Starting phenix.real_space_refine on Fri Mar 15 01:25:32 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uuk_42588/03_2024/8uuk_42588_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uuk_42588/03_2024/8uuk_42588.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uuk_42588/03_2024/8uuk_42588.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uuk_42588/03_2024/8uuk_42588.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uuk_42588/03_2024/8uuk_42588_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uuk_42588/03_2024/8uuk_42588_updated.pdb" } resolution = 2.5 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= 0.002 sd= 0.095 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: 5 Type Number sf(0) Gaussians P 2 5.49 5 S 36 5.16 5 C 6896 2.51 5 N 1542 2.21 5 O 1766 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C TYR 377": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 682": "OE1" <-> "OE2" Residue "C GLU 701": "OE1" <-> "OE2" Residue "C GLU 704": "OE1" <-> "OE2" Residue "D GLU 320": "OE1" <-> "OE2" Residue "D TYR 377": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 540": "OE1" <-> "OE2" Residue "D GLU 682": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 10242 Number of models: 1 Model: "" Number of chains: 4 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: 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: 366 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 366 Unusual residues: {'AV0': 2, 'CLR': 6, 'LBN': 7} Classifications: {'undetermined': 15} Link IDs: {None: 14} Unresolved non-hydrogen bonds: 306 Unresolved non-hydrogen angles: 378 Unresolved non-hydrogen dihedrals: 317 Unresolved non-hydrogen chiralities: 16 Planarities with less than four sites: {'LBN:plan-2': 6, 'LBN:plan-3': 7, 'LBN:plan-1': 6} Unresolved non-hydrogen planarities: 68 Chain: "D" Number of atoms: 366 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 366 Unusual residues: {'AV0': 2, 'CLR': 6, 'LBN': 7} Classifications: {'undetermined': 15} Link IDs: {None: 14} Unresolved non-hydrogen bonds: 306 Unresolved non-hydrogen angles: 378 Unresolved non-hydrogen dihedrals: 317 Unresolved non-hydrogen chiralities: 16 Planarities with less than four sites: {'LBN:plan-2': 6, 'LBN:plan-3': 7, 'LBN:plan-1': 6} Unresolved non-hydrogen planarities: 68 Time building chain proxies: 5.77, per 1000 atoms: 0.56 Number of scatterers: 10242 At special positions: 0 Unit cell: (116.325, 104.775, 105.6, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 36 16.00 P 2 15.00 O 1766 8.00 N 1542 7.00 C 6896 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 - 3.50 Amino acid : False - 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: 4.00 Conformation dependent library (CDL) restraints added in 1.6 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... running ksdssp... Secondary structure from input PDB file: 54 helices and 2 sheets defined 62.5% alpha, 3.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.10 Creating SS restraints... Processing helix chain 'C' and resid 29 through 35 Processing helix chain 'C' and resid 71 through 73 No H-bonds generated for 'chain 'C' and resid 71 through 73' Processing helix chain 'C' and resid 83 through 108 removed outlier: 3.707A pdb=" N LEU C 100 " --> pdb=" O LEU C 96 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N LEU C 107 " --> pdb=" O MET C 103 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N LEU C 108 " --> pdb=" O ALA C 104 " (cutoff:3.500A) Processing helix chain 'C' and resid 115 through 130 Proline residue: C 123 - end of helix removed outlier: 4.038A pdb=" N ILE C 129 " --> pdb=" O LEU C 125 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N PHE C 130 " --> pdb=" O THR C 126 " (cutoff:3.500A) Processing helix chain 'C' and resid 142 through 155 Processing helix chain 'C' and resid 158 through 161 No H-bonds generated for 'chain 'C' and resid 158 through 161' Processing helix chain 'C' and resid 178 through 205 Processing helix chain 'C' and resid 210 through 213 Processing helix chain 'C' and resid 217 through 239 Processing helix chain 'C' and resid 252 through 266 removed outlier: 5.467A pdb=" N GLY C 265 " --> pdb=" O PHE C 261 " (cutoff:3.500A) removed outlier: 6.036A pdb=" N ASN C 266 " --> pdb=" O GLN C 262 " (cutoff:3.500A) Processing helix chain 'C' and resid 269 through 291 Processing helix chain 'C' and resid 302 through 317 Processing helix chain 'C' and resid 319 through 322 No H-bonds generated for 'chain 'C' and resid 319 through 322' Processing helix chain 'C' and resid 343 through 348 removed outlier: 4.118A pdb=" N SER C 347 " --> pdb=" O SER C 344 " (cutoff:3.500A) Processing helix chain 'C' and resid 350 through 375 removed outlier: 3.815A pdb=" N SER C 355 " --> pdb=" O THR C 351 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LYS C 374 " --> pdb=" O VAL C 370 " (cutoff:3.500A) Processing helix chain 'C' and resid 381 through 397 Processing helix chain 'C' and resid 407 through 415 Processing helix chain 'C' and resid 422 through 436 Processing helix chain 'C' and resid 447 through 474 removed outlier: 4.332A pdb=" N LYS C 459 " --> pdb=" O ILE C 455 " (cutoff:3.500A) removed outlier: 5.776A pdb=" N GLY C 460 " --> pdb=" O ALA C 456 " (cutoff:3.500A) removed outlier: 4.836A pdb=" N MET C 461 " --> pdb=" O ASN C 457 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N GLN C 464 " --> pdb=" O GLY C 460 " (cutoff:3.500A) removed outlier: 5.708A pdb=" N VAL C 465 " --> pdb=" O MET C 461 " (cutoff:3.500A) removed outlier: 5.287A pdb=" N CYS C 466 " --> pdb=" O PHE C 462 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N ASP C 467 " --> pdb=" O MET C 463 " (cutoff:3.500A) Proline residue: C 469 - end of helix Processing helix chain 'C' and resid 476 through 490 Processing helix chain 'C' and resid 494 through 514 Processing helix chain 'C' and resid 533 through 536 No H-bonds generated for 'chain 'C' and resid 533 through 536' Processing helix chain 'C' and resid 556 through 570 Processing helix chain 'C' and resid 574 through 584 Processing helix chain 'C' and resid 670 through 686 removed outlier: 3.742A pdb=" N ILE C 686 " --> pdb=" O GLU C 682 " (cutoff:3.500A) Processing helix chain 'C' and resid 697 through 705 Processing helix chain 'C' and resid 724 through 730 Processing helix chain 'D' and resid 29 through 35 Processing helix chain 'D' and resid 71 through 73 No H-bonds generated for 'chain 'D' and resid 71 through 73' Processing helix chain 'D' and resid 83 through 108 removed outlier: 3.712A pdb=" N LEU D 100 " --> pdb=" O LEU D 96 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N LEU D 107 " --> pdb=" O MET D 103 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N LEU D 108 " --> pdb=" O ALA D 104 " (cutoff:3.500A) Processing helix chain 'D' and resid 115 through 130 Proline residue: D 123 - end of helix removed outlier: 4.039A pdb=" N ILE D 129 " --> pdb=" O LEU D 125 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N PHE D 130 " --> pdb=" O THR D 126 " (cutoff:3.500A) Processing helix chain 'D' and resid 142 through 155 Processing helix chain 'D' and resid 158 through 161 No H-bonds generated for 'chain 'D' and resid 158 through 161' Processing helix chain 'D' and resid 178 through 205 Processing helix chain 'D' and resid 210 through 213 Processing helix chain 'D' and resid 217 through 239 Processing helix chain 'D' and resid 252 through 266 removed outlier: 5.472A pdb=" N GLY D 265 " --> pdb=" O PHE D 261 " (cutoff:3.500A) removed outlier: 6.036A pdb=" N ASN D 266 " --> pdb=" O GLN D 262 " (cutoff:3.500A) Processing helix chain 'D' and resid 269 through 291 Processing helix chain 'D' and resid 302 through 317 Processing helix chain 'D' and resid 319 through 322 No H-bonds generated for 'chain 'D' and resid 319 through 322' Processing helix chain 'D' and resid 343 through 348 removed outlier: 4.111A pdb=" N SER D 347 " --> pdb=" O SER D 344 " (cutoff:3.500A) Processing helix chain 'D' and resid 350 through 375 removed outlier: 3.809A pdb=" N SER D 355 " --> pdb=" O THR D 351 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LYS D 374 " --> pdb=" O VAL D 370 " (cutoff:3.500A) Processing helix chain 'D' and resid 381 through 397 Processing helix chain 'D' and resid 407 through 415 Processing helix chain 'D' and resid 422 through 436 Processing helix chain 'D' and resid 447 through 474 removed outlier: 4.324A pdb=" N LYS D 459 " --> pdb=" O ILE D 455 " (cutoff:3.500A) removed outlier: 5.769A pdb=" N GLY D 460 " --> pdb=" O ALA D 456 " (cutoff:3.500A) removed outlier: 4.848A pdb=" N MET D 461 " --> pdb=" O ASN D 457 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N GLN D 464 " --> pdb=" O GLY D 460 " (cutoff:3.500A) removed outlier: 5.727A pdb=" N VAL D 465 " --> pdb=" O MET D 461 " (cutoff:3.500A) removed outlier: 5.356A pdb=" N CYS D 466 " --> pdb=" O PHE D 462 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N ASP D 467 " --> pdb=" O MET D 463 " (cutoff:3.500A) Proline residue: D 469 - end of helix Processing helix chain 'D' and resid 476 through 490 Processing helix chain 'D' and resid 494 through 514 Processing helix chain 'D' and resid 533 through 536 No H-bonds generated for 'chain 'D' and resid 533 through 536' Processing helix chain 'D' and resid 556 through 570 Processing helix chain 'D' and resid 574 through 584 Processing helix chain 'D' and resid 670 through 686 removed outlier: 3.720A pdb=" N ILE D 686 " --> pdb=" O GLU D 682 " (cutoff:3.500A) Processing helix chain 'D' and resid 697 through 705 Processing helix chain 'D' and resid 724 through 730 Processing sheet with id= A, first strand: chain 'C' and resid 530 through 532 removed outlier: 4.110A pdb=" N ILE C 547 " --> pdb=" O LEU C 521 " (cutoff:3.500A) removed outlier: 8.280A pdb=" N SER C 523 " --> pdb=" O VAL C 545 " (cutoff:3.500A) removed outlier: 12.522A pdb=" N VAL C 545 " --> pdb=" O SER C 523 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N SER C 657 " --> pdb=" O LYS C 546 " (cutoff:3.500A) removed outlier: 7.923A pdb=" N LEU C 548 " --> pdb=" O SER C 657 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N VAL C 659 " --> pdb=" O LEU C 548 " (cutoff:3.500A) removed outlier: 7.539A pdb=" N PHE C 550 " --> pdb=" O VAL C 659 " (cutoff:3.500A) removed outlier: 7.072A pdb=" N ASP C 661 " --> pdb=" O PHE C 550 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N HIS C 689 " --> pdb=" O LEU C 658 " (cutoff:3.500A) removed outlier: 7.451A pdb=" N LEU C 660 " --> pdb=" O HIS C 689 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N TYR C 691 " --> pdb=" O LEU C 660 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'D' and resid 530 through 532 removed outlier: 4.117A pdb=" N ILE D 547 " --> pdb=" O LEU D 521 " (cutoff:3.500A) removed outlier: 8.282A pdb=" N SER D 523 " --> pdb=" O VAL D 545 " (cutoff:3.500A) removed outlier: 12.521A pdb=" N VAL D 545 " --> pdb=" O SER D 523 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N SER D 657 " --> pdb=" O LYS D 546 " (cutoff:3.500A) removed outlier: 7.933A pdb=" N LEU D 548 " --> pdb=" O SER D 657 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N VAL D 659 " --> pdb=" O LEU D 548 " (cutoff:3.500A) removed outlier: 7.533A pdb=" N PHE D 550 " --> pdb=" O VAL D 659 " (cutoff:3.500A) removed outlier: 7.067A pdb=" N ASP D 661 " --> pdb=" O PHE D 550 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N HIS D 689 " --> pdb=" O LEU D 658 " (cutoff:3.500A) removed outlier: 7.445A pdb=" N LEU D 660 " --> pdb=" O HIS D 689 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N TYR D 691 " --> pdb=" O LEU D 660 " (cutoff:3.500A) 518 hydrogen bonds defined for protein. 1536 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: 2.76 Time building geometry restraints manager: 4.32 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1554 1.32 - 1.44: 2596 1.44 - 1.57: 6258 1.57 - 1.69: 6 1.69 - 1.81: 56 Bond restraints: 10470 Sorted by residual: bond pdb=" O2 LBN C 806 " pdb=" P1 LBN C 806 " ideal model delta sigma weight residual 1.650 1.596 0.054 2.00e-02 2.50e+03 7.31e+00 bond pdb=" O2 LBN D 806 " pdb=" P1 LBN D 806 " ideal model delta sigma weight residual 1.650 1.597 0.053 2.00e-02 2.50e+03 7.15e+00 bond pdb=" O1 LBN D 806 " pdb=" P1 LBN D 806 " ideal model delta sigma weight residual 1.632 1.595 0.037 2.00e-02 2.50e+03 3.45e+00 bond pdb=" O1 LBN C 806 " pdb=" P1 LBN C 806 " ideal model delta sigma weight residual 1.632 1.596 0.036 2.00e-02 2.50e+03 3.27e+00 bond pdb=" C1 LBN D 806 " pdb=" O1 LBN D 806 " ideal model delta sigma weight residual 1.410 1.444 -0.034 2.00e-02 2.50e+03 2.81e+00 ... (remaining 10465 not shown) Histogram of bond angle deviations from ideal: 99.35 - 106.29: 289 106.29 - 113.23: 6057 113.23 - 120.16: 3665 120.16 - 127.10: 4138 127.10 - 134.04: 81 Bond angle restraints: 14230 Sorted by residual: angle pdb=" CA LYS D 66 " pdb=" CB LYS D 66 " pdb=" CG LYS D 66 " ideal model delta sigma weight residual 114.10 122.36 -8.26 2.00e+00 2.50e-01 1.71e+01 angle pdb=" CA LYS C 66 " pdb=" CB LYS C 66 " pdb=" CG LYS C 66 " ideal model delta sigma weight residual 114.10 122.32 -8.22 2.00e+00 2.50e-01 1.69e+01 angle pdb=" C ILE C 491 " pdb=" N LEU C 492 " pdb=" CA LEU C 492 " ideal model delta sigma weight residual 121.54 128.79 -7.25 1.91e+00 2.74e-01 1.44e+01 angle pdb=" C ILE D 491 " pdb=" N LEU D 492 " pdb=" CA LEU D 492 " ideal model delta sigma weight residual 121.54 128.69 -7.15 1.91e+00 2.74e-01 1.40e+01 angle pdb=" CB LYS D 66 " pdb=" CG LYS D 66 " pdb=" CD LYS D 66 " ideal model delta sigma weight residual 111.30 119.75 -8.45 2.30e+00 1.89e-01 1.35e+01 ... (remaining 14225 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.26: 6651 33.26 - 66.51: 285 66.51 - 99.77: 40 99.77 - 133.02: 56 133.02 - 166.28: 6 Dihedral angle restraints: 7038 sinusoidal: 3488 harmonic: 3550 Sorted by residual: 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 180.00 150.95 29.05 0 5.00e+00 4.00e-02 3.38e+01 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 180.00 150.98 29.02 0 5.00e+00 4.00e-02 3.37e+01 dihedral pdb=" CBS AV0 D 815 " pdb=" C1 AV0 D 815 " pdb=" O1 AV0 D 815 " pdb=" O5 AV0 D 815 " ideal model delta sinusoidal sigma weight residual 85.89 -80.39 166.28 1 3.00e+01 1.11e-03 2.10e+01 ... (remaining 7035 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 1403 0.052 - 0.105: 298 0.105 - 0.157: 42 0.157 - 0.209: 9 0.209 - 0.262: 4 Chirality restraints: 1756 Sorted by residual: chirality pdb=" CB VAL C 559 " pdb=" CA VAL C 559 " pdb=" CG1 VAL C 559 " pdb=" CG2 VAL C 559 " both_signs ideal model delta sigma weight residual False -2.63 -2.37 -0.26 2.00e-01 2.50e+01 1.71e+00 chirality pdb=" C2 LBN D 806 " pdb=" C1 LBN D 806 " pdb=" C3 LBN D 806 " pdb=" O7 LBN D 806 " both_signs ideal model delta sigma weight residual False -2.36 -2.59 0.22 2.00e-01 2.50e+01 1.24e+00 chirality pdb=" C2 LBN C 806 " pdb=" C1 LBN C 806 " pdb=" C3 LBN C 806 " pdb=" O7 LBN C 806 " both_signs ideal model delta sigma weight residual False -2.36 -2.58 0.22 2.00e-01 2.50e+01 1.21e+00 ... (remaining 1753 not shown) Planarity restraints: 1628 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE D 141 " -0.047 5.00e-02 4.00e+02 7.15e-02 8.18e+00 pdb=" N PRO D 142 " 0.124 5.00e-02 4.00e+02 pdb=" CA PRO D 142 " -0.038 5.00e-02 4.00e+02 pdb=" CD PRO D 142 " -0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE C 141 " 0.047 5.00e-02 4.00e+02 7.11e-02 8.09e+00 pdb=" N PRO C 142 " -0.123 5.00e-02 4.00e+02 pdb=" CA PRO C 142 " 0.038 5.00e-02 4.00e+02 pdb=" CD PRO C 142 " 0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY D 139 " -0.033 5.00e-02 4.00e+02 5.09e-02 4.14e+00 pdb=" N PRO D 140 " 0.088 5.00e-02 4.00e+02 pdb=" CA PRO D 140 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO D 140 " -0.028 5.00e-02 4.00e+02 ... (remaining 1625 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.72: 412 2.72 - 3.27: 10652 3.27 - 3.81: 17635 3.81 - 4.36: 21838 4.36 - 4.90: 36296 Nonbonded interactions: 86833 Sorted by model distance: nonbonded pdb=" O PRO C 553 " pdb=" ND2 ASN C 558 " model vdw 2.180 2.520 nonbonded pdb=" O PRO D 553 " pdb=" ND2 ASN D 558 " model vdw 2.188 2.520 nonbonded pdb=" OH TYR D 247 " pdb=" OE1 GLU D 259 " model vdw 2.229 2.440 nonbonded pdb=" OH TYR C 247 " pdb=" OE1 GLU C 259 " model vdw 2.233 2.440 nonbonded pdb=" OH TYR D 78 " pdb=" OD2 ASP D 87 " model vdw 2.240 2.440 ... (remaining 86828 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'C' selection = chain 'D' } 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: 0.670 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: 4.040 Check model and map are aligned: 0.140 Set scattering table: 0.080 Process input model: 29.480 Find NCS groups from input model: 0.490 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.990 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8006 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 : 0.004 0.054 10470 Z= 0.247 Angle : 0.665 10.383 14230 Z= 0.325 Chirality : 0.045 0.262 1756 Planarity : 0.004 0.072 1628 Dihedral : 21.914 166.280 4750 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 11.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 1.53 % Allowed : 17.02 % Favored : 81.45 % 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: 1.07 (0.24), residues: 1210 helix: 1.74 (0.19), residues: 788 sheet: 1.90 (0.71), residues: 34 loop : -1.65 (0.30), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 74 HIS 0.003 0.001 HIS C 656 PHE 0.017 0.001 PHE D 141 TYR 0.012 0.001 TYR D 371 ARG 0.009 0.000 ARG C 79 *********************** 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 143 residues out of total 1046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 127 time to evaluate : 1.152 Fit side-chains REVERT: C 187 LEU cc_start: 0.8288 (mt) cc_final: 0.7987 (mm) REVERT: D 187 LEU cc_start: 0.8299 (mt) cc_final: 0.7992 (mm) outliers start: 16 outliers final: 14 residues processed: 141 average time/residue: 0.6457 time to fit residues: 104.3387 Evaluate side-chains 141 residues out of total 1046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 127 time to evaluate : 1.062 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 93 SER Chi-restraints excluded: chain C residue 154 SER 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 552 SER Chi-restraints excluded: chain D residue 93 SER Chi-restraints excluded: chain D residue 154 SER Chi-restraints excluded: chain D residue 219 LEU Chi-restraints excluded: chain D residue 385 PHE Chi-restraints excluded: chain D residue 407 LEU Chi-restraints excluded: chain D residue 545 VAL Chi-restraints excluded: chain D residue 552 SER Chi-restraints excluded: chain D residue 559 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 103 optimal weight: 0.8980 chunk 92 optimal weight: 0.8980 chunk 51 optimal weight: 3.9990 chunk 31 optimal weight: 3.9990 chunk 62 optimal weight: 4.9990 chunk 49 optimal weight: 0.9990 chunk 95 optimal weight: 4.9990 chunk 37 optimal weight: 7.9990 chunk 58 optimal weight: 1.9990 chunk 71 optimal weight: 0.5980 chunk 110 optimal weight: 1.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 248 ASN C 684 GLN C 689 HIS D 684 GLN D 689 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8049 moved from start: 0.0686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 10470 Z= 0.219 Angle : 0.640 8.222 14230 Z= 0.303 Chirality : 0.046 0.275 1756 Planarity : 0.004 0.075 1628 Dihedral : 16.376 160.152 2621 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 10.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 4.02 % Allowed : 13.96 % Favored : 82.03 % 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: 1.19 (0.25), residues: 1210 helix: 1.81 (0.19), residues: 790 sheet: 0.99 (0.69), residues: 50 loop : -1.54 (0.32), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 74 HIS 0.002 0.001 HIS D 656 PHE 0.020 0.002 PHE D 141 TYR 0.015 0.002 TYR C 556 ARG 0.005 0.000 ARG C 79 *********************** 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 169 residues out of total 1046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 127 time to evaluate : 1.069 Fit side-chains REVERT: C 187 LEU cc_start: 0.8290 (mt) cc_final: 0.7992 (mm) REVERT: D 187 LEU cc_start: 0.8299 (mt) cc_final: 0.7995 (mm) REVERT: D 503 MET cc_start: 0.7913 (OUTLIER) cc_final: 0.7661 (mmp) outliers start: 42 outliers final: 17 residues processed: 156 average time/residue: 0.7785 time to fit residues: 135.7672 Evaluate side-chains 131 residues out of total 1046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 113 time to evaluate : 1.094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 100 LEU Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain C residue 333 ARG Chi-restraints excluded: chain C residue 385 PHE Chi-restraints excluded: chain C residue 404 THR Chi-restraints excluded: chain C residue 407 LEU Chi-restraints excluded: chain C residue 545 VAL Chi-restraints excluded: chain C residue 556 TYR Chi-restraints excluded: chain D residue 100 LEU Chi-restraints excluded: chain D residue 219 LEU Chi-restraints excluded: chain D residue 385 PHE Chi-restraints excluded: chain D residue 404 THR Chi-restraints excluded: chain D residue 407 LEU Chi-restraints excluded: chain D residue 503 MET Chi-restraints excluded: chain D residue 545 VAL Chi-restraints excluded: chain D residue 556 TYR Chi-restraints excluded: chain D residue 559 VAL Chi-restraints excluded: chain D residue 678 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 61 optimal weight: 2.9990 chunk 34 optimal weight: 2.9990 chunk 92 optimal weight: 3.9990 chunk 75 optimal weight: 4.9990 chunk 30 optimal weight: 0.7980 chunk 110 optimal weight: 0.9990 chunk 119 optimal weight: 2.9990 chunk 98 optimal weight: 5.9990 chunk 37 optimal weight: 5.9990 chunk 89 optimal weight: 7.9990 chunk 109 optimal weight: 0.7980 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 248 ASN C 266 ASN C 684 GLN C 689 HIS D 684 GLN D 689 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8098 moved from start: 0.1220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 10470 Z= 0.290 Angle : 0.639 8.446 14230 Z= 0.315 Chirality : 0.046 0.299 1756 Planarity : 0.005 0.078 1628 Dihedral : 15.758 157.623 2615 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 9.61 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.88 % Favored : 94.96 % Rotamer: Outliers : 4.40 % Allowed : 15.58 % Favored : 80.02 % 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: 1.01 (0.24), residues: 1210 helix: 1.59 (0.18), residues: 798 sheet: 1.04 (0.68), residues: 50 loop : -1.51 (0.32), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 74 HIS 0.003 0.001 HIS C 656 PHE 0.021 0.002 PHE C 141 TYR 0.017 0.002 TYR C 371 ARG 0.007 0.000 ARG C 79 *********************** 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 170 residues out of total 1046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 124 time to evaluate : 1.026 Fit side-chains REVERT: C 103 MET cc_start: 0.8636 (OUTLIER) cc_final: 0.8423 (mtp) REVERT: C 187 LEU cc_start: 0.8301 (mt) cc_final: 0.8003 (mm) REVERT: D 187 LEU cc_start: 0.8310 (mt) cc_final: 0.8008 (mm) outliers start: 46 outliers final: 19 residues processed: 154 average time/residue: 0.9296 time to fit residues: 157.4552 Evaluate side-chains 130 residues out of total 1046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 110 time to evaluate : 1.143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 22 VAL Chi-restraints excluded: chain C residue 100 LEU Chi-restraints excluded: chain C residue 103 MET Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 333 ARG Chi-restraints excluded: chain C residue 385 PHE Chi-restraints excluded: chain C residue 404 THR Chi-restraints excluded: chain C residue 407 LEU Chi-restraints excluded: chain C residue 545 VAL Chi-restraints excluded: chain C residue 556 TYR Chi-restraints excluded: chain D residue 22 VAL Chi-restraints excluded: chain D residue 100 LEU Chi-restraints excluded: chain D residue 219 LEU Chi-restraints excluded: chain D residue 277 LEU Chi-restraints excluded: chain D residue 385 PHE Chi-restraints excluded: chain D residue 404 THR Chi-restraints excluded: chain D residue 545 VAL Chi-restraints excluded: chain D residue 556 TYR Chi-restraints excluded: chain D residue 559 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 83 optimal weight: 7.9990 chunk 57 optimal weight: 0.0070 chunk 12 optimal weight: 0.0270 chunk 52 optimal weight: 4.9990 chunk 74 optimal weight: 0.6980 chunk 111 optimal weight: 0.9980 chunk 117 optimal weight: 0.8980 chunk 58 optimal weight: 0.9990 chunk 105 optimal weight: 4.9990 chunk 31 optimal weight: 3.9990 chunk 98 optimal weight: 8.9990 overall best weight: 0.5256 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 684 GLN C 689 HIS D 684 GLN D 689 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8042 moved from start: 0.1251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 10470 Z= 0.159 Angle : 0.610 16.668 14230 Z= 0.289 Chirality : 0.045 0.347 1756 Planarity : 0.004 0.075 1628 Dihedral : 14.454 153.219 2613 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 11.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 4.11 % Allowed : 17.88 % Favored : 78.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.31 (0.25), residues: 1210 helix: 1.89 (0.19), residues: 790 sheet: 1.02 (0.68), residues: 50 loop : -1.47 (0.32), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 74 HIS 0.002 0.001 HIS D 689 PHE 0.017 0.001 PHE D 141 TYR 0.013 0.001 TYR D 371 ARG 0.007 0.000 ARG D 79 *********************** 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 166 residues out of total 1046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 123 time to evaluate : 0.887 Fit side-chains REVERT: C 187 LEU cc_start: 0.8308 (mt) cc_final: 0.8009 (mm) REVERT: C 704 GLU cc_start: 0.7991 (OUTLIER) cc_final: 0.7709 (pt0) REVERT: D 103 MET cc_start: 0.8546 (OUTLIER) cc_final: 0.8301 (mtm) REVERT: D 187 LEU cc_start: 0.8307 (mt) cc_final: 0.8001 (mm) outliers start: 43 outliers final: 24 residues processed: 148 average time/residue: 0.7537 time to fit residues: 125.1405 Evaluate side-chains 144 residues out of total 1046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 118 time to evaluate : 1.079 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 22 VAL Chi-restraints excluded: chain C residue 85 LEU Chi-restraints excluded: chain C residue 100 LEU Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 324 ASN Chi-restraints excluded: chain C residue 385 PHE Chi-restraints excluded: chain C residue 404 THR Chi-restraints excluded: chain C residue 407 LEU Chi-restraints excluded: chain C residue 545 VAL Chi-restraints excluded: chain C residue 556 TYR Chi-restraints excluded: chain C residue 678 MET Chi-restraints excluded: chain C residue 704 GLU Chi-restraints excluded: chain D residue 22 VAL Chi-restraints excluded: chain D residue 85 LEU Chi-restraints excluded: chain D residue 100 LEU Chi-restraints excluded: chain D residue 103 MET Chi-restraints excluded: chain D residue 219 LEU Chi-restraints excluded: chain D residue 277 LEU Chi-restraints excluded: chain D residue 385 PHE Chi-restraints excluded: chain D residue 404 THR Chi-restraints excluded: chain D residue 407 LEU Chi-restraints excluded: chain D residue 545 VAL Chi-restraints excluded: chain D residue 556 TYR Chi-restraints excluded: chain D residue 559 VAL Chi-restraints excluded: chain D residue 678 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 66 optimal weight: 9.9990 chunk 1 optimal weight: 0.0980 chunk 87 optimal weight: 7.9990 chunk 48 optimal weight: 4.9990 chunk 100 optimal weight: 0.8980 chunk 81 optimal weight: 0.9990 chunk 0 optimal weight: 6.9990 chunk 60 optimal weight: 0.9980 chunk 105 optimal weight: 5.9990 chunk 29 optimal weight: 0.3980 chunk 39 optimal weight: 0.8980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 684 GLN C 689 HIS D 684 GLN D 689 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8036 moved from start: 0.1341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10470 Z= 0.168 Angle : 0.579 10.245 14230 Z= 0.279 Chirality : 0.044 0.298 1756 Planarity : 0.004 0.069 1628 Dihedral : 13.684 149.418 2613 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 11.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer: Outliers : 4.11 % Allowed : 17.78 % Favored : 78.11 % 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: 1.34 (0.25), residues: 1210 helix: 1.91 (0.19), residues: 792 sheet: 0.90 (0.67), residues: 50 loop : -1.46 (0.32), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 74 HIS 0.002 0.001 HIS C 656 PHE 0.019 0.001 PHE C 141 TYR 0.013 0.001 TYR D 371 ARG 0.005 0.000 ARG D 79 *********************** 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 167 residues out of total 1046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 124 time to evaluate : 0.917 Fit side-chains REVERT: C 187 LEU cc_start: 0.8306 (mt) cc_final: 0.8006 (mm) REVERT: C 573 ASP cc_start: 0.7335 (OUTLIER) cc_final: 0.7042 (t70) REVERT: C 704 GLU cc_start: 0.8002 (OUTLIER) cc_final: 0.7750 (pt0) REVERT: D 187 LEU cc_start: 0.8315 (mt) cc_final: 0.8010 (mm) REVERT: D 320 GLU cc_start: 0.7973 (tp30) cc_final: 0.7734 (tp30) REVERT: D 573 ASP cc_start: 0.7331 (OUTLIER) cc_final: 0.7002 (t70) REVERT: D 704 GLU cc_start: 0.7973 (OUTLIER) cc_final: 0.7694 (pt0) outliers start: 43 outliers final: 25 residues processed: 148 average time/residue: 0.7822 time to fit residues: 129.8682 Evaluate side-chains 146 residues out of total 1046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 117 time to evaluate : 1.117 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 22 VAL Chi-restraints excluded: chain C residue 85 LEU Chi-restraints excluded: chain C residue 100 LEU Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain C residue 248 ASN Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 324 ASN Chi-restraints excluded: chain C residue 385 PHE Chi-restraints excluded: chain C residue 404 THR Chi-restraints excluded: chain C residue 407 LEU Chi-restraints excluded: chain C residue 545 VAL Chi-restraints excluded: chain C residue 556 TYR Chi-restraints excluded: chain C residue 573 ASP Chi-restraints excluded: chain C residue 678 MET Chi-restraints excluded: chain C residue 704 GLU Chi-restraints excluded: chain D residue 22 VAL Chi-restraints excluded: chain D residue 85 LEU Chi-restraints excluded: chain D residue 100 LEU Chi-restraints excluded: chain D residue 219 LEU Chi-restraints excluded: chain D residue 277 LEU Chi-restraints excluded: chain D residue 385 PHE Chi-restraints excluded: chain D residue 404 THR Chi-restraints excluded: chain D residue 407 LEU Chi-restraints excluded: chain D residue 545 VAL Chi-restraints excluded: chain D residue 556 TYR Chi-restraints excluded: chain D residue 559 VAL Chi-restraints excluded: chain D residue 573 ASP Chi-restraints excluded: chain D residue 678 MET Chi-restraints excluded: chain D residue 704 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 106 optimal weight: 2.9990 chunk 23 optimal weight: 8.9990 chunk 69 optimal weight: 0.1980 chunk 29 optimal weight: 1.9990 chunk 118 optimal weight: 4.9990 chunk 97 optimal weight: 9.9990 chunk 54 optimal weight: 5.9990 chunk 9 optimal weight: 7.9990 chunk 39 optimal weight: 1.9990 chunk 61 optimal weight: 0.0470 chunk 113 optimal weight: 0.8980 overall best weight: 1.0282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 684 GLN C 689 HIS D 689 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8059 moved from start: 0.1451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10470 Z= 0.202 Angle : 0.598 9.861 14230 Z= 0.289 Chirality : 0.044 0.278 1756 Planarity : 0.004 0.074 1628 Dihedral : 13.381 147.144 2613 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 10.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 3.92 % Allowed : 17.88 % Favored : 78.20 % 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: 1.32 (0.25), residues: 1210 helix: 1.89 (0.19), residues: 790 sheet: 0.92 (0.66), residues: 50 loop : -1.45 (0.33), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 74 HIS 0.002 0.001 HIS C 656 PHE 0.019 0.001 PHE D 141 TYR 0.014 0.001 TYR D 371 ARG 0.006 0.000 ARG C 79 *********************** 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 158 residues out of total 1046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 117 time to evaluate : 1.074 Fit side-chains REVERT: C 187 LEU cc_start: 0.8303 (mt) cc_final: 0.7993 (mm) REVERT: C 320 GLU cc_start: 0.8031 (OUTLIER) cc_final: 0.7665 (tp30) REVERT: C 573 ASP cc_start: 0.7339 (OUTLIER) cc_final: 0.7020 (t70) REVERT: C 704 GLU cc_start: 0.7988 (OUTLIER) cc_final: 0.7782 (pt0) REVERT: D 187 LEU cc_start: 0.8311 (mt) cc_final: 0.8006 (mm) REVERT: D 320 GLU cc_start: 0.8029 (tp30) cc_final: 0.7661 (tp30) REVERT: D 573 ASP cc_start: 0.7324 (OUTLIER) cc_final: 0.6997 (t70) REVERT: D 704 GLU cc_start: 0.7960 (OUTLIER) cc_final: 0.7708 (pt0) outliers start: 41 outliers final: 26 residues processed: 143 average time/residue: 0.8862 time to fit residues: 140.3602 Evaluate side-chains 146 residues out of total 1046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 115 time to evaluate : 1.066 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 22 VAL Chi-restraints excluded: chain C residue 85 LEU Chi-restraints excluded: chain C residue 100 LEU Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain C residue 248 ASN Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 320 GLU Chi-restraints excluded: chain C residue 324 ASN Chi-restraints excluded: chain C residue 385 PHE Chi-restraints excluded: chain C residue 404 THR Chi-restraints excluded: chain C residue 407 LEU Chi-restraints excluded: chain C residue 545 VAL Chi-restraints excluded: chain C residue 556 TYR Chi-restraints excluded: chain C residue 573 ASP Chi-restraints excluded: chain C residue 678 MET Chi-restraints excluded: chain C residue 704 GLU Chi-restraints excluded: chain D residue 22 VAL Chi-restraints excluded: chain D residue 85 LEU Chi-restraints excluded: chain D residue 100 LEU Chi-restraints excluded: chain D residue 219 LEU Chi-restraints excluded: chain D residue 277 LEU Chi-restraints excluded: chain D residue 324 ASN Chi-restraints excluded: chain D residue 385 PHE Chi-restraints excluded: chain D residue 404 THR Chi-restraints excluded: chain D residue 407 LEU Chi-restraints excluded: chain D residue 545 VAL Chi-restraints excluded: chain D residue 556 TYR Chi-restraints excluded: chain D residue 559 VAL Chi-restraints excluded: chain D residue 573 ASP Chi-restraints excluded: chain D residue 678 MET Chi-restraints excluded: chain D residue 704 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 13 optimal weight: 2.9990 chunk 67 optimal weight: 2.9990 chunk 86 optimal weight: 0.9980 chunk 66 optimal weight: 3.9990 chunk 99 optimal weight: 0.9980 chunk 65 optimal weight: 4.9990 chunk 117 optimal weight: 1.9990 chunk 73 optimal weight: 0.7980 chunk 71 optimal weight: 0.9980 chunk 54 optimal weight: 0.7980 chunk 72 optimal weight: 0.6980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 689 HIS D 266 ASN D 689 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8046 moved from start: 0.1519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10470 Z= 0.183 Angle : 0.580 8.230 14230 Z= 0.282 Chirality : 0.044 0.314 1756 Planarity : 0.004 0.071 1628 Dihedral : 12.922 146.033 2613 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 10.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer: Outliers : 3.44 % Allowed : 18.64 % Favored : 77.92 % 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: 1.34 (0.25), residues: 1210 helix: 1.92 (0.19), residues: 790 sheet: 0.86 (0.66), residues: 50 loop : -1.44 (0.33), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 74 HIS 0.002 0.001 HIS D 656 PHE 0.018 0.001 PHE C 141 TYR 0.013 0.001 TYR D 371 ARG 0.008 0.000 ARG C 79 *********************** 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 159 residues out of total 1046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 123 time to evaluate : 1.140 Fit side-chains REVERT: C 187 LEU cc_start: 0.8297 (mt) cc_final: 0.7995 (mm) REVERT: C 573 ASP cc_start: 0.7330 (OUTLIER) cc_final: 0.7003 (t70) REVERT: C 701 GLU cc_start: 0.7760 (mm-30) cc_final: 0.7460 (mm-30) REVERT: C 704 GLU cc_start: 0.7984 (OUTLIER) cc_final: 0.7686 (pt0) REVERT: D 187 LEU cc_start: 0.8306 (mt) cc_final: 0.8000 (mm) REVERT: D 573 ASP cc_start: 0.7327 (OUTLIER) cc_final: 0.6993 (t70) REVERT: D 704 GLU cc_start: 0.7954 (OUTLIER) cc_final: 0.7738 (pt0) outliers start: 36 outliers final: 26 residues processed: 143 average time/residue: 0.8063 time to fit residues: 128.5369 Evaluate side-chains 148 residues out of total 1046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 118 time to evaluate : 1.088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 22 VAL Chi-restraints excluded: chain C residue 85 LEU Chi-restraints excluded: chain C residue 100 LEU Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain C residue 248 ASN Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 324 ASN Chi-restraints excluded: chain C residue 385 PHE Chi-restraints excluded: chain C residue 404 THR Chi-restraints excluded: chain C residue 407 LEU Chi-restraints excluded: chain C residue 545 VAL Chi-restraints excluded: chain C residue 556 TYR Chi-restraints excluded: chain C residue 573 ASP Chi-restraints excluded: chain C residue 678 MET Chi-restraints excluded: chain C residue 704 GLU Chi-restraints excluded: chain D residue 22 VAL Chi-restraints excluded: chain D residue 85 LEU Chi-restraints excluded: chain D residue 100 LEU Chi-restraints excluded: chain D residue 219 LEU Chi-restraints excluded: chain D residue 277 LEU Chi-restraints excluded: chain D residue 324 ASN Chi-restraints excluded: chain D residue 385 PHE Chi-restraints excluded: chain D residue 404 THR Chi-restraints excluded: chain D residue 407 LEU Chi-restraints excluded: chain D residue 545 VAL Chi-restraints excluded: chain D residue 556 TYR Chi-restraints excluded: chain D residue 559 VAL Chi-restraints excluded: chain D residue 573 ASP Chi-restraints excluded: chain D residue 678 MET Chi-restraints excluded: chain D residue 704 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: 0.4980 chunk 35 optimal weight: 2.9990 chunk 23 optimal weight: 10.0000 chunk 22 optimal weight: 2.9990 chunk 74 optimal weight: 3.9990 chunk 80 optimal weight: 10.0000 chunk 58 optimal weight: 2.9990 chunk 10 optimal weight: 0.6980 chunk 92 optimal weight: 0.9990 chunk 106 optimal weight: 0.7980 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8073 moved from start: 0.1637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10470 Z= 0.223 Angle : 0.614 7.998 14230 Z= 0.298 Chirality : 0.045 0.340 1756 Planarity : 0.004 0.075 1628 Dihedral : 12.831 144.265 2613 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 10.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer: Outliers : 3.73 % Allowed : 18.36 % Favored : 77.92 % 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: 1.30 (0.25), residues: 1210 helix: 1.85 (0.19), residues: 790 sheet: 0.96 (0.67), residues: 50 loop : -1.40 (0.33), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 74 HIS 0.002 0.001 HIS D 698 PHE 0.020 0.001 PHE C 141 TYR 0.015 0.001 TYR D 371 ARG 0.008 0.000 ARG C 79 *********************** 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 152 residues out of total 1046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 113 time to evaluate : 1.182 Fit side-chains REVERT: C 187 LEU cc_start: 0.8314 (mt) cc_final: 0.8012 (mm) REVERT: C 320 GLU cc_start: 0.7981 (OUTLIER) cc_final: 0.7108 (pm20) REVERT: C 573 ASP cc_start: 0.7316 (OUTLIER) cc_final: 0.6972 (t70) REVERT: C 704 GLU cc_start: 0.7997 (OUTLIER) cc_final: 0.7749 (pt0) REVERT: D 187 LEU cc_start: 0.8327 (mt) cc_final: 0.8020 (mm) REVERT: D 573 ASP cc_start: 0.7311 (OUTLIER) cc_final: 0.6963 (t70) REVERT: D 704 GLU cc_start: 0.7960 (OUTLIER) cc_final: 0.7747 (pt0) outliers start: 39 outliers final: 24 residues processed: 137 average time/residue: 0.8268 time to fit residues: 126.1496 Evaluate side-chains 138 residues out of total 1046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 109 time to evaluate : 1.082 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 22 VAL Chi-restraints excluded: chain C residue 85 LEU Chi-restraints excluded: chain C residue 100 LEU Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain C residue 248 ASN Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 320 GLU Chi-restraints excluded: chain C residue 385 PHE Chi-restraints excluded: chain C residue 404 THR Chi-restraints excluded: chain C residue 407 LEU Chi-restraints excluded: chain C residue 545 VAL Chi-restraints excluded: chain C residue 556 TYR Chi-restraints excluded: chain C residue 573 ASP Chi-restraints excluded: chain C residue 678 MET Chi-restraints excluded: chain C residue 704 GLU Chi-restraints excluded: chain D residue 22 VAL Chi-restraints excluded: chain D residue 85 LEU Chi-restraints excluded: chain D residue 100 LEU Chi-restraints excluded: chain D residue 219 LEU Chi-restraints excluded: chain D residue 277 LEU Chi-restraints excluded: chain D residue 385 PHE Chi-restraints excluded: chain D residue 404 THR Chi-restraints excluded: chain D residue 407 LEU Chi-restraints excluded: chain D residue 545 VAL Chi-restraints excluded: chain D residue 556 TYR Chi-restraints excluded: chain D residue 559 VAL Chi-restraints excluded: chain D residue 573 ASP Chi-restraints excluded: chain D residue 678 MET Chi-restraints excluded: chain D residue 704 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 112 optimal weight: 2.9990 chunk 102 optimal weight: 0.7980 chunk 109 optimal weight: 1.9990 chunk 65 optimal weight: 4.9990 chunk 47 optimal weight: 0.9980 chunk 86 optimal weight: 2.9990 chunk 33 optimal weight: 3.9990 chunk 99 optimal weight: 6.9990 chunk 103 optimal weight: 0.9980 chunk 71 optimal weight: 0.6980 chunk 115 optimal weight: 0.9980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8053 moved from start: 0.1659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10470 Z= 0.190 Angle : 0.589 7.577 14230 Z= 0.286 Chirality : 0.044 0.369 1756 Planarity : 0.004 0.072 1628 Dihedral : 12.439 143.597 2613 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 10.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 3.44 % Allowed : 18.55 % Favored : 78.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.88 (0.19), residues: 794 sheet: 0.92 (0.67), residues: 50 loop : -1.34 (0.33), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 74 HIS 0.002 0.001 HIS D 656 PHE 0.018 0.001 PHE C 141 TYR 0.013 0.001 TYR C 371 ARG 0.007 0.000 ARG C 79 *********************** 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 153 residues out of total 1046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 117 time to evaluate : 1.003 Fit side-chains REVERT: C 37 GLU cc_start: 0.7988 (OUTLIER) cc_final: 0.7656 (pm20) REVERT: C 187 LEU cc_start: 0.8307 (mt) cc_final: 0.7999 (mm) REVERT: C 320 GLU cc_start: 0.7987 (OUTLIER) cc_final: 0.7191 (pm20) REVERT: C 573 ASP cc_start: 0.7304 (OUTLIER) cc_final: 0.6960 (t70) REVERT: C 704 GLU cc_start: 0.7988 (pt0) cc_final: 0.7737 (pt0) REVERT: D 187 LEU cc_start: 0.8316 (mt) cc_final: 0.8007 (mm) REVERT: D 320 GLU cc_start: 0.7933 (tp30) cc_final: 0.7253 (pm20) REVERT: D 573 ASP cc_start: 0.7299 (OUTLIER) cc_final: 0.6952 (t70) REVERT: D 704 GLU cc_start: 0.8002 (pt0) cc_final: 0.7751 (pt0) outliers start: 36 outliers final: 23 residues processed: 140 average time/residue: 0.8184 time to fit residues: 127.4096 Evaluate side-chains 142 residues out of total 1046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 115 time to evaluate : 1.013 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 22 VAL Chi-restraints excluded: chain C residue 37 GLU Chi-restraints excluded: chain C residue 85 LEU Chi-restraints excluded: chain C residue 100 LEU Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 320 GLU Chi-restraints excluded: chain C residue 385 PHE Chi-restraints excluded: chain C residue 404 THR Chi-restraints excluded: chain C residue 407 LEU Chi-restraints excluded: chain C residue 545 VAL Chi-restraints excluded: chain C residue 556 TYR Chi-restraints excluded: chain C residue 573 ASP Chi-restraints excluded: chain C residue 678 MET Chi-restraints excluded: chain D residue 22 VAL Chi-restraints excluded: chain D residue 85 LEU Chi-restraints excluded: chain D residue 100 LEU Chi-restraints excluded: chain D residue 219 LEU Chi-restraints excluded: chain D residue 277 LEU Chi-restraints excluded: chain D residue 385 PHE Chi-restraints excluded: chain D residue 404 THR Chi-restraints excluded: chain D residue 407 LEU Chi-restraints excluded: chain D residue 545 VAL Chi-restraints excluded: chain D residue 556 TYR Chi-restraints excluded: chain D residue 559 VAL Chi-restraints excluded: chain D residue 573 ASP Chi-restraints excluded: chain D residue 678 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 70 optimal weight: 6.9990 chunk 54 optimal weight: 0.8980 chunk 80 optimal weight: 8.9990 chunk 121 optimal weight: 3.9990 chunk 111 optimal weight: 0.3980 chunk 96 optimal weight: 0.9990 chunk 10 optimal weight: 1.9990 chunk 74 optimal weight: 0.6980 chunk 59 optimal weight: 0.0050 chunk 76 optimal weight: 2.9990 chunk 103 optimal weight: 0.9980 overall best weight: 0.5994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 684 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8024 moved from start: 0.1683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 10470 Z= 0.164 Angle : 0.569 8.118 14230 Z= 0.278 Chirality : 0.043 0.316 1756 Planarity : 0.004 0.070 1628 Dihedral : 11.964 141.208 2613 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 11.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 2.87 % Allowed : 19.12 % Favored : 78.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.99 (0.19), residues: 790 sheet: 0.87 (0.67), residues: 50 loop : -1.36 (0.33), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 74 HIS 0.002 0.001 HIS C 656 PHE 0.017 0.001 PHE D 141 TYR 0.012 0.001 TYR D 371 ARG 0.007 0.000 ARG D 79 ********************** 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 154 residues out of total 1046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 124 time to evaluate : 1.003 Fit side-chains REVERT: C 37 GLU cc_start: 0.7978 (OUTLIER) cc_final: 0.7645 (pm20) REVERT: C 187 LEU cc_start: 0.8287 (mt) cc_final: 0.7987 (mm) REVERT: C 320 GLU cc_start: 0.7964 (OUTLIER) cc_final: 0.7260 (pm20) REVERT: C 503 MET cc_start: 0.7537 (mmm) cc_final: 0.7014 (mmm) REVERT: C 573 ASP cc_start: 0.7327 (OUTLIER) cc_final: 0.6979 (t70) REVERT: C 701 GLU cc_start: 0.7763 (mm-30) cc_final: 0.7513 (mm-30) REVERT: C 704 GLU cc_start: 0.7984 (pt0) cc_final: 0.7755 (pt0) REVERT: D 187 LEU cc_start: 0.8296 (mt) cc_final: 0.7992 (mm) REVERT: D 320 GLU cc_start: 0.7936 (tp30) cc_final: 0.7282 (pm20) REVERT: D 503 MET cc_start: 0.7615 (mmt) cc_final: 0.7143 (mmp) REVERT: D 573 ASP cc_start: 0.7314 (OUTLIER) cc_final: 0.6972 (t70) REVERT: D 704 GLU cc_start: 0.7968 (pt0) cc_final: 0.7757 (pt0) outliers start: 30 outliers final: 24 residues processed: 143 average time/residue: 0.8182 time to fit residues: 131.2224 Evaluate side-chains 147 residues out of total 1046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 119 time to evaluate : 1.167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 22 VAL Chi-restraints excluded: chain C residue 37 GLU Chi-restraints excluded: chain C residue 85 LEU Chi-restraints excluded: chain C residue 100 LEU Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 320 GLU Chi-restraints excluded: chain C residue 385 PHE Chi-restraints excluded: chain C residue 404 THR Chi-restraints excluded: chain C residue 407 LEU Chi-restraints excluded: chain C residue 545 VAL Chi-restraints excluded: chain C residue 556 TYR Chi-restraints excluded: chain C residue 573 ASP Chi-restraints excluded: chain C residue 678 MET Chi-restraints excluded: chain D residue 22 VAL Chi-restraints excluded: chain D residue 85 LEU Chi-restraints excluded: chain D residue 100 LEU Chi-restraints excluded: chain D residue 219 LEU Chi-restraints excluded: chain D residue 277 LEU Chi-restraints excluded: chain D residue 385 PHE Chi-restraints excluded: chain D residue 404 THR Chi-restraints excluded: chain D residue 407 LEU Chi-restraints excluded: chain D residue 463 MET Chi-restraints excluded: chain D residue 545 VAL Chi-restraints excluded: chain D residue 556 TYR Chi-restraints excluded: chain D residue 559 VAL Chi-restraints excluded: chain D residue 573 ASP Chi-restraints excluded: chain D residue 678 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 29 optimal weight: 0.7980 chunk 89 optimal weight: 0.2980 chunk 14 optimal weight: 0.9980 chunk 26 optimal weight: 8.9990 chunk 96 optimal weight: 2.9990 chunk 40 optimal weight: 0.7980 chunk 99 optimal weight: 1.9990 chunk 12 optimal weight: 0.7980 chunk 17 optimal weight: 6.9990 chunk 85 optimal weight: 0.0670 chunk 5 optimal weight: 7.9990 overall best weight: 0.5518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 689 HIS D 684 GLN D 689 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.144751 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.113090 restraints weight = 12673.947| |-----------------------------------------------------------------------------| r_work (start): 0.3475 rms_B_bonded: 2.15 r_work: 0.3358 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3246 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3246 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7951 moved from start: 0.1764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 10470 Z= 0.160 Angle : 0.556 7.356 14230 Z= 0.273 Chirality : 0.042 0.249 1756 Planarity : 0.004 0.069 1628 Dihedral : 11.622 138.304 2613 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 11.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer: Outliers : 2.77 % Allowed : 19.69 % Favored : 77.53 % 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: 1.50 (0.25), residues: 1210 helix: 2.07 (0.19), residues: 784 sheet: 0.81 (0.66), residues: 50 loop : -1.37 (0.33), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 74 HIS 0.002 0.001 HIS D 689 PHE 0.018 0.001 PHE D 141 TYR 0.012 0.001 TYR C 371 ARG 0.008 0.000 ARG C 79 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3231.33 seconds wall clock time: 58 minutes 12.47 seconds (3492.47 seconds total)