Starting phenix.real_space_refine on Fri Jul 3 01:15:56 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8woq_37695/07_2026/8woq_37695.cif Found real_map, /net/cci-nas-00/data/ceres_data/8woq_37695/07_2026/8woq_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_2026/8woq_37695.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8woq_37695/07_2026/8woq_37695.map" model { file = "/net/cci-nas-00/data/ceres_data/8woq_37695/07_2026/8woq_37695.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8woq_37695/07_2026/8woq_37695.cif" } resolution = 2.85 write_initial_geo_file = False refinement { macro_cycles = 10 } 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/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, 275 Ad-hoc single atom residues: {' CA': 1} Unusual residues: {' ZN': 1, 'CLR': 7, 'NAG': 2, 'OLA': 1, 'SPL': 1} Classifications: {'undetermined': 12} Link IDs: {None: 10} Chain breaks: 1 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, 303 Ad-hoc single atom residues: {' CA': 1} Unusual residues: {' ZN': 1, 'CLR': 8, 'NAG': 2, 'OLA': 1, 'SPL': 1} Classifications: {'undetermined': 13} Link IDs: {None: 11} Chain breaks: 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: 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: 4.41, per 1000 atoms: 0.39 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: 1.06 Conformation dependent library (CDL) restraints added in 827.3 milliseconds 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: 0.30 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: 1.96 Time building geometry restraints manager: 1.40 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 905 or resid 907 through \ 911)) selection = (chain 'B' and (resid 35 through 80 or resid 82 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: 4.600 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: 0.220 Check model and map are aligned: 0.050 Set scattering table: 0.020 Process input model: 15.180 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:8.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.140 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8396 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. 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 ARG 0.007 0.000 ARG A 118 TYR 0.021 0.001 TYR A 332 PHE 0.030 0.001 PHE B 275 TRP 0.009 0.001 TRP A 700 HIS 0.005 0.001 HIS A 636 Details of bonding type rmsd/Z covalent geometry : bond 0.00415 / 0.19 (11541) covalent geometry : angle 0.81976 / 0.38 (15748) SS BOND : bond 0.00126 / 0.07 ( 8) SS BOND : angle 1.00091 / 0.47 ( 16) hydrogen bonds : bond 0.08980 / 5.80 ( 629) hydrogen bonds : angle 4.30078 / 2.96 ( 1795) metal coordination : bond 0.00178 / 0.11 ( 6) link_BETA1-4 : bond 0.00293 / 0.18 ( 4) link_BETA1-4 : angle 1.61835 / 0.86 ( 12) link_NAG-ASN : bond 0.00396 / 0.20 ( 8) link_NAG-ASN : angle 2.67637 / 2.17 ( 24) *********************** 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 : 0.416 Fit side-chains revert: symmetry clash outliers start: 46 outliers final: 40 residues processed: 145 average time/residue: 0.3611 time to fit residues: 59.4690 Evaluate side-chains 140 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 100 time to evaluate : 0.395 ------------------------------------------------------------------------------- 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 98 optimal weight: 0.5980 chunk 107 optimal weight: 4.9990 chunk 10 optimal weight: 0.4980 chunk 66 optimal weight: 6.9990 chunk 124 optimal weight: 0.8980 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 0.8980 chunk 91 optimal weight: 3.9990 chunk 55 optimal weight: 0.8980 chunk 35 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.121221 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.077103 restraints weight = 28991.564| |-----------------------------------------------------------------------------| r_work (start): 0.3033 rms_B_bonded: 3.67 r_work: 0.2867 rms_B_bonded: 4.28 restraints_weight: 0.5000 r_work (final): 0.2867 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2865 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2865 r_free = 0.2865 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.21 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 = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (8 function evaluations) r_final: 0.2864 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8369 moved from start: 0.0574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 11567 Z= 0.131 Angle : 0.699 16.920 15800 Z= 0.327 Chirality : 0.044 0.286 1840 Planarity : 0.004 0.052 1850 Dihedral : 9.157 59.888 2786 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.00 % Favored : 95.92 % Rotamer: Outliers : 3.53 % Allowed : 25.39 % Favored : 71.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.16 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.24 (0.23), residues: 1276 helix: 2.26 (0.21), residues: 578 sheet: 1.82 (0.28), residues: 272 loop : -2.08 (0.27), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 118 TYR 0.016 0.001 TYR A 332 PHE 0.014 0.001 PHE A 577 TRP 0.008 0.001 TRP A 700 HIS 0.005 0.001 HIS A 636 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.13 (11541) covalent geometry : angle 0.69054 / 0.32 (15748) SS BOND : bond 0.00117 / 0.08 ( 8) SS BOND : angle 0.88097 / 0.45 ( 16) hydrogen bonds : bond 0.04874 / 3.23 ( 629) hydrogen bonds : angle 3.89170 / 2.65 ( 1795) metal coordination : bond 0.00207 / 0.13 ( 6) link_BETA1-4 : bond 0.00345 / 0.20 ( 4) link_BETA1-4 : angle 1.38387 / 0.74 ( 12) link_NAG-ASN : bond 0.00380 / 0.19 ( 8) link_NAG-ASN : angle 2.61827 / 2.09 ( 24) *********************** 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 153 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 112 time to evaluate : 0.444 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 123 GLN cc_start: 0.8180 (mt0) cc_final: 0.7780 (mm110) REVERT: A 207 GLU cc_start: 0.8877 (tm-30) cc_final: 0.8596 (mp0) REVERT: A 208 MET cc_start: 0.8485 (ttm) cc_final: 0.8217 (ttm) REVERT: A 443 ILE cc_start: 0.7668 (OUTLIER) cc_final: 0.7182 (tt) REVERT: B 590 TYR cc_start: 0.7985 (OUTLIER) cc_final: 0.7732 (t80) outliers start: 41 outliers final: 21 residues processed: 144 average time/residue: 0.3722 time to fit residues: 60.4959 Evaluate side-chains 130 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 107 time to evaluate : 0.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 220 ILE 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 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 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 322 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 791 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 97 optimal weight: 4.9990 chunk 123 optimal weight: 0.2980 chunk 106 optimal weight: 3.9990 chunk 83 optimal weight: 0.0670 chunk 38 optimal weight: 6.9990 chunk 1 optimal weight: 4.9990 chunk 55 optimal weight: 1.9990 chunk 53 optimal weight: 8.9990 chunk 102 optimal weight: 6.9990 chunk 101 optimal weight: 0.9980 chunk 33 optimal weight: 0.9980 overall best weight: 0.8720 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.121229 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.075399 restraints weight = 34556.265| |-----------------------------------------------------------------------------| r_work (start): 0.3016 rms_B_bonded: 4.04 r_work: 0.2844 rms_B_bonded: 4.53 restraints_weight: 0.5000 r_work (final): 0.2844 ------------------------------------------------------------------------------- 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 = 0.39 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 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (7 function evaluations) r_final: 0.2842 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8373 moved from start: 0.0748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 11567 Z= 0.131 Angle : 0.691 15.550 15800 Z= 0.319 Chirality : 0.043 0.289 1840 Planarity : 0.004 0.049 1850 Dihedral : 8.319 59.910 2749 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.92 % Favored : 96.00 % Rotamer: Outliers : 3.44 % Allowed : 24.78 % Favored : 71.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.16 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.26 (0.23), residues: 1276 helix: 2.29 (0.21), residues: 578 sheet: 1.74 (0.28), residues: 276 loop : -2.06 (0.27), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 118 TYR 0.013 0.001 TYR B 188 PHE 0.036 0.001 PHE B 722 TRP 0.008 0.001 TRP A 700 HIS 0.005 0.001 HIS A 636 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.13 (11541) covalent geometry : angle 0.68350 / 0.32 (15748) SS BOND : bond 0.00089 / 0.05 ( 8) SS BOND : angle 0.82913 / 0.41 ( 16) hydrogen bonds : bond 0.04706 / 3.12 ( 629) hydrogen bonds : angle 3.83576 / 2.62 ( 1795) metal coordination : bond 0.00206 / 0.12 ( 6) link_BETA1-4 : bond 0.00439 / 0.26 ( 4) link_BETA1-4 : angle 1.36342 / 0.74 ( 12) link_NAG-ASN : bond 0.00405 / 0.20 ( 8) link_NAG-ASN : angle 2.49484 / 2.02 ( 24) *********************** 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 156 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 116 time to evaluate : 0.408 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 123 GLN cc_start: 0.8227 (mt0) cc_final: 0.7774 (mm110) REVERT: A 443 ILE cc_start: 0.7640 (OUTLIER) cc_final: 0.7152 (tt) REVERT: A 590 TYR cc_start: 0.7816 (OUTLIER) cc_final: 0.7596 (t80) REVERT: B 590 TYR cc_start: 0.7976 (OUTLIER) cc_final: 0.7757 (t80) outliers start: 40 outliers final: 19 residues processed: 144 average time/residue: 0.3938 time to fit residues: 63.6572 Evaluate side-chains 133 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 111 time to evaluate : 0.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 190 LEU 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 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 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 287 LEU Chi-restraints excluded: chain B residue 322 LEU 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 87 optimal weight: 0.9980 chunk 69 optimal weight: 2.9990 chunk 94 optimal weight: 6.9990 chunk 1 optimal weight: 4.9990 chunk 76 optimal weight: 1.9990 chunk 123 optimal weight: 3.9990 chunk 102 optimal weight: 5.9990 chunk 64 optimal weight: 10.0000 chunk 111 optimal weight: 4.9990 chunk 21 optimal weight: 3.9990 chunk 66 optimal weight: 0.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 768 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.119023 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.074049 restraints weight = 35074.732| |-----------------------------------------------------------------------------| r_work (start): 0.2974 rms_B_bonded: 3.98 r_work: 0.2798 rms_B_bonded: 4.46 restraints_weight: 0.5000 r_work (final): 0.2798 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2797 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2797 r_free = 0.2797 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2797 r_free = 0.2797 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2797 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8422 moved from start: 0.0840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 11567 Z= 0.221 Angle : 0.738 14.505 15800 Z= 0.348 Chirality : 0.046 0.287 1840 Planarity : 0.004 0.050 1850 Dihedral : 7.994 59.977 2740 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.71 % Favored : 95.21 % Rotamer: Outliers : 4.22 % Allowed : 24.87 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.12 (0.23), residues: 1276 helix: 2.18 (0.21), residues: 578 sheet: 1.75 (0.29), residues: 264 loop : -2.08 (0.26), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 118 TYR 0.020 0.001 TYR A 188 PHE 0.033 0.002 PHE B 722 TRP 0.008 0.001 TRP A 799 HIS 0.005 0.001 HIS A 636 Details of bonding type rmsd/Z covalent geometry : bond 0.00530 / 0.22 (11541) covalent geometry : angle 0.73146 / 0.35 (15748) SS BOND : bond 0.00156 / 0.09 ( 8) SS BOND : angle 1.29272 / 0.67 ( 16) hydrogen bonds : bond 0.05556 / 3.67 ( 629) hydrogen bonds : angle 4.01745 / 2.74 ( 1795) metal coordination : bond 0.00522 / 0.31 ( 6) link_BETA1-4 : bond 0.00447 / 0.27 ( 4) link_BETA1-4 : angle 1.36516 / 0.72 ( 12) link_NAG-ASN : bond 0.00345 / 0.14 ( 8) link_NAG-ASN : angle 2.32479 / 1.87 ( 24) *********************** 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 154 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 105 time to evaluate : 0.411 Fit side-chains revert: symmetry clash REVERT: A 123 GLN cc_start: 0.8304 (mt0) cc_final: 0.7802 (mm110) REVERT: A 207 GLU cc_start: 0.8895 (tm-30) cc_final: 0.8500 (mp0) REVERT: A 443 ILE cc_start: 0.7678 (OUTLIER) cc_final: 0.7212 (tt) REVERT: A 590 TYR cc_start: 0.7813 (OUTLIER) cc_final: 0.7552 (t80) REVERT: B 44 ARG cc_start: 0.8086 (OUTLIER) cc_final: 0.7834 (ptp-110) REVERT: B 513 LEU cc_start: 0.8304 (OUTLIER) cc_final: 0.8076 (mp) REVERT: B 590 TYR cc_start: 0.7975 (OUTLIER) cc_final: 0.7719 (t80) outliers start: 49 outliers final: 23 residues processed: 144 average time/residue: 0.3738 time to fit residues: 60.3890 Evaluate side-chains 126 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 98 time to evaluate : 0.424 ------------------------------------------------------------------------------- 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 260 VAL 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 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 605 TYR Chi-restraints excluded: chain A residue 726 LEU Chi-restraints excluded: chain A residue 728 LEU Chi-restraints excluded: chain A residue 787 CYS Chi-restraints excluded: chain B residue 44 ARG 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 459 VAL Chi-restraints excluded: chain B residue 513 LEU 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 127 optimal weight: 8.9990 chunk 47 optimal weight: 0.8980 chunk 78 optimal weight: 0.9990 chunk 91 optimal weight: 0.8980 chunk 24 optimal weight: 0.3980 chunk 11 optimal weight: 0.8980 chunk 74 optimal weight: 6.9990 chunk 53 optimal weight: 3.9990 chunk 15 optimal weight: 1.9990 chunk 77 optimal weight: 0.7980 chunk 1 optimal weight: 3.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.120967 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.074967 restraints weight = 38613.924| |-----------------------------------------------------------------------------| r_work (start): 0.3004 rms_B_bonded: 4.23 r_work: 0.2827 rms_B_bonded: 4.65 restraints_weight: 0.5000 r_work (final): 0.2827 ------------------------------------------------------------------------------- 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 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2827 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8388 moved from start: 0.0860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 11567 Z= 0.129 Angle : 0.697 14.900 15800 Z= 0.324 Chirality : 0.043 0.291 1840 Planarity : 0.004 0.047 1850 Dihedral : 7.631 59.139 2739 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.08 % Favored : 95.84 % Rotamer: Outliers : 3.53 % Allowed : 25.65 % Favored : 70.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.16 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.24 (0.23), residues: 1276 helix: 2.26 (0.21), residues: 578 sheet: 1.74 (0.28), residues: 276 loop : -2.05 (0.27), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 118 TYR 0.013 0.001 TYR B 188 PHE 0.049 0.001 PHE A 732 TRP 0.008 0.001 TRP A 700 HIS 0.005 0.001 HIS A 636 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.13 (11541) covalent geometry : angle 0.68939 / 0.32 (15748) SS BOND : bond 0.00112 / 0.06 ( 8) SS BOND : angle 0.89868 / 0.43 ( 16) hydrogen bonds : bond 0.04748 / 3.15 ( 629) hydrogen bonds : angle 3.86069 / 2.63 ( 1795) metal coordination : bond 0.00201 / 0.12 ( 6) link_BETA1-4 : bond 0.00442 / 0.26 ( 4) link_BETA1-4 : angle 1.41803 / 0.77 ( 12) link_NAG-ASN : bond 0.00424 / 0.21 ( 8) link_NAG-ASN : angle 2.54405 / 2.03 ( 24) *********************** 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: 41 poor density : 111 time to evaluate : 0.430 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 123 GLN cc_start: 0.8282 (mt0) cc_final: 0.7840 (mm110) REVERT: A 443 ILE cc_start: 0.7626 (OUTLIER) cc_final: 0.7148 (tt) REVERT: B 513 LEU cc_start: 0.8301 (OUTLIER) cc_final: 0.8088 (mp) outliers start: 41 outliers final: 22 residues processed: 141 average time/residue: 0.3372 time to fit residues: 53.9935 Evaluate side-chains 130 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 106 time to evaluate : 0.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 220 ILE Chi-restraints excluded: chain A residue 260 VAL 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 521 LEU 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 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 319 SER Chi-restraints excluded: chain B residue 459 VAL Chi-restraints excluded: chain B residue 513 LEU Chi-restraints excluded: chain B residue 597 ILE Chi-restraints excluded: chain B residue 726 LEU 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 87 optimal weight: 0.9980 chunk 51 optimal weight: 10.0000 chunk 66 optimal weight: 5.9990 chunk 91 optimal weight: 0.0170 chunk 81 optimal weight: 2.9990 chunk 67 optimal weight: 2.9990 chunk 122 optimal weight: 3.9990 chunk 4 optimal weight: 2.9990 chunk 97 optimal weight: 4.9990 chunk 28 optimal weight: 5.9990 chunk 19 optimal weight: 0.4980 overall best weight: 1.5022 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.120355 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.075788 restraints weight = 34887.789| |-----------------------------------------------------------------------------| r_work (start): 0.2997 rms_B_bonded: 3.96 r_work: 0.2821 rms_B_bonded: 4.46 restraints_weight: 0.5000 r_work (final): 0.2821 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2819 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2819 r_free = 0.2819 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 = 0.2819 r_free = 0.2819 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2819 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8402 moved from start: 0.0907 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= 0.169 Angle : 0.732 17.748 15800 Z= 0.338 Chirality : 0.044 0.293 1840 Planarity : 0.004 0.049 1850 Dihedral : 7.514 59.114 2737 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 3.10 % Allowed : 25.56 % Favored : 71.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.16 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.21 (0.23), residues: 1276 helix: 2.25 (0.21), residues: 578 sheet: 1.79 (0.29), residues: 264 loop : -2.03 (0.26), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 118 TYR 0.019 0.001 TYR A 332 PHE 0.028 0.001 PHE B 329 TRP 0.009 0.001 TRP A 700 HIS 0.004 0.001 HIS A 636 Details of bonding type rmsd/Z covalent geometry : bond 0.00397 / 0.17 (11541) covalent geometry : angle 0.72501 / 0.34 (15748) SS BOND : bond 0.00124 / 0.08 ( 8) SS BOND : angle 1.06730 / 0.53 ( 16) hydrogen bonds : bond 0.05057 / 3.34 ( 629) hydrogen bonds : angle 3.91768 / 2.67 ( 1795) metal coordination : bond 0.00344 / 0.21 ( 6) link_BETA1-4 : bond 0.00423 / 0.25 ( 4) link_BETA1-4 : angle 1.38588 / 0.73 ( 12) link_NAG-ASN : bond 0.00376 / 0.17 ( 8) link_NAG-ASN : angle 2.41019 / 1.94 ( 24) *********************** 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 : 0.254 Fit side-chains revert: symmetry clash REVERT: A 123 GLN cc_start: 0.8300 (mt0) cc_final: 0.7808 (mm110) REVERT: A 207 GLU cc_start: 0.8932 (tm-30) cc_final: 0.8493 (mp0) REVERT: A 443 ILE cc_start: 0.7650 (OUTLIER) cc_final: 0.7175 (tt) REVERT: B 44 ARG cc_start: 0.8135 (OUTLIER) cc_final: 0.7929 (ptp-110) REVERT: B 513 LEU cc_start: 0.8303 (OUTLIER) cc_final: 0.8074 (mp) outliers start: 36 outliers final: 25 residues processed: 139 average time/residue: 0.3597 time to fit residues: 56.4198 Evaluate side-chains 130 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 102 time to evaluate : 0.403 ------------------------------------------------------------------------------- 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 260 VAL 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 521 LEU 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 44 ARG 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 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 597 ILE Chi-restraints excluded: chain B residue 726 LEU 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 10 optimal weight: 4.9990 chunk 23 optimal weight: 0.9990 chunk 86 optimal weight: 1.9990 chunk 28 optimal weight: 4.9990 chunk 26 optimal weight: 0.6980 chunk 19 optimal weight: 2.9990 chunk 14 optimal weight: 0.5980 chunk 54 optimal weight: 5.9990 chunk 122 optimal weight: 3.9990 chunk 25 optimal weight: 0.9980 chunk 59 optimal weight: 0.8980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 461 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.121252 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.076270 restraints weight = 38443.179| |-----------------------------------------------------------------------------| r_work (start): 0.3012 rms_B_bonded: 4.15 r_work: 0.2833 rms_B_bonded: 4.62 restraints_weight: 0.5000 r_work (final): 0.2833 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2833 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2833 r_free = 0.2833 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 = 0.2833 r_free = 0.2833 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2833 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8380 moved from start: 0.0982 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= 0.132 Angle : 0.717 19.715 15800 Z= 0.330 Chirality : 0.044 0.294 1840 Planarity : 0.004 0.047 1850 Dihedral : 7.226 58.472 2734 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 3.10 % Allowed : 25.65 % Favored : 71.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.16 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.29 (0.23), residues: 1276 helix: 2.28 (0.21), residues: 576 sheet: 1.78 (0.28), residues: 276 loop : -1.98 (0.27), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 118 TYR 0.013 0.001 TYR B 188 PHE 0.037 0.001 PHE A 732 TRP 0.009 0.001 TRP A 700 HIS 0.004 0.001 HIS A 636 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.13 (11541) covalent geometry : angle 0.70975 / 0.33 (15748) SS BOND : bond 0.00119 / 0.07 ( 8) SS BOND : angle 0.88139 / 0.42 ( 16) hydrogen bonds : bond 0.04662 / 3.10 ( 629) hydrogen bonds : angle 3.84742 / 2.62 ( 1795) metal coordination : bond 0.00191 / 0.11 ( 6) link_BETA1-4 : bond 0.00456 / 0.27 ( 4) link_BETA1-4 : angle 1.43181 / 0.77 ( 12) link_NAG-ASN : bond 0.00416 / 0.21 ( 8) link_NAG-ASN : angle 2.51739 / 2.02 ( 24) *********************** 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 144 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 108 time to evaluate : 0.400 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 123 GLN cc_start: 0.8269 (mt0) cc_final: 0.7805 (mm110) REVERT: A 207 GLU cc_start: 0.8945 (tm-30) cc_final: 0.8505 (mp0) REVERT: A 443 ILE cc_start: 0.7616 (OUTLIER) cc_final: 0.7136 (tt) REVERT: A 444 TYR cc_start: 0.8042 (t80) cc_final: 0.7823 (t80) REVERT: A 829 ILE cc_start: 0.8634 (OUTLIER) cc_final: 0.8390 (tp) REVERT: B 513 LEU cc_start: 0.8290 (OUTLIER) cc_final: 0.8077 (mp) REVERT: B 689 MET cc_start: 0.7258 (pmm) cc_final: 0.5587 (pp-130) outliers start: 36 outliers final: 23 residues processed: 137 average time/residue: 0.3192 time to fit residues: 49.5229 Evaluate side-chains 131 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 105 time to evaluate : 0.248 ------------------------------------------------------------------------------- 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 260 VAL 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 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 829 ILE 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 521 LEU Chi-restraints excluded: chain B residue 559 SER 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 28 optimal weight: 5.9990 chunk 102 optimal weight: 0.2980 chunk 44 optimal weight: 9.9990 chunk 100 optimal weight: 3.9990 chunk 114 optimal weight: 20.0000 chunk 25 optimal weight: 5.9990 chunk 57 optimal weight: 0.9990 chunk 85 optimal weight: 0.7980 chunk 110 optimal weight: 9.9990 chunk 61 optimal weight: 0.6980 chunk 103 optimal weight: 5.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 461 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.120674 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.076131 restraints weight = 32428.018| |-----------------------------------------------------------------------------| r_work (start): 0.3009 rms_B_bonded: 3.86 r_work: 0.2836 rms_B_bonded: 4.40 restraints_weight: 0.5000 r_work (final): 0.2836 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2836 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2836 r_free = 0.2836 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 = 0.2836 r_free = 0.2836 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2836 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8391 moved from start: 0.1010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 11567 Z= 0.161 Angle : 0.738 19.527 15800 Z= 0.340 Chirality : 0.044 0.297 1840 Planarity : 0.004 0.049 1850 Dihedral : 7.177 58.738 2734 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 2.84 % Allowed : 25.99 % Favored : 71.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.16 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.25 (0.23), residues: 1276 helix: 2.25 (0.21), residues: 576 sheet: 1.76 (0.28), residues: 276 loop : -2.00 (0.27), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 118 TYR 0.048 0.001 TYR A 717 PHE 0.049 0.001 PHE A 732 TRP 0.009 0.001 TRP A 700 HIS 0.003 0.001 HIS B 594 Details of bonding type rmsd/Z covalent geometry : bond 0.00375 / 0.16 (11541) covalent geometry : angle 0.73089 / 0.34 (15748) SS BOND : bond 0.00120 / 0.07 ( 8) SS BOND : angle 0.99056 / 0.49 ( 16) hydrogen bonds : bond 0.04905 / 3.25 ( 629) hydrogen bonds : angle 3.90033 / 2.66 ( 1795) metal coordination : bond 0.00307 / 0.18 ( 6) link_BETA1-4 : bond 0.00435 / 0.25 ( 4) link_BETA1-4 : angle 1.39874 / 0.74 ( 12) link_NAG-ASN : bond 0.00376 / 0.18 ( 8) link_NAG-ASN : angle 2.43312 / 1.96 ( 24) *********************** 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 138 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 105 time to evaluate : 0.429 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 123 GLN cc_start: 0.8270 (mt0) cc_final: 0.7791 (mm110) REVERT: A 195 LYS cc_start: 0.9148 (OUTLIER) cc_final: 0.8855 (tmmm) REVERT: A 443 ILE cc_start: 0.7592 (OUTLIER) cc_final: 0.7110 (tt) REVERT: A 444 TYR cc_start: 0.8059 (t80) cc_final: 0.7844 (t80) REVERT: A 829 ILE cc_start: 0.8632 (OUTLIER) cc_final: 0.8390 (tp) REVERT: B 513 LEU cc_start: 0.8296 (OUTLIER) cc_final: 0.8068 (mp) REVERT: B 689 MET cc_start: 0.7242 (pmm) cc_final: 0.5554 (pp-130) outliers start: 33 outliers final: 24 residues processed: 131 average time/residue: 0.3460 time to fit residues: 51.4548 Evaluate side-chains 130 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 102 time to evaluate : 0.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 195 LYS 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 322 LEU Chi-restraints excluded: chain A residue 325 LEU 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 829 ILE 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 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 597 ILE 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 71 optimal weight: 0.9990 chunk 6 optimal weight: 4.9990 chunk 122 optimal weight: 0.4980 chunk 121 optimal weight: 0.8980 chunk 98 optimal weight: 0.7980 chunk 114 optimal weight: 20.0000 chunk 101 optimal weight: 0.9980 chunk 85 optimal weight: 0.8980 chunk 124 optimal weight: 0.8980 chunk 91 optimal weight: 3.9990 chunk 87 optimal weight: 0.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 461 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.121478 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.077101 restraints weight = 30345.648| |-----------------------------------------------------------------------------| r_work (start): 0.3034 rms_B_bonded: 3.78 r_work: 0.2864 rms_B_bonded: 4.34 restraints_weight: 0.5000 r_work (final): 0.2864 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2863 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2863 r_free = 0.2863 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 = 0.2863 r_free = 0.2863 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2863 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8364 moved from start: 0.1085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 11567 Z= 0.132 Angle : 0.728 20.182 15800 Z= 0.336 Chirality : 0.044 0.296 1840 Planarity : 0.004 0.048 1850 Dihedral : 7.038 57.974 2733 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 2.93 % Allowed : 25.99 % Favored : 71.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.16 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.29 (0.23), residues: 1276 helix: 2.27 (0.21), residues: 576 sheet: 1.79 (0.28), residues: 276 loop : -1.98 (0.27), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 118 TYR 0.044 0.001 TYR A 717 PHE 0.029 0.001 PHE B 329 TRP 0.009 0.001 TRP A 700 HIS 0.004 0.001 HIS B 594 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.13 (11541) covalent geometry : angle 0.72135 / 0.33 (15748) SS BOND : bond 0.00117 / 0.07 ( 8) SS BOND : angle 0.85928 / 0.40 ( 16) hydrogen bonds : bond 0.04612 / 3.06 ( 629) hydrogen bonds : angle 3.86934 / 2.63 ( 1795) metal coordination : bond 0.00180 / 0.11 ( 6) link_BETA1-4 : bond 0.00442 / 0.26 ( 4) link_BETA1-4 : angle 1.41680 / 0.75 ( 12) link_NAG-ASN : bond 0.00411 / 0.21 ( 8) link_NAG-ASN : angle 2.50987 / 2.02 ( 24) *********************** 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 141 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 107 time to evaluate : 0.248 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 123 GLN cc_start: 0.8243 (mt0) cc_final: 0.7768 (mm110) REVERT: A 195 LYS cc_start: 0.9143 (OUTLIER) cc_final: 0.8836 (tmmm) REVERT: A 207 GLU cc_start: 0.8934 (tm-30) cc_final: 0.8465 (mp0) REVERT: A 443 ILE cc_start: 0.7575 (OUTLIER) cc_final: 0.7096 (tt) REVERT: A 829 ILE cc_start: 0.8605 (OUTLIER) cc_final: 0.8352 (tp) REVERT: B 513 LEU cc_start: 0.8276 (OUTLIER) cc_final: 0.8065 (mp) outliers start: 34 outliers final: 24 residues processed: 134 average time/residue: 0.3129 time to fit residues: 47.1550 Evaluate side-chains 132 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 104 time to evaluate : 0.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 195 LYS 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 322 LEU Chi-restraints excluded: chain A residue 325 LEU 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 605 TYR Chi-restraints excluded: chain A residue 704 LEU Chi-restraints excluded: chain A residue 787 CYS Chi-restraints excluded: chain A residue 829 ILE 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 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 597 ILE 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 98 optimal weight: 0.3980 chunk 10 optimal weight: 0.7980 chunk 34 optimal weight: 2.9990 chunk 53 optimal weight: 8.9990 chunk 7 optimal weight: 0.1980 chunk 66 optimal weight: 0.6980 chunk 110 optimal weight: 10.0000 chunk 105 optimal weight: 0.6980 chunk 20 optimal weight: 1.9990 chunk 109 optimal weight: 8.9990 chunk 104 optimal weight: 6.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 461 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 784 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.122546 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.077230 restraints weight = 35092.265| |-----------------------------------------------------------------------------| r_work (start): 0.3048 rms_B_bonded: 4.07 r_work: 0.2876 rms_B_bonded: 4.57 restraints_weight: 0.5000 r_work (final): 0.2876 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2869 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2869 r_free = 0.2869 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 = 0.2869 r_free = 0.2869 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2869 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8344 moved from start: 0.1249 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= 0.123 Angle : 0.727 18.138 15800 Z= 0.333 Chirality : 0.044 0.298 1840 Planarity : 0.004 0.046 1850 Dihedral : 6.925 57.590 2733 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 2.41 % Allowed : 26.59 % Favored : 71.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.16 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.31 (0.23), residues: 1276 helix: 2.27 (0.21), residues: 576 sheet: 1.82 (0.28), residues: 276 loop : -1.96 (0.27), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 118 TYR 0.042 0.001 TYR A 717 PHE 0.053 0.001 PHE A 732 TRP 0.010 0.001 TRP A 700 HIS 0.004 0.001 HIS B 594 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.12 (11541) covalent geometry : angle 0.71965 / 0.33 (15748) SS BOND : bond 0.00103 / 0.06 ( 8) SS BOND : angle 1.15326 / 0.52 ( 16) hydrogen bonds : bond 0.04361 / 2.89 ( 629) hydrogen bonds : angle 3.81244 / 2.60 ( 1795) metal coordination : bond 0.00134 / 0.08 ( 6) link_BETA1-4 : bond 0.00489 / 0.29 ( 4) link_BETA1-4 : angle 1.42211 / 0.76 ( 12) link_NAG-ASN : bond 0.00426 / 0.22 ( 8) link_NAG-ASN : angle 2.53247 / 2.05 ( 24) ********************** 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 138 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 110 time to evaluate : 0.388 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 123 GLN cc_start: 0.8241 (mt0) cc_final: 0.7729 (mm110) REVERT: A 207 GLU cc_start: 0.8921 (tm-30) cc_final: 0.8449 (mp0) REVERT: A 829 ILE cc_start: 0.8484 (OUTLIER) cc_final: 0.8256 (tp) REVERT: B 513 LEU cc_start: 0.8255 (OUTLIER) cc_final: 0.8050 (mp) REVERT: B 689 MET cc_start: 0.7220 (pmm) cc_final: 0.5546 (pp-130) outliers start: 28 outliers final: 18 residues processed: 132 average time/residue: 0.3097 time to fit residues: 46.0440 Evaluate side-chains 126 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 106 time to evaluate : 0.385 ------------------------------------------------------------------------------- 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 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 829 ILE Chi-restraints excluded: chain B residue 164 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 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 597 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 74 optimal weight: 3.9990 chunk 3 optimal weight: 0.0040 chunk 71 optimal weight: 1.9990 chunk 8 optimal weight: 0.9990 chunk 29 optimal weight: 0.0030 chunk 5 optimal weight: 0.6980 chunk 32 optimal weight: 0.8980 chunk 25 optimal weight: 2.9990 chunk 36 optimal weight: 4.9990 chunk 122 optimal weight: 4.9990 chunk 70 optimal weight: 2.9990 overall best weight: 0.5204 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.123101 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.080266 restraints weight = 19810.483| |-----------------------------------------------------------------------------| r_work (start): 0.3103 rms_B_bonded: 3.16 r_work: 0.2946 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.2946 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2941 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2941 r_free = 0.2941 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2941 r_free = 0.2941 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2941 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8315 moved from start: 0.1347 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= 0.121 Angle : 0.732 19.670 15800 Z= 0.335 Chirality : 0.044 0.297 1840 Planarity : 0.004 0.045 1850 Dihedral : 6.810 57.807 2733 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 1.72 % Allowed : 27.37 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.30 (0.23), residues: 1276 helix: 2.15 (0.21), residues: 590 sheet: 1.85 (0.28), residues: 276 loop : -1.93 (0.28), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 118 TYR 0.041 0.001 TYR A 717 PHE 0.029 0.001 PHE B 329 TRP 0.010 0.001 TRP A 700 HIS 0.004 0.001 HIS B 594 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.12 (11541) covalent geometry : angle 0.72494 / 0.33 (15748) SS BOND : bond 0.00141 / 0.06 ( 8) SS BOND : angle 0.97636 / 0.45 ( 16) hydrogen bonds : bond 0.04251 / 2.84 ( 629) hydrogen bonds : angle 3.78468 / 2.58 ( 1795) metal coordination : bond 0.00120 / 0.07 ( 6) link_BETA1-4 : bond 0.00447 / 0.26 ( 4) link_BETA1-4 : angle 1.39804 / 0.74 ( 12) link_NAG-ASN : bond 0.00423 / 0.23 ( 8) link_NAG-ASN : angle 2.50303 / 2.03 ( 24) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3535.59 seconds wall clock time: 61 minutes 8.71 seconds (3668.71 seconds total)