Starting phenix.real_space_refine on Fri Feb 14 14:16:16 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8sgw_40470/02_2025/8sgw_40470.cif Found real_map, /net/cci-nas-00/data/ceres_data/8sgw_40470/02_2025/8sgw_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_40470/02_2025/8sgw_40470.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8sgw_40470/02_2025/8sgw_40470.map" model { file = "/net/cci-nas-00/data/ceres_data/8sgw_40470/02_2025/8sgw_40470.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8sgw_40470/02_2025/8sgw_40470.cif" } resolution = 2.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.004 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/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-2': 6, 'LBN:plan-3': 7, 'LBN:plan-1': 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-2': 6, 'LBN:plan-3': 7, 'LBN:plan-1': 6} Unresolved non-hydrogen planarities: 68 Time building chain proxies: 6.78, per 1000 atoms: 0.65 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: 2.99 Conformation dependent library (CDL) restraints added in 1.4 seconds 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2288 Finding SS restraints... Secondary structure from input PDB file: 62 helices and 5 sheets defined 71.9% alpha, 4.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.09 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: 3.49 Time building geometry restraints manager: 3.44 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: 0.05 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: 0.430 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: 0.020 Extract box with map and model: 0.350 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 27.320 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.200 ------------------------------------------------------------------------------- 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= 0.255 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 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 TRP 0.009 0.001 TRP D 74 HIS 0.003 0.001 HIS C 656 PHE 0.017 0.001 PHE D 141 TYR 0.020 0.002 TYR D 27 ARG 0.003 0.000 ARG D 409 *********************** 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 : 1.112 Fit side-chains outliers start: 0 outliers final: 1 residues processed: 167 average time/residue: 1.0164 time to fit residues: 185.8415 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 : 1.125 ------------------------------------------------------------------------------- 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 103 optimal weight: 0.7980 chunk 92 optimal weight: 2.9990 chunk 51 optimal weight: 2.9990 chunk 31 optimal weight: 2.9990 chunk 62 optimal weight: 0.8980 chunk 49 optimal weight: 2.9990 chunk 95 optimal weight: 6.9990 chunk 37 optimal weight: 5.9990 chunk 58 optimal weight: 0.7980 chunk 71 optimal weight: 1.9990 chunk 110 optimal weight: 1.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 289 ASN 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4071 r_free = 0.4071 target = 0.169995 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.136341 restraints weight = 12588.916| |-----------------------------------------------------------------------------| r_work (start): 0.3688 rms_B_bonded: 1.94 r_work: 0.3556 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3423 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.3423 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7546 moved from start: 0.1151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 10634 Z= 0.229 Angle : 0.722 11.243 14414 Z= 0.345 Chirality : 0.047 0.253 1760 Planarity : 0.005 0.070 1640 Dihedral : 19.669 161.685 2744 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 9.65 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.29 % Favored : 94.55 % Rotamer: Outliers : 1.15 % Allowed : 11.57 % Favored : 87.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.85 (0.24), residues: 1210 helix: 1.50 (0.18), residues: 816 sheet: 0.42 (0.55), residues: 50 loop : -1.73 (0.33), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 74 HIS 0.003 0.001 HIS D 656 PHE 0.019 0.002 PHE C 141 TYR 0.013 0.002 TYR C 371 ARG 0.004 0.000 ARG D 24 *********************** 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 148 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 136 time to evaluate : 1.262 Fit side-chains REVERT: C 27 TYR cc_start: 0.7659 (m-80) cc_final: 0.7059 (m-80) REVERT: D 27 TYR cc_start: 0.7666 (m-80) cc_final: 0.7058 (m-80) outliers start: 12 outliers final: 8 residues processed: 144 average time/residue: 0.8790 time to fit residues: 140.7402 Evaluate side-chains 125 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 117 time to evaluate : 1.150 ------------------------------------------------------------------------------- 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 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 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 110 optimal weight: 0.7980 chunk 106 optimal weight: 4.9990 chunk 1 optimal weight: 3.9990 chunk 55 optimal weight: 0.9990 chunk 28 optimal weight: 7.9990 chunk 99 optimal weight: 7.9990 chunk 20 optimal weight: 0.9990 chunk 64 optimal weight: 0.9990 chunk 91 optimal weight: 2.9990 chunk 73 optimal weight: 5.9990 chunk 29 optimal weight: 0.8980 overall best weight: 0.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4060 r_free = 0.4060 target = 0.170185 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.135408 restraints weight = 12777.823| |-----------------------------------------------------------------------------| r_work (start): 0.3664 rms_B_bonded: 2.09 r_work: 0.3532 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.3397 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.3397 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7519 moved from start: 0.1317 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= 0.190 Angle : 0.632 8.068 14414 Z= 0.313 Chirality : 0.045 0.286 1760 Planarity : 0.005 0.076 1640 Dihedral : 17.665 164.845 2742 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 9.79 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.62 % Favored : 94.21 % Rotamer: Outliers : 2.20 % Allowed : 13.00 % Favored : 84.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.95 (0.24), residues: 1210 helix: 1.56 (0.18), residues: 820 sheet: 0.51 (0.53), residues: 50 loop : -1.70 (0.33), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 482 HIS 0.003 0.001 HIS C 656 PHE 0.016 0.001 PHE C 401 TYR 0.013 0.001 TYR C 371 ARG 0.002 0.000 ARG C 24 *********************** 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 153 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 130 time to evaluate : 1.078 Fit side-chains REVERT: C 27 TYR cc_start: 0.7684 (m-80) cc_final: 0.6804 (m-80) REVERT: C 464 GLN cc_start: 0.8319 (OUTLIER) cc_final: 0.8090 (mt0) REVERT: C 682 GLU cc_start: 0.8102 (mt-10) cc_final: 0.7703 (mt-10) REVERT: C 684 GLN cc_start: 0.8156 (OUTLIER) cc_final: 0.7823 (tt0) REVERT: D 27 TYR cc_start: 0.7678 (m-80) cc_final: 0.6803 (m-80) REVERT: D 464 GLN cc_start: 0.8305 (OUTLIER) cc_final: 0.8072 (mt0) REVERT: D 682 GLU cc_start: 0.8114 (mt-10) cc_final: 0.7716 (mt-10) REVERT: D 684 GLN cc_start: 0.8179 (OUTLIER) cc_final: 0.7846 (tt0) outliers start: 23 outliers final: 10 residues processed: 142 average time/residue: 0.8749 time to fit residues: 138.3876 Evaluate side-chains 134 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 120 time to evaluate : 1.101 ------------------------------------------------------------------------------- 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 464 GLN 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 464 GLN 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 103 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 chunk 99 optimal weight: 9.9990 chunk 46 optimal weight: 3.9990 chunk 118 optimal weight: 4.9990 chunk 41 optimal weight: 0.5980 chunk 7 optimal weight: 1.9990 chunk 1 optimal weight: 2.9990 chunk 69 optimal weight: 0.8980 chunk 45 optimal weight: 0.6980 chunk 54 optimal weight: 5.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 33 GLN C 324 ASN D 33 GLN D 324 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4053 r_free = 0.4053 target = 0.168946 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.134478 restraints weight = 12671.699| |-----------------------------------------------------------------------------| r_work (start): 0.3652 rms_B_bonded: 2.02 r_work: 0.3519 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.3383 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.3383 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7491 moved from start: 0.1557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 10634 Z= 0.210 Angle : 0.641 7.530 14414 Z= 0.319 Chirality : 0.046 0.327 1760 Planarity : 0.005 0.077 1640 Dihedral : 16.460 166.328 2742 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.95 % Favored : 93.88 % Rotamer: Outliers : 2.77 % Allowed : 13.00 % Favored : 84.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.04 (0.24), residues: 1210 helix: 1.63 (0.18), residues: 816 sheet: 0.46 (0.51), residues: 50 loop : -1.62 (0.34), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 482 HIS 0.003 0.001 HIS C 656 PHE 0.017 0.002 PHE D 401 TYR 0.018 0.002 TYR D 315 ARG 0.002 0.000 ARG C 470 *********************** 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 160 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 131 time to evaluate : 1.040 Fit side-chains REVERT: C 27 TYR cc_start: 0.7717 (m-80) cc_final: 0.6762 (m-80) REVERT: C 81 LYS cc_start: 0.7872 (mmpt) cc_final: 0.7026 (mmtm) REVERT: C 678 MET cc_start: 0.8033 (mmt) cc_final: 0.7831 (mmt) REVERT: C 684 GLN cc_start: 0.8139 (OUTLIER) cc_final: 0.7800 (tt0) REVERT: D 27 TYR cc_start: 0.7724 (m-80) cc_final: 0.6763 (m-80) REVERT: D 81 LYS cc_start: 0.7875 (mmpt) cc_final: 0.7025 (mmtm) REVERT: D 684 GLN cc_start: 0.8166 (OUTLIER) cc_final: 0.7830 (tt0) outliers start: 29 outliers final: 17 residues processed: 154 average time/residue: 0.8454 time to fit residues: 144.9439 Evaluate side-chains 139 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 120 time to evaluate : 1.033 ------------------------------------------------------------------------------- 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 52 optimal weight: 0.3980 chunk 65 optimal weight: 6.9990 chunk 108 optimal weight: 0.0370 chunk 120 optimal weight: 0.3980 chunk 1 optimal weight: 0.5980 chunk 95 optimal weight: 6.9990 chunk 12 optimal weight: 5.9990 chunk 29 optimal weight: 2.9990 chunk 96 optimal weight: 2.9990 chunk 118 optimal weight: 5.9990 chunk 7 optimal weight: 1.9990 overall best weight: 0.6860 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 464 GLN D 324 ASN D 464 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4082 r_free = 0.4082 target = 0.171695 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.138085 restraints weight = 12665.272| |-----------------------------------------------------------------------------| r_work (start): 0.3697 rms_B_bonded: 2.02 r_work: 0.3566 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.3430 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.3430 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7448 moved from start: 0.1623 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= 0.167 Angle : 0.611 8.525 14414 Z= 0.303 Chirality : 0.044 0.307 1760 Planarity : 0.005 0.078 1640 Dihedral : 15.493 166.050 2742 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 9.84 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.03 % Favored : 93.80 % Rotamer: Outliers : 2.96 % Allowed : 13.19 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.18 (0.25), residues: 1210 helix: 1.77 (0.18), residues: 818 sheet: 0.44 (0.50), residues: 50 loop : -1.66 (0.33), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 482 HIS 0.004 0.001 HIS C 656 PHE 0.016 0.001 PHE C 141 TYR 0.012 0.001 TYR C 371 ARG 0.002 0.000 ARG C 409 *********************** 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 174 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 143 time to evaluate : 1.061 Fit side-chains REVERT: C 27 TYR cc_start: 0.7703 (m-80) cc_final: 0.6690 (m-80) REVERT: C 79 ARG cc_start: 0.7394 (mtp180) cc_final: 0.7022 (mtp-110) REVERT: C 81 LYS cc_start: 0.7828 (mmpt) cc_final: 0.6997 (mmtm) REVERT: C 678 MET cc_start: 0.7908 (mmt) cc_final: 0.7587 (mpm) REVERT: C 682 GLU cc_start: 0.8093 (mt-10) cc_final: 0.7657 (mt-10) REVERT: C 684 GLN cc_start: 0.8115 (OUTLIER) cc_final: 0.7787 (tt0) REVERT: D 27 TYR cc_start: 0.7702 (m-80) cc_final: 0.6686 (m-80) REVERT: D 79 ARG cc_start: 0.7410 (mtp180) cc_final: 0.7041 (mtp-110) REVERT: D 81 LYS cc_start: 0.7834 (mmpt) cc_final: 0.6990 (mmtm) REVERT: D 678 MET cc_start: 0.8052 (mmt) cc_final: 0.7758 (mmt) REVERT: D 682 GLU cc_start: 0.8082 (mt-10) cc_final: 0.7642 (mt-10) REVERT: D 684 GLN cc_start: 0.8115 (OUTLIER) cc_final: 0.7785 (tt0) outliers start: 31 outliers final: 16 residues processed: 165 average time/residue: 0.7956 time to fit residues: 147.3671 Evaluate side-chains 139 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 121 time to evaluate : 1.352 ------------------------------------------------------------------------------- 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 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 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 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 30 optimal weight: 1.9990 chunk 48 optimal weight: 3.9990 chunk 64 optimal weight: 0.8980 chunk 5 optimal weight: 10.0000 chunk 89 optimal weight: 4.9990 chunk 32 optimal weight: 5.9990 chunk 10 optimal weight: 1.9990 chunk 79 optimal weight: 0.9990 chunk 99 optimal weight: 4.9990 chunk 61 optimal weight: 8.9990 chunk 112 optimal weight: 0.7980 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 33 GLN C 464 GLN D 33 GLN D 464 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4053 r_free = 0.4053 target = 0.168734 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.134456 restraints weight = 12677.823| |-----------------------------------------------------------------------------| r_work (start): 0.3652 rms_B_bonded: 2.03 r_work: 0.3520 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.3384 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3384 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7497 moved from start: 0.1748 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= 0.221 Angle : 0.645 9.224 14414 Z= 0.321 Chirality : 0.046 0.308 1760 Planarity : 0.005 0.076 1640 Dihedral : 15.027 166.372 2742 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 9.05 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.28 % Favored : 93.55 % Rotamer: Outliers : 3.82 % Allowed : 13.38 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.09 (0.24), residues: 1210 helix: 1.69 (0.18), residues: 816 sheet: 0.45 (0.51), residues: 50 loop : -1.66 (0.33), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 74 HIS 0.003 0.001 HIS D 656 PHE 0.017 0.002 PHE D 141 TYR 0.015 0.002 TYR D 315 ARG 0.003 0.000 ARG C 185 *********************** 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: 40 poor density : 122 time to evaluate : 1.138 Fit side-chains REVERT: C 27 TYR cc_start: 0.7744 (m-80) cc_final: 0.6766 (m-80) REVERT: C 81 LYS cc_start: 0.7931 (mmpt) cc_final: 0.7084 (mmtm) REVERT: C 678 MET cc_start: 0.7972 (mmt) cc_final: 0.7647 (mpm) REVERT: C 682 GLU cc_start: 0.8129 (mt-10) cc_final: 0.7729 (mt-10) REVERT: C 684 GLN cc_start: 0.8139 (OUTLIER) cc_final: 0.7802 (tt0) REVERT: D 27 TYR cc_start: 0.7743 (m-80) cc_final: 0.6765 (m-80) REVERT: D 81 LYS cc_start: 0.7968 (mmpt) cc_final: 0.7104 (mmtm) REVERT: D 678 MET cc_start: 0.8062 (mmt) cc_final: 0.7685 (mpm) REVERT: D 682 GLU cc_start: 0.8124 (mt-10) cc_final: 0.7720 (mt-10) REVERT: D 684 GLN cc_start: 0.8157 (OUTLIER) cc_final: 0.7822 (tt0) outliers start: 40 outliers final: 18 residues processed: 154 average time/residue: 0.8306 time to fit residues: 142.8805 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 : 1.121 ------------------------------------------------------------------------------- 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 370 VAL Chi-restraints excluded: chain C residue 385 PHE Chi-restraints excluded: chain C residue 527 THR 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 527 THR 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 7 optimal weight: 1.9990 chunk 41 optimal weight: 0.9980 chunk 96 optimal weight: 4.9990 chunk 82 optimal weight: 8.9990 chunk 23 optimal weight: 10.0000 chunk 38 optimal weight: 6.9990 chunk 111 optimal weight: 4.9990 chunk 39 optimal weight: 3.9990 chunk 9 optimal weight: 7.9990 chunk 84 optimal weight: 9.9990 chunk 91 optimal weight: 0.6980 overall best weight: 2.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 34 GLN C 464 GLN ** C 705 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 34 GLN D 464 GLN ** 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 = 0.4005 r_free = 0.4005 target = 0.164389 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.129437 restraints weight = 12823.726| |-----------------------------------------------------------------------------| r_work (start): 0.3588 rms_B_bonded: 2.02 r_work: 0.3453 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3318 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3318 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7550 moved from start: 0.1946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 10634 Z= 0.343 Angle : 0.725 9.477 14414 Z= 0.361 Chirality : 0.049 0.312 1760 Planarity : 0.005 0.076 1640 Dihedral : 15.323 167.890 2742 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 9.38 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.95 % Favored : 93.88 % Rotamer: Outliers : 3.73 % Allowed : 13.48 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.71 (0.24), residues: 1210 helix: 1.40 (0.18), residues: 816 sheet: 0.14 (0.51), residues: 50 loop : -1.76 (0.32), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 74 HIS 0.004 0.001 HIS D 698 PHE 0.019 0.002 PHE C 401 TYR 0.017 0.002 TYR C 371 ARG 0.004 0.001 ARG C 549 *********************** 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 152 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 113 time to evaluate : 1.154 Fit side-chains REVERT: C 81 LYS cc_start: 0.7962 (mmpt) cc_final: 0.7070 (mmtm) REVERT: C 556 TYR cc_start: 0.7371 (OUTLIER) cc_final: 0.6994 (p90) REVERT: C 678 MET cc_start: 0.7979 (mmt) cc_final: 0.7670 (mpm) REVERT: C 684 GLN cc_start: 0.8150 (OUTLIER) cc_final: 0.7828 (tt0) REVERT: D 81 LYS cc_start: 0.7968 (mmpt) cc_final: 0.7077 (mmtm) REVERT: D 556 TYR cc_start: 0.7371 (OUTLIER) cc_final: 0.6989 (p90) REVERT: D 678 MET cc_start: 0.8026 (mmt) cc_final: 0.7665 (mpm) REVERT: D 684 GLN cc_start: 0.8138 (OUTLIER) cc_final: 0.7823 (tt0) outliers start: 39 outliers final: 18 residues processed: 148 average time/residue: 0.8829 time to fit residues: 145.8588 Evaluate side-chains 130 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 108 time to evaluate : 1.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 80 ILE Chi-restraints excluded: chain C residue 126 THR 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 527 THR 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 126 THR 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 527 THR 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 16 optimal weight: 1.9990 chunk 121 optimal weight: 2.9990 chunk 53 optimal weight: 0.9980 chunk 29 optimal weight: 0.0030 chunk 7 optimal weight: 0.7980 chunk 68 optimal weight: 0.7980 chunk 39 optimal weight: 0.4980 chunk 108 optimal weight: 1.9990 chunk 45 optimal weight: 0.9990 chunk 52 optimal weight: 0.9990 chunk 50 optimal weight: 0.8980 overall best weight: 0.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 34 GLN C 464 GLN C 728 HIS D 34 GLN D 464 GLN D 728 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4073 r_free = 0.4073 target = 0.170665 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.136741 restraints weight = 12642.654| |-----------------------------------------------------------------------------| r_work (start): 0.3678 rms_B_bonded: 2.03 r_work: 0.3548 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.3413 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.3413 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7469 moved from start: 0.1856 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= 0.176 Angle : 0.635 8.182 14414 Z= 0.318 Chirality : 0.045 0.336 1760 Planarity : 0.005 0.082 1640 Dihedral : 14.160 165.723 2742 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 10.02 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.54 % Favored : 94.30 % Rotamer: Outliers : 2.96 % Allowed : 14.91 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.98 (0.24), residues: 1210 helix: 1.63 (0.18), residues: 820 sheet: 0.24 (0.50), residues: 50 loop : -1.75 (0.33), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 482 HIS 0.004 0.001 HIS C 656 PHE 0.019 0.001 PHE D 141 TYR 0.012 0.001 TYR C 371 ARG 0.002 0.000 ARG D 409 *********************** 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 154 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 123 time to evaluate : 1.002 Fit side-chains REVERT: C 27 TYR cc_start: 0.7754 (m-80) cc_final: 0.6489 (m-80) REVERT: C 79 ARG cc_start: 0.7333 (mtp180) cc_final: 0.6972 (mtp-110) REVERT: C 81 LYS cc_start: 0.7846 (mmpt) cc_final: 0.7114 (mmtm) REVERT: C 678 MET cc_start: 0.7901 (mmt) cc_final: 0.7421 (mmt) REVERT: C 682 GLU cc_start: 0.7821 (mt-10) cc_final: 0.7543 (mp0) REVERT: C 684 GLN cc_start: 0.8063 (OUTLIER) cc_final: 0.7752 (tt0) REVERT: D 27 TYR cc_start: 0.7755 (m-80) cc_final: 0.6492 (m-80) REVERT: D 79 ARG cc_start: 0.7347 (mtp180) cc_final: 0.6988 (mtp-110) REVERT: D 81 LYS cc_start: 0.7850 (mmpt) cc_final: 0.7115 (mmtm) REVERT: D 678 MET cc_start: 0.7894 (mmt) cc_final: 0.7454 (mmt) REVERT: D 682 GLU cc_start: 0.7825 (mt-10) cc_final: 0.7539 (mp0) REVERT: D 684 GLN cc_start: 0.8053 (OUTLIER) cc_final: 0.7730 (tt0) outliers start: 31 outliers final: 14 residues processed: 146 average time/residue: 0.8538 time to fit residues: 138.8343 Evaluate side-chains 132 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 116 time to evaluate : 1.066 ------------------------------------------------------------------------------- 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 385 PHE Chi-restraints excluded: chain C residue 527 THR 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 385 PHE Chi-restraints excluded: chain D residue 527 THR 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 24 optimal weight: 0.1980 chunk 62 optimal weight: 2.9990 chunk 76 optimal weight: 3.9990 chunk 112 optimal weight: 1.9990 chunk 83 optimal weight: 8.9990 chunk 22 optimal weight: 8.9990 chunk 29 optimal weight: 0.0570 chunk 117 optimal weight: 5.9990 chunk 87 optimal weight: 10.0000 chunk 53 optimal weight: 9.9990 chunk 89 optimal weight: 3.9990 overall best weight: 1.8504 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 34 GLN C 464 GLN D 34 GLN D 464 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4032 r_free = 0.4032 target = 0.166579 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.131742 restraints weight = 12754.078| |-----------------------------------------------------------------------------| r_work (start): 0.3620 rms_B_bonded: 2.03 r_work: 0.3487 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.3352 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3352 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7523 moved from start: 0.1978 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= 0.273 Angle : 0.689 9.094 14414 Z= 0.345 Chirality : 0.048 0.365 1760 Planarity : 0.005 0.074 1640 Dihedral : 14.143 165.077 2742 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 9.93 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.03 % Favored : 93.80 % Rotamer: Outliers : 2.29 % Allowed : 16.06 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.83 (0.24), residues: 1210 helix: 1.51 (0.18), residues: 816 sheet: 0.20 (0.50), residues: 50 loop : -1.78 (0.33), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 74 HIS 0.003 0.001 HIS D 656 PHE 0.018 0.002 PHE D 401 TYR 0.015 0.002 TYR C 371 ARG 0.003 0.000 ARG C 549 *********************** 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 132 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 108 time to evaluate : 1.020 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 81 LYS cc_start: 0.7988 (mmpt) cc_final: 0.7103 (mmtm) REVERT: C 556 TYR cc_start: 0.7184 (OUTLIER) cc_final: 0.6831 (p90) REVERT: C 684 GLN cc_start: 0.8075 (OUTLIER) cc_final: 0.7749 (tt0) REVERT: D 81 LYS cc_start: 0.7985 (mmpt) cc_final: 0.7101 (mmtm) REVERT: D 556 TYR cc_start: 0.7191 (OUTLIER) cc_final: 0.6829 (p90) REVERT: D 678 MET cc_start: 0.7933 (mmt) cc_final: 0.7709 (mpm) REVERT: D 684 GLN cc_start: 0.8056 (OUTLIER) cc_final: 0.7735 (tt0) outliers start: 24 outliers final: 14 residues processed: 128 average time/residue: 0.9514 time to fit residues: 134.5486 Evaluate side-chains 126 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 108 time to evaluate : 1.171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 154 SER Chi-restraints excluded: chain C residue 208 ILE 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 154 SER Chi-restraints excluded: chain D residue 208 ILE 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 94 optimal weight: 0.8980 chunk 96 optimal weight: 1.9990 chunk 4 optimal weight: 2.9990 chunk 8 optimal weight: 0.2980 chunk 99 optimal weight: 6.9990 chunk 97 optimal weight: 5.9990 chunk 37 optimal weight: 0.9990 chunk 101 optimal weight: 5.9990 chunk 28 optimal weight: 0.0770 chunk 46 optimal weight: 1.9990 chunk 10 optimal weight: 0.7980 overall best weight: 0.6140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 34 GLN C 464 GLN D 34 GLN D 464 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4079 r_free = 0.4079 target = 0.171283 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.137443 restraints weight = 12641.203| |-----------------------------------------------------------------------------| r_work (start): 0.3690 rms_B_bonded: 2.02 r_work: 0.3560 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.3424 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.3424 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7455 moved from start: 0.1930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10634 Z= 0.171 Angle : 0.631 8.380 14414 Z= 0.318 Chirality : 0.044 0.344 1760 Planarity : 0.005 0.078 1640 Dihedral : 13.417 162.250 2742 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 9.98 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.95 % Favored : 93.88 % Rotamer: Outliers : 2.01 % Allowed : 16.83 % Favored : 81.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.01 (0.24), residues: 1210 helix: 1.66 (0.18), residues: 816 sheet: 0.30 (0.50), residues: 50 loop : -1.75 (0.33), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 482 HIS 0.004 0.001 HIS C 656 PHE 0.019 0.001 PHE D 141 TYR 0.012 0.001 TYR D 371 ARG 0.002 0.000 ARG C 409 ********************** 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 146 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 125 time to evaluate : 1.119 Fit side-chains revert: symmetry clash REVERT: C 27 TYR cc_start: 0.7795 (m-80) cc_final: 0.6493 (m-80) REVERT: C 79 ARG cc_start: 0.7361 (mtp180) cc_final: 0.7038 (mtp-110) REVERT: C 81 LYS cc_start: 0.7984 (mmpt) cc_final: 0.7115 (mmtm) REVERT: C 461 MET cc_start: 0.8526 (mtt) cc_final: 0.8167 (ttm) REVERT: C 682 GLU cc_start: 0.7719 (mt-10) cc_final: 0.7034 (mp0) REVERT: C 684 GLN cc_start: 0.8058 (OUTLIER) cc_final: 0.7747 (tt0) REVERT: D 27 TYR cc_start: 0.7785 (m-80) cc_final: 0.6487 (m-80) REVERT: D 79 ARG cc_start: 0.7362 (mtp180) cc_final: 0.7040 (mtp-110) REVERT: D 81 LYS cc_start: 0.7986 (mmpt) cc_final: 0.7113 (mmtm) REVERT: D 461 MET cc_start: 0.8519 (mtt) cc_final: 0.8152 (ttm) REVERT: D 678 MET cc_start: 0.7909 (mmt) cc_final: 0.7690 (mpm) REVERT: D 684 GLN cc_start: 0.8056 (OUTLIER) cc_final: 0.7732 (tt0) outliers start: 21 outliers final: 12 residues processed: 140 average time/residue: 0.8444 time to fit residues: 131.8415 Evaluate side-chains 132 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 118 time to evaluate : 1.056 ------------------------------------------------------------------------------- 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 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 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 68 optimal weight: 1.9990 chunk 54 optimal weight: 3.9990 chunk 97 optimal weight: 2.9990 chunk 5 optimal weight: 0.9990 chunk 111 optimal weight: 2.9990 chunk 42 optimal weight: 4.9990 chunk 101 optimal weight: 5.9990 chunk 46 optimal weight: 3.9990 chunk 63 optimal weight: 5.9990 chunk 14 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 overall best weight: 2.5990 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.164740 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.129419 restraints weight = 12673.674| |-----------------------------------------------------------------------------| r_work (start): 0.3590 rms_B_bonded: 2.03 r_work: 0.3454 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.3319 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3319 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7543 moved from start: 0.2112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 10634 Z= 0.343 Angle : 0.730 9.750 14414 Z= 0.365 Chirality : 0.050 0.387 1760 Planarity : 0.005 0.075 1640 Dihedral : 13.785 162.205 2742 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 9.24 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.12 % Favored : 93.72 % Rotamer: Outliers : 1.82 % Allowed : 16.54 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.67 (0.24), residues: 1210 helix: 1.37 (0.18), residues: 816 sheet: -0.04 (0.50), residues: 50 loop : -1.75 (0.33), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 74 HIS 0.004 0.001 HIS C 698 PHE 0.019 0.002 PHE C 394 TYR 0.015 0.002 TYR D 371 ARG 0.004 0.001 ARG D 549 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8112.41 seconds wall clock time: 144 minutes 17.25 seconds (8657.25 seconds total)