Starting phenix.real_space_refine on Sun Apr 5 15:32:06 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9u68_63899/04_2026/9u68_63899.cif Found real_map, /net/cci-nas-00/data/ceres_data/9u68_63899/04_2026/9u68_63899.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.46 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9u68_63899/04_2026/9u68_63899.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9u68_63899/04_2026/9u68_63899.map" model { file = "/net/cci-nas-00/data/ceres_data/9u68_63899/04_2026/9u68_63899.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9u68_63899/04_2026/9u68_63899.cif" } resolution = 2.46 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.029 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: 4 Type Number sf(0) Gaussians S 54 5.16 5 C 7112 2.51 5 N 1963 2.21 5 O 2180 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 11309 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 2515 Number of conformers: 1 Conformer: "" Number of residues, atoms: 321, 2515 Classifications: {'peptide': 321} Link IDs: {'PTRANS': 15, 'TRANS': 305} Chain: "B" Number of atoms: 1250 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1250 Classifications: {'peptide': 156} Link IDs: {'TRANS': 155} Chain: "C" Number of atoms: 2515 Number of conformers: 1 Conformer: "" Number of residues, atoms: 321, 2515 Classifications: {'peptide': 321} Link IDs: {'PTRANS': 15, 'TRANS': 305} Chain: "D" Number of atoms: 1250 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1250 Classifications: {'peptide': 156} Link IDs: {'TRANS': 155} Chain: "E" Number of atoms: 2515 Number of conformers: 1 Conformer: "" Number of residues, atoms: 321, 2515 Classifications: {'peptide': 321} Link IDs: {'PTRANS': 15, 'TRANS': 305} Chain: "F" Number of atoms: 1250 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1250 Classifications: {'peptide': 156} Link IDs: {'TRANS': 155} Chain: "E" 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 Time building chain proxies: 2.59, per 1000 atoms: 0.23 Number of scatterers: 11309 At special positions: 0 Unit cell: (86.92, 87.74, 141.04, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 54 16.00 O 2180 8.00 N 1963 7.00 C 7112 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=18, symmetry=0 Simple disulfide: pdb=" SG CYS A 4 " - pdb=" SG CYS B 137 " distance=2.03 Simple disulfide: pdb=" SG CYS A 42 " - pdb=" SG CYS A 275 " distance=2.03 Simple disulfide: pdb=" SG CYS A 55 " - pdb=" SG CYS A 67 " distance=2.02 Simple disulfide: pdb=" SG CYS A 90 " - pdb=" SG CYS A 136 " distance=2.03 Simple disulfide: pdb=" SG CYS A 279 " - pdb=" SG CYS A 303 " distance=2.03 Simple disulfide: pdb=" SG CYS B 144 " - pdb=" SG CYS B 148 " distance=2.03 Simple disulfide: pdb=" SG CYS C 4 " - pdb=" SG CYS D 137 " distance=2.03 Simple disulfide: pdb=" SG CYS C 42 " - pdb=" SG CYS C 275 " distance=2.03 Simple disulfide: pdb=" SG CYS C 55 " - pdb=" SG CYS C 67 " distance=2.02 Simple disulfide: pdb=" SG CYS C 90 " - pdb=" SG CYS C 136 " distance=2.03 Simple disulfide: pdb=" SG CYS C 279 " - pdb=" SG CYS C 303 " distance=2.03 Simple disulfide: pdb=" SG CYS D 144 " - pdb=" SG CYS D 148 " distance=2.03 Simple disulfide: pdb=" SG CYS E 4 " - pdb=" SG CYS F 137 " distance=2.03 Simple disulfide: pdb=" SG CYS E 42 " - pdb=" SG CYS E 275 " distance=2.03 Simple disulfide: pdb=" SG CYS E 55 " - pdb=" SG CYS E 67 " distance=2.03 Simple disulfide: pdb=" SG CYS E 90 " - pdb=" SG CYS E 136 " distance=2.03 Simple disulfide: pdb=" SG CYS E 279 " - pdb=" SG CYS E 303 " distance=2.03 Simple disulfide: pdb=" SG CYS F 144 " - pdb=" SG CYS F 148 " 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 NAG-ASN " NAG E 401 " - " ASN E 11 " Time building additional restraints: 0.89 Conformation dependent library (CDL) restraints added in 571.9 milliseconds 2838 Ramachandran restraints generated. 1419 Oldfield, 0 Emsley, 1419 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2634 Finding SS restraints... Secondary structure from input PDB file: 21 helices and 35 sheets defined 25.5% alpha, 23.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.30 Creating SS restraints... Processing helix chain 'A' and resid 56 through 63 Processing helix chain 'A' and resid 64 through 73 removed outlier: 3.511A pdb=" N ASP A 68 " --> pdb=" O PRO A 65 " (cutoff:3.500A) removed outlier: 5.828A pdb=" N LEU A 69 " --> pdb=" O LYS A 66 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N LEU A 70 " --> pdb=" O CYS A 67 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LEU A 71 " --> pdb=" O ASP A 68 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N THR A 72 " --> pdb=" O LEU A 69 " (cutoff:3.500A) Processing helix chain 'A' and resid 97 through 106 Processing helix chain 'A' and resid 184 through 192 Processing helix chain 'B' and resid 38 through 58 removed outlier: 3.530A pdb=" N GLN B 42 " --> pdb=" O GLN B 38 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ILE B 43 " --> pdb=" O LYS B 39 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N ALA B 44 " --> pdb=" O SER B 40 " (cutoff:3.500A) Processing helix chain 'B' and resid 74 through 123 removed outlier: 3.822A pdb=" N LYS B 121 " --> pdb=" O ASN B 117 " (cutoff:3.500A) Processing helix chain 'B' and resid 145 through 155 Processing helix chain 'C' and resid 56 through 63 Processing helix chain 'C' and resid 64 through 72 removed outlier: 3.685A pdb=" N ASP C 68 " --> pdb=" O PRO C 65 " (cutoff:3.500A) removed outlier: 5.860A pdb=" N LEU C 69 " --> pdb=" O LYS C 66 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LEU C 70 " --> pdb=" O CYS C 67 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LEU C 71 " --> pdb=" O ASP C 68 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N THR C 72 " --> pdb=" O LEU C 69 " (cutoff:3.500A) Processing helix chain 'C' and resid 97 through 106 Processing helix chain 'C' and resid 184 through 192 Processing helix chain 'D' and resid 37 through 58 Processing helix chain 'D' and resid 74 through 127 removed outlier: 3.515A pdb=" N GLU D 105 " --> pdb=" O LEU D 101 " (cutoff:3.500A) Processing helix chain 'D' and resid 145 through 155 Processing helix chain 'E' and resid 56 through 63 Processing helix chain 'E' and resid 64 through 73 removed outlier: 3.541A pdb=" N ASP E 68 " --> pdb=" O PRO E 65 " (cutoff:3.500A) removed outlier: 5.234A pdb=" N LEU E 69 " --> pdb=" O LYS E 66 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N THR E 72 " --> pdb=" O LEU E 69 " (cutoff:3.500A) Processing helix chain 'E' and resid 97 through 106 Processing helix chain 'E' and resid 184 through 192 Processing helix chain 'F' and resid 37 through 58 removed outlier: 3.546A pdb=" N THR F 41 " --> pdb=" O ASP F 37 " (cutoff:3.500A) Processing helix chain 'F' and resid 74 through 126 removed outlier: 3.621A pdb=" N GLN F 125 " --> pdb=" O LYS F 121 " (cutoff:3.500A) Processing helix chain 'F' and resid 145 through 155 Processing sheet with id=AA1, first strand: chain 'B' and resid 32 through 34 removed outlier: 3.849A pdb=" N GLY B 23 " --> pdb=" O GLY A 6 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 15 through 16 Processing sheet with id=AA3, first strand: chain 'A' and resid 29 through 31 Processing sheet with id=AA4, first strand: chain 'A' and resid 33 through 34 Processing sheet with id=AA5, first strand: chain 'A' and resid 40 through 44 removed outlier: 7.855A pdb=" N LEU A 41 " --> pdb=" O CYS A 275 " (cutoff:3.500A) removed outlier: 8.045A pdb=" N THR A 277 " --> pdb=" O LEU A 41 " (cutoff:3.500A) removed outlier: 6.050A pdb=" N SER A 43 " --> pdb=" O THR A 277 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 50 through 53 removed outlier: 6.784A pdb=" N LEU A 50 " --> pdb=" O ILE A 80 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N ILE A 79 " --> pdb=" O MET A 266 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'A' and resid 108 through 110 removed outlier: 6.694A pdb=" N LYS A 258 " --> pdb=" O SER A 109 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 113 through 114 removed outlier: 8.049A pdb=" N ILE A 176 " --> pdb=" O PRO A 251 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 113 through 114 Processing sheet with id=AB1, first strand: chain 'A' and resid 133 through 138 removed outlier: 7.771A pdb=" N SER A 135 " --> pdb=" O ALA A 141 " (cutoff:3.500A) removed outlier: 10.208A pdb=" N ALA A 141 " --> pdb=" O SER A 135 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 161 through 166 Processing sheet with id=AB3, first strand: chain 'A' and resid 285 through 286 removed outlier: 3.936A pdb=" N CYS A 279 " --> pdb=" O LEU A 286 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N THR B 64 " --> pdb=" O GLY A 301 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 32 through 34 removed outlier: 3.611A pdb=" N GLY D 23 " --> pdb=" O GLY C 6 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 15 through 16 Processing sheet with id=AB6, first strand: chain 'C' and resid 29 through 31 Processing sheet with id=AB7, first strand: chain 'C' and resid 33 through 34 Processing sheet with id=AB8, first strand: chain 'C' and resid 40 through 44 removed outlier: 7.721A pdb=" N LEU C 41 " --> pdb=" O CYS C 275 " (cutoff:3.500A) removed outlier: 8.015A pdb=" N THR C 277 " --> pdb=" O LEU C 41 " (cutoff:3.500A) removed outlier: 5.769A pdb=" N SER C 43 " --> pdb=" O THR C 277 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'C' and resid 50 through 51 removed outlier: 6.750A pdb=" N LEU C 50 " --> pdb=" O ILE C 80 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N ILE C 79 " --> pdb=" O MET C 266 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'C' and resid 108 through 110 removed outlier: 6.633A pdb=" N LYS C 258 " --> pdb=" O SER C 109 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 113 through 115 removed outlier: 6.557A pdb=" N HIS C 253 " --> pdb=" O ILE C 176 " (cutoff:3.500A) removed outlier: 5.500A pdb=" N ILE C 176 " --> pdb=" O HIS C 253 " (cutoff:3.500A) removed outlier: 7.989A pdb=" N ILE C 176 " --> pdb=" O PRO C 251 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 113 through 115 removed outlier: 6.557A pdb=" N HIS C 253 " --> pdb=" O ILE C 176 " (cutoff:3.500A) removed outlier: 5.500A pdb=" N ILE C 176 " --> pdb=" O HIS C 253 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 133 through 138 removed outlier: 7.834A pdb=" N SER C 135 " --> pdb=" O ALA C 141 " (cutoff:3.500A) removed outlier: 10.462A pdb=" N ALA C 141 " --> pdb=" O SER C 135 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 161 through 166 Processing sheet with id=AC6, first strand: chain 'C' and resid 279 through 280 removed outlier: 3.597A pdb=" N ILE C 300 " --> pdb=" O GLN C 280 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'F' and resid 32 through 33 removed outlier: 3.524A pdb=" N HIS F 26 " --> pdb=" O GLY F 33 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLY F 23 " --> pdb=" O GLY E 6 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 15 through 16 Processing sheet with id=AC9, first strand: chain 'E' and resid 29 through 31 Processing sheet with id=AD1, first strand: chain 'E' and resid 33 through 34 Processing sheet with id=AD2, first strand: chain 'E' and resid 40 through 44 removed outlier: 8.233A pdb=" N LEU E 41 " --> pdb=" O CYS E 275 " (cutoff:3.500A) removed outlier: 8.057A pdb=" N THR E 277 " --> pdb=" O LEU E 41 " (cutoff:3.500A) removed outlier: 6.019A pdb=" N SER E 43 " --> pdb=" O THR E 277 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD2 Processing sheet with id=AD3, first strand: chain 'E' and resid 50 through 51 removed outlier: 6.632A pdb=" N LEU E 50 " --> pdb=" O ILE E 80 " (cutoff:3.500A) removed outlier: 6.277A pdb=" N ILE E 79 " --> pdb=" O MET E 266 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD3 Processing sheet with id=AD4, first strand: chain 'E' and resid 110 through 115 removed outlier: 6.690A pdb=" N HIS E 253 " --> pdb=" O ILE E 176 " (cutoff:3.500A) removed outlier: 5.705A pdb=" N ILE E 176 " --> pdb=" O HIS E 253 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N GLU E 172 " --> pdb=" O LEU E 257 " (cutoff:3.500A) removed outlier: 7.885A pdb=" N ILE E 176 " --> pdb=" O PRO E 251 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'E' and resid 110 through 115 removed outlier: 6.690A pdb=" N HIS E 253 " --> pdb=" O ILE E 176 " (cutoff:3.500A) removed outlier: 5.705A pdb=" N ILE E 176 " --> pdb=" O HIS E 253 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N GLU E 172 " --> pdb=" O LEU E 257 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'E' and resid 133 through 138 removed outlier: 4.842A pdb=" N CYS E 136 " --> pdb=" O SER E 143 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'E' and resid 161 through 166 Processing sheet with id=AD8, first strand: chain 'E' and resid 284 through 286 removed outlier: 3.787A pdb=" N CYS E 279 " --> pdb=" O LEU E 286 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N THR F 64 " --> pdb=" O GLY E 301 " (cutoff:3.500A) 454 hydrogen bonds defined for protein. 1257 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.21 Time building geometry restraints manager: 1.25 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.13 - 1.27: 1897 1.27 - 1.41: 2984 1.41 - 1.55: 6604 1.55 - 1.68: 10 1.68 - 1.82: 72 Bond restraints: 11567 Sorted by residual: bond pdb=" CA ARG B 127 " pdb=" C ARG B 127 " ideal model delta sigma weight residual 1.523 1.413 0.111 1.34e-02 5.57e+03 6.80e+01 bond pdb=" CA ARG D 127 " pdb=" C ARG D 127 " ideal model delta sigma weight residual 1.529 1.453 0.077 9.30e-03 1.16e+04 6.80e+01 bond pdb=" C ASN C 320 " pdb=" O ASN C 320 " ideal model delta sigma weight residual 1.235 1.135 0.100 1.23e-02 6.61e+03 6.66e+01 bond pdb=" CA SER F 113 " pdb=" C SER F 113 " ideal model delta sigma weight residual 1.524 1.430 0.094 1.27e-02 6.20e+03 5.50e+01 bond pdb=" N ALA D 130 " pdb=" CA ALA D 130 " ideal model delta sigma weight residual 1.458 1.372 0.086 1.16e-02 7.43e+03 5.44e+01 ... (remaining 11562 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.42: 15401 2.42 - 4.84: 231 4.84 - 7.26: 33 7.26 - 9.68: 6 9.68 - 12.10: 2 Bond angle restraints: 15673 Sorted by residual: angle pdb=" N ASN B 129 " pdb=" CA ASN B 129 " pdb=" C ASN B 129 " ideal model delta sigma weight residual 112.30 102.04 10.26 1.36e+00 5.41e-01 5.69e+01 angle pdb=" C ARG D 127 " pdb=" CA ARG D 127 " pdb=" CB ARG D 127 " ideal model delta sigma weight residual 116.54 109.24 7.30 1.15e+00 7.56e-01 4.03e+01 angle pdb=" N GLY D 4 " pdb=" CA GLY D 4 " pdb=" C GLY D 4 " ideal model delta sigma weight residual 115.30 122.73 -7.43 1.39e+00 5.18e-01 2.85e+01 angle pdb=" N ASN B 128 " pdb=" CA ASN B 128 " pdb=" C ASN B 128 " ideal model delta sigma weight residual 112.86 119.24 -6.38 1.22e+00 6.72e-01 2.73e+01 angle pdb=" N GLY B 8 " pdb=" CA GLY B 8 " pdb=" C GLY B 8 " ideal model delta sigma weight residual 113.18 101.08 12.10 2.37e+00 1.78e-01 2.61e+01 ... (remaining 15668 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.64: 5676 17.64 - 35.28: 850 35.28 - 52.92: 292 52.92 - 70.56: 54 70.56 - 88.20: 16 Dihedral angle restraints: 6888 sinusoidal: 2766 harmonic: 4122 Sorted by residual: dihedral pdb=" C ASN B 128 " pdb=" N ASN B 128 " pdb=" CA ASN B 128 " pdb=" CB ASN B 128 " ideal model delta harmonic sigma weight residual -122.60 -139.62 17.02 0 2.50e+00 1.60e-01 4.64e+01 dihedral pdb=" CB CYS D 144 " pdb=" SG CYS D 144 " pdb=" SG CYS D 148 " pdb=" CB CYS D 148 " ideal model delta sinusoidal sigma weight residual 93.00 40.86 52.14 1 1.00e+01 1.00e-02 3.71e+01 dihedral pdb=" N ASN B 128 " pdb=" C ASN B 128 " pdb=" CA ASN B 128 " pdb=" CB ASN B 128 " ideal model delta harmonic sigma weight residual 122.80 137.07 -14.27 0 2.50e+00 1.60e-01 3.26e+01 ... (remaining 6885 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.151: 1670 0.151 - 0.302: 21 0.302 - 0.453: 8 0.453 - 0.604: 3 0.604 - 0.755: 1 Chirality restraints: 1703 Sorted by residual: chirality pdb=" CA ASN B 128 " pdb=" N ASN B 128 " pdb=" C ASN B 128 " pdb=" CB ASN B 128 " both_signs ideal model delta sigma weight residual False 2.51 1.76 0.75 2.00e-01 2.50e+01 1.42e+01 chirality pdb=" CA GLN B 125 " pdb=" N GLN B 125 " pdb=" C GLN B 125 " pdb=" CB GLN B 125 " both_signs ideal model delta sigma weight residual False 2.51 1.95 0.56 2.00e-01 2.50e+01 7.81e+00 chirality pdb=" CA PHE B 3 " pdb=" N PHE B 3 " pdb=" C PHE B 3 " pdb=" CB PHE B 3 " both_signs ideal model delta sigma weight residual False 2.51 1.99 0.52 2.00e-01 2.50e+01 6.69e+00 ... (remaining 1700 not shown) Planarity restraints: 2024 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER D 113 " -0.018 2.00e-02 2.50e+03 3.71e-02 1.37e+01 pdb=" C SER D 113 " 0.064 2.00e-02 2.50e+03 pdb=" O SER D 113 " -0.025 2.00e-02 2.50e+03 pdb=" N ASN D 114 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS D 123 " 0.015 2.00e-02 2.50e+03 3.04e-02 9.24e+00 pdb=" C LYS D 123 " -0.053 2.00e-02 2.50e+03 pdb=" O LYS D 123 " 0.019 2.00e-02 2.50e+03 pdb=" N SER D 124 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ARG E 217 " 0.041 5.00e-02 4.00e+02 6.10e-02 5.95e+00 pdb=" N PRO E 218 " -0.105 5.00e-02 4.00e+02 pdb=" CA PRO E 218 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO E 218 " 0.034 5.00e-02 4.00e+02 ... (remaining 2021 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 612 2.71 - 3.26: 10369 3.26 - 3.81: 18250 3.81 - 4.35: 22331 4.35 - 4.90: 39313 Nonbonded interactions: 90875 Sorted by model distance: nonbonded pdb=" OD1 ASN D 28 " pdb=" N GLU D 29 " model vdw 2.163 3.120 nonbonded pdb=" N GLU E 99 " pdb=" OE1 GLU E 99 " model vdw 2.201 3.120 nonbonded pdb=" N GLU F 147 " pdb=" OE1 GLU F 147 " model vdw 2.219 3.120 nonbonded pdb=" OD1 ASP A 238 " pdb=" N THR A 239 " model vdw 2.240 3.120 nonbonded pdb=" O CYS C 42 " pdb=" OH TYR C 78 " model vdw 2.245 3.040 ... (remaining 90870 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' selection = chain 'C' selection = (chain 'E' and resid 1 through 321) } ncs_group { reference = chain 'B' selection = chain 'D' 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=1.00 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: 2.340 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: 0.190 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 10.730 Find NCS groups from input model: 0.170 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: 0.000 Load rotamer database and sin/cos tables:6.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.520 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8121 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 : 0.009 0.111 11586 Z= 0.574 Angle : 0.745 12.103 15712 Z= 0.439 Chirality : 0.062 0.755 1703 Planarity : 0.005 0.061 2023 Dihedral : 18.854 88.196 4200 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 4.17 % Allowed : 34.62 % Favored : 61.22 % Cbeta Deviations : 0.23 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.70 (0.21), residues: 1419 helix: 1.40 (0.28), residues: 351 sheet: -0.09 (0.33), residues: 264 loop : -1.52 (0.19), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG E 217 TYR 0.018 0.002 TYR A 145 PHE 0.029 0.002 PHE F 3 TRP 0.011 0.001 TRP A 60 HIS 0.015 0.001 HIS B 111 Details of bonding type rmsd covalent geometry : bond 0.00917 (11567) covalent geometry : angle 0.74436 (15673) SS BOND : bond 0.00360 ( 18) SS BOND : angle 1.11027 ( 36) hydrogen bonds : bond 0.15404 ( 437) hydrogen bonds : angle 6.24935 ( 1257) link_NAG-ASN : bond 0.00265 ( 1) link_NAG-ASN : angle 0.82713 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2838 Ramachandran restraints generated. 1419 Oldfield, 0 Emsley, 1419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2838 Ramachandran restraints generated. 1419 Oldfield, 0 Emsley, 1419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 389 residues out of total 1248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 337 time to evaluate : 0.402 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 78 TYR cc_start: 0.8522 (p90) cc_final: 0.8247 (p90) REVERT: C 321 ILE cc_start: 0.8302 (OUTLIER) cc_final: 0.7953 (mt) REVERT: D 77 MET cc_start: 0.8229 (mtm) cc_final: 0.8006 (mtp) REVERT: D 128 ASN cc_start: 0.8814 (p0) cc_final: 0.8596 (p0) REVERT: F 57 GLU cc_start: 0.6891 (mp0) cc_final: 0.6639 (mp0) outliers start: 52 outliers final: 37 residues processed: 380 average time/residue: 0.6298 time to fit residues: 255.5775 Evaluate side-chains 368 residues out of total 1248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 330 time to evaluate : 0.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 THR Chi-restraints excluded: chain A residue 67 CYS Chi-restraints excluded: chain A residue 82 THR Chi-restraints excluded: chain A residue 111 PHE Chi-restraints excluded: chain A residue 162 SER Chi-restraints excluded: chain A residue 171 LYS Chi-restraints excluded: chain A residue 192 TYR Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain B residue 127 ARG Chi-restraints excluded: chain B residue 128 ASN Chi-restraints excluded: chain B residue 131 LYS Chi-restraints excluded: chain B residue 157 TYR Chi-restraints excluded: chain C residue 2 THR Chi-restraints excluded: chain C residue 67 CYS Chi-restraints excluded: chain C residue 82 THR Chi-restraints excluded: chain C residue 94 GLU Chi-restraints excluded: chain C residue 111 PHE Chi-restraints excluded: chain C residue 162 SER Chi-restraints excluded: chain C residue 200 SER Chi-restraints excluded: chain C residue 281 THR Chi-restraints excluded: chain C residue 299 THR Chi-restraints excluded: chain C residue 321 ILE Chi-restraints excluded: chain D residue 2 LEU Chi-restraints excluded: chain D residue 27 ARG Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 72 SER Chi-restraints excluded: chain D residue 98 LEU Chi-restraints excluded: chain E residue 110 SER Chi-restraints excluded: chain E residue 125 ASN Chi-restraints excluded: chain E residue 136 CYS Chi-restraints excluded: chain E residue 171 LYS Chi-restraints excluded: chain F residue 17 MET Chi-restraints excluded: chain F residue 39 LYS Chi-restraints excluded: chain F residue 61 ILE Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain F residue 100 ILE Chi-restraints excluded: chain F residue 148 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 98 optimal weight: 0.3980 chunk 107 optimal weight: 0.0070 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 0.7980 chunk 124 optimal weight: 0.7980 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 0.3980 chunk 122 optimal weight: 2.9990 chunk 91 optimal weight: 0.7980 chunk 55 optimal weight: 3.9990 overall best weight: 0.4798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 54 ASN A 193 GLN A 223 GLN A 280 GLN B 50 ASN B 128 ASN C 64 ASN ** C 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 50 ASN D 62 GLN D 129 ASN D 135 ASN E 104 GLN E 223 GLN F 50 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.117860 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.110939 restraints weight = 16111.575| |-----------------------------------------------------------------------------| r_work (start): 0.3608 rms_B_bonded: 1.57 r_work: 0.3515 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.3392 rms_B_bonded: 3.54 restraints_weight: 0.2500 r_work (final): 0.3392 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8061 moved from start: 0.0932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 11586 Z= 0.118 Angle : 0.505 6.596 15712 Z= 0.275 Chirality : 0.041 0.176 1703 Planarity : 0.004 0.053 2023 Dihedral : 7.754 59.508 1622 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 5.85 % Allowed : 29.57 % Favored : 64.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.24 (0.22), residues: 1419 helix: 2.30 (0.28), residues: 345 sheet: 0.07 (0.34), residues: 258 loop : -1.41 (0.19), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 217 TYR 0.010 0.001 TYR B 119 PHE 0.010 0.001 PHE F 3 TRP 0.006 0.001 TRP D 21 HIS 0.006 0.001 HIS C 8 Details of bonding type rmsd covalent geometry : bond 0.00264 (11567) covalent geometry : angle 0.50412 (15673) SS BOND : bond 0.00291 ( 18) SS BOND : angle 0.91897 ( 36) hydrogen bonds : bond 0.04437 ( 437) hydrogen bonds : angle 4.52795 ( 1257) link_NAG-ASN : bond 0.00258 ( 1) link_NAG-ASN : angle 0.39925 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2838 Ramachandran restraints generated. 1419 Oldfield, 0 Emsley, 1419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2838 Ramachandran restraints generated. 1419 Oldfield, 0 Emsley, 1419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 389 residues out of total 1248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 316 time to evaluate : 0.264 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 120 GLU cc_start: 0.7599 (mm-30) cc_final: 0.7254 (mm-30) REVERT: F 57 GLU cc_start: 0.7198 (mp0) cc_final: 0.6785 (mp0) outliers start: 73 outliers final: 37 residues processed: 359 average time/residue: 0.6082 time to fit residues: 233.7713 Evaluate side-chains 345 residues out of total 1248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 308 time to evaluate : 0.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 THR Chi-restraints excluded: chain A residue 111 PHE Chi-restraints excluded: chain A residue 171 LYS Chi-restraints excluded: chain A residue 186 SER Chi-restraints excluded: chain A residue 275 CYS Chi-restraints excluded: chain A residue 276 THR Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain B residue 127 ARG Chi-restraints excluded: chain B residue 128 ASN Chi-restraints excluded: chain B residue 157 TYR Chi-restraints excluded: chain C residue 3 ILE Chi-restraints excluded: chain C residue 15 THR Chi-restraints excluded: chain C residue 67 CYS Chi-restraints excluded: chain C residue 82 THR Chi-restraints excluded: chain C residue 94 GLU Chi-restraints excluded: chain C residue 111 PHE Chi-restraints excluded: chain C residue 215 VAL Chi-restraints excluded: chain C residue 268 SER Chi-restraints excluded: chain C residue 276 THR Chi-restraints excluded: chain C residue 299 THR Chi-restraints excluded: chain C residue 308 LYS Chi-restraints excluded: chain D residue 11 GLU Chi-restraints excluded: chain D residue 27 ARG Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain E residue 2 THR Chi-restraints excluded: chain E residue 15 THR Chi-restraints excluded: chain E residue 125 ASN Chi-restraints excluded: chain E residue 136 CYS Chi-restraints excluded: chain E residue 171 LYS Chi-restraints excluded: chain E residue 276 THR Chi-restraints excluded: chain F residue 29 GLU Chi-restraints excluded: chain F residue 59 MET Chi-restraints excluded: chain F residue 61 ILE Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain F residue 69 GLU Chi-restraints excluded: chain F residue 143 LYS Chi-restraints excluded: chain F residue 148 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 19 optimal weight: 2.9990 chunk 35 optimal weight: 3.9990 chunk 30 optimal weight: 0.8980 chunk 16 optimal weight: 2.9990 chunk 136 optimal weight: 2.9990 chunk 62 optimal weight: 1.9990 chunk 14 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 86 optimal weight: 1.9990 chunk 24 optimal weight: 0.6980 chunk 44 optimal weight: 0.0370 overall best weight: 1.1262 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 54 ASN A 189 GLN A 223 GLN ** A 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 125 GLN ** C 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 188 GLN C 311 GLN ** D 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 50 ASN E 294 ASN F 28 ASN F 50 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.115847 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.109114 restraints weight = 15962.184| |-----------------------------------------------------------------------------| r_work (start): 0.3587 rms_B_bonded: 1.52 r_work: 0.3495 rms_B_bonded: 1.86 restraints_weight: 0.5000 r_work: 0.3374 rms_B_bonded: 3.43 restraints_weight: 0.2500 r_work (final): 0.3374 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8095 moved from start: 0.1045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 11586 Z= 0.204 Angle : 0.539 6.131 15712 Z= 0.292 Chirality : 0.044 0.237 1703 Planarity : 0.004 0.054 2023 Dihedral : 7.022 59.573 1591 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 7.21 % Allowed : 26.68 % Favored : 66.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.23 (0.22), residues: 1419 helix: 2.36 (0.28), residues: 354 sheet: 0.05 (0.34), residues: 258 loop : -1.47 (0.19), residues: 807 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 217 TYR 0.015 0.002 TYR B 94 PHE 0.012 0.002 PHE E 111 TRP 0.008 0.001 TRP E 60 HIS 0.010 0.001 HIS A 8 Details of bonding type rmsd covalent geometry : bond 0.00479 (11567) covalent geometry : angle 0.53658 (15673) SS BOND : bond 0.00317 ( 18) SS BOND : angle 1.11534 ( 36) hydrogen bonds : bond 0.04818 ( 437) hydrogen bonds : angle 4.48609 ( 1257) link_NAG-ASN : bond 0.00272 ( 1) link_NAG-ASN : angle 0.59883 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2838 Ramachandran restraints generated. 1419 Oldfield, 0 Emsley, 1419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2838 Ramachandran restraints generated. 1419 Oldfield, 0 Emsley, 1419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 410 residues out of total 1248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 320 time to evaluate : 0.299 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 128 ASN cc_start: 0.7837 (OUTLIER) cc_final: 0.7522 (t0) REVERT: C 130 ARG cc_start: 0.8126 (ptt90) cc_final: 0.7908 (ptt90) REVERT: D 68 LYS cc_start: 0.8895 (OUTLIER) cc_final: 0.8577 (mttm) REVERT: D 105 GLU cc_start: 0.7561 (tp30) cc_final: 0.7342 (tp30) REVERT: D 120 GLU cc_start: 0.7630 (mm-30) cc_final: 0.7301 (mm-30) REVERT: D 123 LYS cc_start: 0.8374 (ttpp) cc_final: 0.7693 (ttpp) REVERT: E 66 LYS cc_start: 0.8419 (OUTLIER) cc_final: 0.7938 (mmtm) REVERT: E 265 ILE cc_start: 0.8982 (OUTLIER) cc_final: 0.8704 (mm) REVERT: F 68 LYS cc_start: 0.8577 (OUTLIER) cc_final: 0.8342 (mttp) outliers start: 90 outliers final: 46 residues processed: 372 average time/residue: 0.6148 time to fit residues: 244.7377 Evaluate side-chains 363 residues out of total 1248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 312 time to evaluate : 0.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 ILE Chi-restraints excluded: chain A residue 48 ILE Chi-restraints excluded: chain A residue 67 CYS Chi-restraints excluded: chain A residue 82 THR Chi-restraints excluded: chain A residue 111 PHE Chi-restraints excluded: chain A residue 112 GLU Chi-restraints excluded: chain A residue 171 LYS Chi-restraints excluded: chain A residue 186 SER Chi-restraints excluded: chain A residue 189 GLN Chi-restraints excluded: chain A residue 192 TYR Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 275 CYS Chi-restraints excluded: chain A residue 276 THR Chi-restraints excluded: chain B residue 32 SER Chi-restraints excluded: chain B residue 127 ARG Chi-restraints excluded: chain B residue 128 ASN Chi-restraints excluded: chain B residue 157 TYR Chi-restraints excluded: chain C residue 3 ILE Chi-restraints excluded: chain C residue 15 THR Chi-restraints excluded: chain C residue 44 LEU Chi-restraints excluded: chain C residue 82 THR Chi-restraints excluded: chain C residue 94 GLU Chi-restraints excluded: chain C residue 111 PHE Chi-restraints excluded: chain C residue 192 TYR Chi-restraints excluded: chain C residue 215 VAL Chi-restraints excluded: chain C residue 266 MET Chi-restraints excluded: chain C residue 268 SER Chi-restraints excluded: chain C residue 276 THR Chi-restraints excluded: chain C residue 281 THR Chi-restraints excluded: chain D residue 27 ARG Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 68 LYS Chi-restraints excluded: chain D residue 148 CYS Chi-restraints excluded: chain E residue 2 THR Chi-restraints excluded: chain E residue 15 THR Chi-restraints excluded: chain E residue 23 ASN Chi-restraints excluded: chain E residue 66 LYS Chi-restraints excluded: chain E residue 69 LEU Chi-restraints excluded: chain E residue 136 CYS Chi-restraints excluded: chain E residue 162 SER Chi-restraints excluded: chain E residue 171 LYS Chi-restraints excluded: chain E residue 172 GLU Chi-restraints excluded: chain E residue 194 ASN Chi-restraints excluded: chain E residue 265 ILE Chi-restraints excluded: chain F residue 59 MET Chi-restraints excluded: chain F residue 61 ILE Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain F residue 68 LYS Chi-restraints excluded: chain F residue 69 GLU Chi-restraints excluded: chain F residue 143 LYS Chi-restraints excluded: chain F residue 148 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 138 optimal weight: 2.9990 chunk 40 optimal weight: 1.9990 chunk 101 optimal weight: 0.6980 chunk 125 optimal weight: 2.9990 chunk 24 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 73 optimal weight: 5.9990 chunk 136 optimal weight: 2.9990 chunk 72 optimal weight: 2.9990 chunk 133 optimal weight: 1.9990 overall best weight: 1.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 51 GLN A 54 ASN A 156 ASN A 189 GLN A 223 GLN ** A 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 28 ASN C 64 ASN C 138 HIS ** C 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 50 ASN D 62 GLN ** E 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.114343 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.107665 restraints weight = 15929.186| |-----------------------------------------------------------------------------| r_work (start): 0.3564 rms_B_bonded: 1.52 r_work: 0.3472 rms_B_bonded: 1.85 restraints_weight: 0.5000 r_work: 0.3351 rms_B_bonded: 3.40 restraints_weight: 0.2500 r_work (final): 0.3351 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8123 moved from start: 0.1270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.070 11586 Z= 0.299 Angle : 0.606 9.068 15712 Z= 0.324 Chirality : 0.046 0.189 1703 Planarity : 0.004 0.054 2023 Dihedral : 6.869 58.762 1586 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 3.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 6.73 % Allowed : 26.52 % Favored : 66.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.43 (0.21), residues: 1419 helix: 2.16 (0.28), residues: 354 sheet: -0.01 (0.33), residues: 264 loop : -1.62 (0.19), residues: 801 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 217 TYR 0.017 0.002 TYR E 145 PHE 0.014 0.002 PHE E 111 TRP 0.011 0.001 TRP C 123 HIS 0.013 0.001 HIS A 8 Details of bonding type rmsd covalent geometry : bond 0.00712 (11567) covalent geometry : angle 0.60243 (15673) SS BOND : bond 0.00491 ( 18) SS BOND : angle 1.55576 ( 36) hydrogen bonds : bond 0.05160 ( 437) hydrogen bonds : angle 4.60571 ( 1257) link_NAG-ASN : bond 0.00157 ( 1) link_NAG-ASN : angle 0.67322 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2838 Ramachandran restraints generated. 1419 Oldfield, 0 Emsley, 1419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2838 Ramachandran restraints generated. 1419 Oldfield, 0 Emsley, 1419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 405 residues out of total 1248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 321 time to evaluate : 0.475 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 105 GLU cc_start: 0.7771 (tp30) cc_final: 0.7486 (tp30) REVERT: B 128 ASN cc_start: 0.7828 (OUTLIER) cc_final: 0.7500 (t0) REVERT: C 130 ARG cc_start: 0.8136 (ptt90) cc_final: 0.7906 (ptt90) REVERT: D 68 LYS cc_start: 0.8912 (OUTLIER) cc_final: 0.8592 (mttm) REVERT: D 120 GLU cc_start: 0.7669 (mm-30) cc_final: 0.7356 (mm-30) REVERT: D 123 LYS cc_start: 0.8346 (ttpp) cc_final: 0.7686 (ttpp) REVERT: E 66 LYS cc_start: 0.8420 (OUTLIER) cc_final: 0.7898 (mmtm) REVERT: E 265 ILE cc_start: 0.9016 (OUTLIER) cc_final: 0.8741 (mm) REVERT: F 68 LYS cc_start: 0.8616 (OUTLIER) cc_final: 0.8384 (mttp) outliers start: 84 outliers final: 54 residues processed: 366 average time/residue: 0.6153 time to fit residues: 240.9104 Evaluate side-chains 374 residues out of total 1248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 315 time to evaluate : 0.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 82 THR Chi-restraints excluded: chain A residue 111 PHE Chi-restraints excluded: chain A residue 112 GLU Chi-restraints excluded: chain A residue 121 THR Chi-restraints excluded: chain A residue 171 LYS Chi-restraints excluded: chain A residue 186 SER Chi-restraints excluded: chain A residue 189 GLN Chi-restraints excluded: chain A residue 192 TYR Chi-restraints excluded: chain A residue 200 SER Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 235 ASP Chi-restraints excluded: chain A residue 275 CYS Chi-restraints excluded: chain A residue 276 THR Chi-restraints excluded: chain B residue 32 SER Chi-restraints excluded: chain B residue 127 ARG Chi-restraints excluded: chain B residue 128 ASN Chi-restraints excluded: chain B residue 157 TYR Chi-restraints excluded: chain C residue 3 ILE Chi-restraints excluded: chain C residue 15 THR Chi-restraints excluded: chain C residue 44 LEU Chi-restraints excluded: chain C residue 82 THR Chi-restraints excluded: chain C residue 94 GLU Chi-restraints excluded: chain C residue 111 PHE Chi-restraints excluded: chain C residue 112 GLU Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 192 TYR Chi-restraints excluded: chain C residue 215 VAL Chi-restraints excluded: chain C residue 219 LYS Chi-restraints excluded: chain C residue 258 LYS Chi-restraints excluded: chain C residue 266 MET Chi-restraints excluded: chain C residue 268 SER Chi-restraints excluded: chain C residue 276 THR Chi-restraints excluded: chain C residue 281 THR Chi-restraints excluded: chain D residue 11 GLU Chi-restraints excluded: chain D residue 27 ARG Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 68 LYS Chi-restraints excluded: chain D residue 148 CYS Chi-restraints excluded: chain E residue 2 THR Chi-restraints excluded: chain E residue 15 THR Chi-restraints excluded: chain E residue 23 ASN Chi-restraints excluded: chain E residue 25 THR Chi-restraints excluded: chain E residue 66 LYS Chi-restraints excluded: chain E residue 69 LEU Chi-restraints excluded: chain E residue 136 CYS Chi-restraints excluded: chain E residue 172 GLU Chi-restraints excluded: chain E residue 220 VAL Chi-restraints excluded: chain E residue 222 GLU Chi-restraints excluded: chain E residue 265 ILE Chi-restraints excluded: chain E residue 276 THR Chi-restraints excluded: chain E residue 314 LEU Chi-restraints excluded: chain F residue 17 MET Chi-restraints excluded: chain F residue 61 ILE Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain F residue 68 LYS Chi-restraints excluded: chain F residue 69 GLU Chi-restraints excluded: chain F residue 143 LYS Chi-restraints excluded: chain F residue 148 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 95 optimal weight: 2.9990 chunk 44 optimal weight: 0.9980 chunk 51 optimal weight: 0.9980 chunk 130 optimal weight: 2.9990 chunk 25 optimal weight: 0.9990 chunk 62 optimal weight: 0.7980 chunk 81 optimal weight: 0.9980 chunk 21 optimal weight: 0.8980 chunk 101 optimal weight: 0.5980 chunk 134 optimal weight: 0.8980 chunk 39 optimal weight: 1.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 51 GLN A 54 ASN A 223 GLN ** A 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 37 HIS C 64 ASN ** C 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 50 ASN E 64 ASN F 50 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.116152 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.109410 restraints weight = 15766.841| |-----------------------------------------------------------------------------| r_work (start): 0.3586 rms_B_bonded: 1.52 r_work: 0.3495 rms_B_bonded: 1.86 restraints_weight: 0.5000 r_work: 0.3375 rms_B_bonded: 3.42 restraints_weight: 0.2500 r_work (final): 0.3375 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8092 moved from start: 0.1314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 11586 Z= 0.164 Angle : 0.531 8.308 15712 Z= 0.288 Chirality : 0.042 0.158 1703 Planarity : 0.004 0.057 2023 Dihedral : 6.497 59.519 1582 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 6.09 % Allowed : 28.29 % Favored : 65.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.28 (0.22), residues: 1419 helix: 2.38 (0.28), residues: 354 sheet: -0.10 (0.34), residues: 249 loop : -1.47 (0.19), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 217 TYR 0.010 0.001 TYR E 145 PHE 0.012 0.001 PHE C 111 TRP 0.005 0.001 TRP A 60 HIS 0.008 0.001 HIS A 8 Details of bonding type rmsd covalent geometry : bond 0.00387 (11567) covalent geometry : angle 0.52791 (15673) SS BOND : bond 0.00340 ( 18) SS BOND : angle 1.26998 ( 36) hydrogen bonds : bond 0.04534 ( 437) hydrogen bonds : angle 4.41295 ( 1257) link_NAG-ASN : bond 0.00271 ( 1) link_NAG-ASN : angle 0.63864 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2838 Ramachandran restraints generated. 1419 Oldfield, 0 Emsley, 1419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2838 Ramachandran restraints generated. 1419 Oldfield, 0 Emsley, 1419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 406 residues out of total 1248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 330 time to evaluate : 0.413 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 128 ASN cc_start: 0.7707 (OUTLIER) cc_final: 0.7404 (t0) REVERT: C 130 ARG cc_start: 0.8117 (ptt90) cc_final: 0.7883 (ptt90) REVERT: C 236 GLN cc_start: 0.7529 (tp40) cc_final: 0.7256 (tp40) REVERT: C 257 LEU cc_start: 0.8888 (OUTLIER) cc_final: 0.8671 (mt) REVERT: D 68 LYS cc_start: 0.8864 (OUTLIER) cc_final: 0.8554 (mttm) REVERT: D 120 GLU cc_start: 0.7633 (mm-30) cc_final: 0.7335 (mm-30) REVERT: D 123 LYS cc_start: 0.8328 (ttpp) cc_final: 0.7627 (ttpp) REVERT: E 66 LYS cc_start: 0.8414 (OUTLIER) cc_final: 0.7915 (mmtm) REVERT: E 265 ILE cc_start: 0.8940 (OUTLIER) cc_final: 0.8669 (mm) REVERT: F 68 LYS cc_start: 0.8553 (OUTLIER) cc_final: 0.8316 (mttp) outliers start: 76 outliers final: 47 residues processed: 373 average time/residue: 0.6095 time to fit residues: 243.2522 Evaluate side-chains 379 residues out of total 1248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 326 time to evaluate : 0.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 THR Chi-restraints excluded: chain A residue 111 PHE Chi-restraints excluded: chain A residue 112 GLU Chi-restraints excluded: chain A residue 171 LYS Chi-restraints excluded: chain A residue 186 SER Chi-restraints excluded: chain A residue 200 SER Chi-restraints excluded: chain A residue 275 CYS Chi-restraints excluded: chain A residue 276 THR Chi-restraints excluded: chain B residue 11 GLU Chi-restraints excluded: chain B residue 32 SER Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain B residue 127 ARG Chi-restraints excluded: chain B residue 128 ASN Chi-restraints excluded: chain B residue 157 TYR Chi-restraints excluded: chain C residue 3 ILE Chi-restraints excluded: chain C residue 15 THR Chi-restraints excluded: chain C residue 44 LEU Chi-restraints excluded: chain C residue 67 CYS Chi-restraints excluded: chain C residue 82 THR Chi-restraints excluded: chain C residue 111 PHE Chi-restraints excluded: chain C residue 112 GLU Chi-restraints excluded: chain C residue 192 TYR Chi-restraints excluded: chain C residue 215 VAL Chi-restraints excluded: chain C residue 257 LEU Chi-restraints excluded: chain C residue 258 LYS Chi-restraints excluded: chain C residue 266 MET Chi-restraints excluded: chain C residue 276 THR Chi-restraints excluded: chain C residue 281 THR Chi-restraints excluded: chain D residue 27 ARG Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 68 LYS Chi-restraints excluded: chain D residue 148 CYS Chi-restraints excluded: chain E residue 2 THR Chi-restraints excluded: chain E residue 15 THR Chi-restraints excluded: chain E residue 25 THR Chi-restraints excluded: chain E residue 44 LEU Chi-restraints excluded: chain E residue 66 LYS Chi-restraints excluded: chain E residue 69 LEU Chi-restraints excluded: chain E residue 136 CYS Chi-restraints excluded: chain E residue 172 GLU Chi-restraints excluded: chain E residue 194 ASN Chi-restraints excluded: chain E residue 222 GLU Chi-restraints excluded: chain E residue 265 ILE Chi-restraints excluded: chain E residue 276 THR Chi-restraints excluded: chain F residue 57 GLU Chi-restraints excluded: chain F residue 61 ILE Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain F residue 68 LYS Chi-restraints excluded: chain F residue 69 GLU Chi-restraints excluded: chain F residue 100 ILE Chi-restraints excluded: chain F residue 143 LYS Chi-restraints excluded: chain F residue 148 CYS Chi-restraints excluded: chain F residue 150 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 71 optimal weight: 0.0370 chunk 66 optimal weight: 1.9990 chunk 91 optimal weight: 0.0980 chunk 2 optimal weight: 2.9990 chunk 83 optimal weight: 2.9990 chunk 140 optimal weight: 2.9990 chunk 131 optimal weight: 0.9980 chunk 40 optimal weight: 1.9990 chunk 120 optimal weight: 1.9990 chunk 18 optimal weight: 2.9990 chunk 1 optimal weight: 4.9990 overall best weight: 1.0262 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 51 GLN A 54 ASN A 223 GLN ** A 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 37 HIS C 64 ASN ** C 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 223 GLN C 280 GLN ** D 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 50 ASN E 64 ASN F 50 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.115959 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.109234 restraints weight = 15941.112| |-----------------------------------------------------------------------------| r_work (start): 0.3583 rms_B_bonded: 1.53 r_work: 0.3492 rms_B_bonded: 1.86 restraints_weight: 0.5000 r_work: 0.3371 rms_B_bonded: 3.43 restraints_weight: 0.2500 r_work (final): 0.3371 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8099 moved from start: 0.1396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 11586 Z= 0.189 Angle : 0.543 8.277 15712 Z= 0.294 Chirality : 0.043 0.251 1703 Planarity : 0.004 0.058 2023 Dihedral : 6.400 59.413 1579 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 6.65 % Allowed : 27.96 % Favored : 65.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.19 (0.22), residues: 1419 helix: 2.40 (0.28), residues: 354 sheet: 0.12 (0.34), residues: 258 loop : -1.46 (0.19), residues: 807 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 217 TYR 0.013 0.001 TYR E 145 PHE 0.012 0.001 PHE E 111 TRP 0.006 0.001 TRP A 60 HIS 0.008 0.001 HIS A 8 Details of bonding type rmsd covalent geometry : bond 0.00446 (11567) covalent geometry : angle 0.54097 (15673) SS BOND : bond 0.00315 ( 18) SS BOND : angle 1.15542 ( 36) hydrogen bonds : bond 0.04608 ( 437) hydrogen bonds : angle 4.40388 ( 1257) link_NAG-ASN : bond 0.00258 ( 1) link_NAG-ASN : angle 0.62890 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2838 Ramachandran restraints generated. 1419 Oldfield, 0 Emsley, 1419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2838 Ramachandran restraints generated. 1419 Oldfield, 0 Emsley, 1419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 409 residues out of total 1248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 326 time to evaluate : 0.435 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 128 ASN cc_start: 0.7655 (OUTLIER) cc_final: 0.7390 (t0) REVERT: C 130 ARG cc_start: 0.8128 (ptt90) cc_final: 0.7917 (ptt90) REVERT: D 68 LYS cc_start: 0.8879 (OUTLIER) cc_final: 0.8565 (mttm) REVERT: D 120 GLU cc_start: 0.7647 (mm-30) cc_final: 0.7356 (mm-30) REVERT: D 123 LYS cc_start: 0.8309 (ttpp) cc_final: 0.7601 (ttpp) REVERT: E 66 LYS cc_start: 0.8407 (OUTLIER) cc_final: 0.7916 (mmtm) REVERT: E 265 ILE cc_start: 0.8954 (OUTLIER) cc_final: 0.8686 (mm) REVERT: F 68 LYS cc_start: 0.8563 (OUTLIER) cc_final: 0.8317 (mttp) REVERT: F 105 GLU cc_start: 0.7594 (tp30) cc_final: 0.7328 (tp30) outliers start: 83 outliers final: 49 residues processed: 375 average time/residue: 0.6125 time to fit residues: 245.6677 Evaluate side-chains 377 residues out of total 1248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 323 time to evaluate : 0.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 ILE Chi-restraints excluded: chain A residue 82 THR Chi-restraints excluded: chain A residue 111 PHE Chi-restraints excluded: chain A residue 112 GLU Chi-restraints excluded: chain A residue 121 THR Chi-restraints excluded: chain A residue 171 LYS Chi-restraints excluded: chain A residue 186 SER Chi-restraints excluded: chain A residue 192 TYR Chi-restraints excluded: chain A residue 200 SER Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 275 CYS Chi-restraints excluded: chain A residue 276 THR Chi-restraints excluded: chain B residue 32 SER Chi-restraints excluded: chain B residue 127 ARG Chi-restraints excluded: chain B residue 128 ASN Chi-restraints excluded: chain B residue 157 TYR Chi-restraints excluded: chain C residue 3 ILE Chi-restraints excluded: chain C residue 15 THR Chi-restraints excluded: chain C residue 44 LEU Chi-restraints excluded: chain C residue 67 CYS Chi-restraints excluded: chain C residue 82 THR Chi-restraints excluded: chain C residue 111 PHE Chi-restraints excluded: chain C residue 112 GLU Chi-restraints excluded: chain C residue 192 TYR Chi-restraints excluded: chain C residue 215 VAL Chi-restraints excluded: chain C residue 258 LYS Chi-restraints excluded: chain C residue 266 MET Chi-restraints excluded: chain C residue 276 THR Chi-restraints excluded: chain C residue 281 THR Chi-restraints excluded: chain D residue 27 ARG Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 68 LYS Chi-restraints excluded: chain D residue 148 CYS Chi-restraints excluded: chain E residue 2 THR Chi-restraints excluded: chain E residue 15 THR Chi-restraints excluded: chain E residue 25 THR Chi-restraints excluded: chain E residue 66 LYS Chi-restraints excluded: chain E residue 69 LEU Chi-restraints excluded: chain E residue 135 SER Chi-restraints excluded: chain E residue 136 CYS Chi-restraints excluded: chain E residue 172 GLU Chi-restraints excluded: chain E residue 222 GLU Chi-restraints excluded: chain E residue 265 ILE Chi-restraints excluded: chain E residue 276 THR Chi-restraints excluded: chain E residue 314 LEU Chi-restraints excluded: chain F residue 57 GLU Chi-restraints excluded: chain F residue 61 ILE Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain F residue 68 LYS Chi-restraints excluded: chain F residue 69 GLU Chi-restraints excluded: chain F residue 100 ILE Chi-restraints excluded: chain F residue 143 LYS Chi-restraints excluded: chain F residue 148 CYS Chi-restraints excluded: chain F residue 150 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 63 optimal weight: 3.9990 chunk 1 optimal weight: 0.8980 chunk 11 optimal weight: 1.9990 chunk 70 optimal weight: 2.9990 chunk 46 optimal weight: 0.1980 chunk 125 optimal weight: 2.9990 chunk 103 optimal weight: 0.2980 chunk 73 optimal weight: 0.1980 chunk 78 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 chunk 99 optimal weight: 0.8980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 51 GLN A 54 ASN A 223 GLN ** A 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 320 ASN C 37 HIS C 64 ASN ** C 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 223 GLN ** C 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 50 ASN E 193 GLN F 50 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.117699 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.110754 restraints weight = 16010.341| |-----------------------------------------------------------------------------| r_work (start): 0.3601 rms_B_bonded: 1.56 r_work: 0.3508 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.3386 rms_B_bonded: 3.51 restraints_weight: 0.2500 r_work (final): 0.3386 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8071 moved from start: 0.1535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 11586 Z= 0.120 Angle : 0.502 6.033 15712 Z= 0.273 Chirality : 0.041 0.146 1703 Planarity : 0.003 0.056 2023 Dihedral : 6.220 59.936 1579 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 5.21 % Allowed : 29.57 % Favored : 65.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.14 (0.22), residues: 1419 helix: 3.07 (0.27), residues: 336 sheet: 0.07 (0.36), residues: 243 loop : -1.24 (0.19), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 217 TYR 0.011 0.001 TYR C 207 PHE 0.010 0.001 PHE C 111 TRP 0.004 0.001 TRP E 123 HIS 0.005 0.001 HIS A 8 Details of bonding type rmsd covalent geometry : bond 0.00277 (11567) covalent geometry : angle 0.50051 (15673) SS BOND : bond 0.00317 ( 18) SS BOND : angle 0.99286 ( 36) hydrogen bonds : bond 0.04116 ( 437) hydrogen bonds : angle 4.25130 ( 1257) link_NAG-ASN : bond 0.00289 ( 1) link_NAG-ASN : angle 0.60791 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2838 Ramachandran restraints generated. 1419 Oldfield, 0 Emsley, 1419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2838 Ramachandran restraints generated. 1419 Oldfield, 0 Emsley, 1419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 385 residues out of total 1248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 320 time to evaluate : 0.327 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 128 ASN cc_start: 0.7522 (OUTLIER) cc_final: 0.7293 (t0) REVERT: C 130 ARG cc_start: 0.8044 (ptt90) cc_final: 0.7725 (ptt90) REVERT: C 219 LYS cc_start: 0.8079 (OUTLIER) cc_final: 0.7640 (ptpt) REVERT: D 68 LYS cc_start: 0.8854 (OUTLIER) cc_final: 0.8532 (mttm) REVERT: D 105 GLU cc_start: 0.7577 (tp30) cc_final: 0.7232 (tp30) REVERT: D 120 GLU cc_start: 0.7675 (mm-30) cc_final: 0.7294 (mm-30) REVERT: D 123 LYS cc_start: 0.8266 (ttpp) cc_final: 0.7453 (ttpp) REVERT: E 66 LYS cc_start: 0.8403 (OUTLIER) cc_final: 0.7985 (mmtm) REVERT: E 321 ILE cc_start: 0.7861 (mm) cc_final: 0.7217 (mm) REVERT: F 68 LYS cc_start: 0.8515 (OUTLIER) cc_final: 0.8281 (mttp) REVERT: F 105 GLU cc_start: 0.7584 (tp30) cc_final: 0.7353 (tp30) outliers start: 65 outliers final: 42 residues processed: 354 average time/residue: 0.6085 time to fit residues: 230.7466 Evaluate side-chains 362 residues out of total 1248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 315 time to evaluate : 0.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 THR Chi-restraints excluded: chain A residue 48 ILE Chi-restraints excluded: chain A residue 82 THR Chi-restraints excluded: chain A residue 111 PHE Chi-restraints excluded: chain A residue 112 GLU Chi-restraints excluded: chain A residue 171 LYS Chi-restraints excluded: chain A residue 186 SER Chi-restraints excluded: chain A residue 200 SER Chi-restraints excluded: chain A residue 235 ASP Chi-restraints excluded: chain A residue 275 CYS Chi-restraints excluded: chain A residue 276 THR Chi-restraints excluded: chain B residue 127 ARG Chi-restraints excluded: chain B residue 128 ASN Chi-restraints excluded: chain B residue 157 TYR Chi-restraints excluded: chain C residue 3 ILE Chi-restraints excluded: chain C residue 15 THR Chi-restraints excluded: chain C residue 44 LEU Chi-restraints excluded: chain C residue 67 CYS Chi-restraints excluded: chain C residue 82 THR Chi-restraints excluded: chain C residue 111 PHE Chi-restraints excluded: chain C residue 112 GLU Chi-restraints excluded: chain C residue 192 TYR Chi-restraints excluded: chain C residue 215 VAL Chi-restraints excluded: chain C residue 219 LYS Chi-restraints excluded: chain C residue 276 THR Chi-restraints excluded: chain C residue 308 LYS Chi-restraints excluded: chain D residue 27 ARG Chi-restraints excluded: chain D residue 50 ASN Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 68 LYS Chi-restraints excluded: chain D residue 148 CYS Chi-restraints excluded: chain E residue 2 THR Chi-restraints excluded: chain E residue 15 THR Chi-restraints excluded: chain E residue 66 LYS Chi-restraints excluded: chain E residue 69 LEU Chi-restraints excluded: chain E residue 136 CYS Chi-restraints excluded: chain E residue 172 GLU Chi-restraints excluded: chain E residue 222 GLU Chi-restraints excluded: chain E residue 276 THR Chi-restraints excluded: chain F residue 29 GLU Chi-restraints excluded: chain F residue 57 GLU Chi-restraints excluded: chain F residue 61 ILE Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain F residue 68 LYS Chi-restraints excluded: chain F residue 69 GLU Chi-restraints excluded: chain F residue 143 LYS Chi-restraints excluded: chain F residue 150 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 126 optimal weight: 0.0870 chunk 140 optimal weight: 2.9990 chunk 93 optimal weight: 2.9990 chunk 57 optimal weight: 0.0010 chunk 15 optimal weight: 0.2980 chunk 136 optimal weight: 3.9990 chunk 135 optimal weight: 2.9990 chunk 27 optimal weight: 0.9980 chunk 128 optimal weight: 2.9990 chunk 43 optimal weight: 1.9990 chunk 18 optimal weight: 2.9990 overall best weight: 0.6766 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 51 GLN A 54 ASN A 223 GLN ** A 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 320 ASN C 37 HIS C 64 ASN ** C 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 188 GLN ** C 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 50 ASN F 50 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.117110 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.110262 restraints weight = 16033.323| |-----------------------------------------------------------------------------| r_work (start): 0.3597 rms_B_bonded: 1.55 r_work: 0.3504 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.3383 rms_B_bonded: 3.48 restraints_weight: 0.2500 r_work (final): 0.3383 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8079 moved from start: 0.1577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 11586 Z= 0.141 Angle : 0.524 7.454 15712 Z= 0.282 Chirality : 0.041 0.180 1703 Planarity : 0.003 0.058 2023 Dihedral : 6.172 59.863 1578 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 5.13 % Allowed : 29.81 % Favored : 65.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.16 (0.22), residues: 1419 helix: 3.09 (0.27), residues: 336 sheet: 0.08 (0.36), residues: 243 loop : -1.22 (0.19), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 217 TYR 0.012 0.001 TYR E 145 PHE 0.011 0.001 PHE C 111 TRP 0.005 0.001 TRP A 60 HIS 0.006 0.001 HIS A 8 Details of bonding type rmsd covalent geometry : bond 0.00330 (11567) covalent geometry : angle 0.52219 (15673) SS BOND : bond 0.00287 ( 18) SS BOND : angle 0.99158 ( 36) hydrogen bonds : bond 0.04229 ( 437) hydrogen bonds : angle 4.27333 ( 1257) link_NAG-ASN : bond 0.00269 ( 1) link_NAG-ASN : angle 0.62636 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2838 Ramachandran restraints generated. 1419 Oldfield, 0 Emsley, 1419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2838 Ramachandran restraints generated. 1419 Oldfield, 0 Emsley, 1419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 388 residues out of total 1248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 324 time to evaluate : 0.454 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 128 ASN cc_start: 0.7468 (OUTLIER) cc_final: 0.7250 (t0) REVERT: C 130 ARG cc_start: 0.8062 (ptt90) cc_final: 0.7759 (ptt90) REVERT: D 68 LYS cc_start: 0.8873 (OUTLIER) cc_final: 0.8555 (mttm) REVERT: D 105 GLU cc_start: 0.7569 (tp30) cc_final: 0.7227 (tp30) REVERT: D 120 GLU cc_start: 0.7658 (mm-30) cc_final: 0.7236 (mm-30) REVERT: D 123 LYS cc_start: 0.8257 (ttpp) cc_final: 0.7409 (ttpp) REVERT: E 66 LYS cc_start: 0.8413 (OUTLIER) cc_final: 0.7966 (mmtm) REVERT: E 321 ILE cc_start: 0.7883 (mm) cc_final: 0.7233 (mm) REVERT: F 68 LYS cc_start: 0.8525 (OUTLIER) cc_final: 0.8291 (mttp) REVERT: F 105 GLU cc_start: 0.7603 (tp30) cc_final: 0.7374 (tp30) outliers start: 64 outliers final: 46 residues processed: 357 average time/residue: 0.6134 time to fit residues: 234.5320 Evaluate side-chains 369 residues out of total 1248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 319 time to evaluate : 0.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 THR Chi-restraints excluded: chain A residue 48 ILE Chi-restraints excluded: chain A residue 82 THR Chi-restraints excluded: chain A residue 111 PHE Chi-restraints excluded: chain A residue 112 GLU Chi-restraints excluded: chain A residue 171 LYS Chi-restraints excluded: chain A residue 186 SER Chi-restraints excluded: chain A residue 200 SER Chi-restraints excluded: chain A residue 235 ASP Chi-restraints excluded: chain A residue 275 CYS Chi-restraints excluded: chain A residue 276 THR Chi-restraints excluded: chain B residue 32 SER Chi-restraints excluded: chain B residue 127 ARG Chi-restraints excluded: chain B residue 128 ASN Chi-restraints excluded: chain B residue 157 TYR Chi-restraints excluded: chain C residue 3 ILE Chi-restraints excluded: chain C residue 15 THR Chi-restraints excluded: chain C residue 44 LEU Chi-restraints excluded: chain C residue 67 CYS Chi-restraints excluded: chain C residue 82 THR Chi-restraints excluded: chain C residue 112 GLU Chi-restraints excluded: chain C residue 192 TYR Chi-restraints excluded: chain C residue 215 VAL Chi-restraints excluded: chain C residue 219 LYS Chi-restraints excluded: chain C residue 276 THR Chi-restraints excluded: chain C residue 281 THR Chi-restraints excluded: chain C residue 308 LYS Chi-restraints excluded: chain D residue 11 GLU Chi-restraints excluded: chain D residue 27 ARG Chi-restraints excluded: chain D residue 61 ILE Chi-restraints excluded: chain D residue 68 LYS Chi-restraints excluded: chain D residue 132 GLU Chi-restraints excluded: chain D residue 148 CYS Chi-restraints excluded: chain E residue 2 THR Chi-restraints excluded: chain E residue 15 THR Chi-restraints excluded: chain E residue 44 LEU Chi-restraints excluded: chain E residue 66 LYS Chi-restraints excluded: chain E residue 69 LEU Chi-restraints excluded: chain E residue 136 CYS Chi-restraints excluded: chain E residue 172 GLU Chi-restraints excluded: chain E residue 222 GLU Chi-restraints excluded: chain E residue 276 THR Chi-restraints excluded: chain F residue 17 MET Chi-restraints excluded: chain F residue 57 GLU Chi-restraints excluded: chain F residue 61 ILE Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain F residue 68 LYS Chi-restraints excluded: chain F residue 69 GLU Chi-restraints excluded: chain F residue 100 ILE Chi-restraints excluded: chain F residue 143 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 47 optimal weight: 3.9990 chunk 7 optimal weight: 0.6980 chunk 93 optimal weight: 3.9990 chunk 2 optimal weight: 1.9990 chunk 66 optimal weight: 0.0770 chunk 45 optimal weight: 0.2980 chunk 51 optimal weight: 0.5980 chunk 97 optimal weight: 3.9990 chunk 128 optimal weight: 2.9990 chunk 121 optimal weight: 1.9990 chunk 90 optimal weight: 1.9990 overall best weight: 0.7340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 51 GLN A 54 ASN A 223 GLN ** A 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 320 ASN C 37 HIS C 64 ASN ** C 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 188 GLN ** C 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 50 ASN E 54 ASN E 64 ASN F 50 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.116969 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.110123 restraints weight = 15910.340| |-----------------------------------------------------------------------------| r_work (start): 0.3598 rms_B_bonded: 1.54 r_work: 0.3505 rms_B_bonded: 1.89 restraints_weight: 0.5000 r_work: 0.3384 rms_B_bonded: 3.48 restraints_weight: 0.2500 r_work (final): 0.3384 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8081 moved from start: 0.1595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 11586 Z= 0.149 Angle : 0.533 6.760 15712 Z= 0.287 Chirality : 0.042 0.209 1703 Planarity : 0.003 0.059 2023 Dihedral : 6.013 59.872 1575 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 4.81 % Allowed : 30.29 % Favored : 64.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.02 (0.22), residues: 1419 helix: 2.65 (0.28), residues: 354 sheet: 0.05 (0.36), residues: 243 loop : -1.32 (0.19), residues: 822 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 217 TYR 0.013 0.001 TYR E 145 PHE 0.011 0.001 PHE C 111 TRP 0.006 0.001 TRP A 60 HIS 0.006 0.001 HIS A 8 Details of bonding type rmsd covalent geometry : bond 0.00349 (11567) covalent geometry : angle 0.53097 (15673) SS BOND : bond 0.00291 ( 18) SS BOND : angle 1.01610 ( 36) hydrogen bonds : bond 0.04286 ( 437) hydrogen bonds : angle 4.27901 ( 1257) link_NAG-ASN : bond 0.00261 ( 1) link_NAG-ASN : angle 0.63523 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2838 Ramachandran restraints generated. 1419 Oldfield, 0 Emsley, 1419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2838 Ramachandran restraints generated. 1419 Oldfield, 0 Emsley, 1419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 385 residues out of total 1248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 325 time to evaluate : 0.594 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 128 ASN cc_start: 0.7449 (OUTLIER) cc_final: 0.7232 (t0) REVERT: C 130 ARG cc_start: 0.8045 (ptt90) cc_final: 0.7749 (ptt90) REVERT: D 105 GLU cc_start: 0.7566 (tp30) cc_final: 0.7241 (tp30) REVERT: D 120 GLU cc_start: 0.7657 (mm-30) cc_final: 0.7247 (mm-30) REVERT: D 123 LYS cc_start: 0.8244 (ttpp) cc_final: 0.7395 (ttpp) REVERT: E 66 LYS cc_start: 0.8390 (OUTLIER) cc_final: 0.7893 (mmtm) REVERT: E 321 ILE cc_start: 0.7869 (mm) cc_final: 0.7225 (mm) REVERT: F 68 LYS cc_start: 0.8534 (OUTLIER) cc_final: 0.8281 (mttp) REVERT: F 105 GLU cc_start: 0.7606 (tp30) cc_final: 0.7365 (tp30) outliers start: 60 outliers final: 48 residues processed: 354 average time/residue: 0.6140 time to fit residues: 232.3480 Evaluate side-chains 369 residues out of total 1248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 318 time to evaluate : 0.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 THR Chi-restraints excluded: chain A residue 48 ILE Chi-restraints excluded: chain A residue 82 THR Chi-restraints excluded: chain A residue 111 PHE Chi-restraints excluded: chain A residue 112 GLU Chi-restraints excluded: chain A residue 171 LYS Chi-restraints excluded: chain A residue 186 SER Chi-restraints excluded: chain A residue 200 SER Chi-restraints excluded: chain A residue 235 ASP Chi-restraints excluded: chain A residue 275 CYS Chi-restraints excluded: chain A residue 276 THR Chi-restraints excluded: chain B residue 32 SER Chi-restraints excluded: chain B residue 127 ARG Chi-restraints excluded: chain B residue 128 ASN Chi-restraints excluded: chain B residue 157 TYR Chi-restraints excluded: chain C residue 3 ILE Chi-restraints excluded: chain C residue 15 THR Chi-restraints excluded: chain C residue 44 LEU Chi-restraints excluded: chain C residue 67 CYS Chi-restraints excluded: chain C residue 82 THR Chi-restraints excluded: chain C residue 112 GLU Chi-restraints excluded: chain C residue 192 TYR Chi-restraints excluded: chain C residue 215 VAL Chi-restraints excluded: chain C residue 276 THR Chi-restraints excluded: chain C residue 281 THR Chi-restraints excluded: chain D residue 11 GLU Chi-restraints excluded: chain D residue 27 ARG Chi-restraints excluded: chain D residue 61 ILE Chi-restraints excluded: chain D residue 68 LYS Chi-restraints excluded: chain D residue 132 GLU Chi-restraints excluded: chain D residue 148 CYS Chi-restraints excluded: chain E residue 2 THR Chi-restraints excluded: chain E residue 15 THR Chi-restraints excluded: chain E residue 25 THR Chi-restraints excluded: chain E residue 44 LEU Chi-restraints excluded: chain E residue 66 LYS Chi-restraints excluded: chain E residue 69 LEU Chi-restraints excluded: chain E residue 125 ASN Chi-restraints excluded: chain E residue 136 CYS Chi-restraints excluded: chain E residue 172 GLU Chi-restraints excluded: chain E residue 222 GLU Chi-restraints excluded: chain E residue 276 THR Chi-restraints excluded: chain F residue 17 MET Chi-restraints excluded: chain F residue 57 GLU Chi-restraints excluded: chain F residue 61 ILE Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain F residue 68 LYS Chi-restraints excluded: chain F residue 69 GLU Chi-restraints excluded: chain F residue 100 ILE Chi-restraints excluded: chain F residue 143 LYS Chi-restraints excluded: chain F residue 150 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 16 optimal weight: 2.9990 chunk 102 optimal weight: 4.9990 chunk 53 optimal weight: 1.9990 chunk 11 optimal weight: 0.5980 chunk 113 optimal weight: 2.9990 chunk 19 optimal weight: 0.4980 chunk 10 optimal weight: 1.9990 chunk 105 optimal weight: 1.9990 chunk 42 optimal weight: 1.9990 chunk 90 optimal weight: 0.9980 chunk 91 optimal weight: 0.4980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 51 GLN A 54 ASN A 223 GLN ** A 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 320 ASN C 37 HIS C 64 ASN ** C 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 188 GLN ** C 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 30 GLN D 50 ASN E 64 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.116519 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.109660 restraints weight = 16101.250| |-----------------------------------------------------------------------------| r_work (start): 0.3588 rms_B_bonded: 1.56 r_work: 0.3495 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.3373 rms_B_bonded: 3.50 restraints_weight: 0.2500 r_work (final): 0.3373 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8093 moved from start: 0.1620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 11586 Z= 0.176 Angle : 0.558 7.110 15712 Z= 0.299 Chirality : 0.042 0.264 1703 Planarity : 0.004 0.059 2023 Dihedral : 6.069 59.351 1575 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 4.97 % Allowed : 30.21 % Favored : 64.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.08 (0.22), residues: 1419 helix: 2.99 (0.28), residues: 336 sheet: 0.04 (0.35), residues: 243 loop : -1.26 (0.19), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 217 TYR 0.017 0.001 TYR A 145 PHE 0.013 0.001 PHE C 111 TRP 0.007 0.001 TRP A 60 HIS 0.007 0.001 HIS A 8 Details of bonding type rmsd covalent geometry : bond 0.00415 (11567) covalent geometry : angle 0.55611 (15673) SS BOND : bond 0.00321 ( 18) SS BOND : angle 1.15110 ( 36) hydrogen bonds : bond 0.04451 ( 437) hydrogen bonds : angle 4.34374 ( 1257) link_NAG-ASN : bond 0.00256 ( 1) link_NAG-ASN : angle 0.69876 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2838 Ramachandran restraints generated. 1419 Oldfield, 0 Emsley, 1419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2838 Ramachandran restraints generated. 1419 Oldfield, 0 Emsley, 1419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 383 residues out of total 1248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 321 time to evaluate : 0.435 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 128 ASN cc_start: 0.7451 (OUTLIER) cc_final: 0.7211 (t0) REVERT: C 130 ARG cc_start: 0.8052 (ptt90) cc_final: 0.7761 (ptt90) REVERT: D 30 GLN cc_start: 0.8337 (OUTLIER) cc_final: 0.8118 (mt0) REVERT: D 68 LYS cc_start: 0.8887 (OUTLIER) cc_final: 0.8565 (mttm) REVERT: D 105 GLU cc_start: 0.7586 (tp30) cc_final: 0.7265 (tp30) REVERT: D 120 GLU cc_start: 0.7668 (mm-30) cc_final: 0.7256 (mm-30) REVERT: D 123 LYS cc_start: 0.8258 (ttpp) cc_final: 0.7417 (ttpp) REVERT: E 66 LYS cc_start: 0.8389 (OUTLIER) cc_final: 0.7887 (mmtm) REVERT: E 265 ILE cc_start: 0.8930 (OUTLIER) cc_final: 0.8652 (mm) REVERT: E 321 ILE cc_start: 0.7883 (mm) cc_final: 0.7321 (mm) REVERT: F 68 LYS cc_start: 0.8536 (OUTLIER) cc_final: 0.8295 (mttp) REVERT: F 105 GLU cc_start: 0.7620 (tp30) cc_final: 0.7373 (tp30) outliers start: 62 outliers final: 46 residues processed: 354 average time/residue: 0.6087 time to fit residues: 230.6277 Evaluate side-chains 372 residues out of total 1248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 320 time to evaluate : 0.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 THR Chi-restraints excluded: chain A residue 48 ILE Chi-restraints excluded: chain A residue 82 THR Chi-restraints excluded: chain A residue 111 PHE Chi-restraints excluded: chain A residue 112 GLU Chi-restraints excluded: chain A residue 171 LYS Chi-restraints excluded: chain A residue 186 SER Chi-restraints excluded: chain A residue 200 SER Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 275 CYS Chi-restraints excluded: chain A residue 276 THR Chi-restraints excluded: chain A residue 318 LEU Chi-restraints excluded: chain B residue 32 SER Chi-restraints excluded: chain B residue 127 ARG Chi-restraints excluded: chain B residue 128 ASN Chi-restraints excluded: chain B residue 157 TYR Chi-restraints excluded: chain C residue 3 ILE Chi-restraints excluded: chain C residue 15 THR Chi-restraints excluded: chain C residue 44 LEU Chi-restraints excluded: chain C residue 67 CYS Chi-restraints excluded: chain C residue 82 THR Chi-restraints excluded: chain C residue 112 GLU Chi-restraints excluded: chain C residue 192 TYR Chi-restraints excluded: chain C residue 215 VAL Chi-restraints excluded: chain C residue 276 THR Chi-restraints excluded: chain C residue 281 THR Chi-restraints excluded: chain D residue 11 GLU Chi-restraints excluded: chain D residue 30 GLN Chi-restraints excluded: chain D residue 61 ILE Chi-restraints excluded: chain D residue 68 LYS Chi-restraints excluded: chain D residue 132 GLU Chi-restraints excluded: chain D residue 148 CYS Chi-restraints excluded: chain E residue 2 THR Chi-restraints excluded: chain E residue 15 THR Chi-restraints excluded: chain E residue 25 THR Chi-restraints excluded: chain E residue 44 LEU Chi-restraints excluded: chain E residue 66 LYS Chi-restraints excluded: chain E residue 69 LEU Chi-restraints excluded: chain E residue 136 CYS Chi-restraints excluded: chain E residue 172 GLU Chi-restraints excluded: chain E residue 222 GLU Chi-restraints excluded: chain E residue 265 ILE Chi-restraints excluded: chain E residue 276 THR Chi-restraints excluded: chain F residue 17 MET Chi-restraints excluded: chain F residue 57 GLU Chi-restraints excluded: chain F residue 61 ILE Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain F residue 68 LYS Chi-restraints excluded: chain F residue 69 GLU Chi-restraints excluded: chain F residue 100 ILE Chi-restraints excluded: chain F residue 143 LYS Chi-restraints excluded: chain F residue 150 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 14 optimal weight: 2.9990 chunk 26 optimal weight: 1.9990 chunk 41 optimal weight: 0.7980 chunk 135 optimal weight: 1.9990 chunk 77 optimal weight: 0.9990 chunk 7 optimal weight: 0.6980 chunk 0 optimal weight: 3.9990 chunk 69 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 11 optimal weight: 0.0000 chunk 62 optimal weight: 0.9990 overall best weight: 0.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 51 GLN A 54 ASN ** A 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 223 GLN A 236 GLN ** A 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 320 ASN C 37 HIS C 64 ASN ** C 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 188 GLN ** C 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 50 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.116672 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.109834 restraints weight = 16105.216| |-----------------------------------------------------------------------------| r_work (start): 0.3591 rms_B_bonded: 1.55 r_work: 0.3497 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.3376 rms_B_bonded: 3.50 restraints_weight: 0.2500 r_work (final): 0.3376 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8089 moved from start: 0.1631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 11586 Z= 0.162 Angle : 0.825 59.199 15712 Z= 0.471 Chirality : 0.042 0.263 1703 Planarity : 0.004 0.060 2023 Dihedral : 5.813 59.358 1571 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 4.65 % Allowed : 30.85 % Favored : 64.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.09 (0.22), residues: 1419 helix: 3.02 (0.28), residues: 336 sheet: 0.04 (0.35), residues: 243 loop : -1.26 (0.19), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 217 TYR 0.015 0.001 TYR C 207 PHE 0.012 0.001 PHE C 111 TRP 0.006 0.001 TRP A 60 HIS 0.007 0.001 HIS C 8 Details of bonding type rmsd covalent geometry : bond 0.00376 (11567) covalent geometry : angle 0.82399 (15673) SS BOND : bond 0.00394 ( 18) SS BOND : angle 1.19753 ( 36) hydrogen bonds : bond 0.04415 ( 437) hydrogen bonds : angle 4.34250 ( 1257) link_NAG-ASN : bond 0.00241 ( 1) link_NAG-ASN : angle 0.70792 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5168.20 seconds wall clock time: 88 minutes 27.75 seconds (5307.75 seconds total)