Starting phenix.real_space_refine on Thu Jul 2 21:17:16 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8shc_40483/07_2026/8shc_40483.cif Found real_map, /net/cci-nas-00/data/ceres_data/8shc_40483/07_2026/8shc_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_40483/07_2026/8shc_40483.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8shc_40483/07_2026/8shc_40483.map" model { file = "/net/cci-nas-00/data/ceres_data/8shc_40483/07_2026/8shc_40483.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8shc_40483/07_2026/8shc_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-dev-6108/lib/python3.11/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, 476 Ad-hoc single atom residues: {' CL': 1} Unusual residues: {'AV0': 2, 'CLR': 6, 'LBN': 9, 'NFL': 2} Classifications: {'undetermined': 19} Link IDs: {None: 18} Chain breaks: 1 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, 476 Ad-hoc single atom residues: {' CL': 1} Unusual residues: {'AV0': 2, 'CLR': 6, 'LBN': 9, 'NFL': 2} Classifications: {'undetermined': 19} Link IDs: {None: 17} Chain breaks: 1 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: 2.14, per 1000 atoms: 0.20 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: 0.75 Conformation dependent library (CDL) restraints added in 330.0 milliseconds 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: 0.17 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: 1.31 Time building geometry restraints manager: 0.94 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: 0.01 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: 0.450 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: 0.110 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 8.630 Find NCS groups from input model: 0.150 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:5.500 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7848 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 are 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/Z covalent geometry : bond 0.00466 / 0.23 (10690) covalent geometry : angle 0.69788 / 0.33 (14502) hydrogen bonds : bond 0.11888 / 7.54 ( 608) hydrogen bonds : angle 4.98518 / 3.51 ( 1782) Misc. bond : bond 0.00006 / 0.00 ( 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 : 0.291 Fit side-chains outliers start: 2 outliers final: 0 residues processed: 159 average time/residue: 0.3750 time to fit residues: 65.1899 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 : 0.281 ------------------------------------------------------------------------------- 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... D 35 GLN D 266 ASN D 656 HIS C 35 GLN C 266 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 = 0.3996 r_free = 0.3996 target = 0.182889 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.149708 restraints weight = 10609.288| |-----------------------------------------------------------------------------| r_work (start): 0.3598 rms_B_bonded: 1.48 r_work: 0.3424 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3287 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3287 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8197 moved from start: 0.1367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10691 Z= 0.161 Angle : 0.707 10.929 14502 Z= 0.343 Chirality : 0.047 0.259 1758 Planarity : 0.005 0.068 1650 Dihedral : 19.455 165.596 2730 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.12 % Favored : 94.71 % Rotamer: Outliers : 2.20 % Allowed : 8.80 % 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 are not related in a simple way. whole: 0.96 (0.25), residues: 1210 helix: 1.69 (0.18), residues: 814 sheet: 1.37 (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 C 371 PHE 0.030 0.002 PHE C 385 TRP 0.012 0.002 TRP C 482 HIS 0.006 0.001 HIS C 698 Details of bonding type rmsd/Z covalent geometry : bond 0.00344 / 0.16 (10690) covalent geometry : angle 0.70741 / 0.34 (14502) hydrogen bonds : bond 0.06418 / 4.22 ( 608) hydrogen bonds : angle 4.09293 / 2.85 ( 1782) Misc. bond : bond 0.00086 / 0.05 ( 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 136 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 113 time to evaluate : 0.241 Fit side-chains REVERT: D 250 ILE cc_start: 0.7983 (pt) cc_final: 0.7734 (pt) outliers start: 23 outliers final: 11 residues processed: 126 average time/residue: 0.3452 time to fit residues: 48.2917 Evaluate side-chains 118 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 107 time to evaluate : 0.272 ------------------------------------------------------------------------------- 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: 7.9990 chunk 26 optimal weight: 7.9990 chunk 21 optimal weight: 7.9990 chunk 71 optimal weight: 0.9990 chunk 91 optimal weight: 3.9990 chunk 2 optimal weight: 1.9990 chunk 8 optimal weight: 3.9990 chunk 19 optimal weight: 0.6980 chunk 68 optimal weight: 0.7980 chunk 99 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.4006 r_free = 0.4006 target = 0.184016 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.150327 restraints weight = 10679.820| |-----------------------------------------------------------------------------| r_work (start): 0.3576 rms_B_bonded: 1.52 r_work: 0.3415 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3274 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3274 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8171 moved from start: 0.1464 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= 0.135 Angle : 0.596 7.981 14502 Z= 0.303 Chirality : 0.045 0.274 1758 Planarity : 0.005 0.071 1650 Dihedral : 17.928 161.004 2730 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.95 % Favored : 94.05 % Rotamer: Outliers : 2.20 % Allowed : 11.09 % Favored : 86.71 % 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 are not related in a simple way. whole: 1.14 (0.25), residues: 1210 helix: 1.87 (0.19), residues: 814 sheet: 1.71 (0.74), residues: 50 loop : -2.25 (0.30), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 549 TYR 0.018 0.001 TYR D 315 PHE 0.019 0.001 PHE C 385 TRP 0.013 0.002 TRP C 482 HIS 0.008 0.001 HIS D 656 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.14 (10690) covalent geometry : angle 0.59591 / 0.30 (14502) hydrogen bonds : bond 0.05725 / 3.76 ( 608) hydrogen bonds : angle 3.96380 / 2.76 ( 1782) Misc. bond : bond 0.00027 / 0.01 ( 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 133 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 110 time to evaluate : 0.281 Fit side-chains REVERT: D 250 ILE cc_start: 0.7925 (pt) cc_final: 0.7651 (pt) REVERT: D 684 GLN cc_start: 0.7767 (OUTLIER) cc_final: 0.7520 (tt0) REVERT: C 684 GLN cc_start: 0.7771 (OUTLIER) cc_final: 0.7526 (tt0) outliers start: 23 outliers final: 13 residues processed: 124 average time/residue: 0.3415 time to fit residues: 46.8400 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 : 0.241 ------------------------------------------------------------------------------- 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: 2.9990 chunk 1 optimal weight: 0.9990 chunk 109 optimal weight: 1.9990 chunk 100 optimal weight: 6.9990 chunk 29 optimal weight: 0.1980 chunk 35 optimal weight: 2.9990 chunk 82 optimal weight: 0.0980 chunk 31 optimal weight: 4.9990 chunk 34 optimal weight: 0.7980 chunk 87 optimal weight: 0.7980 chunk 121 optimal weight: 2.9990 overall best weight: 0.5782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3993 r_free = 0.3993 target = 0.183439 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.148526 restraints weight = 10818.397| |-----------------------------------------------------------------------------| r_work (start): 0.3605 rms_B_bonded: 1.40 r_work: 0.3462 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3323 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3323 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8101 moved from start: 0.1497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 10691 Z= 0.115 Angle : 0.559 7.079 14502 Z= 0.281 Chirality : 0.044 0.314 1758 Planarity : 0.005 0.063 1650 Dihedral : 16.603 154.176 2730 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.62 % Favored : 94.38 % Rotamer: Outliers : 3.15 % Allowed : 11.09 % 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 are not related in a simple way. whole: 1.40 (0.25), residues: 1210 helix: 2.13 (0.19), residues: 804 sheet: 1.49 (0.72), residues: 50 loop : -2.15 (0.31), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 38 TYR 0.012 0.001 TYR C 371 PHE 0.014 0.001 PHE D 385 TRP 0.012 0.001 TRP D 482 HIS 0.002 0.001 HIS D 698 Details of bonding type rmsd/Z covalent geometry : bond 0.00229 / 0.12 (10690) covalent geometry : angle 0.55910 / 0.28 (14502) hydrogen bonds : bond 0.04643 / 3.06 ( 608) hydrogen bonds : angle 3.80677 / 2.64 ( 1782) Misc. bond : bond 0.00001 / 0.00 ( 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 144 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 111 time to evaluate : 0.232 Fit side-chains REVERT: D 250 ILE cc_start: 0.7746 (pt) cc_final: 0.7480 (pt) REVERT: D 442 LEU cc_start: 0.8289 (mm) cc_final: 0.7996 (mt) REVERT: D 556 TYR cc_start: 0.5867 (OUTLIER) cc_final: 0.5538 (p90) REVERT: D 701 GLU cc_start: 0.7386 (OUTLIER) cc_final: 0.7087 (mt-10) REVERT: C 442 LEU cc_start: 0.8287 (mm) cc_final: 0.7998 (mt) outliers start: 33 outliers final: 12 residues processed: 130 average time/residue: 0.3352 time to fit residues: 48.2167 Evaluate side-chains 119 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 105 time to evaluate : 0.215 ------------------------------------------------------------------------------- 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 556 TYR 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: 2.9990 chunk 78 optimal weight: 5.9990 chunk 19 optimal weight: 0.2980 chunk 24 optimal weight: 0.0570 chunk 107 optimal weight: 0.9980 chunk 114 optimal weight: 6.9990 chunk 93 optimal weight: 0.1980 chunk 119 optimal weight: 0.8980 chunk 1 optimal weight: 8.9990 chunk 15 optimal weight: 4.9990 chunk 75 optimal weight: 3.9990 overall best weight: 0.4898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3974 r_free = 0.3974 target = 0.182001 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.148049 restraints weight = 10699.439| |-----------------------------------------------------------------------------| r_work (start): 0.3645 rms_B_bonded: 1.43 r_work: 0.3471 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3333 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3333 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8097 moved from start: 0.1602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 10691 Z= 0.112 Angle : 0.547 7.587 14502 Z= 0.275 Chirality : 0.044 0.309 1758 Planarity : 0.004 0.058 1650 Dihedral : 15.552 145.264 2730 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.70 % Favored : 94.30 % Rotamer: Outliers : 2.68 % Allowed : 13.10 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.56 (0.25), residues: 1210 helix: 2.25 (0.19), residues: 804 sheet: 1.53 (0.72), 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 0.021 0.001 TYR D 315 PHE 0.012 0.001 PHE D 385 TRP 0.011 0.001 TRP C 482 HIS 0.002 0.001 HIS C 698 Details of bonding type rmsd/Z covalent geometry : bond 0.00221 / 0.11 (10690) covalent geometry : angle 0.54650 / 0.28 (14502) hydrogen bonds : bond 0.04411 / 2.91 ( 608) hydrogen bonds : angle 3.73115 / 2.59 ( 1782) Misc. bond : bond 0.00032 / 0.02 ( 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 142 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 114 time to evaluate : 0.276 Fit side-chains REVERT: D 250 ILE cc_start: 0.7805 (pt) cc_final: 0.7544 (pt) REVERT: D 442 LEU cc_start: 0.8429 (mm) cc_final: 0.8155 (mt) REVERT: D 556 TYR cc_start: 0.5799 (OUTLIER) cc_final: 0.5494 (p90) REVERT: D 701 GLU cc_start: 0.7437 (OUTLIER) cc_final: 0.7107 (mt-10) REVERT: C 442 LEU cc_start: 0.8424 (mm) cc_final: 0.8149 (mt) outliers start: 28 outliers final: 11 residues processed: 127 average time/residue: 0.3772 time to fit residues: 53.0693 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 : 0.292 ------------------------------------------------------------------------------- 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 556 TYR 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 95 optimal weight: 4.9990 chunk 48 optimal weight: 0.4980 chunk 27 optimal weight: 5.9990 chunk 20 optimal weight: 2.9990 chunk 110 optimal weight: 0.8980 chunk 40 optimal weight: 5.9990 chunk 53 optimal weight: 3.9990 chunk 80 optimal weight: 0.9980 chunk 120 optimal weight: 0.0670 chunk 113 optimal weight: 4.9990 chunk 76 optimal weight: 0.0770 overall best weight: 0.5076 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.4045 r_free = 0.4045 target = 0.188157 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.156018 restraints weight = 10767.376| |-----------------------------------------------------------------------------| r_work (start): 0.3691 rms_B_bonded: 1.45 r_work: 0.3522 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3385 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3385 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8087 moved from start: 0.1770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 10691 Z= 0.110 Angle : 0.544 7.113 14502 Z= 0.277 Chirality : 0.044 0.364 1758 Planarity : 0.004 0.058 1650 Dihedral : 14.193 141.693 2730 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.95 % Favored : 94.05 % Rotamer: Outliers : 3.35 % Allowed : 13.00 % Favored : 83.65 % 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 are not related in a simple way. whole: 1.64 (0.25), residues: 1210 helix: 2.28 (0.19), residues: 804 sheet: 1.59 (0.73), residues: 50 loop : -1.97 (0.31), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 409 TYR 0.015 0.001 TYR D 315 PHE 0.014 0.001 PHE D 385 TRP 0.011 0.001 TRP C 482 HIS 0.002 0.001 HIS C 698 Details of bonding type rmsd/Z covalent geometry : bond 0.00219 / 0.11 (10690) covalent geometry : angle 0.54351 / 0.28 (14502) hydrogen bonds : bond 0.04325 / 2.87 ( 608) hydrogen bonds : angle 3.60337 / 2.48 ( 1782) Misc. bond : bond 0.00022 / 0.01 ( 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 149 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 114 time to evaluate : 0.293 Fit side-chains REVERT: D 250 ILE cc_start: 0.7843 (pt) cc_final: 0.7570 (pt) REVERT: D 442 LEU cc_start: 0.8431 (mm) cc_final: 0.8161 (mt) REVERT: D 701 GLU cc_start: 0.7419 (OUTLIER) cc_final: 0.7069 (mt-10) REVERT: C 442 LEU cc_start: 0.8430 (mm) cc_final: 0.8157 (mt) outliers start: 35 outliers final: 11 residues processed: 130 average time/residue: 0.3723 time to fit residues: 53.8814 Evaluate side-chains 117 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 105 time to evaluate : 0.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 111 VAL Chi-restraints excluded: chain D residue 155 MET 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 155 MET Chi-restraints excluded: chain C residue 349 MET Chi-restraints excluded: chain C residue 385 PHE Chi-restraints excluded: chain C residue 432 MET 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: 0.8980 chunk 109 optimal weight: 2.9990 chunk 8 optimal weight: 3.9990 chunk 120 optimal weight: 4.9990 chunk 22 optimal weight: 0.7980 chunk 31 optimal weight: 1.9990 chunk 56 optimal weight: 5.9990 chunk 53 optimal weight: 7.9990 chunk 6 optimal weight: 3.9990 chunk 38 optimal weight: 3.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 289 ASN D 705 GLN D 723 HIS C 289 ASN C 705 GLN C 723 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.176187 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.139621 restraints weight = 10656.558| |-----------------------------------------------------------------------------| r_work (start): 0.3514 rms_B_bonded: 1.63 r_work: 0.3362 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3220 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3220 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8249 moved from start: 0.2073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 10691 Z= 0.186 Angle : 0.682 12.858 14502 Z= 0.345 Chirality : 0.048 0.396 1758 Planarity : 0.005 0.070 1650 Dihedral : 14.452 139.047 2730 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 3.97 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.54 % Favored : 94.30 % Rotamer: Outliers : 2.77 % Allowed : 13.77 % Favored : 83.46 % 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 are not related in a simple way. whole: 1.18 (0.25), residues: 1210 helix: 1.95 (0.18), residues: 798 sheet: 1.52 (0.73), residues: 50 loop : -2.15 (0.30), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 549 TYR 0.018 0.002 TYR C 371 PHE 0.021 0.002 PHE D 385 TRP 0.012 0.002 TRP C 74 HIS 0.004 0.001 HIS C 698 Details of bonding type rmsd/Z covalent geometry : bond 0.00433 / 0.19 (10690) covalent geometry : angle 0.68244 / 0.34 (14502) hydrogen bonds : bond 0.07155 / 4.73 ( 608) hydrogen bonds : angle 3.92791 / 2.71 ( 1782) Misc. bond : bond 0.00092 / 0.05 ( 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 143 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 114 time to evaluate : 0.418 Fit side-chains REVERT: D 288 LEU cc_start: 0.7497 (OUTLIER) cc_final: 0.7290 (mp) REVERT: D 385 PHE cc_start: 0.8871 (OUTLIER) cc_final: 0.8502 (m-80) REVERT: D 442 LEU cc_start: 0.8583 (mm) cc_final: 0.8279 (mt) REVERT: D 684 GLN cc_start: 0.7866 (OUTLIER) cc_final: 0.7641 (tt0) REVERT: D 701 GLU cc_start: 0.7546 (OUTLIER) cc_final: 0.7224 (mt-10) REVERT: C 288 LEU cc_start: 0.7505 (OUTLIER) cc_final: 0.7296 (mp) REVERT: C 385 PHE cc_start: 0.8880 (OUTLIER) cc_final: 0.8516 (m-80) REVERT: C 442 LEU cc_start: 0.8571 (mm) cc_final: 0.8268 (mt) REVERT: C 684 GLN cc_start: 0.7857 (OUTLIER) cc_final: 0.7635 (tt0) outliers start: 29 outliers final: 15 residues processed: 128 average time/residue: 0.4231 time to fit residues: 59.4539 Evaluate side-chains 129 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 107 time to evaluate : 0.378 ------------------------------------------------------------------------------- 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 288 LEU 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 684 GLN 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 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 545 VAL Chi-restraints excluded: chain C residue 684 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 14 optimal weight: 3.9990 chunk 52 optimal weight: 7.9990 chunk 56 optimal weight: 4.9990 chunk 19 optimal weight: 0.0970 chunk 109 optimal weight: 3.9990 chunk 35 optimal weight: 2.9990 chunk 77 optimal weight: 0.6980 chunk 87 optimal weight: 4.9990 chunk 102 optimal weight: 0.9980 chunk 46 optimal weight: 2.9990 chunk 36 optimal weight: 2.9990 overall best weight: 1.5582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 266 ASN D 289 ASN C 33 GLN C 266 ASN C 289 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.180649 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.145657 restraints weight = 10579.063| |-----------------------------------------------------------------------------| r_work (start): 0.3477 rms_B_bonded: 1.64 r_work: 0.3315 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3170 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3170 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8198 moved from start: 0.2115 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= 0.153 Angle : 0.624 9.667 14502 Z= 0.320 Chirality : 0.046 0.341 1758 Planarity : 0.005 0.075 1650 Dihedral : 14.144 139.455 2730 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.79 % Favored : 94.21 % Rotamer: Outliers : 1.91 % Allowed : 15.39 % Favored : 82.70 % 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 are not related in a simple way. whole: 1.24 (0.25), residues: 1210 helix: 1.98 (0.19), residues: 802 sheet: 1.35 (0.72), residues: 50 loop : -2.08 (0.31), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 333 TYR 0.016 0.002 TYR C 371 PHE 0.019 0.002 PHE D 385 TRP 0.012 0.002 TRP D 74 HIS 0.003 0.001 HIS C 698 Details of bonding type rmsd/Z covalent geometry : bond 0.00337 / 0.15 (10690) covalent geometry : angle 0.62421 / 0.32 (14502) hydrogen bonds : bond 0.06179 / 4.08 ( 608) hydrogen bonds : angle 3.80881 / 2.63 ( 1782) Misc. bond : bond 0.00052 / 0.03 ( 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 124 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 104 time to evaluate : 0.380 Fit side-chains REVERT: D 442 LEU cc_start: 0.8479 (mm) cc_final: 0.8184 (mt) REVERT: D 684 GLN cc_start: 0.7588 (OUTLIER) cc_final: 0.7357 (tt0) REVERT: D 701 GLU cc_start: 0.7504 (OUTLIER) cc_final: 0.7129 (mt-10) REVERT: C 134 ARG cc_start: 0.7905 (mtm-85) cc_final: 0.7652 (mtm-85) REVERT: C 442 LEU cc_start: 0.8482 (mm) cc_final: 0.8187 (mt) REVERT: C 684 GLN cc_start: 0.7586 (OUTLIER) cc_final: 0.7360 (tt0) outliers start: 20 outliers final: 13 residues processed: 113 average time/residue: 0.4824 time to fit residues: 59.6257 Evaluate side-chains 115 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 99 time to evaluate : 0.401 ------------------------------------------------------------------------------- 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 684 GLN 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 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 Chi-restraints excluded: chain C residue 684 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 51 optimal weight: 0.7980 chunk 43 optimal weight: 3.9990 chunk 53 optimal weight: 9.9990 chunk 21 optimal weight: 8.9990 chunk 31 optimal weight: 2.9990 chunk 13 optimal weight: 6.9990 chunk 70 optimal weight: 2.9990 chunk 75 optimal weight: 3.9990 chunk 12 optimal weight: 20.0000 chunk 25 optimal weight: 5.9990 chunk 117 optimal weight: 2.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3878 r_free = 0.3878 target = 0.171370 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.134730 restraints weight = 10680.346| |-----------------------------------------------------------------------------| r_work (start): 0.3489 rms_B_bonded: 1.41 r_work: 0.3329 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3185 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3185 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8303 moved from start: 0.2427 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= 0.217 Angle : 0.724 13.410 14502 Z= 0.367 Chirality : 0.049 0.338 1758 Planarity : 0.006 0.071 1650 Dihedral : 14.399 136.485 2730 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.62 % Favored : 94.21 % Rotamer: Outliers : 2.87 % Allowed : 15.30 % Favored : 81.84 % 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 are not related in a simple way. whole: 0.85 (0.25), residues: 1210 helix: 1.68 (0.18), residues: 798 sheet: 1.44 (0.72), residues: 50 loop : -2.24 (0.30), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 333 TYR 0.020 0.002 TYR C 371 PHE 0.022 0.002 PHE C 385 TRP 0.016 0.002 TRP D 74 HIS 0.005 0.001 HIS D 698 Details of bonding type rmsd/Z covalent geometry : bond 0.00514 / 0.22 (10690) covalent geometry : angle 0.72359 / 0.37 (14502) hydrogen bonds : bond 0.08080 / 5.35 ( 608) hydrogen bonds : angle 4.06780 / 2.81 ( 1782) Misc. bond : bond 0.00106 / 0.06 ( 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 136 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 106 time to evaluate : 0.356 Fit side-chains REVERT: D 684 GLN cc_start: 0.7931 (OUTLIER) cc_final: 0.7523 (tt0) REVERT: D 701 GLU cc_start: 0.7569 (OUTLIER) cc_final: 0.7205 (mt-10) REVERT: C 134 ARG cc_start: 0.8075 (mtm-85) cc_final: 0.7836 (mtm-85) REVERT: C 503 MET cc_start: 0.8239 (OUTLIER) cc_final: 0.7576 (mmt) REVERT: C 684 GLN cc_start: 0.7949 (OUTLIER) cc_final: 0.7552 (tt0) outliers start: 30 outliers final: 20 residues processed: 119 average time/residue: 0.4914 time to fit residues: 63.9265 Evaluate side-chains 127 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 103 time to evaluate : 0.380 ------------------------------------------------------------------------------- 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 219 LEU Chi-restraints excluded: chain D residue 248 ASN 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 684 GLN 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 219 LEU Chi-restraints excluded: chain C residue 248 ASN 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 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 22 optimal weight: 8.9990 chunk 68 optimal weight: 0.0870 chunk 37 optimal weight: 2.9990 chunk 119 optimal weight: 0.6980 chunk 90 optimal weight: 6.9990 chunk 86 optimal weight: 5.9990 chunk 50 optimal weight: 0.9990 chunk 32 optimal weight: 0.7980 chunk 98 optimal weight: 2.9990 chunk 42 optimal weight: 0.5980 chunk 62 optimal weight: 1.9990 overall best weight: 0.6360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3995 r_free = 0.3995 target = 0.182606 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.148394 restraints weight = 10539.717| |-----------------------------------------------------------------------------| r_work (start): 0.3593 rms_B_bonded: 1.36 r_work: 0.3445 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3302 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.3302 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8157 moved from start: 0.2144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 10691 Z= 0.121 Angle : 0.574 7.550 14502 Z= 0.297 Chirality : 0.043 0.217 1758 Planarity : 0.005 0.064 1650 Dihedral : 13.576 135.586 2730 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.54 % Favored : 94.46 % Rotamer: Outliers : 1.53 % Allowed : 17.11 % Favored : 81.36 % 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 are not related in a simple way. whole: 1.44 (0.25), residues: 1210 helix: 2.13 (0.19), residues: 802 sheet: 1.39 (0.72), residues: 50 loop : -2.00 (0.32), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 333 TYR 0.012 0.001 TYR C 323 PHE 0.012 0.001 PHE C 401 TRP 0.017 0.002 TRP C 482 HIS 0.001 0.001 HIS C 698 Details of bonding type rmsd/Z covalent geometry : bond 0.00246 / 0.12 (10690) covalent geometry : angle 0.57376 / 0.30 (14502) hydrogen bonds : bond 0.05019 / 3.31 ( 608) hydrogen bonds : angle 3.76005 / 2.60 ( 1782) Misc. bond : bond 0.00005 / 0.00 ( 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: 16 poor density : 104 time to evaluate : 0.377 Fit side-chains REVERT: D 250 ILE cc_start: 0.7837 (pt) cc_final: 0.7622 (pt) REVERT: D 701 GLU cc_start: 0.7495 (OUTLIER) cc_final: 0.7131 (mt-10) outliers start: 16 outliers final: 11 residues processed: 113 average time/residue: 0.4901 time to fit residues: 60.6866 Evaluate side-chains 114 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 102 time to evaluate : 0.292 ------------------------------------------------------------------------------- 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 273 ILE 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 111 VAL Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain C residue 248 ASN Chi-restraints excluded: chain C residue 273 ILE 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: 0.8980 chunk 56 optimal weight: 0.2980 chunk 25 optimal weight: 7.9990 chunk 70 optimal weight: 0.5980 chunk 115 optimal weight: 1.9990 chunk 33 optimal weight: 3.9990 chunk 30 optimal weight: 2.9990 chunk 71 optimal weight: 0.5980 chunk 68 optimal weight: 0.4980 chunk 67 optimal weight: 0.9980 chunk 121 optimal weight: 2.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 289 ASN C 289 ASN C 464 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4021 r_free = 0.4021 target = 0.185299 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.152795 restraints weight = 10654.039| |-----------------------------------------------------------------------------| r_work (start): 0.3686 rms_B_bonded: 1.50 r_work: 0.3507 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3365 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.3365 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8132 moved from start: 0.2139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 10691 Z= 0.118 Angle : 0.560 8.640 14502 Z= 0.291 Chirality : 0.043 0.204 1758 Planarity : 0.005 0.057 1650 Dihedral : 12.854 130.708 2730 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.29 % Favored : 94.71 % Rotamer: Outliers : 1.53 % Allowed : 16.63 % Favored : 81.84 % 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 are not related in a simple way. whole: 1.60 (0.25), residues: 1210 helix: 2.24 (0.19), residues: 804 sheet: 1.31 (0.72), residues: 50 loop : -1.90 (0.33), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 333 TYR 0.020 0.001 TYR D 315 PHE 0.014 0.001 PHE C 385 TRP 0.013 0.001 TRP C 482 HIS 0.002 0.001 HIS D 698 Details of bonding type rmsd/Z covalent geometry : bond 0.00237 / 0.12 (10690) covalent geometry : angle 0.56018 / 0.29 (14502) hydrogen bonds : bond 0.04816 / 3.19 ( 608) hydrogen bonds : angle 3.66593 / 2.52 ( 1782) Misc. bond : bond 0.00001 / 0.00 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2809.77 seconds wall clock time: 48 minutes 39.26 seconds (2919.26 seconds total)