Starting phenix.real_space_refine on Sun Apr 5 16:08:58 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9u66_63897/04_2026/9u66_63897.cif Found real_map, /net/cci-nas-00/data/ceres_data/9u66_63897/04_2026/9u66_63897.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.49 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9u66_63897/04_2026/9u66_63897.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9u66_63897/04_2026/9u66_63897.map" model { file = "/net/cci-nas-00/data/ceres_data/9u66_63897/04_2026/9u66_63897.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9u66_63897/04_2026/9u66_63897.cif" } resolution = 3.49 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= 0.030 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 7186 2.51 5 N 1985 2.21 5 O 2218 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 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: 11443 Number of models: 1 Model: "" Number of chains: 9 Chain: "E" Number of atoms: 2506 Number of conformers: 1 Conformer: "" Number of residues, atoms: 321, 2506 Classifications: {'peptide': 321} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 16, 'TRANS': 304} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "F" Number of atoms: 1285 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1285 Classifications: {'peptide': 157} Link IDs: {'PTRANS': 1, 'TRANS': 155} Chain: "A" Number of atoms: 2506 Number of conformers: 1 Conformer: "" Number of residues, atoms: 321, 2506 Classifications: {'peptide': 321} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 16, 'TRANS': 304} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "B" Number of atoms: 1285 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1285 Classifications: {'peptide': 157} Link IDs: {'PTRANS': 1, 'TRANS': 155} Chain: "C" Number of atoms: 2506 Number of conformers: 1 Conformer: "" Number of residues, atoms: 321, 2506 Classifications: {'peptide': 321} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 16, 'TRANS': 304} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "D" Number of atoms: 1285 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1285 Classifications: {'peptide': 157} Link IDs: {'PTRANS': 1, 'TRANS': 155} Chain: "E" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "C" 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: 2.75, per 1000 atoms: 0.24 Number of scatterers: 11443 At special positions: 0 Unit cell: (87.74, 86.92, 150.88, 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 2218 8.00 N 1985 7.00 C 7186 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=9, symmetry=0 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 A 55 " - pdb=" SG CYS A 67 " distance=2.03 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 C 55 " - pdb=" SG CYS C 67 " distance=2.03 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 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 A 401 " - " ASN A 23 " " NAG C 401 " - " ASN C 23 " " NAG E 401 " - " ASN E 23 " " NAG E 402 " - " ASN E 11 " " NAG E 403 " - " ASN E 195 " Time building additional restraints: 0.72 Conformation dependent library (CDL) restraints added in 474.8 milliseconds 2844 Ramachandran restraints generated. 1422 Oldfield, 0 Emsley, 1422 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2664 Finding SS restraints... Secondary structure from input PDB file: 26 helices and 30 sheets defined 28.4% alpha, 17.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.41 Creating SS restraints... Processing helix chain 'E' and resid 56 through 63 Processing helix chain 'E' and resid 67 through 71 removed outlier: 3.506A pdb=" N LEU E 71 " --> pdb=" O ASP E 68 " (cutoff:3.500A) Processing helix chain 'E' and resid 97 through 106 Processing helix chain 'E' and resid 118 through 123 removed outlier: 3.611A pdb=" N SER E 122 " --> pdb=" O PRO E 118 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N TRP E 123 " --> pdb=" O LYS E 119 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 118 through 123' Processing helix chain 'E' and resid 184 through 192 Processing helix chain 'F' and resid 37 through 58 removed outlier: 3.537A pdb=" N ILE F 43 " --> pdb=" O LYS F 39 " (cutoff:3.500A) Processing helix chain 'F' and resid 74 through 127 removed outlier: 3.610A pdb=" N GLU F 78 " --> pdb=" O GLU F 74 " (cutoff:3.500A) Processing helix chain 'F' and resid 145 through 155 Processing helix chain 'F' and resid 158 through 170 removed outlier: 3.743A pdb=" N TYR F 162 " --> pdb=" O ASN F 158 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N GLU F 164 " --> pdb=" O PRO F 160 " (cutoff:3.500A) removed outlier: 4.676A pdb=" N GLU F 165 " --> pdb=" O LYS F 161 " (cutoff:3.500A) Processing helix chain 'A' and resid 56 through 63 Processing helix chain 'A' and resid 64 through 71 removed outlier: 3.998A pdb=" N ASP A 68 " --> pdb=" O PRO A 65 " (cutoff:3.500A) removed outlier: 5.527A pdb=" N LEU A 69 " --> pdb=" O LYS A 66 " (cutoff:3.500A) Processing helix chain 'A' and resid 97 through 106 removed outlier: 3.566A pdb=" N LYS A 102 " --> pdb=" O TYR A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 184 through 192 Processing helix chain 'B' and resid 37 through 58 removed outlier: 3.573A pdb=" N ILE B 43 " --> pdb=" O LYS B 39 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N LYS B 58 " --> pdb=" O SER B 54 " (cutoff:3.500A) Processing helix chain 'B' and resid 74 through 127 removed outlier: 3.731A pdb=" N ASP B 112 " --> pdb=" O LEU B 108 " (cutoff:3.500A) Processing helix chain 'B' and resid 145 through 155 Processing helix chain 'B' and resid 158 through 170 removed outlier: 3.826A pdb=" N TYR B 162 " --> pdb=" O ASN B 158 " (cutoff:3.500A) removed outlier: 4.649A pdb=" N GLU B 164 " --> pdb=" O PRO B 160 " (cutoff:3.500A) removed outlier: 5.572A pdb=" N GLU B 165 " --> pdb=" O LYS B 161 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N SER B 166 " --> pdb=" O TYR B 162 " (cutoff:3.500A) Processing helix chain 'C' and resid 56 through 63 Processing helix chain 'C' and resid 67 through 71 removed outlier: 3.655A pdb=" N LEU C 71 " --> pdb=" O ASP C 68 " (cutoff:3.500A) Processing helix chain 'C' and resid 97 through 106 Processing helix chain 'C' and resid 184 through 193 Processing helix chain 'D' and resid 37 through 58 removed outlier: 3.562A pdb=" N ILE D 43 " --> pdb=" O LYS D 39 " (cutoff:3.500A) Processing helix chain 'D' and resid 74 through 127 removed outlier: 3.577A pdb=" N GLU D 78 " --> pdb=" O GLU D 74 " (cutoff:3.500A) Processing helix chain 'D' and resid 145 through 155 Processing helix chain 'D' and resid 158 through 163 removed outlier: 3.856A pdb=" N TYR D 162 " --> pdb=" O ASN D 158 " (cutoff:3.500A) Processing helix chain 'D' and resid 163 through 170 Processing sheet with id=AA1, first strand: chain 'E' and resid 5 through 7 removed outlier: 3.526A pdb=" N GLY E 6 " --> pdb=" O GLY F 23 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N GLY F 23 " --> pdb=" O GLY E 6 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'E' and resid 15 through 16 Processing sheet with id=AA3, first strand: chain 'E' and resid 29 through 31 Processing sheet with id=AA4, first strand: chain 'E' and resid 41 through 44 removed outlier: 6.075A pdb=" N LEU E 41 " --> pdb=" O HIS E 273 " (cutoff:3.500A) removed outlier: 5.579A pdb=" N CYS E 275 " --> pdb=" O LEU E 41 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 50 through 51 removed outlier: 6.692A pdb=" N LEU E 50 " --> pdb=" O ILE E 80 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N ILE E 79 " --> pdb=" O MET E 266 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'E' and resid 114 through 115 removed outlier: 3.671A pdb=" N PHE E 114 " --> pdb=" O ALA E 254 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N HIS E 253 " --> pdb=" O ILE E 176 " (cutoff:3.500A) removed outlier: 5.589A pdb=" N ILE E 176 " --> pdb=" O HIS E 253 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 148 through 150 Processing sheet with id=AA8, first strand: chain 'E' and resid 161 through 166 removed outlier: 3.705A pdb=" N VAL E 201 " --> pdb=" O LYS E 208 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LYS E 208 " --> pdb=" O VAL E 201 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 284 through 285 Processing sheet with id=AB1, first strand: chain 'F' and resid 130 through 131 Processing sheet with id=AB2, first strand: chain 'B' and resid 32 through 34 removed outlier: 4.259A pdb=" N GLY B 23 " --> pdb=" O GLY A 6 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N GLY A 6 " --> pdb=" O GLY B 23 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N HIS B 25 " --> pdb=" O CYS A 4 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N CYS A 4 " --> pdb=" O HIS B 25 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 14 through 18 removed outlier: 3.921A pdb=" N ASP A 14 " --> pdb=" O VAL A 26 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N THR A 18 " --> pdb=" O LYS A 22 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N LYS A 22 " --> pdb=" O THR A 18 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 29 through 31 Processing sheet with id=AB5, first strand: chain 'A' and resid 41 through 44 removed outlier: 6.310A pdb=" N LEU A 41 " --> pdb=" O HIS A 273 " (cutoff:3.500A) removed outlier: 5.934A pdb=" N CYS A 275 " --> pdb=" O LEU A 41 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 50 through 51 removed outlier: 6.683A pdb=" N LEU A 50 " --> pdb=" O ILE A 80 " (cutoff:3.500A) removed outlier: 6.111A pdb=" N ILE A 79 " --> pdb=" O MET A 266 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'A' and resid 148 through 150 removed outlier: 7.764A pdb=" N ILE A 176 " --> pdb=" O PRO A 251 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 148 through 150 removed outlier: 7.764A pdb=" N ILE A 176 " --> pdb=" O PRO A 251 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 161 through 166 Processing sheet with id=AC1, first strand: chain 'A' and resid 284 through 286 removed outlier: 3.770A pdb=" N LEU A 286 " --> pdb=" O CYS A 279 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N CYS A 279 " --> pdb=" O LEU A 286 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 292 through 293 Processing sheet with id=AC3, first strand: chain 'D' and resid 32 through 34 removed outlier: 4.277A pdb=" N GLY D 23 " --> pdb=" O GLY C 6 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N GLY C 6 " --> pdb=" O GLY D 23 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 14 through 16 removed outlier: 3.959A pdb=" N ASP C 14 " --> pdb=" O VAL C 26 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 29 through 31 Processing sheet with id=AC6, first strand: chain 'C' and resid 41 through 44 removed outlier: 7.670A pdb=" N LEU C 41 " --> pdb=" O CYS C 275 " (cutoff:3.500A) removed outlier: 8.573A pdb=" N THR C 277 " --> pdb=" O LEU C 41 " (cutoff:3.500A) removed outlier: 5.755A pdb=" N SER C 43 " --> pdb=" O THR C 277 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain 'C' and resid 50 through 51 removed outlier: 6.704A pdb=" N LEU C 50 " --> pdb=" O ILE C 80 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N ILE C 79 " --> pdb=" O MET C 266 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain 'C' and resid 148 through 150 Processing sheet with id=AC9, first strand: chain 'C' and resid 161 through 166 Processing sheet with id=AD1, first strand: chain 'C' and resid 226 through 234 Processing sheet with id=AD2, first strand: chain 'C' and resid 280 through 281 Processing sheet with id=AD3, first strand: chain 'C' and resid 292 through 293 423 hydrogen bonds defined for protein. 1179 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: 1.70 Time building geometry restraints manager: 1.06 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3746 1.34 - 1.46: 2549 1.46 - 1.58: 5340 1.58 - 1.69: 0 1.69 - 1.81: 72 Bond restraints: 11707 Sorted by residual: bond pdb=" C1 NAG E 402 " pdb=" O5 NAG E 402 " ideal model delta sigma weight residual 1.406 1.441 -0.035 2.00e-02 2.50e+03 3.03e+00 bond pdb=" C ALA C 315 " pdb=" N THR C 316 " ideal model delta sigma weight residual 1.333 1.311 0.022 1.52e-02 4.33e+03 2.03e+00 bond pdb=" C1 NAG E 403 " pdb=" O5 NAG E 403 " ideal model delta sigma weight residual 1.406 1.434 -0.028 2.00e-02 2.50e+03 1.95e+00 bond pdb=" C1 NAG E 401 " pdb=" O5 NAG E 401 " ideal model delta sigma weight residual 1.406 1.433 -0.027 2.00e-02 2.50e+03 1.85e+00 bond pdb=" C1 NAG A 401 " pdb=" O5 NAG A 401 " ideal model delta sigma weight residual 1.406 1.433 -0.027 2.00e-02 2.50e+03 1.81e+00 ... (remaining 11702 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.61: 15374 1.61 - 3.22: 396 3.22 - 4.82: 79 4.82 - 6.43: 24 6.43 - 8.04: 2 Bond angle restraints: 15875 Sorted by residual: angle pdb=" N THR E 316 " pdb=" CA THR E 316 " pdb=" C THR E 316 " ideal model delta sigma weight residual 112.54 105.47 7.07 1.51e+00 4.39e-01 2.19e+01 angle pdb=" N GLY E 317 " pdb=" CA GLY E 317 " pdb=" C GLY E 317 " ideal model delta sigma weight residual 111.10 116.43 -5.33 1.46e+00 4.69e-01 1.33e+01 angle pdb=" C ASN C 289 " pdb=" N LEU C 290 " pdb=" CA LEU C 290 " ideal model delta sigma weight residual 120.68 125.97 -5.29 1.52e+00 4.33e-01 1.21e+01 angle pdb=" C TYR D 162 " pdb=" N SER D 163 " pdb=" CA SER D 163 " ideal model delta sigma weight residual 121.54 127.54 -6.00 1.91e+00 2.74e-01 9.87e+00 angle pdb=" C TYR B 162 " pdb=" N SER B 163 " pdb=" CA SER B 163 " ideal model delta sigma weight residual 121.54 127.31 -5.77 1.91e+00 2.74e-01 9.13e+00 ... (remaining 15870 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.11: 6303 17.11 - 34.21: 605 34.21 - 51.32: 88 51.32 - 68.42: 25 68.42 - 85.53: 8 Dihedral angle restraints: 7029 sinusoidal: 2868 harmonic: 4161 Sorted by residual: dihedral pdb=" CA ILE B 133 " pdb=" C ILE B 133 " pdb=" N GLY B 134 " pdb=" CA GLY B 134 " ideal model delta harmonic sigma weight residual -180.00 -155.28 -24.72 0 5.00e+00 4.00e-02 2.44e+01 dihedral pdb=" CA ILE F 133 " pdb=" C ILE F 133 " pdb=" N GLY F 134 " pdb=" CA GLY F 134 " ideal model delta harmonic sigma weight residual -180.00 -156.05 -23.95 0 5.00e+00 4.00e-02 2.29e+01 dihedral pdb=" CA ILE D 133 " pdb=" C ILE D 133 " pdb=" N GLY D 134 " pdb=" CA GLY D 134 " ideal model delta harmonic sigma weight residual -180.00 -156.94 -23.06 0 5.00e+00 4.00e-02 2.13e+01 ... (remaining 7026 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.080: 1585 0.080 - 0.159: 143 0.159 - 0.239: 6 0.239 - 0.318: 0 0.318 - 0.398: 1 Chirality restraints: 1735 Sorted by residual: chirality pdb=" C1 NAG E 403 " pdb=" ND2 ASN E 195 " pdb=" C2 NAG E 403 " pdb=" O5 NAG E 403 " both_signs ideal model delta sigma weight residual False -2.40 -2.00 -0.40 2.00e-01 2.50e+01 3.96e+00 chirality pdb=" CA ILE A 265 " pdb=" N ILE A 265 " pdb=" C ILE A 265 " pdb=" CB ILE A 265 " both_signs ideal model delta sigma weight residual False 2.43 2.66 -0.22 2.00e-01 2.50e+01 1.26e+00 chirality pdb=" C2 NAG A 401 " pdb=" C1 NAG A 401 " pdb=" C3 NAG A 401 " pdb=" N2 NAG A 401 " both_signs ideal model delta sigma weight residual False -2.49 -2.29 -0.21 2.00e-01 2.50e+01 1.07e+00 ... (remaining 1732 not shown) Planarity restraints: 2050 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR E 281 " -0.037 5.00e-02 4.00e+02 5.67e-02 5.14e+00 pdb=" N PRO E 282 " 0.098 5.00e-02 4.00e+02 pdb=" CA PRO E 282 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO E 282 " -0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE E 117 " 0.037 5.00e-02 4.00e+02 5.55e-02 4.93e+00 pdb=" N PRO E 118 " -0.096 5.00e-02 4.00e+02 pdb=" CA PRO E 118 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO E 118 " 0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR C 91 " -0.032 5.00e-02 4.00e+02 4.93e-02 3.90e+00 pdb=" N PRO C 92 " 0.085 5.00e-02 4.00e+02 pdb=" CA PRO C 92 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO C 92 " -0.027 5.00e-02 4.00e+02 ... (remaining 2047 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1394 2.75 - 3.29: 10726 3.29 - 3.83: 18376 3.83 - 4.36: 20481 4.36 - 4.90: 36794 Nonbonded interactions: 87771 Sorted by model distance: nonbonded pdb=" OG SER E 106 " pdb=" O SER E 263 " model vdw 2.215 3.040 nonbonded pdb=" O CYS E 42 " pdb=" OH TYR E 78 " model vdw 2.217 3.040 nonbonded pdb=" O CYS C 42 " pdb=" OH TYR C 78 " model vdw 2.229 3.040 nonbonded pdb=" O SER B 49 " pdb=" ND2 ASN B 53 " model vdw 2.231 3.120 nonbonded pdb=" O CYS A 42 " pdb=" OH TYR A 78 " model vdw 2.234 3.040 ... (remaining 87766 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 2 through 401) } 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: 2.090 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: 0.040 Set scattering table: 0.040 Process input model: 11.080 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.020 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:1.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.780 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7305 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 11721 Z= 0.174 Angle : 0.665 12.169 15908 Z= 0.354 Chirality : 0.046 0.398 1735 Planarity : 0.005 0.058 2045 Dihedral : 13.414 85.526 4338 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.56 % Allowed : 6.47 % Favored : 92.97 % Rotamer: Outliers : 0.00 % Allowed : 0.08 % Favored : 99.92 % 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: 1422 helix: 2.40 (0.27), residues: 375 sheet: 0.26 (0.33), residues: 285 loop : -1.77 (0.20), residues: 762 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 113 TYR 0.026 0.002 TYR C 98 PHE 0.025 0.002 PHE E 210 TRP 0.022 0.001 TRP A 252 HIS 0.005 0.001 HIS C 37 Details of bonding type rmsd covalent geometry : bond 0.00372 (11707) covalent geometry : angle 0.65311 (15875) SS BOND : bond 0.00375 ( 9) SS BOND : angle 0.73571 ( 18) hydrogen bonds : bond 0.15012 ( 419) hydrogen bonds : angle 5.94385 ( 1179) link_NAG-ASN : bond 0.00799 ( 5) link_NAG-ASN : angle 4.11106 ( 15) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2844 Ramachandran restraints generated. 1422 Oldfield, 0 Emsley, 1422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2844 Ramachandran restraints generated. 1422 Oldfield, 0 Emsley, 1422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 335 residues out of total 1269 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 335 time to evaluate : 0.421 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 21 GLU cc_start: 0.7017 (pt0) cc_final: 0.6759 (pt0) REVERT: E 22 LYS cc_start: 0.8071 (mmpt) cc_final: 0.7862 (mmpt) REVERT: E 278 LYS cc_start: 0.8288 (mmpt) cc_final: 0.7841 (mmpt) REVERT: E 290 LEU cc_start: 0.7664 (mm) cc_final: 0.7451 (mm) REVERT: E 294 ASN cc_start: 0.7827 (t0) cc_final: 0.7500 (t0) REVERT: E 306 TYR cc_start: 0.8250 (t80) cc_final: 0.7895 (t80) REVERT: F 58 LYS cc_start: 0.7647 (mmmt) cc_final: 0.7446 (mmmt) REVERT: F 74 GLU cc_start: 0.7440 (mt-10) cc_final: 0.6751 (mt-10) REVERT: F 97 GLU cc_start: 0.6263 (pt0) cc_final: 0.5985 (pt0) REVERT: F 116 LYS cc_start: 0.7941 (tptt) cc_final: 0.7667 (tptt) REVERT: F 149 MET cc_start: 0.7312 (mmp) cc_final: 0.6520 (mmp) REVERT: A 22 LYS cc_start: 0.8239 (mmpt) cc_final: 0.7928 (mmpt) REVERT: A 112 GLU cc_start: 0.6983 (mm-30) cc_final: 0.6752 (mm-30) REVERT: A 119 LYS cc_start: 0.7965 (mmtm) cc_final: 0.7598 (mmtm) REVERT: A 134 VAL cc_start: 0.8660 (p) cc_final: 0.8425 (t) REVERT: A 161 LEU cc_start: 0.8770 (tt) cc_final: 0.8551 (tp) REVERT: A 213 GLU cc_start: 0.6935 (tt0) cc_final: 0.6646 (tt0) REVERT: A 243 GLU cc_start: 0.6997 (tt0) cc_final: 0.6703 (tt0) REVERT: A 265 ILE cc_start: 0.8501 (mm) cc_final: 0.8214 (mm) REVERT: A 275 CYS cc_start: 0.8044 (t) cc_final: 0.7769 (t) REVERT: B 74 GLU cc_start: 0.7352 (mt-10) cc_final: 0.6692 (mt-10) REVERT: B 121 LYS cc_start: 0.7681 (mtmm) cc_final: 0.7291 (mtmm) REVERT: C 18 THR cc_start: 0.8016 (p) cc_final: 0.7534 (p) REVERT: C 21 GLU cc_start: 0.6121 (tm-30) cc_final: 0.5785 (tm-30) REVERT: C 22 LYS cc_start: 0.7365 (mmpt) cc_final: 0.6902 (mmpt) REVERT: C 40 LYS cc_start: 0.7619 (tppt) cc_final: 0.7341 (tppt) REVERT: C 64 ASN cc_start: 0.8206 (t0) cc_final: 0.7664 (t0) REVERT: C 80 ILE cc_start: 0.7858 (tt) cc_final: 0.7589 (mt) REVERT: C 112 GLU cc_start: 0.7152 (mm-30) cc_final: 0.6847 (mm-30) REVERT: C 265 ILE cc_start: 0.8386 (mm) cc_final: 0.8071 (mm) REVERT: D 70 PHE cc_start: 0.7696 (m-80) cc_final: 0.7398 (m-80) REVERT: D 121 LYS cc_start: 0.7810 (mtmm) cc_final: 0.7559 (mtmm) REVERT: D 149 MET cc_start: 0.7424 (mmp) cc_final: 0.6580 (mmp) outliers start: 0 outliers final: 0 residues processed: 335 average time/residue: 0.1313 time to fit residues: 58.5281 Evaluate side-chains 318 residues out of total 1269 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 318 time to evaluate : 0.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 98 optimal weight: 2.9990 chunk 107 optimal weight: 8.9990 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 0.7980 chunk 77 optimal weight: 0.0070 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 9.9990 chunk 55 optimal weight: 6.9990 overall best weight: 1.3604 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 10 ASN ** A 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 283 HIS A 311 GLN ** B 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 311 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.138021 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.116677 restraints weight = 16817.137| |-----------------------------------------------------------------------------| r_work (start): 0.3459 rms_B_bonded: 2.89 r_work: 0.3330 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3330 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7567 moved from start: 0.1056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 11721 Z= 0.223 Angle : 0.648 11.032 15908 Z= 0.335 Chirality : 0.045 0.350 1735 Planarity : 0.005 0.050 2045 Dihedral : 6.174 55.488 1647 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.56 % Allowed : 5.98 % Favored : 93.46 % Rotamer: Outliers : 0.87 % Allowed : 9.58 % Favored : 89.55 % 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: -0.37 (0.22), residues: 1422 helix: 2.37 (0.26), residues: 369 sheet: 0.39 (0.34), residues: 264 loop : -1.89 (0.19), residues: 789 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 217 TYR 0.022 0.002 TYR C 91 PHE 0.019 0.002 PHE E 111 TRP 0.016 0.001 TRP A 252 HIS 0.006 0.001 HIS B 26 Details of bonding type rmsd covalent geometry : bond 0.00496 (11707) covalent geometry : angle 0.63774 (15875) SS BOND : bond 0.00485 ( 9) SS BOND : angle 0.93714 ( 18) hydrogen bonds : bond 0.05079 ( 419) hydrogen bonds : angle 4.94686 ( 1179) link_NAG-ASN : bond 0.00655 ( 5) link_NAG-ASN : angle 3.66379 ( 15) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2844 Ramachandran restraints generated. 1422 Oldfield, 0 Emsley, 1422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2844 Ramachandran restraints generated. 1422 Oldfield, 0 Emsley, 1422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 374 residues out of total 1269 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 363 time to evaluate : 0.362 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 21 GLU cc_start: 0.7429 (pt0) cc_final: 0.7058 (pt0) REVERT: E 22 LYS cc_start: 0.8297 (mmpt) cc_final: 0.7989 (mmpt) REVERT: E 30 VAL cc_start: 0.8489 (t) cc_final: 0.8240 (m) REVERT: E 100 GLU cc_start: 0.7596 (mm-30) cc_final: 0.7070 (mm-30) REVERT: E 134 VAL cc_start: 0.8587 (OUTLIER) cc_final: 0.8365 (t) REVERT: E 278 LYS cc_start: 0.8575 (mmpt) cc_final: 0.8164 (mmpt) REVERT: E 290 LEU cc_start: 0.7847 (mm) cc_final: 0.7622 (mm) REVERT: E 294 ASN cc_start: 0.8109 (t0) cc_final: 0.7630 (t0) REVERT: F 74 GLU cc_start: 0.7785 (mt-10) cc_final: 0.7086 (mt-10) REVERT: F 103 GLU cc_start: 0.7508 (mm-30) cc_final: 0.6847 (mm-30) REVERT: F 116 LYS cc_start: 0.8221 (tptt) cc_final: 0.8000 (tptt) REVERT: F 125 GLN cc_start: 0.7823 (tp-100) cc_final: 0.7601 (tp40) REVERT: F 149 MET cc_start: 0.7633 (mmp) cc_final: 0.6863 (mmp) REVERT: A 22 LYS cc_start: 0.8400 (mmpt) cc_final: 0.8079 (mmpt) REVERT: A 102 LYS cc_start: 0.8310 (mttp) cc_final: 0.8077 (mttp) REVERT: A 112 GLU cc_start: 0.7559 (mm-30) cc_final: 0.7316 (mm-30) REVERT: A 119 LYS cc_start: 0.8009 (mmtm) cc_final: 0.7243 (mmtm) REVERT: A 134 VAL cc_start: 0.8779 (p) cc_final: 0.8532 (t) REVERT: A 213 GLU cc_start: 0.7449 (tt0) cc_final: 0.7164 (tt0) REVERT: A 229 TYR cc_start: 0.8554 (m-80) cc_final: 0.8242 (m-80) REVERT: A 236 GLN cc_start: 0.8471 (mp10) cc_final: 0.8011 (mp10) REVERT: A 243 GLU cc_start: 0.7626 (tt0) cc_final: 0.7188 (tt0) REVERT: A 275 CYS cc_start: 0.8457 (t) cc_final: 0.8203 (t) REVERT: A 293 GLN cc_start: 0.7770 (pp30) cc_final: 0.6868 (pp30) REVERT: B 38 GLN cc_start: 0.7817 (mp10) cc_final: 0.7282 (mp10) REVERT: B 74 GLU cc_start: 0.7732 (mt-10) cc_final: 0.6983 (mt-10) REVERT: B 117 ASN cc_start: 0.8405 (m-40) cc_final: 0.8153 (m-40) REVERT: B 128 ASN cc_start: 0.8126 (p0) cc_final: 0.7924 (p0) REVERT: C 18 THR cc_start: 0.8191 (p) cc_final: 0.7654 (p) REVERT: C 40 LYS cc_start: 0.7872 (tppt) cc_final: 0.7513 (tppt) REVERT: C 80 ILE cc_start: 0.8227 (tt) cc_final: 0.7666 (mt) REVERT: C 81 GLU cc_start: 0.7739 (tp30) cc_final: 0.7504 (tp30) REVERT: C 100 GLU cc_start: 0.7634 (mm-30) cc_final: 0.7433 (mm-30) REVERT: C 103 GLU cc_start: 0.7854 (tp30) cc_final: 0.7532 (tp30) REVERT: C 112 GLU cc_start: 0.7711 (mm-30) cc_final: 0.7419 (mm-30) REVERT: C 243 GLU cc_start: 0.7863 (tt0) cc_final: 0.7658 (tt0) REVERT: C 266 MET cc_start: 0.7772 (ttp) cc_final: 0.7476 (ttp) REVERT: C 293 GLN cc_start: 0.7760 (pp30) cc_final: 0.7363 (pp30) REVERT: D 70 PHE cc_start: 0.7872 (m-80) cc_final: 0.7542 (m-80) REVERT: D 121 LYS cc_start: 0.8022 (mtmm) cc_final: 0.7749 (mtmm) REVERT: D 149 MET cc_start: 0.7640 (mmp) cc_final: 0.6806 (mmp) outliers start: 11 outliers final: 9 residues processed: 365 average time/residue: 0.1282 time to fit residues: 62.3816 Evaluate side-chains 364 residues out of total 1269 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 354 time to evaluate : 0.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 134 VAL Chi-restraints excluded: chain F residue 54 SER Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 80 ILE Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain C residue 275 CYS Chi-restraints excluded: chain D residue 59 MET Chi-restraints excluded: chain D residue 69 GLU Chi-restraints excluded: chain D residue 143 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 20 optimal weight: 0.7980 chunk 61 optimal weight: 1.9990 chunk 73 optimal weight: 3.9990 chunk 129 optimal weight: 3.9990 chunk 57 optimal weight: 0.8980 chunk 5 optimal weight: 1.9990 chunk 106 optimal weight: 3.9990 chunk 21 optimal weight: 0.0020 chunk 135 optimal weight: 0.5980 chunk 67 optimal weight: 0.6980 chunk 25 optimal weight: 0.5980 overall best weight: 0.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 293 GLN A 10 ASN B 53 ASN B 60 ASN B 146 ASN C 180 HIS C 280 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.139618 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.118297 restraints weight = 16907.696| |-----------------------------------------------------------------------------| r_work (start): 0.3489 rms_B_bonded: 2.92 r_work: 0.3359 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3359 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7520 moved from start: 0.1301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 11721 Z= 0.122 Angle : 0.587 10.613 15908 Z= 0.300 Chirality : 0.043 0.312 1735 Planarity : 0.004 0.046 2045 Dihedral : 5.801 55.214 1647 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.49 % Allowed : 5.41 % Favored : 94.09 % Rotamer: Outliers : 1.27 % Allowed : 13.30 % Favored : 85.43 % 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: -0.13 (0.22), residues: 1422 helix: 2.69 (0.26), residues: 378 sheet: 0.39 (0.34), residues: 264 loop : -1.81 (0.20), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 217 TYR 0.019 0.001 TYR C 91 PHE 0.011 0.001 PHE D 138 TRP 0.008 0.001 TRP A 252 HIS 0.003 0.001 HIS C 138 Details of bonding type rmsd covalent geometry : bond 0.00267 (11707) covalent geometry : angle 0.57756 (15875) SS BOND : bond 0.00275 ( 9) SS BOND : angle 0.42553 ( 18) hydrogen bonds : bond 0.04507 ( 419) hydrogen bonds : angle 4.60533 ( 1179) link_NAG-ASN : bond 0.00776 ( 5) link_NAG-ASN : angle 3.47280 ( 15) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2844 Ramachandran restraints generated. 1422 Oldfield, 0 Emsley, 1422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2844 Ramachandran restraints generated. 1422 Oldfield, 0 Emsley, 1422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 351 residues out of total 1269 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 335 time to evaluate : 0.355 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 21 GLU cc_start: 0.7419 (pt0) cc_final: 0.6995 (pt0) REVERT: E 22 LYS cc_start: 0.8261 (mmpt) cc_final: 0.7927 (mmpt) REVERT: E 30 VAL cc_start: 0.8510 (t) cc_final: 0.8216 (m) REVERT: E 100 GLU cc_start: 0.7589 (mm-30) cc_final: 0.7105 (mm-30) REVERT: E 134 VAL cc_start: 0.8523 (OUTLIER) cc_final: 0.8299 (t) REVERT: E 149 LEU cc_start: 0.8755 (tp) cc_final: 0.8554 (tt) REVERT: E 278 LYS cc_start: 0.8516 (mmpt) cc_final: 0.8066 (mmpt) REVERT: E 280 GLN cc_start: 0.7867 (tp40) cc_final: 0.7628 (tp-100) REVERT: E 294 ASN cc_start: 0.8086 (t0) cc_final: 0.7580 (t0) REVERT: E 319 ARG cc_start: 0.7992 (ttm-80) cc_final: 0.7713 (ttm-80) REVERT: F 74 GLU cc_start: 0.7737 (mt-10) cc_final: 0.7014 (mt-10) REVERT: F 116 LYS cc_start: 0.8124 (tptt) cc_final: 0.7862 (tptt) REVERT: F 125 GLN cc_start: 0.7756 (tp-100) cc_final: 0.7546 (tp40) REVERT: F 149 MET cc_start: 0.7586 (mmp) cc_final: 0.6787 (mmp) REVERT: A 22 LYS cc_start: 0.8392 (mmpt) cc_final: 0.8060 (mmpt) REVERT: A 102 LYS cc_start: 0.8210 (mttp) cc_final: 0.7938 (mttm) REVERT: A 112 GLU cc_start: 0.7527 (mm-30) cc_final: 0.7281 (mm-30) REVERT: A 119 LYS cc_start: 0.7999 (mmtm) cc_final: 0.7231 (mmtm) REVERT: A 134 VAL cc_start: 0.8757 (p) cc_final: 0.8502 (t) REVERT: A 213 GLU cc_start: 0.7435 (tt0) cc_final: 0.7146 (tt0) REVERT: A 229 TYR cc_start: 0.8458 (m-80) cc_final: 0.7999 (m-80) REVERT: A 275 CYS cc_start: 0.8362 (t) cc_final: 0.8084 (t) REVERT: B 38 GLN cc_start: 0.7821 (mp10) cc_final: 0.7282 (mp10) REVERT: B 74 GLU cc_start: 0.7690 (mt-10) cc_final: 0.6956 (mt-10) REVERT: B 143 LYS cc_start: 0.7457 (tmtt) cc_final: 0.6950 (tmtt) REVERT: C 18 THR cc_start: 0.7983 (p) cc_final: 0.7768 (p) REVERT: C 40 LYS cc_start: 0.7849 (tppt) cc_final: 0.7459 (tppt) REVERT: C 80 ILE cc_start: 0.8125 (tt) cc_final: 0.7691 (pt) REVERT: C 81 GLU cc_start: 0.7718 (tp30) cc_final: 0.7407 (tp30) REVERT: C 100 GLU cc_start: 0.7605 (mm-30) cc_final: 0.7399 (mm-30) REVERT: C 112 GLU cc_start: 0.7671 (mm-30) cc_final: 0.7369 (mm-30) REVERT: C 243 GLU cc_start: 0.7859 (tt0) cc_final: 0.7658 (tt0) REVERT: C 275 CYS cc_start: 0.8619 (p) cc_final: 0.8185 (p) REVERT: C 278 LYS cc_start: 0.8723 (mttt) cc_final: 0.8352 (mttt) REVERT: D 58 LYS cc_start: 0.8219 (tppt) cc_final: 0.7204 (tppt) REVERT: D 121 LYS cc_start: 0.8007 (mtmm) cc_final: 0.7728 (mtmm) REVERT: D 149 MET cc_start: 0.7648 (mmp) cc_final: 0.6839 (mmp) outliers start: 16 outliers final: 10 residues processed: 339 average time/residue: 0.1356 time to fit residues: 60.7882 Evaluate side-chains 346 residues out of total 1269 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 335 time to evaluate : 0.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 69 LEU Chi-restraints excluded: chain E residue 80 ILE Chi-restraints excluded: chain E residue 134 VAL Chi-restraints excluded: chain E residue 208 LYS Chi-restraints excluded: chain F residue 54 SER Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 40 LYS Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain C residue 169 LYS Chi-restraints excluded: chain D residue 69 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 41 optimal weight: 0.5980 chunk 70 optimal weight: 0.9980 chunk 11 optimal weight: 0.0970 chunk 22 optimal weight: 2.9990 chunk 7 optimal weight: 0.8980 chunk 123 optimal weight: 1.9990 chunk 50 optimal weight: 0.9990 chunk 76 optimal weight: 0.5980 chunk 102 optimal weight: 0.7980 chunk 79 optimal weight: 3.9990 chunk 138 optimal weight: 8.9990 overall best weight: 0.5978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 146 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.139730 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.118334 restraints weight = 16963.403| |-----------------------------------------------------------------------------| r_work (start): 0.3469 rms_B_bonded: 2.91 r_work: 0.3339 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3339 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7526 moved from start: 0.1467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 11721 Z= 0.126 Angle : 0.576 10.309 15908 Z= 0.293 Chirality : 0.043 0.314 1735 Planarity : 0.004 0.047 2045 Dihedral : 5.564 55.413 1647 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.49 % Allowed : 5.41 % Favored : 94.09 % Rotamer: Outliers : 1.66 % Allowed : 15.76 % Favored : 82.58 % 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: -0.06 (0.22), residues: 1422 helix: 2.74 (0.26), residues: 378 sheet: 0.47 (0.34), residues: 264 loop : -1.77 (0.20), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 217 TYR 0.021 0.001 TYR E 98 PHE 0.010 0.001 PHE B 70 TRP 0.007 0.001 TRP A 252 HIS 0.003 0.001 HIS C 138 Details of bonding type rmsd covalent geometry : bond 0.00279 (11707) covalent geometry : angle 0.56674 (15875) SS BOND : bond 0.00292 ( 9) SS BOND : angle 0.41917 ( 18) hydrogen bonds : bond 0.04367 ( 419) hydrogen bonds : angle 4.48607 ( 1179) link_NAG-ASN : bond 0.00726 ( 5) link_NAG-ASN : angle 3.40197 ( 15) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2844 Ramachandran restraints generated. 1422 Oldfield, 0 Emsley, 1422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2844 Ramachandran restraints generated. 1422 Oldfield, 0 Emsley, 1422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 353 residues out of total 1269 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 332 time to evaluate : 0.320 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 18 THR cc_start: 0.8390 (p) cc_final: 0.8187 (p) REVERT: E 21 GLU cc_start: 0.7394 (pt0) cc_final: 0.7048 (pt0) REVERT: E 22 LYS cc_start: 0.8270 (mmpt) cc_final: 0.7927 (mmpt) REVERT: E 30 VAL cc_start: 0.8540 (t) cc_final: 0.8236 (m) REVERT: E 100 GLU cc_start: 0.7542 (mm-30) cc_final: 0.7096 (mm-30) REVERT: E 134 VAL cc_start: 0.8567 (OUTLIER) cc_final: 0.8355 (t) REVERT: E 149 LEU cc_start: 0.8778 (tp) cc_final: 0.8577 (tt) REVERT: E 278 LYS cc_start: 0.8545 (mmpt) cc_final: 0.8086 (mmpt) REVERT: E 280 GLN cc_start: 0.7839 (tp40) cc_final: 0.7638 (tp-100) REVERT: E 294 ASN cc_start: 0.8085 (t0) cc_final: 0.7571 (t0) REVERT: E 319 ARG cc_start: 0.8002 (ttm-80) cc_final: 0.7718 (ttm-80) REVERT: F 50 ASN cc_start: 0.8275 (t0) cc_final: 0.7923 (t0) REVERT: F 74 GLU cc_start: 0.7737 (mt-10) cc_final: 0.6965 (mt-10) REVERT: F 116 LYS cc_start: 0.8102 (tptt) cc_final: 0.7862 (tptt) REVERT: F 121 LYS cc_start: 0.8095 (ptpp) cc_final: 0.7788 (mtmm) REVERT: F 125 GLN cc_start: 0.7724 (tp-100) cc_final: 0.7509 (tp40) REVERT: F 149 MET cc_start: 0.7605 (mmp) cc_final: 0.6798 (mmp) REVERT: A 22 LYS cc_start: 0.8410 (mmpt) cc_final: 0.8057 (mmpt) REVERT: A 102 LYS cc_start: 0.8273 (mttp) cc_final: 0.8042 (mttp) REVERT: A 112 GLU cc_start: 0.7559 (mm-30) cc_final: 0.7315 (mm-30) REVERT: A 119 LYS cc_start: 0.7994 (mmtm) cc_final: 0.7272 (mmtm) REVERT: A 134 VAL cc_start: 0.8773 (p) cc_final: 0.8520 (t) REVERT: A 213 GLU cc_start: 0.7426 (tt0) cc_final: 0.7142 (tt0) REVERT: A 227 MET cc_start: 0.7985 (ttp) cc_final: 0.7650 (ttp) REVERT: A 229 TYR cc_start: 0.8503 (m-80) cc_final: 0.7945 (m-80) REVERT: A 265 ILE cc_start: 0.8339 (mm) cc_final: 0.7792 (tp) REVERT: A 266 MET cc_start: 0.8206 (ptm) cc_final: 0.7843 (ptm) REVERT: A 275 CYS cc_start: 0.8362 (t) cc_final: 0.8101 (t) REVERT: B 38 GLN cc_start: 0.7837 (mp10) cc_final: 0.7318 (mp10) REVERT: B 74 GLU cc_start: 0.7677 (mt-10) cc_final: 0.6978 (mt-10) REVERT: C 40 LYS cc_start: 0.7878 (tppt) cc_final: 0.7322 (tppt) REVERT: C 80 ILE cc_start: 0.8183 (tt) cc_final: 0.7666 (mt) REVERT: C 81 GLU cc_start: 0.7733 (tp30) cc_final: 0.7486 (tp30) REVERT: C 100 GLU cc_start: 0.7634 (mm-30) cc_final: 0.7410 (mm-30) REVERT: C 112 GLU cc_start: 0.7675 (mm-30) cc_final: 0.7364 (mm-30) REVERT: C 205 LYS cc_start: 0.8708 (ptpt) cc_final: 0.8435 (pttt) REVERT: C 275 CYS cc_start: 0.8622 (OUTLIER) cc_final: 0.8189 (p) REVERT: D 121 LYS cc_start: 0.8029 (mtmm) cc_final: 0.7713 (mtmm) REVERT: D 149 MET cc_start: 0.7646 (mmp) cc_final: 0.6831 (mmp) outliers start: 21 outliers final: 16 residues processed: 339 average time/residue: 0.1337 time to fit residues: 59.9488 Evaluate side-chains 347 residues out of total 1269 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 329 time to evaluate : 0.465 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 68 ASP Chi-restraints excluded: chain E residue 69 LEU Chi-restraints excluded: chain E residue 77 SER Chi-restraints excluded: chain E residue 80 ILE Chi-restraints excluded: chain E residue 134 VAL Chi-restraints excluded: chain E residue 318 LEU Chi-restraints excluded: chain F residue 54 SER Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 40 LYS Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 133 THR Chi-restraints excluded: chain A residue 184 THR Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain B residue 54 SER Chi-restraints excluded: chain C residue 70 LEU Chi-restraints excluded: chain C residue 169 LYS Chi-restraints excluded: chain C residue 275 CYS Chi-restraints excluded: chain D residue 69 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 37 optimal weight: 0.8980 chunk 34 optimal weight: 5.9990 chunk 16 optimal weight: 2.9990 chunk 140 optimal weight: 4.9990 chunk 133 optimal weight: 1.9990 chunk 89 optimal weight: 4.9990 chunk 25 optimal weight: 3.9990 chunk 30 optimal weight: 2.9990 chunk 6 optimal weight: 1.9990 chunk 70 optimal weight: 0.0980 chunk 1 optimal weight: 3.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 311 GLN B 62 GLN C 283 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.136621 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.115402 restraints weight = 16959.401| |-----------------------------------------------------------------------------| r_work (start): 0.3444 rms_B_bonded: 2.87 r_work: 0.3314 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3314 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7584 moved from start: 0.1731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 11721 Z= 0.255 Angle : 0.656 10.130 15908 Z= 0.335 Chirality : 0.046 0.338 1735 Planarity : 0.004 0.053 2045 Dihedral : 5.633 54.881 1647 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.35 % Allowed : 6.89 % Favored : 92.76 % Rotamer: Outliers : 2.69 % Allowed : 16.71 % Favored : 80.60 % 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: -0.27 (0.22), residues: 1422 helix: 2.27 (0.26), residues: 384 sheet: 0.36 (0.32), residues: 291 loop : -1.85 (0.20), residues: 747 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 217 TYR 0.042 0.002 TYR E 98 PHE 0.015 0.002 PHE B 110 TRP 0.012 0.002 TRP C 60 HIS 0.006 0.002 HIS B 26 Details of bonding type rmsd covalent geometry : bond 0.00566 (11707) covalent geometry : angle 0.64768 (15875) SS BOND : bond 0.00523 ( 9) SS BOND : angle 0.65459 ( 18) hydrogen bonds : bond 0.05140 ( 419) hydrogen bonds : angle 4.63780 ( 1179) link_NAG-ASN : bond 0.00588 ( 5) link_NAG-ASN : angle 3.40327 ( 15) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2844 Ramachandran restraints generated. 1422 Oldfield, 0 Emsley, 1422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2844 Ramachandran restraints generated. 1422 Oldfield, 0 Emsley, 1422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 413 residues out of total 1269 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 379 time to evaluate : 0.493 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 21 GLU cc_start: 0.7426 (pt0) cc_final: 0.7110 (pt0) REVERT: E 22 LYS cc_start: 0.8299 (mmpt) cc_final: 0.7948 (mmpt) REVERT: E 41 LEU cc_start: 0.7360 (OUTLIER) cc_final: 0.7153 (mp) REVERT: E 100 GLU cc_start: 0.7595 (mm-30) cc_final: 0.7160 (mm-30) REVERT: E 149 LEU cc_start: 0.8813 (tp) cc_final: 0.8601 (tt) REVERT: E 258 LYS cc_start: 0.8467 (tppp) cc_final: 0.8223 (tppp) REVERT: E 278 LYS cc_start: 0.8534 (mmpt) cc_final: 0.8069 (mmpt) REVERT: E 280 GLN cc_start: 0.7869 (tp40) cc_final: 0.7641 (tp-100) REVERT: E 294 ASN cc_start: 0.8141 (t0) cc_final: 0.7623 (t0) REVERT: E 319 ARG cc_start: 0.8046 (ttm-80) cc_final: 0.7741 (ttm-80) REVERT: F 50 ASN cc_start: 0.8316 (t0) cc_final: 0.7990 (t0) REVERT: F 74 GLU cc_start: 0.7828 (mt-10) cc_final: 0.7070 (mt-10) REVERT: F 82 LYS cc_start: 0.7855 (ttmt) cc_final: 0.7563 (ttmt) REVERT: F 121 LYS cc_start: 0.8102 (ptpp) cc_final: 0.7818 (mtmm) REVERT: F 149 MET cc_start: 0.7689 (mmp) cc_final: 0.6887 (mmp) REVERT: A 22 LYS cc_start: 0.8447 (mmpt) cc_final: 0.8087 (mmpt) REVERT: A 102 LYS cc_start: 0.8241 (mttp) cc_final: 0.8029 (mttp) REVERT: A 112 GLU cc_start: 0.7659 (mm-30) cc_final: 0.7377 (mm-30) REVERT: A 115 GLU cc_start: 0.7365 (mt-10) cc_final: 0.7148 (mp0) REVERT: A 119 LYS cc_start: 0.8018 (mmtm) cc_final: 0.7403 (mmtm) REVERT: A 134 VAL cc_start: 0.8807 (p) cc_final: 0.8535 (t) REVERT: A 213 GLU cc_start: 0.7475 (tt0) cc_final: 0.7189 (tt0) REVERT: A 223 GLN cc_start: 0.8630 (mm-40) cc_final: 0.8235 (mm-40) REVERT: A 229 TYR cc_start: 0.8575 (m-80) cc_final: 0.8138 (m-80) REVERT: A 236 GLN cc_start: 0.8495 (mp10) cc_final: 0.8078 (mp10) REVERT: A 243 GLU cc_start: 0.7727 (tt0) cc_final: 0.7473 (tt0) REVERT: A 275 CYS cc_start: 0.8429 (t) cc_final: 0.8167 (t) REVERT: A 278 LYS cc_start: 0.8386 (tttp) cc_final: 0.8183 (tttp) REVERT: A 293 GLN cc_start: 0.7725 (pp30) cc_final: 0.6811 (pp30) REVERT: A 316 THR cc_start: 0.7994 (m) cc_final: 0.7635 (p) REVERT: B 38 GLN cc_start: 0.7850 (mp10) cc_final: 0.7307 (mp10) REVERT: B 74 GLU cc_start: 0.7750 (mt-10) cc_final: 0.7043 (mt-10) REVERT: B 121 LYS cc_start: 0.7908 (mtmm) cc_final: 0.7435 (mtmm) REVERT: B 128 ASN cc_start: 0.8244 (p0) cc_final: 0.7808 (p0) REVERT: C 21 GLU cc_start: 0.7337 (tt0) cc_final: 0.6727 (tm-30) REVERT: C 22 LYS cc_start: 0.7896 (mmpt) cc_final: 0.7424 (mmpt) REVERT: C 40 LYS cc_start: 0.7865 (tppt) cc_final: 0.7413 (tppt) REVERT: C 80 ILE cc_start: 0.8250 (tt) cc_final: 0.7718 (mt) REVERT: C 81 GLU cc_start: 0.7750 (tp30) cc_final: 0.7476 (tp30) REVERT: C 112 GLU cc_start: 0.7747 (mm-30) cc_final: 0.7424 (mm-30) REVERT: C 205 LYS cc_start: 0.8754 (ptpt) cc_final: 0.8492 (pttt) REVERT: C 206 TYR cc_start: 0.8243 (t80) cc_final: 0.7937 (t80) REVERT: C 221 ARG cc_start: 0.8538 (ttp80) cc_final: 0.8218 (ptp-110) REVERT: C 243 GLU cc_start: 0.7888 (tt0) cc_final: 0.7477 (tp30) REVERT: C 278 LYS cc_start: 0.8768 (mttt) cc_final: 0.8542 (mttt) REVERT: C 293 GLN cc_start: 0.7796 (pp30) cc_final: 0.7511 (pp30) REVERT: D 105 GLU cc_start: 0.7536 (tm-30) cc_final: 0.7229 (tm-30) REVERT: D 149 MET cc_start: 0.7708 (mmp) cc_final: 0.6859 (mmp) REVERT: D 154 ASN cc_start: 0.7826 (t0) cc_final: 0.7500 (t0) outliers start: 34 outliers final: 26 residues processed: 389 average time/residue: 0.1352 time to fit residues: 70.0734 Evaluate side-chains 395 residues out of total 1269 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 368 time to evaluate : 0.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 41 LEU Chi-restraints excluded: chain E residue 68 ASP Chi-restraints excluded: chain E residue 69 LEU Chi-restraints excluded: chain E residue 77 SER Chi-restraints excluded: chain E residue 80 ILE Chi-restraints excluded: chain E residue 171 LYS Chi-restraints excluded: chain F residue 54 SER Chi-restraints excluded: chain A residue 8 HIS Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 40 LYS Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 80 ILE Chi-restraints excluded: chain A residue 82 THR Chi-restraints excluded: chain A residue 133 THR Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 171 LYS Chi-restraints excluded: chain A residue 184 THR Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain B residue 54 SER Chi-restraints excluded: chain B residue 77 MET Chi-restraints excluded: chain C residue 70 LEU Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 151 ILE Chi-restraints excluded: chain C residue 184 THR Chi-restraints excluded: chain C residue 275 CYS Chi-restraints excluded: chain D residue 69 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 2 optimal weight: 0.9980 chunk 108 optimal weight: 0.9980 chunk 115 optimal weight: 0.8980 chunk 64 optimal weight: 0.8980 chunk 131 optimal weight: 0.0050 chunk 68 optimal weight: 0.9990 chunk 117 optimal weight: 1.9990 chunk 45 optimal weight: 2.9990 chunk 30 optimal weight: 0.9980 chunk 1 optimal weight: 0.8980 chunk 90 optimal weight: 2.9990 overall best weight: 0.7394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 53 ASN F 125 GLN A 311 GLN B 53 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.136716 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.115048 restraints weight = 17126.397| |-----------------------------------------------------------------------------| r_work (start): 0.3460 rms_B_bonded: 3.10 r_work: 0.3324 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3324 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7575 moved from start: 0.1808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 11721 Z= 0.146 Angle : 0.603 9.897 15908 Z= 0.308 Chirality : 0.044 0.316 1735 Planarity : 0.004 0.052 2045 Dihedral : 5.468 54.930 1647 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.28 % Allowed : 5.63 % Favored : 94.09 % Rotamer: Outliers : 3.01 % Allowed : 17.97 % Favored : 79.02 % 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: -0.25 (0.22), residues: 1422 helix: 2.37 (0.26), residues: 384 sheet: 0.43 (0.34), residues: 264 loop : -1.83 (0.20), residues: 774 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 313 TYR 0.040 0.002 TYR E 98 PHE 0.031 0.002 PHE D 70 TRP 0.007 0.001 TRP C 252 HIS 0.003 0.001 HIS C 28 Details of bonding type rmsd covalent geometry : bond 0.00321 (11707) covalent geometry : angle 0.59509 (15875) SS BOND : bond 0.00319 ( 9) SS BOND : angle 0.43539 ( 18) hydrogen bonds : bond 0.04670 ( 419) hydrogen bonds : angle 4.47757 ( 1179) link_NAG-ASN : bond 0.00700 ( 5) link_NAG-ASN : angle 3.26578 ( 15) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2844 Ramachandran restraints generated. 1422 Oldfield, 0 Emsley, 1422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2844 Ramachandran restraints generated. 1422 Oldfield, 0 Emsley, 1422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 388 residues out of total 1269 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 350 time to evaluate : 0.350 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 8 HIS cc_start: 0.6676 (OUTLIER) cc_final: 0.5962 (t70) REVERT: E 21 GLU cc_start: 0.7425 (pt0) cc_final: 0.7069 (pt0) REVERT: E 98 TYR cc_start: 0.8213 (t80) cc_final: 0.8006 (t80) REVERT: E 102 LYS cc_start: 0.8307 (mttp) cc_final: 0.8049 (mttp) REVERT: E 258 LYS cc_start: 0.8504 (tppp) cc_final: 0.8253 (tppp) REVERT: E 278 LYS cc_start: 0.8568 (mmpt) cc_final: 0.8109 (mmpt) REVERT: E 280 GLN cc_start: 0.7826 (tp40) cc_final: 0.7599 (tp-100) REVERT: E 294 ASN cc_start: 0.8122 (t0) cc_final: 0.7640 (t0) REVERT: E 319 ARG cc_start: 0.8069 (ttm-80) cc_final: 0.7771 (ttm-80) REVERT: F 50 ASN cc_start: 0.8292 (t0) cc_final: 0.7959 (t0) REVERT: F 82 LYS cc_start: 0.7792 (ttmt) cc_final: 0.7502 (ttmt) REVERT: F 100 ILE cc_start: 0.7646 (OUTLIER) cc_final: 0.7352 (mp) REVERT: F 121 LYS cc_start: 0.8108 (ptpp) cc_final: 0.7798 (mtmm) REVERT: F 149 MET cc_start: 0.7676 (mmp) cc_final: 0.6851 (mmp) REVERT: A 22 LYS cc_start: 0.8422 (mmpt) cc_final: 0.8080 (mmpt) REVERT: A 102 LYS cc_start: 0.8273 (mttp) cc_final: 0.8034 (mttp) REVERT: A 111 PHE cc_start: 0.8234 (OUTLIER) cc_final: 0.7391 (m-10) REVERT: A 112 GLU cc_start: 0.7664 (mm-30) cc_final: 0.7401 (mm-30) REVERT: A 119 LYS cc_start: 0.7948 (mmtm) cc_final: 0.7320 (mmtm) REVERT: A 134 VAL cc_start: 0.8809 (p) cc_final: 0.8550 (t) REVERT: A 213 GLU cc_start: 0.7444 (tt0) cc_final: 0.7134 (tt0) REVERT: A 229 TYR cc_start: 0.8568 (m-80) cc_final: 0.8236 (m-80) REVERT: A 259 LYS cc_start: 0.8284 (mttp) cc_final: 0.8035 (mmtp) REVERT: A 275 CYS cc_start: 0.8432 (t) cc_final: 0.8167 (t) REVERT: A 278 LYS cc_start: 0.8348 (tttp) cc_final: 0.8124 (tttp) REVERT: A 316 THR cc_start: 0.7915 (m) cc_final: 0.7577 (p) REVERT: A 320 ASN cc_start: 0.8418 (t0) cc_final: 0.8129 (t0) REVERT: B 38 GLN cc_start: 0.7842 (mp10) cc_final: 0.7308 (mp10) REVERT: B 74 GLU cc_start: 0.7631 (mt-10) cc_final: 0.6934 (mt-10) REVERT: B 97 GLU cc_start: 0.7199 (tt0) cc_final: 0.6616 (tt0) REVERT: B 121 LYS cc_start: 0.7847 (mtmm) cc_final: 0.7389 (mtmm) REVERT: B 128 ASN cc_start: 0.8235 (p0) cc_final: 0.7816 (p0) REVERT: B 153 LYS cc_start: 0.8658 (ptmm) cc_final: 0.8326 (ptmm) REVERT: C 21 GLU cc_start: 0.7307 (tt0) cc_final: 0.6682 (tm-30) REVERT: C 22 LYS cc_start: 0.7978 (mmpt) cc_final: 0.7459 (mmpt) REVERT: C 40 LYS cc_start: 0.7839 (tppt) cc_final: 0.7373 (tppt) REVERT: C 80 ILE cc_start: 0.8281 (tt) cc_final: 0.7593 (mt) REVERT: C 81 GLU cc_start: 0.7755 (tp30) cc_final: 0.7481 (tp30) REVERT: C 112 GLU cc_start: 0.7776 (mm-30) cc_final: 0.7447 (mm-30) REVERT: C 205 LYS cc_start: 0.8782 (ptpt) cc_final: 0.8546 (pttt) REVERT: C 206 TYR cc_start: 0.8187 (t80) cc_final: 0.7944 (t80) REVERT: C 221 ARG cc_start: 0.8533 (ttp80) cc_final: 0.8195 (ptp-110) REVERT: C 229 TYR cc_start: 0.8506 (m-80) cc_final: 0.8109 (m-10) REVERT: C 243 GLU cc_start: 0.7903 (tt0) cc_final: 0.7496 (tp30) REVERT: C 275 CYS cc_start: 0.8599 (OUTLIER) cc_final: 0.8264 (p) REVERT: C 278 LYS cc_start: 0.8735 (mttt) cc_final: 0.8464 (mttt) REVERT: C 293 GLN cc_start: 0.7757 (pp30) cc_final: 0.7488 (pp30) REVERT: D 58 LYS cc_start: 0.8035 (tppt) cc_final: 0.7762 (tppp) REVERT: D 149 MET cc_start: 0.7676 (mmp) cc_final: 0.6833 (mmp) outliers start: 38 outliers final: 23 residues processed: 365 average time/residue: 0.1339 time to fit residues: 64.7628 Evaluate side-chains 375 residues out of total 1269 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 348 time to evaluate : 0.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 8 HIS Chi-restraints excluded: chain E residue 68 ASP Chi-restraints excluded: chain E residue 69 LEU Chi-restraints excluded: chain E residue 77 SER Chi-restraints excluded: chain E residue 80 ILE Chi-restraints excluded: chain E residue 234 LEU Chi-restraints excluded: chain F residue 54 SER Chi-restraints excluded: chain F residue 69 GLU Chi-restraints excluded: chain F residue 100 ILE Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 80 ILE Chi-restraints excluded: chain A residue 82 THR Chi-restraints excluded: chain A residue 111 PHE Chi-restraints excluded: chain A residue 133 THR Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 171 LYS Chi-restraints excluded: chain A residue 184 THR Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain B residue 54 SER Chi-restraints excluded: chain B residue 77 MET Chi-restraints excluded: chain C residue 7 TYR Chi-restraints excluded: chain C residue 275 CYS Chi-restraints excluded: chain C residue 318 LEU Chi-restraints excluded: chain D residue 59 MET Chi-restraints excluded: chain D residue 69 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 139 optimal weight: 0.9980 chunk 40 optimal weight: 2.9990 chunk 90 optimal weight: 2.9990 chunk 120 optimal weight: 5.9990 chunk 113 optimal weight: 3.9990 chunk 89 optimal weight: 0.8980 chunk 112 optimal weight: 0.9990 chunk 99 optimal weight: 1.9990 chunk 43 optimal weight: 0.8980 chunk 124 optimal weight: 4.9990 chunk 4 optimal weight: 0.4980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 53 ASN B 53 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.136580 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.114853 restraints weight = 17156.177| |-----------------------------------------------------------------------------| r_work (start): 0.3451 rms_B_bonded: 3.12 r_work: 0.3312 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3312 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7582 moved from start: 0.1913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 11721 Z= 0.156 Angle : 0.604 9.664 15908 Z= 0.305 Chirality : 0.044 0.317 1735 Planarity : 0.004 0.053 2045 Dihedral : 5.314 55.131 1647 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.21 % Allowed : 5.98 % Favored : 93.81 % Rotamer: Outliers : 2.93 % Allowed : 18.53 % Favored : 78.54 % 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: -0.20 (0.22), residues: 1422 helix: 2.42 (0.26), residues: 384 sheet: 0.48 (0.35), residues: 264 loop : -1.82 (0.20), residues: 774 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 313 TYR 0.026 0.002 TYR E 98 PHE 0.026 0.002 PHE D 70 TRP 0.009 0.001 TRP C 252 HIS 0.003 0.001 HIS A 283 Details of bonding type rmsd covalent geometry : bond 0.00346 (11707) covalent geometry : angle 0.59684 (15875) SS BOND : bond 0.00327 ( 9) SS BOND : angle 0.44537 ( 18) hydrogen bonds : bond 0.04585 ( 419) hydrogen bonds : angle 4.42069 ( 1179) link_NAG-ASN : bond 0.00666 ( 5) link_NAG-ASN : angle 3.20919 ( 15) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2844 Ramachandran restraints generated. 1422 Oldfield, 0 Emsley, 1422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2844 Ramachandran restraints generated. 1422 Oldfield, 0 Emsley, 1422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 381 residues out of total 1269 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 344 time to evaluate : 0.420 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 8 HIS cc_start: 0.6689 (OUTLIER) cc_final: 0.5992 (t70) REVERT: E 21 GLU cc_start: 0.7408 (pt0) cc_final: 0.7056 (pt0) REVERT: E 102 LYS cc_start: 0.8280 (mttp) cc_final: 0.8031 (mttp) REVERT: E 229 TYR cc_start: 0.8528 (m-80) cc_final: 0.8248 (m-80) REVERT: E 258 LYS cc_start: 0.8508 (tppp) cc_final: 0.8268 (tppp) REVERT: E 278 LYS cc_start: 0.8583 (mmpt) cc_final: 0.8146 (mmpt) REVERT: E 294 ASN cc_start: 0.8135 (t0) cc_final: 0.7648 (t0) REVERT: E 319 ARG cc_start: 0.8076 (ttm-80) cc_final: 0.7783 (ttm-80) REVERT: F 50 ASN cc_start: 0.8297 (t0) cc_final: 0.7966 (t0) REVERT: F 82 LYS cc_start: 0.7801 (ttmt) cc_final: 0.7517 (ttmt) REVERT: F 100 ILE cc_start: 0.7725 (OUTLIER) cc_final: 0.7241 (mp) REVERT: F 104 ASN cc_start: 0.8161 (m-40) cc_final: 0.7757 (m110) REVERT: F 121 LYS cc_start: 0.8112 (ptpp) cc_final: 0.7792 (mtmm) REVERT: F 125 GLN cc_start: 0.7891 (tp40) cc_final: 0.7646 (tp40) REVERT: F 149 MET cc_start: 0.7706 (mmp) cc_final: 0.6879 (mmp) REVERT: A 22 LYS cc_start: 0.8444 (mmpt) cc_final: 0.8066 (mmpt) REVERT: A 102 LYS cc_start: 0.8288 (mttp) cc_final: 0.8043 (mttp) REVERT: A 111 PHE cc_start: 0.8232 (OUTLIER) cc_final: 0.7397 (m-10) REVERT: A 112 GLU cc_start: 0.7662 (mm-30) cc_final: 0.7389 (mm-30) REVERT: A 119 LYS cc_start: 0.7955 (mmtm) cc_final: 0.7336 (mmtm) REVERT: A 134 VAL cc_start: 0.8816 (p) cc_final: 0.8554 (t) REVERT: A 213 GLU cc_start: 0.7410 (tt0) cc_final: 0.7120 (tt0) REVERT: A 275 CYS cc_start: 0.8400 (t) cc_final: 0.8122 (t) REVERT: A 278 LYS cc_start: 0.8355 (tttp) cc_final: 0.8128 (tttp) REVERT: A 316 THR cc_start: 0.7932 (m) cc_final: 0.7592 (p) REVERT: A 320 ASN cc_start: 0.8402 (t0) cc_final: 0.8099 (t0) REVERT: B 38 GLN cc_start: 0.7830 (mp10) cc_final: 0.7313 (mp10) REVERT: B 97 GLU cc_start: 0.7200 (tt0) cc_final: 0.6642 (tt0) REVERT: B 118 LEU cc_start: 0.8535 (mt) cc_final: 0.8205 (mt) REVERT: B 121 LYS cc_start: 0.7882 (mtmm) cc_final: 0.7380 (mtmm) REVERT: B 128 ASN cc_start: 0.8259 (p0) cc_final: 0.7812 (p0) REVERT: C 21 GLU cc_start: 0.7355 (tt0) cc_final: 0.6709 (tm-30) REVERT: C 22 LYS cc_start: 0.7995 (mmtt) cc_final: 0.7425 (mmpt) REVERT: C 40 LYS cc_start: 0.7877 (tppt) cc_final: 0.7435 (tppt) REVERT: C 80 ILE cc_start: 0.8317 (tt) cc_final: 0.7624 (mt) REVERT: C 81 GLU cc_start: 0.7770 (tp30) cc_final: 0.7512 (tp30) REVERT: C 112 GLU cc_start: 0.7792 (mm-30) cc_final: 0.7472 (mm-30) REVERT: C 205 LYS cc_start: 0.8776 (ptpt) cc_final: 0.8535 (pttt) REVERT: C 206 TYR cc_start: 0.8208 (t80) cc_final: 0.7998 (t80) REVERT: C 221 ARG cc_start: 0.8529 (ttp80) cc_final: 0.8077 (ptm160) REVERT: C 229 TYR cc_start: 0.8519 (m-80) cc_final: 0.8036 (m-80) REVERT: C 265 ILE cc_start: 0.8484 (mm) cc_final: 0.8117 (mm) REVERT: C 275 CYS cc_start: 0.8596 (OUTLIER) cc_final: 0.8262 (p) REVERT: C 278 LYS cc_start: 0.8721 (mttt) cc_final: 0.8449 (mttt) REVERT: C 293 GLN cc_start: 0.7779 (pp30) cc_final: 0.7493 (pp30) REVERT: D 58 LYS cc_start: 0.8050 (tppt) cc_final: 0.7691 (tppp) REVERT: D 149 MET cc_start: 0.7681 (mmp) cc_final: 0.6843 (mmp) outliers start: 37 outliers final: 27 residues processed: 356 average time/residue: 0.1349 time to fit residues: 63.8354 Evaluate side-chains 372 residues out of total 1269 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 341 time to evaluate : 0.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 8 HIS Chi-restraints excluded: chain E residue 34 GLU Chi-restraints excluded: chain E residue 68 ASP Chi-restraints excluded: chain E residue 69 LEU Chi-restraints excluded: chain E residue 77 SER Chi-restraints excluded: chain E residue 80 ILE Chi-restraints excluded: chain E residue 234 LEU Chi-restraints excluded: chain F residue 54 SER Chi-restraints excluded: chain F residue 100 ILE Chi-restraints excluded: chain A residue 8 HIS Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 80 ILE Chi-restraints excluded: chain A residue 82 THR Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 111 PHE Chi-restraints excluded: chain A residue 133 THR Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 171 LYS Chi-restraints excluded: chain A residue 184 THR Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain B residue 54 SER Chi-restraints excluded: chain B residue 77 MET Chi-restraints excluded: chain C residue 7 TYR Chi-restraints excluded: chain C residue 18 THR Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 275 CYS Chi-restraints excluded: chain C residue 299 THR Chi-restraints excluded: chain C residue 318 LEU Chi-restraints excluded: chain D residue 69 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 13 optimal weight: 3.9990 chunk 109 optimal weight: 3.9990 chunk 67 optimal weight: 0.5980 chunk 32 optimal weight: 0.4980 chunk 56 optimal weight: 0.8980 chunk 33 optimal weight: 6.9990 chunk 58 optimal weight: 0.8980 chunk 133 optimal weight: 1.9990 chunk 60 optimal weight: 2.9990 chunk 24 optimal weight: 2.9990 chunk 128 optimal weight: 0.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 53 ASN B 53 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.137311 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.115522 restraints weight = 17084.429| |-----------------------------------------------------------------------------| r_work (start): 0.3461 rms_B_bonded: 3.12 r_work: 0.3326 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3326 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7574 moved from start: 0.1988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 11721 Z= 0.147 Angle : 0.608 10.381 15908 Z= 0.310 Chirality : 0.045 0.355 1735 Planarity : 0.004 0.054 2045 Dihedral : 5.257 55.050 1647 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.21 % Allowed : 5.91 % Favored : 93.88 % Rotamer: Outliers : 2.69 % Allowed : 19.16 % Favored : 78.15 % 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: 1422 helix: 2.40 (0.26), residues: 384 sheet: 0.50 (0.35), residues: 264 loop : -1.81 (0.20), residues: 774 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 217 TYR 0.025 0.002 TYR E 98 PHE 0.026 0.002 PHE B 70 TRP 0.009 0.001 TRP C 252 HIS 0.003 0.001 HIS A 283 Details of bonding type rmsd covalent geometry : bond 0.00328 (11707) covalent geometry : angle 0.60032 (15875) SS BOND : bond 0.00296 ( 9) SS BOND : angle 0.44723 ( 18) hydrogen bonds : bond 0.04545 ( 419) hydrogen bonds : angle 4.41387 ( 1179) link_NAG-ASN : bond 0.00677 ( 5) link_NAG-ASN : angle 3.13777 ( 15) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2844 Ramachandran restraints generated. 1422 Oldfield, 0 Emsley, 1422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2844 Ramachandran restraints generated. 1422 Oldfield, 0 Emsley, 1422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 372 residues out of total 1269 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 338 time to evaluate : 0.423 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 8 HIS cc_start: 0.6721 (OUTLIER) cc_final: 0.6005 (t70) REVERT: E 21 GLU cc_start: 0.7403 (pt0) cc_final: 0.7042 (pt0) REVERT: E 132 THR cc_start: 0.8248 (p) cc_final: 0.7568 (t) REVERT: E 229 TYR cc_start: 0.8525 (m-80) cc_final: 0.8254 (m-80) REVERT: E 258 LYS cc_start: 0.8491 (tppp) cc_final: 0.8251 (tppp) REVERT: E 278 LYS cc_start: 0.8584 (mmpt) cc_final: 0.8146 (mmpt) REVERT: E 294 ASN cc_start: 0.8127 (t0) cc_final: 0.7675 (t0) REVERT: E 319 ARG cc_start: 0.8057 (ttm-80) cc_final: 0.7770 (ttm-80) REVERT: F 82 LYS cc_start: 0.7758 (ttmt) cc_final: 0.7469 (ttmt) REVERT: F 100 ILE cc_start: 0.7672 (OUTLIER) cc_final: 0.7317 (mp) REVERT: F 149 MET cc_start: 0.7694 (mmp) cc_final: 0.6898 (mmp) REVERT: A 22 LYS cc_start: 0.8423 (mmpt) cc_final: 0.8052 (mmpt) REVERT: A 102 LYS cc_start: 0.8275 (mttp) cc_final: 0.8045 (mttp) REVERT: A 111 PHE cc_start: 0.8224 (OUTLIER) cc_final: 0.7817 (m-10) REVERT: A 112 GLU cc_start: 0.7678 (mm-30) cc_final: 0.7328 (mm-30) REVERT: A 119 LYS cc_start: 0.7949 (mmtm) cc_final: 0.7332 (mmtm) REVERT: A 134 VAL cc_start: 0.8822 (p) cc_final: 0.8558 (t) REVERT: A 213 GLU cc_start: 0.7392 (tt0) cc_final: 0.7110 (tt0) REVERT: A 275 CYS cc_start: 0.8393 (t) cc_final: 0.8119 (t) REVERT: A 278 LYS cc_start: 0.8341 (tttp) cc_final: 0.8108 (tttp) REVERT: A 316 THR cc_start: 0.7927 (m) cc_final: 0.7572 (p) REVERT: A 320 ASN cc_start: 0.8375 (t0) cc_final: 0.8073 (t0) REVERT: B 38 GLN cc_start: 0.7819 (mp10) cc_final: 0.7298 (mp10) REVERT: B 97 GLU cc_start: 0.7170 (tt0) cc_final: 0.6550 (tt0) REVERT: B 118 LEU cc_start: 0.8535 (mt) cc_final: 0.8173 (mt) REVERT: B 121 LYS cc_start: 0.7875 (mtmm) cc_final: 0.7366 (mtmm) REVERT: B 128 ASN cc_start: 0.8291 (p0) cc_final: 0.7860 (p0) REVERT: B 153 LYS cc_start: 0.8651 (ptmm) cc_final: 0.8317 (ptmm) REVERT: C 21 GLU cc_start: 0.7379 (tt0) cc_final: 0.6748 (tm-30) REVERT: C 22 LYS cc_start: 0.7982 (mmtt) cc_final: 0.7435 (mmpt) REVERT: C 40 LYS cc_start: 0.7865 (tppt) cc_final: 0.7363 (tppt) REVERT: C 80 ILE cc_start: 0.8332 (OUTLIER) cc_final: 0.7643 (mt) REVERT: C 81 GLU cc_start: 0.7765 (tp30) cc_final: 0.7496 (tp30) REVERT: C 112 GLU cc_start: 0.7773 (mm-30) cc_final: 0.7447 (mm-30) REVERT: C 205 LYS cc_start: 0.8777 (ptpt) cc_final: 0.8566 (pttt) REVERT: C 206 TYR cc_start: 0.8211 (t80) cc_final: 0.8003 (t80) REVERT: C 221 ARG cc_start: 0.8505 (ttp80) cc_final: 0.7670 (ttp80) REVERT: C 243 GLU cc_start: 0.7873 (tt0) cc_final: 0.7565 (tp30) REVERT: C 265 ILE cc_start: 0.8498 (mm) cc_final: 0.8103 (mm) REVERT: C 275 CYS cc_start: 0.8634 (OUTLIER) cc_final: 0.8344 (p) REVERT: C 278 LYS cc_start: 0.8725 (mttt) cc_final: 0.8454 (mttt) REVERT: C 293 GLN cc_start: 0.7750 (pp30) cc_final: 0.7457 (pp30) REVERT: D 58 LYS cc_start: 0.8100 (tppt) cc_final: 0.7695 (tppp) REVERT: D 149 MET cc_start: 0.7682 (mmp) cc_final: 0.6843 (mmp) outliers start: 34 outliers final: 26 residues processed: 349 average time/residue: 0.1376 time to fit residues: 63.1649 Evaluate side-chains 370 residues out of total 1269 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 339 time to evaluate : 0.410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 8 HIS Chi-restraints excluded: chain E residue 68 ASP Chi-restraints excluded: chain E residue 69 LEU Chi-restraints excluded: chain E residue 77 SER Chi-restraints excluded: chain E residue 80 ILE Chi-restraints excluded: chain E residue 234 LEU Chi-restraints excluded: chain F residue 54 SER Chi-restraints excluded: chain F residue 100 ILE Chi-restraints excluded: chain A residue 8 HIS Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 80 ILE Chi-restraints excluded: chain A residue 82 THR Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 111 PHE Chi-restraints excluded: chain A residue 133 THR Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 171 LYS Chi-restraints excluded: chain A residue 184 THR Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain A residue 318 LEU Chi-restraints excluded: chain B residue 54 SER Chi-restraints excluded: chain B residue 77 MET Chi-restraints excluded: chain C residue 7 TYR Chi-restraints excluded: chain C residue 18 THR Chi-restraints excluded: chain C residue 80 ILE Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 275 CYS Chi-restraints excluded: chain C residue 318 LEU Chi-restraints excluded: chain D residue 69 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 2 optimal weight: 0.7980 chunk 95 optimal weight: 0.5980 chunk 4 optimal weight: 0.8980 chunk 130 optimal weight: 0.9980 chunk 124 optimal weight: 2.9990 chunk 78 optimal weight: 2.9990 chunk 86 optimal weight: 2.9990 chunk 104 optimal weight: 1.9990 chunk 74 optimal weight: 2.9990 chunk 122 optimal weight: 1.9990 chunk 58 optimal weight: 0.9980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 53 ASN F 125 GLN ** A 180 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 53 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.137510 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.115628 restraints weight = 16976.770| |-----------------------------------------------------------------------------| r_work (start): 0.3455 rms_B_bonded: 3.12 r_work: 0.3318 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3318 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7576 moved from start: 0.2066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 11721 Z= 0.157 Angle : 0.614 9.583 15908 Z= 0.313 Chirality : 0.044 0.317 1735 Planarity : 0.004 0.054 2045 Dihedral : 5.208 55.141 1647 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.21 % Allowed : 6.26 % Favored : 93.53 % Rotamer: Outliers : 2.69 % Allowed : 20.59 % Favored : 76.72 % 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: -0.20 (0.22), residues: 1422 helix: 2.40 (0.26), residues: 384 sheet: 0.51 (0.35), residues: 264 loop : -1.81 (0.20), residues: 774 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 217 TYR 0.019 0.002 TYR A 192 PHE 0.023 0.002 PHE D 70 TRP 0.010 0.001 TRP C 252 HIS 0.003 0.001 HIS A 283 Details of bonding type rmsd covalent geometry : bond 0.00349 (11707) covalent geometry : angle 0.60673 (15875) SS BOND : bond 0.00318 ( 9) SS BOND : angle 0.45532 ( 18) hydrogen bonds : bond 0.04569 ( 419) hydrogen bonds : angle 4.41418 ( 1179) link_NAG-ASN : bond 0.00655 ( 5) link_NAG-ASN : angle 3.08694 ( 15) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2844 Ramachandran restraints generated. 1422 Oldfield, 0 Emsley, 1422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2844 Ramachandran restraints generated. 1422 Oldfield, 0 Emsley, 1422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 382 residues out of total 1269 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 348 time to evaluate : 0.352 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 21 GLU cc_start: 0.7411 (pt0) cc_final: 0.7076 (pt0) REVERT: E 132 THR cc_start: 0.8251 (p) cc_final: 0.7583 (t) REVERT: E 229 TYR cc_start: 0.8523 (m-80) cc_final: 0.8271 (m-80) REVERT: E 258 LYS cc_start: 0.8500 (tppp) cc_final: 0.8258 (tppp) REVERT: E 278 LYS cc_start: 0.8585 (mmpt) cc_final: 0.8157 (mmpt) REVERT: E 294 ASN cc_start: 0.8128 (t0) cc_final: 0.7647 (t0) REVERT: E 319 ARG cc_start: 0.8055 (ttm-80) cc_final: 0.7770 (ttm-80) REVERT: F 74 GLU cc_start: 0.7749 (mt-10) cc_final: 0.6958 (mt-10) REVERT: F 82 LYS cc_start: 0.7788 (ttmt) cc_final: 0.7494 (ttmt) REVERT: F 100 ILE cc_start: 0.7632 (OUTLIER) cc_final: 0.7306 (mp) REVERT: F 149 MET cc_start: 0.7710 (mmp) cc_final: 0.6899 (mmp) REVERT: A 10 ASN cc_start: 0.8458 (m-40) cc_final: 0.8099 (m-40) REVERT: A 22 LYS cc_start: 0.8454 (mmpt) cc_final: 0.8062 (mmpt) REVERT: A 102 LYS cc_start: 0.8279 (mttp) cc_final: 0.8035 (mttm) REVERT: A 111 PHE cc_start: 0.8216 (OUTLIER) cc_final: 0.7795 (m-10) REVERT: A 112 GLU cc_start: 0.7682 (mm-30) cc_final: 0.7324 (mm-30) REVERT: A 119 LYS cc_start: 0.7959 (mmtm) cc_final: 0.7345 (mmtm) REVERT: A 134 VAL cc_start: 0.8818 (p) cc_final: 0.8557 (t) REVERT: A 213 GLU cc_start: 0.7418 (tt0) cc_final: 0.7135 (tt0) REVERT: A 275 CYS cc_start: 0.8411 (t) cc_final: 0.8132 (t) REVERT: A 278 LYS cc_start: 0.8382 (tttp) cc_final: 0.8115 (tttp) REVERT: A 316 THR cc_start: 0.7914 (m) cc_final: 0.7561 (p) REVERT: B 38 GLN cc_start: 0.7807 (mp10) cc_final: 0.7171 (mp10) REVERT: B 97 GLU cc_start: 0.7207 (tt0) cc_final: 0.6585 (tt0) REVERT: B 118 LEU cc_start: 0.8535 (mt) cc_final: 0.8167 (mt) REVERT: B 121 LYS cc_start: 0.7874 (mtmm) cc_final: 0.7365 (mtmm) REVERT: B 123 LYS cc_start: 0.8668 (tttt) cc_final: 0.8391 (tttt) REVERT: B 128 ASN cc_start: 0.8311 (p0) cc_final: 0.7872 (p0) REVERT: B 153 LYS cc_start: 0.8660 (ptmm) cc_final: 0.8324 (ptmm) REVERT: C 21 GLU cc_start: 0.7389 (tt0) cc_final: 0.6745 (tm-30) REVERT: C 22 LYS cc_start: 0.8005 (mmtt) cc_final: 0.7442 (mmpt) REVERT: C 40 LYS cc_start: 0.7866 (tppt) cc_final: 0.7351 (tppt) REVERT: C 80 ILE cc_start: 0.8361 (OUTLIER) cc_final: 0.7680 (mt) REVERT: C 81 GLU cc_start: 0.7784 (tp30) cc_final: 0.7483 (tp30) REVERT: C 112 GLU cc_start: 0.7806 (mm-30) cc_final: 0.7483 (mm-30) REVERT: C 205 LYS cc_start: 0.8772 (ptpt) cc_final: 0.8552 (pttt) REVERT: C 221 ARG cc_start: 0.8547 (ttp80) cc_final: 0.7666 (ttp80) REVERT: C 243 GLU cc_start: 0.7882 (OUTLIER) cc_final: 0.7561 (tp30) REVERT: C 265 ILE cc_start: 0.8516 (mm) cc_final: 0.8274 (mm) REVERT: C 275 CYS cc_start: 0.8623 (OUTLIER) cc_final: 0.8330 (p) REVERT: C 278 LYS cc_start: 0.8729 (mttt) cc_final: 0.8441 (mttt) REVERT: C 293 GLN cc_start: 0.7771 (pp30) cc_final: 0.7476 (pp30) REVERT: D 58 LYS cc_start: 0.8111 (tppt) cc_final: 0.7625 (tppp) REVERT: D 105 GLU cc_start: 0.7553 (tm-30) cc_final: 0.7235 (tm-30) REVERT: D 149 MET cc_start: 0.7668 (mmp) cc_final: 0.6856 (mmp) outliers start: 34 outliers final: 28 residues processed: 358 average time/residue: 0.1351 time to fit residues: 63.8833 Evaluate side-chains 381 residues out of total 1269 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 348 time to evaluate : 0.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 8 HIS Chi-restraints excluded: chain E residue 68 ASP Chi-restraints excluded: chain E residue 69 LEU Chi-restraints excluded: chain E residue 77 SER Chi-restraints excluded: chain E residue 80 ILE Chi-restraints excluded: chain E residue 234 LEU Chi-restraints excluded: chain F residue 54 SER Chi-restraints excluded: chain F residue 100 ILE Chi-restraints excluded: chain F residue 125 GLN Chi-restraints excluded: chain A residue 8 HIS Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 80 ILE Chi-restraints excluded: chain A residue 82 THR Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 111 PHE Chi-restraints excluded: chain A residue 133 THR Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 171 LYS Chi-restraints excluded: chain A residue 184 THR Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain A residue 318 LEU Chi-restraints excluded: chain B residue 54 SER Chi-restraints excluded: chain C residue 7 TYR Chi-restraints excluded: chain C residue 18 THR Chi-restraints excluded: chain C residue 80 ILE Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 243 GLU Chi-restraints excluded: chain C residue 275 CYS Chi-restraints excluded: chain C residue 318 LEU Chi-restraints excluded: chain D residue 69 GLU Chi-restraints excluded: chain D residue 143 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 66 optimal weight: 1.9990 chunk 33 optimal weight: 9.9990 chunk 17 optimal weight: 0.9990 chunk 110 optimal weight: 2.9990 chunk 60 optimal weight: 4.9990 chunk 61 optimal weight: 0.9990 chunk 0 optimal weight: 6.9990 chunk 18 optimal weight: 1.9990 chunk 52 optimal weight: 1.9990 chunk 44 optimal weight: 3.9990 chunk 106 optimal weight: 0.8980 overall best weight: 1.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 53 ASN F 125 GLN ** C 253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.137112 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.115848 restraints weight = 16900.448| |-----------------------------------------------------------------------------| r_work (start): 0.3447 rms_B_bonded: 2.88 r_work: 0.3317 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3317 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7576 moved from start: 0.2154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 11721 Z= 0.224 Angle : 0.659 9.737 15908 Z= 0.338 Chirality : 0.046 0.328 1735 Planarity : 0.004 0.056 2045 Dihedral : 5.336 55.083 1647 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.21 % Allowed : 6.96 % Favored : 92.83 % Rotamer: Outliers : 2.69 % Allowed : 20.90 % Favored : 76.41 % 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: -0.33 (0.22), residues: 1422 helix: 2.21 (0.26), residues: 384 sheet: 0.46 (0.35), residues: 264 loop : -1.87 (0.20), residues: 774 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 217 TYR 0.019 0.002 TYR A 192 PHE 0.027 0.002 PHE B 70 TRP 0.011 0.002 TRP A 252 HIS 0.006 0.001 HIS A 283 Details of bonding type rmsd covalent geometry : bond 0.00498 (11707) covalent geometry : angle 0.65286 (15875) SS BOND : bond 0.00444 ( 9) SS BOND : angle 0.59593 ( 18) hydrogen bonds : bond 0.04888 ( 419) hydrogen bonds : angle 4.53397 ( 1179) link_NAG-ASN : bond 0.00597 ( 5) link_NAG-ASN : angle 3.09302 ( 15) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2844 Ramachandran restraints generated. 1422 Oldfield, 0 Emsley, 1422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2844 Ramachandran restraints generated. 1422 Oldfield, 0 Emsley, 1422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 395 residues out of total 1269 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 361 time to evaluate : 0.406 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 21 GLU cc_start: 0.7485 (pt0) cc_final: 0.7087 (pt0) REVERT: E 132 THR cc_start: 0.8244 (p) cc_final: 0.7540 (t) REVERT: E 221 ARG cc_start: 0.8409 (ttm-80) cc_final: 0.7949 (ttm-80) REVERT: E 222 GLU cc_start: 0.7943 (tp30) cc_final: 0.7741 (tp30) REVERT: E 229 TYR cc_start: 0.8538 (m-80) cc_final: 0.8325 (m-80) REVERT: E 258 LYS cc_start: 0.8502 (tppp) cc_final: 0.8236 (tppp) REVERT: E 267 ARG cc_start: 0.7842 (ttm-80) cc_final: 0.7400 (ttm-80) REVERT: E 278 LYS cc_start: 0.8543 (mmpt) cc_final: 0.8105 (mmpt) REVERT: E 294 ASN cc_start: 0.8142 (t0) cc_final: 0.7635 (t0) REVERT: E 319 ARG cc_start: 0.8062 (ttm-80) cc_final: 0.7765 (ttm-80) REVERT: F 74 GLU cc_start: 0.7787 (mt-10) cc_final: 0.7005 (mt-10) REVERT: F 82 LYS cc_start: 0.7823 (ttmt) cc_final: 0.7517 (ttmt) REVERT: F 100 ILE cc_start: 0.7658 (OUTLIER) cc_final: 0.7314 (mp) REVERT: F 103 GLU cc_start: 0.7468 (mm-30) cc_final: 0.6878 (mm-30) REVERT: F 149 MET cc_start: 0.7699 (mmp) cc_final: 0.6894 (mmp) REVERT: A 10 ASN cc_start: 0.8485 (m-40) cc_final: 0.8124 (m-40) REVERT: A 22 LYS cc_start: 0.8458 (mmpt) cc_final: 0.8053 (mmpt) REVERT: A 102 LYS cc_start: 0.8263 (mttp) cc_final: 0.8033 (mttp) REVERT: A 111 PHE cc_start: 0.8213 (OUTLIER) cc_final: 0.7761 (m-10) REVERT: A 112 GLU cc_start: 0.7659 (mm-30) cc_final: 0.7288 (mm-30) REVERT: A 119 LYS cc_start: 0.8010 (mmtm) cc_final: 0.7438 (mmtm) REVERT: A 134 VAL cc_start: 0.8831 (p) cc_final: 0.8568 (t) REVERT: A 213 GLU cc_start: 0.7421 (tt0) cc_final: 0.7177 (tt0) REVERT: A 227 MET cc_start: 0.8004 (ttp) cc_final: 0.7542 (ttm) REVERT: A 249 ILE cc_start: 0.8487 (mm) cc_final: 0.8235 (mm) REVERT: A 275 CYS cc_start: 0.8413 (t) cc_final: 0.8133 (t) REVERT: A 278 LYS cc_start: 0.8432 (tttp) cc_final: 0.8158 (tttp) REVERT: A 316 THR cc_start: 0.7936 (m) cc_final: 0.7575 (p) REVERT: B 97 GLU cc_start: 0.7273 (tt0) cc_final: 0.6595 (tt0) REVERT: B 118 LEU cc_start: 0.8524 (mt) cc_final: 0.8167 (mt) REVERT: B 121 LYS cc_start: 0.7914 (mtmm) cc_final: 0.7410 (mtmm) REVERT: B 123 LYS cc_start: 0.8701 (tttt) cc_final: 0.8434 (tttt) REVERT: B 128 ASN cc_start: 0.8357 (p0) cc_final: 0.7929 (p0) REVERT: B 153 LYS cc_start: 0.8687 (ptmm) cc_final: 0.8301 (ptmm) REVERT: C 21 GLU cc_start: 0.7403 (tt0) cc_final: 0.6760 (tm-30) REVERT: C 22 LYS cc_start: 0.7982 (mmtt) cc_final: 0.7422 (mmpt) REVERT: C 40 LYS cc_start: 0.7885 (tppt) cc_final: 0.7367 (tppt) REVERT: C 80 ILE cc_start: 0.8348 (OUTLIER) cc_final: 0.7819 (mt) REVERT: C 81 GLU cc_start: 0.7756 (tp30) cc_final: 0.7442 (tp30) REVERT: C 112 GLU cc_start: 0.7767 (mm-30) cc_final: 0.7454 (mm-30) REVERT: C 205 LYS cc_start: 0.8761 (ptpt) cc_final: 0.8524 (pttt) REVERT: C 221 ARG cc_start: 0.8540 (ttp80) cc_final: 0.7515 (ttp80) REVERT: C 243 GLU cc_start: 0.7894 (OUTLIER) cc_final: 0.7544 (tp30) REVERT: C 267 ARG cc_start: 0.7819 (tpp80) cc_final: 0.7591 (ttp80) REVERT: C 275 CYS cc_start: 0.8553 (OUTLIER) cc_final: 0.8202 (p) REVERT: C 278 LYS cc_start: 0.8731 (mttt) cc_final: 0.8432 (mttt) REVERT: C 293 GLN cc_start: 0.7834 (pp30) cc_final: 0.7618 (pp30) REVERT: D 58 LYS cc_start: 0.8161 (tppt) cc_final: 0.7613 (tppp) REVERT: D 149 MET cc_start: 0.7679 (mmp) cc_final: 0.6859 (mmp) outliers start: 34 outliers final: 28 residues processed: 371 average time/residue: 0.1399 time to fit residues: 68.2749 Evaluate side-chains 392 residues out of total 1269 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 359 time to evaluate : 0.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 8 HIS Chi-restraints excluded: chain E residue 68 ASP Chi-restraints excluded: chain E residue 69 LEU Chi-restraints excluded: chain E residue 77 SER Chi-restraints excluded: chain E residue 80 ILE Chi-restraints excluded: chain E residue 234 LEU Chi-restraints excluded: chain F residue 54 SER Chi-restraints excluded: chain F residue 100 ILE Chi-restraints excluded: chain F residue 125 GLN Chi-restraints excluded: chain A residue 8 HIS Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 80 ILE Chi-restraints excluded: chain A residue 82 THR Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 111 PHE Chi-restraints excluded: chain A residue 133 THR Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 171 LYS Chi-restraints excluded: chain A residue 184 THR Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain B residue 54 SER Chi-restraints excluded: chain C residue 7 TYR Chi-restraints excluded: chain C residue 18 THR Chi-restraints excluded: chain C residue 69 LEU Chi-restraints excluded: chain C residue 80 ILE Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 243 GLU Chi-restraints excluded: chain C residue 275 CYS Chi-restraints excluded: chain C residue 307 VAL Chi-restraints excluded: chain D residue 69 GLU Chi-restraints excluded: chain D residue 143 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 44 optimal weight: 4.9990 chunk 36 optimal weight: 0.8980 chunk 54 optimal weight: 0.9980 chunk 25 optimal weight: 0.6980 chunk 8 optimal weight: 0.7980 chunk 11 optimal weight: 0.9990 chunk 77 optimal weight: 0.6980 chunk 47 optimal weight: 7.9990 chunk 17 optimal weight: 2.9990 chunk 68 optimal weight: 0.8980 chunk 91 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 53 ASN F 125 GLN B 53 ASN C 253 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.137462 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.115570 restraints weight = 17082.732| |-----------------------------------------------------------------------------| r_work (start): 0.3459 rms_B_bonded: 3.15 r_work: 0.3321 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3321 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7578 moved from start: 0.2169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 11721 Z= 0.151 Angle : 0.627 9.595 15908 Z= 0.322 Chirality : 0.045 0.316 1735 Planarity : 0.004 0.055 2045 Dihedral : 5.263 55.017 1647 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.21 % Allowed : 5.84 % Favored : 93.95 % Rotamer: Outliers : 2.77 % Allowed : 21.14 % Favored : 76.09 % 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: -0.30 (0.22), residues: 1422 helix: 2.25 (0.26), residues: 384 sheet: 0.47 (0.35), residues: 264 loop : -1.84 (0.20), residues: 774 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 217 TYR 0.041 0.002 TYR E 98 PHE 0.021 0.002 PHE D 70 TRP 0.009 0.001 TRP C 60 HIS 0.003 0.001 HIS A 138 Details of bonding type rmsd covalent geometry : bond 0.00338 (11707) covalent geometry : angle 0.62108 (15875) SS BOND : bond 0.00315 ( 9) SS BOND : angle 0.45094 ( 18) hydrogen bonds : bond 0.04609 ( 419) hydrogen bonds : angle 4.46732 ( 1179) link_NAG-ASN : bond 0.00662 ( 5) link_NAG-ASN : angle 3.01257 ( 15) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2309.22 seconds wall clock time: 40 minutes 37.49 seconds (2437.49 seconds total)