Starting phenix.real_space_refine on Sat Aug 23 06:46:16 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8shc_40483/08_2025/8shc_40483.cif Found real_map, /net/cci-nas-00/data/ceres_data/8shc_40483/08_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_40483/08_2025/8shc_40483.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8shc_40483/08_2025/8shc_40483.map" model { file = "/net/cci-nas-00/data/ceres_data/8shc_40483/08_2025/8shc_40483.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8shc_40483/08_2025/8shc_40483.cif" } resolution = 3.0 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= 0.041 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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-1': 7, 'LBN:plan-3': 7, 'LBN:plan-2': 6} 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-1': 7, 'LBN:plan-3': 7, 'LBN:plan-2': 6} Unresolved non-hydrogen planarities: 72 Time building chain proxies: 3.00, per 1000 atoms: 0.29 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: 0.89 Conformation dependent library (CDL) restraints added in 410.1 milliseconds Enol-peptide restraints added in 1.2 microseconds 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: 0.26 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: 1.72 Time building geometry restraints manager: 1.19 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: 0.02 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: 0.540 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: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 10.870 Find NCS groups from input model: 0.350 Set up NCS constraints: 0.020 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:6.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.460 ------------------------------------------------------------------------------- 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 : 6.97 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 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: 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 ARG 0.002 0.000 ARG D 409 TYR 0.013 0.001 TYR C 323 PHE 0.026 0.001 PHE C 385 TRP 0.011 0.001 TRP C 482 HIS 0.003 0.001 HIS D 698 Details of bonding type rmsd covalent geometry : bond 0.00466 (10690) covalent geometry : angle 0.69788 (14502) hydrogen bonds : bond 0.11888 ( 608) hydrogen bonds : angle 4.98518 ( 1782) 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 : 0.366 Fit side-chains outliers start: 2 outliers final: 0 residues processed: 159 average time/residue: 0.4647 time to fit residues: 80.4669 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 : 0.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 108 optimal weight: 0.0370 chunk 49 optimal weight: 2.9990 chunk 97 optimal weight: 7.9990 chunk 113 optimal weight: 8.9990 chunk 53 optimal weight: 7.9990 chunk 5 optimal weight: 8.9990 chunk 33 optimal weight: 4.9990 chunk 65 optimal weight: 0.2980 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 0.8980 chunk 117 optimal weight: 3.9990 overall best weight: 1.4462 ------------------------------------------------------------------------------- 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 656 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.182926 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.149534 restraints weight = 10605.249| |-----------------------------------------------------------------------------| r_work (start): 0.3595 rms_B_bonded: 1.53 r_work: 0.3429 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3289 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.3289 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7927 moved from start: 0.1356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10691 Z= 0.160 Angle : 0.709 10.757 14502 Z= 0.344 Chirality : 0.047 0.265 1758 Planarity : 0.005 0.067 1650 Dihedral : 19.519 165.364 2730 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.21 % Favored : 94.63 % Rotamer: Outliers : 2.29 % Allowed : 8.70 % Favored : 89.01 % 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: 0.97 (0.25), residues: 1210 helix: 1.69 (0.19), residues: 814 sheet: 1.36 (0.75), residues: 54 loop : -2.17 (0.31), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 38 TYR 0.013 0.002 TYR D 20 PHE 0.031 0.002 PHE C 385 TRP 0.012 0.002 TRP C 482 HIS 0.005 0.001 HIS C 698 Details of bonding type rmsd covalent geometry : bond 0.00342 (10690) covalent geometry : angle 0.70935 (14502) hydrogen bonds : bond 0.06405 ( 608) hydrogen bonds : angle 4.09122 ( 1782) Misc. bond : bond 0.00087 ( 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: 24 poor density : 113 time to evaluate : 0.285 Fit side-chains REVERT: D 250 ILE cc_start: 0.7982 (pt) cc_final: 0.7738 (pt) outliers start: 24 outliers final: 11 residues processed: 127 average time/residue: 0.4042 time to fit residues: 56.6401 Evaluate side-chains 119 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 108 time to evaluate : 0.362 ------------------------------------------------------------------------------- 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 321 LYS 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 321 LYS Chi-restraints excluded: chain C residue 349 MET 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 5 optimal weight: 0.9980 chunk 26 optimal weight: 6.9990 chunk 21 optimal weight: 2.9990 chunk 71 optimal weight: 0.9980 chunk 91 optimal weight: 2.9990 chunk 2 optimal weight: 3.9990 chunk 8 optimal weight: 4.9990 chunk 19 optimal weight: 0.9990 chunk 68 optimal weight: 0.1980 chunk 99 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 overall best weight: 1.2384 ------------------------------------------------------------------------------- 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 = 0.3920 r_free = 0.3920 target = 0.176649 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.139544 restraints weight = 10753.631| |-----------------------------------------------------------------------------| r_work (start): 0.3558 rms_B_bonded: 1.65 r_work: 0.3400 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3253 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3253 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7944 moved from start: 0.1511 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= 0.141 Angle : 0.605 8.266 14502 Z= 0.307 Chirality : 0.046 0.279 1758 Planarity : 0.005 0.071 1650 Dihedral : 17.937 160.648 2730 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.79 % Favored : 94.21 % Rotamer: Outliers : 2.39 % Allowed : 11.09 % Favored : 86.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % 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: 1.09 (0.25), residues: 1210 helix: 1.83 (0.19), residues: 814 sheet: 1.69 (0.74), residues: 50 loop : -2.26 (0.30), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 549 TYR 0.019 0.002 TYR D 315 PHE 0.021 0.001 PHE C 385 TRP 0.013 0.002 TRP D 482 HIS 0.009 0.002 HIS D 656 Details of bonding type rmsd covalent geometry : bond 0.00299 (10690) covalent geometry : angle 0.60489 (14502) hydrogen bonds : bond 0.05887 ( 608) hydrogen bonds : angle 3.97252 ( 1782) Misc. bond : bond 0.00032 ( 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 135 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 110 time to evaluate : 0.462 Fit side-chains REVERT: D 250 ILE cc_start: 0.7924 (pt) cc_final: 0.7705 (pt) REVERT: D 684 GLN cc_start: 0.7807 (OUTLIER) cc_final: 0.7566 (tt0) REVERT: C 684 GLN cc_start: 0.7808 (OUTLIER) cc_final: 0.7565 (tt0) outliers start: 25 outliers final: 13 residues processed: 126 average time/residue: 0.4283 time to fit residues: 59.6301 Evaluate side-chains 119 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 104 time to evaluate : 0.390 ------------------------------------------------------------------------------- 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 432 MET 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 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 110 optimal weight: 5.9990 chunk 1 optimal weight: 0.9990 chunk 109 optimal weight: 0.0870 chunk 100 optimal weight: 5.9990 chunk 29 optimal weight: 0.8980 chunk 35 optimal weight: 3.9990 chunk 82 optimal weight: 6.9990 chunk 31 optimal weight: 3.9990 chunk 34 optimal weight: 2.9990 chunk 87 optimal weight: 0.9980 chunk 121 optimal weight: 0.9990 overall best weight: 0.7962 ------------------------------------------------------------------------------- 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 = 0.4009 r_free = 0.4009 target = 0.184524 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.150110 restraints weight = 10767.483| |-----------------------------------------------------------------------------| r_work (start): 0.3603 rms_B_bonded: 1.38 r_work: 0.3457 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3319 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3319 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7878 moved from start: 0.1563 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= 0.122 Angle : 0.571 7.321 14502 Z= 0.289 Chirality : 0.045 0.316 1758 Planarity : 0.005 0.065 1650 Dihedral : 16.587 154.673 2730 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 4.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.79 % Favored : 94.21 % Rotamer: Outliers : 3.25 % Allowed : 10.99 % Favored : 85.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % 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: 1.29 (0.25), residues: 1210 helix: 2.00 (0.19), residues: 814 sheet: 1.44 (0.72), residues: 50 loop : -2.20 (0.31), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 38 TYR 0.013 0.001 TYR C 371 PHE 0.016 0.001 PHE C 385 TRP 0.012 0.001 TRP D 482 HIS 0.002 0.001 HIS D 698 Details of bonding type rmsd covalent geometry : bond 0.00248 (10690) covalent geometry : angle 0.57148 (14502) hydrogen bonds : bond 0.05046 ( 608) hydrogen bonds : angle 3.83588 ( 1782) Misc. bond : bond 0.00006 ( 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 140 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 106 time to evaluate : 0.336 Fit side-chains REVERT: D 250 ILE cc_start: 0.7808 (pt) cc_final: 0.7554 (pt) REVERT: D 442 LEU cc_start: 0.8324 (mm) cc_final: 0.8028 (mt) REVERT: D 701 GLU cc_start: 0.7415 (OUTLIER) cc_final: 0.7124 (mt-10) REVERT: C 442 LEU cc_start: 0.8316 (mm) cc_final: 0.8025 (mt) outliers start: 34 outliers final: 12 residues processed: 124 average time/residue: 0.3969 time to fit residues: 54.1447 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 : 0.307 ------------------------------------------------------------------------------- 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 Chi-restraints excluded: chain C residue 545 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 35 optimal weight: 3.9990 chunk 78 optimal weight: 5.9990 chunk 19 optimal weight: 0.0030 chunk 24 optimal weight: 0.0020 chunk 107 optimal weight: 2.9990 chunk 114 optimal weight: 9.9990 chunk 93 optimal weight: 0.3980 chunk 119 optimal weight: 0.9990 chunk 1 optimal weight: 0.9990 chunk 15 optimal weight: 4.9990 chunk 75 optimal weight: 4.9990 overall best weight: 0.4802 ------------------------------------------------------------------------------- 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 C 35 GLN C 266 ASN C 289 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.182252 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.148707 restraints weight = 10701.176| |-----------------------------------------------------------------------------| r_work (start): 0.3650 rms_B_bonded: 1.51 r_work: 0.3485 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3344 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3344 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7839 moved from start: 0.1642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 10691 Z= 0.113 Angle : 0.547 7.505 14502 Z= 0.276 Chirality : 0.044 0.302 1758 Planarity : 0.005 0.059 1650 Dihedral : 15.668 146.085 2730 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.95 % Favored : 94.05 % Rotamer: Outliers : 3.25 % Allowed : 11.95 % Favored : 84.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % 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: 1.52 (0.25), residues: 1210 helix: 2.22 (0.19), residues: 804 sheet: 1.43 (0.71), residues: 50 loop : -2.07 (0.31), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 38 TYR 0.020 0.001 TYR D 315 PHE 0.012 0.001 PHE D 385 TRP 0.012 0.001 TRP D 482 HIS 0.002 0.001 HIS C 698 Details of bonding type rmsd covalent geometry : bond 0.00222 (10690) covalent geometry : angle 0.54742 (14502) hydrogen bonds : bond 0.04432 ( 608) hydrogen bonds : angle 3.74074 ( 1782) Misc. bond : bond 0.00029 ( 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 145 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 111 time to evaluate : 0.457 Fit side-chains REVERT: D 250 ILE cc_start: 0.7831 (pt) cc_final: 0.7567 (pt) REVERT: D 442 LEU cc_start: 0.8424 (mm) cc_final: 0.8144 (mt) REVERT: D 701 GLU cc_start: 0.7421 (OUTLIER) cc_final: 0.7103 (mt-10) REVERT: C 442 LEU cc_start: 0.8414 (mm) cc_final: 0.8136 (mt) outliers start: 34 outliers final: 12 residues processed: 126 average time/residue: 0.3964 time to fit residues: 55.4574 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 : 0.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 385 PHE 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 111 VAL Chi-restraints excluded: chain C residue 248 ASN 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 545 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 95 optimal weight: 3.9990 chunk 48 optimal weight: 2.9990 chunk 27 optimal weight: 7.9990 chunk 20 optimal weight: 0.9980 chunk 110 optimal weight: 0.4980 chunk 40 optimal weight: 4.9990 chunk 53 optimal weight: 0.9990 chunk 80 optimal weight: 0.6980 chunk 120 optimal weight: 4.9990 chunk 113 optimal weight: 0.9990 chunk 76 optimal weight: 3.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- 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 464 GLN C 35 GLN C 289 ASN C 464 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.182656 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.147482 restraints weight = 10704.355| |-----------------------------------------------------------------------------| r_work (start): 0.3640 rms_B_bonded: 1.56 r_work: 0.3493 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3357 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3357 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7864 moved from start: 0.1767 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= 0.123 Angle : 0.576 9.168 14502 Z= 0.291 Chirality : 0.044 0.348 1758 Planarity : 0.005 0.063 1650 Dihedral : 14.875 142.147 2730 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 3.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.79 % Favored : 94.21 % Rotamer: Outliers : 3.15 % Allowed : 13.00 % Favored : 83.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % 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: 1.53 (0.25), residues: 1210 helix: 2.21 (0.19), residues: 804 sheet: 1.46 (0.72), residues: 50 loop : -2.00 (0.31), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 38 TYR 0.013 0.001 TYR C 371 PHE 0.018 0.001 PHE D 385 TRP 0.010 0.001 TRP C 482 HIS 0.002 0.001 HIS C 698 Details of bonding type rmsd covalent geometry : bond 0.00250 (10690) covalent geometry : angle 0.57644 (14502) hydrogen bonds : bond 0.05051 ( 608) hydrogen bonds : angle 3.75559 ( 1782) Misc. bond : bond 0.00000 ( 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: 33 poor density : 108 time to evaluate : 0.317 Fit side-chains REVERT: D 250 ILE cc_start: 0.7915 (pt) cc_final: 0.7700 (pt) REVERT: D 442 LEU cc_start: 0.8483 (mm) cc_final: 0.8217 (mt) REVERT: D 701 GLU cc_start: 0.7456 (OUTLIER) cc_final: 0.7112 (mt-10) REVERT: C 442 LEU cc_start: 0.8470 (mm) cc_final: 0.8204 (mt) outliers start: 33 outliers final: 12 residues processed: 125 average time/residue: 0.3885 time to fit residues: 53.8656 Evaluate side-chains 116 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 103 time to evaluate : 0.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 111 VAL Chi-restraints excluded: chain D residue 219 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 701 GLU 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 385 PHE Chi-restraints excluded: chain C residue 432 MET Chi-restraints excluded: chain C residue 545 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 0 optimal weight: 10.0000 chunk 81 optimal weight: 0.9990 chunk 109 optimal weight: 2.9990 chunk 8 optimal weight: 3.9990 chunk 120 optimal weight: 3.9990 chunk 22 optimal weight: 3.9990 chunk 31 optimal weight: 1.9990 chunk 56 optimal weight: 3.9990 chunk 53 optimal weight: 6.9990 chunk 6 optimal weight: 3.9990 chunk 38 optimal weight: 1.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 289 ASN D 705 GLN D 723 HIS C 35 GLN C 289 ASN C 705 GLN C 723 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.173236 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.136519 restraints weight = 10704.051| |-----------------------------------------------------------------------------| r_work (start): 0.3545 rms_B_bonded: 1.57 r_work: 0.3377 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3233 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3233 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8025 moved from start: 0.2118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 10691 Z= 0.197 Angle : 0.692 12.486 14502 Z= 0.349 Chirality : 0.048 0.381 1758 Planarity : 0.006 0.070 1650 Dihedral : 15.102 140.458 2730 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.79 % Favored : 94.05 % Rotamer: Outliers : 3.15 % Allowed : 13.48 % 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 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: 1.06 (0.25), residues: 1210 helix: 1.88 (0.18), residues: 798 sheet: 1.35 (0.72), residues: 50 loop : -2.22 (0.30), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 549 TYR 0.019 0.002 TYR C 371 PHE 0.021 0.002 PHE D 385 TRP 0.012 0.002 TRP D 74 HIS 0.004 0.001 HIS D 698 Details of bonding type rmsd covalent geometry : bond 0.00461 (10690) covalent geometry : angle 0.69195 (14502) hydrogen bonds : bond 0.07387 ( 608) hydrogen bonds : angle 4.00077 ( 1782) Misc. bond : bond 0.00095 ( 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 149 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 116 time to evaluate : 0.404 Fit side-chains REVERT: D 556 TYR cc_start: 0.6420 (OUTLIER) cc_final: 0.6207 (p90) REVERT: D 701 GLU cc_start: 0.7561 (OUTLIER) cc_final: 0.7207 (mt-10) REVERT: C 556 TYR cc_start: 0.6425 (OUTLIER) cc_final: 0.6215 (p90) outliers start: 33 outliers final: 21 residues processed: 134 average time/residue: 0.4667 time to fit residues: 68.5024 Evaluate side-chains 132 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 108 time to evaluate : 0.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 23 SER Chi-restraints excluded: chain D residue 80 ILE Chi-restraints excluded: chain D residue 96 LEU 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 349 MET Chi-restraints excluded: chain D residue 370 VAL 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 556 TYR Chi-restraints excluded: chain D residue 701 GLU Chi-restraints excluded: chain C residue 23 SER Chi-restraints excluded: chain C residue 80 ILE 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 273 ILE 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 545 VAL Chi-restraints excluded: chain C residue 556 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 14 optimal weight: 2.9990 chunk 52 optimal weight: 6.9990 chunk 56 optimal weight: 1.9990 chunk 19 optimal weight: 10.0000 chunk 109 optimal weight: 3.9990 chunk 35 optimal weight: 0.7980 chunk 77 optimal weight: 1.9990 chunk 87 optimal weight: 3.9990 chunk 102 optimal weight: 4.9990 chunk 46 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 289 ASN C 33 GLN 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 = 0.3902 r_free = 0.3902 target = 0.173975 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.136200 restraints weight = 10589.171| |-----------------------------------------------------------------------------| r_work (start): 0.3436 rms_B_bonded: 1.50 r_work: 0.3275 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3127 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3127 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7963 moved from start: 0.2171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 10691 Z= 0.162 Angle : 0.642 10.411 14502 Z= 0.326 Chirality : 0.047 0.375 1758 Planarity : 0.005 0.073 1650 Dihedral : 14.716 141.200 2730 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.79 % Favored : 94.05 % Rotamer: Outliers : 2.77 % Allowed : 15.01 % Favored : 82.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % 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: 1.13 (0.25), residues: 1210 helix: 1.94 (0.19), residues: 798 sheet: 1.25 (0.72), residues: 50 loop : -2.19 (0.30), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 333 TYR 0.015 0.002 TYR C 371 PHE 0.020 0.002 PHE D 385 TRP 0.013 0.002 TRP D 74 HIS 0.003 0.001 HIS D 698 Details of bonding type rmsd covalent geometry : bond 0.00363 (10690) covalent geometry : angle 0.64222 (14502) hydrogen bonds : bond 0.06518 ( 608) hydrogen bonds : angle 3.91351 ( 1782) Misc. bond : bond 0.00059 ( 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 134 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 105 time to evaluate : 0.360 Fit side-chains REVERT: D 491 ILE cc_start: 0.8032 (pp) cc_final: 0.7791 (pt) REVERT: D 701 GLU cc_start: 0.7553 (OUTLIER) cc_final: 0.7182 (mt-10) REVERT: C 491 ILE cc_start: 0.8015 (pp) cc_final: 0.7784 (pt) outliers start: 29 outliers final: 19 residues processed: 121 average time/residue: 0.4949 time to fit residues: 65.6630 Evaluate side-chains 123 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 103 time to evaluate : 0.371 ------------------------------------------------------------------------------- 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 219 LEU Chi-restraints excluded: chain D residue 273 ILE 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 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 273 ILE Chi-restraints excluded: chain C residue 349 MET Chi-restraints excluded: chain C residue 370 VAL Chi-restraints excluded: chain C residue 385 PHE Chi-restraints excluded: chain C residue 432 MET Chi-restraints excluded: chain C residue 545 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 51 optimal weight: 0.9980 chunk 43 optimal weight: 2.9990 chunk 53 optimal weight: 7.9990 chunk 21 optimal weight: 10.0000 chunk 31 optimal weight: 0.7980 chunk 13 optimal weight: 6.9990 chunk 70 optimal weight: 5.9990 chunk 75 optimal weight: 3.9990 chunk 12 optimal weight: 20.0000 chunk 25 optimal weight: 4.9990 chunk 117 optimal weight: 2.9990 overall best weight: 2.3586 ------------------------------------------------------------------------------- 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 35 GLN C 289 ASN C 464 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.176047 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.140622 restraints weight = 10684.971| |-----------------------------------------------------------------------------| r_work (start): 0.3435 rms_B_bonded: 1.62 r_work: 0.3271 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3124 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3124 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8009 moved from start: 0.2412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 10691 Z= 0.197 Angle : 0.697 12.407 14502 Z= 0.353 Chirality : 0.048 0.381 1758 Planarity : 0.006 0.070 1650 Dihedral : 14.609 138.699 2730 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.95 % Favored : 93.88 % Rotamer: Outliers : 3.25 % Allowed : 14.82 % Favored : 81.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % 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: 0.91 (0.25), residues: 1210 helix: 1.75 (0.18), residues: 798 sheet: 1.35 (0.72), residues: 50 loop : -2.25 (0.30), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 333 TYR 0.017 0.002 TYR C 371 PHE 0.021 0.002 PHE C 385 TRP 0.016 0.002 TRP C 74 HIS 0.004 0.001 HIS D 698 Details of bonding type rmsd covalent geometry : bond 0.00456 (10690) covalent geometry : angle 0.69734 (14502) hydrogen bonds : bond 0.07635 ( 608) hydrogen bonds : angle 4.05977 ( 1782) Misc. bond : bond 0.00082 ( 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 139 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 105 time to evaluate : 0.381 Fit side-chains REVERT: D 491 ILE cc_start: 0.8132 (pp) cc_final: 0.7924 (pt) REVERT: D 701 GLU cc_start: 0.7559 (OUTLIER) cc_final: 0.7177 (mt-10) REVERT: C 503 MET cc_start: 0.8167 (OUTLIER) cc_final: 0.7543 (mmt) outliers start: 34 outliers final: 20 residues processed: 122 average time/residue: 0.5109 time to fit residues: 68.2601 Evaluate side-chains 126 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 104 time to evaluate : 0.371 ------------------------------------------------------------------------------- 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 219 LEU Chi-restraints excluded: chain D residue 273 ILE Chi-restraints excluded: chain D residue 349 MET Chi-restraints excluded: chain D residue 370 VAL 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 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 273 ILE Chi-restraints excluded: chain C residue 349 MET Chi-restraints excluded: chain C residue 370 VAL Chi-restraints excluded: chain C residue 385 PHE Chi-restraints excluded: chain C residue 432 MET Chi-restraints excluded: chain C residue 503 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 22 optimal weight: 6.9990 chunk 68 optimal weight: 0.0970 chunk 37 optimal weight: 1.9990 chunk 119 optimal weight: 0.7980 chunk 90 optimal weight: 0.0000 chunk 86 optimal weight: 5.9990 chunk 50 optimal weight: 0.9980 chunk 32 optimal weight: 0.9980 chunk 98 optimal weight: 2.9990 chunk 42 optimal weight: 0.5980 chunk 62 optimal weight: 4.9990 overall best weight: 0.4982 ------------------------------------------------------------------------------- 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 = 0.4026 r_free = 0.4026 target = 0.185981 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.154056 restraints weight = 10592.555| |-----------------------------------------------------------------------------| r_work (start): 0.3719 rms_B_bonded: 1.41 r_work: 0.3555 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3423 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.3423 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7833 moved from start: 0.2127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 10691 Z= 0.119 Angle : 0.561 7.388 14502 Z= 0.289 Chirality : 0.043 0.264 1758 Planarity : 0.005 0.061 1650 Dihedral : 13.652 137.195 2730 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.37 % Favored : 94.63 % Rotamer: Outliers : 1.24 % Allowed : 17.59 % Favored : 81.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % 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: 1.46 (0.25), residues: 1210 helix: 2.18 (0.19), residues: 802 sheet: 1.22 (0.71), residues: 50 loop : -2.04 (0.32), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 333 TYR 0.011 0.001 TYR C 371 PHE 0.013 0.001 PHE D 555 TRP 0.017 0.002 TRP C 482 HIS 0.002 0.001 HIS C 698 Details of bonding type rmsd covalent geometry : bond 0.00230 (10690) covalent geometry : angle 0.56122 (14502) hydrogen bonds : bond 0.04684 ( 608) hydrogen bonds : angle 3.75175 ( 1782) Misc. bond : bond 0.00013 ( 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 120 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 107 time to evaluate : 0.414 Fit side-chains REVERT: D 250 ILE cc_start: 0.7744 (pt) cc_final: 0.7509 (pt) REVERT: D 442 LEU cc_start: 0.8371 (mm) cc_final: 0.8099 (mt) REVERT: D 701 GLU cc_start: 0.7459 (OUTLIER) cc_final: 0.7109 (mt-10) REVERT: C 442 LEU cc_start: 0.8380 (mm) cc_final: 0.8122 (mt) outliers start: 13 outliers final: 6 residues processed: 114 average time/residue: 0.5311 time to fit residues: 66.1731 Evaluate side-chains 111 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 104 time to evaluate : 0.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 219 LEU 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 219 LEU Chi-restraints excluded: chain C residue 385 PHE 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 109 optimal weight: 4.9990 chunk 56 optimal weight: 0.6980 chunk 25 optimal weight: 6.9990 chunk 70 optimal weight: 7.9990 chunk 115 optimal weight: 0.6980 chunk 33 optimal weight: 4.9990 chunk 30 optimal weight: 3.9990 chunk 71 optimal weight: 0.0980 chunk 68 optimal weight: 0.6980 chunk 67 optimal weight: 0.9980 chunk 121 optimal weight: 2.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 289 ASN C 266 ASN C 289 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.182896 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.148296 restraints weight = 10581.783| |-----------------------------------------------------------------------------| r_work (start): 0.3639 rms_B_bonded: 1.37 r_work: 0.3500 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3364 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3364 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7869 moved from start: 0.2137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 10691 Z= 0.119 Angle : 0.553 8.582 14502 Z= 0.288 Chirality : 0.043 0.213 1758 Planarity : 0.005 0.061 1650 Dihedral : 13.142 133.585 2730 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Rotamer: Outliers : 1.34 % Allowed : 17.11 % Favored : 81.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % 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: 1.58 (0.25), residues: 1210 helix: 2.26 (0.19), residues: 802 sheet: 1.23 (0.72), residues: 50 loop : -1.94 (0.32), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 333 TYR 0.020 0.001 TYR C 315 PHE 0.015 0.001 PHE D 385 TRP 0.014 0.001 TRP C 482 HIS 0.002 0.001 HIS C 698 Details of bonding type rmsd covalent geometry : bond 0.00241 (10690) covalent geometry : angle 0.55286 (14502) hydrogen bonds : bond 0.04927 ( 608) hydrogen bonds : angle 3.71692 ( 1782) Misc. bond : bond 0.00002 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3092.79 seconds wall clock time: 53 minutes 37.57 seconds (3217.57 seconds total)