Starting phenix.real_space_refine on Sat Oct 11 03:35:37 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8woq_37695/10_2025/8woq_37695.cif Found real_map, /net/cci-nas-00/data/ceres_data/8woq_37695/10_2025/8woq_37695.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.85 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8woq_37695/10_2025/8woq_37695.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8woq_37695/10_2025/8woq_37695.map" model { file = "/net/cci-nas-00/data/ceres_data/8woq_37695/10_2025/8woq_37695.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8woq_37695/10_2025/8woq_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-2.0-5842/lib/python3.9/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, 276 Unusual residues: {' CA': 1, ' ZN': 1, 'CLR': 7, 'NAG': 2, 'OLA': 1, 'SPL': 1} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 304 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 304 Unusual residues: {' CA': 1, ' ZN': 1, 'CLR': 8, 'NAG': 2, 'OLA': 1, 'SPL': 1} Classifications: {'undetermined': 14} Link IDs: {None: 13} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Time building chain proxies: 4.82, per 1000 atoms: 0.43 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: 0.90 Conformation dependent library (CDL) restraints added in 874.5 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 0.40 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: 2.06 Time building geometry restraints manager: 1.22 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: 3.150 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.160 Check model and map are aligned: 0.050 Set scattering table: 0.030 Process input model: 15.810 Find NCS groups from input model: 0.260 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:7.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.610 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8185 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.136 11567 Z= 0.193 Angle : 0.827 20.220 15800 Z= 0.377 Chirality : 0.046 0.320 1840 Planarity : 0.007 0.155 1850 Dihedral : 15.764 86.946 5135 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.79 % Favored : 95.13 % Rotamer: Outliers : 3.96 % Allowed : 27.37 % Favored : 68.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.16 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren 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 covalent geometry : bond 0.00415 (11541) covalent geometry : angle 0.81976 (15748) SS BOND : bond 0.00126 ( 8) SS BOND : angle 1.00091 ( 16) hydrogen bonds : bond 0.08980 ( 629) hydrogen bonds : angle 4.30078 ( 1795) metal coordination : bond 0.00178 ( 6) link_BETA1-4 : bond 0.00293 ( 4) link_BETA1-4 : angle 1.61835 ( 12) link_NAG-ASN : bond 0.00396 ( 8) link_NAG-ASN : angle 2.67637 ( 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 : 0.413 Fit side-chains revert: symmetry clash outliers start: 46 outliers final: 40 residues processed: 145 average time/residue: 0.3599 time to fit residues: 59.1288 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 : 0.423 ------------------------------------------------------------------------------- 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... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.121110 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.077028 restraints weight = 29024.822| |-----------------------------------------------------------------------------| r_work (start): 0.3033 rms_B_bonded: 3.68 r_work: 0.2866 rms_B_bonded: 4.29 restraints_weight: 0.5000 r_work (final): 0.2866 ------------------------------------------------------------------------------- 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 | |-----------------------------------------------------------------------------| r_final: 0.2864 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8151 moved from start: 0.0578 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 : 0.698 16.788 15800 Z= 0.326 Chirality : 0.044 0.288 1840 Planarity : 0.004 0.052 1850 Dihedral : 9.144 59.775 2786 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.92 % Favored : 96.00 % 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 aren not related in a simple way. whole: 1.23 (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 0.017 0.001 TYR A 332 PHE 0.014 0.001 PHE B 276 TRP 0.008 0.001 TRP A 700 HIS 0.005 0.001 HIS A 636 Details of bonding type rmsd covalent geometry : bond 0.00291 (11541) covalent geometry : angle 0.68986 (15748) SS BOND : bond 0.00103 ( 8) SS BOND : angle 0.85964 ( 16) hydrogen bonds : bond 0.04878 ( 629) hydrogen bonds : angle 3.88920 ( 1795) metal coordination : bond 0.00211 ( 6) link_BETA1-4 : bond 0.00314 ( 4) link_BETA1-4 : angle 1.35002 ( 12) link_NAG-ASN : bond 0.00389 ( 8) link_NAG-ASN : angle 2.61738 ( 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 : 0.481 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 123 GLN cc_start: 0.8187 (mt0) cc_final: 0.7781 (mm110) REVERT: A 207 GLU cc_start: 0.8874 (tm-30) cc_final: 0.8591 (mp0) REVERT: A 208 MET cc_start: 0.8486 (ttm) cc_final: 0.8217 (ttm) REVERT: A 443 ILE cc_start: 0.7667 (OUTLIER) cc_final: 0.7183 (tt) REVERT: B 590 TYR cc_start: 0.7977 (OUTLIER) cc_final: 0.7755 (t80) outliers start: 41 outliers final: 21 residues processed: 144 average time/residue: 0.3790 time to fit residues: 61.6340 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 : 0.418 ------------------------------------------------------------------------------- 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: 0.3980 chunk 106 optimal weight: 3.9990 chunk 83 optimal weight: 0.2980 chunk 38 optimal weight: 7.9990 chunk 1 optimal weight: 4.9990 chunk 55 optimal weight: 1.9990 chunk 53 optimal weight: 3.9990 chunk 102 optimal weight: 5.9990 chunk 101 optimal weight: 0.6980 chunk 33 optimal weight: 0.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.121290 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.076587 restraints weight = 34523.843| |-----------------------------------------------------------------------------| r_work (start): 0.3022 rms_B_bonded: 3.97 r_work: 0.2851 rms_B_bonded: 4.45 restraints_weight: 0.5000 r_work (final): 0.2851 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2849 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2849 r_free = 0.2849 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 = 0.2849 r_free = 0.2849 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2849 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8158 moved from start: 0.0736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 11567 Z= 0.132 Angle : 0.690 15.517 15800 Z= 0.319 Chirality : 0.043 0.288 1840 Planarity : 0.004 0.049 1850 Dihedral : 8.356 59.879 2749 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.92 % Favored : 96.00 % Rotamer: Outliers : 3.27 % Allowed : 24.78 % Favored : 71.94 % 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 aren not related in a simple way. whole: 1.25 (0.23), residues: 1276 helix: 2.28 (0.21), residues: 578 sheet: 1.75 (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 covalent geometry : bond 0.00297 (11541) covalent geometry : angle 0.68311 (15748) SS BOND : bond 0.00085 ( 8) SS BOND : angle 0.83273 ( 16) hydrogen bonds : bond 0.04718 ( 629) hydrogen bonds : angle 3.84244 ( 1795) metal coordination : bond 0.00207 ( 6) link_BETA1-4 : bond 0.00462 ( 4) link_BETA1-4 : angle 1.36446 ( 12) link_NAG-ASN : bond 0.00402 ( 8) link_NAG-ASN : angle 2.50215 ( 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 154 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 116 time to evaluate : 0.429 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 123 GLN cc_start: 0.8212 (mt0) cc_final: 0.7756 (mm110) REVERT: A 443 ILE cc_start: 0.7644 (OUTLIER) cc_final: 0.7156 (tt) REVERT: A 590 TYR cc_start: 0.7828 (OUTLIER) cc_final: 0.7568 (t80) REVERT: B 590 TYR cc_start: 0.7987 (OUTLIER) cc_final: 0.7764 (t80) outliers start: 38 outliers final: 19 residues processed: 142 average time/residue: 0.3747 time to fit residues: 59.5960 Evaluate side-chains 134 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 112 time to evaluate : 0.491 ------------------------------------------------------------------------------- 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: 0.5980 chunk 69 optimal weight: 2.9990 chunk 94 optimal weight: 7.9990 chunk 1 optimal weight: 4.9990 chunk 76 optimal weight: 0.9980 chunk 123 optimal weight: 0.0970 chunk 102 optimal weight: 4.9990 chunk 64 optimal weight: 9.9990 chunk 111 optimal weight: 9.9990 chunk 21 optimal weight: 0.7980 chunk 66 optimal weight: 0.9980 overall best weight: 0.6978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 784 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.122001 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.077213 restraints weight = 34862.067| |-----------------------------------------------------------------------------| r_work (start): 0.3037 rms_B_bonded: 3.99 r_work: 0.2860 rms_B_bonded: 4.51 restraints_weight: 0.5000 r_work (final): 0.2860 ------------------------------------------------------------------------------- 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 | |-----------------------------------------------------------------------------| r_final: 0.2863 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8143 moved from start: 0.0931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 11567 Z= 0.122 Angle : 0.691 15.764 15800 Z= 0.319 Chirality : 0.043 0.292 1840 Planarity : 0.004 0.049 1850 Dihedral : 7.677 59.352 2740 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.85 % Favored : 96.08 % Rotamer: Outliers : 3.53 % Allowed : 24.70 % 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 aren not related in a simple way. whole: 1.29 (0.23), residues: 1276 helix: 2.30 (0.21), residues: 578 sheet: 1.80 (0.28), residues: 276 loop : -2.04 (0.27), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 118 TYR 0.018 0.001 TYR A 332 PHE 0.032 0.001 PHE B 722 TRP 0.008 0.001 TRP A 700 HIS 0.006 0.001 HIS A 636 Details of bonding type rmsd covalent geometry : bond 0.00267 (11541) covalent geometry : angle 0.68344 (15748) SS BOND : bond 0.00085 ( 8) SS BOND : angle 0.76700 ( 16) hydrogen bonds : bond 0.04511 ( 629) hydrogen bonds : angle 3.79211 ( 1795) metal coordination : bond 0.00160 ( 6) link_BETA1-4 : bond 0.00494 ( 4) link_BETA1-4 : angle 1.37270 ( 12) link_NAG-ASN : bond 0.00415 ( 8) link_NAG-ASN : angle 2.51328 ( 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 156 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 115 time to evaluate : 0.499 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 123 GLN cc_start: 0.8232 (mt0) cc_final: 0.7799 (mm110) REVERT: A 207 GLU cc_start: 0.8908 (tm-30) cc_final: 0.8563 (mp0) REVERT: A 590 TYR cc_start: 0.7822 (OUTLIER) cc_final: 0.7596 (t80) outliers start: 41 outliers final: 20 residues processed: 145 average time/residue: 0.3688 time to fit residues: 60.1026 Evaluate side-chains 129 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 108 time to evaluate : 0.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 220 ILE Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain A residue 585 CYS Chi-restraints excluded: chain A residue 590 TYR Chi-restraints excluded: chain A residue 597 ILE Chi-restraints excluded: chain A residue 726 LEU Chi-restraints excluded: chain A residue 787 CYS Chi-restraints excluded: chain B residue 76 THR Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 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 521 LEU Chi-restraints excluded: chain B residue 597 ILE Chi-restraints excluded: chain B residue 763 LEU 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: 0.8980 chunk 47 optimal weight: 0.8980 chunk 78 optimal weight: 0.8980 chunk 91 optimal weight: 3.9990 chunk 24 optimal weight: 8.9990 chunk 11 optimal weight: 1.9990 chunk 74 optimal weight: 0.0670 chunk 53 optimal weight: 4.9990 chunk 15 optimal weight: 0.9980 chunk 77 optimal weight: 2.9990 chunk 1 optimal weight: 4.9990 overall best weight: 0.7518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 461 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.121922 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.076322 restraints weight = 38648.747| |-----------------------------------------------------------------------------| r_work (start): 0.3030 rms_B_bonded: 4.21 r_work: 0.2855 rms_B_bonded: 4.65 restraints_weight: 0.5000 r_work (final): 0.2855 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2855 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2855 r_free = 0.2855 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 = 0.2855 r_free = 0.2855 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2855 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8151 moved from start: 0.1013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 11567 Z= 0.124 Angle : 0.685 15.778 15800 Z= 0.317 Chirality : 0.043 0.293 1840 Planarity : 0.004 0.048 1850 Dihedral : 7.288 57.391 2734 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.08 % Favored : 95.84 % 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 aren not related in a simple way. whole: 1.34 (0.23), residues: 1276 helix: 2.32 (0.21), residues: 576 sheet: 1.82 (0.28), residues: 276 loop : -1.95 (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 0.027 0.001 PHE B 329 TRP 0.008 0.001 TRP A 700 HIS 0.005 0.001 HIS A 636 Details of bonding type rmsd covalent geometry : bond 0.00276 (11541) covalent geometry : angle 0.67750 (15748) SS BOND : bond 0.00097 ( 8) SS BOND : angle 0.84149 ( 16) hydrogen bonds : bond 0.04448 ( 629) hydrogen bonds : angle 3.76477 ( 1795) metal coordination : bond 0.00172 ( 6) link_BETA1-4 : bond 0.00445 ( 4) link_BETA1-4 : angle 1.37221 ( 12) link_NAG-ASN : bond 0.00409 ( 8) link_NAG-ASN : angle 2.47812 ( 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 156 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 116 time to evaluate : 0.373 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 123 GLN cc_start: 0.8241 (mt0) cc_final: 0.7802 (mm110) REVERT: A 590 TYR cc_start: 0.7851 (OUTLIER) cc_final: 0.7597 (t80) outliers start: 40 outliers final: 19 residues processed: 144 average time/residue: 0.3627 time to fit residues: 58.7740 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 : 0.470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 521 LEU Chi-restraints excluded: chain A residue 585 CYS Chi-restraints excluded: chain A residue 590 TYR Chi-restraints excluded: chain A residue 597 ILE Chi-restraints excluded: chain A residue 787 CYS Chi-restraints excluded: chain A residue 788 ILE Chi-restraints excluded: chain B residue 76 THR Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 220 ILE Chi-restraints excluded: chain B residue 260 VAL Chi-restraints excluded: chain B residue 287 LEU Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain B residue 521 LEU Chi-restraints excluded: chain B residue 597 ILE Chi-restraints excluded: chain B residue 763 LEU 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: 0.7980 chunk 51 optimal weight: 9.9990 chunk 66 optimal weight: 0.2980 chunk 91 optimal weight: 3.9990 chunk 81 optimal weight: 0.8980 chunk 67 optimal weight: 2.9990 chunk 122 optimal weight: 0.0970 chunk 4 optimal weight: 2.9990 chunk 97 optimal weight: 4.9990 chunk 28 optimal weight: 5.9990 chunk 19 optimal weight: 0.6980 overall best weight: 0.5578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3835 r_free = 0.3835 target = 0.122897 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.078161 restraints weight = 34648.956| |-----------------------------------------------------------------------------| r_work (start): 0.3061 rms_B_bonded: 4.01 r_work: 0.2886 rms_B_bonded: 4.54 restraints_weight: 0.5000 r_work (final): 0.2886 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2881 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2881 r_free = 0.2881 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2881 r_free = 0.2881 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2881 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8120 moved from start: 0.1142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 11567 Z= 0.119 Angle : 0.706 16.024 15800 Z= 0.323 Chirality : 0.043 0.293 1840 Planarity : 0.004 0.046 1850 Dihedral : 7.104 59.415 2734 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 2.84 % Allowed : 25.65 % Favored : 71.51 % 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 aren not related in a simple way. whole: 1.36 (0.23), residues: 1276 helix: 2.30 (0.21), residues: 576 sheet: 1.85 (0.28), residues: 276 loop : -1.91 (0.27), residues: 424 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 covalent geometry : bond 0.00260 (11541) covalent geometry : angle 0.69866 (15748) SS BOND : bond 0.00123 ( 8) SS BOND : angle 0.84374 ( 16) hydrogen bonds : bond 0.04297 ( 629) hydrogen bonds : angle 3.76215 ( 1795) metal coordination : bond 0.00127 ( 6) link_BETA1-4 : bond 0.00413 ( 4) link_BETA1-4 : angle 1.38363 ( 12) link_NAG-ASN : bond 0.00431 ( 8) link_NAG-ASN : angle 2.51438 ( 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: 33 poor density : 113 time to evaluate : 0.419 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 123 GLN cc_start: 0.8239 (mt0) cc_final: 0.7797 (mm110) REVERT: A 207 GLU cc_start: 0.8914 (tm-30) cc_final: 0.8485 (mp0) REVERT: A 461 GLN cc_start: 0.8798 (OUTLIER) cc_final: 0.8573 (mp10) REVERT: A 591 GLN cc_start: 0.6719 (pp30) cc_final: 0.6519 (pp30) outliers start: 33 outliers final: 21 residues processed: 136 average time/residue: 0.3842 time to fit residues: 58.9413 Evaluate side-chains 131 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 109 time to evaluate : 0.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 GLU Chi-restraints excluded: chain A residue 190 LEU 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 461 GLN Chi-restraints excluded: chain A residue 521 LEU Chi-restraints excluded: chain A residue 585 CYS Chi-restraints excluded: chain A residue 597 ILE Chi-restraints excluded: chain A residue 787 CYS Chi-restraints excluded: chain A residue 788 ILE Chi-restraints excluded: chain B residue 76 THR 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 521 LEU Chi-restraints excluded: chain B residue 597 ILE Chi-restraints excluded: chain B residue 763 LEU 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: 0.9980 chunk 23 optimal weight: 0.0870 chunk 86 optimal weight: 3.9990 chunk 28 optimal weight: 5.9990 chunk 26 optimal weight: 1.9990 chunk 19 optimal weight: 0.9980 chunk 14 optimal weight: 0.6980 chunk 54 optimal weight: 2.9990 chunk 122 optimal weight: 4.9990 chunk 25 optimal weight: 2.9990 chunk 59 optimal weight: 2.9990 overall best weight: 0.9560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 461 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 624 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.121960 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.076787 restraints weight = 38393.728| |-----------------------------------------------------------------------------| r_work (start): 0.3039 rms_B_bonded: 4.15 r_work: 0.2863 rms_B_bonded: 4.60 restraints_weight: 0.5000 r_work (final): 0.2863 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2857 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2857 r_free = 0.2857 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 = 0.2857 r_free = 0.2857 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2857 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8143 moved from start: 0.1132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 11567 Z= 0.135 Angle : 0.709 16.883 15800 Z= 0.325 Chirality : 0.043 0.295 1840 Planarity : 0.004 0.047 1850 Dihedral : 7.019 57.273 2734 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 2.75 % Allowed : 25.56 % Favored : 71.69 % 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 aren not related in a simple way. whole: 1.37 (0.23), residues: 1276 helix: 2.33 (0.21), residues: 576 sheet: 1.85 (0.28), residues: 276 loop : -1.93 (0.27), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 118 TYR 0.014 0.001 TYR A 188 PHE 0.056 0.001 PHE A 732 TRP 0.008 0.001 TRP A 700 HIS 0.003 0.001 HIS A 636 Details of bonding type rmsd covalent geometry : bond 0.00307 (11541) covalent geometry : angle 0.70195 (15748) SS BOND : bond 0.00104 ( 8) SS BOND : angle 0.93086 ( 16) hydrogen bonds : bond 0.04430 ( 629) hydrogen bonds : angle 3.76971 ( 1795) metal coordination : bond 0.00210 ( 6) link_BETA1-4 : bond 0.00419 ( 4) link_BETA1-4 : angle 1.35727 ( 12) link_NAG-ASN : bond 0.00381 ( 8) link_NAG-ASN : angle 2.46053 ( 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: 32 poor density : 112 time to evaluate : 0.446 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 123 GLN cc_start: 0.8254 (mt0) cc_final: 0.7801 (mm110) REVERT: A 207 GLU cc_start: 0.8916 (tm-30) cc_final: 0.8487 (mp0) REVERT: A 829 ILE cc_start: 0.8569 (OUTLIER) cc_final: 0.8320 (tp) REVERT: B 513 LEU cc_start: 0.8300 (OUTLIER) cc_final: 0.8094 (mp) REVERT: B 689 MET cc_start: 0.7254 (pmm) cc_final: 0.5545 (pp-130) outliers start: 32 outliers final: 19 residues processed: 135 average time/residue: 0.3801 time to fit residues: 58.1719 Evaluate side-chains 128 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 107 time to evaluate : 0.421 ------------------------------------------------------------------------------- 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 521 LEU Chi-restraints excluded: chain A residue 585 CYS Chi-restraints excluded: chain A residue 597 ILE Chi-restraints excluded: chain A residue 787 CYS Chi-restraints excluded: chain A residue 788 ILE 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 597 ILE Chi-restraints excluded: chain B residue 763 LEU 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: 5.9990 chunk 44 optimal weight: 7.9990 chunk 100 optimal weight: 3.9990 chunk 114 optimal weight: 20.0000 chunk 25 optimal weight: 5.9990 chunk 57 optimal weight: 0.8980 chunk 85 optimal weight: 3.9990 chunk 110 optimal weight: 10.0000 chunk 61 optimal weight: 0.7980 chunk 103 optimal weight: 5.9990 overall best weight: 3.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 461 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 768 GLN A 784 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.117730 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.073059 restraints weight = 32300.435| |-----------------------------------------------------------------------------| r_work (start): 0.2955 rms_B_bonded: 3.84 r_work: 0.2781 rms_B_bonded: 4.37 restraints_weight: 0.5000 r_work (final): 0.2781 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2779 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2779 r_free = 0.2779 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2779 r_free = 0.2779 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2779 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8235 moved from start: 0.1163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.058 11567 Z= 0.294 Angle : 0.815 17.591 15800 Z= 0.385 Chirality : 0.048 0.295 1840 Planarity : 0.005 0.051 1850 Dihedral : 7.462 59.128 2733 Min Nonbonded Distance : 1.896 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer: Outliers : 2.93 % Allowed : 25.39 % Favored : 71.69 % 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 aren not related in a simple way. whole: 1.06 (0.23), residues: 1276 helix: 2.10 (0.21), residues: 578 sheet: 1.78 (0.29), residues: 264 loop : -2.10 (0.26), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 118 TYR 0.026 0.002 TYR A 188 PHE 0.030 0.002 PHE B 329 TRP 0.014 0.002 TRP A 799 HIS 0.005 0.001 HIS A 50 Details of bonding type rmsd covalent geometry : bond 0.00704 (11541) covalent geometry : angle 0.80906 (15748) SS BOND : bond 0.00197 ( 8) SS BOND : angle 1.71983 ( 16) hydrogen bonds : bond 0.06143 ( 629) hydrogen bonds : angle 4.14891 ( 1795) metal coordination : bond 0.00733 ( 6) link_BETA1-4 : bond 0.00446 ( 4) link_BETA1-4 : angle 1.42271 ( 12) link_NAG-ASN : bond 0.00358 ( 8) link_NAG-ASN : angle 2.25285 ( 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: 34 poor density : 104 time to evaluate : 0.474 Fit side-chains revert: symmetry clash REVERT: A 123 GLN cc_start: 0.8321 (mt0) cc_final: 0.7818 (mm110) REVERT: A 461 GLN cc_start: 0.8818 (OUTLIER) cc_final: 0.8574 (mp10) REVERT: A 829 ILE cc_start: 0.8608 (OUTLIER) cc_final: 0.8375 (tp) REVERT: B 36 ARG cc_start: 0.8302 (mpp-170) cc_final: 0.6692 (mmt-90) REVERT: B 513 LEU cc_start: 0.8325 (OUTLIER) cc_final: 0.8077 (mp) REVERT: B 689 MET cc_start: 0.7255 (pmm) cc_final: 0.5604 (pp-130) outliers start: 34 outliers final: 15 residues processed: 130 average time/residue: 0.4585 time to fit residues: 66.1785 Evaluate side-chains 118 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 100 time to evaluate : 0.467 ------------------------------------------------------------------------------- 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 461 GLN Chi-restraints excluded: chain A residue 585 CYS Chi-restraints excluded: chain A residue 597 ILE Chi-restraints excluded: chain A residue 605 TYR Chi-restraints excluded: chain A residue 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 459 VAL Chi-restraints excluded: chain B residue 513 LEU Chi-restraints excluded: chain B residue 559 SER 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: 0.6980 chunk 6 optimal weight: 0.9980 chunk 122 optimal weight: 0.9990 chunk 121 optimal weight: 2.9990 chunk 98 optimal weight: 0.8980 chunk 114 optimal weight: 20.0000 chunk 101 optimal weight: 3.9990 chunk 85 optimal weight: 1.9990 chunk 124 optimal weight: 1.9990 chunk 91 optimal weight: 0.9980 chunk 87 optimal weight: 0.6980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3800 r_free = 0.3800 target = 0.120345 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.074883 restraints weight = 30510.526| |-----------------------------------------------------------------------------| r_work (start): 0.3013 rms_B_bonded: 3.87 r_work: 0.2846 rms_B_bonded: 4.40 restraints_weight: 0.5000 r_work (final): 0.2846 ------------------------------------------------------------------------------- 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 | |-----------------------------------------------------------------------------| r_final: 0.2842 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8162 moved from start: 0.1039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 11567 Z= 0.142 Angle : 0.744 18.656 15800 Z= 0.344 Chirality : 0.044 0.292 1840 Planarity : 0.004 0.048 1850 Dihedral : 7.174 59.391 2733 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 2.32 % Allowed : 26.42 % 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 aren not related in a simple way. whole: 1.18 (0.23), residues: 1276 helix: 2.19 (0.21), residues: 572 sheet: 1.76 (0.29), residues: 276 loop : -2.02 (0.27), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 118 TYR 0.023 0.001 TYR A 717 PHE 0.048 0.001 PHE A 732 TRP 0.007 0.001 TRP A 446 HIS 0.006 0.001 HIS A 636 Details of bonding type rmsd covalent geometry : bond 0.00321 (11541) covalent geometry : angle 0.73663 (15748) SS BOND : bond 0.00155 ( 8) SS BOND : angle 1.07292 ( 16) hydrogen bonds : bond 0.04902 ( 629) hydrogen bonds : angle 3.94310 ( 1795) metal coordination : bond 0.00180 ( 6) link_BETA1-4 : bond 0.00414 ( 4) link_BETA1-4 : angle 1.43827 ( 12) link_NAG-ASN : bond 0.00447 ( 8) link_NAG-ASN : angle 2.56907 ( 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 132 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 105 time to evaluate : 0.464 Fit side-chains revert: symmetry clash REVERT: A 123 GLN cc_start: 0.8275 (mt0) cc_final: 0.7743 (mm110) REVERT: A 207 GLU cc_start: 0.8913 (tm-30) cc_final: 0.8485 (mp0) REVERT: A 208 MET cc_start: 0.8361 (ttm) cc_final: 0.8061 (ttm) REVERT: A 461 GLN cc_start: 0.8819 (OUTLIER) cc_final: 0.8600 (mp10) REVERT: A 829 ILE cc_start: 0.8543 (OUTLIER) cc_final: 0.8307 (tp) REVERT: B 513 LEU cc_start: 0.8287 (OUTLIER) cc_final: 0.8072 (mp) outliers start: 27 outliers final: 15 residues processed: 126 average time/residue: 0.3929 time to fit residues: 55.8805 Evaluate side-chains 120 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 102 time to evaluate : 0.427 ------------------------------------------------------------------------------- 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 461 GLN 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 728 LEU Chi-restraints excluded: chain A residue 787 CYS Chi-restraints excluded: chain A residue 829 ILE Chi-restraints excluded: chain B residue 75 VAL Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 220 ILE 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 559 SER Chi-restraints excluded: chain B residue 791 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 98 optimal weight: 1.9990 chunk 10 optimal weight: 0.9990 chunk 34 optimal weight: 1.9990 chunk 53 optimal weight: 10.0000 chunk 7 optimal weight: 0.6980 chunk 66 optimal weight: 0.7980 chunk 110 optimal weight: 9.9990 chunk 105 optimal weight: 0.8980 chunk 20 optimal weight: 0.7980 chunk 109 optimal weight: 9.9990 chunk 104 optimal weight: 7.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3812 r_free = 0.3812 target = 0.121114 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.076191 restraints weight = 35135.725| |-----------------------------------------------------------------------------| r_work (start): 0.3015 rms_B_bonded: 4.02 r_work: 0.2839 rms_B_bonded: 4.52 restraints_weight: 0.5000 r_work (final): 0.2839 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2843 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2843 r_free = 0.2843 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 = 0.2843 r_free = 0.2843 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2843 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8163 moved from start: 0.1153 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= 0.137 Angle : 0.744 18.388 15800 Z= 0.343 Chirality : 0.044 0.300 1840 Planarity : 0.004 0.046 1850 Dihedral : 7.036 58.714 2733 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 1.55 % Allowed : 26.85 % Favored : 71.60 % 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 aren not related in a simple way. whole: 1.29 (0.23), residues: 1276 helix: 2.25 (0.21), residues: 576 sheet: 1.81 (0.29), residues: 276 loop : -1.94 (0.27), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 118 TYR 0.024 0.001 TYR A 717 PHE 0.029 0.001 PHE B 329 TRP 0.007 0.001 TRP A 700 HIS 0.004 0.001 HIS B 594 Details of bonding type rmsd covalent geometry : bond 0.00308 (11541) covalent geometry : angle 0.73733 (15748) SS BOND : bond 0.00109 ( 8) SS BOND : angle 0.91294 ( 16) hydrogen bonds : bond 0.04698 ( 629) hydrogen bonds : angle 3.88846 ( 1795) metal coordination : bond 0.00209 ( 6) link_BETA1-4 : bond 0.00409 ( 4) link_BETA1-4 : angle 1.38987 ( 12) link_NAG-ASN : bond 0.00409 ( 8) link_NAG-ASN : angle 2.50415 ( 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 124 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 106 time to evaluate : 0.397 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 123 GLN cc_start: 0.8268 (mt0) cc_final: 0.7750 (mm110) REVERT: A 207 GLU cc_start: 0.8936 (tm-30) cc_final: 0.8495 (mp0) REVERT: A 208 MET cc_start: 0.8402 (ttm) cc_final: 0.8098 (ttm) REVERT: A 461 GLN cc_start: 0.8803 (OUTLIER) cc_final: 0.8576 (mp10) REVERT: A 829 ILE cc_start: 0.8496 (OUTLIER) cc_final: 0.8268 (tp) REVERT: B 513 LEU cc_start: 0.8275 (OUTLIER) cc_final: 0.8050 (mp) REVERT: B 689 MET cc_start: 0.7244 (pmm) cc_final: 0.5573 (pp-130) outliers start: 18 outliers final: 13 residues processed: 121 average time/residue: 0.4128 time to fit residues: 56.1648 Evaluate side-chains 120 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 104 time to evaluate : 0.412 ------------------------------------------------------------------------------- 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 461 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 A residue 829 ILE Chi-restraints excluded: chain B residue 75 VAL Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 220 ILE 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 559 SER Chi-restraints excluded: chain B residue 791 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 74 optimal weight: 0.1980 chunk 3 optimal weight: 0.0370 chunk 71 optimal weight: 0.9980 chunk 8 optimal weight: 0.9990 chunk 29 optimal weight: 0.9980 chunk 5 optimal weight: 2.9990 chunk 32 optimal weight: 3.9990 chunk 25 optimal weight: 1.9990 chunk 36 optimal weight: 4.9990 chunk 122 optimal weight: 0.4980 chunk 70 optimal weight: 1.9990 overall best weight: 0.5458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3833 r_free = 0.3833 target = 0.122606 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.079551 restraints weight = 19873.991| |-----------------------------------------------------------------------------| r_work (start): 0.3095 rms_B_bonded: 3.18 r_work: 0.2942 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.2942 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2939 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2939 r_free = 0.2939 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 = 0.2939 r_free = 0.2939 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2939 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8101 moved from start: 0.1289 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= 0.123 Angle : 0.732 17.449 15800 Z= 0.337 Chirality : 0.044 0.296 1840 Planarity : 0.004 0.046 1850 Dihedral : 6.859 57.694 2733 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 1.64 % Allowed : 26.85 % Favored : 71.51 % 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 aren not related in a simple way. whole: 1.27 (0.23), residues: 1276 helix: 2.20 (0.21), residues: 572 sheet: 1.86 (0.29), residues: 276 loop : -1.93 (0.27), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 118 TYR 0.023 0.001 TYR A 717 PHE 0.057 0.001 PHE A 732 TRP 0.008 0.001 TRP A 700 HIS 0.004 0.001 HIS B 594 Details of bonding type rmsd covalent geometry : bond 0.00273 (11541) covalent geometry : angle 0.72550 (15748) SS BOND : bond 0.00094 ( 8) SS BOND : angle 0.76054 ( 16) hydrogen bonds : bond 0.04277 ( 629) hydrogen bonds : angle 3.80360 ( 1795) metal coordination : bond 0.00114 ( 6) link_BETA1-4 : bond 0.00461 ( 4) link_BETA1-4 : angle 1.41132 ( 12) link_NAG-ASN : bond 0.00445 ( 8) link_NAG-ASN : angle 2.54085 ( 24) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4068.88 seconds wall clock time: 70 minutes 3.10 seconds (4203.10 seconds total)