Starting phenix.real_space_refine on Wed Mar 4 02:51:13 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8sgw_40470/03_2026/8sgw_40470.cif Found real_map, /net/cci-nas-00/data/ceres_data/8sgw_40470/03_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_40470/03_2026/8sgw_40470.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8sgw_40470/03_2026/8sgw_40470.map" model { file = "/net/cci-nas-00/data/ceres_data/8sgw_40470/03_2026/8sgw_40470.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8sgw_40470/03_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-5986/lib/python3.9/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, 452 Unusual residues: {' CL': 2, 'AV0': 1, 'CLR': 6, 'DMU': 1, 'LBN': 9} Classifications: {'undetermined': 19} Link IDs: {None: 18} 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, 452 Unusual residues: {' CL': 2, 'AV0': 1, 'CLR': 6, 'DMU': 1, 'LBN': 9} Classifications: {'undetermined': 19} Link IDs: {None: 18} 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: 2.51, per 1000 atoms: 0.24 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: 0.90 Conformation dependent library (CDL) restraints added in 503.6 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: 0.33 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: 1.61 Time building geometry restraints manager: 1.11 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: 0.520 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: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 10.840 Find NCS groups from input model: 0.070 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:6.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.400 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7450 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 covalent geometry : bond 0.00418 (10634) covalent geometry : angle 0.68791 (14414) hydrogen bonds : bond 0.12462 ( 638) hydrogen bonds : angle 5.41916 ( 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 : 0.370 Fit side-chains outliers start: 0 outliers final: 1 residues processed: 167 average time/residue: 0.5008 time to fit residues: 91.2620 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 : 0.316 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4066 r_free = 0.4066 target = 0.169445 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.135713 restraints weight = 12636.571| |-----------------------------------------------------------------------------| r_work (start): 0.3679 rms_B_bonded: 1.95 r_work: 0.3547 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3413 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.3413 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7555 moved from start: 0.1138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 10634 Z= 0.174 Angle : 0.727 11.276 14414 Z= 0.348 Chirality : 0.046 0.241 1760 Planarity : 0.005 0.069 1640 Dihedral : 19.897 161.888 2744 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 9.61 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.29 % Favored : 94.55 % Rotamer: Outliers : 1.15 % Allowed : 11.28 % Favored : 87.57 % 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 (0.24), residues: 1210 helix: 1.48 (0.18), residues: 816 sheet: 0.41 (0.56), residues: 50 loop : -1.72 (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 D 371 PHE 0.019 0.002 PHE C 141 TRP 0.009 0.001 TRP C 74 HIS 0.003 0.001 HIS C 656 Details of bonding type rmsd covalent geometry : bond 0.00378 (10634) covalent geometry : angle 0.72723 (14414) hydrogen bonds : bond 0.05361 ( 638) hydrogen bonds : angle 4.56327 ( 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 146 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 134 time to evaluate : 0.365 Fit side-chains REVERT: D 503 MET cc_start: 0.8656 (mpp) cc_final: 0.8379 (mmt) outliers start: 12 outliers final: 6 residues processed: 142 average time/residue: 0.4174 time to fit residues: 65.4420 Evaluate side-chains 122 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 116 time to evaluate : 0.380 ------------------------------------------------------------------------------- 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 552 SER Chi-restraints excluded: chain D residue 154 SER Chi-restraints excluded: chain D residue 219 LEU Chi-restraints excluded: chain D residue 552 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 52 optimal weight: 0.0070 chunk 43 optimal weight: 2.9990 chunk 4 optimal weight: 5.9990 chunk 56 optimal weight: 0.8980 chunk 117 optimal weight: 0.2980 chunk 114 optimal weight: 7.9990 chunk 78 optimal weight: 4.9990 chunk 22 optimal weight: 9.9990 chunk 45 optimal weight: 0.8980 chunk 59 optimal weight: 0.0670 chunk 102 optimal weight: 0.0000 overall best weight: 0.2540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 33 GLN C 289 ASN C 324 ASN C 705 GLN C 728 HIS D 33 GLN D 324 ASN D 705 GLN D 728 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4102 r_free = 0.4102 target = 0.174174 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.140280 restraints weight = 12777.026| |-----------------------------------------------------------------------------| r_work (start): 0.3725 rms_B_bonded: 2.12 r_work: 0.3594 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3594 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7379 moved from start: 0.1408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 10634 Z= 0.119 Angle : 0.601 7.719 14414 Z= 0.297 Chirality : 0.045 0.297 1760 Planarity : 0.004 0.072 1640 Dihedral : 17.185 165.251 2742 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 10.21 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.12 % Favored : 94.71 % Rotamer: Outliers : 1.91 % Allowed : 14.05 % Favored : 84.03 % 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: 1.04 (0.24), residues: 1210 helix: 1.68 (0.18), residues: 818 sheet: 0.54 (0.52), residues: 50 loop : -1.78 (0.33), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 24 TYR 0.015 0.001 TYR D 315 PHE 0.015 0.001 PHE D 141 TRP 0.009 0.001 TRP C 482 HIS 0.004 0.001 HIS D 656 Details of bonding type rmsd covalent geometry : bond 0.00236 (10634) covalent geometry : angle 0.60108 (14414) hydrogen bonds : bond 0.04354 ( 638) hydrogen bonds : angle 4.27503 ( 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 159 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 139 time to evaluate : 0.359 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 27 TYR cc_start: 0.7540 (m-80) cc_final: 0.6795 (m-80) REVERT: C 464 GLN cc_start: 0.8191 (OUTLIER) cc_final: 0.7946 (mt0) REVERT: D 27 TYR cc_start: 0.7544 (m-80) cc_final: 0.6801 (m-80) REVERT: D 464 GLN cc_start: 0.8176 (OUTLIER) cc_final: 0.7929 (mt0) outliers start: 20 outliers final: 10 residues processed: 149 average time/residue: 0.3866 time to fit residues: 64.1342 Evaluate side-chains 132 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 120 time to evaluate : 0.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 80 ILE Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain C residue 370 VAL Chi-restraints excluded: chain C residue 464 GLN Chi-restraints excluded: chain C residue 552 SER Chi-restraints excluded: chain C residue 559 VAL Chi-restraints excluded: chain D residue 80 ILE Chi-restraints excluded: chain D residue 219 LEU Chi-restraints excluded: chain D residue 370 VAL Chi-restraints excluded: chain D residue 464 GLN Chi-restraints excluded: chain D residue 552 SER Chi-restraints excluded: chain D residue 559 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 105 optimal weight: 4.9990 chunk 46 optimal weight: 4.9990 chunk 60 optimal weight: 5.9990 chunk 92 optimal weight: 3.9990 chunk 9 optimal weight: 0.6980 chunk 55 optimal weight: 0.7980 chunk 24 optimal weight: 0.5980 chunk 23 optimal weight: 10.0000 chunk 36 optimal weight: 1.9990 chunk 77 optimal weight: 0.7980 chunk 49 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4083 r_free = 0.4083 target = 0.171940 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.137696 restraints weight = 12892.103| |-----------------------------------------------------------------------------| r_work (start): 0.3695 rms_B_bonded: 2.11 r_work: 0.3564 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3564 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7411 moved from start: 0.1553 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= 0.129 Angle : 0.615 8.025 14414 Z= 0.302 Chirality : 0.045 0.319 1760 Planarity : 0.004 0.072 1640 Dihedral : 16.080 163.352 2742 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 9.61 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.37 % Favored : 94.46 % Rotamer: Outliers : 2.01 % Allowed : 15.11 % Favored : 82.89 % 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: 1.17 (0.25), residues: 1210 helix: 1.77 (0.18), residues: 818 sheet: 0.61 (0.52), residues: 50 loop : -1.71 (0.33), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 24 TYR 0.016 0.001 TYR C 315 PHE 0.016 0.001 PHE C 141 TRP 0.009 0.001 TRP C 482 HIS 0.003 0.001 HIS C 656 Details of bonding type rmsd covalent geometry : bond 0.00271 (10634) covalent geometry : angle 0.61524 (14414) hydrogen bonds : bond 0.04477 ( 638) hydrogen bonds : angle 4.23352 ( 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 150 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 129 time to evaluate : 0.381 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 27 TYR cc_start: 0.7560 (m-80) cc_final: 0.6783 (m-80) REVERT: C 684 GLN cc_start: 0.8068 (OUTLIER) cc_final: 0.7723 (tt0) REVERT: D 27 TYR cc_start: 0.7569 (m-80) cc_final: 0.6788 (m-80) REVERT: D 684 GLN cc_start: 0.8078 (OUTLIER) cc_final: 0.7734 (tt0) outliers start: 21 outliers final: 10 residues processed: 140 average time/residue: 0.3947 time to fit residues: 61.4407 Evaluate side-chains 136 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 124 time to evaluate : 0.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 80 ILE Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain C residue 370 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 219 LEU Chi-restraints excluded: chain D residue 370 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 55 optimal weight: 1.9990 chunk 73 optimal weight: 3.9990 chunk 46 optimal weight: 4.9990 chunk 77 optimal weight: 0.8980 chunk 61 optimal weight: 2.9990 chunk 32 optimal weight: 2.9990 chunk 50 optimal weight: 0.0470 chunk 104 optimal weight: 0.5980 chunk 12 optimal weight: 4.9990 chunk 7 optimal weight: 1.9990 chunk 88 optimal weight: 7.9990 overall best weight: 1.1082 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 33 GLN D 33 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4072 r_free = 0.4072 target = 0.170466 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.136105 restraints weight = 12681.053| |-----------------------------------------------------------------------------| r_work (start): 0.3675 rms_B_bonded: 2.03 r_work: 0.3544 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.3408 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.3408 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7473 moved from start: 0.1656 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 10634 Z= 0.143 Angle : 0.638 9.776 14414 Z= 0.314 Chirality : 0.046 0.317 1760 Planarity : 0.005 0.078 1640 Dihedral : 15.486 165.405 2742 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 9.19 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.12 % Favored : 93.72 % Rotamer: Outliers : 3.15 % Allowed : 14.34 % Favored : 82.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.17 (0.25), residues: 1210 helix: 1.75 (0.18), residues: 818 sheet: 0.60 (0.52), residues: 50 loop : -1.65 (0.33), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 24 TYR 0.013 0.001 TYR C 371 PHE 0.017 0.002 PHE D 141 TRP 0.009 0.001 TRP D 482 HIS 0.003 0.001 HIS D 656 Details of bonding type rmsd covalent geometry : bond 0.00310 (10634) covalent geometry : angle 0.63845 (14414) hydrogen bonds : bond 0.04718 ( 638) hydrogen bonds : angle 4.24808 ( 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 156 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 123 time to evaluate : 0.334 Fit side-chains REVERT: C 27 TYR cc_start: 0.7701 (m-80) cc_final: 0.6750 (m-80) REVERT: C 79 ARG cc_start: 0.7360 (mtp85) cc_final: 0.6998 (mtp-110) REVERT: C 81 LYS cc_start: 0.7795 (mmpt) cc_final: 0.6945 (mmtm) REVERT: C 684 GLN cc_start: 0.8141 (OUTLIER) cc_final: 0.7815 (tt0) REVERT: D 27 TYR cc_start: 0.7703 (m-80) cc_final: 0.6749 (m-80) REVERT: D 79 ARG cc_start: 0.7368 (mtp85) cc_final: 0.7007 (mtp-110) REVERT: D 81 LYS cc_start: 0.7799 (mmpt) cc_final: 0.6945 (mmtm) REVERT: D 684 GLN cc_start: 0.8152 (OUTLIER) cc_final: 0.7822 (tt0) outliers start: 33 outliers final: 18 residues processed: 148 average time/residue: 0.3789 time to fit residues: 62.6323 Evaluate side-chains 139 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 119 time to evaluate : 0.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 67 THR 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 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 67 THR 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: 4.9990 chunk 65 optimal weight: 9.9990 chunk 46 optimal weight: 3.9990 chunk 14 optimal weight: 4.9990 chunk 49 optimal weight: 0.9980 chunk 7 optimal weight: 2.9990 chunk 76 optimal weight: 1.9990 chunk 79 optimal weight: 0.2980 chunk 41 optimal weight: 0.5980 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 464 GLN D 464 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4067 r_free = 0.4067 target = 0.170049 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.135477 restraints weight = 12759.751| |-----------------------------------------------------------------------------| r_work (start): 0.3666 rms_B_bonded: 2.04 r_work: 0.3535 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.3398 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.3398 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7482 moved from start: 0.1747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 10634 Z= 0.146 Angle : 0.633 8.813 14414 Z= 0.315 Chirality : 0.046 0.320 1760 Planarity : 0.005 0.079 1640 Dihedral : 14.924 165.744 2742 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 9.89 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.03 % Favored : 93.80 % Rotamer: Outliers : 3.25 % Allowed : 13.96 % Favored : 82.79 % 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: 1.12 (0.24), residues: 1210 helix: 1.71 (0.18), residues: 818 sheet: 0.67 (0.55), residues: 50 loop : -1.68 (0.33), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 409 TYR 0.015 0.002 TYR C 315 PHE 0.017 0.001 PHE D 141 TRP 0.009 0.001 TRP D 482 HIS 0.003 0.001 HIS C 656 Details of bonding type rmsd covalent geometry : bond 0.00318 (10634) covalent geometry : angle 0.63323 (14414) hydrogen bonds : bond 0.04761 ( 638) hydrogen bonds : angle 4.24831 ( 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 162 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 128 time to evaluate : 0.317 Fit side-chains REVERT: C 27 TYR cc_start: 0.7736 (m-80) cc_final: 0.6773 (m-80) REVERT: C 81 LYS cc_start: 0.7911 (mmpt) cc_final: 0.7055 (mmtm) REVERT: C 682 GLU cc_start: 0.8048 (mt-10) cc_final: 0.7631 (mt-10) REVERT: C 684 GLN cc_start: 0.8139 (OUTLIER) cc_final: 0.7815 (tt0) REVERT: D 27 TYR cc_start: 0.7739 (m-80) cc_final: 0.6789 (m-80) REVERT: D 81 LYS cc_start: 0.7913 (mmpt) cc_final: 0.7051 (mmtm) REVERT: D 682 GLU cc_start: 0.8052 (mt-10) cc_final: 0.7635 (mt-10) REVERT: D 684 GLN cc_start: 0.8149 (OUTLIER) cc_final: 0.7820 (tt0) outliers start: 34 outliers final: 18 residues processed: 154 average time/residue: 0.3579 time to fit residues: 61.6278 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 : 0.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 67 THR 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 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 67 THR 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 71 optimal weight: 2.9990 chunk 93 optimal weight: 8.9990 chunk 77 optimal weight: 0.6980 chunk 20 optimal weight: 2.9990 chunk 21 optimal weight: 4.9990 chunk 62 optimal weight: 0.6980 chunk 28 optimal weight: 5.9990 chunk 108 optimal weight: 0.5980 chunk 78 optimal weight: 4.9990 chunk 14 optimal weight: 4.9990 chunk 80 optimal weight: 5.9990 overall best weight: 1.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4043 r_free = 0.4043 target = 0.167657 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.133235 restraints weight = 12685.786| |-----------------------------------------------------------------------------| r_work (start): 0.3640 rms_B_bonded: 2.01 r_work: 0.3506 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.3369 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.3369 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7510 moved from start: 0.1842 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= 0.172 Angle : 0.665 8.890 14414 Z= 0.333 Chirality : 0.047 0.351 1760 Planarity : 0.005 0.077 1640 Dihedral : 14.618 165.869 2742 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 9.75 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.53 % Favored : 93.31 % Rotamer: Outliers : 3.63 % Allowed : 14.53 % Favored : 81.84 % 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: 1.03 (0.24), residues: 1210 helix: 1.65 (0.18), residues: 816 sheet: 0.49 (0.53), residues: 50 loop : -1.69 (0.33), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 409 TYR 0.016 0.002 TYR D 371 PHE 0.018 0.002 PHE C 401 TRP 0.010 0.001 TRP C 74 HIS 0.003 0.001 HIS D 656 Details of bonding type rmsd covalent geometry : bond 0.00383 (10634) covalent geometry : angle 0.66498 (14414) hydrogen bonds : bond 0.05068 ( 638) hydrogen bonds : angle 4.36823 ( 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 155 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 117 time to evaluate : 0.383 Fit side-chains REVERT: C 27 TYR cc_start: 0.7738 (m-80) cc_final: 0.6594 (m-80) REVERT: C 79 ARG cc_start: 0.7313 (mtp180) cc_final: 0.6958 (mtp-110) REVERT: C 81 LYS cc_start: 0.7962 (mmpt) cc_final: 0.7103 (mmtm) REVERT: C 339 GLU cc_start: 0.7594 (OUTLIER) cc_final: 0.6890 (mp0) REVERT: C 678 MET cc_start: 0.8026 (mmt) cc_final: 0.7629 (mpm) REVERT: C 682 GLU cc_start: 0.8085 (mt-10) cc_final: 0.7665 (mt-10) REVERT: C 684 GLN cc_start: 0.8147 (OUTLIER) cc_final: 0.7816 (tt0) REVERT: D 27 TYR cc_start: 0.7752 (m-80) cc_final: 0.6620 (m-80) REVERT: D 79 ARG cc_start: 0.7321 (mtp180) cc_final: 0.6966 (mtp-110) REVERT: D 81 LYS cc_start: 0.7935 (mmpt) cc_final: 0.7083 (mmtm) REVERT: D 678 MET cc_start: 0.8026 (mmt) cc_final: 0.7631 (mpm) REVERT: D 682 GLU cc_start: 0.8094 (mt-10) cc_final: 0.7674 (mt-10) REVERT: D 684 GLN cc_start: 0.8168 (OUTLIER) cc_final: 0.7838 (tt0) outliers start: 38 outliers final: 17 residues processed: 150 average time/residue: 0.3962 time to fit residues: 66.2269 Evaluate side-chains 134 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 114 time to evaluate : 0.236 ------------------------------------------------------------------------------- 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 67 THR 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=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: 0.5980 chunk 13 optimal weight: 0.9980 chunk 43 optimal weight: 0.8980 chunk 97 optimal weight: 0.8980 chunk 35 optimal weight: 0.9990 chunk 103 optimal weight: 3.9990 chunk 62 optimal weight: 0.8980 chunk 0 optimal weight: 6.9990 chunk 53 optimal weight: 0.0870 overall best weight: 0.6758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 464 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4083 r_free = 0.4083 target = 0.171497 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.137737 restraints weight = 12704.294| |-----------------------------------------------------------------------------| r_work (start): 0.3694 rms_B_bonded: 2.02 r_work: 0.3563 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.3427 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.3427 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7451 moved from start: 0.1857 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= 0.127 Angle : 0.620 8.500 14414 Z= 0.310 Chirality : 0.045 0.351 1760 Planarity : 0.005 0.078 1640 Dihedral : 13.680 163.622 2742 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 9.98 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.70 % Favored : 94.13 % Rotamer: Outliers : 2.87 % Allowed : 15.01 % 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: 1.18 (0.25), residues: 1210 helix: 1.79 (0.18), residues: 818 sheet: 0.52 (0.52), residues: 50 loop : -1.73 (0.33), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 409 TYR 0.013 0.001 TYR C 371 PHE 0.017 0.001 PHE D 141 TRP 0.010 0.001 TRP D 482 HIS 0.003 0.001 HIS D 656 Details of bonding type rmsd covalent geometry : bond 0.00266 (10634) covalent geometry : angle 0.62038 (14414) hydrogen bonds : bond 0.04457 ( 638) hydrogen bonds : angle 4.21702 ( 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 158 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 128 time to evaluate : 0.305 Fit side-chains REVERT: C 27 TYR cc_start: 0.7720 (m-80) cc_final: 0.6689 (m-80) REVERT: C 79 ARG cc_start: 0.7394 (mtp180) cc_final: 0.7073 (mtp-110) REVERT: C 81 LYS cc_start: 0.7879 (mmpt) cc_final: 0.7151 (mmtm) REVERT: C 339 GLU cc_start: 0.7596 (OUTLIER) cc_final: 0.6892 (mp0) REVERT: C 682 GLU cc_start: 0.8100 (mt-10) cc_final: 0.7687 (mt-10) REVERT: C 684 GLN cc_start: 0.8135 (OUTLIER) cc_final: 0.7819 (tt0) REVERT: D 27 TYR cc_start: 0.7732 (m-80) cc_final: 0.6607 (m-80) REVERT: D 79 ARG cc_start: 0.7403 (mtp180) cc_final: 0.7082 (mtp-110) REVERT: D 81 LYS cc_start: 0.7879 (mmpt) cc_final: 0.7143 (mmtm) REVERT: D 682 GLU cc_start: 0.8091 (mt-10) cc_final: 0.7672 (mt-10) REVERT: D 684 GLN cc_start: 0.8140 (OUTLIER) cc_final: 0.7823 (tt0) outliers start: 30 outliers final: 15 residues processed: 150 average time/residue: 0.4028 time to fit residues: 67.0242 Evaluate side-chains 138 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 120 time to evaluate : 0.347 ------------------------------------------------------------------------------- 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 7 optimal weight: 1.9990 chunk 41 optimal weight: 3.9990 chunk 12 optimal weight: 5.9990 chunk 58 optimal weight: 4.9990 chunk 52 optimal weight: 0.9990 chunk 117 optimal weight: 1.9990 chunk 120 optimal weight: 0.0970 chunk 37 optimal weight: 2.9990 chunk 75 optimal weight: 5.9990 chunk 50 optimal weight: 1.9990 chunk 15 optimal weight: 2.9990 overall best weight: 1.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 464 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4052 r_free = 0.4052 target = 0.168555 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.134269 restraints weight = 12675.751| |-----------------------------------------------------------------------------| r_work (start): 0.3652 rms_B_bonded: 2.02 r_work: 0.3520 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.3384 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3384 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7496 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 : 0.004 0.032 10634 Z= 0.164 Angle : 0.660 8.424 14414 Z= 0.330 Chirality : 0.046 0.357 1760 Planarity : 0.005 0.075 1640 Dihedral : 13.459 162.795 2742 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 9.38 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.61 % Favored : 93.22 % Rotamer: Outliers : 3.06 % Allowed : 15.30 % Favored : 81.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.08 (0.25), residues: 1210 helix: 1.70 (0.18), residues: 816 sheet: 0.51 (0.54), residues: 50 loop : -1.74 (0.33), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 549 TYR 0.014 0.002 TYR C 371 PHE 0.017 0.002 PHE D 401 TRP 0.010 0.001 TRP C 74 HIS 0.003 0.001 HIS D 656 Details of bonding type rmsd covalent geometry : bond 0.00366 (10634) covalent geometry : angle 0.65982 (14414) hydrogen bonds : bond 0.04880 ( 638) hydrogen bonds : angle 4.30962 ( 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 147 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 115 time to evaluate : 0.407 Fit side-chains REVERT: C 27 TYR cc_start: 0.7723 (m-80) cc_final: 0.6549 (m-80) REVERT: C 81 LYS cc_start: 0.7901 (mmpt) cc_final: 0.7175 (mmtm) REVERT: C 339 GLU cc_start: 0.7586 (OUTLIER) cc_final: 0.6880 (mp0) REVERT: C 678 MET cc_start: 0.8041 (mmt) cc_final: 0.7674 (mpm) REVERT: C 682 GLU cc_start: 0.8094 (mt-10) cc_final: 0.7717 (mt-10) REVERT: C 684 GLN cc_start: 0.8135 (OUTLIER) cc_final: 0.7805 (tt0) REVERT: D 27 TYR cc_start: 0.7738 (m-80) cc_final: 0.6520 (m-80) REVERT: D 81 LYS cc_start: 0.7907 (mmpt) cc_final: 0.7180 (mmtm) REVERT: D 678 MET cc_start: 0.8025 (mmt) cc_final: 0.7662 (mpm) REVERT: D 682 GLU cc_start: 0.8095 (mt-10) cc_final: 0.7715 (mt-10) REVERT: D 684 GLN cc_start: 0.8164 (OUTLIER) cc_final: 0.7837 (tt0) outliers start: 32 outliers final: 15 residues processed: 135 average time/residue: 0.4587 time to fit residues: 68.3237 Evaluate side-chains 133 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 115 time to evaluate : 0.376 ------------------------------------------------------------------------------- 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 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 67 THR 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 66 optimal weight: 0.9980 chunk 106 optimal weight: 0.9980 chunk 91 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 33 optimal weight: 0.9990 chunk 6 optimal weight: 4.9990 chunk 29 optimal weight: 2.9990 chunk 97 optimal weight: 5.9990 chunk 77 optimal weight: 0.7980 chunk 18 optimal weight: 0.0980 chunk 116 optimal weight: 2.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 34 GLN D 34 GLN D 464 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4079 r_free = 0.4079 target = 0.171159 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.137352 restraints weight = 12627.565| |-----------------------------------------------------------------------------| r_work (start): 0.3689 rms_B_bonded: 2.03 r_work: 0.3555 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.3419 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3419 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7464 moved from start: 0.1906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 10634 Z= 0.132 Angle : 0.625 8.367 14414 Z= 0.315 Chirality : 0.044 0.290 1760 Planarity : 0.005 0.077 1640 Dihedral : 12.936 160.060 2742 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 10.02 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.53 % Favored : 93.31 % Rotamer: Outliers : 2.29 % Allowed : 15.77 % 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: 1.15 (0.25), residues: 1210 helix: 1.78 (0.18), residues: 816 sheet: 0.50 (0.54), residues: 50 loop : -1.75 (0.33), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 409 TYR 0.013 0.001 TYR C 556 PHE 0.018 0.001 PHE D 141 TRP 0.010 0.001 TRP D 482 HIS 0.003 0.001 HIS D 656 Details of bonding type rmsd covalent geometry : bond 0.00280 (10634) covalent geometry : angle 0.62506 (14414) hydrogen bonds : bond 0.04520 ( 638) hydrogen bonds : angle 4.22193 ( 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 148 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 124 time to evaluate : 0.358 Fit side-chains REVERT: C 27 TYR cc_start: 0.7741 (m-80) cc_final: 0.6568 (m-80) REVERT: C 79 ARG cc_start: 0.7362 (mtp180) cc_final: 0.7024 (mtp-110) REVERT: C 81 LYS cc_start: 0.7873 (mmpt) cc_final: 0.7148 (mmtm) REVERT: C 339 GLU cc_start: 0.7602 (OUTLIER) cc_final: 0.6896 (mp0) REVERT: C 373 ILE cc_start: 0.8197 (pp) cc_final: 0.7983 (pt) REVERT: C 678 MET cc_start: 0.8064 (mmt) cc_final: 0.7706 (mpm) REVERT: C 682 GLU cc_start: 0.8116 (mt-10) cc_final: 0.7728 (mt-10) REVERT: C 684 GLN cc_start: 0.8128 (OUTLIER) cc_final: 0.7812 (tt0) REVERT: D 27 TYR cc_start: 0.7731 (m-80) cc_final: 0.6508 (m-80) REVERT: D 79 ARG cc_start: 0.7365 (mtp180) cc_final: 0.7022 (mtp-110) REVERT: D 81 LYS cc_start: 0.7880 (mmpt) cc_final: 0.7148 (mmtm) REVERT: D 678 MET cc_start: 0.8064 (mmt) cc_final: 0.7706 (mpm) REVERT: D 682 GLU cc_start: 0.8109 (mt-10) cc_final: 0.7716 (mt-10) REVERT: D 684 GLN cc_start: 0.8143 (OUTLIER) cc_final: 0.7827 (tt0) outliers start: 24 outliers final: 14 residues processed: 138 average time/residue: 0.4302 time to fit residues: 65.7164 Evaluate side-chains 137 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 120 time to evaluate : 0.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 67 THR 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 86 optimal weight: 0.9980 chunk 38 optimal weight: 7.9990 chunk 74 optimal weight: 5.9990 chunk 111 optimal weight: 2.9990 chunk 29 optimal weight: 0.0010 chunk 107 optimal weight: 0.9990 chunk 41 optimal weight: 0.0970 chunk 5 optimal weight: 0.9990 chunk 6 optimal weight: 0.9980 chunk 27 optimal weight: 5.9990 chunk 115 optimal weight: 3.9990 overall best weight: 0.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 34 GLN D 464 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4088 r_free = 0.4088 target = 0.172062 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.138500 restraints weight = 12772.964| |-----------------------------------------------------------------------------| r_work (start): 0.3703 rms_B_bonded: 2.02 r_work: 0.3572 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.3436 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.3436 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7441 moved from start: 0.1951 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= 0.127 Angle : 0.653 16.441 14414 Z= 0.319 Chirality : 0.043 0.239 1760 Planarity : 0.005 0.075 1640 Dihedral : 12.639 157.634 2742 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 10.58 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.61 % Favored : 93.22 % Rotamer: Outliers : 2.10 % Allowed : 16.35 % Favored : 81.55 % 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: 1.19 (0.25), residues: 1210 helix: 1.81 (0.18), residues: 816 sheet: 0.55 (0.55), residues: 50 loop : -1.73 (0.33), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 409 TYR 0.013 0.001 TYR D 556 PHE 0.018 0.001 PHE D 141 TRP 0.010 0.001 TRP D 482 HIS 0.003 0.001 HIS D 656 Details of bonding type rmsd covalent geometry : bond 0.00263 (10634) covalent geometry : angle 0.65322 (14414) hydrogen bonds : bond 0.04413 ( 638) hydrogen bonds : angle 4.19353 ( 1860) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3814.43 seconds wall clock time: 65 minutes 42.77 seconds (3942.77 seconds total)