Starting phenix.real_space_refine on Thu Jul 31 00:46:12 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7s8v_24927/07_2025/7s8v_24927_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/7s8v_24927/07_2025/7s8v_24927.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.73 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7s8v_24927/07_2025/7s8v_24927.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7s8v_24927/07_2025/7s8v_24927.map" model { file = "/net/cci-nas-00/data/ceres_data/7s8v_24927/07_2025/7s8v_24927_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7s8v_24927/07_2025/7s8v_24927_trim.cif" } resolution = 3.73 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= 0.011 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: 5 Type Number sf(0) Gaussians S 48 5.16 5 C 4070 2.51 5 N 1102 2.21 5 O 1237 1.98 5 H 6045 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 12502 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 4190 Number of conformers: 1 Conformer: "" Number of residues, atoms: 264, 4190 Classifications: {'peptide': 264} Link IDs: {'PTRANS': 22, 'TRANS': 241} Chain breaks: 2 Chain: "B" Number of atoms: 8147 Number of conformers: 1 Conformer: "" Number of residues, atoms: 518, 8147 Classifications: {'peptide': 518} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 31, 'TRANS': 485} Chain breaks: 3 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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 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: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Time building chain proxies: 7.06, per 1000 atoms: 0.56 Number of scatterers: 12502 At special positions: 0 Unit cell: (95.4, 118.72, 106, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 48 16.00 O 1237 8.00 N 1102 7.00 C 4070 6.00 H 6045 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=17, symmetry=0 Simple disulfide: pdb=" SG CYS A 633 " - pdb=" SG CYS A 849 " distance=2.03 Simple disulfide: pdb=" SG CYS A 776 " - pdb=" SG CYS A 785 " distance=2.03 Simple disulfide: pdb=" SG CYS B 8 " - pdb=" SG CYS B 26 " distance=2.03 Simple disulfide: pdb=" SG CYS B 126 " - pdb=" SG CYS B 155 " distance=2.03 Simple disulfide: pdb=" SG CYS B 159 " - pdb=" SG CYS B 182 " distance=2.03 Simple disulfide: pdb=" SG CYS B 169 " - pdb=" SG CYS B 188 " distance=2.03 Simple disulfide: pdb=" SG CYS B 192 " - pdb=" SG CYS B 201 " distance=2.03 Simple disulfide: pdb=" SG CYS B 196 " - pdb=" SG CYS B 207 " distance=2.03 Simple disulfide: pdb=" SG CYS B 208 " - pdb=" SG CYS B 216 " distance=2.03 Simple disulfide: pdb=" SG CYS B 212 " - pdb=" SG CYS B 225 " distance=2.03 Simple disulfide: pdb=" SG CYS B 228 " - pdb=" SG CYS B 237 " distance=2.03 Simple disulfide: pdb=" SG CYS B 241 " - pdb=" SG CYS B 253 " distance=2.03 Simple disulfide: pdb=" SG CYS B 259 " - pdb=" SG CYS B 284 " distance=2.04 Simple disulfide: pdb=" SG CYS B 266 " - pdb=" SG CYS B 274 " distance=2.03 Simple disulfide: pdb=" SG CYS B 288 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 647 " - pdb=" SG CYS B 872 " distance=2.03 Simple disulfide: pdb=" SG CYS B 798 " - pdb=" SG CYS B 807 " distance=2.04 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 D 2 " - " BMA D 3 " " NAG E 1 " - " NAG E 2 " NAG-ASN " NAG A6101 " - " ASN A 610 " " NAG B1601 " - " ASN B 16 " " NAG B1602 " - " ASN B 25 " " NAG B1603 " - " ASN B 624 " " NAG B1604 " - " ASN B 606 " " NAG C 1 " - " ASN A 592 " " NAG D 1 " - " ASN B 111 " " NAG E 1 " - " ASN B 215 " Time building additional restraints: 3.14 Conformation dependent library (CDL) restraints added in 990.1 milliseconds 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1480 Finding SS restraints... Secondary structure from input PDB file: 12 helices and 17 sheets defined 11.8% alpha, 35.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.13 Creating SS restraints... Processing helix chain 'A' and resid 625 through 629 Processing helix chain 'A' and resid 644 through 649 removed outlier: 3.700A pdb=" N ASP A 649 " --> pdb=" O GLY A 646 " (cutoff:3.500A) Processing helix chain 'A' and resid 676 through 684 Processing helix chain 'A' and resid 686 through 698 Processing helix chain 'A' and resid 852 through 857 removed outlier: 4.139A pdb=" N ARG A 856 " --> pdb=" O ARG A 852 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N LYS A 857 " --> pdb=" O GLN A 853 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 852 through 857' Processing helix chain 'B' and resid 18 through 24 Processing helix chain 'B' and resid 42 through 47 removed outlier: 3.656A pdb=" N PHE B 46 " --> pdb=" O ARG B 42 " (cutoff:3.500A) Processing helix chain 'B' and resid 149 through 153 Processing helix chain 'B' and resid 193 through 197 removed outlier: 3.730A pdb=" N CYS B 196 " --> pdb=" O PRO B 193 " (cutoff:3.500A) Processing helix chain 'B' and resid 255 through 270 removed outlier: 3.537A pdb=" N HIS B 263 " --> pdb=" O CYS B 259 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N CYS B 266 " --> pdb=" O LEU B 262 " (cutoff:3.500A) Processing helix chain 'B' and resid 638 through 643 Processing helix chain 'B' and resid 874 through 881 removed outlier: 3.729A pdb=" N PHE B 878 " --> pdb=" O SER B 874 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 585 through 590 removed outlier: 5.340A pdb=" N ASP A 586 " --> pdb=" O ASN A 602 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ASN A 602 " --> pdb=" O ASP A 586 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 747 through 752 removed outlier: 3.533A pdb=" N HIS A 774 " --> pdb=" O ILE A 615 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 809 through 813 Processing sheet with id=AA4, first strand: chain 'A' and resid 846 through 851 removed outlier: 4.061A pdb=" N THR A 872 " --> pdb=" O GLY A 840 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 846 through 851 removed outlier: 4.061A pdb=" N THR A 872 " --> pdb=" O GLY A 840 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 6 through 14 removed outlier: 4.579A pdb=" N VAL B 7 " --> pdb=" O VAL B 28 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N GLU B 30 " --> pdb=" O VAL B 7 " (cutoff:3.500A) removed outlier: 6.028A pdb=" N HIS B 32 " --> pdb=" O PRO B 9 " (cutoff:3.500A) removed outlier: 6.224A pdb=" N SER B 27 " --> pdb=" O MET B 56 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ILE B 82 " --> pdb=" O ASN B 111 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 6 through 14 removed outlier: 4.579A pdb=" N VAL B 7 " --> pdb=" O VAL B 28 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N GLU B 30 " --> pdb=" O VAL B 7 " (cutoff:3.500A) removed outlier: 6.028A pdb=" N HIS B 32 " --> pdb=" O PRO B 9 " (cutoff:3.500A) removed outlier: 8.825A pdb=" N LEU B 62 " --> pdb=" O GLY B 31 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N LEU B 33 " --> pdb=" O LEU B 62 " (cutoff:3.500A) removed outlier: 8.033A pdb=" N PHE B 64 " --> pdb=" O LEU B 33 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N ILE B 35 " --> pdb=" O PHE B 64 " (cutoff:3.500A) removed outlier: 5.840A pdb=" N VAL B 66 " --> pdb=" O ILE B 35 " (cutoff:3.500A) removed outlier: 7.487A pdb=" N LEU B 37 " --> pdb=" O VAL B 66 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N LEU B 61 " --> pdb=" O VAL B 94 " (cutoff:3.500A) removed outlier: 8.224A pdb=" N PHE B 96 " --> pdb=" O LEU B 61 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N LEU B 63 " --> pdb=" O PHE B 96 " (cutoff:3.500A) removed outlier: 7.437A pdb=" N ARG B 118 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N VAL B 94 " --> pdb=" O ARG B 118 " (cutoff:3.500A) removed outlier: 7.851A pdb=" N GLU B 120 " --> pdb=" O VAL B 94 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N PHE B 96 " --> pdb=" O GLU B 120 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N ASN B 122 " --> pdb=" O PHE B 96 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N TYR B 144 " --> pdb=" O VAL B 117 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N VAL B 146 " --> pdb=" O ILE B 119 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N ASN B 148 " --> pdb=" O LYS B 121 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 171 through 173 removed outlier: 3.573A pdb=" N THR B 172 " --> pdb=" O VAL B 179 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N VAL B 179 " --> pdb=" O THR B 172 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'B' and resid 182 through 184 removed outlier: 6.718A pdb=" N HIS B 187 " --> pdb=" O TRP B 183 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 232 through 233 Processing sheet with id=AB2, first strand: chain 'B' and resid 252 through 254 removed outlier: 5.990A pdb=" N HIS B 247 " --> pdb=" O CYS B 284 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 293 through 294 Processing sheet with id=AB4, first strand: chain 'B' and resid 599 through 604 removed outlier: 5.381A pdb=" N ASP B 600 " --> pdb=" O LYS B 616 " (cutoff:3.500A) removed outlier: 4.719A pdb=" N LYS B 616 " --> pdb=" O ASP B 600 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 771 through 774 Processing sheet with id=AB6, first strand: chain 'B' and resid 827 through 832 removed outlier: 5.291A pdb=" N GLN B 845 " --> pdb=" O PRO B 829 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 869 through 873 removed outlier: 3.627A pdb=" N LEU B 856 " --> pdb=" O THR B 901 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N THR B 901 " --> pdb=" O LEU B 856 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N ILE B 898 " --> pdb=" O TRP B 909 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N TRP B 909 " --> pdb=" O ILE B 898 " (cutoff:3.500A) removed outlier: 5.861A pdb=" N ALA B 900 " --> pdb=" O GLY B 907 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 869 through 873 removed outlier: 3.627A pdb=" N LEU B 856 " --> pdb=" O THR B 901 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N THR B 901 " --> pdb=" O LEU B 856 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N TYR B 894 " --> pdb=" O PHE B 915 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N PHE B 915 " --> pdb=" O TYR B 894 " (cutoff:3.500A) 194 hydrogen bonds defined for protein. 474 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: 4.74 Time building geometry restraints manager: 3.85 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.04: 6041 1.04 - 1.24: 693 1.24 - 1.44: 2206 1.44 - 1.64: 3667 1.64 - 1.84: 58 Bond restraints: 12665 Sorted by residual: bond pdb=" C1 NAG D 1 " pdb=" O5 NAG D 1 " ideal model delta sigma weight residual 1.406 1.440 -0.034 2.00e-02 2.50e+03 2.92e+00 bond pdb=" C1 NAG A6101 " pdb=" O5 NAG A6101 " ideal model delta sigma weight residual 1.406 1.434 -0.028 2.00e-02 2.50e+03 2.01e+00 bond pdb=" C1 NAG B1601 " pdb=" O5 NAG B1601 " ideal model delta sigma weight residual 1.406 1.432 -0.026 2.00e-02 2.50e+03 1.74e+00 bond pdb=" CB CYS B 288 " pdb=" SG CYS B 288 " ideal model delta sigma weight residual 1.808 1.765 0.043 3.30e-02 9.18e+02 1.73e+00 bond pdb=" C1 NAG B1604 " pdb=" O5 NAG B1604 " ideal model delta sigma weight residual 1.406 1.432 -0.026 2.00e-02 2.50e+03 1.72e+00 ... (remaining 12660 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.40: 21911 1.40 - 2.80: 795 2.80 - 4.19: 64 4.19 - 5.59: 7 5.59 - 6.99: 3 Bond angle restraints: 22780 Sorted by residual: angle pdb=" CA CYS B 288 " pdb=" CB CYS B 288 " pdb=" SG CYS B 288 " ideal model delta sigma weight residual 114.40 121.39 -6.99 2.30e+00 1.89e-01 9.24e+00 angle pdb=" N CYS B 288 " pdb=" CA CYS B 288 " pdb=" CB CYS B 288 " ideal model delta sigma weight residual 110.14 114.02 -3.88 1.41e+00 5.03e-01 7.56e+00 angle pdb=" C LEU B 599 " pdb=" N ASP B 600 " pdb=" CA ASP B 600 " ideal model delta sigma weight residual 121.80 128.06 -6.26 2.44e+00 1.68e-01 6.58e+00 angle pdb=" CA CYS B 301 " pdb=" CB CYS B 301 " pdb=" SG CYS B 301 " ideal model delta sigma weight residual 114.40 109.02 5.38 2.30e+00 1.89e-01 5.48e+00 angle pdb=" C CYS B 288 " pdb=" CA CYS B 288 " pdb=" CB CYS B 288 " ideal model delta sigma weight residual 109.26 112.58 -3.32 1.47e+00 4.63e-01 5.11e+00 ... (remaining 22775 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.93: 5792 21.93 - 43.86: 356 43.86 - 65.80: 85 65.80 - 87.73: 14 87.73 - 109.66: 5 Dihedral angle restraints: 6252 sinusoidal: 3511 harmonic: 2741 Sorted by residual: dihedral pdb=" CA LEU B 305 " pdb=" C LEU B 305 " pdb=" N GLY B 306 " pdb=" CA GLY B 306 " ideal model delta harmonic sigma weight residual 180.00 149.11 30.89 0 5.00e+00 4.00e-02 3.82e+01 dihedral pdb=" CB CYS B 8 " pdb=" SG CYS B 8 " pdb=" SG CYS B 26 " pdb=" CB CYS B 26 " ideal model delta sinusoidal sigma weight residual 93.00 143.03 -50.03 1 1.00e+01 1.00e-02 3.43e+01 dihedral pdb=" CB CYS B 798 " pdb=" SG CYS B 798 " pdb=" SG CYS B 807 " pdb=" CB CYS B 807 " ideal model delta sinusoidal sigma weight residual 93.00 46.02 46.98 1 1.00e+01 1.00e-02 3.05e+01 ... (remaining 6249 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.330: 990 0.330 - 0.661: 0 0.661 - 0.991: 0 0.991 - 1.322: 1 1.322 - 1.652: 2 Chirality restraints: 993 Sorted by residual: chirality pdb=" C1 NAG D 2 " pdb=" O4 NAG D 1 " pdb=" C2 NAG D 2 " pdb=" O5 NAG D 2 " both_signs ideal model delta sigma weight residual False -2.40 -0.75 -1.65 2.00e-02 2.50e+03 6.82e+03 chirality pdb=" C1 BMA D 3 " pdb=" O4 NAG D 2 " pdb=" C2 BMA D 3 " pdb=" O5 BMA D 3 " both_signs ideal model delta sigma weight residual False -2.40 -0.77 -1.63 2.00e-02 2.50e+03 6.61e+03 chirality pdb=" C1 NAG C 2 " pdb=" O4 NAG C 1 " pdb=" C2 NAG C 2 " pdb=" O5 NAG C 2 " both_signs ideal model delta sigma weight residual False -2.40 -1.30 -1.10 2.00e-02 2.50e+03 3.01e+03 ... (remaining 990 not shown) Planarity restraints: 1890 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY B 306 " 0.036 5.00e-02 4.00e+02 5.46e-02 4.78e+00 pdb=" N PRO B 307 " -0.095 5.00e-02 4.00e+02 pdb=" CA PRO B 307 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO B 307 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CG GLN A 842 " 0.004 2.00e-02 2.50e+03 1.15e-02 1.98e+00 pdb=" CD GLN A 842 " -0.023 2.00e-02 2.50e+03 pdb=" OE1 GLN A 842 " 0.013 2.00e-02 2.50e+03 pdb=" NE2 GLN A 842 " 0.003 2.00e-02 2.50e+03 pdb="HE21 GLN A 842 " 0.007 2.00e-02 2.50e+03 pdb="HE22 GLN A 842 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS B 616 " -0.020 5.00e-02 4.00e+02 3.09e-02 1.52e+00 pdb=" N PRO B 617 " 0.053 5.00e-02 4.00e+02 pdb=" CA PRO B 617 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO B 617 " -0.017 5.00e-02 4.00e+02 ... (remaining 1887 not shown) Histogram of nonbonded interaction distances: 1.53 - 2.15: 608 2.15 - 2.76: 23669 2.76 - 3.37: 34404 3.37 - 3.99: 45992 3.99 - 4.60: 69424 Nonbonded interactions: 174097 Sorted by model distance: nonbonded pdb=" H PHE A 766 " pdb=" OG1 THR A 795 " model vdw 1.535 2.450 nonbonded pdb="HE21 GLN A 876 " pdb=" O GLY A 884 " model vdw 1.545 2.450 nonbonded pdb=" O TRP A 822 " pdb=" HH TYR A 855 " model vdw 1.555 2.450 nonbonded pdb=" O ALA A 644 " pdb=" HG1 THR A 647 " model vdw 1.556 2.450 nonbonded pdb=" O CYS B 266 " pdb="HH11 ARG B 270 " model vdw 1.572 2.450 ... (remaining 174092 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 'C' selection = chain 'E' } 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 5.610 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: 0.190 Extract box with map and model: 0.470 Check model and map are aligned: 0.090 Set scattering table: 0.120 Process input model: 30.200 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6603 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 0.066 6649 Z= 0.184 Angle : 1.413 60.368 9056 Z= 0.532 Chirality : 0.093 1.652 993 Planarity : 0.004 0.055 1160 Dihedral : 13.875 109.661 2664 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.03 % Favored : 92.97 % Rotamer: Outliers : 0.14 % Allowed : 3.81 % Favored : 96.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: -3.48 (0.27), residues: 768 helix: -3.77 (0.47), residues: 54 sheet: -1.79 (0.32), residues: 216 loop : -2.50 (0.25), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 822 HIS 0.003 0.001 HIS B 247 PHE 0.012 0.001 PHE B 51 TYR 0.011 0.001 TYR A 689 ARG 0.009 0.001 ARG B 806 Details of bonding type rmsd link_NAG-ASN : bond 0.00328 ( 8) link_NAG-ASN : angle 1.92474 ( 24) link_BETA1-4 : bond 0.06525 ( 4) link_BETA1-4 : angle 34.34311 ( 12) hydrogen bonds : bond 0.25967 ( 165) hydrogen bonds : angle 10.36512 ( 474) SS BOND : bond 0.00412 ( 17) SS BOND : angle 1.57304 ( 34) covalent geometry : bond 0.00358 ( 6620) covalent geometry : angle 0.64612 ( 8986) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 130 time to evaluate : 1.072 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 585 LEU cc_start: 0.8520 (mt) cc_final: 0.8214 (mt) REVERT: A 602 ASN cc_start: 0.8309 (m-40) cc_final: 0.7727 (m110) REVERT: A 691 LYS cc_start: 0.9275 (tptt) cc_final: 0.8952 (tppt) REVERT: A 778 HIS cc_start: 0.6277 (m90) cc_final: 0.5981 (p90) REVERT: A 834 MET cc_start: 0.7055 (ptm) cc_final: 0.6665 (ptp) REVERT: B 90 ASN cc_start: 0.9082 (t0) cc_final: 0.8365 (t0) REVERT: B 110 MET cc_start: 0.6112 (mmt) cc_final: 0.5603 (mmt) REVERT: B 611 ILE cc_start: 0.8117 (mt) cc_final: 0.7774 (mt) REVERT: B 845 GLN cc_start: 0.8265 (tp40) cc_final: 0.6923 (mp10) outliers start: 1 outliers final: 0 residues processed: 131 average time/residue: 0.5490 time to fit residues: 89.0186 Evaluate side-chains 91 residues out of total 709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 91 time to evaluate : 0.995 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 65 optimal weight: 0.9980 chunk 58 optimal weight: 0.2980 chunk 32 optimal weight: 3.9990 chunk 19 optimal weight: 2.9990 chunk 39 optimal weight: 0.6980 chunk 31 optimal weight: 2.9990 chunk 60 optimal weight: 3.9990 chunk 23 optimal weight: 5.9990 chunk 36 optimal weight: 0.3980 chunk 44 optimal weight: 0.8980 chunk 69 optimal weight: 4.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 32 HIS B 34 GLN B 123 ASN B 594 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4083 r_free = 0.4083 target = 0.085136 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.071943 restraints weight = 98030.209| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.074087 restraints weight = 49777.500| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.075354 restraints weight = 30267.750| |-----------------------------------------------------------------------------| r_work (final): 0.3875 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6680 moved from start: 0.2087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 6649 Z= 0.148 Angle : 0.720 8.335 9056 Z= 0.354 Chirality : 0.047 0.186 993 Planarity : 0.005 0.087 1160 Dihedral : 9.614 64.927 1110 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.77 % Favored : 93.23 % Rotamer: Outliers : 1.41 % Allowed : 8.74 % Favored : 89.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % Cis-general : 0.00 % 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: -2.94 (0.28), residues: 768 helix: -3.21 (0.51), residues: 62 sheet: -1.37 (0.32), residues: 228 loop : -2.15 (0.26), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 618 HIS 0.006 0.001 HIS B 280 PHE 0.012 0.002 PHE B 88 TYR 0.015 0.001 TYR A 689 ARG 0.008 0.001 ARG B 236 Details of bonding type rmsd link_NAG-ASN : bond 0.00538 ( 8) link_NAG-ASN : angle 1.92145 ( 24) link_BETA1-4 : bond 0.00423 ( 4) link_BETA1-4 : angle 4.53158 ( 12) hydrogen bonds : bond 0.05270 ( 165) hydrogen bonds : angle 7.58088 ( 474) SS BOND : bond 0.00520 ( 17) SS BOND : angle 1.45840 ( 34) covalent geometry : bond 0.00328 ( 6620) covalent geometry : angle 0.69102 ( 8986) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 94 time to evaluate : 0.922 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 691 LYS cc_start: 0.9259 (tptt) cc_final: 0.9015 (tppt) REVERT: A 834 MET cc_start: 0.7435 (ptm) cc_final: 0.6889 (ptp) REVERT: B 34 GLN cc_start: 0.7057 (mt0) cc_final: 0.6700 (mp10) REVERT: B 287 GLU cc_start: 0.8052 (mp0) cc_final: 0.6600 (tp30) REVERT: B 845 GLN cc_start: 0.8425 (tp40) cc_final: 0.7352 (mp10) outliers start: 10 outliers final: 6 residues processed: 102 average time/residue: 0.4980 time to fit residues: 63.7350 Evaluate side-chains 83 residues out of total 709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 77 time to evaluate : 0.940 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 698 HIS Chi-restraints excluded: chain A residue 871 TYR Chi-restraints excluded: chain B residue 89 PHE Chi-restraints excluded: chain B residue 255 ASN Chi-restraints excluded: chain B residue 256 PHE Chi-restraints excluded: chain B residue 614 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 44 optimal weight: 0.4980 chunk 6 optimal weight: 5.9990 chunk 43 optimal weight: 3.9990 chunk 45 optimal weight: 0.0270 chunk 60 optimal weight: 3.9990 chunk 41 optimal weight: 0.9980 chunk 28 optimal weight: 1.9990 chunk 75 optimal weight: 7.9990 chunk 55 optimal weight: 4.9990 chunk 14 optimal weight: 0.9990 chunk 63 optimal weight: 3.9990 overall best weight: 0.9042 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 870 ASN B 148 ASN ** B 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4072 r_free = 0.4072 target = 0.084250 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.071079 restraints weight = 99135.758| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.073159 restraints weight = 49806.648| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 56)----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.074398 restraints weight = 31189.277| |-----------------------------------------------------------------------------| r_work (final): 0.3865 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6774 moved from start: 0.3077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6649 Z= 0.145 Angle : 0.652 8.455 9056 Z= 0.325 Chirality : 0.046 0.256 993 Planarity : 0.006 0.086 1160 Dihedral : 7.645 59.578 1110 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.20 % Favored : 91.80 % Rotamer: Outliers : 1.27 % Allowed : 11.28 % Favored : 87.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % Cis-general : 0.00 % 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: -2.65 (0.28), residues: 768 helix: -2.86 (0.53), residues: 62 sheet: -1.07 (0.32), residues: 227 loop : -2.02 (0.27), residues: 479 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 618 HIS 0.005 0.001 HIS B 787 PHE 0.012 0.002 PHE B 788 TYR 0.016 0.001 TYR A 689 ARG 0.005 0.001 ARG B 882 Details of bonding type rmsd link_NAG-ASN : bond 0.00493 ( 8) link_NAG-ASN : angle 1.95034 ( 24) link_BETA1-4 : bond 0.00711 ( 4) link_BETA1-4 : angle 3.51532 ( 12) hydrogen bonds : bond 0.04507 ( 165) hydrogen bonds : angle 6.79143 ( 474) SS BOND : bond 0.00541 ( 17) SS BOND : angle 1.80089 ( 34) covalent geometry : bond 0.00317 ( 6620) covalent geometry : angle 0.62428 ( 8986) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 79 time to evaluate : 1.494 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 691 LYS cc_start: 0.9262 (tptt) cc_final: 0.9024 (tppt) REVERT: A 834 MET cc_start: 0.7578 (ptm) cc_final: 0.6940 (ptp) REVERT: B 287 GLU cc_start: 0.8249 (mp0) cc_final: 0.6799 (tp30) REVERT: B 845 GLN cc_start: 0.8405 (tp40) cc_final: 0.7200 (mp10) outliers start: 9 outliers final: 7 residues processed: 84 average time/residue: 0.5023 time to fit residues: 53.7420 Evaluate side-chains 79 residues out of total 709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 72 time to evaluate : 1.051 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 698 HIS Chi-restraints excluded: chain A residue 871 TYR Chi-restraints excluded: chain B residue 255 ASN Chi-restraints excluded: chain B residue 256 PHE Chi-restraints excluded: chain B residue 613 LEU Chi-restraints excluded: chain B residue 614 LYS Chi-restraints excluded: chain B residue 896 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 1 optimal weight: 3.9990 chunk 52 optimal weight: 0.5980 chunk 34 optimal weight: 2.9990 chunk 53 optimal weight: 0.8980 chunk 42 optimal weight: 2.9990 chunk 63 optimal weight: 3.9990 chunk 50 optimal weight: 0.9980 chunk 64 optimal weight: 3.9990 chunk 61 optimal weight: 6.9990 chunk 31 optimal weight: 0.6980 chunk 35 optimal weight: 2.9990 overall best weight: 1.2382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 608 ASN A 619 GLN A 699 ASN ** B 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4053 r_free = 0.4053 target = 0.083440 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.070286 restraints weight = 98519.082| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.072349 restraints weight = 50812.364| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.073620 restraints weight = 31145.616| |-----------------------------------------------------------------------------| r_work (final): 0.3840 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6931 moved from start: 0.4104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 6649 Z= 0.169 Angle : 0.648 5.866 9056 Z= 0.328 Chirality : 0.045 0.184 993 Planarity : 0.005 0.090 1160 Dihedral : 6.798 57.984 1110 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.98 % Favored : 91.02 % Rotamer: Outliers : 1.41 % Allowed : 11.99 % Favored : 86.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % Cis-general : 0.00 % 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: -2.40 (0.28), residues: 768 helix: -2.48 (0.54), residues: 62 sheet: -0.94 (0.34), residues: 222 loop : -1.86 (0.27), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 618 HIS 0.005 0.001 HIS B 787 PHE 0.016 0.002 PHE A 747 TYR 0.021 0.001 TYR A 689 ARG 0.004 0.001 ARG B 19 Details of bonding type rmsd link_NAG-ASN : bond 0.00467 ( 8) link_NAG-ASN : angle 2.12998 ( 24) link_BETA1-4 : bond 0.00243 ( 4) link_BETA1-4 : angle 2.68991 ( 12) hydrogen bonds : bond 0.03806 ( 165) hydrogen bonds : angle 6.22590 ( 474) SS BOND : bond 0.00836 ( 17) SS BOND : angle 1.67988 ( 34) covalent geometry : bond 0.00363 ( 6620) covalent geometry : angle 0.62460 ( 8986) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 73 time to evaluate : 0.940 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 691 LYS cc_start: 0.9249 (tptt) cc_final: 0.9018 (tppt) REVERT: A 834 MET cc_start: 0.7984 (ptm) cc_final: 0.7478 (ptp) REVERT: B 13 ILE cc_start: 0.7980 (mp) cc_final: 0.7753 (mp) REVERT: B 34 GLN cc_start: 0.7362 (mp10) cc_final: 0.6916 (mp10) REVERT: B 110 MET cc_start: 0.7487 (mmt) cc_final: 0.7171 (mmt) REVERT: B 845 GLN cc_start: 0.8358 (tp40) cc_final: 0.7218 (mp10) outliers start: 10 outliers final: 8 residues processed: 80 average time/residue: 0.4202 time to fit residues: 44.1854 Evaluate side-chains 76 residues out of total 709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 68 time to evaluate : 0.964 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 698 HIS Chi-restraints excluded: chain A residue 871 TYR Chi-restraints excluded: chain B residue 113 THR Chi-restraints excluded: chain B residue 256 PHE Chi-restraints excluded: chain B residue 259 CYS Chi-restraints excluded: chain B residue 613 LEU Chi-restraints excluded: chain B residue 782 ILE Chi-restraints excluded: chain B residue 871 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 46 optimal weight: 3.9990 chunk 76 optimal weight: 6.9990 chunk 61 optimal weight: 4.9990 chunk 73 optimal weight: 3.9990 chunk 70 optimal weight: 4.9990 chunk 8 optimal weight: 0.9980 chunk 25 optimal weight: 0.7980 chunk 18 optimal weight: 2.9990 chunk 5 optimal weight: 2.9990 chunk 23 optimal weight: 0.7980 chunk 32 optimal weight: 2.9990 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 619 GLN A 631 ASN ** B 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.081838 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.068844 restraints weight = 100504.174| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.070824 restraints weight = 51123.005| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.071988 restraints weight = 32716.631| |-----------------------------------------------------------------------------| r_work (final): 0.3800 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7105 moved from start: 0.5230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 6649 Z= 0.211 Angle : 0.680 5.883 9056 Z= 0.347 Chirality : 0.046 0.185 993 Planarity : 0.006 0.088 1160 Dihedral : 6.821 59.587 1110 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 10.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.03 % Favored : 89.97 % Rotamer: Outliers : 1.97 % Allowed : 13.68 % Favored : 84.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % Cis-general : 0.00 % 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: -2.47 (0.28), residues: 768 helix: -2.28 (0.55), residues: 63 sheet: -1.01 (0.35), residues: 213 loop : -1.93 (0.26), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 183 HIS 0.007 0.002 HIS B 247 PHE 0.014 0.002 PHE B 788 TYR 0.017 0.002 TYR A 689 ARG 0.005 0.001 ARG B 19 Details of bonding type rmsd link_NAG-ASN : bond 0.00698 ( 8) link_NAG-ASN : angle 2.38821 ( 24) link_BETA1-4 : bond 0.00254 ( 4) link_BETA1-4 : angle 2.51319 ( 12) hydrogen bonds : bond 0.04012 ( 165) hydrogen bonds : angle 6.07807 ( 474) SS BOND : bond 0.00641 ( 17) SS BOND : angle 1.74013 ( 34) covalent geometry : bond 0.00454 ( 6620) covalent geometry : angle 0.65686 ( 8986) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 65 time to evaluate : 1.014 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 834 MET cc_start: 0.8353 (ptm) cc_final: 0.7802 (ptp) REVERT: B 90 ASN cc_start: 0.9115 (t0) cc_final: 0.8852 (t0) REVERT: B 110 MET cc_start: 0.7728 (mmt) cc_final: 0.7408 (mmt) outliers start: 14 outliers final: 10 residues processed: 76 average time/residue: 0.4490 time to fit residues: 44.8968 Evaluate side-chains 71 residues out of total 709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 61 time to evaluate : 0.923 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 698 HIS Chi-restraints excluded: chain A residue 796 MET Chi-restraints excluded: chain A residue 871 TYR Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 87 LEU Chi-restraints excluded: chain B residue 256 PHE Chi-restraints excluded: chain B residue 259 CYS Chi-restraints excluded: chain B residue 613 LEU Chi-restraints excluded: chain B residue 614 LYS Chi-restraints excluded: chain B residue 782 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 8 optimal weight: 0.8980 chunk 0 optimal weight: 2.9990 chunk 72 optimal weight: 3.9990 chunk 15 optimal weight: 2.9990 chunk 32 optimal weight: 0.9990 chunk 40 optimal weight: 2.9990 chunk 36 optimal weight: 0.9990 chunk 3 optimal weight: 1.9990 chunk 47 optimal weight: 1.9990 chunk 58 optimal weight: 3.9990 chunk 46 optimal weight: 2.9990 overall best weight: 1.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 816 ASN ** B 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.081944 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.068992 restraints weight = 100263.351| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.071027 restraints weight = 51192.290| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.072238 restraints weight = 31761.559| |-----------------------------------------------------------------------------| r_work (final): 0.3800 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7134 moved from start: 0.5754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 6649 Z= 0.163 Angle : 0.635 5.659 9056 Z= 0.320 Chirality : 0.045 0.181 993 Planarity : 0.005 0.088 1160 Dihedral : 6.628 59.684 1110 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.33 % Favored : 91.67 % Rotamer: Outliers : 1.83 % Allowed : 14.39 % Favored : 83.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % Cis-general : 0.00 % 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: -2.36 (0.29), residues: 768 helix: -2.22 (0.56), residues: 63 sheet: -1.02 (0.36), residues: 213 loop : -1.79 (0.27), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 183 HIS 0.005 0.001 HIS B 247 PHE 0.012 0.002 PHE B 788 TYR 0.017 0.001 TYR A 689 ARG 0.004 0.000 ARG A 705 Details of bonding type rmsd link_NAG-ASN : bond 0.00425 ( 8) link_NAG-ASN : angle 2.11344 ( 24) link_BETA1-4 : bond 0.00274 ( 4) link_BETA1-4 : angle 2.29838 ( 12) hydrogen bonds : bond 0.03707 ( 165) hydrogen bonds : angle 5.83210 ( 474) SS BOND : bond 0.00812 ( 17) SS BOND : angle 1.39247 ( 34) covalent geometry : bond 0.00351 ( 6620) covalent geometry : angle 0.61619 ( 8986) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 64 time to evaluate : 0.927 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 834 MET cc_start: 0.8459 (ptm) cc_final: 0.7946 (ptp) REVERT: A 893 TYR cc_start: 0.5744 (OUTLIER) cc_final: 0.4595 (m-10) REVERT: B 90 ASN cc_start: 0.9271 (t0) cc_final: 0.9011 (t0) REVERT: B 110 MET cc_start: 0.7855 (mmt) cc_final: 0.7559 (mmt) REVERT: B 844 TRP cc_start: 0.4060 (p90) cc_final: 0.2953 (p90) outliers start: 13 outliers final: 10 residues processed: 73 average time/residue: 0.4303 time to fit residues: 41.6365 Evaluate side-chains 72 residues out of total 709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 61 time to evaluate : 1.075 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 616 VAL Chi-restraints excluded: chain A residue 694 GLU Chi-restraints excluded: chain A residue 698 HIS Chi-restraints excluded: chain A residue 796 MET Chi-restraints excluded: chain A residue 871 TYR Chi-restraints excluded: chain A residue 893 TYR Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 256 PHE Chi-restraints excluded: chain B residue 259 CYS Chi-restraints excluded: chain B residue 613 LEU Chi-restraints excluded: chain B residue 782 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 54 optimal weight: 1.9990 chunk 18 optimal weight: 3.9990 chunk 20 optimal weight: 3.9990 chunk 72 optimal weight: 3.9990 chunk 11 optimal weight: 2.9990 chunk 52 optimal weight: 0.7980 chunk 50 optimal weight: 0.9980 chunk 23 optimal weight: 1.9990 chunk 67 optimal weight: 6.9990 chunk 64 optimal weight: 0.9980 chunk 3 optimal weight: 2.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 827 ASN B 90 ASN ** B 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.081250 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.068514 restraints weight = 99451.486| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.070392 restraints weight = 51466.531| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.071615 restraints weight = 32260.969| |-----------------------------------------------------------------------------| r_work (final): 0.3784 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7183 moved from start: 0.6274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 6649 Z= 0.170 Angle : 0.635 7.868 9056 Z= 0.321 Chirality : 0.045 0.187 993 Planarity : 0.005 0.086 1160 Dihedral : 6.602 59.425 1110 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 9.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.51 % Favored : 90.49 % Rotamer: Outliers : 1.83 % Allowed : 15.37 % Favored : 82.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % Cis-general : 0.00 % 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: -2.27 (0.29), residues: 768 helix: -2.17 (0.55), residues: 63 sheet: -0.99 (0.36), residues: 210 loop : -1.71 (0.27), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 183 HIS 0.004 0.001 HIS B 100 PHE 0.022 0.002 PHE B 231 TYR 0.014 0.001 TYR A 689 ARG 0.003 0.000 ARG A 705 Details of bonding type rmsd link_NAG-ASN : bond 0.00470 ( 8) link_NAG-ASN : angle 2.20285 ( 24) link_BETA1-4 : bond 0.00336 ( 4) link_BETA1-4 : angle 2.32204 ( 12) hydrogen bonds : bond 0.03641 ( 165) hydrogen bonds : angle 5.67856 ( 474) SS BOND : bond 0.00726 ( 17) SS BOND : angle 1.33987 ( 34) covalent geometry : bond 0.00365 ( 6620) covalent geometry : angle 0.61552 ( 8986) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 59 time to evaluate : 1.000 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 763 LEU cc_start: 0.7776 (mp) cc_final: 0.7517 (mt) REVERT: A 834 MET cc_start: 0.8526 (ptm) cc_final: 0.8042 (ptp) REVERT: A 893 TYR cc_start: 0.5593 (OUTLIER) cc_final: 0.4153 (m-10) REVERT: B 90 ASN cc_start: 0.9339 (t160) cc_final: 0.9125 (t0) REVERT: B 110 MET cc_start: 0.7891 (mmt) cc_final: 0.7628 (mmt) REVERT: B 844 TRP cc_start: 0.4032 (p90) cc_final: 0.2963 (p90) outliers start: 13 outliers final: 10 residues processed: 71 average time/residue: 0.3963 time to fit residues: 37.5473 Evaluate side-chains 67 residues out of total 709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 56 time to evaluate : 0.987 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 616 VAL Chi-restraints excluded: chain A residue 698 HIS Chi-restraints excluded: chain A residue 871 TYR Chi-restraints excluded: chain A residue 893 TYR Chi-restraints excluded: chain B residue 87 LEU Chi-restraints excluded: chain B residue 120 GLU Chi-restraints excluded: chain B residue 256 PHE Chi-restraints excluded: chain B residue 259 CYS Chi-restraints excluded: chain B residue 613 LEU Chi-restraints excluded: chain B residue 782 ILE Chi-restraints excluded: chain B residue 871 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 2 optimal weight: 3.9990 chunk 45 optimal weight: 0.0170 chunk 35 optimal weight: 2.9990 chunk 36 optimal weight: 0.0980 chunk 13 optimal weight: 0.9980 chunk 16 optimal weight: 0.9980 chunk 40 optimal weight: 1.9990 chunk 7 optimal weight: 4.9990 chunk 46 optimal weight: 0.9980 chunk 22 optimal weight: 3.9990 chunk 12 optimal weight: 0.7980 overall best weight: 0.5818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4019 r_free = 0.4019 target = 0.082351 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.069397 restraints weight = 99327.689| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.071447 restraints weight = 50328.444| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.072639 restraints weight = 31377.809| |-----------------------------------------------------------------------------| r_work (final): 0.3808 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7158 moved from start: 0.6455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 6649 Z= 0.111 Angle : 0.592 5.322 9056 Z= 0.299 Chirality : 0.045 0.176 993 Planarity : 0.005 0.084 1160 Dihedral : 6.234 57.494 1110 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.68 % Favored : 92.32 % Rotamer: Outliers : 1.41 % Allowed : 15.94 % Favored : 82.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % Cis-general : 0.00 % 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: -2.06 (0.30), residues: 768 helix: -2.07 (0.56), residues: 63 sheet: -0.82 (0.36), residues: 215 loop : -1.57 (0.28), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 810 HIS 0.012 0.001 HIS B 247 PHE 0.015 0.001 PHE B 39 TYR 0.012 0.001 TYR A 689 ARG 0.003 0.000 ARG A 705 Details of bonding type rmsd link_NAG-ASN : bond 0.00344 ( 8) link_NAG-ASN : angle 1.94911 ( 24) link_BETA1-4 : bond 0.00332 ( 4) link_BETA1-4 : angle 2.13045 ( 12) hydrogen bonds : bond 0.03439 ( 165) hydrogen bonds : angle 5.55115 ( 474) SS BOND : bond 0.00489 ( 17) SS BOND : angle 1.04563 ( 34) covalent geometry : bond 0.00252 ( 6620) covalent geometry : angle 0.57703 ( 8986) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 62 time to evaluate : 0.961 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 834 MET cc_start: 0.8479 (ptm) cc_final: 0.7992 (ptp) REVERT: A 841 SER cc_start: 0.7040 (p) cc_final: 0.6790 (p) REVERT: A 893 TYR cc_start: 0.5209 (OUTLIER) cc_final: 0.4162 (m-10) REVERT: B 90 ASN cc_start: 0.9305 (t160) cc_final: 0.8981 (t0) REVERT: B 97 GLU cc_start: 0.8262 (mm-30) cc_final: 0.7789 (mm-30) REVERT: B 110 MET cc_start: 0.7817 (mmt) cc_final: 0.7575 (mmt) REVERT: B 305 LEU cc_start: 0.8692 (OUTLIER) cc_final: 0.8419 (tt) REVERT: B 818 MET cc_start: 0.7907 (mtp) cc_final: 0.7584 (mtp) REVERT: B 844 TRP cc_start: 0.4018 (p90) cc_final: 0.2928 (p90) outliers start: 10 outliers final: 8 residues processed: 71 average time/residue: 0.4189 time to fit residues: 39.0827 Evaluate side-chains 71 residues out of total 709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 61 time to evaluate : 0.928 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 616 VAL Chi-restraints excluded: chain A residue 698 HIS Chi-restraints excluded: chain A residue 871 TYR Chi-restraints excluded: chain A residue 893 TYR Chi-restraints excluded: chain B residue 256 PHE Chi-restraints excluded: chain B residue 259 CYS Chi-restraints excluded: chain B residue 305 LEU Chi-restraints excluded: chain B residue 613 LEU Chi-restraints excluded: chain B residue 782 ILE Chi-restraints excluded: chain B residue 855 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 21 optimal weight: 4.9990 chunk 24 optimal weight: 7.9990 chunk 6 optimal weight: 0.8980 chunk 74 optimal weight: 8.9990 chunk 3 optimal weight: 2.9990 chunk 27 optimal weight: 3.9990 chunk 53 optimal weight: 0.0980 chunk 72 optimal weight: 4.9990 chunk 37 optimal weight: 2.9990 chunk 31 optimal weight: 1.9990 chunk 50 optimal weight: 0.7980 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.080909 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.068125 restraints weight = 100632.983| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.070109 restraints weight = 51733.741| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.071258 restraints weight = 32168.841| |-----------------------------------------------------------------------------| r_work (final): 0.3771 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7240 moved from start: 0.6973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 6649 Z= 0.178 Angle : 0.634 5.670 9056 Z= 0.322 Chirality : 0.045 0.182 993 Planarity : 0.005 0.086 1160 Dihedral : 6.519 58.773 1110 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 9.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.38 % Favored : 90.62 % Rotamer: Outliers : 1.41 % Allowed : 15.80 % Favored : 82.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % Cis-general : 0.00 % 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: -2.13 (0.29), residues: 768 helix: -1.96 (0.59), residues: 63 sheet: -0.93 (0.36), residues: 211 loop : -1.61 (0.27), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 183 HIS 0.011 0.001 HIS B 247 PHE 0.018 0.002 PHE A 891 TYR 0.018 0.001 TYR A 689 ARG 0.003 0.001 ARG B 47 Details of bonding type rmsd link_NAG-ASN : bond 0.00446 ( 8) link_NAG-ASN : angle 2.27753 ( 24) link_BETA1-4 : bond 0.00331 ( 4) link_BETA1-4 : angle 2.25993 ( 12) hydrogen bonds : bond 0.03543 ( 165) hydrogen bonds : angle 5.55543 ( 474) SS BOND : bond 0.00559 ( 17) SS BOND : angle 1.28978 ( 34) covalent geometry : bond 0.00387 ( 6620) covalent geometry : angle 0.61512 ( 8986) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 56 time to evaluate : 1.074 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 763 LEU cc_start: 0.7670 (mp) cc_final: 0.7450 (mt) REVERT: A 834 MET cc_start: 0.8551 (ptm) cc_final: 0.8028 (ptp) REVERT: A 893 TYR cc_start: 0.5564 (OUTLIER) cc_final: 0.4596 (m-10) REVERT: B 90 ASN cc_start: 0.9358 (t160) cc_final: 0.9045 (t0) REVERT: B 97 GLU cc_start: 0.8026 (mm-30) cc_final: 0.7570 (mm-30) REVERT: B 110 MET cc_start: 0.7925 (mmt) cc_final: 0.7648 (mmt) REVERT: B 305 LEU cc_start: 0.8537 (OUTLIER) cc_final: 0.8299 (tt) REVERT: B 844 TRP cc_start: 0.4110 (p90) cc_final: 0.2962 (p90) outliers start: 10 outliers final: 8 residues processed: 64 average time/residue: 0.4430 time to fit residues: 37.3821 Evaluate side-chains 65 residues out of total 709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 55 time to evaluate : 0.894 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 616 VAL Chi-restraints excluded: chain A residue 698 HIS Chi-restraints excluded: chain A residue 871 TYR Chi-restraints excluded: chain A residue 893 TYR Chi-restraints excluded: chain B residue 256 PHE Chi-restraints excluded: chain B residue 259 CYS Chi-restraints excluded: chain B residue 305 LEU Chi-restraints excluded: chain B residue 613 LEU Chi-restraints excluded: chain B residue 782 ILE Chi-restraints excluded: chain B residue 855 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 20 optimal weight: 3.9990 chunk 21 optimal weight: 0.8980 chunk 26 optimal weight: 0.8980 chunk 64 optimal weight: 1.9990 chunk 17 optimal weight: 2.9990 chunk 61 optimal weight: 2.9990 chunk 32 optimal weight: 3.9990 chunk 41 optimal weight: 7.9990 chunk 73 optimal weight: 0.7980 chunk 30 optimal weight: 1.9990 chunk 34 optimal weight: 3.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.080875 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.068039 restraints weight = 98261.709| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.070041 restraints weight = 50430.666| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.071233 restraints weight = 31572.596| |-----------------------------------------------------------------------------| r_work (final): 0.3772 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7252 moved from start: 0.7347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 6649 Z= 0.150 Angle : 0.619 6.051 9056 Z= 0.312 Chirality : 0.045 0.169 993 Planarity : 0.005 0.084 1160 Dihedral : 6.486 58.734 1110 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.55 % Favored : 92.45 % Rotamer: Outliers : 1.55 % Allowed : 15.80 % Favored : 82.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % Cis-general : 0.00 % 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: -2.07 (0.29), residues: 768 helix: -1.83 (0.61), residues: 63 sheet: -0.83 (0.37), residues: 197 loop : -1.60 (0.27), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 632 HIS 0.011 0.001 HIS B 247 PHE 0.011 0.002 PHE B 96 TYR 0.013 0.001 TYR A 689 ARG 0.003 0.000 ARG A 705 Details of bonding type rmsd link_NAG-ASN : bond 0.00395 ( 8) link_NAG-ASN : angle 2.11436 ( 24) link_BETA1-4 : bond 0.00315 ( 4) link_BETA1-4 : angle 2.16173 ( 12) hydrogen bonds : bond 0.03471 ( 165) hydrogen bonds : angle 5.54013 ( 474) SS BOND : bond 0.00534 ( 17) SS BOND : angle 1.03735 ( 34) covalent geometry : bond 0.00327 ( 6620) covalent geometry : angle 0.60287 ( 8986) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 61 time to evaluate : 0.878 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 763 LEU cc_start: 0.7723 (mp) cc_final: 0.7513 (mt) REVERT: A 834 MET cc_start: 0.8646 (ptm) cc_final: 0.8140 (ptp) REVERT: A 841 SER cc_start: 0.7218 (p) cc_final: 0.6974 (p) REVERT: A 891 PHE cc_start: 0.6140 (p90) cc_final: 0.5909 (p90) REVERT: A 893 TYR cc_start: 0.5717 (OUTLIER) cc_final: 0.4717 (m-10) REVERT: B 38 MET cc_start: 0.6551 (tpp) cc_final: 0.5545 (tpp) REVERT: B 90 ASN cc_start: 0.9361 (t160) cc_final: 0.9053 (t0) REVERT: B 97 GLU cc_start: 0.8262 (mm-30) cc_final: 0.7644 (mm-30) REVERT: B 110 MET cc_start: 0.7937 (mmt) cc_final: 0.7681 (mmt) REVERT: B 818 MET cc_start: 0.7750 (mtp) cc_final: 0.7307 (mtp) REVERT: B 844 TRP cc_start: 0.4163 (p90) cc_final: 0.2955 (p90) outliers start: 11 outliers final: 8 residues processed: 69 average time/residue: 0.4550 time to fit residues: 42.2026 Evaluate side-chains 64 residues out of total 709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 55 time to evaluate : 1.099 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 616 VAL Chi-restraints excluded: chain A residue 698 HIS Chi-restraints excluded: chain A residue 871 TYR Chi-restraints excluded: chain A residue 893 TYR Chi-restraints excluded: chain B residue 256 PHE Chi-restraints excluded: chain B residue 259 CYS Chi-restraints excluded: chain B residue 613 LEU Chi-restraints excluded: chain B residue 782 ILE Chi-restraints excluded: chain B residue 855 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 7 optimal weight: 5.9990 chunk 21 optimal weight: 1.9990 chunk 34 optimal weight: 2.9990 chunk 1 optimal weight: 4.9990 chunk 62 optimal weight: 1.9990 chunk 47 optimal weight: 0.9980 chunk 72 optimal weight: 0.9990 chunk 40 optimal weight: 0.5980 chunk 16 optimal weight: 0.5980 chunk 15 optimal weight: 1.9990 chunk 52 optimal weight: 0.7980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 249 GLN ** B 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3993 r_free = 0.3993 target = 0.081183 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.068355 restraints weight = 99140.607| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.070279 restraints weight = 50489.017| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.071477 restraints weight = 31699.812| |-----------------------------------------------------------------------------| r_work (final): 0.3781 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7242 moved from start: 0.7566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6649 Z= 0.126 Angle : 0.614 5.859 9056 Z= 0.308 Chirality : 0.045 0.172 993 Planarity : 0.005 0.083 1160 Dihedral : 6.308 56.979 1110 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.38 % Favored : 90.62 % Rotamer: Outliers : 1.27 % Allowed : 16.64 % Favored : 82.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % Cis-general : 0.00 % 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: -1.95 (0.30), residues: 768 helix: -1.77 (0.61), residues: 63 sheet: -0.73 (0.37), residues: 203 loop : -1.53 (0.27), residues: 502 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 886 HIS 0.012 0.001 HIS B 247 PHE 0.010 0.001 PHE B 96 TYR 0.015 0.001 TYR A 626 ARG 0.009 0.000 ARG B 882 Details of bonding type rmsd link_NAG-ASN : bond 0.00346 ( 8) link_NAG-ASN : angle 2.05905 ( 24) link_BETA1-4 : bond 0.00344 ( 4) link_BETA1-4 : angle 2.12751 ( 12) hydrogen bonds : bond 0.03366 ( 165) hydrogen bonds : angle 5.42117 ( 474) SS BOND : bond 0.00490 ( 17) SS BOND : angle 1.00850 ( 34) covalent geometry : bond 0.00280 ( 6620) covalent geometry : angle 0.59854 ( 8986) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4952.09 seconds wall clock time: 85 minutes 42.33 seconds (5142.33 seconds total)