Starting phenix.real_space_refine on Sat Aug 23 06:01:19 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8uuk_42588/08_2025/8uuk_42588.cif Found real_map, /net/cci-nas-00/data/ceres_data/8uuk_42588/08_2025/8uuk_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/cci-nas-00/data/ceres_data/8uuk_42588/08_2025/8uuk_42588.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8uuk_42588/08_2025/8uuk_42588.map" model { file = "/net/cci-nas-00/data/ceres_data/8uuk_42588/08_2025/8uuk_42588.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8uuk_42588/08_2025/8uuk_42588.cif" } resolution = 2.5 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 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. Time to flip 8 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 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-3': 7, 'LBN:plan-1': 6, 'LBN:plan-2': 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-3': 7, 'LBN:plan-1': 6, 'LBN:plan-2': 6} Unresolved non-hydrogen planarities: 68 Time building chain proxies: 2.71, per 1000 atoms: 0.26 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 - 3.00 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: 1.15 Conformation dependent library (CDL) restraints added in 402.7 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 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 5 sheets defined 71.1% alpha, 4.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.40 Creating SS restraints... Processing helix chain 'C' and resid 28 through 36 Processing helix chain 'C' and resid 70 through 74 Processing helix chain 'C' and resid 82 through 109 removed outlier: 4.221A pdb=" N SER C 86 " --> pdb=" O GLU C 82 " (cutoff:3.500A) 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 114 through 131 removed outlier: 3.626A pdb=" N TYR C 118 " --> pdb=" O GLY C 114 " (cutoff:3.500A) 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 141 through 156 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: 4.073A pdb=" N VAL C 212 " --> pdb=" O GLY C 209 " (cutoff:3.500A) Processing helix chain 'C' and resid 216 through 240 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 Processing helix chain 'C' and resid 342 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 349 through 376 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 380 through 398 Processing helix chain 'C' and resid 406 through 416 removed outlier: 3.506A 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 446 through 458 removed outlier: 3.976A 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 464 through 466 No H-bonds generated for 'chain 'C' and resid 464 through 466' Processing helix chain 'C' and resid 467 through 475 Processing helix chain 'C' and resid 475 through 491 Processing helix chain 'C' and resid 493 through 515 Processing helix chain 'C' and resid 533 through 537 removed outlier: 4.217A 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 Processing helix chain 'C' and resid 669 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 696 through 706 Processing helix chain 'C' and resid 723 through 731 Processing helix chain 'D' and resid 28 through 36 Processing helix chain 'D' and resid 70 through 74 Processing helix chain 'D' and resid 82 through 109 removed outlier: 4.215A pdb=" N SER D 86 " --> pdb=" O GLU D 82 " (cutoff:3.500A) 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 114 through 131 removed outlier: 3.625A pdb=" N TYR D 118 " --> pdb=" O GLY D 114 " (cutoff:3.500A) 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 141 through 156 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: 4.033A pdb=" N VAL D 212 " --> pdb=" O GLY D 209 " (cutoff:3.500A) Processing helix chain 'D' and resid 216 through 240 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 Processing helix chain 'D' and resid 342 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 349 through 376 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 380 through 398 Processing helix chain 'D' and resid 406 through 416 removed outlier: 3.505A 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 446 through 458 removed outlier: 3.978A 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 464 through 466 No H-bonds generated for 'chain 'D' and resid 464 through 466' Processing helix chain 'D' and resid 467 through 475 Processing helix chain 'D' and resid 475 through 491 Processing helix chain 'D' and resid 493 through 515 Processing helix chain 'D' and resid 533 through 537 removed outlier: 4.216A 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 Processing helix chain 'D' and resid 669 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 696 through 706 Processing helix chain 'D' and resid 723 through 731 Processing sheet with id=AA1, first strand: chain 'C' and resid 19 through 25 removed outlier: 3.643A pdb=" N VAL C 22 " --> pdb=" O VAL D 22 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N VAL D 22 " --> pdb=" O VAL C 22 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 138 through 139 Processing sheet with id=AA3, 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: 6.416A pdb=" N LYS C 546 " --> pdb=" O VAL C 659 " (cutoff:3.500A) removed outlier: 7.263A pdb=" N ASP C 661 " --> pdb=" O LYS C 546 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N LEU C 548 " --> pdb=" O ASP C 661 " (cutoff:3.500A) removed outlier: 8.476A pdb=" N PHE C 719 " --> pdb=" O VAL C 690 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N PHE C 692 " --> pdb=" O PHE C 719 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 138 through 139 Processing sheet with id=AA5, 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: 6.418A pdb=" N LYS D 546 " --> pdb=" O VAL D 659 " (cutoff:3.500A) removed outlier: 7.269A pdb=" N ASP D 661 " --> pdb=" O LYS D 546 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N LEU D 548 " --> pdb=" O ASP D 661 " (cutoff:3.500A) removed outlier: 8.475A pdb=" N PHE D 719 " --> pdb=" O VAL D 690 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N PHE D 692 " --> pdb=" O PHE D 719 " (cutoff:3.500A) 624 hydrogen bonds defined for protein. 1818 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.85 Time building geometry restraints manager: 1.46 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: 0.00 - 2.08: 13935 2.08 - 4.15: 251 4.15 - 6.23: 29 6.23 - 8.31: 11 8.31 - 10.38: 4 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: 392 2.72 - 3.27: 10565 3.27 - 3.81: 17515 3.81 - 4.36: 21654 4.36 - 4.90: 36283 Nonbonded interactions: 86409 Sorted by model distance: nonbonded pdb=" O PRO C 553 " pdb=" ND2 ASN C 558 " model vdw 2.180 3.120 nonbonded pdb=" O PRO D 553 " pdb=" ND2 ASN D 558 " model vdw 2.188 3.120 nonbonded pdb=" OH TYR D 247 " pdb=" OE1 GLU D 259 " model vdw 2.229 3.040 nonbonded pdb=" OH TYR C 247 " pdb=" OE1 GLU C 259 " model vdw 2.233 3.040 nonbonded pdb=" OH TYR D 78 " pdb=" OD2 ASP D 87 " model vdw 2.240 3.040 ... (remaining 86404 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.02 Found NCS groups: ncs_group { reference = chain 'C' 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: 1.050 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.240 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 11.860 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.010 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:9.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.050 ------------------------------------------------------------------------------- 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 10471 Z= 0.191 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 : 11.07 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.07 (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 ARG 0.009 0.000 ARG C 79 TYR 0.012 0.001 TYR D 371 PHE 0.017 0.001 PHE D 141 TRP 0.013 0.001 TRP D 74 HIS 0.003 0.001 HIS C 656 Details of bonding type rmsd covalent geometry : bond 0.00397 (10470) covalent geometry : angle 0.66532 (14230) hydrogen bonds : bond 0.12004 ( 624) hydrogen bonds : angle 5.26453 ( 1818) Misc. bond : bond 0.00037 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 127 time to evaluate : 0.429 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: 0.3389 time to fit residues: 54.5299 Evaluate side-chains 141 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 127 time to evaluate : 0.408 ------------------------------------------------------------------------------- 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 108 optimal weight: 0.9980 chunk 49 optimal weight: 0.9990 chunk 97 optimal weight: 9.9990 chunk 113 optimal weight: 4.9990 chunk 53 optimal weight: 0.9990 chunk 5 optimal weight: 10.0000 chunk 33 optimal weight: 3.9990 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 4.9990 chunk 51 optimal weight: 0.8980 chunk 117 optimal weight: 0.7980 overall best weight: 0.9384 ------------------------------------------------------------------------------- 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 248 ASN D 684 GLN D 689 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.144020 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.110988 restraints weight = 12076.894| |-----------------------------------------------------------------------------| r_work (start): 0.3421 rms_B_bonded: 2.04 r_work: 0.3300 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3175 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.3175 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8086 moved from start: 0.0885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 10471 Z= 0.155 Angle : 0.661 9.989 14230 Z= 0.322 Chirality : 0.045 0.233 1756 Planarity : 0.005 0.076 1628 Dihedral : 16.919 159.003 2621 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 9.61 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.37 % Favored : 94.46 % Rotamer: Outliers : 3.44 % Allowed : 14.44 % Favored : 82.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.15 (0.25), residues: 1210 helix: 1.71 (0.18), residues: 798 sheet: 0.95 (0.68), residues: 50 loop : -1.47 (0.33), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 79 TYR 0.014 0.002 TYR C 371 PHE 0.023 0.002 PHE D 141 TRP 0.013 0.001 TRP C 74 HIS 0.002 0.001 HIS D 698 Details of bonding type rmsd covalent geometry : bond 0.00351 (10470) covalent geometry : angle 0.66110 (14230) hydrogen bonds : bond 0.04734 ( 624) hydrogen bonds : angle 4.32639 ( 1818) Misc. bond : bond 0.00051 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 134 time to evaluate : 0.419 Fit side-chains REVERT: C 187 LEU cc_start: 0.8297 (mt) cc_final: 0.8027 (mm) REVERT: C 560 ASP cc_start: 0.7333 (m-30) cc_final: 0.7077 (m-30) REVERT: C 576 ARG cc_start: 0.7301 (ttt180) cc_final: 0.7091 (ttm-80) REVERT: D 187 LEU cc_start: 0.8305 (mt) cc_final: 0.8030 (mm) outliers start: 36 outliers final: 16 residues processed: 158 average time/residue: 0.4243 time to fit residues: 74.5260 Evaluate side-chains 133 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 117 time to evaluate : 0.397 ------------------------------------------------------------------------------- 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 385 PHE 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 704 GLU Chi-restraints excluded: chain D residue 100 LEU Chi-restraints excluded: chain D residue 219 LEU Chi-restraints excluded: chain D residue 252 SER 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 559 VAL Chi-restraints excluded: chain D residue 678 MET Chi-restraints excluded: chain D residue 704 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 42 optimal weight: 3.9990 chunk 93 optimal weight: 4.9990 chunk 44 optimal weight: 5.9990 chunk 77 optimal weight: 1.9990 chunk 103 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 39 optimal weight: 2.9990 chunk 73 optimal weight: 0.9990 chunk 58 optimal weight: 0.6980 chunk 18 optimal weight: 2.9990 chunk 66 optimal weight: 2.9990 overall best weight: 1.5388 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.140375 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.107640 restraints weight = 12872.374| |-----------------------------------------------------------------------------| r_work (start): 0.3405 rms_B_bonded: 2.15 r_work: 0.3288 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3176 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3176 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8039 moved from start: 0.1216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 10471 Z= 0.182 Angle : 0.642 8.359 14230 Z= 0.319 Chirality : 0.046 0.276 1756 Planarity : 0.005 0.078 1628 Dihedral : 15.993 158.390 2613 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.71 % Favored : 95.12 % Rotamer: Outliers : 3.82 % Allowed : 15.11 % Favored : 81.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.08 (0.25), residues: 1210 helix: 1.66 (0.18), residues: 798 sheet: 0.93 (0.66), residues: 50 loop : -1.49 (0.33), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 79 TYR 0.016 0.002 TYR D 371 PHE 0.019 0.002 PHE C 141 TRP 0.012 0.001 TRP D 74 HIS 0.002 0.001 HIS D 656 Details of bonding type rmsd covalent geometry : bond 0.00419 (10470) covalent geometry : angle 0.64218 (14230) hydrogen bonds : bond 0.05124 ( 624) hydrogen bonds : angle 4.35323 ( 1818) Misc. bond : bond 0.00102 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 115 time to evaluate : 0.402 Fit side-chains REVERT: C 103 MET cc_start: 0.8600 (OUTLIER) cc_final: 0.8386 (mtp) REVERT: C 187 LEU cc_start: 0.8225 (mt) cc_final: 0.7947 (mm) REVERT: C 560 ASP cc_start: 0.7302 (m-30) cc_final: 0.6948 (m-30) REVERT: C 576 ARG cc_start: 0.7311 (ttt180) cc_final: 0.7067 (ttm-80) REVERT: D 103 MET cc_start: 0.8613 (OUTLIER) cc_final: 0.8402 (mtp) REVERT: D 187 LEU cc_start: 0.8226 (mt) cc_final: 0.7944 (mm) outliers start: 40 outliers final: 20 residues processed: 143 average time/residue: 0.4308 time to fit residues: 68.2954 Evaluate side-chains 133 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 111 time to evaluate : 0.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 22 VAL Chi-restraints excluded: chain C residue 80 ILE 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 385 PHE 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 704 GLU Chi-restraints excluded: chain D residue 22 VAL 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 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 704 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 77 optimal weight: 2.9990 chunk 33 optimal weight: 0.6980 chunk 89 optimal weight: 8.9990 chunk 120 optimal weight: 2.9990 chunk 93 optimal weight: 6.9990 chunk 1 optimal weight: 1.9990 chunk 74 optimal weight: 0.6980 chunk 114 optimal weight: 0.5980 chunk 57 optimal weight: 2.9990 chunk 30 optimal weight: 2.9990 chunk 91 optimal weight: 0.8980 overall best weight: 0.9782 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.141989 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.109467 restraints weight = 12840.818| |-----------------------------------------------------------------------------| r_work (start): 0.3425 rms_B_bonded: 2.16 r_work: 0.3309 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3196 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3196 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8008 moved from start: 0.1396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10471 Z= 0.140 Angle : 0.609 7.545 14230 Z= 0.302 Chirality : 0.045 0.332 1756 Planarity : 0.005 0.084 1628 Dihedral : 14.823 154.588 2613 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 9.37 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.88 % Favored : 94.96 % Rotamer: Outliers : 3.44 % Allowed : 16.16 % Favored : 80.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.22 (0.25), residues: 1210 helix: 1.73 (0.18), residues: 808 sheet: 0.84 (0.64), residues: 50 loop : -1.43 (0.33), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 79 TYR 0.015 0.001 TYR D 371 PHE 0.021 0.001 PHE C 141 TRP 0.011 0.001 TRP C 74 HIS 0.003 0.001 HIS D 656 Details of bonding type rmsd covalent geometry : bond 0.00313 (10470) covalent geometry : angle 0.60909 (14230) hydrogen bonds : bond 0.04585 ( 624) hydrogen bonds : angle 4.18913 ( 1818) Misc. bond : bond 0.00038 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 128 time to evaluate : 0.381 Fit side-chains REVERT: C 103 MET cc_start: 0.8579 (OUTLIER) cc_final: 0.8377 (mtp) REVERT: C 187 LEU cc_start: 0.8229 (mt) cc_final: 0.7947 (mm) REVERT: C 560 ASP cc_start: 0.7299 (m-30) cc_final: 0.6971 (m-30) REVERT: C 576 ARG cc_start: 0.7311 (ttt180) cc_final: 0.7082 (ttm-80) REVERT: D 187 LEU cc_start: 0.8215 (mt) cc_final: 0.7929 (mm) outliers start: 36 outliers final: 19 residues processed: 150 average time/residue: 0.4415 time to fit residues: 73.3603 Evaluate side-chains 133 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 113 time to evaluate : 0.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 248 ASN Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 385 PHE 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 D residue 100 LEU Chi-restraints excluded: chain D residue 219 LEU Chi-restraints excluded: chain D residue 252 SER Chi-restraints excluded: chain D residue 277 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 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 94 optimal weight: 0.9990 chunk 65 optimal weight: 3.9990 chunk 62 optimal weight: 3.9990 chunk 103 optimal weight: 0.6980 chunk 47 optimal weight: 0.6980 chunk 10 optimal weight: 0.6980 chunk 53 optimal weight: 10.0000 chunk 26 optimal weight: 6.9990 chunk 111 optimal weight: 0.5980 chunk 109 optimal weight: 0.9990 chunk 105 optimal weight: 4.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.143072 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.110932 restraints weight = 12822.424| |-----------------------------------------------------------------------------| r_work (start): 0.3444 rms_B_bonded: 2.15 r_work: 0.3329 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3216 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3216 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7992 moved from start: 0.1507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10471 Z= 0.130 Angle : 0.635 16.650 14230 Z= 0.304 Chirality : 0.045 0.334 1756 Planarity : 0.005 0.080 1628 Dihedral : 14.209 151.730 2613 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 9.70 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.96 % Favored : 94.88 % Rotamer: Outliers : 3.63 % Allowed : 16.06 % Favored : 80.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.24 (0.24), residues: 1210 helix: 1.76 (0.18), residues: 802 sheet: 0.65 (0.63), residues: 50 loop : -1.37 (0.33), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 79 TYR 0.015 0.001 TYR D 371 PHE 0.021 0.001 PHE D 141 TRP 0.008 0.001 TRP C 74 HIS 0.002 0.001 HIS D 656 Details of bonding type rmsd covalent geometry : bond 0.00280 (10470) covalent geometry : angle 0.63510 (14230) hydrogen bonds : bond 0.04508 ( 624) hydrogen bonds : angle 4.14207 ( 1818) Misc. bond : bond 0.00011 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 118 time to evaluate : 0.427 Fit side-chains REVERT: C 66 LYS cc_start: 0.6038 (tppt) cc_final: 0.5817 (tppt) REVERT: C 103 MET cc_start: 0.8561 (OUTLIER) cc_final: 0.8356 (mtp) REVERT: C 187 LEU cc_start: 0.8216 (mt) cc_final: 0.7932 (mm) REVERT: C 560 ASP cc_start: 0.7324 (m-30) cc_final: 0.6936 (m-30) REVERT: C 576 ARG cc_start: 0.7307 (ttt180) cc_final: 0.7058 (ttm-80) REVERT: D 66 LYS cc_start: 0.6095 (tppt) cc_final: 0.5877 (tppt) REVERT: D 187 LEU cc_start: 0.8216 (mt) cc_final: 0.7929 (mm) outliers start: 38 outliers final: 26 residues processed: 142 average time/residue: 0.4352 time to fit residues: 68.2974 Evaluate side-chains 143 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 116 time to evaluate : 0.398 ------------------------------------------------------------------------------- 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 103 MET 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 407 LEU Chi-restraints excluded: chain C residue 545 VAL Chi-restraints excluded: chain C residue 552 SER Chi-restraints excluded: chain C residue 556 TYR 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 248 ASN Chi-restraints excluded: chain D residue 252 SER 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 118 optimal weight: 2.9990 chunk 70 optimal weight: 4.9990 chunk 61 optimal weight: 7.9990 chunk 24 optimal weight: 0.0770 chunk 93 optimal weight: 1.9990 chunk 22 optimal weight: 6.9990 chunk 88 optimal weight: 2.9990 chunk 34 optimal weight: 2.9990 chunk 56 optimal weight: 2.9990 chunk 55 optimal weight: 0.9990 chunk 15 optimal weight: 0.0980 overall best weight: 1.2344 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.140241 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.107777 restraints weight = 12954.138| |-----------------------------------------------------------------------------| r_work (start): 0.3401 rms_B_bonded: 2.16 r_work: 0.3284 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3171 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3171 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8028 moved from start: 0.1697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 10471 Z= 0.160 Angle : 0.636 11.812 14230 Z= 0.310 Chirality : 0.046 0.328 1756 Planarity : 0.005 0.078 1628 Dihedral : 13.912 148.770 2613 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 9.42 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.96 % Favored : 94.88 % Rotamer: Outliers : 3.54 % Allowed : 16.16 % Favored : 80.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.19 (0.24), residues: 1210 helix: 1.72 (0.18), residues: 802 sheet: 0.56 (0.62), residues: 50 loop : -1.33 (0.33), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 79 TYR 0.016 0.002 TYR D 371 PHE 0.021 0.001 PHE C 141 TRP 0.011 0.001 TRP C 74 HIS 0.002 0.001 HIS D 656 Details of bonding type rmsd covalent geometry : bond 0.00358 (10470) covalent geometry : angle 0.63569 (14230) hydrogen bonds : bond 0.04806 ( 624) hydrogen bonds : angle 4.19588 ( 1818) Misc. bond : bond 0.00034 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 121 time to evaluate : 0.409 Fit side-chains REVERT: C 103 MET cc_start: 0.8627 (OUTLIER) cc_final: 0.8423 (mtp) REVERT: C 187 LEU cc_start: 0.8256 (mt) cc_final: 0.7964 (mm) REVERT: C 560 ASP cc_start: 0.7393 (m-30) cc_final: 0.7010 (m-30) REVERT: C 576 ARG cc_start: 0.7314 (ttt180) cc_final: 0.7043 (ttm-80) REVERT: C 704 GLU cc_start: 0.8129 (OUTLIER) cc_final: 0.7876 (pt0) REVERT: D 187 LEU cc_start: 0.8248 (mt) cc_final: 0.7958 (mm) REVERT: D 704 GLU cc_start: 0.8125 (OUTLIER) cc_final: 0.7878 (pt0) outliers start: 37 outliers final: 25 residues processed: 142 average time/residue: 0.4329 time to fit residues: 67.9359 Evaluate side-chains 142 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 114 time to evaluate : 0.399 ------------------------------------------------------------------------------- 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 103 MET 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 407 LEU Chi-restraints excluded: chain C residue 545 VAL Chi-restraints excluded: chain C residue 552 SER 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 219 LEU Chi-restraints excluded: chain D residue 248 ASN 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 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 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 115 optimal weight: 0.7980 chunk 50 optimal weight: 0.7980 chunk 15 optimal weight: 2.9990 chunk 97 optimal weight: 8.9990 chunk 11 optimal weight: 2.9990 chunk 23 optimal weight: 9.9990 chunk 102 optimal weight: 0.9990 chunk 2 optimal weight: 0.9980 chunk 81 optimal weight: 0.8980 chunk 105 optimal weight: 4.9990 chunk 108 optimal weight: 0.9980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 689 HIS D 689 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.142174 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.109942 restraints weight = 12769.832| |-----------------------------------------------------------------------------| r_work (start): 0.3426 rms_B_bonded: 2.15 r_work: 0.3312 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3198 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.3198 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8004 moved from start: 0.1763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10471 Z= 0.136 Angle : 0.620 10.393 14230 Z= 0.303 Chirality : 0.045 0.292 1756 Planarity : 0.005 0.081 1628 Dihedral : 13.383 148.113 2613 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 10.41 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.71 % Favored : 95.12 % Rotamer: Outliers : 3.35 % Allowed : 17.02 % Favored : 79.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.33 (0.25), residues: 1210 helix: 1.82 (0.18), residues: 802 sheet: 0.56 (0.62), residues: 50 loop : -1.27 (0.34), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 79 TYR 0.015 0.001 TYR D 371 PHE 0.022 0.001 PHE D 141 TRP 0.009 0.001 TRP C 74 HIS 0.002 0.001 HIS C 656 Details of bonding type rmsd covalent geometry : bond 0.00299 (10470) covalent geometry : angle 0.62046 (14230) hydrogen bonds : bond 0.04514 ( 624) hydrogen bonds : angle 4.12187 ( 1818) Misc. bond : bond 0.00014 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 119 time to evaluate : 0.405 Fit side-chains REVERT: C 66 LYS cc_start: 0.6265 (mmmt) cc_final: 0.5525 (tppt) REVERT: C 187 LEU cc_start: 0.8235 (mt) cc_final: 0.7957 (mm) REVERT: C 217 ASP cc_start: 0.8158 (m-30) cc_final: 0.7944 (m-30) REVERT: C 320 GLU cc_start: 0.7924 (tp30) cc_final: 0.6990 (pm20) REVERT: C 560 ASP cc_start: 0.7319 (m-30) cc_final: 0.6950 (m-30) REVERT: C 576 ARG cc_start: 0.7317 (ttt180) cc_final: 0.7035 (ttm-80) REVERT: C 704 GLU cc_start: 0.8117 (OUTLIER) cc_final: 0.7907 (pt0) REVERT: D 66 LYS cc_start: 0.6225 (mmmt) cc_final: 0.5491 (tppt) REVERT: D 187 LEU cc_start: 0.8229 (mt) cc_final: 0.7946 (mm) REVERT: D 704 GLU cc_start: 0.8105 (OUTLIER) cc_final: 0.7898 (pt0) outliers start: 35 outliers final: 23 residues processed: 141 average time/residue: 0.4109 time to fit residues: 63.9736 Evaluate side-chains 143 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 118 time to evaluate : 0.388 ------------------------------------------------------------------------------- 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 385 PHE Chi-restraints excluded: chain C residue 407 LEU Chi-restraints excluded: chain C residue 545 VAL Chi-restraints excluded: chain C residue 552 SER 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 219 LEU Chi-restraints excluded: chain D residue 248 ASN 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 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 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 13 optimal weight: 2.9990 chunk 36 optimal weight: 5.9990 chunk 52 optimal weight: 2.9990 chunk 70 optimal weight: 0.9980 chunk 75 optimal weight: 4.9990 chunk 121 optimal weight: 0.9980 chunk 77 optimal weight: 3.9990 chunk 46 optimal weight: 2.9990 chunk 67 optimal weight: 0.8980 chunk 97 optimal weight: 0.9980 chunk 95 optimal weight: 0.7980 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 689 HIS D 689 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.141646 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.109390 restraints weight = 12841.397| |-----------------------------------------------------------------------------| r_work (start): 0.3425 rms_B_bonded: 2.15 r_work: 0.3308 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3195 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3195 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8009 moved from start: 0.1864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10471 Z= 0.140 Angle : 0.615 8.559 14230 Z= 0.301 Chirality : 0.045 0.330 1756 Planarity : 0.005 0.077 1628 Dihedral : 12.937 145.889 2613 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 10.36 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.04 % Favored : 94.79 % Rotamer: Outliers : 3.54 % Allowed : 17.30 % Favored : 79.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.27 (0.25), residues: 1210 helix: 1.77 (0.18), residues: 814 sheet: 0.58 (0.62), residues: 50 loop : -1.38 (0.34), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 79 TYR 0.015 0.001 TYR D 371 PHE 0.022 0.001 PHE C 141 TRP 0.009 0.001 TRP C 74 HIS 0.002 0.001 HIS D 656 Details of bonding type rmsd covalent geometry : bond 0.00310 (10470) covalent geometry : angle 0.61477 (14230) hydrogen bonds : bond 0.04559 ( 624) hydrogen bonds : angle 4.11911 ( 1818) Misc. bond : bond 0.00018 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 119 time to evaluate : 0.401 Fit side-chains REVERT: C 66 LYS cc_start: 0.6164 (mmmt) cc_final: 0.5410 (tppt) REVERT: C 187 LEU cc_start: 0.8254 (mt) cc_final: 0.7959 (mm) REVERT: C 217 ASP cc_start: 0.8147 (m-30) cc_final: 0.7930 (m-30) REVERT: C 320 GLU cc_start: 0.7892 (tp30) cc_final: 0.7075 (pm20) REVERT: C 576 ARG cc_start: 0.7303 (ttt180) cc_final: 0.7055 (ttm-80) REVERT: C 704 GLU cc_start: 0.8098 (OUTLIER) cc_final: 0.7880 (pt0) REVERT: D 66 LYS cc_start: 0.6172 (mmmt) cc_final: 0.5423 (tppt) REVERT: D 187 LEU cc_start: 0.8236 (mt) cc_final: 0.7945 (mm) REVERT: D 329 LYS cc_start: 0.8424 (OUTLIER) cc_final: 0.8190 (ttmm) REVERT: D 704 GLU cc_start: 0.8100 (OUTLIER) cc_final: 0.7888 (pt0) outliers start: 37 outliers final: 23 residues processed: 143 average time/residue: 0.4017 time to fit residues: 63.4502 Evaluate side-chains 142 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 116 time to evaluate : 0.361 ------------------------------------------------------------------------------- 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 385 PHE Chi-restraints excluded: chain C residue 407 LEU Chi-restraints excluded: chain C residue 545 VAL Chi-restraints excluded: chain C residue 552 SER 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 219 LEU Chi-restraints excluded: chain D residue 248 ASN Chi-restraints excluded: chain D residue 277 LEU Chi-restraints excluded: chain D residue 329 LYS 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 556 TYR Chi-restraints excluded: chain D residue 559 VAL 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 33 optimal weight: 4.9990 chunk 100 optimal weight: 0.4980 chunk 41 optimal weight: 0.9980 chunk 88 optimal weight: 1.9990 chunk 16 optimal weight: 0.8980 chunk 37 optimal weight: 3.9990 chunk 60 optimal weight: 4.9990 chunk 97 optimal weight: 8.9990 chunk 67 optimal weight: 0.9990 chunk 31 optimal weight: 0.8980 chunk 69 optimal weight: 0.7980 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 = 0.3761 r_free = 0.3761 target = 0.142631 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.110553 restraints weight = 12782.702| |-----------------------------------------------------------------------------| r_work (start): 0.3440 rms_B_bonded: 2.14 r_work: 0.3324 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3211 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3211 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7993 moved from start: 0.1904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 10471 Z= 0.131 Angle : 0.604 8.312 14230 Z= 0.297 Chirality : 0.045 0.367 1756 Planarity : 0.005 0.080 1628 Dihedral : 12.478 144.389 2613 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 10.22 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.79 % Favored : 95.04 % Rotamer: Outliers : 2.96 % Allowed : 17.97 % Favored : 79.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.35 (0.25), residues: 1210 helix: 1.81 (0.18), residues: 812 sheet: 0.57 (0.62), residues: 50 loop : -1.30 (0.35), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 79 TYR 0.014 0.001 TYR D 371 PHE 0.022 0.001 PHE C 141 TRP 0.009 0.001 TRP C 74 HIS 0.002 0.001 HIS C 698 Details of bonding type rmsd covalent geometry : bond 0.00286 (10470) covalent geometry : angle 0.60365 (14230) hydrogen bonds : bond 0.04442 ( 624) hydrogen bonds : angle 4.09514 ( 1818) Misc. bond : bond 0.00015 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 125 time to evaluate : 0.243 Fit side-chains REVERT: C 66 LYS cc_start: 0.6185 (mmmt) cc_final: 0.5583 (tppt) REVERT: C 187 LEU cc_start: 0.8246 (mt) cc_final: 0.7953 (mm) REVERT: C 217 ASP cc_start: 0.8133 (m-30) cc_final: 0.7926 (m-30) REVERT: C 320 GLU cc_start: 0.7894 (tp30) cc_final: 0.7106 (pm20) REVERT: C 576 ARG cc_start: 0.7305 (ttt180) cc_final: 0.7059 (ttm-80) REVERT: C 701 GLU cc_start: 0.7650 (mm-30) cc_final: 0.7205 (pt0) REVERT: D 66 LYS cc_start: 0.6163 (mmmt) cc_final: 0.5521 (tppt) REVERT: D 187 LEU cc_start: 0.8242 (mt) cc_final: 0.7957 (mm) REVERT: D 329 LYS cc_start: 0.8404 (OUTLIER) cc_final: 0.8176 (ttmm) REVERT: D 704 GLU cc_start: 0.8088 (OUTLIER) cc_final: 0.7877 (pt0) outliers start: 31 outliers final: 22 residues processed: 145 average time/residue: 0.4309 time to fit residues: 68.6218 Evaluate side-chains 140 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 116 time to evaluate : 0.375 ------------------------------------------------------------------------------- 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 248 ASN Chi-restraints excluded: chain C residue 385 PHE Chi-restraints excluded: chain C residue 407 LEU Chi-restraints excluded: chain C residue 545 VAL Chi-restraints excluded: chain C residue 552 SER Chi-restraints excluded: chain C residue 556 TYR 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 248 ASN Chi-restraints excluded: chain D residue 277 LEU Chi-restraints excluded: chain D residue 329 LYS 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 556 TYR Chi-restraints excluded: chain D residue 559 VAL Chi-restraints excluded: chain D residue 678 MET Chi-restraints excluded: chain D residue 704 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 41 optimal weight: 0.9980 chunk 17 optimal weight: 0.8980 chunk 63 optimal weight: 0.0980 chunk 32 optimal weight: 0.1980 chunk 93 optimal weight: 4.9990 chunk 107 optimal weight: 0.6980 chunk 112 optimal weight: 1.9990 chunk 91 optimal weight: 4.9990 chunk 97 optimal weight: 6.9990 chunk 92 optimal weight: 0.5980 chunk 75 optimal weight: 0.9980 overall best weight: 0.4980 ------------------------------------------------------------------------------- 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 = 0.3785 r_free = 0.3785 target = 0.144655 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.112873 restraints weight = 12630.206| |-----------------------------------------------------------------------------| r_work (start): 0.3467 rms_B_bonded: 2.13 r_work: 0.3355 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3242 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.3242 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7964 moved from start: 0.2001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 10471 Z= 0.117 Angle : 0.588 8.923 14230 Z= 0.289 Chirality : 0.044 0.339 1756 Planarity : 0.005 0.077 1628 Dihedral : 12.049 142.664 2609 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 10.13 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.21 % Favored : 94.63 % Rotamer: Outliers : 2.49 % Allowed : 19.02 % Favored : 78.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.42 (0.25), residues: 1210 helix: 1.91 (0.18), residues: 810 sheet: 0.58 (0.63), residues: 50 loop : -1.37 (0.35), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 79 TYR 0.012 0.001 TYR D 371 PHE 0.023 0.001 PHE C 141 TRP 0.009 0.001 TRP D 482 HIS 0.002 0.001 HIS D 698 Details of bonding type rmsd covalent geometry : bond 0.00245 (10470) covalent geometry : angle 0.58812 (14230) hydrogen bonds : bond 0.04243 ( 624) hydrogen bonds : angle 4.04308 ( 1818) Misc. bond : bond 0.00007 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 126 time to evaluate : 0.380 Fit side-chains REVERT: C 66 LYS cc_start: 0.5992 (mmmt) cc_final: 0.5300 (tppt) REVERT: C 187 LEU cc_start: 0.8215 (mt) cc_final: 0.7929 (mm) REVERT: C 217 ASP cc_start: 0.8086 (m-30) cc_final: 0.7859 (m-30) REVERT: C 320 GLU cc_start: 0.7895 (tp30) cc_final: 0.7142 (pm20) REVERT: C 503 MET cc_start: 0.8010 (mmm) cc_final: 0.7698 (mmm) REVERT: C 576 ARG cc_start: 0.7347 (ttt180) cc_final: 0.7089 (ttm-80) REVERT: C 701 GLU cc_start: 0.7561 (mm-30) cc_final: 0.7253 (pt0) REVERT: D 66 LYS cc_start: 0.6099 (mmmt) cc_final: 0.5402 (tppt) REVERT: D 187 LEU cc_start: 0.8228 (mt) cc_final: 0.7945 (mm) REVERT: D 329 LYS cc_start: 0.8374 (OUTLIER) cc_final: 0.7751 (ttmm) REVERT: D 701 GLU cc_start: 0.7562 (mm-30) cc_final: 0.7180 (pt0) outliers start: 26 outliers final: 21 residues processed: 142 average time/residue: 0.4262 time to fit residues: 66.8203 Evaluate side-chains 141 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 119 time to evaluate : 0.242 ------------------------------------------------------------------------------- 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 248 ASN Chi-restraints excluded: chain C residue 385 PHE Chi-restraints excluded: chain C residue 407 LEU Chi-restraints excluded: chain C residue 545 VAL Chi-restraints excluded: chain C residue 552 SER Chi-restraints excluded: chain C residue 556 TYR 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 248 ASN Chi-restraints excluded: chain D residue 329 LYS 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 556 TYR Chi-restraints excluded: chain D residue 559 VAL 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 64 optimal weight: 0.4980 chunk 107 optimal weight: 0.8980 chunk 111 optimal weight: 0.4980 chunk 40 optimal weight: 6.9990 chunk 48 optimal weight: 0.9990 chunk 121 optimal weight: 3.9990 chunk 112 optimal weight: 0.7980 chunk 21 optimal weight: 0.0170 chunk 52 optimal weight: 4.9990 chunk 0 optimal weight: 6.9990 chunk 1 optimal weight: 2.9990 overall best weight: 0.5418 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.144989 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.113137 restraints weight = 12725.859| |-----------------------------------------------------------------------------| r_work (start): 0.3471 rms_B_bonded: 2.14 r_work: 0.3358 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3244 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.3244 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7960 moved from start: 0.2044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 10471 Z= 0.118 Angle : 0.580 7.976 14230 Z= 0.287 Chirality : 0.043 0.300 1756 Planarity : 0.005 0.077 1628 Dihedral : 11.729 140.177 2609 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 9.89 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.96 % Favored : 94.88 % Rotamer: Outliers : 2.20 % Allowed : 19.31 % Favored : 78.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.46 (0.25), residues: 1210 helix: 1.95 (0.18), residues: 810 sheet: 0.55 (0.63), residues: 50 loop : -1.36 (0.35), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 79 TYR 0.012 0.001 TYR D 371 PHE 0.023 0.001 PHE C 141 TRP 0.008 0.001 TRP D 482 HIS 0.002 0.001 HIS D 698 Details of bonding type rmsd covalent geometry : bond 0.00250 (10470) covalent geometry : angle 0.58002 (14230) hydrogen bonds : bond 0.04225 ( 624) hydrogen bonds : angle 4.02543 ( 1818) Misc. bond : bond 0.00002 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4008.79 seconds wall clock time: 69 minutes 10.88 seconds (4150.88 seconds total)