33 28.67 0 5.00e+00 4.00e-02 3.29e+01 dihedral pdb=" CA VAL D 722 " pdb=" C VAL D 722 " pdb=" N HIS D 723 " pdb=" CA HIS D 723 " ideal model delta harmonic sigma weight residual 180.00 151.36 28.64 0 5.00e+00 4.00e-02 3.28e+01 dihedral pdb=" CA THR C 404 " pdb=" C THR C 404 " pdb=" N THR C 405 " pdb=" CA THR C 405 " ideal model delta harmonic sigma weight residual -180.00 -153.99 -26.01 0 5.00e+00 4.00e-02 2.71e+01 ... (remaining 7163 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.972: 1756 0.972 - 1.944: 0 1.944 - 2.916: 0 2.916 - 3.888: 0 3.888 - 4.860: 2 Chirality restraints: 1758 Sorted by residual: chirality pdb=" C2 LBN C 816 " pdb=" C1 LBN C 816 " pdb=" C3 LBN C 816 " pdb=" O7 LBN C 816 " both_signs ideal model delta sigma weight residual False -2.36 2.50 -4.86 2.00e-01 2.50e+01 5.91e+02 chirality pdb=" C2 LBN D 802 " pdb=" C1 LBN D 802 " pdb=" C3 LBN D 802 " pdb=" O7 LBN D 802 " both_signs ideal model delta sigma weight residual False -2.36 2.49 -4.86 2.00e-01 2.50e+01 5.90e+02 chirality pdb=" C2 LBN D 813 " pdb=" C1 LBN D 813 " pdb=" C3 LBN D 813 " pdb=" O7 LBN D 813 " both_signs ideal model delta sigma weight residual False -2.36 -2.10 -0.27 2.00e-01 2.50e+01 1.76e+00 ... (remaining 1755 not shown) Planarity restraints: 1650 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C41 LBN C 816 " -0.100 2.00e-02 2.50e+03 2.33e-01 5.43e+02 pdb=" C42 LBN C 816 " 0.314 2.00e-02 2.50e+03 pdb=" C5 LBN C 816 " -0.314 2.00e-02 2.50e+03 pdb=" C8 LBN C 816 " 0.101 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C41 LBN D 802 " 0.101 2.00e-02 2.50e+03 2.33e-01 5.41e+02 pdb=" C42 LBN D 802 " -0.313 2.00e-02 2.50e+03 pdb=" C5 LBN D 802 " 0.313 2.00e-02 2.50e+03 pdb=" C8 LBN D 802 " -0.100 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C41 LBN C 806 " 0.062 2.00e-02 2.50e+03 1.17e-01 1.38e+02 pdb=" C42 LBN C 806 " -0.154 2.00e-02 2.50e+03 pdb=" C5 LBN C 806 " 0.154 2.00e-02 2.50e+03 pdb=" C8 LBN C 806 " -0.062 2.00e-02 2.50e+03 ... (remaining 1647 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 630 2.74 - 3.28: 10368 3.28 - 3.82: 16188 3.82 - 4.36: 19632 4.36 - 4.90: 34097 Nonbonded interactions: 80915 Sorted by model distance: nonbonded pdb=" O PRO C 553 " pdb=" ND2 ASN C 558 " model vdw 2.197 3.120 nonbonded pdb=" O PRO D 553 " pdb=" ND2 ASN D 558 " model vdw 2.197 3.120 nonbonded pdb=" NH1 ARG C 38 " pdb=" OE2 GLU C 701 " model vdw 2.257 3.120 nonbonded pdb=" OG1 THR C 132 " pdb=" OE1 GLU C 384 " model vdw 2.270 3.040 nonbonded pdb=" OG1 THR D 132 " pdb=" OE1 GLU D 384 " model vdw 2.274 3.040 ... (remaining 80910 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: 0.05 Found NCS groups: ncs_group { reference = (chain 'C' and (resid 17 through 732 or resid 808 or (resid 813 and (name C25 or \ name C26 or name C27 or name C28 or name C29 or name C30 or name C31 or name C3 \ 2 or name C33)))) selection = (chain 'D' and (resid 17 through 732 or resid 808 or (resid 813 and (name C25 or \ name C26 or name C27 or name C28 or name C29 or name C30 or name C31 or name C3 \ 2 or name C33)))) } 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: 55.440 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: 0.010 Extract box with map and model: 0.420 Check model and map are aligned: 0.090 Set scattering table: 0.110 Process input model: 28.660 Find NCS groups from input model: 0.740 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:119.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 204.540 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7559 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 : 0.005 0.068 10691 Z= 0.235 Angle : 0.698 10.599 14502 Z= 0.329 Chirality : 0.170 4.860 1758 Planarity : 0.010 0.233 1650 Dihedral : 21.902 169.148 4878 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.87 % Favored : 94.13 % Rotamer: Outliers : 0.19 % Allowed : 0.29 % Favored : 99.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.04 (0.25), residues: 1210 helix: 1.80 (0.19), residues: 796 sheet: 1.68 (0.79), residues: 54 loop : -2.16 (0.31), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 482 HIS 0.003 0.001 HIS D 698 PHE 0.026 0.001 PHE C 385 TYR 0.013 0.001 TYR C 323 ARG 0.002 0.000 ARG D 409 Details of bonding type rmsd hydrogen bonds : bond 0.11888 ( 608) hydrogen bonds : angle 4.98518 ( 1782) covalent geometry : bond 0.00466 (10690) covalent geometry : angle 0.69788 (14502) Misc. bond : bond 0.00006 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 159 time to evaluate : 1.576 Fit side-chains outliers start: 2 outliers final: 0 residues processed: 159 average time/residue: 1.2493 time to fit residues: 216.9843 Evaluate side-chains 106 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 106 time to evaluate : 0.946 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 103 optimal weight: 0.6980 chunk 92 optimal weight: 0.8980 chunk 51 optimal weight: 5.9990 chunk 31 optimal weight: 2.9990 chunk 62 optimal weight: 2.9990 chunk 49 optimal weight: 2.9990 chunk 95 optimal weight: 1.9990 chunk 37 optimal weight: 3.9990 chunk 58 optimal weight: 0.8980 chunk 71 optimal weight: 0.4980 chunk 110 optimal weight: 1.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 35 GLN D 266 ASN D 289 ASN D 656 HIS C 35 GLN C 266 ASN C 289 ASN C 656 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4029 r_free = 0.4029 target = 0.186310 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.153948 restraints weight = 10574.905| |-----------------------------------------------------------------------------| r_work (start): 0.3684 rms_B_bonded: 1.45 r_work: 0.3510 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3373 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3373 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7886 moved from start: 0.1154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10691 Z= 0.142 Angle : 0.672 11.016 14502 Z= 0.324 Chirality : 0.045 0.229 1758 Planarity : 0.005 0.063 1650 Dihedral : 19.557 164.615 2730 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.29 % Favored : 94.71 % Rotamer: Outliers : 2.10 % Allowed : 9.18 % Favored : 88.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.17 (0.25), residues: 1210 helix: 1.90 (0.19), residues: 802 sheet: 1.93 (0.77), residues: 50 loop : -2.14 (0.31), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 482 HIS 0.004 0.001 HIS C 698 PHE 0.026 0.001 PHE C 385 TYR 0.012 0.001 TYR C 371 ARG 0.003 0.000 ARG C 38 Details of bonding type rmsd hydrogen bonds : bond 0.05647 ( 608) hydrogen bonds : angle 4.06427 ( 1782) covalent geometry : bond 0.00296 (10690) covalent geometry : angle 0.67242 (14502) Misc. bond : bond 0.00049 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 115 time to evaluate : 0.993 Fit side-chains REVERT: D 250 ILE cc_start: 0.7913 (pt) cc_final: 0.7644 (pt) outliers start: 22 outliers final: 10 residues processed: 129 average time/residue: 0.8702 time to fit residues: 125.0929 Evaluate side-chains 120 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 110 time to evaluate : 0.988 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 80 ILE Chi-restraints excluded: chain D residue 111 VAL Chi-restraints excluded: chain D residue 349 MET Chi-restraints excluded: chain D residue 724 ASP Chi-restraints excluded: chain C residue 80 ILE Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain C residue 155 MET Chi-restraints excluded: chain C residue 349 MET Chi-restraints excluded: chain C residue 532 SER Chi-restraints excluded: chain C residue 724 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 8 optimal weight: 3.9990 chunk 54 optimal weight: 7.9990 chunk 94 optimal weight: 1.9990 chunk 24 optimal weight: 20.0000 chunk 57 optimal weight: 3.9990 chunk 42 optimal weight: 2.9990 chunk 95 optimal weight: 1.9990 chunk 59 optimal weight: 0.2980 chunk 113 optimal weight: 3.9990 chunk 2 optimal weight: 0.5980 chunk 33 optimal weight: 1.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 35 GLN D 289 ASN D 656 HIS C 35 GLN C 289 ASN C 656 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.182798 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.149607 restraints weight = 10634.092| |-----------------------------------------------------------------------------| r_work (start): 0.3608 rms_B_bonded: 1.54 r_work: 0.3438 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3296 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3296 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7922 moved from start: 0.1486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10691 Z= 0.148 Angle : 0.621 9.115 14502 Z= 0.315 Chirality : 0.046 0.284 1758 Planarity : 0.005 0.069 1650 Dihedral : 18.092 160.407 2730 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.95 % Favored : 94.05 % Rotamer: Outliers : 2.20 % Allowed : 10.99 % Favored : 86.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % 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: 1.13 (0.25), residues: 1210 helix: 1.85 (0.19), residues: 814 sheet: 1.79 (0.75), residues: 50 loop : -2.23 (0.30), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP D 482 HIS 0.009 0.002 HIS D 656 PHE 0.022 0.002 PHE D 385 TYR 0.020 0.002 TYR C 315 ARG 0.003 0.000 ARG C 549 Details of bonding type rmsd hydrogen bonds : bond 0.06030 ( 608) hydrogen bonds : angle 4.00216 ( 1782) covalent geometry : bond 0.00318 (10690) covalent geometry : angle 0.62147 (14502) Misc. bond : bond 0.00049 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 111 time to evaluate : 0.890 Fit side-chains REVERT: D 250 ILE cc_start: 0.7964 (pt) cc_final: 0.7748 (pt) REVERT: D 442 LEU cc_start: 0.8409 (mm) cc_final: 0.8106 (mt) REVERT: D 684 GLN cc_start: 0.7804 (OUTLIER) cc_final: 0.7558 (tt0) REVERT: C 442 LEU cc_start: 0.8404 (mm) cc_final: 0.8096 (mt) REVERT: C 684 GLN cc_start: 0.7812 (OUTLIER) cc_final: 0.7569 (tt0) outliers start: 23 outliers final: 16 residues processed: 124 average time/residue: 1.0042 time to fit residues: 138.0839 Evaluate side-chains 123 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 105 time to evaluate : 1.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 96 LEU Chi-restraints excluded: chain D residue 111 VAL Chi-restraints excluded: chain D residue 288 LEU Chi-restraints excluded: chain D residue 349 MET Chi-restraints excluded: chain D residue 385 PHE Chi-restraints excluded: chain D residue 432 MET Chi-restraints excluded: chain D residue 545 VAL Chi-restraints excluded: chain D residue 684 GLN Chi-restraints excluded: chain D residue 724 ASP Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain C residue 155 MET Chi-restraints excluded: chain C residue 288 LEU Chi-restraints excluded: chain C residue 349 MET Chi-restraints excluded: chain C residue 385 PHE Chi-restraints excluded: chain C residue 432 MET Chi-restraints excluded: chain C residue 684 GLN Chi-restraints excluded: chain C residue 724 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 62 optimal weight: 0.8980 chunk 73 optimal weight: 1.9990 chunk 31 optimal weight: 0.9980 chunk 41 optimal weight: 1.9990 chunk 97 optimal weight: 0.9990 chunk 75 optimal weight: 3.9990 chunk 82 optimal weight: 2.9990 chunk 29 optimal weight: 0.0670 chunk 37 optimal weight: 5.9990 chunk 23 optimal weight: 2.9990 chunk 108 optimal weight: 0.9980 overall best weight: 0.7920 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 35 GLN D 289 ASN C 35 GLN C 289 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.183831 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.149660 restraints weight = 10643.025| |-----------------------------------------------------------------------------| r_work (start): 0.3611 rms_B_bonded: 1.36 r_work: 0.3466 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3328 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3328 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7864 moved from start: 0.1536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 10691 Z= 0.121 Angle : 0.568 7.292 14502 Z= 0.287 Chirality : 0.045 0.318 1758 Planarity : 0.005 0.065 1650 Dihedral : 16.668 153.248 2730 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Rotamer: Outliers : 3.15 % Allowed : 11.85 % Favored : 84.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % 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: 1.38 (0.25), residues: 1210 helix: 2.11 (0.19), residues: 804 sheet: 1.56 (0.73), residues: 50 loop : -2.15 (0.30), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 482 HIS 0.002 0.001 HIS D 698 PHE 0.016 0.001 PHE D 385 TYR 0.012 0.001 TYR C 371 ARG 0.003 0.000 ARG C 38 Details of bonding type rmsd hydrogen bonds : bond 0.04924 ( 608) hydrogen bonds : angle 3.81523 ( 1782) covalent geometry : bond 0.00247 (10690) covalent geometry : angle 0.56770 (14502) Misc. bond : bond 0.00011 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 108 time to evaluate : 0.946 Fit side-chains REVERT: D 250 ILE cc_start: 0.7801 (pt) cc_final: 0.7524 (pt) REVERT: D 442 LEU cc_start: 0.8473 (mm) cc_final: 0.8183 (mt) REVERT: D 701 GLU cc_start: 0.7386 (OUTLIER) cc_final: 0.7108 (mt-10) REVERT: C 442 LEU cc_start: 0.8463 (mm) cc_final: 0.8176 (mt) outliers start: 33 outliers final: 11 residues processed: 125 average time/residue: 0.9461 time to fit residues: 130.9543 Evaluate side-chains 116 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 104 time to evaluate : 1.130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 96 LEU Chi-restraints excluded: chain D residue 111 VAL Chi-restraints excluded: chain D residue 288 LEU Chi-restraints excluded: chain D residue 349 MET Chi-restraints excluded: chain D residue 385 PHE Chi-restraints excluded: chain D residue 545 VAL Chi-restraints excluded: chain D residue 701 GLU Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain C residue 288 LEU Chi-restraints excluded: chain C residue 349 MET Chi-restraints excluded: chain C residue 385 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 17 optimal weight: 5.9990 chunk 40 optimal weight: 0.9990 chunk 86 optimal weight: 4.9990 chunk 94 optimal weight: 1.9990 chunk 91 optimal weight: 2.9990 chunk 60 optimal weight: 4.9990 chunk 63 optimal weight: 0.9990 chunk 105 optimal weight: 4.9990 chunk 59 optimal weight: 2.9990 chunk 6 optimal weight: 3.9990 chunk 102 optimal weight: 0.4980 overall best weight: 1.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 35 GLN D 266 ASN D 289 ASN D 464 GLN D 723 HIS C 33 GLN C 35 GLN C 266 ASN C 289 ASN C 464 GLN C 723 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.173037 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.134976 restraints weight = 10667.726| |-----------------------------------------------------------------------------| r_work (start): 0.3554 rms_B_bonded: 1.49 r_work: 0.3405 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3264 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.3264 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7959 moved from start: 0.1799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 10691 Z= 0.152 Angle : 0.622 9.401 14502 Z= 0.315 Chirality : 0.046 0.312 1758 Planarity : 0.005 0.069 1650 Dihedral : 16.243 147.808 2730 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 4.01 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.79 % Favored : 94.05 % Rotamer: Outliers : 3.25 % Allowed : 11.85 % Favored : 84.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % 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: 1.19 (0.25), residues: 1210 helix: 1.96 (0.18), residues: 802 sheet: 1.39 (0.72), residues: 50 loop : -2.16 (0.30), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP D 482 HIS 0.003 0.001 HIS D 698 PHE 0.022 0.002 PHE D 385 TYR 0.020 0.002 TYR D 315 ARG 0.002 0.000 ARG D 549 Details of bonding type rmsd hydrogen bonds : bond 0.06188 ( 608) hydrogen bonds : angle 3.91343 ( 1782) covalent geometry : bond 0.00330 (10690) covalent geometry : angle 0.62182 (14502) Misc. bond : bond 0.00031 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 112 time to evaluate : 1.017 Fit side-chains REVERT: D 250 ILE cc_start: 0.7925 (pt) cc_final: 0.7717 (pt) REVERT: D 701 GLU cc_start: 0.7512 (OUTLIER) cc_final: 0.7193 (mt-10) outliers start: 34 outliers final: 12 residues processed: 128 average time/residue: 0.9917 time to fit residues: 141.4646 Evaluate side-chains 117 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 104 time to evaluate : 1.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 96 LEU Chi-restraints excluded: chain D residue 111 VAL Chi-restraints excluded: chain D residue 248 ASN Chi-restraints excluded: chain D residue 349 MET Chi-restraints excluded: chain D residue 432 MET Chi-restraints excluded: chain D residue 545 VAL Chi-restraints excluded: chain D residue 701 GLU Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain C residue 248 ASN Chi-restraints excluded: chain C residue 349 MET Chi-restraints excluded: chain C residue 432 MET Chi-restraints excluded: chain C residue 545 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 109 optimal weight: 2.9990 chunk 89 optimal weight: 0.9990 chunk 113 optimal weight: 9.9990 chunk 100 optimal weight: 0.7980 chunk 70 optimal weight: 1.9990 chunk 84 optimal weight: 1.9990 chunk 65 optimal weight: 7.9990 chunk 94 optimal weight: 0.9990 chunk 104 optimal weight: 0.8980 chunk 121 optimal weight: 4.9990 chunk 102 optimal weight: 0.0870 overall best weight: 0.7562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 35 GLN D 289 ASN C 35 GLN C 289 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.181044 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.145685 restraints weight = 10628.587| |-----------------------------------------------------------------------------| r_work (start): 0.3639 rms_B_bonded: 1.41 r_work: 0.3495 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3358 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.3358 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7869 moved from start: 0.1778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 10691 Z= 0.120 Angle : 0.566 7.886 14502 Z= 0.287 Chirality : 0.045 0.318 1758 Planarity : 0.005 0.066 1650 Dihedral : 15.400 144.438 2730 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.62 % Favored : 94.38 % Rotamer: Outliers : 3.63 % Allowed : 12.14 % Favored : 84.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % 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: 1.46 (0.25), residues: 1210 helix: 2.18 (0.19), residues: 802 sheet: 1.40 (0.71), residues: 50 loop : -2.08 (0.31), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 482 HIS 0.002 0.001 HIS C 698 PHE 0.017 0.001 PHE C 385 TYR 0.021 0.001 TYR D 315 ARG 0.001 0.000 ARG C 38 Details of bonding type rmsd hydrogen bonds : bond 0.04954 ( 608) hydrogen bonds : angle 3.77566 ( 1782) covalent geometry : bond 0.00243 (10690) covalent geometry : angle 0.56643 (14502) Misc. bond : bond 0.00008 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 103 time to evaluate : 1.438 Fit side-chains REVERT: D 155 MET cc_start: 0.7921 (OUTLIER) cc_final: 0.7708 (ttm) REVERT: D 250 ILE cc_start: 0.7896 (pt) cc_final: 0.7679 (pt) REVERT: D 442 LEU cc_start: 0.8427 (mm) cc_final: 0.8134 (mt) REVERT: D 556 TYR cc_start: 0.5893 (OUTLIER) cc_final: 0.5549 (p90) REVERT: D 701 GLU cc_start: 0.7430 (OUTLIER) cc_final: 0.7119 (mt-10) REVERT: C 442 LEU cc_start: 0.8417 (mm) cc_final: 0.8124 (mt) REVERT: C 556 TYR cc_start: 0.5893 (OUTLIER) cc_final: 0.5546 (p90) outliers start: 38 outliers final: 12 residues processed: 123 average time/residue: 1.0629 time to fit residues: 145.2439 Evaluate side-chains 120 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 104 time to evaluate : 1.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 23 SER Chi-restraints excluded: chain D residue 96 LEU Chi-restraints excluded: chain D residue 111 VAL Chi-restraints excluded: chain D residue 155 MET Chi-restraints excluded: chain D residue 219 LEU Chi-restraints excluded: chain D residue 432 MET Chi-restraints excluded: chain D residue 545 VAL Chi-restraints excluded: chain D residue 556 TYR Chi-restraints excluded: chain D residue 701 GLU Chi-restraints excluded: chain C residue 23 SER Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain C residue 432 MET Chi-restraints excluded: chain C residue 545 VAL Chi-restraints excluded: chain C residue 556 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 39 optimal weight: 0.8980 chunk 2 optimal weight: 4.9990 chunk 110 optimal weight: 0.8980 chunk 71 optimal weight: 2.9990 chunk 46 optimal weight: 5.9990 chunk 54 optimal weight: 0.2980 chunk 40 optimal weight: 0.7980 chunk 72 optimal weight: 0.5980 chunk 116 optimal weight: 5.9990 chunk 113 optimal weight: 1.9990 chunk 92 optimal weight: 0.7980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 35 GLN D 289 ASN C 35 GLN C 289 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.184898 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.150823 restraints weight = 10743.925| |-----------------------------------------------------------------------------| r_work (start): 0.3657 rms_B_bonded: 1.37 r_work: 0.3519 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3384 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.3384 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7850 moved from start: 0.1820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 10691 Z= 0.118 Angle : 0.565 8.453 14502 Z= 0.288 Chirality : 0.044 0.355 1758 Planarity : 0.005 0.060 1650 Dihedral : 14.196 141.344 2730 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 4.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.70 % Favored : 94.30 % Rotamer: Outliers : 3.15 % Allowed : 13.19 % Favored : 83.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % 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: 1.57 (0.25), residues: 1210 helix: 2.26 (0.19), residues: 804 sheet: 1.33 (0.71), residues: 50 loop : -2.02 (0.31), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 482 HIS 0.003 0.001 HIS D 698 PHE 0.019 0.001 PHE D 385 TYR 0.013 0.001 TYR C 371 ARG 0.001 0.000 ARG C 576 Details of bonding type rmsd hydrogen bonds : bond 0.04762 ( 608) hydrogen bonds : angle 3.73573 ( 1782) covalent geometry : bond 0.00237 (10690) covalent geometry : angle 0.56478 (14502) Misc. bond : bond 0.00013 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 112 time to evaluate : 1.061 Fit side-chains REVERT: D 155 MET cc_start: 0.7934 (OUTLIER) cc_final: 0.7725 (ttm) REVERT: D 250 ILE cc_start: 0.7857 (pt) cc_final: 0.7642 (pt) REVERT: D 442 LEU cc_start: 0.8470 (mm) cc_final: 0.8179 (mt) REVERT: D 701 GLU cc_start: 0.7427 (OUTLIER) cc_final: 0.7123 (mt-10) REVERT: C 442 LEU cc_start: 0.8458 (mm) cc_final: 0.8181 (mt) outliers start: 33 outliers final: 12 residues processed: 128 average time/residue: 0.8327 time to fit residues: 118.8812 Evaluate side-chains 117 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 103 time to evaluate : 1.045 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 23 SER Chi-restraints excluded: chain D residue 111 VAL Chi-restraints excluded: chain D residue 155 MET Chi-restraints excluded: chain D residue 219 LEU Chi-restraints excluded: chain D residue 432 MET Chi-restraints excluded: chain D residue 545 VAL Chi-restraints excluded: chain D residue 701 GLU Chi-restraints excluded: chain C residue 23 SER Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain C residue 349 MET Chi-restraints excluded: chain C residue 432 MET Chi-restraints excluded: chain C residue 545 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 17 optimal weight: 4.9990 chunk 6 optimal weight: 3.9990 chunk 56 optimal weight: 5.9990 chunk 99 optimal weight: 3.9990 chunk 10 optimal weight: 0.5980 chunk 41 optimal weight: 0.6980 chunk 82 optimal weight: 4.9990 chunk 68 optimal weight: 0.0870 chunk 80 optimal weight: 0.0470 chunk 75 optimal weight: 3.9990 chunk 92 optimal weight: 1.9990 overall best weight: 0.6858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 289 ASN C 35 GLN C 289 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4034 r_free = 0.4034 target = 0.186783 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.154377 restraints weight = 10663.248| |-----------------------------------------------------------------------------| r_work (start): 0.3670 rms_B_bonded: 1.49 r_work: 0.3502 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3362 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.3362 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7864 moved from start: 0.1928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 10691 Z= 0.116 Angle : 0.552 8.207 14502 Z= 0.285 Chirality : 0.043 0.316 1758 Planarity : 0.005 0.061 1650 Dihedral : 13.443 137.913 2730 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.70 % Favored : 94.30 % Rotamer: Outliers : 2.39 % Allowed : 13.67 % Favored : 83.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % 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: 1.64 (0.25), residues: 1210 helix: 2.29 (0.19), residues: 804 sheet: 1.33 (0.72), residues: 50 loop : -1.95 (0.32), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 482 HIS 0.002 0.001 HIS D 698 PHE 0.018 0.001 PHE D 385 TYR 0.018 0.001 TYR C 315 ARG 0.001 0.000 ARG C 185 Details of bonding type rmsd hydrogen bonds : bond 0.04660 ( 608) hydrogen bonds : angle 3.69652 ( 1782) covalent geometry : bond 0.00235 (10690) covalent geometry : angle 0.55167 (14502) Misc. bond : bond 0.00007 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 113 time to evaluate : 1.113 Fit side-chains REVERT: D 250 ILE cc_start: 0.7727 (pt) cc_final: 0.7526 (pt) REVERT: D 442 LEU cc_start: 0.8444 (mm) cc_final: 0.8168 (mt) REVERT: D 701 GLU cc_start: 0.7509 (OUTLIER) cc_final: 0.7198 (mt-10) REVERT: C 442 LEU cc_start: 0.8442 (mm) cc_final: 0.8165 (mt) REVERT: C 556 TYR cc_start: 0.5798 (OUTLIER) cc_final: 0.5564 (p90) outliers start: 25 outliers final: 12 residues processed: 127 average time/residue: 0.9493 time to fit residues: 132.9214 Evaluate side-chains 117 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 103 time to evaluate : 1.067 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 23 SER Chi-restraints excluded: chain D residue 111 VAL Chi-restraints excluded: chain D residue 219 LEU Chi-restraints excluded: chain D residue 273 ILE Chi-restraints excluded: chain D residue 432 MET Chi-restraints excluded: chain D residue 545 VAL Chi-restraints excluded: chain D residue 701 GLU Chi-restraints excluded: chain C residue 23 SER Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain C residue 273 ILE Chi-restraints excluded: chain C residue 432 MET Chi-restraints excluded: chain C residue 545 VAL Chi-restraints excluded: chain C residue 556 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 79 optimal weight: 4.9990 chunk 63 optimal weight: 10.0000 chunk 20 optimal weight: 0.9980 chunk 16 optimal weight: 2.9990 chunk 101 optimal weight: 0.7980 chunk 10 optimal weight: 0.7980 chunk 49 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 104 optimal weight: 1.9990 chunk 121 optimal weight: 0.1980 chunk 97 optimal weight: 10.0000 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 289 ASN D 464 GLN C 289 ASN C 464 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4038 r_free = 0.4038 target = 0.187094 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.153563 restraints weight = 10768.209| |-----------------------------------------------------------------------------| r_work (start): 0.3662 rms_B_bonded: 1.53 r_work: 0.3512 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3376 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.3376 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7851 moved from start: 0.2000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 10691 Z= 0.119 Angle : 0.556 8.657 14502 Z= 0.288 Chirality : 0.042 0.230 1758 Planarity : 0.005 0.062 1650 Dihedral : 13.016 134.913 2730 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer: Outliers : 2.29 % Allowed : 14.34 % Favored : 83.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % 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: 1.64 (0.25), residues: 1210 helix: 2.27 (0.19), residues: 806 sheet: 1.34 (0.72), residues: 50 loop : -1.91 (0.32), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 482 HIS 0.002 0.001 HIS D 698 PHE 0.017 0.001 PHE C 385 TYR 0.013 0.001 TYR C 371 ARG 0.008 0.000 ARG D 333 Details of bonding type rmsd hydrogen bonds : bond 0.04835 ( 608) hydrogen bonds : angle 3.71639 ( 1782) covalent geometry : bond 0.00244 (10690) covalent geometry : angle 0.55562 (14502) Misc. bond : bond 0.00010 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 104 time to evaluate : 1.020 Fit side-chains REVERT: D 442 LEU cc_start: 0.8477 (mm) cc_final: 0.8208 (mt) REVERT: D 701 GLU cc_start: 0.7524 (OUTLIER) cc_final: 0.7165 (mt-10) REVERT: C 442 LEU cc_start: 0.8471 (mm) cc_final: 0.8205 (mt) outliers start: 24 outliers final: 14 residues processed: 119 average time/residue: 0.8693 time to fit residues: 114.9233 Evaluate side-chains 117 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 102 time to evaluate : 0.973 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 23 SER Chi-restraints excluded: chain D residue 111 VAL Chi-restraints excluded: chain D residue 219 LEU Chi-restraints excluded: chain D residue 273 ILE Chi-restraints excluded: chain D residue 432 MET Chi-restraints excluded: chain D residue 545 VAL Chi-restraints excluded: chain D residue 684 GLN Chi-restraints excluded: chain D residue 701 GLU Chi-restraints excluded: chain C residue 23 SER Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain C residue 273 ILE Chi-restraints excluded: chain C residue 432 MET Chi-restraints excluded: chain C residue 545 VAL Chi-restraints excluded: chain C residue 684 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 16 optimal weight: 1.9990 chunk 31 optimal weight: 3.9990 chunk 118 optimal weight: 0.9990 chunk 29 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 60 optimal weight: 4.9990 chunk 14 optimal weight: 0.6980 chunk 61 optimal weight: 0.8980 chunk 102 optimal weight: 5.9990 chunk 80 optimal weight: 10.0000 chunk 101 optimal weight: 0.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 289 ASN C 289 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.181506 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.146972 restraints weight = 10635.515| |-----------------------------------------------------------------------------| r_work (start): 0.3585 rms_B_bonded: 1.36 r_work: 0.3431 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3289 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3289 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7920 moved from start: 0.2088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 10691 Z= 0.134 Angle : 0.582 9.519 14502 Z= 0.303 Chirality : 0.043 0.209 1758 Planarity : 0.005 0.067 1650 Dihedral : 12.868 131.085 2730 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.54 % Favored : 94.46 % Rotamer: Outliers : 2.10 % Allowed : 14.82 % Favored : 83.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % 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: 1.53 (0.25), residues: 1210 helix: 2.21 (0.19), residues: 802 sheet: 1.31 (0.72), residues: 50 loop : -1.96 (0.32), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 74 HIS 0.003 0.001 HIS C 698 PHE 0.022 0.001 PHE C 385 TYR 0.017 0.001 TYR C 315 ARG 0.006 0.000 ARG C 333 Details of bonding type rmsd hydrogen bonds : bond 0.05533 ( 608) hydrogen bonds : angle 3.77162 ( 1782) covalent geometry : bond 0.00284 (10690) covalent geometry : angle 0.58196 (14502) Misc. bond : bond 0.00040 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 109 time to evaluate : 1.145 Fit side-chains REVERT: D 442 LEU cc_start: 0.8513 (mm) cc_final: 0.8240 (mt) REVERT: D 556 TYR cc_start: 0.6010 (OUTLIER) cc_final: 0.5789 (p90) REVERT: D 701 GLU cc_start: 0.7562 (OUTLIER) cc_final: 0.7268 (mt-10) REVERT: C 442 LEU cc_start: 0.8496 (mm) cc_final: 0.8221 (mt) outliers start: 22 outliers final: 11 residues processed: 122 average time/residue: 0.9192 time to fit residues: 124.0118 Evaluate side-chains 115 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 102 time to evaluate : 0.936 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 23 SER Chi-restraints excluded: chain D residue 111 VAL Chi-restraints excluded: chain D residue 219 LEU Chi-restraints excluded: chain D residue 432 MET Chi-restraints excluded: chain D residue 545 VAL Chi-restraints excluded: chain D residue 556 TYR Chi-restraints excluded: chain D residue 701 GLU Chi-restraints excluded: chain C residue 23 SER Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain C residue 155 MET Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain C residue 432 MET Chi-restraints excluded: chain C residue 545 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 112 optimal weight: 4.9990 chunk 116 optimal weight: 3.9990 chunk 37 optimal weight: 2.9990 chunk 58 optimal weight: 4.9990 chunk 97 optimal weight: 10.0000 chunk 26 optimal weight: 5.9990 chunk 19 optimal weight: 2.9990 chunk 49 optimal weight: 0.9980 chunk 77 optimal weight: 0.0060 chunk 115 optimal weight: 0.5980 chunk 20 optimal weight: 0.9980 overall best weight: 1.1198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 266 ASN D 289 ASN C 266 ASN C 289 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4017 r_free = 0.4017 target = 0.184791 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.150370 restraints weight = 10571.428| |-----------------------------------------------------------------------------| r_work (start): 0.3615 rms_B_bonded: 1.59 r_work: 0.3468 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3329 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3329 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7901 moved from start: 0.2126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 10691 Z= 0.133 Angle : 0.579 9.201 14502 Z= 0.302 Chirality : 0.043 0.215 1758 Planarity : 0.005 0.069 1650 Dihedral : 12.683 128.775 2730 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 2.39 % Allowed : 15.11 % Favored : 82.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % 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 (0.25), residues: 1210 helix: 2.21 (0.19), residues: 802 sheet: 1.36 (0.72), residues: 50 loop : -1.95 (0.33), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 482 HIS 0.002 0.001 HIS D 698 PHE 0.021 0.001 PHE D 385 TYR 0.014 0.001 TYR D 371 ARG 0.007 0.000 ARG D 333 Details of bonding type rmsd hydrogen bonds : bond 0.05440 ( 608) hydrogen bonds : angle 3.77549 ( 1782) covalent geometry : bond 0.00282 (10690) covalent geometry : angle 0.57873 (14502) Misc. bond : bond 0.00042 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7079.87 seconds wall clock time: 125 minutes 37.09 seconds (7537.09 seconds total)