Starting phenix.real_space_refine on Fri Jan 17 00:23:32 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8uuk_42588/01_2025/8uuk_42588.cif Found real_map, /net/cci-nas-00/data/ceres_data/8uuk_42588/01_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_42588/01_2025/8uuk_42588.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8uuk_42588/01_2025/8uuk_42588.map" model { file = "/net/cci-nas-00/data/ceres_data/8uuk_42588/01_2025/8uuk_42588.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8uuk_42588/01_2025/8uuk_42588.cif" } 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. Time to flip 8 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/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: 6.72, per 1000 atoms: 0.66 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: 2.98 Conformation dependent library (CDL) restraints added in 1.4 seconds 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2288 Finding SS restraints... Secondary structure from input PDB file: 62 helices and 5 sheets defined 71.1% alpha, 4.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.17 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: 3.23 Time building geometry restraints manager: 3.37 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: 0.06 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: 1.090 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: 0.400 Check model and map are aligned: 0.080 Set scattering table: 0.110 Process input model: 26.680 Find NCS groups from input model: 0.200 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:14.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.420 ------------------------------------------------------------------------------- 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= 0.256 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 to be fit. rotamer outliers: 16 poor density : 127 time to evaluate : 1.088 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: 0.6818 time to fit residues: 110.2903 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 : 1.080 ------------------------------------------------------------------------------- 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: 0.7980 chunk 92 optimal weight: 1.9990 chunk 51 optimal weight: 4.9990 chunk 31 optimal weight: 3.9990 chunk 62 optimal weight: 4.9990 chunk 49 optimal weight: 2.9990 chunk 95 optimal weight: 3.9990 chunk 37 optimal weight: 4.9990 chunk 58 optimal weight: 0.3980 chunk 71 optimal weight: 0.5980 chunk 110 optimal weight: 4.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- 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 248 ASN D 684 GLN D 689 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.142092 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.109387 restraints weight = 12748.059| |-----------------------------------------------------------------------------| r_work (start): 0.3430 rms_B_bonded: 2.15 r_work: 0.3310 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3197 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3197 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8006 moved from start: 0.0913 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= 0.266 Angle : 0.688 10.448 14230 Z= 0.335 Chirality : 0.046 0.231 1756 Planarity : 0.005 0.080 1628 Dihedral : 17.407 160.161 2621 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.21 % Favored : 94.63 % Rotamer: Outliers : 3.35 % Allowed : 14.72 % Favored : 81.93 % 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: 1.08 (0.25), residues: 1210 helix: 1.64 (0.18), residues: 798 sheet: 0.95 (0.68), residues: 50 loop : -1.44 (0.33), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 74 HIS 0.002 0.001 HIS C 656 PHE 0.022 0.002 PHE D 141 TYR 0.015 0.002 TYR C 371 ARG 0.005 0.001 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 167 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 132 time to evaluate : 1.264 Fit side-chains REVERT: C 187 LEU cc_start: 0.8174 (mt) cc_final: 0.7891 (mm) REVERT: C 576 ARG cc_start: 0.7321 (ttt180) cc_final: 0.7107 (ttm-80) REVERT: D 187 LEU cc_start: 0.8163 (mt) cc_final: 0.7881 (mm) REVERT: D 576 ARG cc_start: 0.7314 (ttt180) cc_final: 0.7107 (ttm-80) outliers start: 35 outliers final: 15 residues processed: 159 average time/residue: 0.7898 time to fit residues: 140.6519 Evaluate side-chains 131 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 116 time to evaluate : 1.042 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 556 TYR Chi-restraints excluded: chain C residue 704 GLU 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 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 Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 52 optimal weight: 4.9990 chunk 57 optimal weight: 3.9990 chunk 81 optimal weight: 0.8980 chunk 54 optimal weight: 3.9990 chunk 46 optimal weight: 2.9990 chunk 14 optimal weight: 3.9990 chunk 73 optimal weight: 0.3980 chunk 96 optimal weight: 2.9990 chunk 39 optimal weight: 0.8980 chunk 50 optimal weight: 4.9990 chunk 91 optimal weight: 2.9990 overall best weight: 1.6384 ------------------------------------------------------------------------------- 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 = 0.3724 r_free = 0.3724 target = 0.139445 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.106903 restraints weight = 12908.159| |-----------------------------------------------------------------------------| r_work (start): 0.3397 rms_B_bonded: 2.14 r_work: 0.3279 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3167 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3167 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8042 moved from start: 0.1258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 10470 Z= 0.282 Angle : 0.646 8.271 14230 Z= 0.321 Chirality : 0.046 0.279 1756 Planarity : 0.005 0.080 1628 Dihedral : 16.124 158.514 2613 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.88 % Favored : 94.96 % Rotamer: Outliers : 3.92 % Allowed : 15.01 % 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 (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 (0.25), residues: 1210 helix: 1.65 (0.18), residues: 798 sheet: 0.88 (0.66), residues: 50 loop : -1.48 (0.33), 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 0.020 0.002 PHE C 141 TYR 0.017 0.002 TYR C 371 ARG 0.004 0.000 ARG D 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 162 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 121 time to evaluate : 1.005 Fit side-chains REVERT: C 103 MET cc_start: 0.8612 (OUTLIER) cc_final: 0.8396 (mtp) REVERT: C 187 LEU cc_start: 0.8222 (mt) cc_final: 0.7944 (mm) REVERT: C 560 ASP cc_start: 0.7278 (m-30) cc_final: 0.7012 (m-30) REVERT: C 576 ARG cc_start: 0.7323 (ttt180) cc_final: 0.7098 (ttm-80) REVERT: D 103 MET cc_start: 0.8623 (OUTLIER) cc_final: 0.8414 (mtp) REVERT: D 187 LEU cc_start: 0.8227 (mt) cc_final: 0.7947 (mm) REVERT: D 576 ARG cc_start: 0.7348 (ttt180) cc_final: 0.7139 (ttm-80) outliers start: 41 outliers final: 22 residues processed: 150 average time/residue: 0.9994 time to fit residues: 165.6428 Evaluate side-chains 136 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 112 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 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 552 SER 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 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 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 87 optimal weight: 3.9990 chunk 98 optimal weight: 2.9990 chunk 38 optimal weight: 0.7980 chunk 88 optimal weight: 7.9990 chunk 72 optimal weight: 1.9990 chunk 17 optimal weight: 0.9980 chunk 103 optimal weight: 0.9990 chunk 42 optimal weight: 3.9990 chunk 62 optimal weight: 0.9980 chunk 121 optimal weight: 0.9990 chunk 57 optimal weight: 0.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- 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 = 0.3742 r_free = 0.3742 target = 0.141396 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.109105 restraints weight = 12741.843| |-----------------------------------------------------------------------------| r_work (start): 0.3420 rms_B_bonded: 2.14 r_work: 0.3303 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3190 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3190 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8013 moved from start: 0.1430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 10470 Z= 0.206 Angle : 0.611 7.495 14230 Z= 0.304 Chirality : 0.045 0.325 1756 Planarity : 0.005 0.083 1628 Dihedral : 15.064 155.065 2613 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 8.95 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.96 % Favored : 94.88 % Rotamer: Outliers : 3.63 % Allowed : 15.87 % Favored : 80.50 % 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: 1.23 (0.25), residues: 1210 helix: 1.76 (0.18), residues: 802 sheet: 0.83 (0.64), residues: 50 loop : -1.42 (0.33), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 74 HIS 0.003 0.001 HIS D 656 PHE 0.021 0.001 PHE D 141 TYR 0.015 0.001 TYR C 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 165 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 127 time to evaluate : 1.130 Fit side-chains REVERT: C 103 MET cc_start: 0.8590 (OUTLIER) cc_final: 0.8386 (mtp) REVERT: C 187 LEU cc_start: 0.8232 (mt) cc_final: 0.7948 (mm) REVERT: C 560 ASP cc_start: 0.7305 (m-30) cc_final: 0.7030 (m-30) REVERT: C 576 ARG cc_start: 0.7291 (ttt180) cc_final: 0.7054 (ttm-80) REVERT: D 187 LEU cc_start: 0.8212 (mt) cc_final: 0.7931 (mm) REVERT: D 576 ARG cc_start: 0.7327 (ttt180) cc_final: 0.7063 (ttm-80) REVERT: D 704 GLU cc_start: 0.8112 (OUTLIER) cc_final: 0.7845 (pt0) outliers start: 38 outliers final: 24 residues processed: 152 average time/residue: 0.8399 time to fit residues: 142.3814 Evaluate side-chains 143 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 117 time to evaluate : 1.035 ------------------------------------------------------------------------------- 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 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 30 optimal weight: 2.9990 chunk 62 optimal weight: 3.9990 chunk 22 optimal weight: 0.7980 chunk 43 optimal weight: 1.9990 chunk 104 optimal weight: 0.7980 chunk 93 optimal weight: 6.9990 chunk 1 optimal weight: 0.8980 chunk 81 optimal weight: 0.6980 chunk 106 optimal weight: 0.7980 chunk 47 optimal weight: 2.9990 chunk 97 optimal weight: 8.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 = 0.3755 r_free = 0.3755 target = 0.142469 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.110396 restraints weight = 12761.669| |-----------------------------------------------------------------------------| r_work (start): 0.3437 rms_B_bonded: 2.14 r_work: 0.3321 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3209 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3209 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8002 moved from start: 0.1516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10470 Z= 0.188 Angle : 0.645 17.493 14230 Z= 0.308 Chirality : 0.045 0.336 1756 Planarity : 0.005 0.081 1628 Dihedral : 14.387 151.906 2613 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 9.56 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.71 % Favored : 95.12 % Rotamer: Outliers : 3.44 % Allowed : 16.54 % 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: 1.23 (0.24), residues: 1210 helix: 1.77 (0.18), residues: 802 sheet: 0.65 (0.64), residues: 50 loop : -1.39 (0.33), residues: 358 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 0.021 0.001 PHE D 141 TYR 0.015 0.001 TYR D 371 ARG 0.010 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 156 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 120 time to evaluate : 1.160 Fit side-chains REVERT: C 103 MET cc_start: 0.8573 (OUTLIER) cc_final: 0.8370 (mtp) REVERT: C 187 LEU cc_start: 0.8230 (mt) cc_final: 0.7948 (mm) REVERT: C 560 ASP cc_start: 0.7299 (m-30) cc_final: 0.6924 (m-30) REVERT: C 576 ARG cc_start: 0.7291 (ttt180) cc_final: 0.7047 (ttm-80) REVERT: D 187 LEU cc_start: 0.8209 (mt) cc_final: 0.7924 (mm) REVERT: D 576 ARG cc_start: 0.7317 (ttt180) cc_final: 0.7062 (ttm-80) REVERT: D 704 GLU cc_start: 0.8100 (OUTLIER) cc_final: 0.7837 (pt0) outliers start: 36 outliers final: 26 residues processed: 143 average time/residue: 0.8837 time to fit residues: 140.7653 Evaluate side-chains 145 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 117 time to evaluate : 1.054 ------------------------------------------------------------------------------- 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 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 32 optimal weight: 0.9990 chunk 6 optimal weight: 1.9990 chunk 25 optimal weight: 0.9990 chunk 51 optimal weight: 4.9990 chunk 74 optimal weight: 2.9990 chunk 35 optimal weight: 2.9990 chunk 22 optimal weight: 0.9990 chunk 100 optimal weight: 0.8980 chunk 12 optimal weight: 1.9990 chunk 95 optimal weight: 2.9990 chunk 9 optimal weight: 0.9990 overall best weight: 0.9788 ------------------------------------------------------------------------------- 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 = 0.3746 r_free = 0.3746 target = 0.141568 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.109363 restraints weight = 12783.876| |-----------------------------------------------------------------------------| r_work (start): 0.3427 rms_B_bonded: 2.14 r_work: 0.3310 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3197 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3197 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8012 moved from start: 0.1651 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10470 Z= 0.205 Angle : 0.629 12.108 14230 Z= 0.305 Chirality : 0.045 0.324 1756 Planarity : 0.005 0.078 1628 Dihedral : 13.887 149.518 2613 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.88 % Favored : 94.96 % Rotamer: Outliers : 3.63 % Allowed : 16.73 % 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 (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: 1.28 (0.24), residues: 1210 helix: 1.79 (0.18), residues: 802 sheet: 0.59 (0.63), residues: 50 loop : -1.32 (0.33), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 74 HIS 0.002 0.001 HIS D 656 PHE 0.021 0.001 PHE C 141 TYR 0.015 0.001 TYR D 371 ARG 0.007 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 160 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 122 time to evaluate : 1.083 Fit side-chains REVERT: C 103 MET cc_start: 0.8609 (OUTLIER) cc_final: 0.8404 (mtp) REVERT: C 187 LEU cc_start: 0.8237 (mt) cc_final: 0.7958 (mm) REVERT: C 560 ASP cc_start: 0.7338 (m-30) cc_final: 0.6984 (m-30) REVERT: C 576 ARG cc_start: 0.7312 (ttt180) cc_final: 0.7045 (ttm-80) REVERT: D 66 LYS cc_start: 0.6060 (tppt) cc_final: 0.5812 (tppt) REVERT: D 187 LEU cc_start: 0.8234 (mt) cc_final: 0.7954 (mm) REVERT: D 576 ARG cc_start: 0.7322 (ttt180) cc_final: 0.7045 (ttm-80) REVERT: D 704 GLU cc_start: 0.8116 (OUTLIER) cc_final: 0.7908 (pt0) outliers start: 38 outliers final: 27 residues processed: 147 average time/residue: 0.9061 time to fit residues: 147.5786 Evaluate side-chains 144 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 115 time to evaluate : 1.054 ------------------------------------------------------------------------------- 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 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 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 28 optimal weight: 0.0570 chunk 116 optimal weight: 0.7980 chunk 35 optimal weight: 0.9980 chunk 68 optimal weight: 1.9990 chunk 44 optimal weight: 4.9990 chunk 31 optimal weight: 2.9990 chunk 120 optimal weight: 3.9990 chunk 22 optimal weight: 0.8980 chunk 33 optimal weight: 0.6980 chunk 50 optimal weight: 0.8980 chunk 73 optimal weight: 0.2980 overall best weight: 0.5498 ------------------------------------------------------------------------------- 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 = 0.3785 r_free = 0.3785 target = 0.144760 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.112790 restraints weight = 12911.167| |-----------------------------------------------------------------------------| r_work (start): 0.3464 rms_B_bonded: 2.16 r_work: 0.3350 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3237 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3237 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7957 moved from start: 0.1739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 10470 Z= 0.161 Angle : 0.597 11.029 14230 Z= 0.291 Chirality : 0.044 0.319 1756 Planarity : 0.005 0.078 1628 Dihedral : 13.024 148.127 2613 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 10.17 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.71 % Favored : 95.12 % Rotamer: Outliers : 3.35 % Allowed : 17.21 % Favored : 79.45 % 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: 1.38 (0.25), residues: 1210 helix: 1.93 (0.18), residues: 798 sheet: 0.58 (0.64), residues: 50 loop : -1.41 (0.33), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 482 HIS 0.002 0.001 HIS C 656 PHE 0.022 0.001 PHE D 141 TYR 0.013 0.001 TYR D 371 ARG 0.008 0.000 ARG D 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 to be fit. rotamer outliers: 35 poor density : 124 time to evaluate : 1.098 Fit side-chains REVERT: C 187 LEU cc_start: 0.8214 (mt) cc_final: 0.7931 (mm) REVERT: C 217 ASP cc_start: 0.8176 (OUTLIER) cc_final: 0.7925 (m-30) REVERT: C 320 GLU cc_start: 0.7869 (tp30) cc_final: 0.6968 (pm20) REVERT: C 576 ARG cc_start: 0.7271 (ttt180) cc_final: 0.6993 (ttm-80) REVERT: D 66 LYS cc_start: 0.5674 (tppt) cc_final: 0.5358 (tppt) REVERT: D 187 LEU cc_start: 0.8206 (mt) cc_final: 0.7922 (mm) REVERT: D 576 ARG cc_start: 0.7306 (ttt180) cc_final: 0.7022 (ttm-80) outliers start: 35 outliers final: 20 residues processed: 145 average time/residue: 0.9101 time to fit residues: 146.1535 Evaluate side-chains 139 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 118 time to evaluate : 1.171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 85 LEU Chi-restraints excluded: chain C residue 100 LEU Chi-restraints excluded: chain C residue 217 ASP 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 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 57 optimal weight: 1.9990 chunk 119 optimal weight: 4.9990 chunk 17 optimal weight: 2.9990 chunk 18 optimal weight: 3.9990 chunk 90 optimal weight: 3.9990 chunk 20 optimal weight: 0.7980 chunk 37 optimal weight: 0.8980 chunk 45 optimal weight: 0.6980 chunk 35 optimal weight: 5.9990 chunk 91 optimal weight: 0.9980 chunk 26 optimal weight: 4.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- 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 = 0.3749 r_free = 0.3749 target = 0.141629 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.109486 restraints weight = 12882.706| |-----------------------------------------------------------------------------| r_work (start): 0.3427 rms_B_bonded: 2.15 r_work: 0.3312 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3199 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3199 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8014 moved from start: 0.1826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10470 Z= 0.214 Angle : 0.621 9.390 14230 Z= 0.303 Chirality : 0.045 0.342 1756 Planarity : 0.005 0.076 1628 Dihedral : 12.858 145.630 2613 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 9.75 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.79 % Favored : 95.04 % Rotamer: Outliers : 2.87 % Allowed : 18.26 % Favored : 78.87 % 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: 1.81 (0.18), residues: 812 sheet: 0.55 (0.63), residues: 50 loop : -1.31 (0.34), residues: 348 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 0.021 0.001 PHE D 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 to be fit. rotamer outliers: 30 poor density : 122 time to evaluate : 1.008 Fit side-chains REVERT: C 187 LEU cc_start: 0.8237 (mt) cc_final: 0.7951 (mm) REVERT: C 217 ASP cc_start: 0.8185 (OUTLIER) cc_final: 0.7935 (m-30) REVERT: C 320 GLU cc_start: 0.7899 (tp30) cc_final: 0.7047 (pm20) REVERT: C 560 ASP cc_start: 0.7341 (m-30) cc_final: 0.6969 (m-30) REVERT: C 576 ARG cc_start: 0.7366 (ttt180) cc_final: 0.7115 (ttm-80) REVERT: D 187 LEU cc_start: 0.8247 (mt) cc_final: 0.7952 (mm) REVERT: D 329 LYS cc_start: 0.8429 (OUTLIER) cc_final: 0.8177 (ttmm) REVERT: D 576 ARG cc_start: 0.7339 (ttt180) cc_final: 0.7077 (ttm-80) REVERT: D 701 GLU cc_start: 0.7611 (mm-30) cc_final: 0.7213 (pt0) outliers start: 30 outliers final: 21 residues processed: 143 average time/residue: 0.9060 time to fit residues: 143.3035 Evaluate side-chains 141 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 118 time to evaluate : 1.025 ------------------------------------------------------------------------------- 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 217 ASP 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 252 SER 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 116 optimal weight: 0.8980 chunk 88 optimal weight: 0.0970 chunk 17 optimal weight: 1.9990 chunk 50 optimal weight: 0.9990 chunk 22 optimal weight: 0.9990 chunk 103 optimal weight: 0.6980 chunk 5 optimal weight: 4.9990 chunk 112 optimal weight: 1.9990 chunk 108 optimal weight: 3.9990 chunk 91 optimal weight: 1.9990 chunk 65 optimal weight: 5.9990 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 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 = 0.3768 r_free = 0.3768 target = 0.143231 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.111106 restraints weight = 12915.233| |-----------------------------------------------------------------------------| r_work (start): 0.3445 rms_B_bonded: 2.15 r_work: 0.3330 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3217 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.3217 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7980 moved from start: 0.1855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10470 Z= 0.177 Angle : 0.605 8.722 14230 Z= 0.296 Chirality : 0.045 0.367 1756 Planarity : 0.005 0.080 1628 Dihedral : 12.436 144.928 2609 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 9.70 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.79 % Favored : 95.04 % Rotamer: Outliers : 3.06 % Allowed : 18.16 % Favored : 78.78 % 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: 1.37 (0.25), residues: 1210 helix: 1.81 (0.18), residues: 814 sheet: 0.52 (0.63), residues: 50 loop : -1.25 (0.35), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 482 HIS 0.002 0.001 HIS D 656 PHE 0.022 0.001 PHE C 141 TYR 0.014 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 151 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 119 time to evaluate : 1.091 Fit side-chains REVERT: C 187 LEU cc_start: 0.8233 (mt) cc_final: 0.7946 (mm) REVERT: C 217 ASP cc_start: 0.8160 (OUTLIER) cc_final: 0.7906 (m-30) REVERT: C 320 GLU cc_start: 0.7899 (tp30) cc_final: 0.7102 (pm20) REVERT: C 576 ARG cc_start: 0.7307 (ttt180) cc_final: 0.7056 (ttm-80) REVERT: D 187 LEU cc_start: 0.8219 (mt) cc_final: 0.7941 (mm) REVERT: D 217 ASP cc_start: 0.8172 (OUTLIER) cc_final: 0.7921 (m-30) REVERT: D 329 LYS cc_start: 0.8406 (OUTLIER) cc_final: 0.8163 (ttmm) REVERT: D 576 ARG cc_start: 0.7331 (ttt180) cc_final: 0.7065 (ttm-80) REVERT: D 701 GLU cc_start: 0.7587 (mm-30) cc_final: 0.7232 (pt0) outliers start: 32 outliers final: 21 residues processed: 139 average time/residue: 0.9211 time to fit residues: 141.9454 Evaluate side-chains 141 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 117 time to evaluate : 1.059 ------------------------------------------------------------------------------- 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 85 LEU Chi-restraints excluded: chain C residue 100 LEU Chi-restraints excluded: chain C residue 217 ASP 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 217 ASP 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 27 optimal weight: 2.9990 chunk 31 optimal weight: 2.9990 chunk 100 optimal weight: 4.9990 chunk 9 optimal weight: 5.9990 chunk 30 optimal weight: 1.9990 chunk 76 optimal weight: 0.6980 chunk 95 optimal weight: 3.9990 chunk 12 optimal weight: 2.9990 chunk 68 optimal weight: 0.9990 chunk 112 optimal weight: 2.9990 chunk 88 optimal weight: 0.9980 overall best weight: 1.5386 ------------------------------------------------------------------------------- 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 = 0.3720 r_free = 0.3720 target = 0.138846 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.106538 restraints weight = 12820.226| |-----------------------------------------------------------------------------| r_work (start): 0.3388 rms_B_bonded: 2.12 r_work: 0.3271 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3158 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.3158 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8040 moved from start: 0.1973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 10470 Z= 0.270 Angle : 0.655 8.200 14230 Z= 0.321 Chirality : 0.047 0.379 1756 Planarity : 0.005 0.077 1628 Dihedral : 12.525 143.014 2609 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 9.47 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.29 % Favored : 94.55 % Rotamer: Outliers : 2.39 % Allowed : 18.83 % Favored : 78.78 % 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: 1.15 (0.25), residues: 1210 helix: 1.68 (0.18), residues: 812 sheet: 0.51 (0.63), residues: 50 loop : -1.42 (0.34), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 74 HIS 0.003 0.001 HIS C 698 PHE 0.021 0.002 PHE C 141 TYR 0.017 0.002 TYR D 371 ARG 0.008 0.001 ARG C 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 141 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 116 time to evaluate : 1.049 Fit side-chains REVERT: C 187 LEU cc_start: 0.8270 (mt) cc_final: 0.7979 (mm) REVERT: C 217 ASP cc_start: 0.8170 (OUTLIER) cc_final: 0.7920 (m-30) REVERT: C 320 GLU cc_start: 0.7942 (tp30) cc_final: 0.7116 (pm20) REVERT: C 560 ASP cc_start: 0.7384 (m-30) cc_final: 0.7005 (m-30) REVERT: C 576 ARG cc_start: 0.7329 (ttt180) cc_final: 0.7085 (ttm-80) REVERT: D 187 LEU cc_start: 0.8246 (mt) cc_final: 0.7954 (mm) REVERT: D 217 ASP cc_start: 0.8186 (OUTLIER) cc_final: 0.7940 (m-30) REVERT: D 318 ASN cc_start: 0.8179 (t0) cc_final: 0.7925 (t0) REVERT: D 329 LYS cc_start: 0.8441 (OUTLIER) cc_final: 0.8204 (ttmm) REVERT: D 576 ARG cc_start: 0.7370 (ttt180) cc_final: 0.7109 (ttm-80) REVERT: D 701 GLU cc_start: 0.7666 (mm-30) cc_final: 0.7247 (pt0) outliers start: 25 outliers final: 18 residues processed: 131 average time/residue: 0.9234 time to fit residues: 133.5192 Evaluate side-chains 135 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 114 time to evaluate : 1.179 ------------------------------------------------------------------------------- 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 217 ASP 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 217 ASP Chi-restraints excluded: chain D residue 329 LYS Chi-restraints excluded: chain D residue 385 PHE 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 18 optimal weight: 0.9990 chunk 40 optimal weight: 2.9990 chunk 46 optimal weight: 1.9990 chunk 28 optimal weight: 0.4980 chunk 19 optimal weight: 7.9990 chunk 68 optimal weight: 0.5980 chunk 56 optimal weight: 0.9980 chunk 9 optimal weight: 4.9990 chunk 100 optimal weight: 0.8980 chunk 89 optimal weight: 1.9990 chunk 98 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 = 0.142569 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.110502 restraints weight = 12795.658| |-----------------------------------------------------------------------------| r_work (start): 0.3441 rms_B_bonded: 2.14 r_work: 0.3325 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3212 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.3212 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7985 moved from start: 0.1966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10470 Z= 0.189 Angle : 0.611 8.206 14230 Z= 0.301 Chirality : 0.044 0.345 1756 Planarity : 0.005 0.085 1628 Dihedral : 12.108 142.673 2609 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 10.46 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.96 % Favored : 94.88 % 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 (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: 1.74 (0.18), residues: 814 sheet: 0.52 (0.63), residues: 50 loop : -1.23 (0.35), residues: 346 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 0.023 0.001 PHE C 141 TYR 0.014 0.001 TYR D 371 ARG 0.007 0.000 ARG C 79 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7586.92 seconds wall clock time: 135 minutes 0.08 seconds (8100.08 seconds total)