Starting phenix.real_space_refine on Tue Jul 29 11:52:52 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8woq_37695/07_2025/8woq_37695.cif Found real_map, /net/cci-nas-00/data/ceres_data/8woq_37695/07_2025/8woq_37695.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.85 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8woq_37695/07_2025/8woq_37695.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8woq_37695/07_2025/8woq_37695.map" model { file = "/net/cci-nas-00/data/ceres_data/8woq_37695/07_2025/8woq_37695.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8woq_37695/07_2025/8woq_37695.cif" } resolution = 2.85 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= 0.013 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. Time to flip 25 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/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: 12.24, per 1000 atoms: 1.09 Number of scatterers: 11218 At special positions: 0 Unit cell: (94.461, 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 - 3.00 Amino acid : True - 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: 2.87 Conformation dependent library (CDL) restraints added in 2.4 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 901 " pdb="ZN ZN A 901 " - pdb=" NE2 HIS A 796 " pdb="ZN ZN A 901 " - pdb=" NE2 HIS A 563 " pdb="ZN ZN A 901 " - pdb=" NE2 HIS A 800 " pdb=" ZN B 901 " pdb="ZN ZN B 901 " - pdb=" NE2 HIS B 796 " pdb="ZN ZN B 901 " - pdb=" NE2 HIS B 563 " 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 50.0% alpha, 16.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.03 Creating SS restraints... Processing helix chain 'A' and resid 38 through 43 removed outlier: 4.389A 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 268 through 272 removed outlier: 3.571A pdb=" N GLY A 272 " --> pdb=" O TYR A 269 " (cutoff:3.500A) Processing helix chain 'A' and resid 302 through 335 removed outlier: 3.911A pdb=" N TYR A 306 " --> pdb=" O LYS A 302 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N PHE A 317 " --> pdb=" O SER A 313 " (cutoff:3.500A) removed outlier: 4.675A pdb=" N PHE A 320 " --> pdb=" O ILE A 316 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N TYR A 321 " --> pdb=" O PHE A 317 " (cutoff:3.500A) Processing helix chain 'A' and resid 441 through 474 Proline residue: A 458 - end of helix removed outlier: 3.633A pdb=" N GLY A 474 " --> pdb=" O VAL A 470 " (cutoff:3.500A) Processing helix chain 'A' and resid 482 through 486 removed outlier: 4.028A 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: 3.960A 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: 4.276A pdb=" N ASP A 574 " --> pdb=" O ASN A 570 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N MET A 578 " --> pdb=" O ASP A 574 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N TYR A 579 " --> pdb=" O THR A 575 " (cutoff:3.500A) Processing helix chain 'A' and resid 602 through 621 removed outlier: 3.720A pdb=" N ALA A 606 " --> pdb=" O TYR A 602 " (cutoff:3.500A) Processing helix chain 'A' and resid 624 through 649 removed outlier: 3.710A pdb=" N PHE A 628 " --> pdb=" O ASN A 624 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N TRP A 629 " --> pdb=" O ASP A 625 " (cutoff:3.500A) 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: 3.603A pdb=" N LEU A 749 " --> pdb=" O LEU A 745 " (cutoff:3.500A) removed outlier: 3.805A 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 794 through 816 Processing helix chain 'A' and resid 819 through 824 Processing helix chain 'B' and resid 38 through 43 removed outlier: 4.152A 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 268 through 272 Processing helix chain 'B' and resid 302 through 335 removed outlier: 3.891A pdb=" N TYR B 306 " --> pdb=" O LYS B 302 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N PHE B 317 " --> pdb=" O SER B 313 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N PHE B 320 " --> pdb=" O ILE B 316 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N TYR B 321 " --> pdb=" O PHE B 317 " (cutoff:3.500A) Processing helix chain 'B' and resid 441 through 474 removed outlier: 4.137A 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: 3.909A 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: 3.873A 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: 4.281A pdb=" N ASP B 574 " --> pdb=" O ASN B 570 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N MET B 578 " --> pdb=" O ASP B 574 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N TYR B 579 " --> pdb=" O THR B 575 " (cutoff:3.500A) Processing helix chain 'B' and resid 602 through 621 removed outlier: 4.093A pdb=" N ALA B 606 " --> pdb=" O TYR B 602 " (cutoff:3.500A) Processing helix chain 'B' and resid 624 through 650 removed outlier: 4.442A pdb=" N TRP B 629 " --> pdb=" O ASP B 625 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N MET B 650 " --> pdb=" O GLN B 646 " (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: 3.637A pdb=" N LEU B 749 " --> pdb=" O LEU B 745 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N PHE B 765 " --> pdb=" O ALA B 761 " (cutoff:3.500A) removed outlier: 4.006A 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 794 through 816 removed outlier: 3.502A 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 removed outlier: 6.201A pdb=" N ARG A 44 " --> pdb=" O SER A 65 " (cutoff:3.500A) removed outlier: 8.064A pdb=" N ASN A 67 " --> pdb=" O ARG A 44 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 51 through 56 removed outlier: 4.473A 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 removed outlier: 6.036A pdb=" N ARG B 44 " --> pdb=" O SER B 65 " (cutoff:3.500A) removed outlier: 7.725A pdb=" N ASN B 67 " --> pdb=" O ARG B 44 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 51 through 56 removed outlier: 4.625A pdb=" N ALA B 77 " --> pdb=" O LEU B 166 " (cutoff:3.500A) removed outlier: 4.481A 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 192 629 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: 3.42 Time building geometry restraints manager: 3.38 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: 3251 1.34 - 1.46: 2724 1.46 - 1.58: 5472 1.58 - 1.70: 0 1.70 - 1.82: 94 Bond restraints: 11541 Sorted by residual: 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 4.62e+01 bond pdb=" C10 OLA A 912 " pdb=" C9 OLA A 912 " ideal model delta sigma weight residual 1.332 1.467 -0.135 2.00e-02 2.50e+03 4.58e+01 bond pdb=" C1 OLA A 912 " pdb=" C2 OLA A 912 " ideal model delta sigma weight residual 1.542 1.510 0.032 2.00e-02 2.50e+03 2.64e+00 bond pdb=" C1 OLA B 914 " pdb=" C2 OLA B 914 " ideal model delta sigma weight residual 1.542 1.510 0.032 2.00e-02 2.50e+03 2.58e+00 bond pdb=" C1 NAG E 2 " pdb=" O5 NAG E 2 " ideal model delta sigma weight residual 1.406 1.437 -0.031 2.00e-02 2.50e+03 2.40e+00 ... (remaining 11536 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.04: 15642 4.04 - 8.09: 77 8.09 - 12.13: 26 12.13 - 16.18: 2 16.18 - 20.22: 1 Bond angle restraints: 15748 Sorted by residual: angle pdb=" C ASN B 598 " pdb=" N ALA B 599 " pdb=" CA ALA B 599 " ideal model delta sigma weight residual 121.70 133.71 -12.01 1.80e+00 3.09e-01 4.45e+01 angle pdb=" C ASN A 598 " pdb=" N ALA A 599 " pdb=" CA ALA A 599 " ideal model delta sigma weight residual 121.70 133.55 -11.85 1.80e+00 3.09e-01 4.33e+01 angle pdb=" CA LEU A 728 " pdb=" CB LEU A 728 " pdb=" CG LEU A 728 " ideal model delta sigma weight residual 116.30 136.52 -20.22 3.50e+00 8.16e-02 3.34e+01 angle pdb=" CA MET B 613 " pdb=" CB MET B 613 " pdb=" CG MET B 613 " ideal model delta sigma weight residual 114.10 124.06 -9.96 2.00e+00 2.50e-01 2.48e+01 angle pdb=" C ILE A 612 " pdb=" N MET A 613 " pdb=" CA MET A 613 " ideal model delta sigma weight residual 121.58 112.24 9.34 1.95e+00 2.63e-01 2.29e+01 ... (remaining 15743 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.39: 6571 17.39 - 34.78: 801 34.78 - 52.17: 217 52.17 - 69.56: 54 69.56 - 86.95: 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 24.23 -24.23 0 5.00e+00 4.00e-02 2.35e+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 21.40 -21.40 0 5.00e+00 4.00e-02 1.83e+01 dihedral pdb=" CB CYS A 212 " pdb=" SG CYS A 212 " pdb=" SG CYS A 271 " pdb=" CB CYS A 271 " ideal model delta sinusoidal sigma weight residual 93.00 58.11 34.89 1 1.00e+01 1.00e-02 1.73e+01 ... (remaining 7648 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.064: 1590 0.064 - 0.128: 229 0.128 - 0.192: 15 0.192 - 0.256: 4 0.256 - 0.320: 2 Chirality restraints: 1840 Sorted by residual: 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 -2.08 -0.32 2.00e-01 2.50e+01 2.56e+00 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 -2.09 -0.31 2.00e-01 2.50e+01 2.45e+00 chirality pdb=" C2 SPL B 906 " pdb=" C1 SPL B 906 " pdb=" C3 SPL B 906 " pdb=" N2 SPL B 906 " both_signs ideal model delta sigma weight residual False -2.45 -2.20 -0.25 2.00e-01 2.50e+01 1.58e+00 ... (remaining 1837 not shown) Planarity restraints: 1858 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C10 OLA B 914 " 0.200 2.00e-02 2.50e+03 1.55e-01 2.42e+02 pdb=" C11 OLA B 914 " -0.090 2.00e-02 2.50e+03 pdb=" C8 OLA B 914 " 0.091 2.00e-02 2.50e+03 pdb=" C9 OLA B 914 " -0.200 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C10 OLA A 912 " -0.186 2.00e-02 2.50e+03 1.44e-01 2.09e+02 pdb=" C11 OLA A 912 " 0.085 2.00e-02 2.50e+03 pdb=" C8 OLA A 912 " -0.085 2.00e-02 2.50e+03 pdb=" C9 OLA A 912 " 0.186 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 710 " -0.214 9.50e-02 1.11e+02 9.57e-02 5.64e+00 pdb=" NE ARG A 710 " 0.013 2.00e-02 2.50e+03 pdb=" CZ ARG A 710 " 0.001 2.00e-02 2.50e+03 pdb=" NH1 ARG A 710 " 0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG A 710 " -0.007 2.00e-02 2.50e+03 ... (remaining 1855 not shown) Histogram of nonbonded interaction distances: 2.05 - 2.62: 105 2.62 - 3.19: 9544 3.19 - 3.76: 16329 3.76 - 4.33: 22475 4.33 - 4.90: 37900 Nonbonded interactions: 86353 Sorted by model distance: nonbonded pdb="ZN ZN B 901 " pdb=" O HOH B1002 " model vdw 2.046 2.230 nonbonded pdb="ZN ZN A 901 " pdb=" O HOH A1002 " model vdw 2.052 2.230 nonbonded pdb=" OG1 THR A 135 " pdb=" OE1 GLU A 137 " model vdw 2.128 3.040 nonbonded pdb=" O LYS B 265 " pdb=" NH1 ARG B 289 " model vdw 2.200 3.120 nonbonded pdb=" OH TYR B 64 " pdb=" OH TYR B 159 " model vdw 2.246 3.040 ... (remaining 86348 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 \ 905 or resid 907 through 911)) selection = (chain 'B' and (resid 35 through 80 or resid 82 through 830 or resid 901 through \ 905 or resid 907 through 911)) } 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: 4.480 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: 0.500 Check model and map are aligned: 0.090 Set scattering table: 0.110 Process input model: 36.760 Find NCS groups from input model: 0.550 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: 0.010 Load rotamer database and sin/cos tables:15.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 58.370 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8185 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 11567 Z= 0.193 Angle : 0.827 20.220 15800 Z= 0.377 Chirality : 0.046 0.320 1840 Planarity : 0.007 0.155 1850 Dihedral : 15.764 86.946 5135 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.79 % Favored : 95.13 % Rotamer: Outliers : 3.96 % Allowed : 27.37 % Favored : 68.67 % 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: 1.00 (0.23), residues: 1276 helix: 1.94 (0.21), residues: 590 sheet: 1.85 (0.28), residues: 260 loop : -2.11 (0.27), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 700 HIS 0.005 0.001 HIS A 636 PHE 0.030 0.001 PHE B 275 TYR 0.021 0.001 TYR A 332 ARG 0.007 0.000 ARG A 118 Details of bonding type rmsd link_NAG-ASN : bond 0.00396 ( 8) link_NAG-ASN : angle 2.67637 ( 24) link_BETA1-4 : bond 0.00293 ( 4) link_BETA1-4 : angle 1.61835 ( 12) hydrogen bonds : bond 0.08980 ( 629) hydrogen bonds : angle 4.30078 ( 1795) metal coordination : bond 0.00178 ( 6) SS BOND : bond 0.00126 ( 8) SS BOND : angle 1.00091 ( 16) covalent geometry : bond 0.00415 (11541) covalent geometry : angle 0.81976 (15748) *********************** 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 149 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 103 time to evaluate : 1.296 Fit side-chains revert: symmetry clash outliers start: 46 outliers final: 40 residues processed: 145 average time/residue: 0.8444 time to fit residues: 138.6037 Evaluate side-chains 142 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 102 time to evaluate : 1.172 ------------------------------------------------------------------------------- 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 286 ASN Chi-restraints excluded: chain A residue 296 THR Chi-restraints excluded: chain A residue 313 SER Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 319 SER Chi-restraints excluded: chain A residue 327 VAL 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 597 ILE Chi-restraints excluded: chain A residue 780 SER Chi-restraints excluded: chain B residue 60 THR Chi-restraints excluded: chain B residue 76 THR Chi-restraints excluded: chain B residue 89 LEU Chi-restraints excluded: chain B residue 119 SER Chi-restraints excluded: chain B residue 135 THR Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 196 ASP 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 324 CYS Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 459 VAL Chi-restraints excluded: chain B residue 520 ILE Chi-restraints excluded: chain B residue 521 LEU Chi-restraints excluded: chain B residue 544 LEU Chi-restraints excluded: chain B residue 572 GLN 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 780 SER Chi-restraints excluded: chain B residue 788 ILE Chi-restraints excluded: chain B residue 810 SER Chi-restraints excluded: chain B residue 814 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 108 optimal weight: 5.9990 chunk 97 optimal weight: 2.9990 chunk 53 optimal weight: 7.9990 chunk 33 optimal weight: 4.9990 chunk 65 optimal weight: 0.9980 chunk 51 optimal weight: 10.0000 chunk 100 optimal weight: 2.9990 chunk 38 optimal weight: 6.9990 chunk 61 optimal weight: 1.9990 chunk 74 optimal weight: 6.9990 chunk 116 optimal weight: 10.0000 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 768 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.118575 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.074393 restraints weight = 26435.264| |-----------------------------------------------------------------------------| r_work (start): 0.3016 rms_B_bonded: 3.50 r_work: 0.2851 rms_B_bonded: 4.12 restraints_weight: 0.5000 r_work (final): 0.2851 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2863 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2863 r_free = 0.2863 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2862 r_free = 0.2862 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2862 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8237 moved from start: 0.0680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.055 11567 Z= 0.271 Angle : 0.770 17.076 15800 Z= 0.369 Chirality : 0.047 0.283 1840 Planarity : 0.005 0.063 1850 Dihedral : 9.569 59.796 2786 Min Nonbonded Distance : 1.896 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.18 % Favored : 94.74 % Rotamer: Outliers : 4.73 % Allowed : 25.73 % Favored : 69.54 % 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: 1.01 (0.23), residues: 1276 helix: 2.12 (0.21), residues: 578 sheet: 1.72 (0.29), residues: 260 loop : -2.16 (0.26), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 799 HIS 0.005 0.001 HIS A 636 PHE 0.020 0.002 PHE B 276 TYR 0.021 0.002 TYR A 188 ARG 0.007 0.001 ARG A 118 Details of bonding type rmsd link_NAG-ASN : bond 0.00390 ( 8) link_NAG-ASN : angle 2.40615 ( 24) link_BETA1-4 : bond 0.00304 ( 4) link_BETA1-4 : angle 1.36581 ( 12) hydrogen bonds : bond 0.06023 ( 629) hydrogen bonds : angle 4.13731 ( 1795) metal coordination : bond 0.00709 ( 6) SS BOND : bond 0.00178 ( 8) SS BOND : angle 1.49214 ( 16) covalent geometry : bond 0.00654 (11541) covalent geometry : angle 0.76339 (15748) *********************** 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 156 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 101 time to evaluate : 1.306 Fit side-chains revert: symmetry clash REVERT: A 207 GLU cc_start: 0.8866 (tm-30) cc_final: 0.8593 (mp0) REVERT: A 443 ILE cc_start: 0.7777 (OUTLIER) cc_final: 0.7318 (tt) REVERT: A 461 GLN cc_start: 0.8710 (OUTLIER) cc_final: 0.7814 (mp10) REVERT: B 590 TYR cc_start: 0.8002 (OUTLIER) cc_final: 0.7717 (t80) outliers start: 55 outliers final: 29 residues processed: 147 average time/residue: 1.1176 time to fit residues: 184.6119 Evaluate side-chains 129 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 97 time to evaluate : 1.445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 205 VAL 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 322 LEU Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain A residue 461 GLN Chi-restraints excluded: chain A residue 510 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 585 CYS Chi-restraints excluded: chain A residue 597 ILE Chi-restraints excluded: chain A residue 605 TYR Chi-restraints excluded: chain A residue 726 LEU Chi-restraints excluded: chain A residue 787 CYS Chi-restraints excluded: chain B residue 76 THR Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 196 ASP Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 220 ILE Chi-restraints excluded: chain B residue 260 VAL Chi-restraints excluded: chain B residue 287 LEU Chi-restraints excluded: chain B residue 521 LEU Chi-restraints excluded: chain B residue 590 TYR Chi-restraints excluded: chain B residue 597 ILE Chi-restraints excluded: chain B residue 726 LEU Chi-restraints excluded: chain B residue 735 ILE Chi-restraints excluded: chain B residue 787 CYS Chi-restraints excluded: chain B residue 791 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 85 optimal weight: 0.7980 chunk 58 optimal weight: 0.9980 chunk 107 optimal weight: 2.9990 chunk 82 optimal weight: 0.9980 chunk 30 optimal weight: 0.9990 chunk 125 optimal weight: 0.6980 chunk 93 optimal weight: 20.0000 chunk 98 optimal weight: 0.8980 chunk 47 optimal weight: 6.9990 chunk 126 optimal weight: 2.9990 chunk 123 optimal weight: 2.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.120539 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.075774 restraints weight = 36908.264| |-----------------------------------------------------------------------------| r_work (start): 0.3002 rms_B_bonded: 4.05 r_work: 0.2827 rms_B_bonded: 4.53 restraints_weight: 0.5000 r_work (final): 0.2827 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2824 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2824 r_free = 0.2824 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2824 r_free = 0.2824 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2824 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8177 moved from start: 0.0631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 11567 Z= 0.133 Angle : 0.700 14.623 15800 Z= 0.326 Chirality : 0.044 0.288 1840 Planarity : 0.004 0.047 1850 Dihedral : 8.571 59.840 2753 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.24 % Favored : 95.68 % Rotamer: Outliers : 3.61 % Allowed : 25.82 % Favored : 70.57 % 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: 1.16 (0.23), residues: 1276 helix: 2.25 (0.21), residues: 578 sheet: 1.67 (0.29), residues: 264 loop : -2.04 (0.26), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 700 HIS 0.006 0.001 HIS A 636 PHE 0.054 0.001 PHE A 732 TYR 0.013 0.001 TYR B 188 ARG 0.006 0.000 ARG A 118 Details of bonding type rmsd link_NAG-ASN : bond 0.00436 ( 8) link_NAG-ASN : angle 2.54274 ( 24) link_BETA1-4 : bond 0.00411 ( 4) link_BETA1-4 : angle 1.42770 ( 12) hydrogen bonds : bond 0.04963 ( 629) hydrogen bonds : angle 3.92443 ( 1795) metal coordination : bond 0.00187 ( 6) SS BOND : bond 0.00110 ( 8) SS BOND : angle 0.94810 ( 16) covalent geometry : bond 0.00296 (11541) covalent geometry : angle 0.69279 (15748) *********************** 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 153 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 111 time to evaluate : 1.216 Fit side-chains revert: symmetry clash REVERT: A 443 ILE cc_start: 0.7664 (OUTLIER) cc_final: 0.7190 (tt) REVERT: A 590 TYR cc_start: 0.7825 (OUTLIER) cc_final: 0.7561 (t80) REVERT: B 513 LEU cc_start: 0.8294 (OUTLIER) cc_final: 0.8082 (mp) REVERT: B 590 TYR cc_start: 0.7994 (OUTLIER) cc_final: 0.7732 (t80) REVERT: B 722 PHE cc_start: 0.8723 (t80) cc_final: 0.8523 (t80) outliers start: 42 outliers final: 17 residues processed: 141 average time/residue: 0.8243 time to fit residues: 131.1076 Evaluate side-chains 125 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 104 time to evaluate : 1.159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 443 ILE 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 585 CYS Chi-restraints excluded: chain A residue 590 TYR Chi-restraints excluded: chain A residue 597 ILE Chi-restraints excluded: chain A residue 728 LEU Chi-restraints excluded: chain B residue 76 THR Chi-restraints excluded: chain B residue 220 ILE Chi-restraints excluded: chain B residue 287 LEU Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain B residue 513 LEU Chi-restraints excluded: chain B residue 521 LEU Chi-restraints excluded: chain B residue 559 SER Chi-restraints excluded: chain B residue 590 TYR Chi-restraints excluded: chain B residue 597 ILE Chi-restraints excluded: chain B residue 735 ILE Chi-restraints excluded: chain B residue 791 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 76 optimal weight: 0.9980 chunk 1 optimal weight: 4.9990 chunk 69 optimal weight: 2.9990 chunk 115 optimal weight: 5.9990 chunk 112 optimal weight: 7.9990 chunk 44 optimal weight: 5.9990 chunk 43 optimal weight: 0.9980 chunk 21 optimal weight: 3.9990 chunk 20 optimal weight: 0.7980 chunk 10 optimal weight: 0.9980 chunk 110 optimal weight: 3.9990 overall best weight: 1.3582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.119930 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.075906 restraints weight = 25807.773| |-----------------------------------------------------------------------------| r_work (start): 0.3010 rms_B_bonded: 3.52 r_work: 0.2844 rms_B_bonded: 4.12 restraints_weight: 0.5000 r_work (final): 0.2844 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2847 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2847 r_free = 0.2847 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2847 r_free = 0.2847 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2847 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8186 moved from start: 0.0757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 11567 Z= 0.160 Angle : 0.716 15.394 15800 Z= 0.334 Chirality : 0.044 0.291 1840 Planarity : 0.004 0.048 1850 Dihedral : 8.107 59.240 2743 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.40 % Favored : 95.53 % Rotamer: Outliers : 3.79 % Allowed : 25.30 % Favored : 70.91 % 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: 2.23 (0.21), residues: 578 sheet: 1.69 (0.29), residues: 264 loop : -2.06 (0.26), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 106 HIS 0.006 0.001 HIS A 636 PHE 0.033 0.001 PHE B 722 TYR 0.016 0.001 TYR B 188 ARG 0.004 0.000 ARG A 118 Details of bonding type rmsd link_NAG-ASN : bond 0.00379 ( 8) link_NAG-ASN : angle 2.41679 ( 24) link_BETA1-4 : bond 0.00423 ( 4) link_BETA1-4 : angle 1.36434 ( 12) hydrogen bonds : bond 0.05102 ( 629) hydrogen bonds : angle 3.94179 ( 1795) metal coordination : bond 0.00316 ( 6) SS BOND : bond 0.00108 ( 8) SS BOND : angle 1.02380 ( 16) covalent geometry : bond 0.00372 (11541) covalent geometry : angle 0.70876 (15748) *********************** 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 153 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 109 time to evaluate : 1.300 Fit side-chains revert: symmetry clash REVERT: A 123 GLN cc_start: 0.8269 (mt0) cc_final: 0.7819 (mm110) REVERT: A 207 GLU cc_start: 0.8875 (tm-30) cc_final: 0.8526 (mp0) REVERT: A 208 MET cc_start: 0.8460 (ttm) cc_final: 0.8158 (ttm) REVERT: A 443 ILE cc_start: 0.7666 (OUTLIER) cc_final: 0.7192 (tt) REVERT: A 591 GLN cc_start: 0.7184 (tm-30) cc_final: 0.6951 (pp30) REVERT: B 513 LEU cc_start: 0.8310 (OUTLIER) cc_final: 0.8090 (mp) REVERT: B 590 TYR cc_start: 0.7993 (OUTLIER) cc_final: 0.7737 (t80) REVERT: B 722 PHE cc_start: 0.8748 (t80) cc_final: 0.8537 (t80) outliers start: 44 outliers final: 25 residues processed: 145 average time/residue: 0.7597 time to fit residues: 125.0301 Evaluate side-chains 134 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 106 time to evaluate : 1.229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 133 GLU Chi-restraints excluded: chain A residue 220 ILE Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain A residue 510 LEU Chi-restraints excluded: chain A residue 559 SER Chi-restraints excluded: chain A residue 572 GLN Chi-restraints excluded: chain A residue 585 CYS Chi-restraints excluded: chain A residue 597 ILE Chi-restraints excluded: chain A residue 726 LEU Chi-restraints excluded: chain A residue 787 CYS Chi-restraints excluded: chain B residue 76 THR Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 220 ILE Chi-restraints excluded: chain B residue 260 VAL Chi-restraints excluded: chain B residue 287 LEU Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain B residue 513 LEU Chi-restraints excluded: chain B residue 559 SER Chi-restraints excluded: chain B residue 590 TYR Chi-restraints excluded: chain B residue 597 ILE Chi-restraints excluded: chain B residue 735 ILE Chi-restraints excluded: chain B residue 787 CYS Chi-restraints excluded: chain B residue 791 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 9 optimal weight: 4.9990 chunk 92 optimal weight: 4.9990 chunk 48 optimal weight: 10.0000 chunk 110 optimal weight: 7.9990 chunk 72 optimal weight: 0.8980 chunk 117 optimal weight: 0.9980 chunk 44 optimal weight: 10.0000 chunk 49 optimal weight: 6.9990 chunk 45 optimal weight: 2.9990 chunk 97 optimal weight: 0.0980 chunk 106 optimal weight: 4.9990 overall best weight: 1.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 768 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.119292 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.074341 restraints weight = 35297.583| |-----------------------------------------------------------------------------| r_work (start): 0.2977 rms_B_bonded: 3.97 r_work: 0.2800 rms_B_bonded: 4.47 restraints_weight: 0.5000 r_work (final): 0.2800 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2798 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2798 r_free = 0.2798 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2798 r_free = 0.2798 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2798 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 moved from start: 0.0804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 11567 Z= 0.206 Angle : 0.731 17.219 15800 Z= 0.342 Chirality : 0.045 0.291 1840 Planarity : 0.004 0.048 1850 Dihedral : 7.972 59.407 2740 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.87 % Favored : 95.05 % Rotamer: Outliers : 4.04 % Allowed : 25.22 % Favored : 70.74 % 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: 2.20 (0.21), residues: 578 sheet: 1.69 (0.29), residues: 264 loop : -2.10 (0.26), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 106 HIS 0.004 0.001 HIS A 636 PHE 0.030 0.001 PHE B 722 TYR 0.020 0.001 TYR A 332 ARG 0.005 0.000 ARG A 118 Details of bonding type rmsd link_NAG-ASN : bond 0.00366 ( 8) link_NAG-ASN : angle 2.36516 ( 24) link_BETA1-4 : bond 0.00413 ( 4) link_BETA1-4 : angle 1.38292 ( 12) hydrogen bonds : bond 0.05382 ( 629) hydrogen bonds : angle 3.98511 ( 1795) metal coordination : bond 0.00460 ( 6) SS BOND : bond 0.00154 ( 8) SS BOND : angle 1.25882 ( 16) covalent geometry : bond 0.00491 (11541) covalent geometry : angle 0.72452 (15748) *********************** 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 152 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 105 time to evaluate : 1.207 Fit side-chains revert: symmetry clash REVERT: A 123 GLN cc_start: 0.8325 (mt0) cc_final: 0.7854 (mm110) REVERT: A 443 ILE cc_start: 0.7704 (OUTLIER) cc_final: 0.7245 (tt) REVERT: A 461 GLN cc_start: 0.8791 (OUTLIER) cc_final: 0.8577 (mp-120) REVERT: B 513 LEU cc_start: 0.8285 (OUTLIER) cc_final: 0.8055 (mp) REVERT: B 590 TYR cc_start: 0.8000 (OUTLIER) cc_final: 0.7699 (t80) REVERT: B 722 PHE cc_start: 0.8739 (t80) cc_final: 0.8490 (t80) outliers start: 47 outliers final: 27 residues processed: 143 average time/residue: 0.8319 time to fit residues: 134.4179 Evaluate side-chains 129 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 98 time to evaluate : 1.171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 220 ILE Chi-restraints excluded: chain A residue 313 SER Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain A residue 461 GLN Chi-restraints excluded: chain A residue 510 LEU Chi-restraints excluded: chain A residue 559 SER Chi-restraints excluded: chain A residue 572 GLN Chi-restraints excluded: chain A residue 585 CYS Chi-restraints excluded: chain A residue 597 ILE Chi-restraints excluded: chain A residue 605 TYR Chi-restraints excluded: chain A residue 704 LEU Chi-restraints excluded: chain A residue 787 CYS Chi-restraints excluded: chain B residue 76 THR Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 220 ILE Chi-restraints excluded: chain B residue 260 VAL Chi-restraints excluded: chain B residue 287 LEU Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain B residue 459 VAL Chi-restraints excluded: chain B residue 513 LEU Chi-restraints excluded: chain B residue 559 SER Chi-restraints excluded: chain B residue 590 TYR Chi-restraints excluded: chain B residue 597 ILE Chi-restraints excluded: chain B residue 735 ILE Chi-restraints excluded: chain B residue 787 CYS Chi-restraints excluded: chain B residue 791 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 54 optimal weight: 0.9990 chunk 79 optimal weight: 0.9980 chunk 4 optimal weight: 2.9990 chunk 84 optimal weight: 0.8980 chunk 58 optimal weight: 1.9990 chunk 80 optimal weight: 3.9990 chunk 22 optimal weight: 2.9990 chunk 113 optimal weight: 7.9990 chunk 108 optimal weight: 7.9990 chunk 23 optimal weight: 0.0870 chunk 43 optimal weight: 0.8980 overall best weight: 0.7760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.120975 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.075931 restraints weight = 41595.372| |-----------------------------------------------------------------------------| r_work (start): 0.3005 rms_B_bonded: 4.25 r_work: 0.2824 rms_B_bonded: 4.69 restraints_weight: 0.5000 r_work (final): 0.2824 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2827 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2827 r_free = 0.2827 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2827 r_free = 0.2827 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2827 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8170 moved from start: 0.0905 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 11567 Z= 0.129 Angle : 0.715 16.357 15800 Z= 0.328 Chirality : 0.043 0.292 1840 Planarity : 0.004 0.046 1850 Dihedral : 7.663 59.238 2740 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 3.10 % Allowed : 26.16 % Favored : 70.74 % 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: 2.25 (0.21), residues: 578 sheet: 1.72 (0.28), residues: 276 loop : -2.06 (0.27), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 700 HIS 0.004 0.001 HIS A 636 PHE 0.029 0.001 PHE B 722 TYR 0.013 0.001 TYR B 188 ARG 0.004 0.000 ARG A 118 Details of bonding type rmsd link_NAG-ASN : bond 0.00435 ( 8) link_NAG-ASN : angle 2.54080 ( 24) link_BETA1-4 : bond 0.00421 ( 4) link_BETA1-4 : angle 1.44306 ( 12) hydrogen bonds : bond 0.04724 ( 629) hydrogen bonds : angle 3.89904 ( 1795) metal coordination : bond 0.00173 ( 6) SS BOND : bond 0.00106 ( 8) SS BOND : angle 0.88592 ( 16) covalent geometry : bond 0.00283 (11541) covalent geometry : angle 0.70741 (15748) *********************** 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 146 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 110 time to evaluate : 1.035 Fit side-chains revert: symmetry clash REVERT: A 123 GLN cc_start: 0.8300 (mt0) cc_final: 0.7825 (mm110) REVERT: A 207 GLU cc_start: 0.8946 (tm-30) cc_final: 0.8494 (mp0) REVERT: A 443 ILE cc_start: 0.7639 (OUTLIER) cc_final: 0.7159 (tt) REVERT: A 590 TYR cc_start: 0.7857 (OUTLIER) cc_final: 0.7591 (t80) REVERT: B 513 LEU cc_start: 0.8295 (OUTLIER) cc_final: 0.8082 (mp) REVERT: B 590 TYR cc_start: 0.7967 (OUTLIER) cc_final: 0.7719 (t80) outliers start: 36 outliers final: 22 residues processed: 138 average time/residue: 1.0338 time to fit residues: 162.3601 Evaluate side-chains 129 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 103 time to evaluate : 1.144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 220 ILE Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain A residue 521 LEU Chi-restraints excluded: chain A residue 585 CYS Chi-restraints excluded: chain A residue 590 TYR Chi-restraints excluded: chain A residue 597 ILE Chi-restraints excluded: chain A residue 704 LEU Chi-restraints excluded: chain A residue 787 CYS Chi-restraints excluded: chain B residue 76 THR Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 220 ILE Chi-restraints excluded: chain B residue 260 VAL Chi-restraints excluded: chain B residue 287 LEU Chi-restraints excluded: chain B residue 319 SER Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain B residue 459 VAL Chi-restraints excluded: chain B residue 513 LEU Chi-restraints excluded: chain B residue 521 LEU Chi-restraints excluded: chain B residue 559 SER Chi-restraints excluded: chain B residue 590 TYR Chi-restraints excluded: chain B residue 597 ILE Chi-restraints excluded: chain B residue 787 CYS Chi-restraints excluded: chain B residue 791 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 60 optimal weight: 2.9990 chunk 58 optimal weight: 1.9990 chunk 29 optimal weight: 3.9990 chunk 17 optimal weight: 3.9990 chunk 24 optimal weight: 8.9990 chunk 74 optimal weight: 0.0980 chunk 1 optimal weight: 4.9990 chunk 96 optimal weight: 3.9990 chunk 42 optimal weight: 0.8980 chunk 18 optimal weight: 1.9990 chunk 70 optimal weight: 4.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 624 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.119879 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.076388 restraints weight = 22922.121| |-----------------------------------------------------------------------------| r_work (start): 0.3024 rms_B_bonded: 3.32 r_work: 0.2863 rms_B_bonded: 3.96 restraints_weight: 0.5000 r_work (final): 0.2863 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2860 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2860 r_free = 0.2860 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2860 r_free = 0.2860 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2860 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8173 moved from start: 0.0908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 11567 Z= 0.175 Angle : 0.729 17.011 15800 Z= 0.339 Chirality : 0.044 0.295 1840 Planarity : 0.004 0.048 1850 Dihedral : 7.473 58.364 2734 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 3.18 % Allowed : 26.08 % Favored : 70.74 % 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: 2.24 (0.21), residues: 576 sheet: 1.69 (0.28), residues: 276 loop : -2.02 (0.27), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 700 HIS 0.004 0.001 HIS A 636 PHE 0.051 0.001 PHE A 732 TYR 0.020 0.001 TYR A 332 ARG 0.004 0.000 ARG A 118 Details of bonding type rmsd link_NAG-ASN : bond 0.00378 ( 8) link_NAG-ASN : angle 2.39315 ( 24) link_BETA1-4 : bond 0.00420 ( 4) link_BETA1-4 : angle 1.40828 ( 12) hydrogen bonds : bond 0.05072 ( 629) hydrogen bonds : angle 3.93558 ( 1795) metal coordination : bond 0.00351 ( 6) SS BOND : bond 0.00128 ( 8) SS BOND : angle 1.09314 ( 16) covalent geometry : bond 0.00412 (11541) covalent geometry : angle 0.72199 (15748) *********************** 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 143 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 106 time to evaluate : 2.190 Fit side-chains revert: symmetry clash REVERT: A 123 GLN cc_start: 0.8263 (mt0) cc_final: 0.7740 (mm110) REVERT: A 207 GLU cc_start: 0.8882 (tm-30) cc_final: 0.8499 (mp0) REVERT: A 443 ILE cc_start: 0.7654 (OUTLIER) cc_final: 0.7179 (tt) REVERT: A 591 GLN cc_start: 0.6888 (pp30) cc_final: 0.6667 (pp30) REVERT: B 513 LEU cc_start: 0.8289 (OUTLIER) cc_final: 0.8055 (mp) REVERT: B 590 TYR cc_start: 0.7981 (OUTLIER) cc_final: 0.7742 (t80) REVERT: B 689 MET cc_start: 0.7269 (pmm) cc_final: 0.5576 (pp-130) REVERT: B 722 PHE cc_start: 0.8728 (t80) cc_final: 0.8467 (t80) outliers start: 37 outliers final: 26 residues processed: 136 average time/residue: 1.1038 time to fit residues: 172.0375 Evaluate side-chains 133 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 104 time to evaluate : 1.696 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 220 ILE Chi-restraints excluded: chain A residue 313 SER Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain A residue 585 CYS Chi-restraints excluded: chain A residue 597 ILE Chi-restraints excluded: chain A residue 605 TYR Chi-restraints excluded: chain A residue 704 LEU Chi-restraints excluded: chain A residue 787 CYS Chi-restraints excluded: chain A residue 788 ILE Chi-restraints excluded: chain B residue 76 THR Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 220 ILE Chi-restraints excluded: chain B residue 260 VAL Chi-restraints excluded: chain B residue 287 LEU Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain B residue 459 VAL Chi-restraints excluded: chain B residue 513 LEU Chi-restraints excluded: chain B residue 521 LEU Chi-restraints excluded: chain B residue 559 SER Chi-restraints excluded: chain B residue 581 ILE Chi-restraints excluded: chain B residue 590 TYR Chi-restraints excluded: chain B residue 597 ILE Chi-restraints excluded: chain B residue 787 CYS Chi-restraints excluded: chain B residue 791 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 51 optimal weight: 8.9990 chunk 14 optimal weight: 0.5980 chunk 42 optimal weight: 0.6980 chunk 49 optimal weight: 9.9990 chunk 98 optimal weight: 0.9980 chunk 3 optimal weight: 0.8980 chunk 40 optimal weight: 4.9990 chunk 22 optimal weight: 3.9990 chunk 93 optimal weight: 6.9990 chunk 15 optimal weight: 0.9980 chunk 41 optimal weight: 0.2980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.121004 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.076351 restraints weight = 28220.747| |-----------------------------------------------------------------------------| r_work (start): 0.3029 rms_B_bonded: 3.70 r_work: 0.2862 rms_B_bonded: 4.28 restraints_weight: 0.5000 r_work (final): 0.2862 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2864 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2864 r_free = 0.2864 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2864 r_free = 0.2864 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2864 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8151 moved from start: 0.1034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 11567 Z= 0.127 Angle : 0.726 18.578 15800 Z= 0.331 Chirality : 0.043 0.294 1840 Planarity : 0.004 0.046 1850 Dihedral : 7.288 59.889 2734 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 2.84 % Allowed : 26.42 % Favored : 70.74 % 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: 1.28 (0.23), residues: 1276 helix: 2.27 (0.21), residues: 576 sheet: 1.74 (0.28), residues: 276 loop : -1.97 (0.27), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 700 HIS 0.004 0.001 HIS A 636 PHE 0.035 0.001 PHE B 722 TYR 0.046 0.001 TYR A 717 ARG 0.004 0.000 ARG A 710 Details of bonding type rmsd link_NAG-ASN : bond 0.00427 ( 8) link_NAG-ASN : angle 2.52468 ( 24) link_BETA1-4 : bond 0.00451 ( 4) link_BETA1-4 : angle 1.44612 ( 12) hydrogen bonds : bond 0.04624 ( 629) hydrogen bonds : angle 3.88634 ( 1795) metal coordination : bond 0.00163 ( 6) SS BOND : bond 0.00113 ( 8) SS BOND : angle 0.85823 ( 16) covalent geometry : bond 0.00280 (11541) covalent geometry : angle 0.71899 (15748) *********************** 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 140 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 107 time to evaluate : 1.302 Fit side-chains revert: symmetry clash REVERT: A 123 GLN cc_start: 0.8260 (mt0) cc_final: 0.7770 (mm110) REVERT: A 207 GLU cc_start: 0.8905 (tm-30) cc_final: 0.8504 (mp0) REVERT: A 443 ILE cc_start: 0.7631 (OUTLIER) cc_final: 0.7157 (tt) REVERT: B 513 LEU cc_start: 0.8278 (OUTLIER) cc_final: 0.8063 (mp) REVERT: B 590 TYR cc_start: 0.7977 (OUTLIER) cc_final: 0.7762 (t80) REVERT: B 689 MET cc_start: 0.7249 (pmm) cc_final: 0.5589 (pp-130) REVERT: B 722 PHE cc_start: 0.8693 (t80) cc_final: 0.8386 (t80) outliers start: 33 outliers final: 25 residues processed: 133 average time/residue: 1.3956 time to fit residues: 210.4317 Evaluate side-chains 131 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 103 time to evaluate : 3.646 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 220 ILE Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain A residue 521 LEU Chi-restraints excluded: chain A residue 585 CYS Chi-restraints excluded: chain A residue 597 ILE Chi-restraints excluded: chain A residue 704 LEU Chi-restraints excluded: chain A residue 787 CYS Chi-restraints excluded: chain A residue 788 ILE Chi-restraints excluded: chain B residue 76 THR Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 220 ILE Chi-restraints excluded: chain B residue 260 VAL Chi-restraints excluded: chain B residue 287 LEU Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain B residue 459 VAL Chi-restraints excluded: chain B residue 513 LEU Chi-restraints excluded: chain B residue 521 LEU Chi-restraints excluded: chain B residue 559 SER Chi-restraints excluded: chain B residue 590 TYR Chi-restraints excluded: chain B residue 597 ILE Chi-restraints excluded: chain B residue 771 SER Chi-restraints excluded: chain B residue 787 CYS Chi-restraints excluded: chain B residue 791 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 89 optimal weight: 2.9990 chunk 93 optimal weight: 5.9990 chunk 104 optimal weight: 6.9990 chunk 90 optimal weight: 0.9990 chunk 43 optimal weight: 0.9990 chunk 127 optimal weight: 3.9990 chunk 74 optimal weight: 6.9990 chunk 87 optimal weight: 0.9980 chunk 26 optimal weight: 0.7980 chunk 23 optimal weight: 0.2980 chunk 115 optimal weight: 3.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.121236 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.076377 restraints weight = 36806.784| |-----------------------------------------------------------------------------| r_work (start): 0.3018 rms_B_bonded: 4.07 r_work: 0.2841 rms_B_bonded: 4.57 restraints_weight: 0.5000 r_work (final): 0.2841 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2842 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2842 r_free = 0.2842 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2842 r_free = 0.2842 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2842 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8161 moved from start: 0.1081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 11567 Z= 0.131 Angle : 0.723 18.291 15800 Z= 0.332 Chirality : 0.044 0.297 1840 Planarity : 0.004 0.047 1850 Dihedral : 7.144 58.275 2734 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 3.18 % Allowed : 26.42 % Favored : 70.40 % 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: 1.28 (0.23), residues: 1276 helix: 2.28 (0.21), residues: 576 sheet: 1.77 (0.28), residues: 276 loop : -1.99 (0.27), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 700 HIS 0.004 0.001 HIS B 594 PHE 0.058 0.001 PHE A 732 TYR 0.043 0.001 TYR A 717 ARG 0.004 0.000 ARG A 118 Details of bonding type rmsd link_NAG-ASN : bond 0.00406 ( 8) link_NAG-ASN : angle 2.46744 ( 24) link_BETA1-4 : bond 0.00435 ( 4) link_BETA1-4 : angle 1.41478 ( 12) hydrogen bonds : bond 0.04572 ( 629) hydrogen bonds : angle 3.85323 ( 1795) metal coordination : bond 0.00189 ( 6) SS BOND : bond 0.00102 ( 8) SS BOND : angle 0.83460 ( 16) covalent geometry : bond 0.00293 (11541) covalent geometry : angle 0.71658 (15748) *********************** 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 145 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 108 time to evaluate : 1.312 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 123 GLN cc_start: 0.8293 (mt0) cc_final: 0.7798 (mm110) REVERT: A 443 ILE cc_start: 0.7627 (OUTLIER) cc_final: 0.7156 (tt) REVERT: A 444 TYR cc_start: 0.8039 (t80) cc_final: 0.7823 (t80) REVERT: A 829 ILE cc_start: 0.8564 (OUTLIER) cc_final: 0.8332 (tp) REVERT: B 513 LEU cc_start: 0.8293 (OUTLIER) cc_final: 0.8084 (mp) REVERT: B 722 PHE cc_start: 0.8701 (t80) cc_final: 0.8404 (OUTLIER) outliers start: 37 outliers final: 24 residues processed: 136 average time/residue: 1.0642 time to fit residues: 164.2502 Evaluate side-chains 132 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 106 time to evaluate : 1.511 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 220 ILE Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain A residue 521 LEU Chi-restraints excluded: chain A residue 585 CYS Chi-restraints excluded: chain A residue 597 ILE Chi-restraints excluded: chain A residue 704 LEU Chi-restraints excluded: chain A residue 787 CYS Chi-restraints excluded: chain A residue 788 ILE Chi-restraints excluded: chain A residue 829 ILE Chi-restraints excluded: chain B residue 76 THR Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 220 ILE Chi-restraints excluded: chain B residue 260 VAL Chi-restraints excluded: chain B residue 287 LEU Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain B residue 459 VAL Chi-restraints excluded: chain B residue 513 LEU Chi-restraints excluded: chain B residue 521 LEU Chi-restraints excluded: chain B residue 597 ILE Chi-restraints excluded: chain B residue 787 CYS Chi-restraints excluded: chain B residue 791 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 21 optimal weight: 2.9990 chunk 73 optimal weight: 2.9990 chunk 56 optimal weight: 0.0170 chunk 35 optimal weight: 0.0970 chunk 48 optimal weight: 10.0000 chunk 41 optimal weight: 0.0770 chunk 103 optimal weight: 5.9990 chunk 54 optimal weight: 1.9990 chunk 97 optimal weight: 3.9990 chunk 31 optimal weight: 0.9980 chunk 14 optimal weight: 0.5980 overall best weight: 0.3574 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 784 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.123065 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.078842 restraints weight = 25804.273| |-----------------------------------------------------------------------------| r_work (start): 0.3081 rms_B_bonded: 3.59 r_work: 0.2921 rms_B_bonded: 4.23 restraints_weight: 0.5000 r_work (final): 0.2921 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2918 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2918 r_free = 0.2918 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2918 r_free = 0.2918 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2918 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8106 moved from start: 0.1328 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 11567 Z= 0.118 Angle : 0.719 18.929 15800 Z= 0.329 Chirality : 0.043 0.296 1840 Planarity : 0.004 0.045 1850 Dihedral : 6.944 57.522 2734 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 2.15 % Allowed : 27.45 % Favored : 70.40 % 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: 1.33 (0.23), residues: 1276 helix: 2.29 (0.21), residues: 576 sheet: 1.83 (0.28), residues: 276 loop : -1.94 (0.27), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 700 HIS 0.004 0.001 HIS B 594 PHE 0.034 0.001 PHE B 722 TYR 0.040 0.001 TYR A 717 ARG 0.003 0.000 ARG A 118 Details of bonding type rmsd link_NAG-ASN : bond 0.00466 ( 8) link_NAG-ASN : angle 2.54397 ( 24) link_BETA1-4 : bond 0.00455 ( 4) link_BETA1-4 : angle 1.42869 ( 12) hydrogen bonds : bond 0.04167 ( 629) hydrogen bonds : angle 3.79240 ( 1795) metal coordination : bond 0.00070 ( 6) SS BOND : bond 0.00095 ( 8) SS BOND : angle 0.69767 ( 16) covalent geometry : bond 0.00253 (11541) covalent geometry : angle 0.71205 (15748) ********************** 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 137 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 112 time to evaluate : 1.303 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 123 GLN cc_start: 0.8239 (mt0) cc_final: 0.7450 (mm-40) REVERT: A 207 GLU cc_start: 0.8897 (tm-30) cc_final: 0.8481 (mp0) REVERT: A 829 ILE cc_start: 0.8524 (OUTLIER) cc_final: 0.8286 (tp) REVERT: B 513 LEU cc_start: 0.8246 (OUTLIER) cc_final: 0.8042 (mp) REVERT: B 689 MET cc_start: 0.7233 (pmm) cc_final: 0.5522 (pp-130) REVERT: B 722 PHE cc_start: 0.8691 (t80) cc_final: 0.8385 (t80) outliers start: 25 outliers final: 14 residues processed: 132 average time/residue: 0.8549 time to fit residues: 127.9272 Evaluate side-chains 122 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 106 time to evaluate : 1.124 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 521 LEU Chi-restraints excluded: chain A residue 585 CYS Chi-restraints excluded: chain A residue 597 ILE Chi-restraints excluded: chain A residue 787 CYS Chi-restraints excluded: chain A residue 829 ILE Chi-restraints excluded: chain B residue 76 THR Chi-restraints excluded: chain B residue 220 ILE Chi-restraints excluded: chain B residue 260 VAL Chi-restraints excluded: chain B residue 287 LEU Chi-restraints excluded: chain B residue 513 LEU Chi-restraints excluded: chain B residue 521 LEU Chi-restraints excluded: chain B residue 559 SER Chi-restraints excluded: chain B residue 597 ILE Chi-restraints excluded: chain B residue 771 SER Chi-restraints excluded: chain B residue 791 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 122 optimal weight: 4.9990 chunk 72 optimal weight: 0.2980 chunk 103 optimal weight: 5.9990 chunk 91 optimal weight: 0.9990 chunk 34 optimal weight: 1.9990 chunk 125 optimal weight: 0.9980 chunk 32 optimal weight: 0.7980 chunk 98 optimal weight: 0.0980 chunk 33 optimal weight: 4.9990 chunk 127 optimal weight: 5.9990 chunk 22 optimal weight: 3.9990 overall best weight: 0.6382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.122590 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.078358 restraints weight = 28929.017| |-----------------------------------------------------------------------------| r_work (start): 0.3065 rms_B_bonded: 3.73 r_work: 0.2902 rms_B_bonded: 4.30 restraints_weight: 0.5000 r_work (final): 0.2902 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2900 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2900 r_free = 0.2900 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2900 r_free = 0.2900 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2900 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8126 moved from start: 0.1335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 11567 Z= 0.124 Angle : 0.731 17.849 15800 Z= 0.335 Chirality : 0.044 0.297 1840 Planarity : 0.004 0.044 1850 Dihedral : 6.891 57.646 2734 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 1.72 % Allowed : 28.14 % Favored : 70.14 % 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: 1.34 (0.23), residues: 1276 helix: 2.28 (0.21), residues: 576 sheet: 1.87 (0.28), residues: 276 loop : -1.93 (0.27), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 700 HIS 0.004 0.001 HIS B 594 PHE 0.055 0.001 PHE A 732 TYR 0.038 0.001 TYR A 717 ARG 0.004 0.000 ARG A 118 Details of bonding type rmsd link_NAG-ASN : bond 0.00412 ( 8) link_NAG-ASN : angle 2.46479 ( 24) link_BETA1-4 : bond 0.00446 ( 4) link_BETA1-4 : angle 1.39955 ( 12) hydrogen bonds : bond 0.04236 ( 629) hydrogen bonds : angle 3.77681 ( 1795) metal coordination : bond 0.00141 ( 6) SS BOND : bond 0.00214 ( 8) SS BOND : angle 1.03916 ( 16) covalent geometry : bond 0.00277 (11541) covalent geometry : angle 0.72426 (15748) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8742.14 seconds wall clock time: 160 minutes 0.48 seconds (9600.48 seconds total)