Starting phenix.real_space_refine on Thu May 1 05:46:52 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8sgw_40470/05_2025/8sgw_40470.cif Found real_map, /net/cci-nas-00/data/ceres_data/8sgw_40470/05_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_40470/05_2025/8sgw_40470.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8sgw_40470/05_2025/8sgw_40470.map" model { file = "/net/cci-nas-00/data/ceres_data/8sgw_40470/05_2025/8sgw_40470.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8sgw_40470/05_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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/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: 6.74, 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: 2.78 Conformation dependent library (CDL) restraints added in 1.2 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: 0.94 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: 3.40 Time building geometry restraints manager: 3.24 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: 1.270 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.370 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 26.370 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.040 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:12.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.190 ------------------------------------------------------------------------------- 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 (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 Details of bonding type rmsd hydrogen bonds : bond 0.12462 ( 638) hydrogen bonds : angle 5.41916 ( 1860) covalent geometry : bond 0.00418 (10634) covalent geometry : angle 0.68791 (14414) *********************** 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 : 0.975 Fit side-chains outliers start: 0 outliers final: 1 residues processed: 167 average time/residue: 0.9572 time to fit residues: 175.4537 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 : 1.004 ------------------------------------------------------------------------------- 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 = 41)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.136341 restraints weight = 12588.853| |-----------------------------------------------------------------------------| r_work (start): 0.3688 rms_B_bonded: 1.94 r_work: 0.3557 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3422 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3422 ------------------------------------------------------------------------------- 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= 0.165 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 Details of bonding type rmsd hydrogen bonds : bond 0.05184 ( 638) hydrogen bonds : angle 4.52826 ( 1860) covalent geometry : bond 0.00357 (10634) covalent geometry : angle 0.72230 (14414) *********************** 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 : 1.077 Fit side-chains REVERT: C 27 TYR cc_start: 0.7660 (m-80) cc_final: 0.7058 (m-80) REVERT: D 27 TYR cc_start: 0.7666 (m-80) cc_final: 0.7057 (m-80) outliers start: 12 outliers final: 8 residues processed: 144 average time/residue: 0.8795 time to fit residues: 140.8531 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 : 1.158 ------------------------------------------------------------------------------- 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: 4.9990 chunk 99 optimal weight: 9.9990 chunk 20 optimal weight: 0.9990 chunk 64 optimal weight: 0.9990 chunk 91 optimal weight: 2.9990 chunk 73 optimal weight: 4.9990 chunk 29 optimal weight: 0.3980 overall best weight: 0.8386 ------------------------------------------------------------------------------- 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 = 0.4066 r_free = 0.4066 target = 0.170641 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.136025 restraints weight = 12779.027| |-----------------------------------------------------------------------------| r_work (start): 0.3671 rms_B_bonded: 2.09 r_work: 0.3540 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.3404 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.3404 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7491 moved from start: 0.1302 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= 0.135 Angle : 0.627 8.159 14414 Z= 0.310 Chirality : 0.045 0.279 1760 Planarity : 0.005 0.076 1640 Dihedral : 17.681 164.798 2742 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 9.70 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.62 % Favored : 94.21 % Rotamer: Outliers : 2.20 % Allowed : 13.19 % Favored : 84.61 % 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: 0.96 (0.24), residues: 1210 helix: 1.59 (0.18), residues: 818 sheet: 0.51 (0.52), residues: 50 loop : -1.73 (0.33), residues: 342 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 D 141 TYR 0.013 0.001 TYR C 371 ARG 0.002 0.000 ARG C 185 Details of bonding type rmsd hydrogen bonds : bond 0.04751 ( 638) hydrogen bonds : angle 4.36217 ( 1860) covalent geometry : bond 0.00283 (10634) covalent geometry : angle 0.62687 (14414) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 132 time to evaluate : 1.100 Fit side-chains REVERT: C 27 TYR cc_start: 0.7688 (m-80) cc_final: 0.6821 (m-80) REVERT: C 464 GLN cc_start: 0.8298 (OUTLIER) cc_final: 0.8051 (mt0) REVERT: C 682 GLU cc_start: 0.8091 (mt-10) cc_final: 0.7692 (mt-10) REVERT: C 684 GLN cc_start: 0.8151 (OUTLIER) cc_final: 0.7823 (tt0) REVERT: D 27 TYR cc_start: 0.7684 (m-80) cc_final: 0.6819 (m-80) REVERT: D 464 GLN cc_start: 0.8280 (OUTLIER) cc_final: 0.8029 (mt0) REVERT: D 682 GLU cc_start: 0.8097 (mt-10) cc_final: 0.7697 (mt-10) REVERT: D 684 GLN cc_start: 0.8165 (OUTLIER) cc_final: 0.7835 (tt0) outliers start: 23 outliers final: 10 residues processed: 144 average time/residue: 0.8205 time to fit residues: 131.8285 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 : 1.001 ------------------------------------------------------------------------------- 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: 0.9990 chunk 62 optimal weight: 0.0570 chunk 99 optimal weight: 10.0000 chunk 46 optimal weight: 3.9990 chunk 118 optimal weight: 4.9990 chunk 41 optimal weight: 0.7980 chunk 7 optimal weight: 2.9990 chunk 1 optimal weight: 2.9990 chunk 69 optimal weight: 0.6980 chunk 45 optimal weight: 0.7980 chunk 54 optimal weight: 2.9990 overall best weight: 0.6700 ------------------------------------------------------------------------------- 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 728 HIS D 33 GLN D 324 ASN D 728 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4081 r_free = 0.4081 target = 0.171862 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.137704 restraints weight = 12738.429| |-----------------------------------------------------------------------------| r_work (start): 0.3693 rms_B_bonded: 2.08 r_work: 0.3564 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3564 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7382 moved from start: 0.1530 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= 0.124 Angle : 0.605 7.185 14414 Z= 0.300 Chirality : 0.045 0.321 1760 Planarity : 0.005 0.076 1640 Dihedral : 15.991 164.692 2742 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 9.56 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.29 % Favored : 94.55 % Rotamer: Outliers : 1.91 % Allowed : 13.86 % 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: 1.18 (0.25), residues: 1210 helix: 1.77 (0.18), residues: 818 sheet: 0.54 (0.50), residues: 50 loop : -1.67 (0.34), residues: 342 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 141 TYR 0.019 0.001 TYR D 315 ARG 0.002 0.000 ARG D 409 Details of bonding type rmsd hydrogen bonds : bond 0.04438 ( 638) hydrogen bonds : angle 4.20751 ( 1860) covalent geometry : bond 0.00257 (10634) covalent geometry : angle 0.60482 (14414) *********************** 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 161 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 141 time to evaluate : 1.013 Fit side-chains REVERT: C 27 TYR cc_start: 0.7546 (m-80) cc_final: 0.6732 (m-80) REVERT: C 79 ARG cc_start: 0.7411 (mtp180) cc_final: 0.7046 (mtp-110) REVERT: C 81 LYS cc_start: 0.7824 (mmpt) cc_final: 0.7113 (mmtm) REVERT: C 684 GLN cc_start: 0.8062 (OUTLIER) cc_final: 0.7725 (tt0) REVERT: D 27 TYR cc_start: 0.7556 (m-80) cc_final: 0.6739 (m-80) REVERT: D 79 ARG cc_start: 0.7400 (mtp180) cc_final: 0.7034 (mtp-110) REVERT: D 81 LYS cc_start: 0.7828 (mmpt) cc_final: 0.7115 (mmtm) REVERT: D 684 GLN cc_start: 0.8068 (OUTLIER) cc_final: 0.7730 (tt0) outliers start: 20 outliers final: 10 residues processed: 153 average time/residue: 0.7737 time to fit residues: 132.8511 Evaluate side-chains 135 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 123 time to evaluate : 0.994 ------------------------------------------------------------------------------- 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 52 optimal weight: 0.9990 chunk 65 optimal weight: 8.9990 chunk 108 optimal weight: 0.8980 chunk 120 optimal weight: 0.0070 chunk 1 optimal weight: 0.5980 chunk 95 optimal weight: 6.9990 chunk 12 optimal weight: 4.9990 chunk 29 optimal weight: 4.9990 chunk 96 optimal weight: 2.9990 chunk 118 optimal weight: 5.9990 chunk 7 optimal weight: 0.9980 overall best weight: 0.7000 ------------------------------------------------------------------------------- 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 = 0.4092 r_free = 0.4092 target = 0.172343 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.138671 restraints weight = 12656.386| |-----------------------------------------------------------------------------| r_work (start): 0.3706 rms_B_bonded: 2.03 r_work: 0.3575 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.3439 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.3439 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7441 moved from start: 0.1628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 10634 Z= 0.126 Angle : 0.614 9.534 14414 Z= 0.302 Chirality : 0.045 0.315 1760 Planarity : 0.004 0.074 1640 Dihedral : 15.401 164.579 2742 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 9.70 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.45 % Favored : 94.38 % Rotamer: Outliers : 3.25 % Allowed : 13.77 % Favored : 82.98 % 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: 1.21 (0.25), residues: 1210 helix: 1.81 (0.18), residues: 818 sheet: 0.50 (0.51), residues: 50 loop : -1.72 (0.33), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 482 HIS 0.003 0.001 HIS D 656 PHE 0.016 0.001 PHE D 141 TYR 0.012 0.001 TYR C 371 ARG 0.002 0.000 ARG D 24 Details of bonding type rmsd hydrogen bonds : bond 0.04425 ( 638) hydrogen bonds : angle 4.18938 ( 1860) covalent geometry : bond 0.00263 (10634) covalent geometry : angle 0.61431 (14414) *********************** 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 162 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 128 time to evaluate : 1.123 Fit side-chains REVERT: C 27 TYR cc_start: 0.7641 (m-80) cc_final: 0.6745 (m-80) REVERT: C 79 ARG cc_start: 0.7349 (mtp180) cc_final: 0.7016 (mtp-110) REVERT: C 81 LYS cc_start: 0.7920 (mmpt) cc_final: 0.7091 (mmtm) REVERT: C 464 GLN cc_start: 0.8334 (OUTLIER) cc_final: 0.8128 (mt0) REVERT: C 684 GLN cc_start: 0.8133 (OUTLIER) cc_final: 0.7802 (tt0) REVERT: D 27 TYR cc_start: 0.7650 (m-80) cc_final: 0.6755 (m-80) REVERT: D 79 ARG cc_start: 0.7352 (mtp180) cc_final: 0.7019 (mtp-110) REVERT: D 81 LYS cc_start: 0.7925 (mmpt) cc_final: 0.7089 (mmtm) REVERT: D 464 GLN cc_start: 0.8326 (OUTLIER) cc_final: 0.8111 (mt0) REVERT: D 684 GLN cc_start: 0.8123 (OUTLIER) cc_final: 0.7784 (tt0) outliers start: 34 outliers final: 18 residues processed: 154 average time/residue: 0.8420 time to fit residues: 145.1694 Evaluate side-chains 144 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 122 time to evaluate : 1.202 ------------------------------------------------------------------------------- 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 464 GLN 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 464 GLN 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 30 optimal weight: 4.9990 chunk 48 optimal weight: 2.9990 chunk 64 optimal weight: 0.6980 chunk 5 optimal weight: 0.7980 chunk 89 optimal weight: 3.9990 chunk 32 optimal weight: 0.3980 chunk 10 optimal weight: 2.9990 chunk 79 optimal weight: 0.8980 chunk 99 optimal weight: 2.9990 chunk 61 optimal weight: 0.0010 chunk 112 optimal weight: 0.9980 overall best weight: 0.5586 ------------------------------------------------------------------------------- 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 = 0.4099 r_free = 0.4099 target = 0.173010 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.139524 restraints weight = 12684.664| |-----------------------------------------------------------------------------| r_work (start): 0.3716 rms_B_bonded: 2.02 r_work: 0.3586 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.3451 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.3451 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7427 moved from start: 0.1718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 10634 Z= 0.121 Angle : 0.604 8.846 14414 Z= 0.298 Chirality : 0.044 0.322 1760 Planarity : 0.004 0.073 1640 Dihedral : 14.908 164.336 2742 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 10.02 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.95 % Favored : 93.88 % Rotamer: Outliers : 3.44 % Allowed : 13.77 % 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: 1.22 (0.25), residues: 1210 helix: 1.83 (0.18), residues: 818 sheet: 0.57 (0.53), residues: 50 loop : -1.77 (0.33), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 482 HIS 0.003 0.001 HIS D 656 PHE 0.016 0.001 PHE D 141 TYR 0.016 0.001 TYR C 315 ARG 0.002 0.000 ARG D 409 Details of bonding type rmsd hydrogen bonds : bond 0.04341 ( 638) hydrogen bonds : angle 4.15433 ( 1860) covalent geometry : bond 0.00247 (10634) covalent geometry : angle 0.60428 (14414) *********************** 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 168 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 132 time to evaluate : 1.028 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 27 TYR cc_start: 0.7695 (m-80) cc_final: 0.6825 (m-80) REVERT: C 79 ARG cc_start: 0.7382 (mtp180) cc_final: 0.7009 (mtp-110) REVERT: C 81 LYS cc_start: 0.7911 (mmpt) cc_final: 0.7083 (mmtm) REVERT: C 464 GLN cc_start: 0.8528 (OUTLIER) cc_final: 0.8250 (mt0) REVERT: C 684 GLN cc_start: 0.8134 (OUTLIER) cc_final: 0.7805 (tt0) REVERT: D 27 TYR cc_start: 0.7713 (m-80) cc_final: 0.6847 (m-80) REVERT: D 79 ARG cc_start: 0.7388 (mtp180) cc_final: 0.7014 (mtp-110) REVERT: D 81 LYS cc_start: 0.7911 (mmpt) cc_final: 0.7076 (mmtm) REVERT: D 464 GLN cc_start: 0.8517 (OUTLIER) cc_final: 0.8239 (mt0) REVERT: D 684 GLN cc_start: 0.8131 (OUTLIER) cc_final: 0.7795 (tt0) outliers start: 36 outliers final: 20 residues processed: 158 average time/residue: 0.7676 time to fit residues: 136.1292 Evaluate side-chains 147 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 123 time to evaluate : 1.037 ------------------------------------------------------------------------------- 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 464 GLN Chi-restraints excluded: chain C residue 465 VAL 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 464 GLN Chi-restraints excluded: chain D residue 465 VAL 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: 3.9990 chunk 96 optimal weight: 0.8980 chunk 82 optimal weight: 10.0000 chunk 23 optimal weight: 10.0000 chunk 38 optimal weight: 0.7980 chunk 111 optimal weight: 2.9990 chunk 39 optimal weight: 0.8980 chunk 9 optimal weight: 6.9990 chunk 84 optimal weight: 10.0000 chunk 91 optimal weight: 3.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- 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 = 0.4059 r_free = 0.4059 target = 0.169042 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.134863 restraints weight = 12755.821| |-----------------------------------------------------------------------------| r_work (start): 0.3659 rms_B_bonded: 2.03 r_work: 0.3525 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.3389 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.3389 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7504 moved from start: 0.1742 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= 0.165 Angle : 0.656 8.901 14414 Z= 0.324 Chirality : 0.046 0.343 1760 Planarity : 0.005 0.073 1640 Dihedral : 14.664 164.971 2742 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 9.05 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.28 % Favored : 93.55 % Rotamer: Outliers : 3.63 % Allowed : 14.05 % Favored : 82.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.08 (0.24), residues: 1210 helix: 1.69 (0.18), residues: 820 sheet: 0.68 (0.55), residues: 50 loop : -1.76 (0.33), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 74 HIS 0.003 0.001 HIS D 656 PHE 0.018 0.002 PHE C 401 TYR 0.014 0.002 TYR C 371 ARG 0.002 0.000 ARG C 409 Details of bonding type rmsd hydrogen bonds : bond 0.04881 ( 638) hydrogen bonds : angle 4.28071 ( 1860) covalent geometry : bond 0.00368 (10634) covalent geometry : angle 0.65630 (14414) *********************** 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 158 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 120 time to evaluate : 1.018 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 27 TYR cc_start: 0.7721 (m-80) cc_final: 0.6725 (m-80) REVERT: C 79 ARG cc_start: 0.7343 (mtp180) cc_final: 0.6975 (mtp-110) REVERT: C 81 LYS cc_start: 0.7919 (mmpt) cc_final: 0.7062 (mmtm) REVERT: C 339 GLU cc_start: 0.7605 (OUTLIER) cc_final: 0.6884 (mp0) REVERT: C 464 GLN cc_start: 0.8635 (OUTLIER) cc_final: 0.8287 (mt0) REVERT: C 684 GLN cc_start: 0.8158 (OUTLIER) cc_final: 0.7814 (tt0) REVERT: D 27 TYR cc_start: 0.7715 (m-80) cc_final: 0.6722 (m-80) REVERT: D 81 LYS cc_start: 0.7920 (mmpt) cc_final: 0.7057 (mmtm) REVERT: D 464 GLN cc_start: 0.8622 (OUTLIER) cc_final: 0.8276 (mt0) REVERT: D 684 GLN cc_start: 0.8162 (OUTLIER) cc_final: 0.7813 (tt0) outliers start: 38 outliers final: 20 residues processed: 148 average time/residue: 0.8466 time to fit residues: 139.5082 Evaluate side-chains 145 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 120 time to evaluate : 0.984 ------------------------------------------------------------------------------- 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 339 GLU Chi-restraints excluded: chain C residue 370 VAL Chi-restraints excluded: chain C residue 385 PHE Chi-restraints excluded: chain C residue 464 GLN Chi-restraints excluded: chain C residue 465 VAL 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 464 GLN Chi-restraints excluded: chain D residue 465 VAL 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 16 optimal weight: 1.9990 chunk 121 optimal weight: 2.9990 chunk 53 optimal weight: 9.9990 chunk 29 optimal weight: 0.0020 chunk 7 optimal weight: 0.9980 chunk 68 optimal weight: 0.9990 chunk 39 optimal weight: 0.8980 chunk 108 optimal weight: 0.8980 chunk 45 optimal weight: 2.9990 chunk 52 optimal weight: 0.0170 chunk 50 optimal weight: 1.9990 overall best weight: 0.5626 ------------------------------------------------------------------------------- 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 = 0.4102 r_free = 0.4102 target = 0.173274 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.139693 restraints weight = 12641.484| |-----------------------------------------------------------------------------| r_work (start): 0.3720 rms_B_bonded: 2.02 r_work: 0.3588 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.3450 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.3450 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7426 moved from start: 0.1841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 10634 Z= 0.123 Angle : 0.608 8.022 14414 Z= 0.302 Chirality : 0.045 0.351 1760 Planarity : 0.004 0.077 1640 Dihedral : 13.621 163.233 2742 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 9.75 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.87 % Favored : 93.97 % Rotamer: Outliers : 2.87 % Allowed : 15.30 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.23 (0.25), residues: 1210 helix: 1.85 (0.18), residues: 816 sheet: 0.60 (0.52), residues: 50 loop : -1.76 (0.33), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 482 HIS 0.003 0.001 HIS C 656 PHE 0.016 0.001 PHE D 141 TYR 0.016 0.001 TYR D 315 ARG 0.002 0.000 ARG C 409 Details of bonding type rmsd hydrogen bonds : bond 0.04316 ( 638) hydrogen bonds : angle 4.15847 ( 1860) covalent geometry : bond 0.00255 (10634) covalent geometry : angle 0.60803 (14414) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 126 time to evaluate : 1.148 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 27 TYR cc_start: 0.7750 (m-80) cc_final: 0.6732 (m-80) REVERT: C 79 ARG cc_start: 0.7381 (mtp180) cc_final: 0.6991 (mtp-110) REVERT: C 81 LYS cc_start: 0.7881 (mmpt) cc_final: 0.7022 (mmtm) REVERT: C 339 GLU cc_start: 0.7583 (OUTLIER) cc_final: 0.6880 (mp0) REVERT: C 684 GLN cc_start: 0.8142 (OUTLIER) cc_final: 0.7828 (tt0) REVERT: D 27 TYR cc_start: 0.7752 (m-80) cc_final: 0.6727 (m-80) REVERT: D 81 LYS cc_start: 0.7880 (mmpt) cc_final: 0.7150 (mmtm) REVERT: D 684 GLN cc_start: 0.8132 (OUTLIER) cc_final: 0.7814 (tt0) outliers start: 30 outliers final: 16 residues processed: 150 average time/residue: 1.0969 time to fit residues: 183.3506 Evaluate side-chains 141 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 122 time to evaluate : 1.059 ------------------------------------------------------------------------------- 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 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 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 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: 1.9990 chunk 62 optimal weight: 3.9990 chunk 76 optimal weight: 3.9990 chunk 112 optimal weight: 0.6980 chunk 83 optimal weight: 8.9990 chunk 22 optimal weight: 8.9990 chunk 29 optimal weight: 0.0050 chunk 117 optimal weight: 10.0000 chunk 87 optimal weight: 9.9990 chunk 53 optimal weight: 8.9990 chunk 89 optimal weight: 1.9990 overall best weight: 1.7400 ------------------------------------------------------------------------------- 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 = 0.4046 r_free = 0.4046 target = 0.167922 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.133051 restraints weight = 12706.206| |-----------------------------------------------------------------------------| r_work (start): 0.3637 rms_B_bonded: 2.03 r_work: 0.3506 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.3368 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3368 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7510 moved from start: 0.1882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 10634 Z= 0.182 Angle : 0.708 15.471 14414 Z= 0.345 Chirality : 0.048 0.378 1760 Planarity : 0.005 0.076 1640 Dihedral : 13.544 163.378 2742 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 9.47 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.28 % Favored : 93.55 % Rotamer: Outliers : 2.96 % Allowed : 14.82 % Favored : 82.22 % 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 (0.25), residues: 1210 helix: 1.65 (0.18), residues: 818 sheet: 0.70 (0.57), residues: 50 loop : -1.71 (0.33), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 74 HIS 0.003 0.001 HIS C 698 PHE 0.019 0.002 PHE C 401 TYR 0.016 0.002 TYR C 371 ARG 0.003 0.000 ARG D 409 Details of bonding type rmsd hydrogen bonds : bond 0.05103 ( 638) hydrogen bonds : angle 4.34175 ( 1860) covalent geometry : bond 0.00408 (10634) covalent geometry : angle 0.70835 (14414) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 114 time to evaluate : 1.140 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 27 TYR cc_start: 0.7741 (m-80) cc_final: 0.6583 (m-80) REVERT: C 81 LYS cc_start: 0.7908 (mmpt) cc_final: 0.7013 (mmtm) REVERT: C 339 GLU cc_start: 0.7615 (OUTLIER) cc_final: 0.6890 (mp0) REVERT: C 464 GLN cc_start: 0.8609 (OUTLIER) cc_final: 0.8304 (mt0) REVERT: C 556 TYR cc_start: 0.7033 (OUTLIER) cc_final: 0.6719 (p90) REVERT: C 684 GLN cc_start: 0.8148 (OUTLIER) cc_final: 0.7810 (tt0) REVERT: D 27 TYR cc_start: 0.7733 (m-80) cc_final: 0.6578 (m-80) REVERT: D 79 ARG cc_start: 0.7314 (mtp85) cc_final: 0.6969 (mtp-110) REVERT: D 81 LYS cc_start: 0.7885 (mmpt) cc_final: 0.7018 (mmtm) REVERT: D 464 GLN cc_start: 0.8598 (OUTLIER) cc_final: 0.8299 (mt0) REVERT: D 556 TYR cc_start: 0.7043 (OUTLIER) cc_final: 0.6715 (p90) REVERT: D 684 GLN cc_start: 0.8148 (OUTLIER) cc_final: 0.7808 (tt0) outliers start: 31 outliers final: 16 residues processed: 141 average time/residue: 0.9567 time to fit residues: 150.0708 Evaluate side-chains 134 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 111 time to evaluate : 1.194 ------------------------------------------------------------------------------- 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 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 464 GLN 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 67 THR 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 464 GLN 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: 0.9990 chunk 96 optimal weight: 4.9990 chunk 4 optimal weight: 4.9990 chunk 8 optimal weight: 0.6980 chunk 99 optimal weight: 9.9990 chunk 97 optimal weight: 6.9990 chunk 37 optimal weight: 8.9990 chunk 101 optimal weight: 4.9990 chunk 28 optimal weight: 0.0570 chunk 46 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 overall best weight: 1.3504 ------------------------------------------------------------------------------- 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 = 0.4055 r_free = 0.4055 target = 0.168874 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.134275 restraints weight = 12585.517| |-----------------------------------------------------------------------------| r_work (start): 0.3649 rms_B_bonded: 2.02 r_work: 0.3518 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.3382 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3382 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7482 moved from start: 0.1913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 10634 Z= 0.160 Angle : 0.676 14.172 14414 Z= 0.335 Chirality : 0.046 0.347 1760 Planarity : 0.005 0.079 1640 Dihedral : 13.363 162.555 2742 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 9.65 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.87 % Favored : 93.97 % Rotamer: Outliers : 2.20 % Allowed : 15.39 % Favored : 82.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.02 (0.25), residues: 1210 helix: 1.64 (0.18), residues: 818 sheet: 0.59 (0.57), residues: 50 loop : -1.74 (0.33), residues: 342 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 0.017 0.002 PHE C 401 TYR 0.015 0.002 TYR C 371 ARG 0.002 0.000 ARG D 185 Details of bonding type rmsd hydrogen bonds : bond 0.04906 ( 638) hydrogen bonds : angle 4.31352 ( 1860) covalent geometry : bond 0.00353 (10634) covalent geometry : angle 0.67638 (14414) ********************** 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 136 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 113 time to evaluate : 1.099 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 27 TYR cc_start: 0.7728 (m-80) cc_final: 0.6530 (m-80) REVERT: C 79 ARG cc_start: 0.7326 (mtp180) cc_final: 0.6988 (mtp-110) REVERT: C 81 LYS cc_start: 0.7884 (mmpt) cc_final: 0.6993 (mmtm) REVERT: C 339 GLU cc_start: 0.7581 (OUTLIER) cc_final: 0.6880 (mp0) REVERT: C 684 GLN cc_start: 0.8132 (OUTLIER) cc_final: 0.7799 (tt0) REVERT: D 27 TYR cc_start: 0.7723 (m-80) cc_final: 0.6530 (m-80) REVERT: D 79 ARG cc_start: 0.7308 (mtp85) cc_final: 0.6951 (mtp-110) REVERT: D 81 LYS cc_start: 0.7901 (mmpt) cc_final: 0.7161 (mmtm) REVERT: D 684 GLN cc_start: 0.8145 (OUTLIER) cc_final: 0.7815 (tt0) outliers start: 23 outliers final: 13 residues processed: 128 average time/residue: 0.8853 time to fit residues: 125.7929 Evaluate side-chains 129 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 113 time to evaluate : 0.967 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 67 THR 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 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 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: 0.9980 chunk 54 optimal weight: 4.9990 chunk 97 optimal weight: 10.0000 chunk 5 optimal weight: 0.9980 chunk 111 optimal weight: 3.9990 chunk 42 optimal weight: 3.9990 chunk 101 optimal weight: 0.9980 chunk 46 optimal weight: 2.9990 chunk 63 optimal weight: 0.0070 chunk 14 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 overall best weight: 1.2000 ------------------------------------------------------------------------------- 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 = 0.4061 r_free = 0.4061 target = 0.169501 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.135099 restraints weight = 12607.537| |-----------------------------------------------------------------------------| r_work (start): 0.3662 rms_B_bonded: 2.02 r_work: 0.3530 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.3394 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3394 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7484 moved from start: 0.1907 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= 0.151 Angle : 0.671 15.757 14414 Z= 0.330 Chirality : 0.045 0.292 1760 Planarity : 0.005 0.082 1640 Dihedral : 13.033 160.006 2742 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 9.93 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.61 % Favored : 93.22 % Rotamer: Outliers : 2.01 % Allowed : 15.58 % Favored : 82.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.03 (0.25), residues: 1210 helix: 1.65 (0.18), residues: 818 sheet: 0.57 (0.56), residues: 50 loop : -1.73 (0.33), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 74 HIS 0.003 0.001 HIS C 656 PHE 0.017 0.002 PHE D 141 TYR 0.014 0.001 TYR D 371 ARG 0.002 0.000 ARG D 409 Details of bonding type rmsd hydrogen bonds : bond 0.04791 ( 638) hydrogen bonds : angle 4.26979 ( 1860) covalent geometry : bond 0.00330 (10634) covalent geometry : angle 0.67113 (14414) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7794.24 seconds wall clock time: 135 minutes 52.84 seconds (8152.84 seconds total)