Starting phenix.real_space_refine on Sat Nov 16 04:36:56 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8shc_40483/11_2024/8shc_40483.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8shc_40483/11_2024/8shc_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8shc_40483/11_2024/8shc_40483.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8shc_40483/11_2024/8shc_40483.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8shc_40483/11_2024/8shc_40483.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8shc_40483/11_2024/8shc_40483.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.041 sd= 0.266 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians P 6 5.49 5 S 36 5.16 5 Cl 2 4.86 5 C 7056 2.51 5 N 1550 2.21 5 O 1802 1.98 5 F 12 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 10464 Number of models: 1 Model: "" Number of chains: 4 Chain: "D" Number of atoms: 4755 Number of conformers: 1 Conformer: "" Number of residues, atoms: 613, 4755 Classifications: {'peptide': 613} Link IDs: {'PTRANS': 24, 'TRANS': 588} Chain breaks: 3 Chain: "C" Number of atoms: 4755 Number of conformers: 1 Conformer: "" Number of residues, atoms: 613, 4755 Classifications: {'peptide': 613} Link IDs: {'PTRANS': 24, 'TRANS': 588} Chain breaks: 3 Chain: "D" Number of atoms: 477 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 477 Unusual residues: {' CL': 1, 'AV0': 2, 'CLR': 6, 'LBN': 9, 'NFL': 2} Classifications: {'undetermined': 20} Link IDs: {None: 19} Unresolved non-hydrogen bonds: 340 Unresolved non-hydrogen angles: 420 Unresolved non-hydrogen dihedrals: 351 Unresolved non-hydrogen chiralities: 17 Planarities with less than four sites: {'LBN:plan-2': 6, 'LBN:plan-3': 7, 'LBN:plan-1': 7} Unresolved non-hydrogen planarities: 72 Chain: "C" Number of atoms: 477 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 477 Unusual residues: {' CL': 1, 'AV0': 2, 'CLR': 6, 'LBN': 9, 'NFL': 2} Classifications: {'undetermined': 20} Link IDs: {None: 19} Unresolved non-hydrogen bonds: 340 Unresolved non-hydrogen angles: 420 Unresolved non-hydrogen dihedrals: 351 Unresolved non-hydrogen chiralities: 17 Planarities with less than four sites: {'LBN:plan-2': 6, 'LBN:plan-3': 7, 'LBN:plan-1': 7} Unresolved non-hydrogen planarities: 72 Time building chain proxies: 6.94, per 1000 atoms: 0.66 Number of scatterers: 10464 At special positions: 0 Unit cell: (122.1, 73.7, 107.8, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Cl 2 17.00 S 36 16.00 P 6 15.00 F 12 9.00 O 1802 8.00 N 1550 7.00 C 7056 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.17 Conformation dependent library (CDL) restraints added in 1.4 seconds 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2288 Finding SS restraints... Secondary structure from input PDB file: 62 helices and 3 sheets defined 71.5% alpha, 4.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.11 Creating SS restraints... Processing helix chain 'D' and resid 28 through 36 Processing helix chain 'D' and resid 70 through 74 removed outlier: 3.724A pdb=" N ASP D 73 " --> pdb=" O PRO D 70 " (cutoff:3.500A) Processing helix chain 'D' and resid 79 through 106 removed outlier: 4.183A pdb=" N LEU D 84 " --> pdb=" O ILE D 80 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N LEU D 85 " --> pdb=" O LYS D 81 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N SER D 86 " --> pdb=" O GLU D 82 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N LEU D 100 " --> pdb=" O LEU D 96 " (cutoff:3.500A) Processing helix chain 'D' and resid 114 through 131 removed outlier: 3.916A pdb=" N TYR D 118 " --> pdb=" O GLY D 114 " (cutoff:3.500A) Proline residue: D 123 - end of helix removed outlier: 4.543A pdb=" N ILE D 129 " --> pdb=" O LEU D 125 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N PHE D 130 " --> pdb=" O THR D 126 " (cutoff:3.500A) Processing helix chain 'D' and resid 141 through 156 removed outlier: 3.841A pdb=" N SER D 145 " --> pdb=" O PHE D 141 " (cutoff:3.500A) Processing helix chain 'D' and resid 157 through 162 Processing helix chain 'D' and resid 177 through 206 Processing helix chain 'D' and resid 209 through 215 removed outlier: 4.077A pdb=" N VAL D 212 " --> pdb=" O GLY D 209 " (cutoff:3.500A) Processing helix chain 'D' and resid 216 through 241 removed outlier: 3.505A pdb=" N ASN D 241 " --> pdb=" O LYS D 237 " (cutoff:3.500A) Processing helix chain 'D' and resid 251 through 264 Processing helix chain 'D' and resid 265 through 267 No H-bonds generated for 'chain 'D' and resid 265 through 267' Processing helix chain 'D' and resid 268 through 292 Processing helix chain 'D' and resid 301 through 318 Processing helix chain 'D' and resid 318 through 323 removed outlier: 3.531A pdb=" N ASN D 322 " --> pdb=" O ASN D 318 " (cutoff:3.500A) Processing helix chain 'D' and resid 342 through 348 removed outlier: 3.897A pdb=" N LEU D 345 " --> pdb=" O PRO D 342 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N SER D 347 " --> pdb=" O SER D 344 " (cutoff:3.500A) Processing helix chain 'D' and resid 349 through 376 removed outlier: 4.006A pdb=" N SER D 355 " --> pdb=" O THR D 351 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LYS D 374 " --> pdb=" O VAL D 370 " (cutoff:3.500A) Processing helix chain 'D' and resid 380 through 397 Processing helix chain 'D' and resid 406 through 416 removed outlier: 3.696A pdb=" N THR D 416 " --> pdb=" O VAL D 412 " (cutoff:3.500A) Processing helix chain 'D' and resid 421 through 437 Processing helix chain 'D' and resid 439 through 443 removed outlier: 3.636A pdb=" N LEU D 442 " --> pdb=" O GLY D 439 " (cutoff:3.500A) Processing helix chain 'D' and resid 446 through 457 removed outlier: 3.952A pdb=" N LEU D 450 " --> pdb=" O GLN D 446 " (cutoff:3.500A) Processing helix chain 'D' and resid 458 through 463 Processing helix chain 'D' and resid 466 through 475 removed outlier: 4.560A pdb=" N ARG D 470 " --> pdb=" O CYS D 466 " (cutoff:3.500A) Processing helix chain 'D' and resid 475 through 491 removed outlier: 3.513A pdb=" N ALA D 479 " --> pdb=" O ASN D 475 " (cutoff:3.500A) Processing helix chain 'D' and resid 493 through 515 Processing helix chain 'D' and resid 533 through 537 removed outlier: 4.201A pdb=" N LYS D 537 " --> pdb=" O THR D 533 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 533 through 537' Processing helix chain 'D' and resid 555 through 571 Processing helix chain 'D' and resid 573 through 585 removed outlier: 3.697A pdb=" N VAL D 577 " --> pdb=" O ASP D 573 " (cutoff:3.500A) Processing helix chain 'D' and resid 669 through 686 removed outlier: 3.839A pdb=" N ILE D 686 " --> pdb=" O GLU D 682 " (cutoff:3.500A) Processing helix chain 'D' and resid 696 through 706 Processing helix chain 'D' and resid 723 through 731 Processing helix chain 'C' and resid 28 through 36 Processing helix chain 'C' and resid 70 through 74 removed outlier: 3.721A pdb=" N ASP C 73 " --> pdb=" O PRO C 70 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 106 removed outlier: 4.183A pdb=" N LEU C 84 " --> pdb=" O ILE C 80 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N LEU C 85 " --> pdb=" O LYS C 81 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N SER C 86 " --> pdb=" O GLU C 82 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N LEU C 100 " --> pdb=" O LEU C 96 " (cutoff:3.500A) Processing helix chain 'C' and resid 114 through 131 removed outlier: 3.917A pdb=" N TYR C 118 " --> pdb=" O GLY C 114 " (cutoff:3.500A) Proline residue: C 123 - end of helix removed outlier: 4.542A pdb=" N ILE C 129 " --> pdb=" O LEU C 125 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N PHE C 130 " --> pdb=" O THR C 126 " (cutoff:3.500A) Processing helix chain 'C' and resid 141 through 156 removed outlier: 3.843A pdb=" N SER C 145 " --> pdb=" O PHE C 141 " (cutoff:3.500A) Processing helix chain 'C' and resid 157 through 162 Processing helix chain 'C' and resid 177 through 206 Processing helix chain 'C' and resid 209 through 215 removed outlier: 4.076A pdb=" N VAL C 212 " --> pdb=" O GLY C 209 " (cutoff:3.500A) Processing helix chain 'C' and resid 216 through 241 removed outlier: 3.504A pdb=" N ASN C 241 " --> pdb=" O LYS C 237 " (cutoff:3.500A) Processing helix chain 'C' and resid 251 through 264 Processing helix chain 'C' and resid 265 through 267 No H-bonds generated for 'chain 'C' and resid 265 through 267' Processing helix chain 'C' and resid 268 through 292 Processing helix chain 'C' and resid 301 through 318 Processing helix chain 'C' and resid 318 through 323 removed outlier: 3.531A pdb=" N ASN C 322 " --> pdb=" O ASN C 318 " (cutoff:3.500A) Processing helix chain 'C' and resid 342 through 348 removed outlier: 3.897A pdb=" N LEU C 345 " --> pdb=" O PRO C 342 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N SER C 347 " --> pdb=" O SER C 344 " (cutoff:3.500A) Processing helix chain 'C' and resid 349 through 376 removed outlier: 4.010A pdb=" N SER C 355 " --> pdb=" O THR C 351 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LYS C 374 " --> pdb=" O VAL C 370 " (cutoff:3.500A) Processing helix chain 'C' and resid 380 through 397 Processing helix chain 'C' and resid 406 through 416 removed outlier: 3.696A pdb=" N THR C 416 " --> pdb=" O VAL C 412 " (cutoff:3.500A) Processing helix chain 'C' and resid 421 through 437 Processing helix chain 'C' and resid 439 through 443 removed outlier: 3.636A pdb=" N LEU C 442 " --> pdb=" O GLY C 439 " (cutoff:3.500A) Processing helix chain 'C' and resid 446 through 457 removed outlier: 3.952A pdb=" N LEU C 450 " --> pdb=" O GLN C 446 " (cutoff:3.500A) Processing helix chain 'C' and resid 458 through 463 Processing helix chain 'C' and resid 466 through 475 removed outlier: 4.560A pdb=" N ARG C 470 " --> pdb=" O CYS C 466 " (cutoff:3.500A) Processing helix chain 'C' and resid 475 through 491 removed outlier: 3.514A pdb=" N ALA C 479 " --> pdb=" O ASN C 475 " (cutoff:3.500A) Processing helix chain 'C' and resid 493 through 515 Processing helix chain 'C' and resid 533 through 537 removed outlier: 4.197A pdb=" N LYS C 537 " --> pdb=" O THR C 533 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 533 through 537' Processing helix chain 'C' and resid 555 through 571 Processing helix chain 'C' and resid 573 through 585 removed outlier: 3.697A pdb=" N VAL C 577 " --> pdb=" O ASP C 573 " (cutoff:3.500A) Processing helix chain 'C' and resid 669 through 686 removed outlier: 3.838A pdb=" N ILE C 686 " --> pdb=" O GLU C 682 " (cutoff:3.500A) Processing helix chain 'C' and resid 696 through 706 Processing helix chain 'C' and resid 723 through 731 Processing sheet with id=AA1, first strand: chain 'D' and resid 19 through 25 removed outlier: 3.718A pdb=" N VAL D 22 " --> pdb=" O VAL C 22 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N VAL C 22 " --> pdb=" O VAL D 22 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 530 through 532 removed outlier: 4.399A pdb=" N SER D 517 " --> pdb=" O SER D 551 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N ILE D 547 " --> pdb=" O LEU D 521 " (cutoff:3.500A) removed outlier: 9.072A pdb=" N SER D 523 " --> pdb=" O VAL D 545 " (cutoff:3.500A) removed outlier: 12.888A pdb=" N VAL D 545 " --> pdb=" O SER D 523 " (cutoff:3.500A) removed outlier: 6.195A pdb=" N LYS D 546 " --> pdb=" O VAL D 659 " (cutoff:3.500A) removed outlier: 7.385A pdb=" N ASP D 661 " --> pdb=" O LYS D 546 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N LEU D 548 " --> pdb=" O ASP D 661 " (cutoff:3.500A) removed outlier: 8.789A pdb=" N PHE D 719 " --> pdb=" O VAL D 690 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N PHE D 692 " --> pdb=" O PHE D 719 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 530 through 532 removed outlier: 4.399A pdb=" N SER C 517 " --> pdb=" O SER C 551 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N ILE C 547 " --> pdb=" O LEU C 521 " (cutoff:3.500A) removed outlier: 9.073A pdb=" N SER C 523 " --> pdb=" O VAL C 545 " (cutoff:3.500A) removed outlier: 12.888A pdb=" N VAL C 545 " --> pdb=" O SER C 523 " (cutoff:3.500A) removed outlier: 6.195A pdb=" N LYS C 546 " --> pdb=" O VAL C 659 " (cutoff:3.500A) removed outlier: 7.384A pdb=" N ASP C 661 " --> pdb=" O LYS C 546 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N LEU C 548 " --> pdb=" O ASP C 661 " (cutoff:3.500A) removed outlier: 8.789A pdb=" N PHE C 719 " --> pdb=" O VAL C 690 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N PHE C 692 " --> pdb=" O PHE C 719 " (cutoff:3.500A) 608 hydrogen bonds defined for protein. 1782 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.38 Time building geometry restraints manager: 3.53 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: 0.00 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: 0.350 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.380 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 26.530 Find NCS groups from input model: 0.650 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:13.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.090 ------------------------------------------------------------------------------- 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 10690 Z= 0.282 Angle : 0.698 10.599 14502 Z= 0.329 Chirality : 0.170 4.860 1758 Planarity : 0.010 0.233 1650 Dihedral : 21.902 169.148 4878 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.87 % Favored : 94.13 % Rotamer: Outliers : 0.19 % Allowed : 0.29 % Favored : 99.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.04 (0.25), residues: 1210 helix: 1.80 (0.19), residues: 796 sheet: 1.68 (0.79), residues: 54 loop : -2.16 (0.31), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 482 HIS 0.003 0.001 HIS D 698 PHE 0.026 0.001 PHE C 385 TYR 0.013 0.001 TYR C 323 ARG 0.002 0.000 ARG D 409 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 159 time to evaluate : 1.032 Fit side-chains outliers start: 2 outliers final: 0 residues processed: 159 average time/residue: 1.0203 time to fit residues: 177.3652 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 : 1.120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 103 optimal weight: 0.6980 chunk 92 optimal weight: 0.8980 chunk 51 optimal weight: 5.9990 chunk 31 optimal weight: 2.9990 chunk 62 optimal weight: 2.9990 chunk 49 optimal weight: 2.9990 chunk 95 optimal weight: 1.9990 chunk 37 optimal weight: 3.9990 chunk 58 optimal weight: 0.8980 chunk 71 optimal weight: 0.4980 chunk 110 optimal weight: 1.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 35 GLN D 266 ASN D 289 ASN D 656 HIS C 35 GLN C 266 ASN C 289 ASN C 656 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7674 moved from start: 0.1154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10690 Z= 0.195 Angle : 0.672 11.015 14502 Z= 0.324 Chirality : 0.045 0.229 1758 Planarity : 0.005 0.063 1650 Dihedral : 19.557 164.614 2730 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.29 % Favored : 94.71 % Rotamer: Outliers : 2.10 % Allowed : 9.18 % Favored : 88.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.17 (0.25), residues: 1210 helix: 1.90 (0.19), residues: 802 sheet: 1.93 (0.77), residues: 50 loop : -2.14 (0.31), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 482 HIS 0.004 0.001 HIS C 698 PHE 0.026 0.001 PHE C 385 TYR 0.012 0.001 TYR C 371 ARG 0.003 0.000 ARG C 38 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 115 time to evaluate : 1.058 Fit side-chains REVERT: D 250 ILE cc_start: 0.7793 (pt) cc_final: 0.7498 (pt) outliers start: 22 outliers final: 10 residues processed: 129 average time/residue: 0.8410 time to fit residues: 121.2486 Evaluate side-chains 120 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 110 time to evaluate : 1.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 80 ILE Chi-restraints excluded: chain D residue 111 VAL Chi-restraints excluded: chain D residue 349 MET Chi-restraints excluded: chain D residue 724 ASP Chi-restraints excluded: chain C residue 80 ILE Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain C residue 155 MET Chi-restraints excluded: chain C residue 349 MET Chi-restraints excluded: chain C residue 532 SER Chi-restraints excluded: chain C residue 724 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 61 optimal weight: 0.9990 chunk 34 optimal weight: 5.9990 chunk 92 optimal weight: 3.9990 chunk 75 optimal weight: 4.9990 chunk 30 optimal weight: 3.9990 chunk 110 optimal weight: 5.9990 chunk 119 optimal weight: 5.9990 chunk 98 optimal weight: 4.9990 chunk 37 optimal weight: 4.9990 chunk 89 optimal weight: 7.9990 chunk 109 optimal weight: 3.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- 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 D 705 GLN D 723 HIS C 33 GLN C 35 GLN C 289 ASN C 656 HIS C 705 GLN C 723 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7874 moved from start: 0.2119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 10690 Z= 0.419 Angle : 0.809 15.387 14502 Z= 0.408 Chirality : 0.052 0.283 1758 Planarity : 0.006 0.073 1650 Dihedral : 19.197 170.288 2730 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.45 % Favored : 94.38 % Rotamer: Outliers : 4.59 % Allowed : 9.18 % Favored : 86.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.30 (0.24), residues: 1210 helix: 1.21 (0.18), residues: 822 sheet: 1.54 (0.72), residues: 50 loop : -2.66 (0.28), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.003 TRP C 74 HIS 0.009 0.002 HIS D 656 PHE 0.030 0.003 PHE D 385 TYR 0.022 0.002 TYR C 371 ARG 0.005 0.001 ARG C 549 *********************** 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 161 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 113 time to evaluate : 1.074 Fit side-chains REVERT: D 464 GLN cc_start: 0.8642 (OUTLIER) cc_final: 0.8306 (mt0) REVERT: D 684 GLN cc_start: 0.7780 (OUTLIER) cc_final: 0.7326 (tt0) REVERT: C 464 GLN cc_start: 0.8634 (OUTLIER) cc_final: 0.8314 (mt0) REVERT: C 503 MET cc_start: 0.6955 (OUTLIER) cc_final: 0.6165 (mmt) REVERT: C 684 GLN cc_start: 0.7776 (OUTLIER) cc_final: 0.7323 (tt0) outliers start: 48 outliers final: 24 residues processed: 137 average time/residue: 1.0767 time to fit residues: 160.9246 Evaluate side-chains 136 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 107 time to evaluate : 1.119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 80 ILE Chi-restraints excluded: chain D residue 96 LEU Chi-restraints excluded: chain D residue 103 MET Chi-restraints excluded: chain D residue 111 VAL Chi-restraints excluded: chain D residue 248 ASN Chi-restraints excluded: chain D residue 288 LEU Chi-restraints excluded: chain D residue 343 ILE Chi-restraints excluded: chain D residue 349 MET Chi-restraints excluded: chain D residue 370 VAL Chi-restraints excluded: chain D residue 432 MET Chi-restraints excluded: chain D residue 464 GLN Chi-restraints excluded: chain D residue 545 VAL Chi-restraints excluded: chain D residue 684 GLN Chi-restraints excluded: chain D residue 724 ASP Chi-restraints excluded: chain C residue 80 ILE Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 103 MET 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 343 ILE Chi-restraints excluded: chain C residue 349 MET Chi-restraints excluded: chain C residue 370 VAL Chi-restraints excluded: chain C residue 432 MET Chi-restraints excluded: chain C residue 464 GLN Chi-restraints excluded: chain C residue 503 MET Chi-restraints excluded: chain C residue 545 VAL 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 83 optimal weight: 8.9990 chunk 57 optimal weight: 0.7980 chunk 12 optimal weight: 6.9990 chunk 52 optimal weight: 6.9990 chunk 74 optimal weight: 2.9990 chunk 111 optimal weight: 0.9980 chunk 117 optimal weight: 1.9990 chunk 58 optimal weight: 0.9980 chunk 105 optimal weight: 0.9990 chunk 31 optimal weight: 0.6980 chunk 98 optimal weight: 6.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7747 moved from start: 0.1851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10690 Z= 0.175 Angle : 0.605 8.064 14502 Z= 0.309 Chirality : 0.046 0.317 1758 Planarity : 0.005 0.070 1650 Dihedral : 17.996 176.600 2730 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.79 % Favored : 94.21 % Rotamer: Outliers : 3.44 % Allowed : 12.62 % Favored : 83.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.98 (0.25), residues: 1210 helix: 1.84 (0.19), residues: 798 sheet: 1.28 (0.71), residues: 50 loop : -2.32 (0.30), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP C 482 HIS 0.002 0.001 HIS C 698 PHE 0.014 0.001 PHE C 385 TYR 0.009 0.001 TYR C 315 ARG 0.003 0.000 ARG C 38 *********************** 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: 36 poor density : 108 time to evaluate : 1.233 Fit side-chains REVERT: D 250 ILE cc_start: 0.7817 (pt) cc_final: 0.7573 (pt) REVERT: D 684 GLN cc_start: 0.7561 (OUTLIER) cc_final: 0.7246 (tt0) REVERT: D 701 GLU cc_start: 0.6847 (OUTLIER) cc_final: 0.6592 (mt-10) REVERT: C 503 MET cc_start: 0.6948 (OUTLIER) cc_final: 0.6198 (mmt) REVERT: C 684 GLN cc_start: 0.7560 (OUTLIER) cc_final: 0.7248 (tt0) outliers start: 36 outliers final: 17 residues processed: 126 average time/residue: 1.0824 time to fit residues: 149.5099 Evaluate side-chains 125 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 104 time to evaluate : 1.026 ------------------------------------------------------------------------------- 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 313 ILE 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 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 155 MET Chi-restraints excluded: chain C residue 248 ASN 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 503 MET Chi-restraints excluded: chain C residue 545 VAL Chi-restraints excluded: chain C residue 556 TYR Chi-restraints excluded: chain C residue 684 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 66 optimal weight: 8.9990 chunk 1 optimal weight: 8.9990 chunk 87 optimal weight: 5.9990 chunk 48 optimal weight: 0.5980 chunk 100 optimal weight: 0.9980 chunk 81 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 60 optimal weight: 4.9990 chunk 105 optimal weight: 0.4980 chunk 29 optimal weight: 0.7980 chunk 39 optimal weight: 5.9990 overall best weight: 1.5782 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7788 moved from start: 0.2008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 10690 Z= 0.232 Angle : 0.644 10.959 14502 Z= 0.325 Chirality : 0.047 0.322 1758 Planarity : 0.005 0.070 1650 Dihedral : 17.132 160.726 2730 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.79 % Favored : 94.05 % Rotamer: Outliers : 3.35 % Allowed : 13.48 % Favored : 83.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.00 (0.25), residues: 1210 helix: 1.86 (0.19), residues: 798 sheet: 1.17 (0.71), residues: 50 loop : -2.28 (0.30), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 482 HIS 0.003 0.001 HIS C 698 PHE 0.019 0.002 PHE D 385 TYR 0.017 0.002 TYR C 315 ARG 0.005 0.000 ARG C 333 *********************** 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: 35 poor density : 110 time to evaluate : 1.152 Fit side-chains REVERT: D 250 ILE cc_start: 0.7883 (pt) cc_final: 0.7641 (pt) REVERT: D 684 GLN cc_start: 0.7613 (OUTLIER) cc_final: 0.7263 (tt0) REVERT: D 701 GLU cc_start: 0.6947 (OUTLIER) cc_final: 0.6663 (mt-10) REVERT: C 503 MET cc_start: 0.6964 (OUTLIER) cc_final: 0.6216 (mmt) REVERT: C 684 GLN cc_start: 0.7610 (OUTLIER) cc_final: 0.7259 (tt0) REVERT: C 701 GLU cc_start: 0.7093 (OUTLIER) cc_final: 0.6764 (mt-10) outliers start: 35 outliers final: 18 residues processed: 130 average time/residue: 1.0819 time to fit residues: 153.5554 Evaluate side-chains 129 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 106 time to evaluate : 1.174 ------------------------------------------------------------------------------- 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 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 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 288 LEU Chi-restraints excluded: chain C residue 349 MET Chi-restraints excluded: chain C residue 385 PHE Chi-restraints excluded: chain C residue 503 MET Chi-restraints excluded: chain C residue 545 VAL Chi-restraints excluded: chain C residue 556 TYR Chi-restraints excluded: chain C residue 684 GLN Chi-restraints excluded: chain C residue 701 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 106 optimal weight: 0.7980 chunk 23 optimal weight: 1.9990 chunk 69 optimal weight: 0.8980 chunk 29 optimal weight: 0.1980 chunk 118 optimal weight: 4.9990 chunk 97 optimal weight: 5.9990 chunk 54 optimal weight: 5.9990 chunk 9 optimal weight: 0.7980 chunk 39 optimal weight: 2.9990 chunk 61 optimal weight: 0.9990 chunk 113 optimal weight: 0.6980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 35 GLN D 266 ASN D 289 ASN D 464 GLN C 35 GLN C 266 ASN C 289 ASN C 464 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7698 moved from start: 0.1886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 10690 Z= 0.161 Angle : 0.571 7.381 14502 Z= 0.291 Chirality : 0.045 0.277 1758 Planarity : 0.005 0.063 1650 Dihedral : 16.015 160.106 2730 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.62 % Favored : 94.38 % Rotamer: Outliers : 3.25 % Allowed : 13.67 % Favored : 83.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.37 (0.25), residues: 1210 helix: 2.13 (0.19), residues: 802 sheet: 1.28 (0.71), residues: 50 loop : -2.16 (0.31), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 482 HIS 0.002 0.001 HIS C 698 PHE 0.012 0.001 PHE C 385 TYR 0.011 0.001 TYR C 371 ARG 0.004 0.000 ARG C 333 *********************** 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: 34 poor density : 107 time to evaluate : 1.165 Fit side-chains REVERT: D 250 ILE cc_start: 0.7685 (pt) cc_final: 0.7443 (pt) REVERT: D 442 LEU cc_start: 0.8519 (mm) cc_final: 0.8278 (mt) REVERT: D 684 GLN cc_start: 0.7410 (OUTLIER) cc_final: 0.7208 (tt0) REVERT: D 701 GLU cc_start: 0.7011 (OUTLIER) cc_final: 0.6675 (mt-10) REVERT: C 442 LEU cc_start: 0.8510 (mm) cc_final: 0.8272 (mt) REVERT: C 684 GLN cc_start: 0.7409 (OUTLIER) cc_final: 0.7185 (tt0) REVERT: C 701 GLU cc_start: 0.7109 (OUTLIER) cc_final: 0.6853 (mt-10) outliers start: 34 outliers final: 11 residues processed: 125 average time/residue: 1.0734 time to fit residues: 147.4309 Evaluate side-chains 123 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 108 time to evaluate : 1.111 ------------------------------------------------------------------------------- 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 385 PHE 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 385 PHE Chi-restraints excluded: chain C residue 545 VAL Chi-restraints excluded: chain C residue 684 GLN Chi-restraints excluded: chain C residue 701 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 13 optimal weight: 7.9990 chunk 67 optimal weight: 3.9990 chunk 86 optimal weight: 5.9990 chunk 66 optimal weight: 3.9990 chunk 99 optimal weight: 6.9990 chunk 65 optimal weight: 10.0000 chunk 117 optimal weight: 5.9990 chunk 73 optimal weight: 0.3980 chunk 71 optimal weight: 0.5980 chunk 54 optimal weight: 8.9990 chunk 72 optimal weight: 0.7980 overall best weight: 1.9584 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7806 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 0.040 10690 Z= 0.259 Angle : 0.671 11.990 14502 Z= 0.339 Chirality : 0.047 0.262 1758 Planarity : 0.006 0.070 1650 Dihedral : 15.938 158.842 2730 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.62 % Favored : 94.21 % Rotamer: Outliers : 3.25 % Allowed : 13.86 % Favored : 82.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.06 (0.25), residues: 1210 helix: 1.90 (0.18), residues: 798 sheet: 1.24 (0.71), residues: 50 loop : -2.27 (0.30), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 74 HIS 0.004 0.001 HIS C 698 PHE 0.019 0.002 PHE D 385 TYR 0.016 0.002 TYR C 371 ARG 0.006 0.001 ARG D 333 *********************** 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 140 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 106 time to evaluate : 1.164 Fit side-chains REVERT: D 288 LEU cc_start: 0.8016 (OUTLIER) cc_final: 0.7786 (mp) REVERT: D 385 PHE cc_start: 0.8789 (OUTLIER) cc_final: 0.8424 (m-80) REVERT: D 491 ILE cc_start: 0.8076 (pp) cc_final: 0.7811 (pt) REVERT: D 684 GLN cc_start: 0.7500 (OUTLIER) cc_final: 0.7107 (tt0) REVERT: D 701 GLU cc_start: 0.6984 (OUTLIER) cc_final: 0.6658 (mt-10) REVERT: C 288 LEU cc_start: 0.8012 (OUTLIER) cc_final: 0.7784 (mp) REVERT: C 491 ILE cc_start: 0.8062 (pp) cc_final: 0.7819 (pt) REVERT: C 503 MET cc_start: 0.6918 (OUTLIER) cc_final: 0.6145 (mmt) REVERT: C 684 GLN cc_start: 0.7494 (OUTLIER) cc_final: 0.7088 (tt0) REVERT: C 701 GLU cc_start: 0.7153 (OUTLIER) cc_final: 0.6896 (mt-10) outliers start: 34 outliers final: 14 residues processed: 125 average time/residue: 1.0504 time to fit residues: 143.9867 Evaluate side-chains 124 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 102 time to evaluate : 1.178 ------------------------------------------------------------------------------- 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 248 ASN 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 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 503 MET Chi-restraints excluded: chain C residue 545 VAL Chi-restraints excluded: chain C residue 684 GLN Chi-restraints excluded: chain C residue 701 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 46 optimal weight: 2.9990 chunk 70 optimal weight: 0.7980 chunk 35 optimal weight: 1.9990 chunk 23 optimal weight: 0.9990 chunk 22 optimal weight: 6.9990 chunk 74 optimal weight: 5.9990 chunk 80 optimal weight: 0.0000 chunk 58 optimal weight: 4.9990 chunk 10 optimal weight: 0.6980 chunk 92 optimal weight: 2.9990 chunk 106 optimal weight: 1.9990 overall best weight: 0.8988 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7729 moved from start: 0.2012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 10690 Z= 0.174 Angle : 0.593 8.055 14502 Z= 0.302 Chirality : 0.045 0.305 1758 Planarity : 0.005 0.065 1650 Dihedral : 15.332 159.763 2730 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.70 % Favored : 94.30 % Rotamer: Outliers : 2.68 % Allowed : 14.82 % Favored : 82.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.36 (0.25), residues: 1210 helix: 2.11 (0.19), residues: 802 sheet: 1.22 (0.71), residues: 50 loop : -2.11 (0.31), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 482 HIS 0.002 0.001 HIS D 698 PHE 0.015 0.001 PHE D 385 TYR 0.013 0.001 TYR C 371 ARG 0.006 0.000 ARG D 333 *********************** 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 136 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 108 time to evaluate : 1.310 Fit side-chains REVERT: D 250 ILE cc_start: 0.7790 (pt) cc_final: 0.7536 (pt) REVERT: D 684 GLN cc_start: 0.7363 (OUTLIER) cc_final: 0.7066 (tt0) REVERT: D 701 GLU cc_start: 0.7063 (OUTLIER) cc_final: 0.6738 (mt-10) REVERT: C 491 ILE cc_start: 0.7783 (pp) cc_final: 0.7572 (pt) REVERT: C 684 GLN cc_start: 0.7361 (OUTLIER) cc_final: 0.7061 (tt0) outliers start: 28 outliers final: 17 residues processed: 125 average time/residue: 1.1136 time to fit residues: 153.4287 Evaluate side-chains 126 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 106 time to evaluate : 1.156 ------------------------------------------------------------------------------- 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 248 ASN 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 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 273 ILE Chi-restraints excluded: chain C residue 349 MET Chi-restraints excluded: chain C residue 385 PHE 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 112 optimal weight: 5.9990 chunk 102 optimal weight: 5.9990 chunk 109 optimal weight: 0.0970 chunk 65 optimal weight: 3.9990 chunk 47 optimal weight: 2.9990 chunk 86 optimal weight: 6.9990 chunk 33 optimal weight: 1.9990 chunk 99 optimal weight: 4.9990 chunk 103 optimal weight: 2.9990 chunk 71 optimal weight: 1.9990 chunk 115 optimal weight: 4.9990 overall best weight: 2.0186 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7809 moved from start: 0.2260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 10690 Z= 0.263 Angle : 0.672 11.872 14502 Z= 0.341 Chirality : 0.047 0.323 1758 Planarity : 0.005 0.068 1650 Dihedral : 15.266 159.667 2730 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.62 % Favored : 94.21 % Rotamer: Outliers : 3.15 % Allowed : 14.15 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.10 (0.25), residues: 1210 helix: 1.92 (0.19), residues: 798 sheet: 1.23 (0.72), residues: 50 loop : -2.22 (0.31), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP D 74 HIS 0.004 0.001 HIS C 698 PHE 0.019 0.002 PHE D 385 TYR 0.016 0.002 TYR D 371 ARG 0.007 0.001 ARG D 333 *********************** 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 138 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 105 time to evaluate : 1.073 Fit side-chains REVERT: D 684 GLN cc_start: 0.7465 (OUTLIER) cc_final: 0.7083 (tt0) REVERT: D 701 GLU cc_start: 0.7103 (OUTLIER) cc_final: 0.6713 (mt-10) REVERT: C 503 MET cc_start: 0.6922 (OUTLIER) cc_final: 0.6148 (mmt) REVERT: C 684 GLN cc_start: 0.7459 (OUTLIER) cc_final: 0.7073 (tt0) outliers start: 33 outliers final: 17 residues processed: 124 average time/residue: 1.0756 time to fit residues: 146.2950 Evaluate side-chains 125 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 104 time to evaluate : 1.205 ------------------------------------------------------------------------------- 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 248 ASN 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 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 273 ILE Chi-restraints excluded: chain C residue 349 MET Chi-restraints excluded: chain C residue 385 PHE 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 70 optimal weight: 0.9990 chunk 54 optimal weight: 5.9990 chunk 80 optimal weight: 0.5980 chunk 121 optimal weight: 3.9990 chunk 111 optimal weight: 0.8980 chunk 96 optimal weight: 1.9990 chunk 10 optimal weight: 0.9990 chunk 74 optimal weight: 6.9990 chunk 59 optimal weight: 3.9990 chunk 76 optimal weight: 2.9990 chunk 103 optimal weight: 4.9990 overall best weight: 1.0986 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7750 moved from start: 0.2181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 10690 Z= 0.188 Angle : 0.609 8.769 14502 Z= 0.312 Chirality : 0.045 0.356 1758 Planarity : 0.005 0.068 1650 Dihedral : 14.714 160.081 2730 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.70 % Favored : 94.30 % Rotamer: Outliers : 2.58 % Allowed : 15.01 % Favored : 82.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.32 (0.25), residues: 1210 helix: 2.08 (0.19), residues: 802 sheet: 1.18 (0.72), residues: 50 loop : -2.12 (0.32), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP C 482 HIS 0.002 0.001 HIS C 698 PHE 0.017 0.001 PHE C 385 TYR 0.014 0.001 TYR C 371 ARG 0.008 0.000 ARG C 333 ********************** 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 135 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 108 time to evaluate : 1.265 Fit side-chains REVERT: D 250 ILE cc_start: 0.7776 (pt) cc_final: 0.7542 (pt) REVERT: D 442 LEU cc_start: 0.8543 (mm) cc_final: 0.8337 (mt) REVERT: D 684 GLN cc_start: 0.7352 (OUTLIER) cc_final: 0.6957 (tt0) REVERT: D 701 GLU cc_start: 0.7084 (OUTLIER) cc_final: 0.6708 (mt-10) REVERT: C 442 LEU cc_start: 0.8539 (mm) cc_final: 0.8331 (mt) REVERT: C 684 GLN cc_start: 0.7348 (OUTLIER) cc_final: 0.6999 (tt0) outliers start: 27 outliers final: 17 residues processed: 124 average time/residue: 1.0642 time to fit residues: 144.7012 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 : 1.696 ------------------------------------------------------------------------------- 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 248 ASN 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 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 273 ILE Chi-restraints excluded: chain C residue 349 MET Chi-restraints excluded: chain C residue 385 PHE 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 29 optimal weight: 1.9990 chunk 89 optimal weight: 0.0670 chunk 14 optimal weight: 1.9990 chunk 26 optimal weight: 4.9990 chunk 96 optimal weight: 0.0570 chunk 40 optimal weight: 0.4980 chunk 99 optimal weight: 1.9990 chunk 12 optimal weight: 20.0000 chunk 17 optimal weight: 4.9990 chunk 85 optimal weight: 5.9990 chunk 5 optimal weight: 9.9990 overall best weight: 0.9240 ------------------------------------------------------------------------------- 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 = 0.3993 r_free = 0.3993 target = 0.182633 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.149127 restraints weight = 10609.189| |-----------------------------------------------------------------------------| r_work (start): 0.3539 rms_B_bonded: 1.50 r_work: 0.3383 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3242 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.3242 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7890 moved from start: 0.2183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 10690 Z= 0.177 Angle : 0.585 8.929 14502 Z= 0.301 Chirality : 0.044 0.350 1758 Planarity : 0.005 0.066 1650 Dihedral : 13.801 154.228 2730 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.70 % Favored : 94.30 % Rotamer: Outliers : 2.39 % Allowed : 15.11 % Favored : 82.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.45 (0.25), residues: 1210 helix: 2.17 (0.19), residues: 802 sheet: 1.18 (0.72), residues: 50 loop : -2.04 (0.33), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 482 HIS 0.003 0.001 HIS C 698 PHE 0.015 0.001 PHE D 385 TYR 0.022 0.002 TYR D 315 ARG 0.008 0.000 ARG C 333 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3203.34 seconds wall clock time: 58 minutes 49.52 seconds (3529.52 seconds total)