Starting phenix.real_space_refine on Wed Feb 12 11:01:54 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6knf_0730/02_2025/6knf_0730.cif Found real_map, /net/cci-nas-00/data/ceres_data/6knf_0730/02_2025/6knf_0730.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.99 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6knf_0730/02_2025/6knf_0730.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6knf_0730/02_2025/6knf_0730.map" model { file = "/net/cci-nas-00/data/ceres_data/6knf_0730/02_2025/6knf_0730.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6knf_0730/02_2025/6knf_0730.cif" } resolution = 2.99 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Cu 6 5.60 5 S 30 5.16 5 C 4935 2.51 5 N 1326 2.21 5 O 1452 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 58 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 7749 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 2581 Number of conformers: 1 Conformer: "" Number of residues, atoms: 334, 2581 Classifications: {'peptide': 334} Link IDs: {'PCIS': 2, 'PTRANS': 20, 'TRANS': 311} Chain: "B" Number of atoms: 2581 Number of conformers: 1 Conformer: "" Number of residues, atoms: 334, 2581 Classifications: {'peptide': 334} Link IDs: {'PCIS': 2, 'PTRANS': 20, 'TRANS': 311} Chain: "C" Number of atoms: 2581 Number of conformers: 1 Conformer: "" Number of residues, atoms: 334, 2581 Classifications: {'peptide': 334} Link IDs: {'PCIS': 2, 'PTRANS': 20, 'TRANS': 311} Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CU': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CU': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CU': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 1005 SG CYS A 136 25.198 25.320 32.458 1.00 57.62 S ATOM 3586 SG CYS B 136 40.865 66.428 32.465 1.00 58.29 S ATOM 6167 SG CYS C 136 68.598 32.343 32.554 1.00 57.18 S Time building chain proxies: 6.59, per 1000 atoms: 0.85 Number of scatterers: 7749 At special positions: 0 Unit cell: (94.16, 94.16, 75.68, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Cu 6 28.99 S 30 16.00 O 1452 8.00 N 1326 7.00 C 4935 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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 Time building additional restraints: 1.71 Conformation dependent library (CDL) restraints added in 1.1 seconds 1992 Ramachandran restraints generated. 996 Oldfield, 0 Emsley, 996 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1806 Finding SS restraints... Secondary structure from input PDB file: 18 helices and 15 sheets defined 14.4% alpha, 41.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.92 Creating SS restraints... Processing helix chain 'A' and resid 8 through 12 Processing helix chain 'A' and resid 105 through 109 Processing helix chain 'A' and resid 141 through 149 removed outlier: 3.597A pdb=" N GLY A 149 " --> pdb=" O HIS A 145 " (cutoff:3.500A) Processing helix chain 'A' and resid 198 through 212 removed outlier: 3.775A pdb=" N ALA A 202 " --> pdb=" O THR A 198 " (cutoff:3.500A) removed outlier: 5.042A pdb=" N GLU A 204 " --> pdb=" O GLY A 200 " (cutoff:3.500A) removed outlier: 5.195A pdb=" N ASP A 205 " --> pdb=" O GLU A 201 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 232 removed outlier: 3.930A pdb=" N HIS A 231 " --> pdb=" O THR A 228 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ALA A 232 " --> pdb=" O GLY A 229 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 228 through 232' Processing helix chain 'A' and resid 307 through 315 removed outlier: 3.519A pdb=" N GLY A 315 " --> pdb=" O ALA A 311 " (cutoff:3.500A) Processing helix chain 'B' and resid 8 through 12 Processing helix chain 'B' and resid 105 through 109 Processing helix chain 'B' and resid 141 through 149 removed outlier: 3.597A pdb=" N GLY B 149 " --> pdb=" O HIS B 145 " (cutoff:3.500A) Processing helix chain 'B' and resid 198 through 212 removed outlier: 3.775A pdb=" N ALA B 202 " --> pdb=" O THR B 198 " (cutoff:3.500A) removed outlier: 5.042A pdb=" N GLU B 204 " --> pdb=" O GLY B 200 " (cutoff:3.500A) removed outlier: 5.196A pdb=" N ASP B 205 " --> pdb=" O GLU B 201 " (cutoff:3.500A) Processing helix chain 'B' and resid 228 through 232 removed outlier: 3.931A pdb=" N HIS B 231 " --> pdb=" O THR B 228 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ALA B 232 " --> pdb=" O GLY B 229 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 228 through 232' Processing helix chain 'B' and resid 307 through 315 removed outlier: 3.519A pdb=" N GLY B 315 " --> pdb=" O ALA B 311 " (cutoff:3.500A) Processing helix chain 'C' and resid 8 through 12 Processing helix chain 'C' and resid 105 through 109 Processing helix chain 'C' and resid 141 through 149 removed outlier: 3.597A pdb=" N GLY C 149 " --> pdb=" O HIS C 145 " (cutoff:3.500A) Processing helix chain 'C' and resid 198 through 212 removed outlier: 3.775A pdb=" N ALA C 202 " --> pdb=" O THR C 198 " (cutoff:3.500A) removed outlier: 5.043A pdb=" N GLU C 204 " --> pdb=" O GLY C 200 " (cutoff:3.500A) removed outlier: 5.196A pdb=" N ASP C 205 " --> pdb=" O GLU C 201 " (cutoff:3.500A) Processing helix chain 'C' and resid 228 through 232 removed outlier: 3.930A pdb=" N HIS C 231 " --> pdb=" O THR C 228 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ALA C 232 " --> pdb=" O GLY C 229 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 228 through 232' Processing helix chain 'C' and resid 307 through 315 removed outlier: 3.520A pdb=" N GLY C 315 " --> pdb=" O ALA C 311 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 14 through 16 Processing sheet with id=AA2, first strand: chain 'A' and resid 14 through 16 removed outlier: 6.364A pdb=" N VAL A 39 " --> pdb=" O GLU A 82 " (cutoff:3.500A) removed outlier: 7.739A pdb=" N ARG A 84 " --> pdb=" O VAL A 39 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N PHE A 41 " --> pdb=" O ARG A 84 " (cutoff:3.500A) removed outlier: 8.153A pdb=" N ILE A 86 " --> pdb=" O PHE A 41 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N MET A 43 " --> pdb=" O ILE A 86 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N ASP A 79 " --> pdb=" O ALA A 126 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N GLU A 119 " --> pdb=" O LYS C 336 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N LYS C 336 " --> pdb=" O GLU A 119 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N THR A 121 " --> pdb=" O VAL C 334 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N VAL C 334 " --> pdb=" O THR A 121 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 73 through 76 removed outlier: 6.121A pdb=" N MET A 73 " --> pdb=" O MET A 155 " (cutoff:3.500A) removed outlier: 7.259A pdb=" N LEU A 157 " --> pdb=" O MET A 73 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N VAL A 75 " --> pdb=" O LEU A 157 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 217 through 220 removed outlier: 8.142A pdb=" N THR A 294 " --> pdb=" O GLY A 261 " (cutoff:3.500A) removed outlier: 8.640A pdb=" N GLY A 261 " --> pdb=" O THR A 294 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N ASP A 262 " --> pdb=" O ASP A 277 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ASP A 277 " --> pdb=" O ASP A 262 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 233 through 236 removed outlier: 3.824A pdb=" N ALA A 302 " --> pdb=" O ILE A 257 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 331 through 338 removed outlier: 3.843A pdb=" N VAL A 334 " --> pdb=" O THR B 121 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N THR B 121 " --> pdb=" O VAL A 334 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N LYS A 336 " --> pdb=" O GLU B 119 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N GLU B 119 " --> pdb=" O LYS A 336 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N ASP B 79 " --> pdb=" O ALA B 126 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N VAL B 39 " --> pdb=" O GLU B 82 " (cutoff:3.500A) removed outlier: 7.739A pdb=" N ARG B 84 " --> pdb=" O VAL B 39 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N PHE B 41 " --> pdb=" O ARG B 84 " (cutoff:3.500A) removed outlier: 8.152A pdb=" N ILE B 86 " --> pdb=" O PHE B 41 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N MET B 43 " --> pdb=" O ILE B 86 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 331 through 338 removed outlier: 3.843A pdb=" N VAL A 334 " --> pdb=" O THR B 121 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N THR B 121 " --> pdb=" O VAL A 334 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N LYS A 336 " --> pdb=" O GLU B 119 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N GLU B 119 " --> pdb=" O LYS A 336 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N ASP B 79 " --> pdb=" O ALA B 126 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N VAL B 39 " --> pdb=" O GLU B 82 " (cutoff:3.500A) removed outlier: 7.739A pdb=" N ARG B 84 " --> pdb=" O VAL B 39 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N PHE B 41 " --> pdb=" O ARG B 84 " (cutoff:3.500A) removed outlier: 8.152A pdb=" N ILE B 86 " --> pdb=" O PHE B 41 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N MET B 43 " --> pdb=" O ILE B 86 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 73 through 76 removed outlier: 6.123A pdb=" N MET B 73 " --> pdb=" O MET B 155 " (cutoff:3.500A) removed outlier: 7.259A pdb=" N LEU B 157 " --> pdb=" O MET B 73 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N VAL B 75 " --> pdb=" O LEU B 157 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 217 through 220 removed outlier: 8.142A pdb=" N THR B 294 " --> pdb=" O GLY B 261 " (cutoff:3.500A) removed outlier: 8.639A pdb=" N GLY B 261 " --> pdb=" O THR B 294 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N ASP B 262 " --> pdb=" O ASP B 277 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ASP B 277 " --> pdb=" O ASP B 262 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 233 through 236 removed outlier: 3.823A pdb=" N ALA B 302 " --> pdb=" O ILE B 257 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 331 through 338 removed outlier: 3.779A pdb=" N VAL B 334 " --> pdb=" O THR C 121 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N THR C 121 " --> pdb=" O VAL B 334 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N LYS B 336 " --> pdb=" O GLU C 119 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N GLU C 119 " --> pdb=" O LYS B 336 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ASP C 79 " --> pdb=" O ALA C 126 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N VAL C 39 " --> pdb=" O GLU C 82 " (cutoff:3.500A) removed outlier: 7.739A pdb=" N ARG C 84 " --> pdb=" O VAL C 39 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N PHE C 41 " --> pdb=" O ARG C 84 " (cutoff:3.500A) removed outlier: 8.152A pdb=" N ILE C 86 " --> pdb=" O PHE C 41 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N MET C 43 " --> pdb=" O ILE C 86 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 331 through 338 removed outlier: 3.779A pdb=" N VAL B 334 " --> pdb=" O THR C 121 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N THR C 121 " --> pdb=" O VAL B 334 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N LYS B 336 " --> pdb=" O GLU C 119 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N GLU C 119 " --> pdb=" O LYS B 336 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ASP C 79 " --> pdb=" O ALA C 126 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N VAL C 39 " --> pdb=" O GLU C 82 " (cutoff:3.500A) removed outlier: 7.739A pdb=" N ARG C 84 " --> pdb=" O VAL C 39 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N PHE C 41 " --> pdb=" O ARG C 84 " (cutoff:3.500A) removed outlier: 8.152A pdb=" N ILE C 86 " --> pdb=" O PHE C 41 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N MET C 43 " --> pdb=" O ILE C 86 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 73 through 76 removed outlier: 6.122A pdb=" N MET C 73 " --> pdb=" O MET C 155 " (cutoff:3.500A) removed outlier: 7.259A pdb=" N LEU C 157 " --> pdb=" O MET C 73 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N VAL C 75 " --> pdb=" O LEU C 157 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 217 through 220 removed outlier: 8.142A pdb=" N THR C 294 " --> pdb=" O GLY C 261 " (cutoff:3.500A) removed outlier: 8.639A pdb=" N GLY C 261 " --> pdb=" O THR C 294 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N ASP C 262 " --> pdb=" O ASP C 277 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ASP C 277 " --> pdb=" O ASP C 262 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 233 through 236 removed outlier: 3.823A pdb=" N ALA C 302 " --> pdb=" O ILE C 257 " (cutoff:3.500A) 273 hydrogen bonds defined for protein. 705 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.29 Time building geometry restraints manager: 2.00 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: 2561 1.34 - 1.45: 1233 1.45 - 1.57: 4102 1.57 - 1.69: 0 1.69 - 1.80: 57 Bond restraints: 7953 Sorted by residual: bond pdb=" CB PRO B 23 " pdb=" CG PRO B 23 " ideal model delta sigma weight residual 1.506 1.455 0.051 3.90e-02 6.57e+02 1.73e+00 bond pdb=" CB PRO C 23 " pdb=" CG PRO C 23 " ideal model delta sigma weight residual 1.506 1.456 0.050 3.90e-02 6.57e+02 1.67e+00 bond pdb=" CB PRO A 23 " pdb=" CG PRO A 23 " ideal model delta sigma weight residual 1.506 1.456 0.050 3.90e-02 6.57e+02 1.66e+00 bond pdb=" CG PRO C 254 " pdb=" CD PRO C 254 " ideal model delta sigma weight residual 1.503 1.467 0.036 3.40e-02 8.65e+02 1.12e+00 bond pdb=" CG PRO A 254 " pdb=" CD PRO A 254 " ideal model delta sigma weight residual 1.503 1.468 0.035 3.40e-02 8.65e+02 1.09e+00 ... (remaining 7948 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.18: 10161 1.18 - 2.37: 557 2.37 - 3.55: 112 3.55 - 4.73: 12 4.73 - 5.91: 3 Bond angle restraints: 10845 Sorted by residual: angle pdb=" C ASN C 305 " pdb=" N HIS C 306 " pdb=" CA HIS C 306 " ideal model delta sigma weight residual 122.55 118.75 3.80 2.03e+00 2.43e-01 3.51e+00 angle pdb=" N ASN A 307 " pdb=" CA ASN A 307 " pdb=" C ASN A 307 " ideal model delta sigma weight residual 108.17 104.74 3.43 1.85e+00 2.92e-01 3.44e+00 angle pdb=" N ASN C 307 " pdb=" CA ASN C 307 " pdb=" C ASN C 307 " ideal model delta sigma weight residual 108.17 104.75 3.42 1.85e+00 2.92e-01 3.43e+00 angle pdb=" C ASN A 305 " pdb=" N HIS A 306 " pdb=" CA HIS A 306 " ideal model delta sigma weight residual 122.55 118.81 3.74 2.03e+00 2.43e-01 3.39e+00 angle pdb=" N ASN B 307 " pdb=" CA ASN B 307 " pdb=" C ASN B 307 " ideal model delta sigma weight residual 108.17 104.77 3.40 1.85e+00 2.92e-01 3.39e+00 ... (remaining 10840 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.02: 4144 17.02 - 34.05: 383 34.05 - 51.07: 84 51.07 - 68.10: 39 68.10 - 85.12: 6 Dihedral angle restraints: 4656 sinusoidal: 1812 harmonic: 2844 Sorted by residual: dihedral pdb=" CA HIS B 306 " pdb=" C HIS B 306 " pdb=" N ASN B 307 " pdb=" CA ASN B 307 " ideal model delta harmonic sigma weight residual 180.00 153.84 26.16 0 5.00e+00 4.00e-02 2.74e+01 dihedral pdb=" CA HIS C 306 " pdb=" C HIS C 306 " pdb=" N ASN C 307 " pdb=" CA ASN C 307 " ideal model delta harmonic sigma weight residual 180.00 153.86 26.14 0 5.00e+00 4.00e-02 2.73e+01 dihedral pdb=" CA HIS A 306 " pdb=" C HIS A 306 " pdb=" N ASN A 307 " pdb=" CA ASN A 307 " ideal model delta harmonic sigma weight residual 180.00 153.87 26.13 0 5.00e+00 4.00e-02 2.73e+01 ... (remaining 4653 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 684 0.034 - 0.067: 298 0.067 - 0.101: 166 0.101 - 0.134: 42 0.134 - 0.168: 7 Chirality restraints: 1197 Sorted by residual: chirality pdb=" CA HIS A 306 " pdb=" N HIS A 306 " pdb=" C HIS A 306 " pdb=" CB HIS A 306 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.02e-01 chirality pdb=" CA HIS B 306 " pdb=" N HIS B 306 " pdb=" C HIS B 306 " pdb=" CB HIS B 306 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 6.85e-01 chirality pdb=" CA HIS C 306 " pdb=" N HIS C 306 " pdb=" C HIS C 306 " pdb=" CB HIS C 306 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.48e-01 ... (remaining 1194 not shown) Planarity restraints: 1422 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS C 336 " 0.024 5.00e-02 4.00e+02 3.70e-02 2.19e+00 pdb=" N PRO C 337 " -0.064 5.00e-02 4.00e+02 pdb=" CA PRO C 337 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO C 337 " 0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS A 336 " 0.024 5.00e-02 4.00e+02 3.70e-02 2.19e+00 pdb=" N PRO A 337 " -0.064 5.00e-02 4.00e+02 pdb=" CA PRO A 337 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO A 337 " 0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS B 336 " -0.024 5.00e-02 4.00e+02 3.67e-02 2.15e+00 pdb=" N PRO B 337 " 0.063 5.00e-02 4.00e+02 pdb=" CA PRO B 337 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO B 337 " -0.020 5.00e-02 4.00e+02 ... (remaining 1419 not shown) Histogram of nonbonded interaction distances: 2.02 - 2.59: 122 2.59 - 3.17: 6302 3.17 - 3.75: 11208 3.75 - 4.32: 16624 4.32 - 4.90: 29170 Nonbonded interactions: 63426 Sorted by model distance: nonbonded pdb=" NE2 HIS B 100 " pdb="CU CU B 501 " model vdw 2.015 2.320 nonbonded pdb=" NE2 HIS A 100 " pdb="CU CU A 501 " model vdw 2.016 2.320 nonbonded pdb=" NE2 HIS C 100 " pdb="CU CU C 501 " model vdw 2.016 2.320 nonbonded pdb=" NE2 HIS C 306 " pdb="CU CU A 501 " model vdw 2.053 2.320 nonbonded pdb=" ND1 HIS A 145 " pdb="CU CU A 500 " model vdw 2.054 2.320 ... (remaining 63421 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: 0.05 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' } 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: 14.600 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: 0.310 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 22.320 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.860 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8797 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 : 0.007 0.061 7953 Z= 0.490 Angle : 0.634 5.914 10845 Z= 0.353 Chirality : 0.048 0.168 1197 Planarity : 0.005 0.037 1422 Dihedral : 15.036 85.119 2850 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 8.82 % Allowed : 15.44 % Favored : 75.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.46 (0.23), residues: 996 helix: -1.79 (0.48), residues: 78 sheet: -0.73 (0.29), residues: 288 loop : -2.16 (0.20), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 281 HIS 0.004 0.001 HIS A 306 PHE 0.011 0.002 PHE B 292 TYR 0.013 0.002 TYR B 134 ARG 0.002 0.000 ARG A 211 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1992 Ramachandran restraints generated. 996 Oldfield, 0 Emsley, 996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1992 Ramachandran restraints generated. 996 Oldfield, 0 Emsley, 996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 75 time to evaluate : 0.889 Fit side-chains REVERT: A 18 ASP cc_start: 0.7396 (OUTLIER) cc_final: 0.7141 (p0) REVERT: A 205 ASP cc_start: 0.7778 (OUTLIER) cc_final: 0.7429 (p0) REVERT: B 205 ASP cc_start: 0.7990 (OUTLIER) cc_final: 0.7465 (p0) REVERT: B 340 MET cc_start: 0.6484 (OUTLIER) cc_final: 0.6267 (mtt) REVERT: C 340 MET cc_start: 0.6163 (OUTLIER) cc_final: 0.5948 (mtt) outliers start: 72 outliers final: 27 residues processed: 140 average time/residue: 0.9734 time to fit residues: 146.3828 Evaluate side-chains 84 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 52 time to evaluate : 0.890 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 VAL Chi-restraints excluded: chain A residue 11 THR Chi-restraints excluded: chain A residue 18 ASP Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain A residue 160 ASP Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain A residue 205 ASP Chi-restraints excluded: chain A residue 294 THR Chi-restraints excluded: chain A residue 322 VAL Chi-restraints excluded: chain B residue 51 VAL Chi-restraints excluded: chain B residue 127 THR Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain B residue 160 ASP Chi-restraints excluded: chain B residue 198 THR Chi-restraints excluded: chain B residue 205 ASP Chi-restraints excluded: chain B residue 267 THR Chi-restraints excluded: chain B residue 322 VAL Chi-restraints excluded: chain B residue 340 MET Chi-restraints excluded: chain C residue 11 THR Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain C residue 127 THR Chi-restraints excluded: chain C residue 131 VAL Chi-restraints excluded: chain C residue 160 ASP Chi-restraints excluded: chain C residue 198 THR Chi-restraints excluded: chain C residue 205 ASP Chi-restraints excluded: chain C residue 267 THR Chi-restraints excluded: chain C residue 294 THR Chi-restraints excluded: chain C residue 340 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 83 optimal weight: 0.7980 chunk 75 optimal weight: 0.8980 chunk 41 optimal weight: 0.7980 chunk 25 optimal weight: 2.9990 chunk 50 optimal weight: 0.7980 chunk 40 optimal weight: 0.9990 chunk 77 optimal weight: 0.8980 chunk 30 optimal weight: 0.5980 chunk 47 optimal weight: 0.1980 chunk 57 optimal weight: 0.9980 chunk 89 optimal weight: 0.7980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 HIS B 76 HIS B 221 ASN C 76 HIS C 221 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.097890 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2902 r_free = 0.2902 target = 0.078290 restraints weight = 11756.154| |-----------------------------------------------------------------------------| r_work (start): 0.2900 rms_B_bonded: 2.27 r_work: 0.2780 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2648 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.2648 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8970 moved from start: 0.1007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 7953 Z= 0.235 Angle : 0.554 5.689 10845 Z= 0.300 Chirality : 0.047 0.138 1197 Planarity : 0.004 0.035 1422 Dihedral : 6.615 59.567 1117 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 5.02 % Allowed : 18.75 % Favored : 76.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.56 (0.24), residues: 996 helix: -2.02 (0.40), residues: 90 sheet: -0.05 (0.29), residues: 282 loop : -1.40 (0.23), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP C 281 HIS 0.004 0.001 HIS A 306 PHE 0.009 0.001 PHE C 124 TYR 0.009 0.001 TYR B 134 ARG 0.002 0.000 ARG B 159 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1992 Ramachandran restraints generated. 996 Oldfield, 0 Emsley, 996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1992 Ramachandran restraints generated. 996 Oldfield, 0 Emsley, 996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 58 time to evaluate : 0.865 Fit side-chains REVERT: A 18 ASP cc_start: 0.7976 (OUTLIER) cc_final: 0.7622 (p0) REVERT: B 340 MET cc_start: 0.7080 (mtt) cc_final: 0.6555 (mtt) REVERT: C 340 MET cc_start: 0.6752 (mtt) cc_final: 0.6233 (mtt) outliers start: 41 outliers final: 14 residues processed: 90 average time/residue: 1.1118 time to fit residues: 107.1235 Evaluate side-chains 66 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 51 time to evaluate : 0.974 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 ASP Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 94 LEU Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain A residue 294 THR Chi-restraints excluded: chain A residue 322 VAL Chi-restraints excluded: chain B residue 51 VAL Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain B residue 198 THR Chi-restraints excluded: chain B residue 322 VAL Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 131 VAL Chi-restraints excluded: chain C residue 198 THR Chi-restraints excluded: chain C residue 294 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 0 optimal weight: 5.9990 chunk 12 optimal weight: 1.9990 chunk 84 optimal weight: 3.9990 chunk 54 optimal weight: 1.9990 chunk 32 optimal weight: 4.9990 chunk 59 optimal weight: 0.2980 chunk 40 optimal weight: 2.9990 chunk 22 optimal weight: 3.9990 chunk 79 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 85 optimal weight: 2.9990 overall best weight: 1.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 297 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.096152 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2874 r_free = 0.2874 target = 0.076577 restraints weight = 11899.521| |-----------------------------------------------------------------------------| r_work (start): 0.2873 rms_B_bonded: 2.26 r_work: 0.2753 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2621 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.2621 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9011 moved from start: 0.1180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.066 7953 Z= 0.486 Angle : 0.617 5.983 10845 Z= 0.333 Chirality : 0.049 0.162 1197 Planarity : 0.005 0.037 1422 Dihedral : 6.656 53.417 1089 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 5.76 % Allowed : 18.75 % Favored : 75.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.36 (0.25), residues: 996 helix: -1.56 (0.45), residues: 90 sheet: -0.15 (0.27), residues: 312 loop : -1.23 (0.24), residues: 594 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 281 HIS 0.004 0.001 HIS B 26 PHE 0.010 0.002 PHE C 124 TYR 0.015 0.002 TYR B 134 ARG 0.002 0.000 ARG A 159 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1992 Ramachandran restraints generated. 996 Oldfield, 0 Emsley, 996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1992 Ramachandran restraints generated. 996 Oldfield, 0 Emsley, 996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 52 time to evaluate : 0.905 Fit side-chains REVERT: A 18 ASP cc_start: 0.8017 (OUTLIER) cc_final: 0.7684 (p0) REVERT: B 29 ASP cc_start: 0.8623 (OUTLIER) cc_final: 0.8416 (t0) REVERT: B 340 MET cc_start: 0.7172 (mtt) cc_final: 0.6707 (mtt) REVERT: C 340 MET cc_start: 0.6993 (mtt) cc_final: 0.6433 (mtt) outliers start: 47 outliers final: 27 residues processed: 88 average time/residue: 1.0146 time to fit residues: 96.3738 Evaluate side-chains 77 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 48 time to evaluate : 0.860 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 ASP Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 94 LEU Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 155 MET Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain A residue 294 THR Chi-restraints excluded: chain A residue 322 VAL Chi-restraints excluded: chain B residue 18 ASP Chi-restraints excluded: chain B residue 29 ASP Chi-restraints excluded: chain B residue 51 VAL Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 127 THR Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain B residue 198 THR Chi-restraints excluded: chain B residue 294 THR Chi-restraints excluded: chain B residue 322 VAL Chi-restraints excluded: chain C residue 18 ASP Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 122 LEU Chi-restraints excluded: chain C residue 127 THR Chi-restraints excluded: chain C residue 131 VAL Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 198 THR Chi-restraints excluded: chain C residue 294 THR Chi-restraints excluded: chain C residue 322 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 45 optimal weight: 0.5980 chunk 1 optimal weight: 0.0370 chunk 67 optimal weight: 2.9990 chunk 73 optimal weight: 2.9990 chunk 21 optimal weight: 1.9990 chunk 74 optimal weight: 0.8980 chunk 49 optimal weight: 3.9990 chunk 10 optimal weight: 0.5980 chunk 71 optimal weight: 0.9990 chunk 18 optimal weight: 0.5980 chunk 69 optimal weight: 2.9990 overall best weight: 0.5458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.098925 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2916 r_free = 0.2916 target = 0.079211 restraints weight = 11540.934| |-----------------------------------------------------------------------------| r_work (start): 0.2922 rms_B_bonded: 2.28 r_work: 0.2803 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2669 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.2669 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8951 moved from start: 0.1441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 7953 Z= 0.199 Angle : 0.515 5.581 10845 Z= 0.277 Chirality : 0.046 0.130 1197 Planarity : 0.004 0.037 1422 Dihedral : 6.279 51.582 1089 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 6.25 % Allowed : 18.26 % Favored : 75.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.09 (0.25), residues: 996 helix: -1.51 (0.43), residues: 93 sheet: 0.48 (0.30), residues: 255 loop : -1.15 (0.24), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP B 281 HIS 0.003 0.000 HIS A 306 PHE 0.009 0.001 PHE B 124 TYR 0.008 0.001 TYR C 184 ARG 0.002 0.000 ARG A 123 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1992 Ramachandran restraints generated. 996 Oldfield, 0 Emsley, 996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1992 Ramachandran restraints generated. 996 Oldfield, 0 Emsley, 996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 57 time to evaluate : 1.360 Fit side-chains REVERT: A 18 ASP cc_start: 0.7975 (OUTLIER) cc_final: 0.7619 (p0) REVERT: A 253 ARG cc_start: 0.9002 (OUTLIER) cc_final: 0.8717 (ptp90) REVERT: B 18 ASP cc_start: 0.8003 (OUTLIER) cc_final: 0.7668 (p0) REVERT: B 29 ASP cc_start: 0.8547 (OUTLIER) cc_final: 0.8343 (t0) REVERT: B 253 ARG cc_start: 0.8931 (OUTLIER) cc_final: 0.8626 (ptp90) REVERT: B 340 MET cc_start: 0.7012 (mtt) cc_final: 0.6568 (mtt) REVERT: C 340 MET cc_start: 0.6915 (mtt) cc_final: 0.6380 (mtt) outliers start: 51 outliers final: 26 residues processed: 97 average time/residue: 1.0323 time to fit residues: 107.9062 Evaluate side-chains 86 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 55 time to evaluate : 0.875 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 ASP Chi-restraints excluded: chain A residue 29 ASP Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 94 LEU Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain A residue 253 ARG Chi-restraints excluded: chain A residue 294 THR Chi-restraints excluded: chain A residue 322 VAL Chi-restraints excluded: chain A residue 340 MET Chi-restraints excluded: chain B residue 18 ASP Chi-restraints excluded: chain B residue 29 ASP Chi-restraints excluded: chain B residue 51 VAL Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain B residue 198 THR Chi-restraints excluded: chain B residue 253 ARG Chi-restraints excluded: chain B residue 322 VAL Chi-restraints excluded: chain C residue 18 ASP Chi-restraints excluded: chain C residue 29 ASP Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 122 LEU Chi-restraints excluded: chain C residue 127 THR Chi-restraints excluded: chain C residue 131 VAL Chi-restraints excluded: chain C residue 198 THR Chi-restraints excluded: chain C residue 294 THR Chi-restraints excluded: chain C residue 322 VAL Chi-restraints excluded: chain C residue 328 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 30 optimal weight: 1.9990 chunk 88 optimal weight: 2.9990 chunk 71 optimal weight: 2.9990 chunk 69 optimal weight: 1.9990 chunk 78 optimal weight: 1.9990 chunk 38 optimal weight: 4.9990 chunk 15 optimal weight: 2.9990 chunk 4 optimal weight: 2.9990 chunk 90 optimal weight: 2.9990 chunk 63 optimal weight: 0.9990 chunk 75 optimal weight: 0.9990 overall best weight: 1.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.096246 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2860 r_free = 0.2860 target = 0.076285 restraints weight = 11810.211| |-----------------------------------------------------------------------------| r_work (start): 0.2861 rms_B_bonded: 2.32 r_work: 0.2735 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2598 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.2598 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8977 moved from start: 0.1399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.068 7953 Z= 0.475 Angle : 0.606 5.966 10845 Z= 0.328 Chirality : 0.049 0.162 1197 Planarity : 0.005 0.037 1422 Dihedral : 6.735 51.210 1089 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 5.39 % Allowed : 19.00 % Favored : 75.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.18 (0.25), residues: 996 helix: -1.80 (0.42), residues: 90 sheet: -0.03 (0.27), residues: 303 loop : -1.02 (0.25), residues: 603 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 281 HIS 0.004 0.001 HIS B 26 PHE 0.011 0.002 PHE C 292 TYR 0.015 0.002 TYR B 134 ARG 0.002 0.000 ARG B 159 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1992 Ramachandran restraints generated. 996 Oldfield, 0 Emsley, 996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1992 Ramachandran restraints generated. 996 Oldfield, 0 Emsley, 996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 50 time to evaluate : 0.739 Fit side-chains REVERT: A 18 ASP cc_start: 0.7949 (OUTLIER) cc_final: 0.7642 (p0) REVERT: B 18 ASP cc_start: 0.8037 (OUTLIER) cc_final: 0.7689 (p0) REVERT: B 29 ASP cc_start: 0.8541 (OUTLIER) cc_final: 0.8330 (t0) REVERT: B 253 ARG cc_start: 0.8966 (OUTLIER) cc_final: 0.8746 (ptp90) REVERT: B 340 MET cc_start: 0.7191 (mtt) cc_final: 0.6649 (mtt) REVERT: C 180 GLU cc_start: 0.8719 (OUTLIER) cc_final: 0.8442 (tp30) REVERT: C 340 MET cc_start: 0.7196 (mtt) cc_final: 0.6764 (mtt) outliers start: 44 outliers final: 30 residues processed: 86 average time/residue: 1.0289 time to fit residues: 95.1921 Evaluate side-chains 85 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 50 time to evaluate : 0.985 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 ASP Chi-restraints excluded: chain A residue 29 ASP Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 94 LEU Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain A residue 294 THR Chi-restraints excluded: chain A residue 322 VAL Chi-restraints excluded: chain A residue 340 MET Chi-restraints excluded: chain B residue 18 ASP Chi-restraints excluded: chain B residue 29 ASP Chi-restraints excluded: chain B residue 51 VAL Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 127 THR Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain B residue 175 ILE Chi-restraints excluded: chain B residue 198 THR Chi-restraints excluded: chain B residue 253 ARG Chi-restraints excluded: chain B residue 294 THR Chi-restraints excluded: chain B residue 322 VAL Chi-restraints excluded: chain C residue 18 ASP Chi-restraints excluded: chain C residue 29 ASP Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 122 LEU Chi-restraints excluded: chain C residue 127 THR Chi-restraints excluded: chain C residue 131 VAL Chi-restraints excluded: chain C residue 180 GLU Chi-restraints excluded: chain C residue 198 THR Chi-restraints excluded: chain C residue 267 THR Chi-restraints excluded: chain C residue 294 THR Chi-restraints excluded: chain C residue 322 VAL Chi-restraints excluded: chain C residue 328 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 92 optimal weight: 0.9990 chunk 61 optimal weight: 0.5980 chunk 41 optimal weight: 0.7980 chunk 96 optimal weight: 0.8980 chunk 76 optimal weight: 0.7980 chunk 6 optimal weight: 0.7980 chunk 64 optimal weight: 0.7980 chunk 30 optimal weight: 0.8980 chunk 38 optimal weight: 1.9990 chunk 86 optimal weight: 0.0970 chunk 26 optimal weight: 0.0970 overall best weight: 0.4776 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.099343 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2921 r_free = 0.2921 target = 0.079535 restraints weight = 11467.540| |-----------------------------------------------------------------------------| r_work (start): 0.2924 rms_B_bonded: 2.27 r_work: 0.2804 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2669 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.2669 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8949 moved from start: 0.1597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7953 Z= 0.196 Angle : 0.510 5.624 10845 Z= 0.276 Chirality : 0.045 0.129 1197 Planarity : 0.004 0.038 1422 Dihedral : 6.380 50.146 1089 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 5.64 % Allowed : 18.14 % Favored : 76.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.92 (0.25), residues: 996 helix: -1.93 (0.41), residues: 93 sheet: 0.73 (0.30), residues: 255 loop : -1.00 (0.24), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP B 281 HIS 0.003 0.000 HIS B 306 PHE 0.009 0.001 PHE C 124 TYR 0.009 0.001 TYR C 184 ARG 0.001 0.000 ARG B 159 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1992 Ramachandran restraints generated. 996 Oldfield, 0 Emsley, 996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1992 Ramachandran restraints generated. 996 Oldfield, 0 Emsley, 996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 61 time to evaluate : 0.882 Fit side-chains REVERT: A 18 ASP cc_start: 0.7887 (OUTLIER) cc_final: 0.7554 (p0) REVERT: A 253 ARG cc_start: 0.8997 (OUTLIER) cc_final: 0.8745 (ptp90) REVERT: A 331 MET cc_start: 0.8814 (OUTLIER) cc_final: 0.8569 (ttp) REVERT: B 18 ASP cc_start: 0.8014 (OUTLIER) cc_final: 0.7677 (p0) REVERT: B 253 ARG cc_start: 0.8937 (OUTLIER) cc_final: 0.8651 (ptp90) REVERT: B 340 MET cc_start: 0.6954 (mtt) cc_final: 0.6493 (mtt) REVERT: C 180 GLU cc_start: 0.8652 (OUTLIER) cc_final: 0.8309 (tp30) REVERT: C 340 MET cc_start: 0.7140 (mtt) cc_final: 0.6629 (mtt) outliers start: 46 outliers final: 28 residues processed: 99 average time/residue: 1.0071 time to fit residues: 107.3887 Evaluate side-chains 87 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 53 time to evaluate : 0.914 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 ASP Chi-restraints excluded: chain A residue 29 ASP Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 94 LEU Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain A residue 253 ARG Chi-restraints excluded: chain A residue 294 THR Chi-restraints excluded: chain A residue 322 VAL Chi-restraints excluded: chain A residue 331 MET Chi-restraints excluded: chain B residue 18 ASP Chi-restraints excluded: chain B residue 51 VAL Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 127 THR Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain B residue 175 ILE Chi-restraints excluded: chain B residue 198 THR Chi-restraints excluded: chain B residue 253 ARG Chi-restraints excluded: chain B residue 267 THR Chi-restraints excluded: chain B residue 322 VAL Chi-restraints excluded: chain C residue 18 ASP Chi-restraints excluded: chain C residue 29 ASP Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 122 LEU Chi-restraints excluded: chain C residue 127 THR Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 180 GLU Chi-restraints excluded: chain C residue 198 THR Chi-restraints excluded: chain C residue 294 THR Chi-restraints excluded: chain C residue 322 VAL Chi-restraints excluded: chain C residue 328 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 21 optimal weight: 1.9990 chunk 96 optimal weight: 0.8980 chunk 44 optimal weight: 2.9990 chunk 81 optimal weight: 0.0060 chunk 25 optimal weight: 2.9990 chunk 23 optimal weight: 2.9990 chunk 18 optimal weight: 2.9990 chunk 2 optimal weight: 6.9990 chunk 11 optimal weight: 0.9990 chunk 42 optimal weight: 1.9990 chunk 29 optimal weight: 0.9980 overall best weight: 0.9800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.098845 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2904 r_free = 0.2904 target = 0.078669 restraints weight = 11690.748| |-----------------------------------------------------------------------------| r_work (start): 0.2908 rms_B_bonded: 2.30 r_work: 0.2786 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2651 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.2651 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8973 moved from start: 0.1592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 7953 Z= 0.311 Angle : 0.555 5.765 10845 Z= 0.299 Chirality : 0.047 0.144 1197 Planarity : 0.004 0.038 1422 Dihedral : 6.415 51.926 1088 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 5.15 % Allowed : 18.14 % Favored : 76.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.96 (0.25), residues: 996 helix: -1.85 (0.42), residues: 93 sheet: 0.15 (0.28), residues: 303 loop : -0.84 (0.25), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 281 HIS 0.003 0.001 HIS A 306 PHE 0.010 0.002 PHE C 124 TYR 0.011 0.001 TYR B 134 ARG 0.001 0.000 ARG B 159 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1992 Ramachandran restraints generated. 996 Oldfield, 0 Emsley, 996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1992 Ramachandran restraints generated. 996 Oldfield, 0 Emsley, 996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 54 time to evaluate : 0.952 Fit side-chains REVERT: A 18 ASP cc_start: 0.7948 (OUTLIER) cc_final: 0.7623 (p0) REVERT: A 331 MET cc_start: 0.8845 (OUTLIER) cc_final: 0.8488 (ttp) REVERT: A 340 MET cc_start: 0.6778 (mtt) cc_final: 0.6310 (mpt) REVERT: B 18 ASP cc_start: 0.8002 (OUTLIER) cc_final: 0.7701 (p0) REVERT: B 159 ARG cc_start: 0.8615 (OUTLIER) cc_final: 0.8329 (mmt180) REVERT: B 253 ARG cc_start: 0.8949 (OUTLIER) cc_final: 0.8686 (ptp90) REVERT: B 340 MET cc_start: 0.7020 (mtt) cc_final: 0.6534 (mtt) REVERT: C 180 GLU cc_start: 0.8693 (OUTLIER) cc_final: 0.8418 (tp30) REVERT: C 340 MET cc_start: 0.7151 (mtt) cc_final: 0.6647 (mtt) outliers start: 42 outliers final: 30 residues processed: 89 average time/residue: 1.1984 time to fit residues: 113.6649 Evaluate side-chains 88 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 52 time to evaluate : 0.936 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 ASP Chi-restraints excluded: chain A residue 29 ASP Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 94 LEU Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain A residue 294 THR Chi-restraints excluded: chain A residue 322 VAL Chi-restraints excluded: chain A residue 331 MET Chi-restraints excluded: chain B residue 18 ASP Chi-restraints excluded: chain B residue 51 VAL Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 127 THR Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain B residue 159 ARG Chi-restraints excluded: chain B residue 175 ILE Chi-restraints excluded: chain B residue 198 THR Chi-restraints excluded: chain B residue 253 ARG Chi-restraints excluded: chain B residue 267 THR Chi-restraints excluded: chain B residue 294 THR Chi-restraints excluded: chain B residue 322 VAL Chi-restraints excluded: chain C residue 18 ASP Chi-restraints excluded: chain C residue 29 ASP Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 122 LEU Chi-restraints excluded: chain C residue 127 THR Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 180 GLU Chi-restraints excluded: chain C residue 198 THR Chi-restraints excluded: chain C residue 267 THR Chi-restraints excluded: chain C residue 294 THR Chi-restraints excluded: chain C residue 322 VAL Chi-restraints excluded: chain C residue 328 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 40 optimal weight: 1.9990 chunk 43 optimal weight: 0.9980 chunk 48 optimal weight: 0.7980 chunk 69 optimal weight: 1.9990 chunk 25 optimal weight: 2.9990 chunk 75 optimal weight: 0.7980 chunk 21 optimal weight: 1.9990 chunk 11 optimal weight: 0.9990 chunk 1 optimal weight: 0.2980 chunk 54 optimal weight: 1.9990 chunk 24 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.099718 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2919 r_free = 0.2919 target = 0.079617 restraints weight = 11584.406| |-----------------------------------------------------------------------------| r_work (start): 0.2918 rms_B_bonded: 2.30 r_work: 0.2796 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.2661 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.2661 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8961 moved from start: 0.1676 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 7953 Z= 0.256 Angle : 0.540 5.681 10845 Z= 0.291 Chirality : 0.046 0.135 1197 Planarity : 0.004 0.038 1422 Dihedral : 6.326 52.756 1088 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 5.51 % Allowed : 17.40 % Favored : 77.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.83 (0.26), residues: 996 helix: -1.82 (0.42), residues: 93 sheet: 0.64 (0.30), residues: 261 loop : -0.89 (0.25), residues: 642 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 281 HIS 0.003 0.001 HIS A 306 PHE 0.010 0.001 PHE C 124 TYR 0.010 0.001 TYR C 184 ARG 0.002 0.000 ARG C 159 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1992 Ramachandran restraints generated. 996 Oldfield, 0 Emsley, 996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1992 Ramachandran restraints generated. 996 Oldfield, 0 Emsley, 996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 57 time to evaluate : 0.854 Fit side-chains revert: symmetry clash REVERT: A 18 ASP cc_start: 0.7935 (OUTLIER) cc_final: 0.7612 (p0) REVERT: A 253 ARG cc_start: 0.9020 (OUTLIER) cc_final: 0.8797 (ptp90) REVERT: A 331 MET cc_start: 0.8805 (OUTLIER) cc_final: 0.8492 (ttp) REVERT: B 18 ASP cc_start: 0.7969 (OUTLIER) cc_final: 0.7665 (p0) REVERT: B 159 ARG cc_start: 0.8609 (OUTLIER) cc_final: 0.8330 (mmt180) REVERT: B 253 ARG cc_start: 0.8920 (OUTLIER) cc_final: 0.8648 (ptp90) REVERT: B 340 MET cc_start: 0.6994 (mtt) cc_final: 0.6515 (mtt) REVERT: C 340 MET cc_start: 0.7157 (mtt) cc_final: 0.6643 (mtt) outliers start: 45 outliers final: 33 residues processed: 92 average time/residue: 1.1964 time to fit residues: 117.0678 Evaluate side-chains 92 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 53 time to evaluate : 0.803 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 ASP Chi-restraints excluded: chain A residue 29 ASP Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 94 LEU Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain A residue 253 ARG Chi-restraints excluded: chain A residue 294 THR Chi-restraints excluded: chain A residue 322 VAL Chi-restraints excluded: chain A residue 331 MET Chi-restraints excluded: chain B residue 18 ASP Chi-restraints excluded: chain B residue 51 VAL Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 127 THR Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain B residue 159 ARG Chi-restraints excluded: chain B residue 175 ILE Chi-restraints excluded: chain B residue 198 THR Chi-restraints excluded: chain B residue 253 ARG Chi-restraints excluded: chain B residue 267 THR Chi-restraints excluded: chain B residue 294 THR Chi-restraints excluded: chain B residue 322 VAL Chi-restraints excluded: chain C residue 18 ASP Chi-restraints excluded: chain C residue 29 ASP Chi-restraints excluded: chain C residue 34 THR Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 98 ASP Chi-restraints excluded: chain C residue 122 LEU Chi-restraints excluded: chain C residue 127 THR Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 180 GLU Chi-restraints excluded: chain C residue 198 THR Chi-restraints excluded: chain C residue 267 THR Chi-restraints excluded: chain C residue 294 THR Chi-restraints excluded: chain C residue 322 VAL Chi-restraints excluded: chain C residue 328 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 45 optimal weight: 0.8980 chunk 81 optimal weight: 0.6980 chunk 50 optimal weight: 0.8980 chunk 75 optimal weight: 1.9990 chunk 62 optimal weight: 0.5980 chunk 17 optimal weight: 1.9990 chunk 87 optimal weight: 0.9990 chunk 33 optimal weight: 0.1980 chunk 37 optimal weight: 1.9990 chunk 15 optimal weight: 2.9990 chunk 85 optimal weight: 0.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.100271 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2929 r_free = 0.2929 target = 0.080222 restraints weight = 11707.014| |-----------------------------------------------------------------------------| r_work (start): 0.2929 rms_B_bonded: 2.31 r_work: 0.2808 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.2672 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.2672 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8956 moved from start: 0.1729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 7953 Z= 0.235 Angle : 0.530 5.654 10845 Z= 0.286 Chirality : 0.046 0.133 1197 Planarity : 0.004 0.038 1422 Dihedral : 6.281 53.017 1088 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 5.02 % Allowed : 17.77 % Favored : 77.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.78 (0.26), residues: 996 helix: -1.79 (0.42), residues: 93 sheet: 0.66 (0.30), residues: 261 loop : -0.85 (0.25), residues: 642 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 281 HIS 0.003 0.001 HIS B 306 PHE 0.010 0.001 PHE C 124 TYR 0.009 0.001 TYR C 184 ARG 0.003 0.000 ARG A 159 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1992 Ramachandran restraints generated. 996 Oldfield, 0 Emsley, 996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1992 Ramachandran restraints generated. 996 Oldfield, 0 Emsley, 996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 56 time to evaluate : 0.900 Fit side-chains revert: symmetry clash REVERT: A 18 ASP cc_start: 0.7919 (OUTLIER) cc_final: 0.7600 (p0) REVERT: A 253 ARG cc_start: 0.9027 (OUTLIER) cc_final: 0.8811 (ptp90) REVERT: A 331 MET cc_start: 0.8787 (OUTLIER) cc_final: 0.8533 (ttp) REVERT: A 340 MET cc_start: 0.6705 (mtt) cc_final: 0.6242 (mpt) REVERT: B 18 ASP cc_start: 0.7946 (OUTLIER) cc_final: 0.7646 (p0) REVERT: B 159 ARG cc_start: 0.8597 (OUTLIER) cc_final: 0.8320 (mmt180) REVERT: B 253 ARG cc_start: 0.8922 (OUTLIER) cc_final: 0.8647 (ptp90) REVERT: B 331 MET cc_start: 0.8717 (OUTLIER) cc_final: 0.8515 (ttp) REVERT: B 340 MET cc_start: 0.7039 (mtt) cc_final: 0.6578 (mtt) REVERT: C 340 MET cc_start: 0.7165 (mtt) cc_final: 0.6641 (mtt) outliers start: 41 outliers final: 32 residues processed: 89 average time/residue: 1.1888 time to fit residues: 112.6445 Evaluate side-chains 93 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 54 time to evaluate : 0.809 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 ASP Chi-restraints excluded: chain A residue 29 ASP Chi-restraints excluded: chain A residue 34 THR Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 94 LEU Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain A residue 253 ARG Chi-restraints excluded: chain A residue 294 THR Chi-restraints excluded: chain A residue 322 VAL Chi-restraints excluded: chain A residue 331 MET Chi-restraints excluded: chain B residue 18 ASP Chi-restraints excluded: chain B residue 51 VAL Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 127 THR Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain B residue 159 ARG Chi-restraints excluded: chain B residue 175 ILE Chi-restraints excluded: chain B residue 198 THR Chi-restraints excluded: chain B residue 253 ARG Chi-restraints excluded: chain B residue 267 THR Chi-restraints excluded: chain B residue 322 VAL Chi-restraints excluded: chain B residue 331 MET Chi-restraints excluded: chain C residue 18 ASP Chi-restraints excluded: chain C residue 29 ASP Chi-restraints excluded: chain C residue 34 THR Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 122 LEU Chi-restraints excluded: chain C residue 127 THR Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 180 GLU Chi-restraints excluded: chain C residue 198 THR Chi-restraints excluded: chain C residue 267 THR Chi-restraints excluded: chain C residue 294 THR Chi-restraints excluded: chain C residue 322 VAL Chi-restraints excluded: chain C residue 328 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 25 optimal weight: 2.9990 chunk 31 optimal weight: 0.6980 chunk 1 optimal weight: 0.0050 chunk 85 optimal weight: 1.9990 chunk 13 optimal weight: 0.9980 chunk 55 optimal weight: 3.9990 chunk 18 optimal weight: 0.6980 chunk 43 optimal weight: 0.8980 chunk 77 optimal weight: 2.9990 chunk 80 optimal weight: 1.9990 chunk 29 optimal weight: 0.6980 overall best weight: 0.5994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.100703 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2935 r_free = 0.2935 target = 0.080672 restraints weight = 11721.422| |-----------------------------------------------------------------------------| r_work (start): 0.2940 rms_B_bonded: 2.30 r_work: 0.2818 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2682 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.2682 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8948 moved from start: 0.1791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 7953 Z= 0.220 Angle : 0.525 5.630 10845 Z= 0.282 Chirality : 0.045 0.131 1197 Planarity : 0.004 0.038 1422 Dihedral : 6.209 53.406 1088 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 4.90 % Allowed : 18.01 % Favored : 77.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.73 (0.26), residues: 996 helix: -1.76 (0.43), residues: 93 sheet: 0.68 (0.30), residues: 261 loop : -0.79 (0.25), residues: 642 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 281 HIS 0.003 0.001 HIS A 306 PHE 0.010 0.001 PHE C 124 TYR 0.009 0.001 TYR C 184 ARG 0.002 0.000 ARG A 159 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1992 Ramachandran restraints generated. 996 Oldfield, 0 Emsley, 996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1992 Ramachandran restraints generated. 996 Oldfield, 0 Emsley, 996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 57 time to evaluate : 0.931 Fit side-chains REVERT: A 18 ASP cc_start: 0.7871 (OUTLIER) cc_final: 0.7576 (p0) REVERT: A 253 ARG cc_start: 0.9039 (OUTLIER) cc_final: 0.8810 (ptp90) REVERT: A 331 MET cc_start: 0.8751 (OUTLIER) cc_final: 0.8517 (ttp) REVERT: A 340 MET cc_start: 0.6695 (mtt) cc_final: 0.6246 (mpt) REVERT: B 18 ASP cc_start: 0.7927 (OUTLIER) cc_final: 0.7588 (p0) REVERT: B 159 ARG cc_start: 0.8593 (OUTLIER) cc_final: 0.8330 (mmt180) REVERT: B 253 ARG cc_start: 0.8907 (OUTLIER) cc_final: 0.8622 (ptp90) REVERT: B 340 MET cc_start: 0.6986 (mtt) cc_final: 0.6446 (mtt) REVERT: C 340 MET cc_start: 0.7109 (mtt) cc_final: 0.6598 (mtt) outliers start: 40 outliers final: 29 residues processed: 90 average time/residue: 1.1900 time to fit residues: 114.3676 Evaluate side-chains 90 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 55 time to evaluate : 0.829 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 ASP Chi-restraints excluded: chain A residue 29 ASP Chi-restraints excluded: chain A residue 34 THR Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 94 LEU Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain A residue 253 ARG Chi-restraints excluded: chain A residue 294 THR Chi-restraints excluded: chain A residue 322 VAL Chi-restraints excluded: chain A residue 331 MET Chi-restraints excluded: chain B residue 18 ASP Chi-restraints excluded: chain B residue 34 THR Chi-restraints excluded: chain B residue 51 VAL Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 127 THR Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain B residue 159 ARG Chi-restraints excluded: chain B residue 175 ILE Chi-restraints excluded: chain B residue 198 THR Chi-restraints excluded: chain B residue 253 ARG Chi-restraints excluded: chain B residue 267 THR Chi-restraints excluded: chain B residue 322 VAL Chi-restraints excluded: chain C residue 29 ASP Chi-restraints excluded: chain C residue 34 THR Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 122 LEU Chi-restraints excluded: chain C residue 127 THR Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 198 THR Chi-restraints excluded: chain C residue 294 THR Chi-restraints excluded: chain C residue 322 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 12 optimal weight: 0.7980 chunk 30 optimal weight: 0.9990 chunk 66 optimal weight: 0.0870 chunk 76 optimal weight: 0.7980 chunk 63 optimal weight: 0.9990 chunk 40 optimal weight: 2.9990 chunk 6 optimal weight: 0.6980 chunk 50 optimal weight: 1.9990 chunk 54 optimal weight: 0.9980 chunk 25 optimal weight: 2.9990 chunk 79 optimal weight: 0.9980 overall best weight: 0.6758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.100429 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2931 r_free = 0.2931 target = 0.080406 restraints weight = 11600.241| |-----------------------------------------------------------------------------| r_work (start): 0.2936 rms_B_bonded: 2.29 r_work: 0.2817 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2682 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.2682 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8948 moved from start: 0.1809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 7953 Z= 0.238 Angle : 0.529 5.654 10845 Z= 0.285 Chirality : 0.046 0.134 1197 Planarity : 0.004 0.038 1422 Dihedral : 6.227 53.739 1088 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 4.53 % Allowed : 17.89 % Favored : 77.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.83 (0.26), residues: 996 helix: -1.73 (0.43), residues: 93 sheet: 0.36 (0.29), residues: 285 loop : -0.80 (0.25), residues: 618 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 281 HIS 0.003 0.001 HIS A 306 PHE 0.009 0.001 PHE C 124 TYR 0.009 0.001 TYR C 184 ARG 0.002 0.000 ARG A 159 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4946.86 seconds wall clock time: 88 minutes 17.68 seconds (5297.68 seconds total)