Starting phenix.real_space_refine on Sat Nov 16 03:47:33 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sgw_40470/11_2024/8sgw_40470.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sgw_40470/11_2024/8sgw_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sgw_40470/11_2024/8sgw_40470.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sgw_40470/11_2024/8sgw_40470.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sgw_40470/11_2024/8sgw_40470.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sgw_40470/11_2024/8sgw_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-5513/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: 6.65, per 1000 atoms: 0.64 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: 2.98 Conformation dependent library (CDL) restraints added in 1.4 seconds 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2288 Finding SS restraints... Secondary structure from input PDB file: 62 helices and 5 sheets defined 71.9% alpha, 4.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.14 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: 3.59 Time building geometry restraints manager: 3.39 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: 0.00 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: 0.650 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: 0.450 Check model and map are aligned: 0.070 Set scattering table: 0.100 Process input model: 26.930 Find NCS groups from input model: 0.300 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:13.540 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.090 ------------------------------------------------------------------------------- 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 : 1.046 Fit side-chains outliers start: 0 outliers final: 1 residues processed: 167 average time/residue: 1.0162 time to fit residues: 185.8866 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 : 1.183 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7531 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 : 1.058 Fit side-chains outliers start: 12 outliers final: 8 residues processed: 144 average time/residue: 0.8889 time to fit residues: 142.3998 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 : 1.094 ------------------------------------------------------------------------------- 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 61 optimal weight: 7.9990 chunk 34 optimal weight: 6.9990 chunk 92 optimal weight: 3.9990 chunk 75 optimal weight: 4.9990 chunk 30 optimal weight: 0.8980 chunk 110 optimal weight: 0.1980 chunk 119 optimal weight: 1.9990 chunk 98 optimal weight: 10.0000 chunk 37 optimal weight: 10.0000 chunk 89 optimal weight: 8.9990 chunk 109 optimal weight: 2.9990 overall best weight: 2.0186 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7583 moved from start: 0.1461 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= 0.287 Angle : 0.689 8.992 14414 Z= 0.343 Chirality : 0.048 0.275 1760 Planarity : 0.005 0.073 1640 Dihedral : 18.214 166.216 2742 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 9.47 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.87 % Favored : 93.97 % Rotamer: Outliers : 2.10 % Allowed : 12.91 % Favored : 84.99 % 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: 0.78 (0.24), residues: 1210 helix: 1.43 (0.18), residues: 816 sheet: 0.39 (0.53), residues: 50 loop : -1.69 (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 C 141 TYR 0.016 0.002 TYR C 371 ARG 0.003 0.000 ARG D 181 *********************** 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 138 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 116 time to evaluate : 1.195 Fit side-chains REVERT: C 684 GLN cc_start: 0.7897 (OUTLIER) cc_final: 0.7542 (tt0) REVERT: D 684 GLN cc_start: 0.7902 (OUTLIER) cc_final: 0.7546 (tt0) outliers start: 22 outliers final: 11 residues processed: 132 average time/residue: 0.8917 time to fit residues: 131.0012 Evaluate side-chains 121 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 108 time to evaluate : 1.203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 80 ILE Chi-restraints excluded: chain C residue 154 SER Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain C residue 552 SER Chi-restraints excluded: chain C residue 559 VAL Chi-restraints excluded: chain C residue 684 GLN Chi-restraints excluded: chain D residue 80 ILE Chi-restraints excluded: chain D residue 154 SER Chi-restraints excluded: chain D residue 219 LEU Chi-restraints excluded: chain D residue 347 SER 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 83 optimal weight: 10.0000 chunk 57 optimal weight: 4.9990 chunk 12 optimal weight: 3.9990 chunk 52 optimal weight: 0.6980 chunk 74 optimal weight: 0.9980 chunk 111 optimal weight: 9.9990 chunk 117 optimal weight: 5.9990 chunk 58 optimal weight: 0.4980 chunk 105 optimal weight: 3.9990 chunk 31 optimal weight: 2.9990 chunk 98 optimal weight: 0.9990 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 324 ASN D 324 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7554 moved from start: 0.1585 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= 0.212 Angle : 0.640 7.590 14414 Z= 0.320 Chirality : 0.046 0.318 1760 Planarity : 0.005 0.078 1640 Dihedral : 17.038 167.545 2742 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 9.24 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.79 % Favored : 94.05 % Rotamer: Outliers : 2.49 % Allowed : 13.29 % 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: 0.95 (0.24), residues: 1210 helix: 1.57 (0.18), residues: 816 sheet: 0.26 (0.50), residues: 50 loop : -1.62 (0.33), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 74 HIS 0.004 0.001 HIS D 656 PHE 0.017 0.002 PHE C 141 TYR 0.016 0.002 TYR D 315 ARG 0.002 0.000 ARG C 24 *********************** 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 154 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 128 time to evaluate : 1.125 Fit side-chains REVERT: C 81 LYS cc_start: 0.7683 (mmpt) cc_final: 0.6971 (mmtm) REVERT: C 684 GLN cc_start: 0.7860 (OUTLIER) cc_final: 0.7530 (tt0) REVERT: D 81 LYS cc_start: 0.7683 (mmpt) cc_final: 0.6973 (mmtm) REVERT: D 684 GLN cc_start: 0.7864 (OUTLIER) cc_final: 0.7530 (tt0) outliers start: 26 outliers final: 14 residues processed: 146 average time/residue: 0.9039 time to fit residues: 147.5614 Evaluate side-chains 136 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 120 time to evaluate : 1.182 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 80 ILE Chi-restraints excluded: chain C residue 154 SER Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain C residue 385 PHE Chi-restraints excluded: chain C residue 545 VAL Chi-restraints excluded: chain C residue 552 SER Chi-restraints excluded: chain C residue 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 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 66 optimal weight: 10.0000 chunk 1 optimal weight: 0.9990 chunk 87 optimal weight: 3.9990 chunk 48 optimal weight: 0.8980 chunk 100 optimal weight: 3.9990 chunk 81 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 60 optimal weight: 1.9990 chunk 105 optimal weight: 5.9990 chunk 29 optimal weight: 0.9990 chunk 39 optimal weight: 4.9990 overall best weight: 1.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 324 ASN C 464 GLN D 464 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7554 moved from start: 0.1646 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= 0.208 Angle : 0.640 9.738 14414 Z= 0.320 Chirality : 0.046 0.322 1760 Planarity : 0.005 0.080 1640 Dihedral : 16.226 167.879 2742 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 9.79 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.20 % Favored : 93.64 % Rotamer: Outliers : 3.63 % Allowed : 12.52 % 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: 1.00 (0.24), residues: 1210 helix: 1.62 (0.18), residues: 820 sheet: 0.20 (0.49), residues: 50 loop : -1.66 (0.33), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 482 HIS 0.004 0.001 HIS C 656 PHE 0.018 0.001 PHE D 141 TYR 0.013 0.002 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 165 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 127 time to evaluate : 1.220 Fit side-chains REVERT: C 27 TYR cc_start: 0.7509 (m-80) cc_final: 0.5876 (m-80) REVERT: C 81 LYS cc_start: 0.7684 (mmpt) cc_final: 0.6961 (mmtm) REVERT: C 339 GLU cc_start: 0.7160 (OUTLIER) cc_final: 0.6761 (mp0) REVERT: C 682 GLU cc_start: 0.7489 (mt-10) cc_final: 0.7143 (mt-10) REVERT: C 684 GLN cc_start: 0.7860 (OUTLIER) cc_final: 0.7521 (tt0) REVERT: D 27 TYR cc_start: 0.7509 (m-80) cc_final: 0.5875 (m-80) REVERT: D 81 LYS cc_start: 0.7717 (mmpt) cc_final: 0.6997 (mmtm) REVERT: D 682 GLU cc_start: 0.7499 (mt-10) cc_final: 0.7150 (mt-10) REVERT: D 684 GLN cc_start: 0.7863 (OUTLIER) cc_final: 0.7524 (tt0) outliers start: 38 outliers final: 16 residues processed: 155 average time/residue: 0.8123 time to fit residues: 140.7736 Evaluate side-chains 134 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 115 time to evaluate : 1.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 80 ILE Chi-restraints excluded: chain C residue 154 SER Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain C residue 339 GLU Chi-restraints excluded: chain C residue 370 VAL Chi-restraints excluded: chain C residue 385 PHE Chi-restraints excluded: chain C residue 545 VAL Chi-restraints excluded: chain C residue 552 SER Chi-restraints excluded: chain C residue 559 VAL Chi-restraints excluded: chain C residue 684 GLN Chi-restraints excluded: chain D residue 80 ILE Chi-restraints excluded: chain D residue 154 SER Chi-restraints excluded: chain D residue 219 LEU Chi-restraints excluded: chain D residue 370 VAL Chi-restraints excluded: chain D residue 385 PHE Chi-restraints excluded: chain D residue 545 VAL Chi-restraints excluded: chain D residue 552 SER Chi-restraints excluded: chain D residue 559 VAL Chi-restraints excluded: chain D residue 684 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 106 optimal weight: 2.9990 chunk 23 optimal weight: 10.0000 chunk 69 optimal weight: 0.5980 chunk 29 optimal weight: 1.9990 chunk 118 optimal weight: 5.9990 chunk 97 optimal weight: 0.9990 chunk 54 optimal weight: 5.9990 chunk 9 optimal weight: 7.9990 chunk 39 optimal weight: 0.9980 chunk 61 optimal weight: 5.9990 chunk 113 optimal weight: 9.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 34 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7574 moved from start: 0.1786 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= 0.237 Angle : 0.664 9.620 14414 Z= 0.332 Chirality : 0.046 0.322 1760 Planarity : 0.005 0.078 1640 Dihedral : 15.693 168.531 2742 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 9.56 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.70 % Favored : 94.13 % Rotamer: Outliers : 4.21 % Allowed : 12.62 % Favored : 83.17 % 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: 0.92 (0.24), residues: 1210 helix: 1.58 (0.18), residues: 816 sheet: 0.15 (0.49), residues: 50 loop : -1.75 (0.32), 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 0.018 0.002 PHE D 141 TYR 0.016 0.002 TYR D 315 ARG 0.002 0.000 ARG D 409 *********************** 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 156 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 112 time to evaluate : 1.081 Fit side-chains REVERT: C 79 ARG cc_start: 0.7140 (mtp180) cc_final: 0.6840 (mtp-110) REVERT: C 81 LYS cc_start: 0.7730 (mmpt) cc_final: 0.6972 (mmtm) REVERT: C 339 GLU cc_start: 0.7169 (OUTLIER) cc_final: 0.6764 (mp0) REVERT: C 678 MET cc_start: 0.7151 (mmt) cc_final: 0.6835 (mpm) REVERT: C 682 GLU cc_start: 0.7548 (mt-10) cc_final: 0.7249 (mt-10) REVERT: C 684 GLN cc_start: 0.7856 (OUTLIER) cc_final: 0.7522 (tt0) REVERT: D 81 LYS cc_start: 0.7740 (mmpt) cc_final: 0.6996 (mmtm) REVERT: D 678 MET cc_start: 0.7153 (mmt) cc_final: 0.6832 (mpm) REVERT: D 682 GLU cc_start: 0.7559 (mt-10) cc_final: 0.7255 (mt-10) REVERT: D 684 GLN cc_start: 0.7862 (OUTLIER) cc_final: 0.7525 (tt0) outliers start: 44 outliers final: 16 residues processed: 148 average time/residue: 0.8641 time to fit residues: 142.9230 Evaluate side-chains 127 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 108 time to evaluate : 1.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 80 ILE Chi-restraints excluded: chain C residue 154 SER Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain C residue 339 GLU Chi-restraints excluded: chain C residue 370 VAL Chi-restraints excluded: chain C residue 385 PHE Chi-restraints excluded: chain C residue 545 VAL Chi-restraints excluded: chain C residue 552 SER Chi-restraints excluded: chain C residue 559 VAL Chi-restraints excluded: chain C residue 684 GLN Chi-restraints excluded: chain D residue 80 ILE Chi-restraints excluded: chain D residue 154 SER Chi-restraints excluded: chain D residue 219 LEU Chi-restraints excluded: chain D residue 370 VAL Chi-restraints excluded: chain D residue 385 PHE Chi-restraints excluded: chain D residue 545 VAL Chi-restraints excluded: chain D residue 552 SER Chi-restraints excluded: chain D residue 559 VAL Chi-restraints excluded: chain D residue 684 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 13 optimal weight: 5.9990 chunk 67 optimal weight: 4.9990 chunk 86 optimal weight: 2.9990 chunk 66 optimal weight: 1.9990 chunk 99 optimal weight: 0.9990 chunk 65 optimal weight: 6.9990 chunk 117 optimal weight: 3.9990 chunk 73 optimal weight: 3.9990 chunk 71 optimal weight: 1.9990 chunk 54 optimal weight: 5.9990 chunk 72 optimal weight: 0.8980 overall best weight: 1.7788 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7588 moved from start: 0.1859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 10634 Z= 0.263 Angle : 0.686 9.915 14414 Z= 0.342 Chirality : 0.047 0.305 1760 Planarity : 0.005 0.077 1640 Dihedral : 15.422 168.991 2742 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 9.38 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.12 % Favored : 93.72 % Rotamer: Outliers : 3.35 % Allowed : 13.96 % Favored : 82.70 % 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: 0.82 (0.24), residues: 1210 helix: 1.52 (0.18), residues: 816 sheet: -0.01 (0.49), residues: 50 loop : -1.79 (0.32), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 74 HIS 0.003 0.001 HIS C 656 PHE 0.019 0.002 PHE C 141 TYR 0.015 0.002 TYR C 371 ARG 0.003 0.000 ARG D 185 *********************** 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 145 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 110 time to evaluate : 1.128 Fit side-chains REVERT: C 81 LYS cc_start: 0.7695 (mmpt) cc_final: 0.6934 (mmtm) REVERT: C 339 GLU cc_start: 0.7185 (OUTLIER) cc_final: 0.6785 (mp0) REVERT: C 678 MET cc_start: 0.7134 (mmt) cc_final: 0.6909 (mpm) REVERT: C 684 GLN cc_start: 0.7814 (OUTLIER) cc_final: 0.7477 (tt0) REVERT: D 79 ARG cc_start: 0.7198 (mtp180) cc_final: 0.6919 (mtp-110) REVERT: D 81 LYS cc_start: 0.7697 (mmpt) cc_final: 0.6942 (mmtm) REVERT: D 678 MET cc_start: 0.7133 (mmt) cc_final: 0.6907 (mpm) REVERT: D 684 GLN cc_start: 0.7819 (OUTLIER) cc_final: 0.7480 (tt0) outliers start: 35 outliers final: 17 residues processed: 137 average time/residue: 0.9059 time to fit residues: 137.6062 Evaluate side-chains 126 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 106 time to evaluate : 1.165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 80 ILE Chi-restraints excluded: chain C residue 154 SER Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain C residue 339 GLU Chi-restraints excluded: chain C residue 347 SER Chi-restraints excluded: chain C residue 370 VAL Chi-restraints excluded: chain C residue 385 PHE Chi-restraints excluded: chain C residue 545 VAL Chi-restraints excluded: chain C residue 552 SER Chi-restraints excluded: chain C residue 559 VAL Chi-restraints excluded: chain C residue 684 GLN Chi-restraints excluded: chain D residue 80 ILE Chi-restraints excluded: chain D residue 154 SER Chi-restraints excluded: chain D residue 219 LEU Chi-restraints excluded: chain D residue 370 VAL Chi-restraints excluded: chain D residue 385 PHE Chi-restraints excluded: chain D residue 545 VAL Chi-restraints excluded: chain D residue 552 SER Chi-restraints excluded: chain D residue 559 VAL Chi-restraints excluded: chain D residue 684 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 46 optimal weight: 1.9990 chunk 70 optimal weight: 9.9990 chunk 35 optimal weight: 4.9990 chunk 23 optimal weight: 10.0000 chunk 22 optimal weight: 7.9990 chunk 74 optimal weight: 5.9990 chunk 80 optimal weight: 6.9990 chunk 58 optimal weight: 0.8980 chunk 10 optimal weight: 0.7980 chunk 92 optimal weight: 3.9990 chunk 106 optimal weight: 0.7980 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 34 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7585 moved from start: 0.1900 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= 0.257 Angle : 0.682 8.799 14414 Z= 0.342 Chirality : 0.047 0.272 1760 Planarity : 0.005 0.077 1640 Dihedral : 15.240 168.745 2742 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 9.65 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.12 % Favored : 93.72 % Rotamer: Outliers : 3.35 % Allowed : 14.63 % Favored : 82.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.80 (0.24), residues: 1210 helix: 1.50 (0.18), residues: 816 sheet: -0.07 (0.49), residues: 50 loop : -1.80 (0.32), 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 0.019 0.002 PHE D 141 TYR 0.015 0.002 TYR C 556 ARG 0.003 0.000 ARG D 185 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 109 time to evaluate : 1.230 Fit side-chains REVERT: C 81 LYS cc_start: 0.7688 (mmpt) cc_final: 0.6954 (mmtm) REVERT: C 339 GLU cc_start: 0.7182 (OUTLIER) cc_final: 0.6782 (mp0) REVERT: C 678 MET cc_start: 0.7129 (mmt) cc_final: 0.6846 (mpm) REVERT: C 682 GLU cc_start: 0.7467 (mt-10) cc_final: 0.7165 (mt-10) REVERT: C 684 GLN cc_start: 0.7807 (OUTLIER) cc_final: 0.7462 (tt0) REVERT: D 81 LYS cc_start: 0.7682 (mmpt) cc_final: 0.6940 (mmtm) REVERT: D 678 MET cc_start: 0.7129 (mmt) cc_final: 0.6843 (mpm) REVERT: D 682 GLU cc_start: 0.7482 (mt-10) cc_final: 0.7177 (mt-10) REVERT: D 684 GLN cc_start: 0.7812 (OUTLIER) cc_final: 0.7467 (tt0) outliers start: 35 outliers final: 16 residues processed: 136 average time/residue: 0.9559 time to fit residues: 144.5961 Evaluate side-chains 125 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 106 time to evaluate : 1.160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 154 SER Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain C residue 339 GLU Chi-restraints excluded: chain C residue 347 SER Chi-restraints excluded: chain C residue 370 VAL Chi-restraints excluded: chain C residue 385 PHE Chi-restraints excluded: chain C residue 545 VAL Chi-restraints excluded: chain C residue 552 SER Chi-restraints excluded: chain C residue 559 VAL Chi-restraints excluded: chain C residue 684 GLN Chi-restraints excluded: chain D residue 154 SER Chi-restraints excluded: chain D residue 219 LEU Chi-restraints excluded: chain D residue 347 SER Chi-restraints excluded: chain D residue 370 VAL Chi-restraints excluded: chain D residue 385 PHE Chi-restraints excluded: chain D residue 545 VAL Chi-restraints excluded: chain D residue 552 SER Chi-restraints excluded: chain D residue 559 VAL Chi-restraints excluded: chain D residue 684 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 112 optimal weight: 0.9980 chunk 102 optimal weight: 2.9990 chunk 109 optimal weight: 0.0980 chunk 65 optimal weight: 3.9990 chunk 47 optimal weight: 0.5980 chunk 86 optimal weight: 2.9990 chunk 33 optimal weight: 0.9990 chunk 99 optimal weight: 4.9990 chunk 103 optimal weight: 0.5980 chunk 71 optimal weight: 0.7980 chunk 115 optimal weight: 0.7980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 34 GLN C 728 HIS D 34 GLN D 728 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7512 moved from start: 0.1838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10634 Z= 0.175 Angle : 0.635 7.998 14414 Z= 0.319 Chirality : 0.045 0.342 1760 Planarity : 0.005 0.081 1640 Dihedral : 14.319 165.955 2742 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 10.21 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.87 % Favored : 93.97 % Rotamer: Outliers : 2.20 % Allowed : 15.77 % Favored : 82.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.06 (0.24), residues: 1210 helix: 1.72 (0.18), residues: 818 sheet: 0.13 (0.48), residues: 50 loop : -1.79 (0.33), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 482 HIS 0.004 0.001 HIS D 656 PHE 0.020 0.001 PHE C 141 TYR 0.015 0.001 TYR C 556 ARG 0.002 0.000 ARG C 185 *********************** 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 157 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 134 time to evaluate : 1.205 Fit side-chains REVERT: C 79 ARG cc_start: 0.7174 (mtp180) cc_final: 0.6892 (mtp-110) REVERT: C 81 LYS cc_start: 0.7562 (mmpt) cc_final: 0.6896 (mmtm) REVERT: C 339 GLU cc_start: 0.7126 (OUTLIER) cc_final: 0.6756 (mp0) REVERT: C 678 MET cc_start: 0.7067 (mmt) cc_final: 0.6771 (mpm) REVERT: C 682 GLU cc_start: 0.7452 (mt-10) cc_final: 0.7166 (mt-10) REVERT: C 684 GLN cc_start: 0.7794 (OUTLIER) cc_final: 0.7480 (tt0) REVERT: D 81 LYS cc_start: 0.7622 (mmpt) cc_final: 0.6981 (mmtm) REVERT: D 678 MET cc_start: 0.7068 (mmt) cc_final: 0.6766 (mpm) REVERT: D 682 GLU cc_start: 0.7463 (mt-10) cc_final: 0.7171 (mt-10) REVERT: D 684 GLN cc_start: 0.7800 (OUTLIER) cc_final: 0.7484 (tt0) outliers start: 23 outliers final: 14 residues processed: 149 average time/residue: 0.8313 time to fit residues: 138.5963 Evaluate side-chains 138 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 121 time to evaluate : 1.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 154 SER Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain C residue 339 GLU Chi-restraints excluded: chain C residue 370 VAL Chi-restraints excluded: chain C residue 385 PHE Chi-restraints excluded: chain C residue 545 VAL Chi-restraints excluded: chain C residue 552 SER Chi-restraints excluded: chain C residue 559 VAL Chi-restraints excluded: chain C residue 684 GLN Chi-restraints excluded: chain D residue 154 SER Chi-restraints excluded: chain D residue 219 LEU Chi-restraints excluded: chain D residue 370 VAL Chi-restraints excluded: chain D residue 385 PHE Chi-restraints excluded: chain D residue 545 VAL Chi-restraints excluded: chain D residue 552 SER Chi-restraints excluded: chain D residue 559 VAL Chi-restraints excluded: chain D residue 684 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 70 optimal weight: 4.9990 chunk 54 optimal weight: 2.9990 chunk 80 optimal weight: 5.9990 chunk 121 optimal weight: 0.9980 chunk 111 optimal weight: 0.8980 chunk 96 optimal weight: 0.7980 chunk 10 optimal weight: 1.9990 chunk 74 optimal weight: 5.9990 chunk 59 optimal weight: 0.8980 chunk 76 optimal weight: 1.9990 chunk 103 optimal weight: 4.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7545 moved from start: 0.1886 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= 0.212 Angle : 0.664 8.545 14414 Z= 0.332 Chirality : 0.046 0.365 1760 Planarity : 0.005 0.076 1640 Dihedral : 14.119 164.791 2742 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 9.79 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.12 % Favored : 93.72 % Rotamer: Outliers : 2.39 % Allowed : 15.97 % 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: 1.03 (0.24), residues: 1210 helix: 1.71 (0.18), residues: 814 sheet: 0.20 (0.48), residues: 50 loop : -1.79 (0.33), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 482 HIS 0.003 0.001 HIS C 656 PHE 0.019 0.002 PHE C 141 TYR 0.014 0.002 TYR D 556 ARG 0.003 0.000 ARG D 24 ********************** 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 143 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 118 time to evaluate : 1.230 Fit side-chains REVERT: C 79 ARG cc_start: 0.7172 (mtp180) cc_final: 0.6873 (mtp-110) REVERT: C 81 LYS cc_start: 0.7625 (mmpt) cc_final: 0.6977 (mmtm) REVERT: C 339 GLU cc_start: 0.7233 (OUTLIER) cc_final: 0.6814 (mp0) REVERT: C 678 MET cc_start: 0.7071 (mmt) cc_final: 0.6723 (mpm) REVERT: C 682 GLU cc_start: 0.7463 (mt-10) cc_final: 0.7174 (mp0) REVERT: C 684 GLN cc_start: 0.7854 (OUTLIER) cc_final: 0.7520 (tt0) REVERT: D 79 ARG cc_start: 0.7149 (mtp85) cc_final: 0.6912 (mtp-110) REVERT: D 81 LYS cc_start: 0.7620 (mmpt) cc_final: 0.6970 (mmtm) REVERT: D 678 MET cc_start: 0.7071 (mmt) cc_final: 0.6717 (mpm) REVERT: D 682 GLU cc_start: 0.7470 (mt-10) cc_final: 0.7176 (mp0) REVERT: D 684 GLN cc_start: 0.7860 (OUTLIER) cc_final: 0.7524 (tt0) outliers start: 25 outliers final: 17 residues processed: 135 average time/residue: 0.9083 time to fit residues: 136.1547 Evaluate side-chains 137 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 117 time to evaluate : 1.117 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 154 SER Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain C residue 339 GLU Chi-restraints excluded: chain C residue 347 SER Chi-restraints excluded: chain C residue 370 VAL Chi-restraints excluded: chain C residue 385 PHE Chi-restraints excluded: chain C residue 386 ILE 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 370 VAL Chi-restraints excluded: chain D residue 385 PHE Chi-restraints excluded: chain D residue 386 ILE 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 29 optimal weight: 0.7980 chunk 89 optimal weight: 4.9990 chunk 14 optimal weight: 0.9980 chunk 26 optimal weight: 9.9990 chunk 96 optimal weight: 0.9990 chunk 40 optimal weight: 0.0370 chunk 99 optimal weight: 0.6980 chunk 12 optimal weight: 1.9990 chunk 17 optimal weight: 2.9990 chunk 85 optimal weight: 0.3980 chunk 5 optimal weight: 0.6980 overall best weight: 0.5258 ------------------------------------------------------------------------------- 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 = 0.4089 r_free = 0.4089 target = 0.172272 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.139011 restraints weight = 12693.365| |-----------------------------------------------------------------------------| r_work (start): 0.3707 rms_B_bonded: 2.01 r_work: 0.3576 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.3440 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.3440 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7428 moved from start: 0.1914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10634 Z= 0.169 Angle : 0.624 8.114 14414 Z= 0.315 Chirality : 0.044 0.316 1760 Planarity : 0.005 0.076 1640 Dihedral : 13.535 161.314 2742 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 10.30 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.95 % Favored : 93.88 % Rotamer: Outliers : 1.82 % Allowed : 16.73 % Favored : 81.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.13 (0.25), residues: 1210 helix: 1.77 (0.18), residues: 822 sheet: 0.25 (0.49), residues: 50 loop : -1.81 (0.33), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 482 HIS 0.004 0.001 HIS D 656 PHE 0.019 0.001 PHE C 141 TYR 0.015 0.001 TYR C 556 ARG 0.003 0.000 ARG C 24 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3375.35 seconds wall clock time: 62 minutes 0.59 seconds (3720.59 seconds total)