Starting phenix.real_space_refine on Sun Aug 4 19:58:11 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wor_37696/08_2024/8wor_37696.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wor_37696/08_2024/8wor_37696.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.66 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wor_37696/08_2024/8wor_37696.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wor_37696/08_2024/8wor_37696.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wor_37696/08_2024/8wor_37696.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wor_37696/08_2024/8wor_37696.cif" } resolution = 2.66 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= 0.000 sd= 0.018 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 Ca 2 9.91 5 Zn 2 6.06 5 S 60 5.16 5 C 7539 2.51 5 N 1696 2.21 5 O 1919 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 188": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 275": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 509": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 722": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 732": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 116": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 148": "OD1" <-> "OD2" Residue "B TYR 188": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 207": "OE1" <-> "OE2" Residue "B TYR 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 275": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 590": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 605": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 11218 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 5261 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 647, 5252 Classifications: {'peptide': 647} Link IDs: {'CIS': 1, 'PCIS': 3, 'PTRANS': 22, 'TRANS': 620} Chain breaks: 4 Conformer: "B" Number of residues, atoms: 647, 5252 Classifications: {'peptide': 647} Link IDs: {'CIS': 1, 'PCIS': 3, 'PTRANS': 22, 'TRANS': 620} Chain breaks: 4 bond proxies already assigned to first conformer: 5384 Chain: "B" Number of atoms: 5261 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 647, 5252 Classifications: {'peptide': 647} Link IDs: {'CIS': 1, 'PCIS': 3, 'PTRANS': 22, 'TRANS': 620} Chain breaks: 4 Conformer: "B" Number of residues, atoms: 647, 5252 Classifications: {'peptide': 647} Link IDs: {'CIS': 1, 'PCIS': 3, 'PTRANS': 22, 'TRANS': 620} Chain breaks: 4 bond proxies already assigned to first conformer: 5384 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 276 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 276 Unusual residues: {' CA': 1, ' ZN': 1, 'CLR': 7, 'NAG': 2, 'OLA': 1, 'SPL': 1} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 304 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 304 Unusual residues: {' CA': 1, ' ZN': 1, 'CLR': 8, 'NAG': 2, 'OLA': 1, 'SPL': 1} Classifications: {'undetermined': 14} Link IDs: {None: 13} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Time building chain proxies: 11.52, per 1000 atoms: 1.03 Number of scatterers: 11218 At special positions: 0 Unit cell: (93.61, 89.355, 135.309, 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) Zn 2 29.99 Ca 2 19.99 S 60 16.00 O 1919 8.00 N 1696 7.00 C 7539 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS A 130 " - pdb=" SG CYS A 222 " distance=2.03 Simple disulfide: pdb=" SG CYS A 212 " - pdb=" SG CYS A 271 " distance=2.03 Simple disulfide: pdb=" SG CYS A 479 " - pdb=" SG CYS A 565 " distance=2.03 Simple disulfide: pdb=" SG CYS A 485 " - pdb=" SG CYS A 787 " distance=2.03 Simple disulfide: pdb=" SG CYS B 130 " - pdb=" SG CYS B 222 " distance=2.03 Simple disulfide: pdb=" SG CYS B 212 " - pdb=" SG CYS B 271 " distance=2.03 Simple disulfide: pdb=" SG CYS B 479 " - pdb=" SG CYS B 565 " distance=2.03 Simple disulfide: pdb=" SG CYS B 485 " - pdb=" SG CYS B 787 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " NAG-ASN " NAG A 903 " - " ASN A 67 " " NAG A 904 " - " ASN A 136 " " NAG B 903 " - " ASN B 67 " " NAG B 904 " - " ASN B 136 " " NAG C 1 " - " ASN A 57 " " NAG D 1 " - " ASN A 83 " " NAG E 1 " - " ASN B 57 " " NAG F 1 " - " ASN B 83 " Time building additional restraints: 4.41 Conformation dependent library (CDL) restraints added in 3.4 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 901 " pdb="ZN ZN A 901 " - pdb=" NE2 HIS A 563 " pdb="ZN ZN A 901 " - pdb=" NE2 HIS A 796 " pdb="ZN ZN A 901 " - pdb=" NE2 HIS A 800 " pdb=" ZN B 901 " pdb="ZN ZN B 901 " - pdb=" NE2 HIS B 563 " pdb="ZN ZN B 901 " - pdb=" NE2 HIS B 796 " pdb="ZN ZN B 901 " - pdb=" NE2 HIS B 800 " 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2492 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 10 sheets defined 49.9% alpha, 15.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.08 Creating SS restraints... Processing helix chain 'A' and resid 38 through 43 removed outlier: 4.270A pdb=" N ALA A 42 " --> pdb=" O ASP A 38 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 253 No H-bonds generated for 'chain 'A' and resid 251 through 253' Processing helix chain 'A' and resid 302 through 335 removed outlier: 3.841A pdb=" N TYR A 306 " --> pdb=" O LYS A 302 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N PHE A 317 " --> pdb=" O SER A 313 " (cutoff:3.500A) removed outlier: 4.606A pdb=" N PHE A 320 " --> pdb=" O ILE A 316 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N TYR A 321 " --> pdb=" O PHE A 317 " (cutoff:3.500A) Processing helix chain 'A' and resid 441 through 474 removed outlier: 4.024A pdb=" N ILE A 448 " --> pdb=" O TYR A 444 " (cutoff:3.500A) Proline residue: A 458 - end of helix Processing helix chain 'A' and resid 482 through 486 removed outlier: 3.948A pdb=" N ALA A 486 " --> pdb=" O PHE A 483 " (cutoff:3.500A) Processing helix chain 'A' and resid 495 through 500 Processing helix chain 'A' and resid 501 through 527 removed outlier: 3.842A pdb=" N VAL A 505 " --> pdb=" O ASN A 501 " (cutoff:3.500A) Processing helix chain 'A' and resid 541 through 563 Processing helix chain 'A' and resid 570 through 594 removed outlier: 4.204A pdb=" N ASP A 574 " --> pdb=" O ASN A 570 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N MET A 578 " --> pdb=" O ASP A 574 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N TYR A 579 " --> pdb=" O THR A 575 " (cutoff:3.500A) Processing helix chain 'A' and resid 602 through 621 removed outlier: 3.741A pdb=" N ALA A 606 " --> pdb=" O TYR A 602 " (cutoff:3.500A) Processing helix chain 'A' and resid 626 through 650 Processing helix chain 'A' and resid 686 through 709 Processing helix chain 'A' and resid 713 through 738 Processing helix chain 'A' and resid 745 through 767 removed outlier: 3.581A pdb=" N LEU A 749 " --> pdb=" O LEU A 745 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N PHE A 765 " --> pdb=" O ALA A 761 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N PHE A 767 " --> pdb=" O LEU A 763 " (cutoff:3.500A) Processing helix chain 'A' and resid 776 through 782 Processing helix chain 'A' and resid 788 through 792 removed outlier: 3.643A pdb=" N ASP A 791 " --> pdb=" O ILE A 788 " (cutoff:3.500A) Processing helix chain 'A' and resid 794 through 816 removed outlier: 3.520A pdb=" N ILE A 798 " --> pdb=" O ASP A 794 " (cutoff:3.500A) Processing helix chain 'A' and resid 819 through 824 Processing helix chain 'B' and resid 38 through 43 removed outlier: 4.202A pdb=" N ALA B 42 " --> pdb=" O ASP B 38 " (cutoff:3.500A) Processing helix chain 'B' and resid 251 through 253 No H-bonds generated for 'chain 'B' and resid 251 through 253' Processing helix chain 'B' and resid 302 through 335 removed outlier: 3.848A pdb=" N TYR B 306 " --> pdb=" O LYS B 302 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N PHE B 317 " --> pdb=" O SER B 313 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N PHE B 320 " --> pdb=" O ILE B 316 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N TYR B 321 " --> pdb=" O PHE B 317 " (cutoff:3.500A) Processing helix chain 'B' and resid 441 through 474 removed outlier: 4.014A pdb=" N ILE B 448 " --> pdb=" O TYR B 444 " (cutoff:3.500A) Proline residue: B 458 - end of helix Processing helix chain 'B' and resid 482 through 486 removed outlier: 3.933A pdb=" N ALA B 486 " --> pdb=" O PHE B 483 " (cutoff:3.500A) Processing helix chain 'B' and resid 495 through 500 Processing helix chain 'B' and resid 501 through 527 removed outlier: 3.860A pdb=" N VAL B 505 " --> pdb=" O ASN B 501 " (cutoff:3.500A) Processing helix chain 'B' and resid 541 through 563 Processing helix chain 'B' and resid 570 through 594 removed outlier: 4.205A pdb=" N ASP B 574 " --> pdb=" O ASN B 570 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N MET B 578 " --> pdb=" O ASP B 574 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N TYR B 579 " --> pdb=" O THR B 575 " (cutoff:3.500A) Processing helix chain 'B' and resid 602 through 621 removed outlier: 3.711A pdb=" N ALA B 606 " --> pdb=" O TYR B 602 " (cutoff:3.500A) Processing helix chain 'B' and resid 624 through 650 removed outlier: 3.547A pdb=" N PHE B 628 " --> pdb=" O ASN B 624 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N TRP B 629 " --> pdb=" O ASP B 625 " (cutoff:3.500A) Processing helix chain 'B' and resid 686 through 709 Processing helix chain 'B' and resid 713 through 738 Processing helix chain 'B' and resid 745 through 767 removed outlier: 3.563A pdb=" N LEU B 749 " --> pdb=" O LEU B 745 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N PHE B 765 " --> pdb=" O ALA B 761 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N PHE B 767 " --> pdb=" O LEU B 763 " (cutoff:3.500A) Processing helix chain 'B' and resid 776 through 782 Processing helix chain 'B' and resid 788 through 792 removed outlier: 3.635A pdb=" N ASP B 791 " --> pdb=" O ILE B 788 " (cutoff:3.500A) Processing helix chain 'B' and resid 794 through 816 removed outlier: 3.514A pdb=" N ILE B 798 " --> pdb=" O ASP B 794 " (cutoff:3.500A) Processing helix chain 'B' and resid 819 through 824 Processing sheet with id=AA1, first strand: chain 'A' and resid 44 through 45 Processing sheet with id=AA2, first strand: chain 'A' and resid 51 through 56 removed outlier: 4.478A pdb=" N VAL A 78 " --> pdb=" O LEU A 129 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 110 through 113 Processing sheet with id=AA4, first strand: chain 'A' and resid 177 through 181 Processing sheet with id=AA5, first strand: chain 'A' and resid 187 through 192 Processing sheet with id=AA6, first strand: chain 'B' and resid 44 through 45 Processing sheet with id=AA7, first strand: chain 'B' and resid 51 through 56 removed outlier: 4.449A pdb=" N VAL B 78 " --> pdb=" O LEU B 129 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 110 through 113 Processing sheet with id=AA9, first strand: chain 'B' and resid 177 through 181 Processing sheet with id=AB1, first strand: chain 'B' and resid 187 through 192 630 hydrogen bonds defined for protein. 1795 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: 3.27 Time building geometry restraints manager: 4.83 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3258 1.34 - 1.46: 2819 1.46 - 1.58: 5368 1.58 - 1.70: 2 1.70 - 1.82: 94 Bond restraints: 11541 Sorted by residual: bond pdb=" C10 OLA A 911 " pdb=" C9 OLA A 911 " ideal model delta sigma weight residual 1.332 1.468 -0.136 2.00e-02 2.50e+03 4.64e+01 bond pdb=" C10 OLA B 914 " pdb=" C9 OLA B 914 " ideal model delta sigma weight residual 1.332 1.468 -0.136 2.00e-02 2.50e+03 4.60e+01 bond pdb=" CB PRO B 748 " pdb=" CG PRO B 748 " ideal model delta sigma weight residual 1.492 1.589 -0.097 5.00e-02 4.00e+02 3.79e+00 bond pdb=" CB PRO A 748 " pdb=" CG PRO A 748 " ideal model delta sigma weight residual 1.492 1.585 -0.093 5.00e-02 4.00e+02 3.43e+00 bond pdb=" C1 OLA A 911 " pdb=" C2 OLA A 911 " ideal model delta sigma weight residual 1.542 1.510 0.032 2.00e-02 2.50e+03 2.60e+00 ... (remaining 11536 not shown) Histogram of bond angle deviations from ideal: 97.20 - 105.30: 253 105.30 - 113.40: 6546 113.40 - 121.51: 6525 121.51 - 129.61: 2362 129.61 - 137.71: 62 Bond angle restraints: 15748 Sorted by residual: angle pdb=" CA LEU B 728 " pdb=" CB LEU B 728 " pdb=" CG LEU B 728 " ideal model delta sigma weight residual 116.30 137.71 -21.41 3.50e+00 8.16e-02 3.74e+01 angle pdb=" CA PRO B 748 " pdb=" N PRO B 748 " pdb=" CD PRO B 748 " ideal model delta sigma weight residual 112.00 104.60 7.40 1.40e+00 5.10e-01 2.79e+01 angle pdb=" CA LEU A 728 " pdb=" CB LEU A 728 " pdb=" CG LEU A 728 " ideal model delta sigma weight residual 116.30 134.47 -18.17 3.50e+00 8.16e-02 2.70e+01 angle pdb=" CA PRO A 748 " pdb=" N PRO A 748 " pdb=" CD PRO A 748 " ideal model delta sigma weight residual 112.00 105.37 6.63 1.40e+00 5.10e-01 2.24e+01 angle pdb=" C ILE B 612 " pdb=" N MET B 613 " pdb=" CA MET B 613 " ideal model delta sigma weight residual 120.72 114.17 6.55 1.67e+00 3.59e-01 1.54e+01 ... (remaining 15743 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.36: 6563 17.36 - 34.73: 800 34.73 - 52.09: 223 52.09 - 69.45: 57 69.45 - 86.82: 8 Dihedral angle restraints: 7651 sinusoidal: 3791 harmonic: 3860 Sorted by residual: dihedral pdb=" CA TYR B 210 " pdb=" C TYR B 210 " pdb=" N PRO B 211 " pdb=" CA PRO B 211 " ideal model delta harmonic sigma weight residual 0.00 20.33 -20.33 0 5.00e+00 4.00e-02 1.65e+01 dihedral pdb=" CA TYR A 210 " pdb=" C TYR A 210 " pdb=" N PRO A 211 " pdb=" CA PRO A 211 " ideal model delta harmonic sigma weight residual 0.00 20.20 -20.20 0 5.00e+00 4.00e-02 1.63e+01 dihedral pdb=" CA CYS A 787 " pdb=" C CYS A 787 " pdb=" N ILE A 788 " pdb=" CA ILE A 788 " ideal model delta harmonic sigma weight residual 180.00 -161.15 -18.85 0 5.00e+00 4.00e-02 1.42e+01 ... (remaining 7648 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 1583 0.057 - 0.115: 232 0.115 - 0.172: 21 0.172 - 0.229: 2 0.229 - 0.287: 2 Chirality restraints: 1840 Sorted by residual: chirality pdb=" C1 NAG E 1 " pdb=" ND2 ASN B 57 " pdb=" C2 NAG E 1 " pdb=" O5 NAG E 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.11 -0.29 2.00e-01 2.50e+01 2.06e+00 chirality pdb=" C1 NAG C 1 " pdb=" ND2 ASN A 57 " pdb=" C2 NAG C 1 " pdb=" O5 NAG C 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.13 -0.27 2.00e-01 2.50e+01 1.88e+00 chirality pdb=" CA MET A 613 " pdb=" N MET A 613 " pdb=" C MET A 613 " pdb=" CB MET A 613 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 8.66e-01 ... (remaining 1837 not shown) Planarity restraints: 1858 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C10 OLA A 911 " -0.185 2.00e-02 2.50e+03 1.44e-01 2.08e+02 pdb=" C11 OLA A 911 " 0.085 2.00e-02 2.50e+03 pdb=" C8 OLA A 911 " -0.085 2.00e-02 2.50e+03 pdb=" C9 OLA A 911 " 0.186 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C10 OLA B 914 " 0.185 2.00e-02 2.50e+03 1.44e-01 2.08e+02 pdb=" C11 OLA B 914 " -0.085 2.00e-02 2.50e+03 pdb=" C8 OLA B 914 " 0.085 2.00e-02 2.50e+03 pdb=" C9 OLA B 914 " -0.185 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL A 747 " 0.082 5.00e-02 4.00e+02 1.21e-01 2.34e+01 pdb=" N PRO A 748 " -0.209 5.00e-02 4.00e+02 pdb=" CA PRO A 748 " 0.062 5.00e-02 4.00e+02 pdb=" CD PRO A 748 " 0.065 5.00e-02 4.00e+02 ... (remaining 1855 not shown) Histogram of nonbonded interaction distances: 1.93 - 2.52: 61 2.52 - 3.12: 8574 3.12 - 3.71: 16133 3.71 - 4.31: 22955 4.31 - 4.90: 39543 Nonbonded interactions: 87266 Sorted by model distance: nonbonded pdb="ZN ZN A 901 " pdb=" O HOH A1001 " model vdw 1.928 2.230 nonbonded pdb="ZN ZN B 901 " pdb=" O HOH B1001 " model vdw 1.928 2.230 nonbonded pdb=" OH TYR A 64 " pdb=" OH TYR A 159 " model vdw 2.080 3.040 nonbonded pdb=" OH TYR B 64 " pdb=" OH TYR B 159 " model vdw 2.085 3.040 nonbonded pdb=" O ASN B 598 " pdb=" OH TYR B 602 " model vdw 2.193 3.040 ... (remaining 87261 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 'A' and (resid 35 through 80 or resid 82 through 830 or resid 901 through \ 906 or resid 908 through 910 or resid 913)) selection = (chain 'B' and (resid 35 through 80 or resid 82 through 830 or resid 901 through \ 906 or resid 908 through 910 or resid 913)) } ncs_group { reference = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } 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=0.21 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: 2.030 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.460 Check model and map are aligned: 0.080 Set scattering table: 0.130 Process input model: 39.800 Find NCS groups from input model: 0.510 Set up NCS constraints: 0.070 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:9.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 53.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7484 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 0.136 11541 Z= 0.245 Angle : 0.636 21.410 15748 Z= 0.307 Chirality : 0.041 0.287 1840 Planarity : 0.007 0.144 1850 Dihedral : 15.745 86.815 5135 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 22.33 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.45 % Favored : 96.39 % Rotamer: Outliers : 5.08 % Allowed : 27.19 % Favored : 67.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.16 % 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: 1.60 (0.24), residues: 1276 helix: 2.90 (0.21), residues: 590 sheet: 1.34 (0.30), residues: 272 loop : -2.08 (0.27), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 446 HIS 0.004 0.001 HIS A 636 PHE 0.038 0.001 PHE A 732 TYR 0.011 0.001 TYR B 188 ARG 0.001 0.000 ARG B 593 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1158 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 116 time to evaluate : 1.141 Fit side-chains revert: symmetry clash REVERT: A 117 GLN cc_start: 0.8957 (mm-40) cc_final: 0.8744 (mp10) REVERT: A 158 GLN cc_start: 0.8522 (mt0) cc_final: 0.8296 (mt0) REVERT: A 554 MET cc_start: 0.7669 (tpp) cc_final: 0.7331 (mmm) REVERT: B 117 GLN cc_start: 0.9001 (mm-40) cc_final: 0.8797 (mp10) REVERT: B 554 MET cc_start: 0.7676 (tpp) cc_final: 0.7338 (mmm) REVERT: B 650 MET cc_start: 0.2997 (tpt) cc_final: 0.2770 (tpt) REVERT: B 686 MET cc_start: 0.5258 (mmt) cc_final: 0.4300 (pmm) REVERT: B 718 MET cc_start: 0.8145 (ttp) cc_final: 0.7940 (ttm) outliers start: 59 outliers final: 47 residues processed: 170 average time/residue: 0.8272 time to fit residues: 157.8904 Evaluate side-chains 160 residues out of total 1158 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 113 time to evaluate : 1.131 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 296 THR Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 318 LEU Chi-restraints excluded: chain A residue 319 SER Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 472 VAL Chi-restraints excluded: chain A residue 521 LEU Chi-restraints excluded: chain A residue 541 HIS Chi-restraints excluded: chain A residue 559 SER Chi-restraints excluded: chain A residue 569 SER Chi-restraints excluded: chain A residue 572 GLN Chi-restraints excluded: chain A residue 589 LEU Chi-restraints excluded: chain A residue 735 ILE Chi-restraints excluded: chain A residue 755 THR Chi-restraints excluded: chain A residue 763 LEU Chi-restraints excluded: chain B residue 60 THR Chi-restraints excluded: chain B residue 76 THR Chi-restraints excluded: chain B residue 196 ASP Chi-restraints excluded: chain B residue 220 ILE Chi-restraints excluded: chain B residue 257 GLN Chi-restraints excluded: chain B residue 260 VAL Chi-restraints excluded: chain B residue 287 LEU Chi-restraints excluded: chain B residue 296 THR Chi-restraints excluded: chain B residue 309 SER Chi-restraints excluded: chain B residue 314 VAL Chi-restraints excluded: chain B residue 319 SER Chi-restraints excluded: chain B residue 324 CYS Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 470 VAL Chi-restraints excluded: chain B residue 472 VAL Chi-restraints excluded: chain B residue 520 ILE Chi-restraints excluded: chain B residue 521 LEU Chi-restraints excluded: chain B residue 541 HIS Chi-restraints excluded: chain B residue 569 SER Chi-restraints excluded: chain B residue 572 GLN Chi-restraints excluded: chain B residue 587 LEU Chi-restraints excluded: chain B residue 589 LEU Chi-restraints excluded: chain B residue 615 THR Chi-restraints excluded: chain B residue 735 ILE Chi-restraints excluded: chain B residue 755 THR Chi-restraints excluded: chain B residue 763 LEU Chi-restraints excluded: chain B residue 813 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 108 optimal weight: 7.9990 chunk 97 optimal weight: 0.6980 chunk 53 optimal weight: 0.8980 chunk 33 optimal weight: 0.8980 chunk 65 optimal weight: 2.9990 chunk 51 optimal weight: 10.0000 chunk 100 optimal weight: 3.9990 chunk 38 optimal weight: 6.9990 chunk 61 optimal weight: 4.9990 chunk 74 optimal weight: 5.9990 chunk 116 optimal weight: 3.9990 overall best weight: 1.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 90 ASN A 123 GLN A 142 GLN ** A 725 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 769 ASN B 71 GLN B 90 ASN B 142 GLN B 286 ASN ** B 725 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 769 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7541 moved from start: 0.0893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 11541 Z= 0.368 Angle : 0.770 18.732 15748 Z= 0.369 Chirality : 0.048 0.301 1840 Planarity : 0.005 0.075 1850 Dihedral : 9.692 59.766 2800 Min Nonbonded Distance : 1.863 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.08 % Favored : 95.76 % Rotamer: Outliers : 5.94 % Allowed : 26.08 % Favored : 67.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.16 % 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 (0.23), residues: 1276 helix: 2.40 (0.21), residues: 590 sheet: 1.30 (0.29), residues: 274 loop : -2.05 (0.27), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP A 627 HIS 0.007 0.001 HIS B 636 PHE 0.016 0.002 PHE A 722 TYR 0.017 0.002 TYR B 188 ARG 0.004 0.001 ARG A 289 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1158 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 116 time to evaluate : 1.113 Fit side-chains REVERT: A 158 GLN cc_start: 0.8535 (mt0) cc_final: 0.8313 (mt0) REVERT: A 554 MET cc_start: 0.7610 (tpp) cc_final: 0.7318 (mmm) REVERT: A 594 HIS cc_start: 0.6581 (OUTLIER) cc_final: 0.6068 (m90) REVERT: A 686 MET cc_start: 0.5205 (mmt) cc_final: 0.4515 (mpt) REVERT: A 736 MET cc_start: 0.7187 (tmm) cc_final: 0.6943 (mmm) REVERT: B 117 GLN cc_start: 0.9016 (mm-40) cc_final: 0.8806 (mp10) REVERT: B 289 ARG cc_start: 0.8997 (OUTLIER) cc_final: 0.8753 (mtm180) REVERT: B 554 MET cc_start: 0.7628 (tpp) cc_final: 0.7331 (mmm) REVERT: B 605 TYR cc_start: 0.3758 (OUTLIER) cc_final: 0.3501 (p90) REVERT: B 686 MET cc_start: 0.5200 (mmt) cc_final: 0.4294 (pmm) REVERT: B 712 ARG cc_start: 0.5086 (mpt180) cc_final: 0.4221 (mpp80) outliers start: 69 outliers final: 32 residues processed: 173 average time/residue: 0.8581 time to fit residues: 166.2660 Evaluate side-chains 149 residues out of total 1158 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 114 time to evaluate : 1.167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 220 ILE Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 296 THR Chi-restraints excluded: chain A residue 309 SER Chi-restraints excluded: chain A residue 521 LEU Chi-restraints excluded: chain A residue 544 LEU Chi-restraints excluded: chain A residue 559 SER Chi-restraints excluded: chain A residue 572 GLN Chi-restraints excluded: chain A residue 594 HIS Chi-restraints excluded: chain A residue 597 ILE Chi-restraints excluded: chain A residue 727 LEU Chi-restraints excluded: chain A residue 735 ILE Chi-restraints excluded: chain A residue 763 LEU Chi-restraints excluded: chain B residue 76 THR Chi-restraints excluded: chain B residue 119 SER Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 220 ILE Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 260 VAL Chi-restraints excluded: chain B residue 286 ASN Chi-restraints excluded: chain B residue 287 LEU Chi-restraints excluded: chain B residue 289 ARG Chi-restraints excluded: chain B residue 296 THR Chi-restraints excluded: chain B residue 521 LEU Chi-restraints excluded: chain B residue 572 GLN Chi-restraints excluded: chain B residue 587 LEU Chi-restraints excluded: chain B residue 605 TYR Chi-restraints excluded: chain B residue 617 LEU Chi-restraints excluded: chain B residue 725 ASN Chi-restraints excluded: chain B residue 727 LEU Chi-restraints excluded: chain B residue 735 ILE Chi-restraints excluded: chain B residue 763 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 64 optimal weight: 9.9990 chunk 36 optimal weight: 0.4980 chunk 96 optimal weight: 0.7980 chunk 79 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 116 optimal weight: 10.0000 chunk 125 optimal weight: 1.9990 chunk 103 optimal weight: 4.9990 chunk 115 optimal weight: 6.9990 chunk 39 optimal weight: 4.9990 chunk 93 optimal weight: 20.0000 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 90 ASN ** A 725 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 769 ASN B 90 ASN B 142 GLN B 286 ASN ** B 725 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 769 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7532 moved from start: 0.1097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 11541 Z= 0.294 Angle : 0.724 18.574 15748 Z= 0.347 Chirality : 0.046 0.273 1840 Planarity : 0.005 0.067 1850 Dihedral : 8.836 59.870 2760 Min Nonbonded Distance : 1.905 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.32 % Favored : 95.60 % Rotamer: Outliers : 4.91 % Allowed : 26.59 % Favored : 68.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.16 % 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: 1.14 (0.23), residues: 1276 helix: 2.26 (0.21), residues: 590 sheet: 1.34 (0.29), residues: 274 loop : -2.07 (0.27), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 629 HIS 0.006 0.001 HIS B 636 PHE 0.026 0.002 PHE B 628 TYR 0.016 0.001 TYR A 188 ARG 0.003 0.000 ARG A 593 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1158 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 111 time to evaluate : 1.219 Fit side-chains REVERT: A 158 GLN cc_start: 0.8537 (mt0) cc_final: 0.8311 (mt0) REVERT: A 554 MET cc_start: 0.7540 (tpp) cc_final: 0.7226 (mmm) REVERT: A 594 HIS cc_start: 0.6682 (OUTLIER) cc_final: 0.6155 (m90) REVERT: A 686 MET cc_start: 0.5139 (mmt) cc_final: 0.4461 (mpt) REVERT: A 736 MET cc_start: 0.7144 (tmm) cc_final: 0.6829 (mmm) REVERT: A 781 ARG cc_start: 0.8187 (OUTLIER) cc_final: 0.7688 (mtm-85) REVERT: B 289 ARG cc_start: 0.8980 (OUTLIER) cc_final: 0.8730 (mtm180) REVERT: B 461 GLN cc_start: 0.8066 (OUTLIER) cc_final: 0.7838 (mt0) REVERT: B 554 MET cc_start: 0.7616 (tpp) cc_final: 0.7335 (mmm) REVERT: B 559 SER cc_start: 0.8260 (OUTLIER) cc_final: 0.7872 (p) REVERT: B 686 MET cc_start: 0.5176 (mmt) cc_final: 0.4309 (pmm) REVERT: B 712 ARG cc_start: 0.4903 (mpt180) cc_final: 0.4180 (mpp80) REVERT: B 781 ARG cc_start: 0.8197 (OUTLIER) cc_final: 0.7533 (mtm-85) outliers start: 57 outliers final: 35 residues processed: 160 average time/residue: 0.8802 time to fit residues: 156.8140 Evaluate side-chains 153 residues out of total 1158 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 112 time to evaluate : 1.140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 220 ILE Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 296 THR Chi-restraints excluded: chain A residue 457 LEU Chi-restraints excluded: chain A residue 521 LEU Chi-restraints excluded: chain A residue 559 SER Chi-restraints excluded: chain A residue 572 GLN Chi-restraints excluded: chain A residue 590 TYR Chi-restraints excluded: chain A residue 594 HIS Chi-restraints excluded: chain A residue 597 ILE Chi-restraints excluded: chain A residue 725 ASN Chi-restraints excluded: chain A residue 727 LEU Chi-restraints excluded: chain A residue 735 ILE Chi-restraints excluded: chain A residue 763 LEU Chi-restraints excluded: chain A residue 781 ARG Chi-restraints excluded: chain B residue 76 THR Chi-restraints excluded: chain B residue 119 SER Chi-restraints excluded: chain B residue 135 THR Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 220 ILE Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 260 VAL Chi-restraints excluded: chain B residue 289 ARG Chi-restraints excluded: chain B residue 296 THR Chi-restraints excluded: chain B residue 324 CYS Chi-restraints excluded: chain B residue 457 LEU Chi-restraints excluded: chain B residue 461 GLN Chi-restraints excluded: chain B residue 521 LEU Chi-restraints excluded: chain B residue 559 SER Chi-restraints excluded: chain B residue 572 GLN Chi-restraints excluded: chain B residue 587 LEU Chi-restraints excluded: chain B residue 605 TYR Chi-restraints excluded: chain B residue 617 LEU Chi-restraints excluded: chain B residue 626 VAL Chi-restraints excluded: chain B residue 704 LEU Chi-restraints excluded: chain B residue 725 ASN Chi-restraints excluded: chain B residue 727 LEU Chi-restraints excluded: chain B residue 735 ILE Chi-restraints excluded: chain B residue 763 LEU Chi-restraints excluded: chain B residue 781 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 115 optimal weight: 5.9990 chunk 87 optimal weight: 0.6980 chunk 60 optimal weight: 1.9990 chunk 12 optimal weight: 0.9980 chunk 55 optimal weight: 0.9990 chunk 78 optimal weight: 0.9980 chunk 116 optimal weight: 5.9990 chunk 123 optimal weight: 2.9990 chunk 61 optimal weight: 3.9990 chunk 110 optimal weight: 0.8980 chunk 33 optimal weight: 1.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 71 GLN A 74 GLN A 90 ASN A 288 GLN ** A 725 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 769 ASN B 71 GLN B 74 GLN B 90 ASN B 142 GLN B 286 ASN B 725 ASN B 769 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7512 moved from start: 0.1186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 11541 Z= 0.219 Angle : 0.687 18.031 15748 Z= 0.327 Chirality : 0.044 0.286 1840 Planarity : 0.004 0.062 1850 Dihedral : 8.364 59.654 2758 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 4.65 % Allowed : 26.25 % Favored : 69.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.16 % 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 (0.23), residues: 1276 helix: 2.30 (0.21), residues: 590 sheet: 1.41 (0.29), residues: 274 loop : -2.04 (0.27), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 629 HIS 0.005 0.001 HIS B 636 PHE 0.015 0.001 PHE B 628 TYR 0.014 0.001 TYR A 188 ARG 0.003 0.000 ARG A 781 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1158 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 113 time to evaluate : 1.134 Fit side-chains REVERT: A 113 GLN cc_start: 0.8561 (mm-40) cc_final: 0.8298 (mm-40) REVERT: A 158 GLN cc_start: 0.8516 (mt0) cc_final: 0.8284 (mt0) REVERT: A 554 MET cc_start: 0.7500 (tpp) cc_final: 0.7213 (mmm) REVERT: A 590 TYR cc_start: 0.6035 (OUTLIER) cc_final: 0.5634 (t80) REVERT: A 650 MET cc_start: 0.3262 (OUTLIER) cc_final: 0.3055 (tpt) REVERT: A 736 MET cc_start: 0.7093 (tmm) cc_final: 0.6822 (tpp) REVERT: A 781 ARG cc_start: 0.8167 (OUTLIER) cc_final: 0.7676 (mtm-85) REVERT: B 289 ARG cc_start: 0.8901 (OUTLIER) cc_final: 0.8607 (mtm180) REVERT: B 461 GLN cc_start: 0.8039 (OUTLIER) cc_final: 0.7825 (mt0) REVERT: B 554 MET cc_start: 0.7524 (tpp) cc_final: 0.7267 (mmm) REVERT: B 586 MET cc_start: 0.7360 (tmm) cc_final: 0.7126 (tmt) REVERT: B 587 LEU cc_start: 0.7697 (OUTLIER) cc_final: 0.7470 (mp) REVERT: B 686 MET cc_start: 0.5111 (mmt) cc_final: 0.4230 (pmm) REVERT: B 781 ARG cc_start: 0.8170 (OUTLIER) cc_final: 0.7626 (ttm110) outliers start: 54 outliers final: 31 residues processed: 157 average time/residue: 0.9660 time to fit residues: 167.6597 Evaluate side-chains 146 residues out of total 1158 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 108 time to evaluate : 1.165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 119 SER Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 220 ILE Chi-restraints excluded: chain A residue 457 LEU Chi-restraints excluded: chain A residue 521 LEU Chi-restraints excluded: chain A residue 544 LEU Chi-restraints excluded: chain A residue 559 SER Chi-restraints excluded: chain A residue 572 GLN Chi-restraints excluded: chain A residue 590 TYR Chi-restraints excluded: chain A residue 597 ILE Chi-restraints excluded: chain A residue 650 MET Chi-restraints excluded: chain A residue 725 ASN Chi-restraints excluded: chain A residue 727 LEU Chi-restraints excluded: chain A residue 735 ILE Chi-restraints excluded: chain A residue 763 LEU Chi-restraints excluded: chain A residue 781 ARG Chi-restraints excluded: chain B residue 76 THR Chi-restraints excluded: chain B residue 119 SER Chi-restraints excluded: chain B residue 135 THR Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 220 ILE Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 289 ARG Chi-restraints excluded: chain B residue 324 CYS Chi-restraints excluded: chain B residue 457 LEU Chi-restraints excluded: chain B residue 461 GLN Chi-restraints excluded: chain B residue 572 GLN Chi-restraints excluded: chain B residue 587 LEU Chi-restraints excluded: chain B residue 605 TYR Chi-restraints excluded: chain B residue 617 LEU Chi-restraints excluded: chain B residue 626 VAL Chi-restraints excluded: chain B residue 704 LEU Chi-restraints excluded: chain B residue 727 LEU Chi-restraints excluded: chain B residue 735 ILE Chi-restraints excluded: chain B residue 763 LEU Chi-restraints excluded: chain B residue 781 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 103 optimal weight: 3.9990 chunk 70 optimal weight: 0.0970 chunk 1 optimal weight: 4.9990 chunk 92 optimal weight: 4.9990 chunk 51 optimal weight: 5.9990 chunk 105 optimal weight: 0.0010 chunk 85 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 63 optimal weight: 3.9990 chunk 111 optimal weight: 7.9990 chunk 31 optimal weight: 3.9990 overall best weight: 1.8190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 74 GLN A 90 ASN A 142 GLN ** A 725 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 769 ASN B 71 GLN B 74 GLN B 90 ASN B 286 ASN B 725 ASN B 769 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7541 moved from start: 0.1313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 11541 Z= 0.346 Angle : 0.736 18.627 15748 Z= 0.356 Chirality : 0.047 0.279 1840 Planarity : 0.005 0.063 1850 Dihedral : 8.277 59.967 2752 Min Nonbonded Distance : 1.862 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 4.82 % Allowed : 26.33 % Favored : 68.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.16 % 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: 1.05 (0.23), residues: 1276 helix: 2.18 (0.21), residues: 590 sheet: 1.37 (0.29), residues: 274 loop : -2.15 (0.27), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP B 629 HIS 0.005 0.001 HIS B 636 PHE 0.014 0.002 PHE B 454 TYR 0.017 0.001 TYR A 188 ARG 0.003 0.000 ARG A 37 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1158 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 107 time to evaluate : 1.064 Fit side-chains REVERT: A 158 GLN cc_start: 0.8526 (mt0) cc_final: 0.8284 (mt0) REVERT: A 554 MET cc_start: 0.7539 (tpp) cc_final: 0.7283 (mmm) REVERT: A 736 MET cc_start: 0.7105 (tmm) cc_final: 0.6809 (tpp) REVERT: A 781 ARG cc_start: 0.8196 (OUTLIER) cc_final: 0.7680 (ttm110) REVERT: B 461 GLN cc_start: 0.8069 (OUTLIER) cc_final: 0.7849 (mt0) REVERT: B 554 MET cc_start: 0.7624 (tpp) cc_final: 0.7363 (mmm) REVERT: B 559 SER cc_start: 0.8230 (OUTLIER) cc_final: 0.7835 (p) REVERT: B 587 LEU cc_start: 0.7714 (OUTLIER) cc_final: 0.7463 (mp) REVERT: B 686 MET cc_start: 0.5157 (mmt) cc_final: 0.4297 (pmm) REVERT: B 781 ARG cc_start: 0.8196 (OUTLIER) cc_final: 0.7691 (mtm-85) outliers start: 56 outliers final: 37 residues processed: 154 average time/residue: 0.8974 time to fit residues: 154.0323 Evaluate side-chains 147 residues out of total 1158 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 105 time to evaluate : 1.044 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 119 SER Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 220 ILE Chi-restraints excluded: chain A residue 296 THR Chi-restraints excluded: chain A residue 309 SER Chi-restraints excluded: chain A residue 544 LEU Chi-restraints excluded: chain A residue 559 SER Chi-restraints excluded: chain A residue 572 GLN Chi-restraints excluded: chain A residue 590 TYR Chi-restraints excluded: chain A residue 597 ILE Chi-restraints excluded: chain A residue 650 MET Chi-restraints excluded: chain A residue 725 ASN Chi-restraints excluded: chain A residue 727 LEU Chi-restraints excluded: chain A residue 735 ILE Chi-restraints excluded: chain A residue 763 LEU Chi-restraints excluded: chain A residue 781 ARG Chi-restraints excluded: chain A residue 787 CYS Chi-restraints excluded: chain B residue 76 THR Chi-restraints excluded: chain B residue 119 SER Chi-restraints excluded: chain B residue 135 THR Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 220 ILE Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 286 ASN Chi-restraints excluded: chain B residue 296 THR Chi-restraints excluded: chain B residue 324 CYS Chi-restraints excluded: chain B residue 461 GLN Chi-restraints excluded: chain B residue 544 LEU Chi-restraints excluded: chain B residue 559 SER Chi-restraints excluded: chain B residue 572 GLN Chi-restraints excluded: chain B residue 587 LEU Chi-restraints excluded: chain B residue 605 TYR Chi-restraints excluded: chain B residue 617 LEU Chi-restraints excluded: chain B residue 704 LEU Chi-restraints excluded: chain B residue 727 LEU Chi-restraints excluded: chain B residue 735 ILE Chi-restraints excluded: chain B residue 763 LEU Chi-restraints excluded: chain B residue 781 ARG Chi-restraints excluded: chain B residue 787 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 41 optimal weight: 0.5980 chunk 111 optimal weight: 9.9990 chunk 24 optimal weight: 7.9990 chunk 72 optimal weight: 0.6980 chunk 30 optimal weight: 10.0000 chunk 123 optimal weight: 0.8980 chunk 102 optimal weight: 3.9990 chunk 57 optimal weight: 2.9990 chunk 10 optimal weight: 8.9990 chunk 40 optimal weight: 2.9990 chunk 65 optimal weight: 0.8980 overall best weight: 1.2182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 71 GLN A 74 GLN A 90 ASN A 288 GLN ** A 725 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 769 ASN B 71 GLN B 74 GLN B 90 ASN B 142 GLN B 286 ASN B 725 ASN B 769 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7525 moved from start: 0.1312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 11541 Z= 0.255 Angle : 0.703 18.745 15748 Z= 0.337 Chirality : 0.045 0.281 1840 Planarity : 0.004 0.060 1850 Dihedral : 8.028 59.576 2750 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 5.42 % Allowed : 25.22 % Favored : 69.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.16 % 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: 1.11 (0.23), residues: 1276 helix: 2.37 (0.21), residues: 578 sheet: 1.41 (0.29), residues: 274 loop : -2.24 (0.26), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 629 HIS 0.005 0.001 HIS B 636 PHE 0.015 0.001 PHE B 732 TYR 0.015 0.001 TYR A 188 ARG 0.004 0.000 ARG B 289 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1158 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 110 time to evaluate : 1.226 Fit side-chains REVERT: A 113 GLN cc_start: 0.8567 (mm-40) cc_final: 0.8306 (mm-40) REVERT: A 158 GLN cc_start: 0.8523 (mt0) cc_final: 0.8278 (mt0) REVERT: A 554 MET cc_start: 0.7527 (tpp) cc_final: 0.7273 (mmm) REVERT: A 605 TYR cc_start: 0.3640 (OUTLIER) cc_final: 0.3433 (p90) REVERT: A 736 MET cc_start: 0.7080 (tmm) cc_final: 0.6794 (tpp) REVERT: A 781 ARG cc_start: 0.8184 (OUTLIER) cc_final: 0.7661 (ttm110) REVERT: B 461 GLN cc_start: 0.8054 (OUTLIER) cc_final: 0.7827 (mt0) REVERT: B 554 MET cc_start: 0.7553 (tpp) cc_final: 0.7283 (mmm) REVERT: B 559 SER cc_start: 0.8249 (OUTLIER) cc_final: 0.7870 (p) REVERT: B 590 TYR cc_start: 0.6221 (OUTLIER) cc_final: 0.5852 (t80) REVERT: B 686 MET cc_start: 0.5128 (mmt) cc_final: 0.4262 (pmm) REVERT: B 781 ARG cc_start: 0.8188 (OUTLIER) cc_final: 0.7653 (ttm110) outliers start: 63 outliers final: 40 residues processed: 161 average time/residue: 0.9040 time to fit residues: 161.4733 Evaluate side-chains 153 residues out of total 1158 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 107 time to evaluate : 1.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 119 SER Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 220 ILE Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 296 THR Chi-restraints excluded: chain A residue 457 LEU Chi-restraints excluded: chain A residue 472 VAL Chi-restraints excluded: chain A residue 544 LEU Chi-restraints excluded: chain A residue 559 SER Chi-restraints excluded: chain A residue 572 GLN Chi-restraints excluded: chain A residue 590 TYR Chi-restraints excluded: chain A residue 597 ILE Chi-restraints excluded: chain A residue 605 TYR Chi-restraints excluded: chain A residue 725 ASN Chi-restraints excluded: chain A residue 727 LEU Chi-restraints excluded: chain A residue 735 ILE Chi-restraints excluded: chain A residue 763 LEU Chi-restraints excluded: chain A residue 781 ARG Chi-restraints excluded: chain A residue 787 CYS Chi-restraints excluded: chain A residue 814 LEU Chi-restraints excluded: chain B residue 76 THR Chi-restraints excluded: chain B residue 119 SER Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 220 ILE Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 260 VAL Chi-restraints excluded: chain B residue 296 THR Chi-restraints excluded: chain B residue 309 SER Chi-restraints excluded: chain B residue 324 CYS Chi-restraints excluded: chain B residue 457 LEU Chi-restraints excluded: chain B residue 461 GLN Chi-restraints excluded: chain B residue 544 LEU Chi-restraints excluded: chain B residue 559 SER Chi-restraints excluded: chain B residue 572 GLN Chi-restraints excluded: chain B residue 590 TYR Chi-restraints excluded: chain B residue 597 ILE Chi-restraints excluded: chain B residue 605 TYR Chi-restraints excluded: chain B residue 617 LEU Chi-restraints excluded: chain B residue 704 LEU Chi-restraints excluded: chain B residue 727 LEU Chi-restraints excluded: chain B residue 735 ILE Chi-restraints excluded: chain B residue 763 LEU Chi-restraints excluded: chain B residue 781 ARG Chi-restraints excluded: chain B residue 787 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 119 optimal weight: 1.9990 chunk 13 optimal weight: 2.9990 chunk 70 optimal weight: 3.9990 chunk 90 optimal weight: 0.9980 chunk 104 optimal weight: 4.9990 chunk 69 optimal weight: 0.9990 chunk 123 optimal weight: 0.0770 chunk 77 optimal weight: 0.8980 chunk 75 optimal weight: 1.9990 chunk 56 optimal weight: 0.0980 chunk 76 optimal weight: 1.9990 overall best weight: 0.6140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 74 GLN A 90 ASN A 142 GLN A 288 GLN ** A 725 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 769 ASN B 74 GLN B 90 ASN B 142 GLN B 286 ASN B 725 ASN B 769 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7490 moved from start: 0.1426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 11541 Z= 0.177 Angle : 0.663 17.005 15748 Z= 0.316 Chirality : 0.043 0.288 1840 Planarity : 0.004 0.057 1850 Dihedral : 7.592 59.520 2748 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 4.04 % Allowed : 26.94 % Favored : 69.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.16 % 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 (0.23), residues: 1276 helix: 2.47 (0.21), residues: 578 sheet: 1.48 (0.29), residues: 274 loop : -2.20 (0.26), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 629 HIS 0.004 0.001 HIS A 636 PHE 0.015 0.001 PHE B 732 TYR 0.012 0.001 TYR A 188 ARG 0.003 0.000 ARG A 781 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1158 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 111 time to evaluate : 1.200 Fit side-chains REVERT: A 158 GLN cc_start: 0.8519 (mt0) cc_final: 0.8275 (mt0) REVERT: A 554 MET cc_start: 0.7542 (tpp) cc_final: 0.7269 (mmm) REVERT: A 590 TYR cc_start: 0.6160 (OUTLIER) cc_final: 0.5665 (t80) REVERT: A 605 TYR cc_start: 0.3710 (OUTLIER) cc_final: 0.3484 (p90) REVERT: A 736 MET cc_start: 0.6965 (tmm) cc_final: 0.6707 (tpp) REVERT: A 781 ARG cc_start: 0.8115 (OUTLIER) cc_final: 0.7644 (mtm-85) REVERT: B 461 GLN cc_start: 0.8020 (OUTLIER) cc_final: 0.7806 (mt0) REVERT: B 554 MET cc_start: 0.7610 (tpp) cc_final: 0.7334 (mmm) REVERT: B 559 SER cc_start: 0.8283 (OUTLIER) cc_final: 0.7911 (p) REVERT: B 590 TYR cc_start: 0.6175 (OUTLIER) cc_final: 0.5822 (t80) REVERT: B 686 MET cc_start: 0.5103 (mmt) cc_final: 0.4290 (pmm) outliers start: 47 outliers final: 32 residues processed: 148 average time/residue: 0.9262 time to fit residues: 151.9910 Evaluate side-chains 145 residues out of total 1158 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 107 time to evaluate : 1.048 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 220 ILE Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 296 THR Chi-restraints excluded: chain A residue 572 GLN Chi-restraints excluded: chain A residue 590 TYR Chi-restraints excluded: chain A residue 597 ILE Chi-restraints excluded: chain A residue 605 TYR Chi-restraints excluded: chain A residue 727 LEU Chi-restraints excluded: chain A residue 735 ILE Chi-restraints excluded: chain A residue 763 LEU Chi-restraints excluded: chain A residue 781 ARG Chi-restraints excluded: chain A residue 787 CYS Chi-restraints excluded: chain B residue 76 THR Chi-restraints excluded: chain B residue 119 SER Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 260 VAL Chi-restraints excluded: chain B residue 277 ILE Chi-restraints excluded: chain B residue 286 ASN Chi-restraints excluded: chain B residue 296 THR Chi-restraints excluded: chain B residue 309 SER Chi-restraints excluded: chain B residue 324 CYS Chi-restraints excluded: chain B residue 443 ILE Chi-restraints excluded: chain B residue 461 GLN Chi-restraints excluded: chain B residue 544 LEU Chi-restraints excluded: chain B residue 559 SER Chi-restraints excluded: chain B residue 572 GLN Chi-restraints excluded: chain B residue 590 TYR Chi-restraints excluded: chain B residue 597 ILE Chi-restraints excluded: chain B residue 605 TYR Chi-restraints excluded: chain B residue 617 LEU Chi-restraints excluded: chain B residue 650 MET Chi-restraints excluded: chain B residue 704 LEU Chi-restraints excluded: chain B residue 727 LEU Chi-restraints excluded: chain B residue 735 ILE Chi-restraints excluded: chain B residue 763 LEU Chi-restraints excluded: chain B residue 771 SER Chi-restraints excluded: chain B residue 787 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 49 optimal weight: 20.0000 chunk 73 optimal weight: 0.5980 chunk 37 optimal weight: 0.9980 chunk 24 optimal weight: 9.9990 chunk 23 optimal weight: 3.9990 chunk 78 optimal weight: 0.8980 chunk 84 optimal weight: 0.7980 chunk 60 optimal weight: 0.8980 chunk 11 optimal weight: 2.9990 chunk 96 optimal weight: 0.8980 chunk 112 optimal weight: 9.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 71 GLN A 74 GLN A 90 ASN ** A 725 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 769 ASN B 71 GLN B 74 GLN B 90 ASN B 286 ASN B 725 ASN B 769 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7499 moved from start: 0.1443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 11541 Z= 0.203 Angle : 0.673 16.826 15748 Z= 0.322 Chirality : 0.044 0.285 1840 Planarity : 0.004 0.057 1850 Dihedral : 7.447 58.979 2745 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 4.56 % Allowed : 26.33 % Favored : 69.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.16 % 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 (0.23), residues: 1276 helix: 2.45 (0.21), residues: 578 sheet: 1.51 (0.29), residues: 274 loop : -2.19 (0.26), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 629 HIS 0.004 0.001 HIS B 636 PHE 0.017 0.001 PHE B 732 TYR 0.014 0.001 TYR A 188 ARG 0.003 0.000 ARG A 781 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1158 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 111 time to evaluate : 1.078 Fit side-chains REVERT: A 158 GLN cc_start: 0.8521 (mt0) cc_final: 0.8278 (mt0) REVERT: A 554 MET cc_start: 0.7515 (tpp) cc_final: 0.7256 (mmm) REVERT: A 590 TYR cc_start: 0.6165 (OUTLIER) cc_final: 0.5673 (t80) REVERT: A 605 TYR cc_start: 0.3667 (OUTLIER) cc_final: 0.3423 (p90) REVERT: A 736 MET cc_start: 0.6960 (tmm) cc_final: 0.6704 (tpp) REVERT: A 781 ARG cc_start: 0.8160 (OUTLIER) cc_final: 0.7625 (ttm110) REVERT: B 461 GLN cc_start: 0.8023 (OUTLIER) cc_final: 0.7816 (mt0) REVERT: B 554 MET cc_start: 0.7577 (tpp) cc_final: 0.7304 (mmm) REVERT: B 559 SER cc_start: 0.8282 (OUTLIER) cc_final: 0.7900 (p) REVERT: B 590 TYR cc_start: 0.6228 (OUTLIER) cc_final: 0.5897 (t80) REVERT: B 686 MET cc_start: 0.5100 (mmt) cc_final: 0.4300 (pmm) REVERT: B 781 ARG cc_start: 0.8146 (OUTLIER) cc_final: 0.7651 (ttm110) outliers start: 53 outliers final: 36 residues processed: 154 average time/residue: 0.9976 time to fit residues: 169.5721 Evaluate side-chains 153 residues out of total 1158 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 110 time to evaluate : 1.038 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 220 ILE Chi-restraints excluded: chain A residue 296 THR Chi-restraints excluded: chain A residue 521 LEU Chi-restraints excluded: chain A residue 572 GLN Chi-restraints excluded: chain A residue 590 TYR Chi-restraints excluded: chain A residue 597 ILE Chi-restraints excluded: chain A residue 605 TYR Chi-restraints excluded: chain A residue 650 MET Chi-restraints excluded: chain A residue 727 LEU Chi-restraints excluded: chain A residue 735 ILE Chi-restraints excluded: chain A residue 763 LEU Chi-restraints excluded: chain A residue 781 ARG Chi-restraints excluded: chain A residue 787 CYS Chi-restraints excluded: chain A residue 814 LEU Chi-restraints excluded: chain B residue 76 THR Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 220 ILE Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 260 VAL Chi-restraints excluded: chain B residue 277 ILE Chi-restraints excluded: chain B residue 296 THR Chi-restraints excluded: chain B residue 309 SER Chi-restraints excluded: chain B residue 324 CYS Chi-restraints excluded: chain B residue 457 LEU Chi-restraints excluded: chain B residue 461 GLN Chi-restraints excluded: chain B residue 510 LEU Chi-restraints excluded: chain B residue 521 LEU Chi-restraints excluded: chain B residue 544 LEU Chi-restraints excluded: chain B residue 559 SER Chi-restraints excluded: chain B residue 572 GLN Chi-restraints excluded: chain B residue 590 TYR Chi-restraints excluded: chain B residue 597 ILE Chi-restraints excluded: chain B residue 605 TYR Chi-restraints excluded: chain B residue 617 LEU Chi-restraints excluded: chain B residue 704 LEU Chi-restraints excluded: chain B residue 727 LEU Chi-restraints excluded: chain B residue 735 ILE Chi-restraints excluded: chain B residue 763 LEU Chi-restraints excluded: chain B residue 771 SER Chi-restraints excluded: chain B residue 781 ARG Chi-restraints excluded: chain B residue 787 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 118 optimal weight: 2.9990 chunk 107 optimal weight: 2.9990 chunk 114 optimal weight: 4.9990 chunk 69 optimal weight: 0.8980 chunk 50 optimal weight: 9.9990 chunk 90 optimal weight: 1.9990 chunk 35 optimal weight: 0.9990 chunk 103 optimal weight: 4.9990 chunk 108 optimal weight: 9.9990 chunk 75 optimal weight: 3.9990 chunk 121 optimal weight: 1.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 74 GLN A 90 ASN A 142 GLN ** A 725 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 769 ASN B 71 GLN B 74 GLN B 90 ASN B 286 ASN B 725 ASN B 769 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7537 moved from start: 0.1488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 11541 Z= 0.341 Angle : 0.726 16.940 15748 Z= 0.352 Chirality : 0.047 0.276 1840 Planarity : 0.005 0.059 1850 Dihedral : 7.584 59.114 2745 Min Nonbonded Distance : 1.872 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 4.73 % Allowed : 26.08 % Favored : 69.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.16 % 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 (0.23), residues: 1276 helix: 2.33 (0.21), residues: 578 sheet: 1.43 (0.29), residues: 274 loop : -2.26 (0.26), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP B 799 HIS 0.004 0.001 HIS B 563 PHE 0.019 0.002 PHE B 732 TYR 0.019 0.002 TYR A 188 ARG 0.003 0.000 ARG A 781 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1158 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 110 time to evaluate : 1.195 Fit side-chains REVERT: A 158 GLN cc_start: 0.8523 (mt0) cc_final: 0.8276 (mt0) REVERT: A 554 MET cc_start: 0.7580 (tpp) cc_final: 0.7339 (mmm) REVERT: A 590 TYR cc_start: 0.6050 (OUTLIER) cc_final: 0.5597 (t80) REVERT: A 605 TYR cc_start: 0.3781 (OUTLIER) cc_final: 0.3527 (p90) REVERT: A 736 MET cc_start: 0.6966 (tmm) cc_final: 0.6721 (tpp) REVERT: A 781 ARG cc_start: 0.8198 (OUTLIER) cc_final: 0.7679 (ttm110) REVERT: B 461 GLN cc_start: 0.8063 (OUTLIER) cc_final: 0.7855 (mt0) REVERT: B 554 MET cc_start: 0.7588 (tpp) cc_final: 0.7342 (mmm) REVERT: B 559 SER cc_start: 0.8226 (OUTLIER) cc_final: 0.7831 (p) REVERT: B 686 MET cc_start: 0.5082 (mmt) cc_final: 0.4278 (pmm) REVERT: B 781 ARG cc_start: 0.8196 (OUTLIER) cc_final: 0.7728 (ttm110) outliers start: 55 outliers final: 39 residues processed: 155 average time/residue: 0.9302 time to fit residues: 159.9469 Evaluate side-chains 152 residues out of total 1158 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 107 time to evaluate : 1.174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 119 SER Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 220 ILE Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 296 THR Chi-restraints excluded: chain A residue 309 SER Chi-restraints excluded: chain A residue 472 VAL Chi-restraints excluded: chain A residue 521 LEU Chi-restraints excluded: chain A residue 572 GLN Chi-restraints excluded: chain A residue 590 TYR Chi-restraints excluded: chain A residue 597 ILE Chi-restraints excluded: chain A residue 605 TYR Chi-restraints excluded: chain A residue 727 LEU Chi-restraints excluded: chain A residue 735 ILE Chi-restraints excluded: chain A residue 763 LEU Chi-restraints excluded: chain A residue 771 SER Chi-restraints excluded: chain A residue 781 ARG Chi-restraints excluded: chain A residue 787 CYS Chi-restraints excluded: chain A residue 814 LEU Chi-restraints excluded: chain B residue 76 THR Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 220 ILE Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 260 VAL Chi-restraints excluded: chain B residue 277 ILE Chi-restraints excluded: chain B residue 296 THR Chi-restraints excluded: chain B residue 309 SER Chi-restraints excluded: chain B residue 324 CYS Chi-restraints excluded: chain B residue 457 LEU Chi-restraints excluded: chain B residue 461 GLN Chi-restraints excluded: chain B residue 510 LEU Chi-restraints excluded: chain B residue 544 LEU Chi-restraints excluded: chain B residue 559 SER Chi-restraints excluded: chain B residue 572 GLN Chi-restraints excluded: chain B residue 597 ILE Chi-restraints excluded: chain B residue 605 TYR Chi-restraints excluded: chain B residue 617 LEU Chi-restraints excluded: chain B residue 650 MET Chi-restraints excluded: chain B residue 727 LEU Chi-restraints excluded: chain B residue 735 ILE Chi-restraints excluded: chain B residue 763 LEU Chi-restraints excluded: chain B residue 771 SER Chi-restraints excluded: chain B residue 781 ARG Chi-restraints excluded: chain B residue 787 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 74 optimal weight: 6.9990 chunk 57 optimal weight: 1.9990 chunk 84 optimal weight: 0.3980 chunk 127 optimal weight: 0.6980 chunk 117 optimal weight: 1.9990 chunk 101 optimal weight: 0.9980 chunk 10 optimal weight: 0.4980 chunk 78 optimal weight: 0.8980 chunk 62 optimal weight: 2.9990 chunk 80 optimal weight: 1.9990 chunk 108 optimal weight: 0.1980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 71 GLN A 74 GLN A 90 ASN A 142 GLN ** A 725 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 769 ASN B 74 GLN B 90 ASN B 142 GLN B 286 ASN B 725 ASN B 769 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7489 moved from start: 0.1508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 11541 Z= 0.174 Angle : 0.663 16.582 15748 Z= 0.317 Chirality : 0.043 0.285 1840 Planarity : 0.004 0.056 1850 Dihedral : 7.320 59.495 2745 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 3.61 % Allowed : 27.11 % Favored : 69.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.16 % 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 (0.23), residues: 1276 helix: 2.45 (0.21), residues: 578 sheet: 1.50 (0.29), residues: 274 loop : -2.21 (0.26), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 629 HIS 0.004 0.001 HIS B 636 PHE 0.016 0.001 PHE B 732 TYR 0.014 0.001 TYR B 210 ARG 0.003 0.000 ARG A 781 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1158 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 109 time to evaluate : 1.077 Fit side-chains REVERT: A 158 GLN cc_start: 0.8518 (mt0) cc_final: 0.8272 (mt0) REVERT: A 554 MET cc_start: 0.7555 (tpp) cc_final: 0.7285 (mmm) REVERT: A 590 TYR cc_start: 0.6149 (OUTLIER) cc_final: 0.5692 (t80) REVERT: A 605 TYR cc_start: 0.3706 (OUTLIER) cc_final: 0.3473 (p90) REVERT: A 736 MET cc_start: 0.6940 (tmm) cc_final: 0.6655 (tpp) REVERT: A 781 ARG cc_start: 0.8113 (OUTLIER) cc_final: 0.7634 (mtm-85) REVERT: B 461 GLN cc_start: 0.8022 (OUTLIER) cc_final: 0.7805 (mt0) REVERT: B 554 MET cc_start: 0.7580 (tpp) cc_final: 0.7338 (mmm) REVERT: B 559 SER cc_start: 0.8280 (OUTLIER) cc_final: 0.7918 (p) REVERT: B 686 MET cc_start: 0.5030 (mmt) cc_final: 0.4267 (pmm) REVERT: B 736 MET cc_start: 0.7725 (tpp) cc_final: 0.6922 (mpp) REVERT: B 781 ARG cc_start: 0.8127 (OUTLIER) cc_final: 0.7591 (ttm110) outliers start: 42 outliers final: 29 residues processed: 143 average time/residue: 0.9717 time to fit residues: 153.2172 Evaluate side-chains 139 residues out of total 1158 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 104 time to evaluate : 1.071 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 220 ILE Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 296 THR Chi-restraints excluded: chain A residue 521 LEU Chi-restraints excluded: chain A residue 572 GLN Chi-restraints excluded: chain A residue 590 TYR Chi-restraints excluded: chain A residue 597 ILE Chi-restraints excluded: chain A residue 605 TYR Chi-restraints excluded: chain A residue 727 LEU Chi-restraints excluded: chain A residue 735 ILE Chi-restraints excluded: chain A residue 763 LEU Chi-restraints excluded: chain A residue 781 ARG Chi-restraints excluded: chain A residue 787 CYS Chi-restraints excluded: chain B residue 76 THR Chi-restraints excluded: chain B residue 220 ILE Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 260 VAL Chi-restraints excluded: chain B residue 277 ILE Chi-restraints excluded: chain B residue 296 THR Chi-restraints excluded: chain B residue 457 LEU Chi-restraints excluded: chain B residue 461 GLN Chi-restraints excluded: chain B residue 510 LEU Chi-restraints excluded: chain B residue 559 SER Chi-restraints excluded: chain B residue 572 GLN Chi-restraints excluded: chain B residue 597 ILE Chi-restraints excluded: chain B residue 605 TYR Chi-restraints excluded: chain B residue 617 LEU Chi-restraints excluded: chain B residue 650 MET Chi-restraints excluded: chain B residue 727 LEU Chi-restraints excluded: chain B residue 763 LEU Chi-restraints excluded: chain B residue 771 SER Chi-restraints excluded: chain B residue 781 ARG Chi-restraints excluded: chain B residue 787 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 31 optimal weight: 0.9980 chunk 93 optimal weight: 4.9990 chunk 14 optimal weight: 0.6980 chunk 28 optimal weight: 4.9990 chunk 101 optimal weight: 4.9990 chunk 42 optimal weight: 2.9990 chunk 104 optimal weight: 3.9990 chunk 12 optimal weight: 1.9990 chunk 18 optimal weight: 0.7980 chunk 89 optimal weight: 3.9990 chunk 5 optimal weight: 0.5980 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 74 GLN A 90 ASN A 142 GLN ** A 725 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 769 ASN B 71 GLN B 74 GLN B 90 ASN B 142 GLN B 286 ASN B 725 ASN B 769 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4101 r_free = 0.4101 target = 0.166312 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.102862 restraints weight = 16542.813| |-----------------------------------------------------------------------------| r_work (start): 0.3275 rms_B_bonded: 2.78 r_work: 0.3136 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3136 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3155 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3155 r_free = 0.3155 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3155 r_free = 0.3155 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3155 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8106 moved from start: 0.1532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 11541 Z= 0.225 Angle : 0.678 16.543 15748 Z= 0.325 Chirality : 0.044 0.282 1840 Planarity : 0.004 0.056 1850 Dihedral : 7.255 59.716 2743 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 3.53 % Allowed : 27.19 % Favored : 69.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.16 % 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: 1.17 (0.23), residues: 1276 helix: 2.40 (0.21), residues: 578 sheet: 1.50 (0.29), residues: 274 loop : -2.21 (0.26), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 629 HIS 0.004 0.001 HIS B 636 PHE 0.018 0.001 PHE B 732 TYR 0.015 0.001 TYR A 188 ARG 0.003 0.000 ARG A 781 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3700.83 seconds wall clock time: 65 minutes 53.89 seconds (3953.89 seconds total)