Starting phenix.real_space_refine on Wed May 14 03:31:21 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8woq_37695/05_2025/8woq_37695.cif Found real_map, /net/cci-nas-00/data/ceres_data/8woq_37695/05_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_37695/05_2025/8woq_37695.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8woq_37695/05_2025/8woq_37695.map" model { file = "/net/cci-nas-00/data/ceres_data/8woq_37695/05_2025/8woq_37695.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8woq_37695/05_2025/8woq_37695.cif" } resolution = 2.85 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.013 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Ca 2 9.91 5 Zn 2 6.06 5 S 60 5.16 5 C 7539 2.51 5 N 1696 2.21 5 O 1919 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 25 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 11218 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 5261 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 647, 5252 Classifications: {'peptide': 647} Link IDs: {'CIS': 1, 'PCIS': 3, 'PTRANS': 22, 'TRANS': 620} Chain breaks: 4 Conformer: "B" Number of residues, atoms: 647, 5252 Classifications: {'peptide': 647} Link IDs: {'CIS': 1, 'PCIS': 3, 'PTRANS': 22, 'TRANS': 620} Chain breaks: 4 bond proxies already assigned to first conformer: 5384 Chain: "B" Number of atoms: 5261 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 647, 5252 Classifications: {'peptide': 647} Link IDs: {'CIS': 1, 'PCIS': 3, 'PTRANS': 22, 'TRANS': 620} Chain breaks: 4 Conformer: "B" Number of residues, atoms: 647, 5252 Classifications: {'peptide': 647} Link IDs: {'CIS': 1, 'PCIS': 3, 'PTRANS': 22, 'TRANS': 620} Chain breaks: 4 bond proxies already assigned to first conformer: 5384 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 276 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 276 Unusual residues: {' CA': 1, ' ZN': 1, 'CLR': 7, 'NAG': 2, 'OLA': 1, 'SPL': 1} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 304 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 304 Unusual residues: {' CA': 1, ' ZN': 1, 'CLR': 8, 'NAG': 2, 'OLA': 1, 'SPL': 1} Classifications: {'undetermined': 14} Link IDs: {None: 13} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Time building chain proxies: 11.76, per 1000 atoms: 1.05 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: 3.00 Conformation dependent library (CDL) restraints added in 2.5 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 901 " pdb="ZN ZN A 901 " - pdb=" NE2 HIS A 796 " pdb="ZN ZN A 901 " - pdb=" NE2 HIS A 563 " pdb="ZN ZN A 901 " - pdb=" NE2 HIS A 800 " pdb=" ZN B 901 " pdb="ZN ZN B 901 " - pdb=" NE2 HIS B 796 " pdb="ZN ZN B 901 " - pdb=" NE2 HIS B 563 " pdb="ZN ZN B 901 " - pdb=" NE2 HIS B 800 " 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2492 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 10 sheets defined 50.0% alpha, 16.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.09 Creating SS restraints... Processing helix chain 'A' and resid 38 through 43 removed outlier: 4.389A pdb=" N ALA A 42 " --> pdb=" O ASP A 38 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 253 No H-bonds generated for 'chain 'A' and resid 251 through 253' Processing helix chain 'A' and resid 268 through 272 removed outlier: 3.571A pdb=" N GLY A 272 " --> pdb=" O TYR A 269 " (cutoff:3.500A) Processing helix chain 'A' and resid 302 through 335 removed outlier: 3.911A pdb=" N TYR A 306 " --> pdb=" O LYS A 302 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N PHE A 317 " --> pdb=" O SER A 313 " (cutoff:3.500A) removed outlier: 4.675A pdb=" N PHE A 320 " --> pdb=" O ILE A 316 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N TYR A 321 " --> pdb=" O PHE A 317 " (cutoff:3.500A) Processing helix chain 'A' and resid 441 through 474 Proline residue: A 458 - end of helix removed outlier: 3.633A pdb=" N GLY A 474 " --> pdb=" O VAL A 470 " (cutoff:3.500A) Processing helix chain 'A' and resid 482 through 486 removed outlier: 4.028A pdb=" N ALA A 486 " --> pdb=" O PHE A 483 " (cutoff:3.500A) Processing helix chain 'A' and resid 495 through 500 Processing helix chain 'A' and resid 501 through 527 removed outlier: 3.960A pdb=" N VAL A 505 " --> pdb=" O ASN A 501 " (cutoff:3.500A) Processing helix chain 'A' and resid 541 through 563 Processing helix chain 'A' and resid 570 through 594 removed outlier: 4.276A pdb=" N ASP A 574 " --> pdb=" O ASN A 570 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N MET A 578 " --> pdb=" O ASP A 574 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N TYR A 579 " --> pdb=" O THR A 575 " (cutoff:3.500A) Processing helix chain 'A' and resid 602 through 621 removed outlier: 3.720A pdb=" N ALA A 606 " --> pdb=" O TYR A 602 " (cutoff:3.500A) Processing helix chain 'A' and resid 624 through 649 removed outlier: 3.710A pdb=" N PHE A 628 " --> pdb=" O ASN A 624 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N TRP A 629 " --> pdb=" O ASP A 625 " (cutoff:3.500A) Processing helix chain 'A' and resid 686 through 709 Processing helix chain 'A' and resid 713 through 738 Processing helix chain 'A' and resid 745 through 767 removed outlier: 3.603A pdb=" N LEU A 749 " --> pdb=" O LEU A 745 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N PHE A 767 " --> pdb=" O LEU A 763 " (cutoff:3.500A) Processing helix chain 'A' and resid 776 through 782 Processing helix chain 'A' and resid 794 through 816 Processing helix chain 'A' and resid 819 through 824 Processing helix chain 'B' and resid 38 through 43 removed outlier: 4.152A pdb=" N ALA B 42 " --> pdb=" O ASP B 38 " (cutoff:3.500A) Processing helix chain 'B' and resid 251 through 253 No H-bonds generated for 'chain 'B' and resid 251 through 253' Processing helix chain 'B' and resid 268 through 272 Processing helix chain 'B' and resid 302 through 335 removed outlier: 3.891A pdb=" N TYR B 306 " --> pdb=" O LYS B 302 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N PHE B 317 " --> pdb=" O SER B 313 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N PHE B 320 " --> pdb=" O ILE B 316 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N TYR B 321 " --> pdb=" O PHE B 317 " (cutoff:3.500A) Processing helix chain 'B' and resid 441 through 474 removed outlier: 4.137A pdb=" N ILE B 448 " --> pdb=" O TYR B 444 " (cutoff:3.500A) Proline residue: B 458 - end of helix Processing helix chain 'B' and resid 482 through 486 removed outlier: 3.909A pdb=" N ALA B 486 " --> pdb=" O PHE B 483 " (cutoff:3.500A) Processing helix chain 'B' and resid 495 through 500 Processing helix chain 'B' and resid 501 through 527 removed outlier: 3.873A pdb=" N VAL B 505 " --> pdb=" O ASN B 501 " (cutoff:3.500A) Processing helix chain 'B' and resid 541 through 563 Processing helix chain 'B' and resid 570 through 594 removed outlier: 4.281A pdb=" N ASP B 574 " --> pdb=" O ASN B 570 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N MET B 578 " --> pdb=" O ASP B 574 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N TYR B 579 " --> pdb=" O THR B 575 " (cutoff:3.500A) Processing helix chain 'B' and resid 602 through 621 removed outlier: 4.093A pdb=" N ALA B 606 " --> pdb=" O TYR B 602 " (cutoff:3.500A) Processing helix chain 'B' and resid 624 through 650 removed outlier: 4.442A pdb=" N TRP B 629 " --> pdb=" O ASP B 625 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N MET B 650 " --> pdb=" O GLN B 646 " (cutoff:3.500A) Processing helix chain 'B' and resid 686 through 709 Processing helix chain 'B' and resid 713 through 738 Processing helix chain 'B' and resid 745 through 767 removed outlier: 3.637A pdb=" N LEU B 749 " --> pdb=" O LEU B 745 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N PHE B 765 " --> pdb=" O ALA B 761 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N PHE B 767 " --> pdb=" O LEU B 763 " (cutoff:3.500A) Processing helix chain 'B' and resid 776 through 782 Processing helix chain 'B' and resid 794 through 816 removed outlier: 3.502A pdb=" N ILE B 798 " --> pdb=" O ASP B 794 " (cutoff:3.500A) Processing helix chain 'B' and resid 819 through 824 Processing sheet with id=AA1, first strand: chain 'A' and resid 44 through 45 removed outlier: 6.201A pdb=" N ARG A 44 " --> pdb=" O SER A 65 " (cutoff:3.500A) removed outlier: 8.064A pdb=" N ASN A 67 " --> pdb=" O ARG A 44 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 51 through 56 removed outlier: 4.473A pdb=" N VAL A 78 " --> pdb=" O LEU A 129 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 110 through 113 Processing sheet with id=AA4, first strand: chain 'A' and resid 177 through 181 Processing sheet with id=AA5, first strand: chain 'A' and resid 187 through 192 Processing sheet with id=AA6, first strand: chain 'B' and resid 44 through 45 removed outlier: 6.036A pdb=" N ARG B 44 " --> pdb=" O SER B 65 " (cutoff:3.500A) removed outlier: 7.725A pdb=" N ASN B 67 " --> pdb=" O ARG B 44 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 51 through 56 removed outlier: 4.625A pdb=" N ALA B 77 " --> pdb=" O LEU B 166 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N VAL B 78 " --> pdb=" O LEU B 129 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 110 through 113 Processing sheet with id=AA9, first strand: chain 'B' and resid 177 through 181 Processing sheet with id=AB1, first strand: chain 'B' and resid 187 through 192 629 hydrogen bonds defined for protein. 1795 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.32 Time building geometry restraints manager: 3.43 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3251 1.34 - 1.46: 2724 1.46 - 1.58: 5472 1.58 - 1.70: 0 1.70 - 1.82: 94 Bond restraints: 11541 Sorted by residual: bond pdb=" C10 OLA B 914 " pdb=" C9 OLA B 914 " ideal model delta sigma weight residual 1.332 1.468 -0.136 2.00e-02 2.50e+03 4.62e+01 bond pdb=" C10 OLA A 912 " pdb=" C9 OLA A 912 " ideal model delta sigma weight residual 1.332 1.467 -0.135 2.00e-02 2.50e+03 4.58e+01 bond pdb=" C1 OLA A 912 " pdb=" C2 OLA A 912 " ideal model delta sigma weight residual 1.542 1.510 0.032 2.00e-02 2.50e+03 2.64e+00 bond pdb=" C1 OLA B 914 " pdb=" C2 OLA B 914 " ideal model delta sigma weight residual 1.542 1.510 0.032 2.00e-02 2.50e+03 2.58e+00 bond pdb=" C1 NAG E 2 " pdb=" O5 NAG E 2 " ideal model delta sigma weight residual 1.406 1.437 -0.031 2.00e-02 2.50e+03 2.40e+00 ... (remaining 11536 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.04: 15642 4.04 - 8.09: 77 8.09 - 12.13: 26 12.13 - 16.18: 2 16.18 - 20.22: 1 Bond angle restraints: 15748 Sorted by residual: angle pdb=" C ASN B 598 " pdb=" N ALA B 599 " pdb=" CA ALA B 599 " ideal model delta sigma weight residual 121.70 133.71 -12.01 1.80e+00 3.09e-01 4.45e+01 angle pdb=" C ASN A 598 " pdb=" N ALA A 599 " pdb=" CA ALA A 599 " ideal model delta sigma weight residual 121.70 133.55 -11.85 1.80e+00 3.09e-01 4.33e+01 angle pdb=" CA LEU A 728 " pdb=" CB LEU A 728 " pdb=" CG LEU A 728 " ideal model delta sigma weight residual 116.30 136.52 -20.22 3.50e+00 8.16e-02 3.34e+01 angle pdb=" CA MET B 613 " pdb=" CB MET B 613 " pdb=" CG MET B 613 " ideal model delta sigma weight residual 114.10 124.06 -9.96 2.00e+00 2.50e-01 2.48e+01 angle pdb=" C ILE A 612 " pdb=" N MET A 613 " pdb=" CA MET A 613 " ideal model delta sigma weight residual 121.58 112.24 9.34 1.95e+00 2.63e-01 2.29e+01 ... (remaining 15743 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.39: 6571 17.39 - 34.78: 801 34.78 - 52.17: 217 52.17 - 69.56: 54 69.56 - 86.95: 8 Dihedral angle restraints: 7651 sinusoidal: 3791 harmonic: 3860 Sorted by residual: dihedral pdb=" CA TYR B 210 " pdb=" C TYR B 210 " pdb=" N PRO B 211 " pdb=" CA PRO B 211 " ideal model delta harmonic sigma weight residual 0.00 24.23 -24.23 0 5.00e+00 4.00e-02 2.35e+01 dihedral pdb=" CA TYR A 210 " pdb=" C TYR A 210 " pdb=" N PRO A 211 " pdb=" CA PRO A 211 " ideal model delta harmonic sigma weight residual 0.00 21.40 -21.40 0 5.00e+00 4.00e-02 1.83e+01 dihedral pdb=" CB CYS A 212 " pdb=" SG CYS A 212 " pdb=" SG CYS A 271 " pdb=" CB CYS A 271 " ideal model delta sinusoidal sigma weight residual 93.00 58.11 34.89 1 1.00e+01 1.00e-02 1.73e+01 ... (remaining 7648 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.064: 1590 0.064 - 0.128: 229 0.128 - 0.192: 15 0.192 - 0.256: 4 0.256 - 0.320: 2 Chirality restraints: 1840 Sorted by residual: chirality pdb=" C1 NAG C 1 " pdb=" ND2 ASN A 57 " pdb=" C2 NAG C 1 " pdb=" O5 NAG C 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.08 -0.32 2.00e-01 2.50e+01 2.56e+00 chirality pdb=" C1 NAG E 1 " pdb=" ND2 ASN B 57 " pdb=" C2 NAG E 1 " pdb=" O5 NAG E 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.09 -0.31 2.00e-01 2.50e+01 2.45e+00 chirality pdb=" C2 SPL B 906 " pdb=" C1 SPL B 906 " pdb=" C3 SPL B 906 " pdb=" N2 SPL B 906 " both_signs ideal model delta sigma weight residual False -2.45 -2.20 -0.25 2.00e-01 2.50e+01 1.58e+00 ... (remaining 1837 not shown) Planarity restraints: 1858 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C10 OLA B 914 " 0.200 2.00e-02 2.50e+03 1.55e-01 2.42e+02 pdb=" C11 OLA B 914 " -0.090 2.00e-02 2.50e+03 pdb=" C8 OLA B 914 " 0.091 2.00e-02 2.50e+03 pdb=" C9 OLA B 914 " -0.200 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C10 OLA A 912 " -0.186 2.00e-02 2.50e+03 1.44e-01 2.09e+02 pdb=" C11 OLA A 912 " 0.085 2.00e-02 2.50e+03 pdb=" C8 OLA A 912 " -0.085 2.00e-02 2.50e+03 pdb=" C9 OLA A 912 " 0.186 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 710 " -0.214 9.50e-02 1.11e+02 9.57e-02 5.64e+00 pdb=" NE ARG A 710 " 0.013 2.00e-02 2.50e+03 pdb=" CZ ARG A 710 " 0.001 2.00e-02 2.50e+03 pdb=" NH1 ARG A 710 " 0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG A 710 " -0.007 2.00e-02 2.50e+03 ... (remaining 1855 not shown) Histogram of nonbonded interaction distances: 2.05 - 2.62: 105 2.62 - 3.19: 9544 3.19 - 3.76: 16329 3.76 - 4.33: 22475 4.33 - 4.90: 37900 Nonbonded interactions: 86353 Sorted by model distance: nonbonded pdb="ZN ZN B 901 " pdb=" O HOH B1002 " model vdw 2.046 2.230 nonbonded pdb="ZN ZN A 901 " pdb=" O HOH A1002 " model vdw 2.052 2.230 nonbonded pdb=" OG1 THR A 135 " pdb=" OE1 GLU A 137 " model vdw 2.128 3.040 nonbonded pdb=" O LYS B 265 " pdb=" NH1 ARG B 289 " model vdw 2.200 3.120 nonbonded pdb=" OH TYR B 64 " pdb=" OH TYR B 159 " model vdw 2.246 3.040 ... (remaining 86348 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 35 through 80 or resid 82 through 830 or resid 901 through \ 905 or resid 907 through 911)) selection = (chain 'B' and (resid 35 through 80 or resid 82 through 830 or resid 901 through \ 905 or resid 907 through 911)) } ncs_group { reference = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.21 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.510 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.430 Check model and map are aligned: 0.070 Set scattering table: 0.120 Process input model: 35.620 Find NCS groups from input model: 0.530 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.400 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8185 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.136 11567 Z= 0.193 Angle : 0.827 20.220 15800 Z= 0.377 Chirality : 0.046 0.320 1840 Planarity : 0.007 0.155 1850 Dihedral : 15.764 86.946 5135 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.79 % Favored : 95.13 % Rotamer: Outliers : 3.96 % Allowed : 27.37 % Favored : 68.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.16 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.00 (0.23), residues: 1276 helix: 1.94 (0.21), residues: 590 sheet: 1.85 (0.28), residues: 260 loop : -2.11 (0.27), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 700 HIS 0.005 0.001 HIS A 636 PHE 0.030 0.001 PHE B 275 TYR 0.021 0.001 TYR A 332 ARG 0.007 0.000 ARG A 118 Details of bonding type rmsd link_NAG-ASN : bond 0.00396 ( 8) link_NAG-ASN : angle 2.67637 ( 24) link_BETA1-4 : bond 0.00293 ( 4) link_BETA1-4 : angle 1.61835 ( 12) hydrogen bonds : bond 0.08980 ( 629) hydrogen bonds : angle 4.30078 ( 1795) metal coordination : bond 0.00178 ( 6) SS BOND : bond 0.00126 ( 8) SS BOND : angle 1.00091 ( 16) covalent geometry : bond 0.00415 (11541) covalent geometry : angle 0.81976 (15748) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 103 time to evaluate : 1.261 Fit side-chains revert: symmetry clash outliers start: 46 outliers final: 40 residues processed: 145 average time/residue: 0.7788 time to fit residues: 127.7617 Evaluate side-chains 142 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 102 time to evaluate : 1.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 220 ILE Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 286 ASN Chi-restraints excluded: chain A residue 296 THR Chi-restraints excluded: chain A residue 313 SER Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 319 SER Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 521 LEU Chi-restraints excluded: chain A residue 559 SER Chi-restraints excluded: chain A residue 572 GLN Chi-restraints excluded: chain A residue 597 ILE Chi-restraints excluded: chain A residue 780 SER Chi-restraints excluded: chain B residue 60 THR Chi-restraints excluded: chain B residue 76 THR Chi-restraints excluded: chain B residue 89 LEU Chi-restraints excluded: chain B residue 119 SER Chi-restraints excluded: chain B residue 135 THR Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 196 ASP Chi-restraints excluded: chain B residue 260 VAL Chi-restraints excluded: chain B residue 287 LEU Chi-restraints excluded: chain B residue 296 THR Chi-restraints excluded: chain B residue 309 SER Chi-restraints excluded: chain B residue 314 VAL Chi-restraints excluded: chain B residue 324 CYS Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 459 VAL Chi-restraints excluded: chain B residue 520 ILE Chi-restraints excluded: chain B residue 521 LEU Chi-restraints excluded: chain B residue 544 LEU Chi-restraints excluded: chain B residue 572 GLN Chi-restraints excluded: chain B residue 615 THR Chi-restraints excluded: chain B residue 735 ILE Chi-restraints excluded: chain B residue 755 THR Chi-restraints excluded: chain B residue 780 SER Chi-restraints excluded: chain B residue 788 ILE Chi-restraints excluded: chain B residue 810 SER Chi-restraints excluded: chain B residue 814 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 108 optimal weight: 5.9990 chunk 97 optimal weight: 2.9990 chunk 53 optimal weight: 7.9990 chunk 33 optimal weight: 4.9990 chunk 65 optimal weight: 0.9980 chunk 51 optimal weight: 10.0000 chunk 100 optimal weight: 2.9990 chunk 38 optimal weight: 6.9990 chunk 61 optimal weight: 1.9990 chunk 74 optimal weight: 6.9990 chunk 116 optimal weight: 10.0000 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 768 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.118575 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.074393 restraints weight = 26435.462| |-----------------------------------------------------------------------------| r_work (start): 0.3016 rms_B_bonded: 3.50 r_work: 0.2851 rms_B_bonded: 4.10 restraints_weight: 0.5000 r_work (final): 0.2851 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2843 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2843 r_free = 0.2843 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2842 r_free = 0.2842 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2842 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8237 moved from start: 0.0680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.055 11567 Z= 0.271 Angle : 0.770 17.076 15800 Z= 0.369 Chirality : 0.047 0.283 1840 Planarity : 0.005 0.063 1850 Dihedral : 9.569 59.796 2786 Min Nonbonded Distance : 1.896 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.18 % Favored : 94.74 % Rotamer: Outliers : 4.73 % Allowed : 25.73 % Favored : 69.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.16 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.01 (0.23), residues: 1276 helix: 2.12 (0.21), residues: 578 sheet: 1.72 (0.29), residues: 260 loop : -2.16 (0.26), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 799 HIS 0.005 0.001 HIS A 636 PHE 0.020 0.002 PHE B 276 TYR 0.021 0.002 TYR A 188 ARG 0.007 0.001 ARG A 118 Details of bonding type rmsd link_NAG-ASN : bond 0.00390 ( 8) link_NAG-ASN : angle 2.40617 ( 24) link_BETA1-4 : bond 0.00303 ( 4) link_BETA1-4 : angle 1.36581 ( 12) hydrogen bonds : bond 0.06023 ( 629) hydrogen bonds : angle 4.13734 ( 1795) metal coordination : bond 0.00709 ( 6) SS BOND : bond 0.00178 ( 8) SS BOND : angle 1.49214 ( 16) covalent geometry : bond 0.00654 (11541) covalent geometry : angle 0.76339 (15748) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 101 time to evaluate : 1.109 Fit side-chains revert: symmetry clash REVERT: A 207 GLU cc_start: 0.8864 (tm-30) cc_final: 0.8591 (mp0) REVERT: A 443 ILE cc_start: 0.7776 (OUTLIER) cc_final: 0.7317 (tt) REVERT: A 461 GLN cc_start: 0.8707 (OUTLIER) cc_final: 0.7807 (mp10) REVERT: B 590 TYR cc_start: 0.7995 (OUTLIER) cc_final: 0.7708 (t80) outliers start: 55 outliers final: 29 residues processed: 147 average time/residue: 0.8012 time to fit residues: 131.9739 Evaluate side-chains 129 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 97 time to evaluate : 1.115 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 220 ILE Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 296 THR Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain A residue 461 GLN Chi-restraints excluded: chain A residue 510 LEU Chi-restraints excluded: chain A residue 521 LEU Chi-restraints excluded: chain A residue 544 LEU Chi-restraints excluded: chain A residue 559 SER Chi-restraints excluded: chain A residue 572 GLN Chi-restraints excluded: chain A residue 585 CYS Chi-restraints excluded: chain A residue 597 ILE Chi-restraints excluded: chain A residue 605 TYR Chi-restraints excluded: chain A residue 726 LEU Chi-restraints excluded: chain A residue 787 CYS Chi-restraints excluded: chain B residue 76 THR Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 196 ASP Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 220 ILE Chi-restraints excluded: chain B residue 260 VAL Chi-restraints excluded: chain B residue 287 LEU Chi-restraints excluded: chain B residue 521 LEU Chi-restraints excluded: chain B residue 590 TYR Chi-restraints excluded: chain B residue 597 ILE Chi-restraints excluded: chain B residue 726 LEU Chi-restraints excluded: chain B residue 735 ILE Chi-restraints excluded: chain B residue 787 CYS Chi-restraints excluded: chain B residue 791 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 85 optimal weight: 0.9990 chunk 58 optimal weight: 1.9990 chunk 107 optimal weight: 2.9990 chunk 82 optimal weight: 0.9990 chunk 30 optimal weight: 0.9990 chunk 125 optimal weight: 0.7980 chunk 93 optimal weight: 20.0000 chunk 98 optimal weight: 0.7980 chunk 47 optimal weight: 4.9990 chunk 126 optimal weight: 2.9990 chunk 123 optimal weight: 3.9990 overall best weight: 0.9186 ------------------------------------------------------------------------------- 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 = 0.3808 r_free = 0.3808 target = 0.120560 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.075625 restraints weight = 36954.272| |-----------------------------------------------------------------------------| r_work (start): 0.3000 rms_B_bonded: 4.05 r_work: 0.2825 rms_B_bonded: 4.53 restraints_weight: 0.5000 r_work (final): 0.2825 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2824 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2824 r_free = 0.2824 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2824 r_free = 0.2824 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2824 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8177 moved from start: 0.0648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 11567 Z= 0.137 Angle : 0.699 15.057 15800 Z= 0.325 Chirality : 0.044 0.288 1840 Planarity : 0.004 0.047 1850 Dihedral : 8.521 59.721 2753 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.40 % Favored : 95.53 % Rotamer: Outliers : 3.53 % Allowed : 25.90 % Favored : 70.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.16 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.17 (0.23), residues: 1276 helix: 2.26 (0.21), residues: 578 sheet: 1.67 (0.29), residues: 264 loop : -2.04 (0.26), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 700 HIS 0.005 0.001 HIS A 636 PHE 0.038 0.001 PHE B 722 TYR 0.014 0.001 TYR B 188 ARG 0.005 0.000 ARG A 118 Details of bonding type rmsd link_NAG-ASN : bond 0.00429 ( 8) link_NAG-ASN : angle 2.52572 ( 24) link_BETA1-4 : bond 0.00508 ( 4) link_BETA1-4 : angle 1.42347 ( 12) hydrogen bonds : bond 0.04951 ( 629) hydrogen bonds : angle 3.92549 ( 1795) metal coordination : bond 0.00185 ( 6) SS BOND : bond 0.00119 ( 8) SS BOND : angle 0.93498 ( 16) covalent geometry : bond 0.00306 (11541) covalent geometry : angle 0.69098 (15748) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 111 time to evaluate : 1.126 Fit side-chains revert: symmetry clash REVERT: A 443 ILE cc_start: 0.7662 (OUTLIER) cc_final: 0.7188 (tt) REVERT: A 590 TYR cc_start: 0.7825 (OUTLIER) cc_final: 0.7560 (t80) REVERT: B 513 LEU cc_start: 0.8287 (OUTLIER) cc_final: 0.8074 (mp) REVERT: B 590 TYR cc_start: 0.7991 (OUTLIER) cc_final: 0.7729 (t80) REVERT: B 722 PHE cc_start: 0.8720 (t80) cc_final: 0.8519 (t80) outliers start: 41 outliers final: 17 residues processed: 141 average time/residue: 0.8255 time to fit residues: 130.5016 Evaluate side-chains 125 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 104 time to evaluate : 1.167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain A residue 544 LEU Chi-restraints excluded: chain A residue 559 SER Chi-restraints excluded: chain A residue 572 GLN Chi-restraints excluded: chain A residue 585 CYS Chi-restraints excluded: chain A residue 590 TYR Chi-restraints excluded: chain A residue 597 ILE Chi-restraints excluded: chain A residue 728 LEU Chi-restraints excluded: chain B residue 76 THR Chi-restraints excluded: chain B residue 220 ILE Chi-restraints excluded: chain B residue 287 LEU Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain B residue 513 LEU Chi-restraints excluded: chain B residue 521 LEU Chi-restraints excluded: chain B residue 559 SER Chi-restraints excluded: chain B residue 590 TYR Chi-restraints excluded: chain B residue 597 ILE Chi-restraints excluded: chain B residue 735 ILE Chi-restraints excluded: chain B residue 791 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 76 optimal weight: 0.8980 chunk 1 optimal weight: 4.9990 chunk 69 optimal weight: 2.9990 chunk 115 optimal weight: 5.9990 chunk 112 optimal weight: 7.9990 chunk 44 optimal weight: 7.9990 chunk 43 optimal weight: 1.9990 chunk 21 optimal weight: 2.9990 chunk 20 optimal weight: 0.8980 chunk 10 optimal weight: 0.6980 chunk 110 optimal weight: 2.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- 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 = 0.3796 r_free = 0.3796 target = 0.119707 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.075645 restraints weight = 25826.461| |-----------------------------------------------------------------------------| r_work (start): 0.3003 rms_B_bonded: 3.52 r_work: 0.2837 rms_B_bonded: 4.13 restraints_weight: 0.5000 r_work (final): 0.2837 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2841 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2841 r_free = 0.2841 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2841 r_free = 0.2841 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2841 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8191 moved from start: 0.0771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 11567 Z= 0.169 Angle : 0.717 14.627 15800 Z= 0.335 Chirality : 0.044 0.291 1840 Planarity : 0.004 0.047 1850 Dihedral : 8.081 59.358 2743 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.63 % Favored : 95.29 % Rotamer: Outliers : 3.61 % Allowed : 25.65 % Favored : 70.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.16 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.13 (0.23), residues: 1276 helix: 2.22 (0.21), residues: 578 sheet: 1.68 (0.29), residues: 264 loop : -2.07 (0.26), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 106 HIS 0.006 0.001 HIS A 636 PHE 0.049 0.001 PHE A 732 TYR 0.018 0.001 TYR A 332 ARG 0.005 0.000 ARG A 118 Details of bonding type rmsd link_NAG-ASN : bond 0.00380 ( 8) link_NAG-ASN : angle 2.39734 ( 24) link_BETA1-4 : bond 0.00452 ( 4) link_BETA1-4 : angle 1.37687 ( 12) hydrogen bonds : bond 0.05184 ( 629) hydrogen bonds : angle 3.95476 ( 1795) metal coordination : bond 0.00363 ( 6) SS BOND : bond 0.00117 ( 8) SS BOND : angle 1.05280 ( 16) covalent geometry : bond 0.00398 (11541) covalent geometry : angle 0.71022 (15748) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 107 time to evaluate : 1.117 Fit side-chains revert: symmetry clash REVERT: A 207 GLU cc_start: 0.8879 (tm-30) cc_final: 0.8503 (mp0) REVERT: A 443 ILE cc_start: 0.7684 (OUTLIER) cc_final: 0.7214 (tt) REVERT: B 513 LEU cc_start: 0.8304 (OUTLIER) cc_final: 0.8071 (mp) REVERT: B 590 TYR cc_start: 0.8009 (OUTLIER) cc_final: 0.7752 (t80) REVERT: B 722 PHE cc_start: 0.8748 (t80) cc_final: 0.8542 (t80) outliers start: 42 outliers final: 24 residues processed: 141 average time/residue: 0.7627 time to fit residues: 121.4147 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 : 1.090 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 220 ILE Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain A residue 510 LEU Chi-restraints excluded: chain A residue 559 SER Chi-restraints excluded: chain A residue 572 GLN Chi-restraints excluded: chain A residue 585 CYS Chi-restraints excluded: chain A residue 597 ILE Chi-restraints excluded: chain A residue 726 LEU Chi-restraints excluded: chain A residue 787 CYS Chi-restraints excluded: chain B residue 76 THR Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 220 ILE Chi-restraints excluded: chain B residue 260 VAL Chi-restraints excluded: chain B residue 287 LEU Chi-restraints excluded: chain B residue 319 SER Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain B residue 513 LEU Chi-restraints excluded: chain B residue 559 SER Chi-restraints excluded: chain B residue 590 TYR Chi-restraints excluded: chain B residue 597 ILE Chi-restraints excluded: chain B residue 735 ILE Chi-restraints excluded: chain B residue 787 CYS Chi-restraints excluded: chain B residue 791 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 9 optimal weight: 2.9990 chunk 92 optimal weight: 4.9990 chunk 48 optimal weight: 9.9990 chunk 110 optimal weight: 5.9990 chunk 72 optimal weight: 0.8980 chunk 117 optimal weight: 0.8980 chunk 44 optimal weight: 5.9990 chunk 49 optimal weight: 6.9990 chunk 45 optimal weight: 9.9990 chunk 97 optimal weight: 2.9990 chunk 106 optimal weight: 4.9990 overall best weight: 2.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 768 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.118203 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.073319 restraints weight = 35255.757| |-----------------------------------------------------------------------------| r_work (start): 0.2957 rms_B_bonded: 3.95 r_work: 0.2780 rms_B_bonded: 4.43 restraints_weight: 0.5000 r_work (final): 0.2780 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2775 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2775 r_free = 0.2775 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2775 r_free = 0.2775 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2775 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8231 moved from start: 0.0894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 11567 Z= 0.248 Angle : 0.762 17.540 15800 Z= 0.359 Chirality : 0.047 0.291 1840 Planarity : 0.004 0.048 1850 Dihedral : 8.064 59.953 2740 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.02 % Favored : 94.90 % Rotamer: Outliers : 4.39 % Allowed : 24.70 % Favored : 70.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.16 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.05 (0.23), residues: 1276 helix: 2.18 (0.21), residues: 578 sheet: 1.64 (0.29), residues: 264 loop : -2.14 (0.26), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 799 HIS 0.005 0.001 HIS A 636 PHE 0.031 0.002 PHE B 722 TYR 0.020 0.001 TYR A 188 ARG 0.005 0.000 ARG A 118 Details of bonding type rmsd link_NAG-ASN : bond 0.00384 ( 8) link_NAG-ASN : angle 2.30928 ( 24) link_BETA1-4 : bond 0.00371 ( 4) link_BETA1-4 : angle 1.41062 ( 12) hydrogen bonds : bond 0.05860 ( 629) hydrogen bonds : angle 4.09423 ( 1795) metal coordination : bond 0.00599 ( 6) SS BOND : bond 0.00171 ( 8) SS BOND : angle 1.43623 ( 16) covalent geometry : bond 0.00594 (11541) covalent geometry : angle 0.75542 (15748) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 102 time to evaluate : 1.241 Fit side-chains revert: symmetry clash REVERT: A 443 ILE cc_start: 0.7724 (OUTLIER) cc_final: 0.7271 (tt) REVERT: B 513 LEU cc_start: 0.8286 (OUTLIER) cc_final: 0.8042 (mp) REVERT: B 590 TYR cc_start: 0.7974 (OUTLIER) cc_final: 0.7670 (t80) REVERT: B 722 PHE cc_start: 0.8739 (t80) cc_final: 0.8468 (t80) outliers start: 51 outliers final: 25 residues processed: 142 average time/residue: 0.8281 time to fit residues: 132.7476 Evaluate side-chains 124 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 96 time to evaluate : 1.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 220 ILE Chi-restraints excluded: chain A residue 313 SER Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain A residue 510 LEU Chi-restraints excluded: chain A residue 559 SER Chi-restraints excluded: chain A residue 572 GLN Chi-restraints excluded: chain A residue 585 CYS Chi-restraints excluded: chain A residue 597 ILE Chi-restraints excluded: chain A residue 605 TYR Chi-restraints excluded: chain A residue 704 LEU Chi-restraints excluded: chain A residue 787 CYS Chi-restraints excluded: chain B residue 76 THR Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 220 ILE Chi-restraints excluded: chain B residue 260 VAL Chi-restraints excluded: chain B residue 287 LEU Chi-restraints excluded: chain B residue 459 VAL Chi-restraints excluded: chain B residue 513 LEU Chi-restraints excluded: chain B residue 559 SER Chi-restraints excluded: chain B residue 590 TYR Chi-restraints excluded: chain B residue 597 ILE Chi-restraints excluded: chain B residue 735 ILE Chi-restraints excluded: chain B residue 787 CYS Chi-restraints excluded: chain B residue 791 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 54 optimal weight: 0.7980 chunk 79 optimal weight: 0.7980 chunk 4 optimal weight: 2.9990 chunk 84 optimal weight: 0.7980 chunk 58 optimal weight: 3.9990 chunk 80 optimal weight: 3.9990 chunk 22 optimal weight: 2.9990 chunk 113 optimal weight: 5.9990 chunk 108 optimal weight: 10.0000 chunk 23 optimal weight: 0.0470 chunk 43 optimal weight: 0.9980 overall best weight: 0.6878 ------------------------------------------------------------------------------- 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 = 0.3809 r_free = 0.3809 target = 0.120965 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.075814 restraints weight = 41524.435| |-----------------------------------------------------------------------------| r_work (start): 0.3002 rms_B_bonded: 4.27 r_work: 0.2820 rms_B_bonded: 4.70 restraints_weight: 0.5000 r_work (final): 0.2820 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2825 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2825 r_free = 0.2825 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2825 r_free = 0.2825 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2825 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8169 moved from start: 0.0938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 11567 Z= 0.128 Angle : 0.731 19.635 15800 Z= 0.334 Chirality : 0.044 0.291 1840 Planarity : 0.004 0.045 1850 Dihedral : 7.710 59.008 2740 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 2.84 % Allowed : 26.68 % Favored : 70.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.16 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.18 (0.23), residues: 1276 helix: 2.23 (0.21), residues: 578 sheet: 1.68 (0.28), residues: 276 loop : -2.09 (0.27), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 700 HIS 0.005 0.001 HIS A 636 PHE 0.030 0.001 PHE B 722 TYR 0.019 0.001 TYR A 332 ARG 0.004 0.000 ARG A 118 Details of bonding type rmsd link_NAG-ASN : bond 0.00466 ( 8) link_NAG-ASN : angle 2.60530 ( 24) link_BETA1-4 : bond 0.00465 ( 4) link_BETA1-4 : angle 1.50108 ( 12) hydrogen bonds : bond 0.04763 ( 629) hydrogen bonds : angle 3.91775 ( 1795) metal coordination : bond 0.00171 ( 6) SS BOND : bond 0.00109 ( 8) SS BOND : angle 0.87124 ( 16) covalent geometry : bond 0.00278 (11541) covalent geometry : angle 0.72313 (15748) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 113 time to evaluate : 1.283 Fit side-chains revert: symmetry clash REVERT: A 123 GLN cc_start: 0.8314 (mt0) cc_final: 0.7831 (mm110) REVERT: A 207 GLU cc_start: 0.8939 (tm-30) cc_final: 0.8483 (mp0) REVERT: A 443 ILE cc_start: 0.7692 (OUTLIER) cc_final: 0.7223 (tt) REVERT: A 591 GLN cc_start: 0.7192 (tm-30) cc_final: 0.6957 (pp30) REVERT: B 513 LEU cc_start: 0.8298 (OUTLIER) cc_final: 0.8084 (mp) REVERT: B 590 TYR cc_start: 0.7968 (OUTLIER) cc_final: 0.7685 (t80) outliers start: 33 outliers final: 20 residues processed: 141 average time/residue: 0.8315 time to fit residues: 131.8830 Evaluate side-chains 128 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 105 time to evaluate : 1.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 220 ILE Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain A residue 521 LEU Chi-restraints excluded: chain A residue 572 GLN Chi-restraints excluded: chain A residue 597 ILE Chi-restraints excluded: chain A residue 704 LEU Chi-restraints excluded: chain A residue 787 CYS Chi-restraints excluded: chain B residue 76 THR Chi-restraints excluded: chain B residue 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 319 SER Chi-restraints excluded: chain B residue 459 VAL Chi-restraints excluded: chain B residue 513 LEU Chi-restraints excluded: chain B residue 559 SER Chi-restraints excluded: chain B residue 590 TYR Chi-restraints excluded: chain B residue 597 ILE Chi-restraints excluded: chain B residue 771 SER Chi-restraints excluded: chain B residue 787 CYS Chi-restraints excluded: chain B residue 791 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 60 optimal weight: 0.4980 chunk 58 optimal weight: 1.9990 chunk 29 optimal weight: 7.9990 chunk 17 optimal weight: 3.9990 chunk 24 optimal weight: 9.9990 chunk 74 optimal weight: 0.0980 chunk 1 optimal weight: 4.9990 chunk 96 optimal weight: 2.9990 chunk 42 optimal weight: 3.9990 chunk 18 optimal weight: 1.9990 chunk 70 optimal weight: 1.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 624 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.119989 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.076435 restraints weight = 22908.956| |-----------------------------------------------------------------------------| r_work (start): 0.3018 rms_B_bonded: 3.35 r_work: 0.2856 rms_B_bonded: 3.99 restraints_weight: 0.5000 r_work (final): 0.2856 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2867 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2867 r_free = 0.2867 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 = 0.2867 r_free = 0.2867 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2867 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8174 moved from start: 0.0907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 11567 Z= 0.158 Angle : 0.731 19.613 15800 Z= 0.337 Chirality : 0.044 0.296 1840 Planarity : 0.004 0.047 1850 Dihedral : 7.549 58.469 2737 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 2.75 % Allowed : 26.76 % Favored : 70.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.16 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.20 (0.23), residues: 1276 helix: 2.27 (0.21), residues: 578 sheet: 1.68 (0.28), residues: 276 loop : -2.11 (0.27), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 106 HIS 0.003 0.001 HIS A 636 PHE 0.051 0.001 PHE A 732 TYR 0.049 0.001 TYR A 717 ARG 0.004 0.000 ARG A 118 Details of bonding type rmsd link_NAG-ASN : bond 0.00392 ( 8) link_NAG-ASN : angle 2.44390 ( 24) link_BETA1-4 : bond 0.00449 ( 4) link_BETA1-4 : angle 1.43483 ( 12) hydrogen bonds : bond 0.04975 ( 629) hydrogen bonds : angle 3.92952 ( 1795) metal coordination : bond 0.00289 ( 6) SS BOND : bond 0.00112 ( 8) SS BOND : angle 0.99449 ( 16) covalent geometry : bond 0.00367 (11541) covalent geometry : angle 0.72370 (15748) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 106 time to evaluate : 1.147 Fit side-chains revert: symmetry clash REVERT: A 123 GLN cc_start: 0.8289 (mt0) cc_final: 0.7787 (mm110) REVERT: A 207 GLU cc_start: 0.8890 (tm-30) cc_final: 0.8507 (mp0) REVERT: A 443 ILE cc_start: 0.7695 (OUTLIER) cc_final: 0.7226 (tt) REVERT: A 829 ILE cc_start: 0.8621 (OUTLIER) cc_final: 0.8383 (tp) REVERT: B 513 LEU cc_start: 0.8310 (OUTLIER) cc_final: 0.8079 (mp) REVERT: B 590 TYR cc_start: 0.7998 (OUTLIER) cc_final: 0.7728 (t80) REVERT: B 689 MET cc_start: 0.7264 (pmm) cc_final: 0.5569 (pp-130) REVERT: B 722 PHE cc_start: 0.8735 (t80) cc_final: 0.8447 (t80) outliers start: 32 outliers final: 23 residues processed: 133 average time/residue: 0.8235 time to fit residues: 123.3038 Evaluate side-chains 131 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 104 time to evaluate : 1.113 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 220 ILE Chi-restraints excluded: chain A residue 313 SER Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain A residue 521 LEU Chi-restraints excluded: chain A residue 597 ILE Chi-restraints excluded: chain A residue 704 LEU Chi-restraints excluded: chain A residue 787 CYS Chi-restraints excluded: chain A residue 829 ILE Chi-restraints excluded: chain B residue 76 THR Chi-restraints excluded: chain B residue 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 319 SER Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain B residue 459 VAL Chi-restraints excluded: chain B residue 513 LEU Chi-restraints excluded: chain B residue 521 LEU Chi-restraints excluded: chain B residue 559 SER Chi-restraints excluded: chain B residue 590 TYR Chi-restraints excluded: chain B residue 597 ILE Chi-restraints excluded: chain B residue 771 SER Chi-restraints excluded: chain B residue 787 CYS Chi-restraints excluded: chain B residue 791 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 51 optimal weight: 0.4980 chunk 14 optimal weight: 0.6980 chunk 42 optimal weight: 0.8980 chunk 49 optimal weight: 7.9990 chunk 98 optimal weight: 0.9980 chunk 3 optimal weight: 0.8980 chunk 40 optimal weight: 4.9990 chunk 22 optimal weight: 3.9990 chunk 93 optimal weight: 8.9990 chunk 15 optimal weight: 0.6980 chunk 41 optimal weight: 0.2980 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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 = 0.3817 r_free = 0.3817 target = 0.121370 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.077315 restraints weight = 28042.061| |-----------------------------------------------------------------------------| r_work (start): 0.3045 rms_B_bonded: 3.66 r_work: 0.2880 rms_B_bonded: 4.25 restraints_weight: 0.5000 r_work (final): 0.2880 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2878 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2878 r_free = 0.2878 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 = 0.2878 r_free = 0.2878 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2878 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8141 moved from start: 0.1128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 11567 Z= 0.123 Angle : 0.719 19.942 15800 Z= 0.328 Chirality : 0.043 0.297 1840 Planarity : 0.004 0.045 1850 Dihedral : 7.248 59.600 2734 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 2.50 % Allowed : 27.19 % Favored : 70.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.16 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.30 (0.23), residues: 1276 helix: 2.32 (0.21), residues: 576 sheet: 1.73 (0.28), residues: 276 loop : -1.99 (0.27), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 106 HIS 0.003 0.001 HIS A 636 PHE 0.035 0.001 PHE B 722 TYR 0.042 0.001 TYR A 717 ARG 0.004 0.000 ARG A 118 Details of bonding type rmsd link_NAG-ASN : bond 0.00436 ( 8) link_NAG-ASN : angle 2.53343 ( 24) link_BETA1-4 : bond 0.00471 ( 4) link_BETA1-4 : angle 1.45192 ( 12) hydrogen bonds : bond 0.04496 ( 629) hydrogen bonds : angle 3.84158 ( 1795) metal coordination : bond 0.00126 ( 6) SS BOND : bond 0.00100 ( 8) SS BOND : angle 0.79436 ( 16) covalent geometry : bond 0.00267 (11541) covalent geometry : angle 0.71135 (15748) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 109 time to evaluate : 1.241 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 123 GLN cc_start: 0.8246 (mt0) cc_final: 0.7755 (mm110) REVERT: A 207 GLU cc_start: 0.8901 (tm-30) cc_final: 0.8499 (mp0) REVERT: A 443 ILE cc_start: 0.7626 (OUTLIER) cc_final: 0.7157 (tt) REVERT: A 829 ILE cc_start: 0.8591 (OUTLIER) cc_final: 0.8355 (tp) REVERT: B 513 LEU cc_start: 0.8278 (OUTLIER) cc_final: 0.8063 (mp) REVERT: B 590 TYR cc_start: 0.7988 (OUTLIER) cc_final: 0.7777 (t80) REVERT: B 689 MET cc_start: 0.7249 (pmm) cc_final: 0.5570 (pp-130) REVERT: B 722 PHE cc_start: 0.8692 (t80) cc_final: 0.8405 (OUTLIER) outliers start: 29 outliers final: 21 residues processed: 133 average time/residue: 0.8781 time to fit residues: 131.2741 Evaluate side-chains 130 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 106 time to evaluate : 1.111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 220 ILE Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain A residue 585 CYS Chi-restraints excluded: chain A residue 597 ILE Chi-restraints excluded: chain A residue 787 CYS Chi-restraints excluded: chain A residue 829 ILE Chi-restraints excluded: chain B residue 76 THR Chi-restraints excluded: chain B residue 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 319 SER Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain B residue 513 LEU Chi-restraints excluded: chain B residue 521 LEU Chi-restraints excluded: chain B residue 590 TYR Chi-restraints excluded: chain B residue 597 ILE Chi-restraints excluded: chain B residue 771 SER Chi-restraints excluded: chain B residue 787 CYS Chi-restraints excluded: chain B residue 791 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 89 optimal weight: 3.9990 chunk 93 optimal weight: 8.9990 chunk 104 optimal weight: 5.9990 chunk 90 optimal weight: 0.6980 chunk 43 optimal weight: 0.8980 chunk 127 optimal weight: 0.9990 chunk 74 optimal weight: 0.0870 chunk 87 optimal weight: 0.6980 chunk 26 optimal weight: 0.9990 chunk 23 optimal weight: 2.9990 chunk 115 optimal weight: 2.9990 overall best weight: 0.6760 ------------------------------------------------------------------------------- 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 = 0.3821 r_free = 0.3821 target = 0.121748 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.076885 restraints weight = 36805.189| |-----------------------------------------------------------------------------| r_work (start): 0.3027 rms_B_bonded: 4.08 r_work: 0.2852 rms_B_bonded: 4.59 restraints_weight: 0.5000 r_work (final): 0.2852 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2852 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2852 r_free = 0.2852 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 = 0.2852 r_free = 0.2852 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2852 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8149 moved from start: 0.1154 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= 0.125 Angle : 0.730 18.502 15800 Z= 0.332 Chirality : 0.043 0.297 1840 Planarity : 0.004 0.047 1850 Dihedral : 7.078 58.831 2734 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 2.50 % Allowed : 27.19 % Favored : 70.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.16 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.31 (0.23), residues: 1276 helix: 2.31 (0.21), residues: 576 sheet: 1.78 (0.28), residues: 276 loop : -1.98 (0.27), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 700 HIS 0.004 0.001 HIS B 594 PHE 0.052 0.001 PHE A 732 TYR 0.039 0.001 TYR A 717 ARG 0.004 0.000 ARG A 118 Details of bonding type rmsd link_NAG-ASN : bond 0.00415 ( 8) link_NAG-ASN : angle 2.48205 ( 24) link_BETA1-4 : bond 0.00423 ( 4) link_BETA1-4 : angle 1.40988 ( 12) hydrogen bonds : bond 0.04468 ( 629) hydrogen bonds : angle 3.84389 ( 1795) metal coordination : bond 0.00154 ( 6) SS BOND : bond 0.00086 ( 8) SS BOND : angle 0.76764 ( 16) covalent geometry : bond 0.00277 (11541) covalent geometry : angle 0.72330 (15748) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 110 time to evaluate : 1.250 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 123 GLN cc_start: 0.8282 (mt0) cc_final: 0.7743 (mm110) REVERT: A 829 ILE cc_start: 0.8552 (OUTLIER) cc_final: 0.8311 (tp) REVERT: B 513 LEU cc_start: 0.8276 (OUTLIER) cc_final: 0.8068 (mp) REVERT: B 722 PHE cc_start: 0.8668 (t80) cc_final: 0.8367 (t80) outliers start: 29 outliers final: 19 residues processed: 134 average time/residue: 0.8250 time to fit residues: 124.3553 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 : 1.282 ------------------------------------------------------------------------------- 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 322 LEU Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 585 CYS Chi-restraints excluded: chain A residue 597 ILE Chi-restraints excluded: chain A residue 704 LEU Chi-restraints excluded: chain A residue 787 CYS Chi-restraints excluded: chain A residue 829 ILE Chi-restraints excluded: chain B residue 76 THR Chi-restraints excluded: chain B residue 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 319 SER 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 771 SER Chi-restraints excluded: chain B residue 787 CYS Chi-restraints excluded: chain B residue 791 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 21 optimal weight: 2.9990 chunk 73 optimal weight: 2.9990 chunk 56 optimal weight: 0.6980 chunk 35 optimal weight: 3.9990 chunk 48 optimal weight: 10.0000 chunk 41 optimal weight: 0.4980 chunk 103 optimal weight: 5.9990 chunk 54 optimal weight: 0.6980 chunk 97 optimal weight: 3.9990 chunk 31 optimal weight: 0.9980 chunk 14 optimal weight: 0.5980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 = 0.3823 r_free = 0.3823 target = 0.121853 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.077966 restraints weight = 25777.922| |-----------------------------------------------------------------------------| r_work (start): 0.3059 rms_B_bonded: 3.54 r_work: 0.2897 rms_B_bonded: 4.18 restraints_weight: 0.5000 r_work (final): 0.2897 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2893 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2893 r_free = 0.2893 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 = 0.2893 r_free = 0.2893 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2893 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8131 moved from start: 0.1275 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= 0.125 Angle : 0.728 19.713 15800 Z= 0.333 Chirality : 0.044 0.295 1840 Planarity : 0.004 0.046 1850 Dihedral : 6.996 57.508 2734 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 1.89 % Allowed : 27.80 % Favored : 70.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.16 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.32 (0.23), residues: 1276 helix: 2.30 (0.21), residues: 576 sheet: 1.79 (0.28), residues: 276 loop : -1.95 (0.27), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 700 HIS 0.004 0.001 HIS B 594 PHE 0.034 0.001 PHE B 722 TYR 0.038 0.001 TYR A 717 ARG 0.004 0.000 ARG A 118 Details of bonding type rmsd link_NAG-ASN : bond 0.00413 ( 8) link_NAG-ASN : angle 2.47923 ( 24) link_BETA1-4 : bond 0.00440 ( 4) link_BETA1-4 : angle 1.41525 ( 12) hydrogen bonds : bond 0.04393 ( 629) hydrogen bonds : angle 3.83634 ( 1795) metal coordination : bond 0.00156 ( 6) SS BOND : bond 0.00101 ( 8) SS BOND : angle 0.78634 ( 16) covalent geometry : bond 0.00278 (11541) covalent geometry : angle 0.72129 (15748) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 110 time to evaluate : 1.207 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 123 GLN cc_start: 0.8243 (mt0) cc_final: 0.7707 (mm110) REVERT: A 207 GLU cc_start: 0.8886 (tm-30) cc_final: 0.8455 (mp0) REVERT: A 591 GLN cc_start: 0.7088 (tm-30) cc_final: 0.6883 (pp30) REVERT: A 829 ILE cc_start: 0.8547 (OUTLIER) cc_final: 0.8304 (tp) REVERT: B 513 LEU cc_start: 0.8255 (OUTLIER) cc_final: 0.8048 (mp) REVERT: B 689 MET cc_start: 0.7236 (pmm) cc_final: 0.5544 (pp-130) REVERT: B 722 PHE cc_start: 0.8679 (t80) cc_final: 0.8389 (t80) outliers start: 22 outliers final: 17 residues processed: 130 average time/residue: 0.8556 time to fit residues: 124.4225 Evaluate side-chains 125 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 106 time to evaluate : 1.100 ------------------------------------------------------------------------------- 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 327 VAL Chi-restraints excluded: chain A residue 597 ILE Chi-restraints excluded: chain A residue 704 LEU Chi-restraints excluded: chain A residue 787 CYS Chi-restraints excluded: chain A residue 829 ILE Chi-restraints excluded: chain B residue 76 THR Chi-restraints excluded: chain B residue 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 513 LEU Chi-restraints excluded: chain B residue 521 LEU Chi-restraints excluded: chain B residue 559 SER Chi-restraints excluded: chain B residue 597 ILE Chi-restraints excluded: chain B residue 771 SER Chi-restraints excluded: chain B residue 787 CYS Chi-restraints excluded: chain B residue 791 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 122 optimal weight: 4.9990 chunk 72 optimal weight: 0.9980 chunk 103 optimal weight: 5.9990 chunk 91 optimal weight: 3.9990 chunk 34 optimal weight: 1.9990 chunk 125 optimal weight: 3.9990 chunk 32 optimal weight: 0.9980 chunk 98 optimal weight: 1.9990 chunk 33 optimal weight: 3.9990 chunk 127 optimal weight: 6.9990 chunk 22 optimal weight: 3.9990 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 768 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.119257 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.075098 restraints weight = 29109.994| |-----------------------------------------------------------------------------| r_work (start): 0.2995 rms_B_bonded: 3.68 r_work: 0.2824 rms_B_bonded: 4.29 restraints_weight: 0.5000 r_work (final): 0.2824 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2821 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2821 r_free = 0.2821 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2821 r_free = 0.2821 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2821 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8196 moved from start: 0.1124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 11567 Z= 0.207 Angle : 0.779 18.159 15800 Z= 0.364 Chirality : 0.046 0.294 1840 Planarity : 0.004 0.049 1850 Dihedral : 7.194 59.430 2734 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer: Outliers : 2.15 % Allowed : 27.71 % Favored : 70.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.16 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.19 (0.23), residues: 1276 helix: 2.21 (0.21), residues: 576 sheet: 1.76 (0.29), residues: 264 loop : -1.96 (0.27), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 799 HIS 0.004 0.001 HIS B 594 PHE 0.052 0.002 PHE A 732 TYR 0.037 0.001 TYR A 717 ARG 0.004 0.000 ARG A 118 Details of bonding type rmsd link_NAG-ASN : bond 0.00330 ( 8) link_NAG-ASN : angle 2.32597 ( 24) link_BETA1-4 : bond 0.00408 ( 4) link_BETA1-4 : angle 1.40136 ( 12) hydrogen bonds : bond 0.05354 ( 629) hydrogen bonds : angle 4.01648 ( 1795) metal coordination : bond 0.00488 ( 6) SS BOND : bond 0.00167 ( 8) SS BOND : angle 1.28510 ( 16) covalent geometry : bond 0.00494 (11541) covalent geometry : angle 0.77325 (15748) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7771.47 seconds wall clock time: 135 minutes 32.55 seconds (8132.55 seconds total)