Starting phenix.real_space_refine on Thu Jul 2 21:05:01 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8sgw_40470/07_2026/8sgw_40470.cif Found real_map, /net/cci-nas-00/data/ceres_data/8sgw_40470/07_2026/8sgw_40470.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/8sgw_40470/07_2026/8sgw_40470.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8sgw_40470/07_2026/8sgw_40470.map" model { file = "/net/cci-nas-00/data/ceres_data/8sgw_40470/07_2026/8sgw_40470.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8sgw_40470/07_2026/8sgw_40470.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= 0.004 sd= 0.118 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: 6 Type Number sf(0) Gaussians P 6 5.49 5 S 36 5.16 5 Cl 4 4.86 5 C 7028 2.51 5 N 1542 2.21 5 O 1798 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 10414 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: 452 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 450 Ad-hoc single atom residues: {' CL': 2} Unusual residues: {'AV0': 1, 'CLR': 6, 'DMU': 1, 'LBN': 9} Classifications: {'undetermined': 17} Link IDs: {None: 15} Chain breaks: 2 Unresolved non-hydrogen bonds: 288 Unresolved non-hydrogen angles: 351 Unresolved non-hydrogen dihedrals: 270 Unresolved non-hydrogen chiralities: 6 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: 452 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 450 Ad-hoc single atom residues: {' CL': 2} Unusual residues: {'AV0': 1, 'CLR': 6, 'DMU': 1, 'LBN': 9} Classifications: {'undetermined': 17} Link IDs: {None: 15} Chain breaks: 2 Unresolved non-hydrogen bonds: 288 Unresolved non-hydrogen angles: 351 Unresolved non-hydrogen dihedrals: 270 Unresolved non-hydrogen chiralities: 6 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: 2.01, per 1000 atoms: 0.19 Number of scatterers: 10414 At special positions: 0 Unit cell: (83.74, 121.9, 104.94, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Cl 4 17.00 S 36 16.00 P 6 15.00 O 1798 8.00 N 1542 7.00 C 7028 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 !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!! Possible link ignored !!! !!! HETATM10316 C18 DMU D 818 41.046 59.711 31.954 1.00 67.13 C !!! !!! HETATM 9864 C18 DMU C 818 41.691 61.056 31.971 1.00 66.94 C !!! !!! N-linked glycan : False !!! !!! O-linked glycan : False !!! !!! Glycan-glycan : True !!! !!! No oxygen atom found !!! !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.67 Conformation dependent library (CDL) restraints added in 350.3 milliseconds 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2288 Finding SS restraints... Secondary structure from input PDB file: 62 helices and 5 sheets defined 71.9% alpha, 4.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.26 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 79 through 109 removed outlier: 4.277A pdb=" N LEU C 84 " --> pdb=" O ILE C 80 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N LEU C 85 " --> pdb=" O LYS C 81 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N SER C 86 " --> pdb=" O GLU C 82 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N LEU C 100 " --> pdb=" O LEU C 96 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N LEU C 107 " --> pdb=" O MET C 103 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N LEU C 108 " --> pdb=" O ALA C 104 " (cutoff:3.500A) Processing helix chain 'C' and resid 114 through 131 removed outlier: 3.602A pdb=" N TYR C 118 " --> pdb=" O GLY C 114 " (cutoff:3.500A) Proline residue: C 123 - end of helix removed outlier: 4.053A pdb=" N ILE C 129 " --> pdb=" O LEU C 125 " (cutoff:3.500A) removed outlier: 4.544A 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 208 through 215 removed outlier: 4.076A pdb=" N ILE C 211 " --> pdb=" O ILE C 208 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N VAL C 212 " --> pdb=" O GLY C 209 " (cutoff:3.500A) Processing helix chain 'C' and resid 216 through 241 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: 3.778A pdb=" N SER C 347 " --> pdb=" O SER C 344 " (cutoff:3.500A) Processing helix chain 'C' and resid 349 through 376 removed outlier: 3.778A pdb=" N SER C 355 " --> pdb=" O THR C 351 " (cutoff:3.500A) removed outlier: 3.559A 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 Processing helix chain 'C' and resid 421 through 437 Processing helix chain 'C' and resid 446 through 458 removed outlier: 3.781A 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: 4.382A pdb=" N LYS C 537 " --> pdb=" O THR C 533 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 533 through 537' Processing helix chain 'C' and resid 555 through 571 Processing helix chain 'C' and resid 573 through 585 removed outlier: 3.507A pdb=" N VAL C 577 " --> pdb=" O ASP C 573 " (cutoff:3.500A) Processing helix chain 'C' and resid 669 through 686 removed outlier: 3.734A 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 79 through 109 removed outlier: 4.277A pdb=" N LEU D 84 " --> pdb=" O ILE D 80 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N LEU D 85 " --> pdb=" O LYS D 81 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N SER D 86 " --> pdb=" O GLU D 82 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N LEU D 100 " --> pdb=" O LEU D 96 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N LEU D 107 " --> pdb=" O MET D 103 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N LEU D 108 " --> pdb=" O ALA D 104 " (cutoff:3.500A) Processing helix chain 'D' and resid 114 through 131 removed outlier: 3.602A pdb=" N TYR D 118 " --> pdb=" O GLY D 114 " (cutoff:3.500A) Proline residue: D 123 - end of helix removed outlier: 4.058A pdb=" N ILE D 129 " --> pdb=" O LEU D 125 " (cutoff:3.500A) removed outlier: 4.533A 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 208 through 215 removed outlier: 4.074A pdb=" N ILE D 211 " --> pdb=" O ILE D 208 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N VAL D 212 " --> pdb=" O GLY D 209 " (cutoff:3.500A) Processing helix chain 'D' and resid 216 through 241 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: 3.771A pdb=" N SER D 347 " --> pdb=" O SER D 344 " (cutoff:3.500A) Processing helix chain 'D' and resid 349 through 376 removed outlier: 3.760A pdb=" N SER D 355 " --> pdb=" O THR D 351 " (cutoff:3.500A) removed outlier: 3.559A 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 Processing helix chain 'D' and resid 421 through 437 Processing helix chain 'D' and resid 446 through 458 removed outlier: 3.782A 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: 4.383A pdb=" N LYS D 537 " --> pdb=" O THR D 533 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 533 through 537' Processing helix chain 'D' and resid 555 through 571 Processing helix chain 'D' and resid 573 through 585 removed outlier: 3.507A pdb=" N VAL D 577 " --> pdb=" O ASP D 573 " (cutoff:3.500A) Processing helix chain 'D' and resid 669 through 686 removed outlier: 3.734A 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: 3.801A pdb=" N VAL C 22 " --> pdb=" O VAL D 22 " (cutoff:3.500A) removed outlier: 3.801A 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: 4.129A pdb=" N ILE C 547 " --> pdb=" O LEU C 521 " (cutoff:3.500A) removed outlier: 8.522A pdb=" N SER C 523 " --> pdb=" O VAL C 545 " (cutoff:3.500A) removed outlier: 12.665A pdb=" N VAL C 545 " --> pdb=" O SER C 523 " (cutoff:3.500A) removed outlier: 8.568A pdb=" N PHE C 719 " --> pdb=" O VAL C 690 " (cutoff:3.500A) removed outlier: 6.545A 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: 4.129A pdb=" N ILE D 547 " --> pdb=" O LEU D 521 " (cutoff:3.500A) removed outlier: 8.520A pdb=" N SER D 523 " --> pdb=" O VAL D 545 " (cutoff:3.500A) removed outlier: 12.663A pdb=" N VAL D 545 " --> pdb=" O SER D 523 " (cutoff:3.500A) removed outlier: 8.567A pdb=" N PHE D 719 " --> pdb=" O VAL D 690 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N PHE D 692 " --> pdb=" O PHE D 719 " (cutoff:3.500A) 638 hydrogen bonds defined for protein. 1860 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: 1.57 Time building geometry restraints manager: 0.89 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: 1572 1.32 - 1.45: 2604 1.45 - 1.57: 6390 1.57 - 1.69: 12 1.69 - 1.81: 56 Bond restraints: 10634 Sorted by residual: bond pdb=" O2 LBN D 809 " pdb=" P1 LBN D 809 " ideal model delta sigma weight residual 1.650 1.595 0.055 2.00e-02 2.50e+03 7.50e+00 bond pdb=" O2 LBN C 807 " pdb=" P1 LBN C 807 " ideal model delta sigma weight residual 1.650 1.595 0.055 2.00e-02 2.50e+03 7.43e+00 bond pdb=" O2 LBN D 806 " pdb=" P1 LBN D 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 807 " pdb=" P1 LBN D 807 " ideal model delta sigma weight residual 1.650 1.596 0.054 2.00e-02 2.50e+03 7.25e+00 bond pdb=" O2 LBN C 809 " pdb=" P1 LBN C 809 " ideal model delta sigma weight residual 1.650 1.596 0.054 2.00e-02 2.50e+03 7.16e+00 ... (remaining 10629 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.11: 14112 2.11 - 4.22: 266 4.22 - 6.33: 23 6.33 - 8.44: 4 8.44 - 10.55: 9 Bond angle restraints: 14414 Sorted by residual: angle pdb=" C ILE C 491 " pdb=" N LEU C 492 " pdb=" CA LEU C 492 " ideal model delta sigma weight residual 121.54 129.26 -7.72 1.91e+00 2.74e-01 1.63e+01 angle pdb=" C ILE D 491 " pdb=" N LEU D 492 " pdb=" CA LEU D 492 " ideal model delta sigma weight residual 121.54 129.24 -7.70 1.91e+00 2.74e-01 1.63e+01 angle pdb=" O1 LBN C 809 " pdb=" P1 LBN C 809 " pdb=" O2 LBN C 809 " ideal model delta sigma weight residual 93.45 104.00 -10.55 3.00e+00 1.11e-01 1.24e+01 angle pdb=" O1 LBN C 807 " pdb=" P1 LBN C 807 " pdb=" O2 LBN C 807 " ideal model delta sigma weight residual 93.45 103.99 -10.54 3.00e+00 1.11e-01 1.23e+01 angle pdb=" O1 LBN D 809 " pdb=" P1 LBN D 809 " pdb=" O2 LBN D 809 " ideal model delta sigma weight residual 93.45 103.97 -10.52 3.00e+00 1.11e-01 1.23e+01 ... (remaining 14409 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.37: 6850 33.37 - 66.75: 209 66.75 - 100.12: 43 100.12 - 133.50: 66 133.50 - 166.87: 10 Dihedral angle restraints: 7178 sinusoidal: 3628 harmonic: 3550 Sorted by residual: dihedral pdb=" CA VAL C 722 " pdb=" C VAL C 722 " pdb=" N HIS C 723 " pdb=" CA HIS C 723 " ideal model delta harmonic sigma weight residual 180.00 151.34 28.66 0 5.00e+00 4.00e-02 3.29e+01 dihedral pdb=" CA VAL D 722 " pdb=" C VAL D 722 " pdb=" N HIS D 723 " pdb=" CA HIS D 723 " ideal model delta harmonic sigma weight residual 180.00 151.34 28.66 0 5.00e+00 4.00e-02 3.29e+01 dihedral pdb=" CBS AV0 D 819 " pdb=" C1 AV0 D 819 " pdb=" O1 AV0 D 819 " pdb=" O5 AV0 D 819 " ideal model delta sinusoidal sigma weight residual 85.89 -80.98 166.87 1 3.00e+01 1.11e-03 2.11e+01 ... (remaining 7175 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.988: 1756 0.988 - 1.976: 0 1.976 - 2.965: 0 2.965 - 3.953: 0 3.953 - 4.941: 4 Chirality restraints: 1760 Sorted by residual: 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 2.58 -4.94 2.00e-01 2.50e+01 6.10e+02 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 -4.94 2.00e-01 2.50e+01 6.10e+02 chirality pdb=" C2 LBN C 809 " pdb=" C1 LBN C 809 " pdb=" C3 LBN C 809 " pdb=" O7 LBN C 809 " both_signs ideal model delta sigma weight residual False -2.36 2.50 -4.86 2.00e-01 2.50e+01 5.91e+02 ... (remaining 1757 not shown) Planarity restraints: 1640 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C41 LBN D 809 " 0.235 2.00e-02 2.50e+03 2.37e-01 5.62e+02 pdb=" C42 LBN D 809 " -0.231 2.00e-02 2.50e+03 pdb=" C5 LBN D 809 " -0.243 2.00e-02 2.50e+03 pdb=" C8 LBN D 809 " 0.239 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C41 LBN C 809 " -0.217 2.00e-02 2.50e+03 2.17e-01 4.71e+02 pdb=" C42 LBN C 809 " 0.217 2.00e-02 2.50e+03 pdb=" C5 LBN C 809 " 0.217 2.00e-02 2.50e+03 pdb=" C8 LBN C 809 " -0.217 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C41 LBN C 806 " 0.094 2.00e-02 2.50e+03 2.05e-01 4.22e+02 pdb=" C42 LBN C 806 " -0.274 2.00e-02 2.50e+03 pdb=" C5 LBN C 806 " 0.275 2.00e-02 2.50e+03 pdb=" C8 LBN C 806 " -0.095 2.00e-02 2.50e+03 ... (remaining 1637 not shown) Histogram of nonbonded interaction distances: 1.49 - 2.17: 3 2.17 - 2.86: 3447 2.86 - 3.54: 15285 3.54 - 4.22: 24541 4.22 - 4.90: 43749 Nonbonded interactions: 87025 Sorted by model distance: nonbonded pdb=" C18 DMU C 818 " pdb=" C18 DMU D 818 " model vdw 1.492 3.840 nonbonded pdb=" O PRO D 553 " pdb=" ND2 ASN D 558 " model vdw 2.135 3.120 nonbonded pdb=" O PRO C 553 " pdb=" ND2 ASN C 558 " model vdw 2.136 3.120 nonbonded pdb=" OH TYR D 78 " pdb=" OD2 ASP D 87 " model vdw 2.208 3.040 nonbonded pdb=" OH TYR C 78 " pdb=" OD2 ASP C 87 " model vdw 2.209 3.040 ... (remaining 87020 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: 0.470 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.100 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 9.430 Find NCS groups from input model: 0.090 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: 0.000 Load rotamer database and sin/cos tables:7.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.260 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7709 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 0.055 10634 Z= 0.206 Angle : 0.688 10.547 14414 Z= 0.328 Chirality : 0.238 4.941 1760 Planarity : 0.012 0.237 1640 Dihedral : 21.885 166.873 4890 Min Nonbonded Distance : 1.492 Molprobity Statistics. All-atom Clashscore : 13.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 0.00 % Allowed : 0.10 % Favored : 99.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.83 (0.25), residues: 1210 helix: 1.58 (0.19), residues: 804 sheet: -0.07 (0.57), residues: 54 loop : -1.82 (0.32), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 409 TYR 0.020 0.002 TYR D 27 PHE 0.017 0.001 PHE D 141 TRP 0.009 0.001 TRP D 74 HIS 0.003 0.001 HIS C 656 Details of bonding type rmsd/Z covalent geometry : bond 0.00418 / 0.21 (10634) covalent geometry : angle 0.68791 / 0.33 (14414) hydrogen bonds : bond 0.12462 / 8.14 ( 638) hydrogen bonds : angle 5.41916 / 3.95 ( 1860) *********************** 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 167 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 167 time to evaluate : 0.238 Fit side-chains outliers start: 0 outliers final: 1 residues processed: 167 average time/residue: 0.4075 time to fit residues: 74.3083 Evaluate side-chains 125 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 124 time to evaluate : 0.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 250 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 108 optimal weight: 3.9990 chunk 49 optimal weight: 3.9990 chunk 97 optimal weight: 9.9990 chunk 113 optimal weight: 3.9990 chunk 53 optimal weight: 9.9990 chunk 5 optimal weight: 9.9990 chunk 33 optimal weight: 4.9990 chunk 65 optimal weight: 0.6980 chunk 62 optimal weight: 0.8980 chunk 51 optimal weight: 0.9980 chunk 117 optimal weight: 0.6980 overall best weight: 1.4582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 324 ASN ** C 705 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 324 ASN ** D 705 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4065 r_free = 0.4065 target = 0.169350 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.135541 restraints weight = 12626.614| |-----------------------------------------------------------------------------| r_work (start): 0.3677 rms_B_bonded: 1.95 r_work: 0.3546 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3410 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3410 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7802 moved from start: 0.1179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 10634 Z= 0.174 Angle : 0.731 11.373 14414 Z= 0.350 Chirality : 0.046 0.244 1760 Planarity : 0.005 0.071 1640 Dihedral : 19.694 162.039 2744 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 9.84 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.29 % Favored : 94.55 % Rotamer: Outliers : 1.34 % Allowed : 11.57 % Favored : 87.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.82 (0.24), residues: 1210 helix: 1.47 (0.18), residues: 816 sheet: 0.43 (0.56), residues: 50 loop : -1.73 (0.33), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG D 24 TYR 0.013 0.002 TYR C 371 PHE 0.019 0.002 PHE C 141 TRP 0.010 0.001 TRP D 74 HIS 0.003 0.001 HIS C 698 Details of bonding type rmsd/Z covalent geometry : bond 0.00379 / 0.17 (10634) covalent geometry : angle 0.73100 / 0.35 (14414) hydrogen bonds : bond 0.05266 / 3.43 ( 638) hydrogen bonds : angle 4.54190 / 3.36 ( 1860) *********************** 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 149 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 135 time to evaluate : 0.386 Fit side-chains REVERT: C 27 TYR cc_start: 0.7665 (m-80) cc_final: 0.7036 (m-80) REVERT: D 27 TYR cc_start: 0.7671 (m-80) cc_final: 0.7032 (m-80) outliers start: 14 outliers final: 10 residues processed: 145 average time/residue: 0.3539 time to fit residues: 57.0039 Evaluate side-chains 126 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 116 time to evaluate : 0.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 154 SER Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain C residue 280 ILE Chi-restraints excluded: chain C residue 552 SER Chi-restraints excluded: chain C residue 559 VAL Chi-restraints excluded: chain D residue 154 SER Chi-restraints excluded: chain D residue 219 LEU Chi-restraints excluded: chain D residue 280 ILE Chi-restraints excluded: chain D residue 552 SER 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: 0.0270 chunk 43 optimal weight: 2.9990 chunk 4 optimal weight: 6.9990 chunk 56 optimal weight: 2.9990 chunk 117 optimal weight: 1.9990 chunk 114 optimal weight: 5.9990 chunk 78 optimal weight: 4.9990 chunk 22 optimal weight: 9.9990 chunk 45 optimal weight: 1.9990 chunk 59 optimal weight: 0.6980 chunk 102 optimal weight: 1.9990 overall best weight: 1.3444 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 33 GLN C 324 ASN ** C 705 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 33 GLN D 324 ASN ** D 705 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4040 r_free = 0.4040 target = 0.168287 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.133410 restraints weight = 12752.551| |-----------------------------------------------------------------------------| r_work (start): 0.3639 rms_B_bonded: 2.08 r_work: 0.3507 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.3371 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.3371 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7775 moved from start: 0.1390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 10634 Z= 0.158 Angle : 0.651 8.822 14414 Z= 0.324 Chirality : 0.046 0.267 1760 Planarity : 0.005 0.075 1640 Dihedral : 17.895 165.268 2742 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 9.75 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.62 % Favored : 94.21 % Rotamer: Outliers : 2.01 % Allowed : 13.48 % Favored : 84.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.87 (0.24), residues: 1210 helix: 1.48 (0.18), residues: 820 sheet: 0.44 (0.54), residues: 50 loop : -1.68 (0.33), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 409 TYR 0.014 0.002 TYR C 371 PHE 0.017 0.002 PHE D 401 TRP 0.010 0.001 TRP C 482 HIS 0.003 0.001 HIS D 656 Details of bonding type rmsd/Z covalent geometry : bond 0.00343 / 0.16 (10634) covalent geometry : angle 0.65096 / 0.32 (14414) hydrogen bonds : bond 0.05058 / 3.30 ( 638) hydrogen bonds : angle 4.41952 / 3.27 ( 1860) *********************** 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 145 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 124 time to evaluate : 0.427 Fit side-chains revert: symmetry clash REVERT: C 27 TYR cc_start: 0.7748 (m-80) cc_final: 0.6806 (m-80) REVERT: C 684 GLN cc_start: 0.8196 (OUTLIER) cc_final: 0.7872 (tt0) REVERT: D 27 TYR cc_start: 0.7743 (m-80) cc_final: 0.6800 (m-80) REVERT: D 684 GLN cc_start: 0.8221 (OUTLIER) cc_final: 0.7898 (tt0) outliers start: 21 outliers final: 10 residues processed: 136 average time/residue: 0.3784 time to fit residues: 57.3675 Evaluate side-chains 129 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 117 time to evaluate : 0.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 80 ILE Chi-restraints excluded: chain C residue 154 SER Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain C residue 552 SER Chi-restraints excluded: chain C residue 559 VAL Chi-restraints excluded: chain C residue 684 GLN Chi-restraints excluded: chain D residue 80 ILE Chi-restraints excluded: chain D residue 154 SER Chi-restraints excluded: chain D residue 219 LEU Chi-restraints excluded: chain D residue 552 SER Chi-restraints excluded: chain D residue 559 VAL Chi-restraints excluded: chain D residue 684 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 105 optimal weight: 6.9990 chunk 46 optimal weight: 3.9990 chunk 60 optimal weight: 3.9990 chunk 92 optimal weight: 2.9990 chunk 9 optimal weight: 9.9990 chunk 55 optimal weight: 0.7980 chunk 24 optimal weight: 6.9990 chunk 23 optimal weight: 9.9990 chunk 36 optimal weight: 6.9990 chunk 77 optimal weight: 0.5980 chunk 49 optimal weight: 0.9990 overall best weight: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 324 ASN D 289 ASN D 324 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.166417 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.131252 restraints weight = 12801.146| |-----------------------------------------------------------------------------| r_work (start): 0.3609 rms_B_bonded: 2.04 r_work: 0.3473 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.3336 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3336 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7778 moved from start: 0.1658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 10634 Z= 0.190 Angle : 0.678 7.844 14414 Z= 0.339 Chirality : 0.047 0.318 1760 Planarity : 0.005 0.076 1640 Dihedral : 17.259 167.510 2742 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 9.24 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.95 % Favored : 93.88 % Rotamer: Outliers : 2.39 % Allowed : 13.77 % Favored : 83.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.79 (0.24), residues: 1210 helix: 1.42 (0.18), residues: 820 sheet: 0.21 (0.50), residues: 50 loop : -1.64 (0.34), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 549 TYR 0.018 0.002 TYR D 315 PHE 0.019 0.002 PHE D 141 TRP 0.011 0.001 TRP C 74 HIS 0.003 0.001 HIS C 656 Details of bonding type rmsd/Z covalent geometry : bond 0.00425 / 0.19 (10634) covalent geometry : angle 0.67823 / 0.34 (14414) hydrogen bonds : bond 0.05362 / 3.49 ( 638) hydrogen bonds : angle 4.47593 / 3.32 ( 1860) *********************** 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 137 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 112 time to evaluate : 0.238 Fit side-chains revert: symmetry clash REVERT: C 27 TYR cc_start: 0.7764 (m-80) cc_final: 0.6727 (m-80) REVERT: C 81 LYS cc_start: 0.7939 (mmpt) cc_final: 0.7086 (mmtm) REVERT: C 556 TYR cc_start: 0.7104 (OUTLIER) cc_final: 0.6753 (p90) REVERT: C 684 GLN cc_start: 0.8117 (OUTLIER) cc_final: 0.7778 (tt0) REVERT: D 27 TYR cc_start: 0.7767 (m-80) cc_final: 0.6726 (m-80) REVERT: D 81 LYS cc_start: 0.7944 (mmpt) cc_final: 0.7092 (mmtm) REVERT: D 556 TYR cc_start: 0.7097 (OUTLIER) cc_final: 0.6739 (p90) REVERT: D 678 MET cc_start: 0.8062 (mmt) cc_final: 0.7842 (mmt) REVERT: D 684 GLN cc_start: 0.8157 (OUTLIER) cc_final: 0.7826 (tt0) outliers start: 25 outliers final: 15 residues processed: 133 average time/residue: 0.3873 time to fit residues: 57.2555 Evaluate side-chains 130 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 111 time to evaluate : 0.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 80 ILE 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 C residue 556 TYR Chi-restraints excluded: chain C residue 559 VAL Chi-restraints excluded: chain C residue 684 GLN Chi-restraints excluded: chain D residue 80 ILE Chi-restraints excluded: chain D residue 100 LEU 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 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 684 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 55 optimal weight: 0.8980 chunk 73 optimal weight: 5.9990 chunk 46 optimal weight: 1.9990 chunk 77 optimal weight: 2.9990 chunk 61 optimal weight: 1.9990 chunk 32 optimal weight: 0.0000 chunk 50 optimal weight: 0.6980 chunk 104 optimal weight: 2.9990 chunk 12 optimal weight: 5.9990 chunk 7 optimal weight: 0.5980 chunk 88 optimal weight: 7.9990 overall best weight: 0.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 289 ASN C 324 ASN D 324 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4064 r_free = 0.4064 target = 0.169871 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.135933 restraints weight = 12742.886| |-----------------------------------------------------------------------------| r_work (start): 0.3670 rms_B_bonded: 2.03 r_work: 0.3539 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.3402 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3402 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7721 moved from start: 0.1660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 10634 Z= 0.132 Angle : 0.614 8.237 14414 Z= 0.308 Chirality : 0.045 0.315 1760 Planarity : 0.005 0.080 1640 Dihedral : 16.132 167.732 2742 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 9.98 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.87 % Favored : 93.97 % Rotamer: Outliers : 3.54 % Allowed : 12.91 % Favored : 83.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.02 (0.24), residues: 1210 helix: 1.63 (0.18), residues: 820 sheet: 0.24 (0.49), residues: 50 loop : -1.67 (0.33), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 409 TYR 0.013 0.001 TYR D 371 PHE 0.018 0.001 PHE D 141 TRP 0.010 0.001 TRP D 482 HIS 0.004 0.001 HIS C 656 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.13 (10634) covalent geometry : angle 0.61417 / 0.31 (14414) hydrogen bonds : bond 0.04637 / 3.03 ( 638) hydrogen bonds : angle 4.27752 / 3.16 ( 1860) *********************** 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 171 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 134 time to evaluate : 0.308 Fit side-chains REVERT: C 27 TYR cc_start: 0.7754 (m-80) cc_final: 0.6633 (m-80) REVERT: C 81 LYS cc_start: 0.7967 (mmpt) cc_final: 0.7134 (mmtm) REVERT: C 339 GLU cc_start: 0.7577 (OUTLIER) cc_final: 0.6878 (mp0) REVERT: C 678 MET cc_start: 0.8068 (mmt) cc_final: 0.7844 (mmt) REVERT: C 682 GLU cc_start: 0.8150 (mt-10) cc_final: 0.7797 (mt-10) REVERT: C 684 GLN cc_start: 0.8095 (OUTLIER) cc_final: 0.7772 (tt0) REVERT: D 27 TYR cc_start: 0.7752 (m-80) cc_final: 0.6633 (m-80) REVERT: D 81 LYS cc_start: 0.7967 (mmpt) cc_final: 0.7127 (mmtm) REVERT: D 684 GLN cc_start: 0.8096 (OUTLIER) cc_final: 0.7758 (tt0) outliers start: 37 outliers final: 16 residues processed: 161 average time/residue: 0.3376 time to fit residues: 61.0654 Evaluate side-chains 137 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 118 time to evaluate : 0.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 80 ILE Chi-restraints excluded: chain C residue 154 SER Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain C residue 339 GLU Chi-restraints excluded: chain C residue 370 VAL 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 C residue 559 VAL Chi-restraints excluded: chain C residue 684 GLN Chi-restraints excluded: chain D residue 80 ILE Chi-restraints excluded: chain D residue 154 SER Chi-restraints excluded: chain D residue 219 LEU Chi-restraints excluded: chain D residue 370 VAL 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 559 VAL Chi-restraints excluded: chain D residue 684 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 67 optimal weight: 4.9990 chunk 110 optimal weight: 1.9990 chunk 73 optimal weight: 3.9990 chunk 65 optimal weight: 8.9990 chunk 46 optimal weight: 4.9990 chunk 14 optimal weight: 5.9990 chunk 49 optimal weight: 0.1980 chunk 7 optimal weight: 2.9990 chunk 76 optimal weight: 0.0050 chunk 79 optimal weight: 0.6980 chunk 41 optimal weight: 1.9990 overall best weight: 0.9798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 34 GLN D 34 GLN D 289 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4061 r_free = 0.4061 target = 0.169453 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.135170 restraints weight = 12840.710| |-----------------------------------------------------------------------------| r_work (start): 0.3659 rms_B_bonded: 2.05 r_work: 0.3527 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.3391 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.3391 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7738 moved from start: 0.1737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 10634 Z= 0.140 Angle : 0.640 11.243 14414 Z= 0.317 Chirality : 0.046 0.310 1760 Planarity : 0.005 0.079 1640 Dihedral : 15.340 167.142 2742 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 9.61 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.95 % Favored : 93.88 % Rotamer: Outliers : 3.35 % Allowed : 13.00 % Favored : 83.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.06 (0.24), residues: 1210 helix: 1.67 (0.18), residues: 820 sheet: 0.23 (0.49), residues: 50 loop : -1.69 (0.33), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 409 TYR 0.017 0.002 TYR D 315 PHE 0.019 0.001 PHE C 141 TRP 0.009 0.001 TRP D 482 HIS 0.003 0.001 HIS C 656 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.14 (10634) covalent geometry : angle 0.64045 / 0.32 (14414) hydrogen bonds : bond 0.04714 / 3.07 ( 638) hydrogen bonds : angle 4.25758 / 3.15 ( 1860) *********************** 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 159 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 124 time to evaluate : 0.358 Fit side-chains revert: symmetry clash REVERT: C 27 TYR cc_start: 0.7733 (m-80) cc_final: 0.6675 (m-80) REVERT: C 81 LYS cc_start: 0.8002 (mmpt) cc_final: 0.7122 (mmtm) REVERT: C 339 GLU cc_start: 0.7586 (OUTLIER) cc_final: 0.6852 (mp0) REVERT: C 678 MET cc_start: 0.7992 (mmt) cc_final: 0.7710 (mmt) REVERT: C 682 GLU cc_start: 0.8203 (mt-10) cc_final: 0.7851 (mt-10) REVERT: C 684 GLN cc_start: 0.8110 (OUTLIER) cc_final: 0.7774 (tt0) REVERT: D 27 TYR cc_start: 0.7740 (m-80) cc_final: 0.6681 (m-80) REVERT: D 81 LYS cc_start: 0.7972 (mmpt) cc_final: 0.7107 (mmtm) REVERT: D 684 GLN cc_start: 0.8116 (OUTLIER) cc_final: 0.7775 (tt0) outliers start: 35 outliers final: 17 residues processed: 151 average time/residue: 0.3419 time to fit residues: 57.7984 Evaluate side-chains 138 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 118 time to evaluate : 0.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 80 ILE Chi-restraints excluded: chain C residue 154 SER Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain C residue 339 GLU Chi-restraints excluded: chain C residue 370 VAL 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 C residue 559 VAL Chi-restraints excluded: chain C residue 684 GLN Chi-restraints excluded: chain D residue 80 ILE Chi-restraints excluded: chain D residue 154 SER Chi-restraints excluded: chain D residue 219 LEU Chi-restraints excluded: chain D residue 347 SER Chi-restraints excluded: chain D residue 370 VAL 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 559 VAL Chi-restraints excluded: chain D residue 684 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 71 optimal weight: 0.7980 chunk 93 optimal weight: 10.0000 chunk 77 optimal weight: 2.9990 chunk 20 optimal weight: 2.9990 chunk 21 optimal weight: 5.9990 chunk 62 optimal weight: 0.8980 chunk 28 optimal weight: 2.9990 chunk 108 optimal weight: 0.9980 chunk 78 optimal weight: 0.9980 chunk 14 optimal weight: 4.9990 chunk 80 optimal weight: 7.9990 overall best weight: 1.3382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 34 GLN D 34 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4048 r_free = 0.4048 target = 0.168185 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.133659 restraints weight = 12755.859| |-----------------------------------------------------------------------------| r_work (start): 0.3642 rms_B_bonded: 2.03 r_work: 0.3510 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.3373 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.3373 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7752 moved from start: 0.1802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 10634 Z= 0.158 Angle : 0.667 10.040 14414 Z= 0.329 Chirality : 0.046 0.294 1760 Planarity : 0.005 0.078 1640 Dihedral : 14.875 167.334 2742 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.12 % Favored : 93.72 % Rotamer: Outliers : 3.73 % Allowed : 13.86 % Favored : 82.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.00 (0.24), residues: 1210 helix: 1.62 (0.18), residues: 820 sheet: 0.22 (0.50), residues: 50 loop : -1.69 (0.33), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 409 TYR 0.014 0.002 TYR D 371 PHE 0.018 0.002 PHE D 141 TRP 0.010 0.001 TRP C 74 HIS 0.003 0.001 HIS D 656 Details of bonding type rmsd/Z covalent geometry : bond 0.00346 / 0.16 (10634) covalent geometry : angle 0.66664 / 0.33 (14414) hydrogen bonds : bond 0.04928 / 3.20 ( 638) hydrogen bonds : angle 4.32175 / 3.20 ( 1860) *********************** 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 157 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 118 time to evaluate : 0.363 Fit side-chains revert: symmetry clash REVERT: C 27 TYR cc_start: 0.7754 (m-80) cc_final: 0.6555 (m-80) REVERT: C 79 ARG cc_start: 0.7339 (mtp180) cc_final: 0.6989 (mtp-110) REVERT: C 81 LYS cc_start: 0.8021 (mmpt) cc_final: 0.7138 (mmtm) REVERT: C 339 GLU cc_start: 0.7589 (OUTLIER) cc_final: 0.6854 (mp0) REVERT: C 678 MET cc_start: 0.8012 (mmt) cc_final: 0.7741 (mpm) REVERT: C 684 GLN cc_start: 0.8103 (OUTLIER) cc_final: 0.7767 (tt0) REVERT: D 27 TYR cc_start: 0.7760 (m-80) cc_final: 0.6561 (m-80) REVERT: D 79 ARG cc_start: 0.7339 (mtp180) cc_final: 0.6988 (mtp-110) REVERT: D 81 LYS cc_start: 0.8022 (mmpt) cc_final: 0.7137 (mmtm) REVERT: D 684 GLN cc_start: 0.8117 (OUTLIER) cc_final: 0.7788 (tt0) outliers start: 39 outliers final: 18 residues processed: 150 average time/residue: 0.3483 time to fit residues: 58.4854 Evaluate side-chains 133 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 112 time to evaluate : 0.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 80 ILE Chi-restraints excluded: chain C residue 154 SER Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain C residue 339 GLU Chi-restraints excluded: chain C residue 347 SER Chi-restraints excluded: chain C residue 370 VAL 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 C residue 559 VAL Chi-restraints excluded: chain C residue 684 GLN Chi-restraints excluded: chain D residue 80 ILE Chi-restraints excluded: chain D residue 154 SER Chi-restraints excluded: chain D residue 219 LEU Chi-restraints excluded: chain D residue 347 SER Chi-restraints excluded: chain D residue 370 VAL 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 559 VAL Chi-restraints excluded: chain D residue 684 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 33 optimal weight: 0.9990 chunk 116 optimal weight: 4.9990 chunk 18 optimal weight: 0.9990 chunk 13 optimal weight: 0.6980 chunk 43 optimal weight: 1.9990 chunk 97 optimal weight: 4.9990 chunk 35 optimal weight: 1.9990 chunk 103 optimal weight: 2.9990 chunk 62 optimal weight: 0.9980 chunk 0 optimal weight: 2.9990 chunk 53 optimal weight: 7.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 34 GLN D 34 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4057 r_free = 0.4057 target = 0.169054 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.134676 restraints weight = 12748.793| |-----------------------------------------------------------------------------| r_work (start): 0.3654 rms_B_bonded: 2.02 r_work: 0.3521 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.3385 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3385 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7737 moved from start: 0.1845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 10634 Z= 0.147 Angle : 0.652 9.287 14414 Z= 0.325 Chirality : 0.046 0.330 1760 Planarity : 0.005 0.079 1640 Dihedral : 14.402 166.447 2742 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 9.52 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.62 % Favored : 94.21 % Rotamer: Outliers : 2.87 % Allowed : 15.20 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.03 (0.24), residues: 1210 helix: 1.67 (0.18), residues: 818 sheet: 0.20 (0.50), residues: 50 loop : -1.70 (0.33), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 409 TYR 0.014 0.002 TYR D 315 PHE 0.018 0.001 PHE D 141 TRP 0.009 0.001 TRP C 74 HIS 0.003 0.001 HIS D 656 Details of bonding type rmsd/Z covalent geometry : bond 0.00318 / 0.15 (10634) covalent geometry : angle 0.65209 / 0.32 (14414) hydrogen bonds : bond 0.04798 / 3.12 ( 638) hydrogen bonds : angle 4.30190 / 3.18 ( 1860) *********************** 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 144 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 114 time to evaluate : 0.371 Fit side-chains revert: symmetry clash REVERT: C 27 TYR cc_start: 0.7750 (m-80) cc_final: 0.6597 (m-80) REVERT: C 81 LYS cc_start: 0.7973 (mmpt) cc_final: 0.7066 (mmtm) REVERT: C 339 GLU cc_start: 0.7559 (OUTLIER) cc_final: 0.6854 (mp0) REVERT: C 678 MET cc_start: 0.7986 (mmt) cc_final: 0.7751 (mpm) REVERT: C 684 GLN cc_start: 0.8104 (OUTLIER) cc_final: 0.7773 (tt0) REVERT: D 27 TYR cc_start: 0.7750 (m-80) cc_final: 0.6594 (m-80) REVERT: D 81 LYS cc_start: 0.7977 (mmpt) cc_final: 0.7067 (mmtm) REVERT: D 682 GLU cc_start: 0.7972 (mt-10) cc_final: 0.7685 (mt-10) REVERT: D 684 GLN cc_start: 0.8133 (OUTLIER) cc_final: 0.7804 (tt0) outliers start: 30 outliers final: 18 residues processed: 136 average time/residue: 0.3933 time to fit residues: 59.3860 Evaluate side-chains 133 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 112 time to evaluate : 0.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 80 ILE Chi-restraints excluded: chain C residue 154 SER Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain C residue 339 GLU Chi-restraints excluded: chain C residue 347 SER Chi-restraints excluded: chain C residue 370 VAL 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 C residue 559 VAL Chi-restraints excluded: chain C residue 684 GLN Chi-restraints excluded: chain D residue 80 ILE Chi-restraints excluded: chain D residue 154 SER Chi-restraints excluded: chain D residue 219 LEU Chi-restraints excluded: chain D residue 347 SER Chi-restraints excluded: chain D residue 370 VAL 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 559 VAL Chi-restraints excluded: chain D residue 684 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 7 optimal weight: 1.9990 chunk 41 optimal weight: 2.9990 chunk 12 optimal weight: 3.9990 chunk 58 optimal weight: 0.3980 chunk 52 optimal weight: 3.9990 chunk 117 optimal weight: 5.9990 chunk 120 optimal weight: 0.0570 chunk 37 optimal weight: 0.9990 chunk 75 optimal weight: 4.9990 chunk 50 optimal weight: 1.9990 chunk 15 optimal weight: 2.9990 overall best weight: 1.0904 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4058 r_free = 0.4058 target = 0.169097 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.134743 restraints weight = 12707.364| |-----------------------------------------------------------------------------| r_work (start): 0.3655 rms_B_bonded: 2.04 r_work: 0.3522 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.3385 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.3385 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7745 moved from start: 0.1833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 10634 Z= 0.147 Angle : 0.653 9.124 14414 Z= 0.326 Chirality : 0.046 0.364 1760 Planarity : 0.005 0.079 1640 Dihedral : 13.942 164.699 2742 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 9.75 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.28 % Favored : 93.55 % Rotamer: Outliers : 2.68 % Allowed : 15.20 % 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 are not related in a simple way. whole: 1.06 (0.24), residues: 1210 helix: 1.72 (0.18), residues: 812 sheet: 0.22 (0.50), residues: 50 loop : -1.74 (0.33), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 134 TYR 0.013 0.001 TYR D 371 PHE 0.019 0.001 PHE D 141 TRP 0.009 0.001 TRP C 74 HIS 0.003 0.001 HIS D 656 Details of bonding type rmsd/Z covalent geometry : bond 0.00316 / 0.15 (10634) covalent geometry : angle 0.65266 / 0.33 (14414) hydrogen bonds : bond 0.04781 / 3.10 ( 638) hydrogen bonds : angle 4.28035 / 3.17 ( 1860) *********************** 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 145 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 117 time to evaluate : 0.265 Fit side-chains revert: symmetry clash REVERT: C 27 TYR cc_start: 0.7756 (m-80) cc_final: 0.6469 (m-80) REVERT: C 79 ARG cc_start: 0.7338 (mtp180) cc_final: 0.6997 (mtp-110) REVERT: C 81 LYS cc_start: 0.7925 (mmpt) cc_final: 0.7195 (mmtm) REVERT: C 339 GLU cc_start: 0.7558 (OUTLIER) cc_final: 0.6856 (mp0) REVERT: C 678 MET cc_start: 0.7995 (mmt) cc_final: 0.7656 (mpm) REVERT: C 682 GLU cc_start: 0.7969 (mt-10) cc_final: 0.7634 (mt-10) REVERT: C 684 GLN cc_start: 0.8107 (OUTLIER) cc_final: 0.7771 (tt0) REVERT: D 27 TYR cc_start: 0.7759 (m-80) cc_final: 0.6470 (m-80) REVERT: D 79 ARG cc_start: 0.7346 (mtp180) cc_final: 0.7008 (mtp-110) REVERT: D 81 LYS cc_start: 0.7944 (mmpt) cc_final: 0.7222 (mmtm) REVERT: D 684 GLN cc_start: 0.8115 (OUTLIER) cc_final: 0.7790 (tt0) outliers start: 28 outliers final: 16 residues processed: 135 average time/residue: 0.3608 time to fit residues: 53.8924 Evaluate side-chains 133 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 114 time to evaluate : 0.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 154 SER Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain C residue 339 GLU Chi-restraints excluded: chain C residue 347 SER Chi-restraints excluded: chain C residue 370 VAL 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 C residue 559 VAL Chi-restraints excluded: chain C residue 684 GLN Chi-restraints excluded: chain D residue 154 SER Chi-restraints excluded: chain D residue 219 LEU Chi-restraints excluded: chain D residue 347 SER Chi-restraints excluded: chain D residue 370 VAL 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 559 VAL Chi-restraints excluded: chain D residue 684 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 66 optimal weight: 1.9990 chunk 106 optimal weight: 1.9990 chunk 91 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 chunk 33 optimal weight: 0.9990 chunk 6 optimal weight: 4.9990 chunk 29 optimal weight: 0.8980 chunk 97 optimal weight: 10.0000 chunk 77 optimal weight: 0.7980 chunk 18 optimal weight: 0.5980 chunk 116 optimal weight: 2.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 34 GLN D 34 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4061 r_free = 0.4061 target = 0.169502 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.135044 restraints weight = 12653.422| |-----------------------------------------------------------------------------| r_work (start): 0.3659 rms_B_bonded: 2.03 r_work: 0.3527 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.3391 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.3391 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7732 moved from start: 0.1875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10634 Z= 0.145 Angle : 0.647 9.047 14414 Z= 0.325 Chirality : 0.045 0.349 1760 Planarity : 0.005 0.079 1640 Dihedral : 13.591 162.584 2742 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 9.52 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.62 % Favored : 94.21 % Rotamer: Outliers : 2.20 % Allowed : 15.77 % Favored : 82.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.07 (0.24), residues: 1210 helix: 1.70 (0.18), residues: 816 sheet: 0.22 (0.50), residues: 50 loop : -1.71 (0.33), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 409 TYR 0.015 0.001 TYR C 556 PHE 0.019 0.001 PHE D 141 TRP 0.009 0.001 TRP C 74 HIS 0.003 0.001 HIS C 656 Details of bonding type rmsd/Z covalent geometry : bond 0.00313 / 0.15 (10634) covalent geometry : angle 0.64737 / 0.33 (14414) hydrogen bonds : bond 0.04750 / 3.08 ( 638) hydrogen bonds : angle 4.26156 / 3.15 ( 1860) ********************** 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 139 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 116 time to evaluate : 0.382 Fit side-chains revert: symmetry clash REVERT: C 27 TYR cc_start: 0.7808 (m-80) cc_final: 0.6514 (m-80) REVERT: C 79 ARG cc_start: 0.7315 (mtp180) cc_final: 0.6921 (mtp-110) REVERT: C 81 LYS cc_start: 0.7920 (mmpt) cc_final: 0.7190 (mmtm) REVERT: C 339 GLU cc_start: 0.7556 (OUTLIER) cc_final: 0.6853 (mp0) REVERT: C 678 MET cc_start: 0.7937 (mmt) cc_final: 0.7627 (mpm) REVERT: C 682 GLU cc_start: 0.7999 (mt-10) cc_final: 0.7634 (mt-10) REVERT: C 684 GLN cc_start: 0.8104 (OUTLIER) cc_final: 0.7771 (tt0) REVERT: D 27 TYR cc_start: 0.7804 (m-80) cc_final: 0.6508 (m-80) REVERT: D 79 ARG cc_start: 0.7330 (mtp180) cc_final: 0.6935 (mtp-110) REVERT: D 81 LYS cc_start: 0.7923 (mmpt) cc_final: 0.7191 (mmtm) REVERT: D 684 GLN cc_start: 0.8109 (OUTLIER) cc_final: 0.7784 (tt0) outliers start: 23 outliers final: 16 residues processed: 131 average time/residue: 0.4005 time to fit residues: 57.9843 Evaluate side-chains 133 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 114 time to evaluate : 0.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 154 SER Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain C residue 339 GLU Chi-restraints excluded: chain C residue 347 SER Chi-restraints excluded: chain C residue 370 VAL 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 C residue 559 VAL Chi-restraints excluded: chain C residue 684 GLN Chi-restraints excluded: chain D residue 154 SER Chi-restraints excluded: chain D residue 219 LEU Chi-restraints excluded: chain D residue 347 SER Chi-restraints excluded: chain D residue 370 VAL 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 559 VAL Chi-restraints excluded: chain D residue 684 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 86 optimal weight: 1.9990 chunk 38 optimal weight: 10.0000 chunk 74 optimal weight: 5.9990 chunk 111 optimal weight: 1.9990 chunk 29 optimal weight: 2.9990 chunk 107 optimal weight: 0.9990 chunk 41 optimal weight: 0.9990 chunk 5 optimal weight: 4.9990 chunk 6 optimal weight: 3.9990 chunk 27 optimal weight: 5.9990 chunk 115 optimal weight: 0.7980 overall best weight: 1.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 34 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4044 r_free = 0.4044 target = 0.167938 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.133223 restraints weight = 12767.229| |-----------------------------------------------------------------------------| r_work (start): 0.3635 rms_B_bonded: 2.04 r_work: 0.3503 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.3366 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3366 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7753 moved from start: 0.1913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 10634 Z= 0.162 Angle : 0.662 9.079 14414 Z= 0.334 Chirality : 0.046 0.316 1760 Planarity : 0.005 0.077 1640 Dihedral : 13.470 160.400 2742 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 9.47 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.28 % Favored : 93.55 % Rotamer: Outliers : 2.39 % Allowed : 15.58 % Favored : 82.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.01 (0.24), residues: 1210 helix: 1.65 (0.18), residues: 814 sheet: 0.19 (0.50), residues: 50 loop : -1.68 (0.33), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 134 TYR 0.018 0.002 TYR D 556 PHE 0.018 0.002 PHE D 141 TRP 0.010 0.001 TRP C 74 HIS 0.003 0.001 HIS D 656 Details of bonding type rmsd/Z covalent geometry : bond 0.00355 / 0.16 (10634) covalent geometry : angle 0.66151 / 0.33 (14414) hydrogen bonds : bond 0.04994 / 3.24 ( 638) hydrogen bonds : angle 4.32500 / 3.21 ( 1860) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3484.79 seconds wall clock time: 60 minutes 10.53 seconds (3610.53 seconds total)