Starting phenix.real_space_refine on Wed Mar 12 11:11:09 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6knf_0730/03_2025/6knf_0730.cif Found real_map, /net/cci-nas-00/data/ceres_data/6knf_0730/03_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_0730/03_2025/6knf_0730.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6knf_0730/03_2025/6knf_0730.map" model { file = "/net/cci-nas-00/data/ceres_data/6knf_0730/03_2025/6knf_0730.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6knf_0730/03_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-5624/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: 6.65, per 1000 atoms: 0.86 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: 1.72 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: 0.93 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: 2.32 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: 284.940 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: 0.280 Check model and map are aligned: 0.050 Set scattering table: 0.080 Process input model: 22.600 Find NCS groups from input model: 0.140 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:13.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 321.450 ------------------------------------------------------------------------------- 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 : 0.864 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: 0.9365 time to fit residues: 141.2200 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 : 0.880 ------------------------------------------------------------------------------- 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: 0.6980 chunk 89 optimal weight: 0.7980 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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 = 0.3207 r_free = 0.3207 target = 0.097968 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2909 r_free = 0.2909 target = 0.078632 restraints weight = 11749.696| |-----------------------------------------------------------------------------| r_work (start): 0.2909 rms_B_bonded: 2.26 r_work: 0.2791 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2660 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.2660 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8965 moved from start: 0.1082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 7953 Z= 0.222 Angle : 0.553 5.687 10845 Z= 0.298 Chirality : 0.047 0.137 1197 Planarity : 0.004 0.036 1422 Dihedral : 6.519 59.133 1117 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % 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: -1.64 (0.24), residues: 996 helix: -2.04 (0.39), residues: 93 sheet: -0.23 (0.29), residues: 273 loop : -1.37 (0.23), residues: 630 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 A 250 *********************** 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 105 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 59 time to evaluate : 0.892 Fit side-chains REVERT: A 18 ASP cc_start: 0.8003 (OUTLIER) cc_final: 0.7630 (p0) REVERT: C 340 MET cc_start: 0.6779 (mtt) cc_final: 0.6100 (mtt) outliers start: 46 outliers final: 14 residues processed: 95 average time/residue: 1.2221 time to fit residues: 124.7703 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 : 1.088 ------------------------------------------------------------------------------- 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: 0.5980 chunk 84 optimal weight: 0.0980 chunk 54 optimal weight: 1.9990 chunk 32 optimal weight: 4.9990 chunk 59 optimal weight: 0.0770 chunk 40 optimal weight: 3.9990 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: 0.9542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 297 GLN C 297 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.097958 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2901 r_free = 0.2901 target = 0.078239 restraints weight = 11597.356| |-----------------------------------------------------------------------------| r_work (start): 0.2905 rms_B_bonded: 2.26 r_work: 0.2785 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2653 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.2653 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8975 moved from start: 0.1253 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= 0.302 Angle : 0.551 5.767 10845 Z= 0.298 Chirality : 0.047 0.144 1197 Planarity : 0.004 0.036 1422 Dihedral : 6.308 52.298 1089 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 5.51 % Allowed : 18.38 % Favored : 76.10 % 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: -1.14 (0.25), residues: 996 helix: -1.62 (0.42), residues: 93 sheet: 0.35 (0.29), residues: 282 loop : -1.18 (0.24), residues: 621 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 0.011 0.001 TYR B 134 ARG 0.002 0.000 ARG B 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 101 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 56 time to evaluate : 0.801 Fit side-chains REVERT: A 18 ASP cc_start: 0.8011 (OUTLIER) cc_final: 0.7667 (p0) REVERT: B 18 ASP cc_start: 0.8040 (OUTLIER) cc_final: 0.7694 (p0) REVERT: B 253 ARG cc_start: 0.8984 (OUTLIER) cc_final: 0.8702 (ptp90) outliers start: 45 outliers final: 25 residues processed: 90 average time/residue: 1.0042 time to fit residues: 97.0610 Evaluate side-chains 76 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 48 time to evaluate : 0.866 ------------------------------------------------------------------------------- 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 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 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 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 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 45 optimal weight: 1.9990 chunk 1 optimal weight: 1.9990 chunk 67 optimal weight: 1.9990 chunk 73 optimal weight: 3.9990 chunk 21 optimal weight: 0.6980 chunk 74 optimal weight: 0.7980 chunk 49 optimal weight: 5.9990 chunk 10 optimal weight: 0.9980 chunk 71 optimal weight: 2.9990 chunk 18 optimal weight: 0.0870 chunk 69 optimal weight: 2.9990 overall best weight: 0.9160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 297 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.098151 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2905 r_free = 0.2905 target = 0.078477 restraints weight = 11522.340| |-----------------------------------------------------------------------------| r_work (start): 0.2908 rms_B_bonded: 2.26 r_work: 0.2787 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2656 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.2656 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8971 moved from start: 0.1395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 7953 Z= 0.287 Angle : 0.535 5.745 10845 Z= 0.289 Chirality : 0.046 0.141 1197 Planarity : 0.004 0.037 1422 Dihedral : 6.314 50.869 1089 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 7.23 % Allowed : 17.28 % 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: -1.02 (0.25), residues: 996 helix: -1.39 (0.42), residues: 96 sheet: 0.35 (0.29), residues: 273 loop : -1.05 (0.24), residues: 627 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP B 281 HIS 0.003 0.001 HIS A 306 PHE 0.009 0.001 PHE C 124 TYR 0.011 0.001 TYR B 134 ARG 0.002 0.000 ARG B 159 *********************** 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 113 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 54 time to evaluate : 0.695 Fit side-chains revert: symmetry clash REVERT: A 18 ASP cc_start: 0.7983 (OUTLIER) cc_final: 0.7656 (p0) REVERT: B 18 ASP cc_start: 0.8064 (OUTLIER) cc_final: 0.7720 (p0) REVERT: B 253 ARG cc_start: 0.8974 (OUTLIER) cc_final: 0.8718 (ptp90) REVERT: B 331 MET cc_start: 0.8812 (OUTLIER) cc_final: 0.8548 (ttp) outliers start: 59 outliers final: 29 residues processed: 101 average time/residue: 0.9501 time to fit residues: 103.5852 Evaluate side-chains 84 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 51 time to evaluate : 0.924 ------------------------------------------------------------------------------- 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 B residue 18 ASP Chi-restraints excluded: chain B residue 50 LEU Chi-restraints excluded: chain B residue 51 VAL Chi-restraints excluded: chain B residue 98 ASP 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 253 ARG Chi-restraints excluded: chain B residue 294 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 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 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: 1.9990 chunk 69 optimal weight: 2.9990 chunk 78 optimal weight: 0.5980 chunk 38 optimal weight: 2.9990 chunk 15 optimal weight: 1.9990 chunk 4 optimal weight: 2.9990 chunk 90 optimal weight: 2.9990 chunk 63 optimal weight: 0.2980 chunk 75 optimal weight: 0.8980 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 297 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.096881 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2879 r_free = 0.2879 target = 0.077389 restraints weight = 11606.714| |-----------------------------------------------------------------------------| r_work (start): 0.2884 rms_B_bonded: 2.25 r_work: 0.2764 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2629 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.2629 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8977 moved from start: 0.1439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 7953 Z= 0.352 Angle : 0.555 5.807 10845 Z= 0.300 Chirality : 0.047 0.149 1197 Planarity : 0.004 0.036 1422 Dihedral : 6.476 50.894 1089 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 5.76 % Allowed : 18.63 % 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: -1.10 (0.25), residues: 996 helix: -1.64 (0.41), residues: 96 sheet: -0.00 (0.27), residues: 303 loop : -0.95 (0.25), residues: 597 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP B 281 HIS 0.003 0.001 HIS A 306 PHE 0.009 0.002 PHE C 124 TYR 0.015 0.001 TYR B 134 ARG 0.003 0.000 ARG A 253 *********************** 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 96 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 49 time to evaluate : 0.906 Fit side-chains REVERT: A 18 ASP cc_start: 0.7913 (OUTLIER) cc_final: 0.7597 (p0) REVERT: B 18 ASP cc_start: 0.8031 (OUTLIER) cc_final: 0.7683 (p0) REVERT: B 253 ARG cc_start: 0.8991 (OUTLIER) cc_final: 0.8763 (ptp90) REVERT: B 331 MET cc_start: 0.8789 (OUTLIER) cc_final: 0.8552 (ttp) outliers start: 47 outliers final: 30 residues processed: 85 average time/residue: 1.3432 time to fit residues: 122.0050 Evaluate side-chains 84 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 50 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 294 THR Chi-restraints excluded: chain A residue 322 VAL Chi-restraints excluded: chain B residue 18 ASP Chi-restraints excluded: chain B residue 50 LEU 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 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 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 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: 0.0040 chunk 61 optimal weight: 0.8980 chunk 41 optimal weight: 0.8980 chunk 96 optimal weight: 0.6980 chunk 76 optimal weight: 0.6980 chunk 6 optimal weight: 0.4980 chunk 64 optimal weight: 0.7980 chunk 30 optimal weight: 0.5980 chunk 38 optimal weight: 1.9990 chunk 86 optimal weight: 1.9990 chunk 26 optimal weight: 0.9980 overall best weight: 0.4992 ------------------------------------------------------------------------------- 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 = 0.3236 r_free = 0.3236 target = 0.099948 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2935 r_free = 0.2935 target = 0.080315 restraints weight = 11604.679| |-----------------------------------------------------------------------------| r_work (start): 0.2939 rms_B_bonded: 2.25 r_work: 0.2819 rms_B_bonded: 2.75 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: 0.8945 moved from start: 0.1640 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 : 0.503 5.619 10845 Z= 0.271 Chirality : 0.045 0.130 1197 Planarity : 0.004 0.035 1422 Dihedral : 6.241 50.201 1089 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 5.15 % Allowed : 18.75 % Favored : 76.10 % 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: -0.89 (0.25), residues: 996 helix: -1.85 (0.40), residues: 96 sheet: 0.73 (0.30), residues: 255 loop : -0.97 (0.24), residues: 645 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP B 281 HIS 0.003 0.001 HIS A 306 PHE 0.008 0.001 PHE C 124 TYR 0.008 0.001 TYR C 184 ARG 0.002 0.000 ARG A 253 *********************** 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 101 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 59 time to evaluate : 0.821 Fit side-chains REVERT: A 18 ASP cc_start: 0.7932 (OUTLIER) cc_final: 0.7584 (p0) REVERT: B 18 ASP cc_start: 0.7975 (OUTLIER) cc_final: 0.7637 (p0) REVERT: B 253 ARG cc_start: 0.8907 (OUTLIER) cc_final: 0.8602 (ptp90) outliers start: 42 outliers final: 27 residues processed: 91 average time/residue: 1.2800 time to fit residues: 124.3068 Evaluate side-chains 83 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 53 time to evaluate : 0.942 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 VAL 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 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 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 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 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 122 LEU 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 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: 0.7980 chunk 44 optimal weight: 2.9990 chunk 81 optimal weight: 0.0980 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: 0.9990 chunk 29 optimal weight: 1.9990 overall best weight: 0.9786 ------------------------------------------------------------------------------- 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 = 0.3224 r_free = 0.3224 target = 0.099087 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2905 r_free = 0.2905 target = 0.078855 restraints weight = 11683.319| |-----------------------------------------------------------------------------| r_work (start): 0.2911 rms_B_bonded: 2.31 r_work: 0.2789 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.2651 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.2651 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8971 moved from start: 0.1608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 7953 Z= 0.309 Angle : 0.553 5.745 10845 Z= 0.298 Chirality : 0.046 0.146 1197 Planarity : 0.004 0.035 1422 Dihedral : 6.346 51.556 1088 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 4.90 % Allowed : 18.14 % Favored : 76.96 % 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: -0.97 (0.25), residues: 996 helix: -1.85 (0.41), residues: 96 sheet: 0.11 (0.27), residues: 303 loop : -0.82 (0.26), residues: 597 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP B 281 HIS 0.003 0.001 HIS A 306 PHE 0.009 0.002 PHE C 124 TYR 0.012 0.001 TYR B 134 ARG 0.003 0.000 ARG A 253 *********************** 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 93 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 53 time to evaluate : 2.186 Fit side-chains REVERT: A 18 ASP cc_start: 0.7954 (OUTLIER) cc_final: 0.7637 (p0) REVERT: A 331 MET cc_start: 0.8820 (OUTLIER) cc_final: 0.8606 (ttp) REVERT: B 18 ASP cc_start: 0.7991 (OUTLIER) cc_final: 0.7679 (p0) REVERT: B 253 ARG cc_start: 0.8933 (OUTLIER) cc_final: 0.8662 (ptp90) outliers start: 40 outliers final: 27 residues processed: 87 average time/residue: 1.9481 time to fit residues: 180.1028 Evaluate side-chains 84 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 53 time to evaluate : 0.923 ------------------------------------------------------------------------------- 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 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 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 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: 2.9990 chunk 43 optimal weight: 0.8980 chunk 48 optimal weight: 0.8980 chunk 69 optimal weight: 2.9990 chunk 25 optimal weight: 2.9990 chunk 75 optimal weight: 1.9990 chunk 21 optimal weight: 0.4980 chunk 11 optimal weight: 1.9990 chunk 1 optimal weight: 0.8980 chunk 54 optimal weight: 1.9990 chunk 24 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 = 0.3230 r_free = 0.3230 target = 0.099498 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2917 r_free = 0.2917 target = 0.079439 restraints weight = 11584.669| |-----------------------------------------------------------------------------| r_work (start): 0.2918 rms_B_bonded: 2.29 r_work: 0.2797 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2661 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.2661 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8964 moved from start: 0.1673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 7953 Z= 0.275 Angle : 0.541 5.713 10845 Z= 0.292 Chirality : 0.046 0.141 1197 Planarity : 0.004 0.035 1422 Dihedral : 6.327 52.808 1088 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 4.78 % Allowed : 18.87 % Favored : 76.35 % 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: -0.91 (0.25), residues: 996 helix: -1.84 (0.41), residues: 96 sheet: 0.18 (0.28), residues: 303 loop : -0.79 (0.26), residues: 597 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP C 281 HIS 0.003 0.001 HIS A 306 PHE 0.009 0.001 PHE C 124 TYR 0.010 0.001 TYR B 134 ARG 0.002 0.000 ARG A 253 *********************** 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 95 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 56 time to evaluate : 0.782 Fit side-chains REVERT: A 18 ASP cc_start: 0.7929 (OUTLIER) cc_final: 0.7623 (p0) REVERT: B 18 ASP cc_start: 0.7959 (OUTLIER) cc_final: 0.7652 (p0) REVERT: B 253 ARG cc_start: 0.8925 (OUTLIER) cc_final: 0.8646 (ptp90) REVERT: B 331 MET cc_start: 0.8721 (ttm) cc_final: 0.8518 (ttp) outliers start: 39 outliers final: 32 residues processed: 87 average time/residue: 1.1863 time to fit residues: 110.3600 Evaluate side-chains 87 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 52 time to evaluate : 0.867 ------------------------------------------------------------------------------- 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 B residue 18 ASP Chi-restraints excluded: chain B residue 51 VAL Chi-restraints excluded: chain B residue 73 MET 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 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 45 optimal weight: 0.8980 chunk 81 optimal weight: 0.5980 chunk 50 optimal weight: 0.7980 chunk 75 optimal weight: 0.6980 chunk 62 optimal weight: 0.9990 chunk 17 optimal weight: 1.9990 chunk 87 optimal weight: 0.1980 chunk 33 optimal weight: 0.7980 chunk 37 optimal weight: 1.9990 chunk 15 optimal weight: 0.5980 chunk 85 optimal weight: 0.3980 overall best weight: 0.4980 ------------------------------------------------------------------------------- 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 = 0.3248 r_free = 0.3248 target = 0.100747 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2937 r_free = 0.2937 target = 0.080655 restraints weight = 11699.750| |-----------------------------------------------------------------------------| r_work (start): 0.2940 rms_B_bonded: 2.31 r_work: 0.2819 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2683 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.2683 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8945 moved from start: 0.1781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 7953 Z= 0.202 Angle : 0.520 5.625 10845 Z= 0.280 Chirality : 0.045 0.129 1197 Planarity : 0.004 0.034 1422 Dihedral : 6.208 53.059 1088 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 4.66 % Allowed : 18.75 % Favored : 76.59 % 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: -1.75 (0.43), residues: 93 sheet: 0.88 (0.30), residues: 255 loop : -0.89 (0.24), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP C 281 HIS 0.003 0.001 HIS A 306 PHE 0.011 0.001 PHE C 99 TYR 0.008 0.001 TYR C 184 ARG 0.002 0.000 ARG A 253 *********************** 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 95 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 57 time to evaluate : 1.013 Fit side-chains REVERT: A 18 ASP cc_start: 0.7877 (OUTLIER) cc_final: 0.7566 (p0) REVERT: B 18 ASP cc_start: 0.7934 (OUTLIER) cc_final: 0.7636 (p0) REVERT: B 159 ARG cc_start: 0.8607 (OUTLIER) cc_final: 0.8340 (mmt180) REVERT: B 253 ARG cc_start: 0.8892 (OUTLIER) cc_final: 0.8587 (ptp90) outliers start: 38 outliers final: 27 residues processed: 87 average time/residue: 1.1406 time to fit residues: 106.1898 Evaluate side-chains 84 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 53 time to evaluate : 0.863 ------------------------------------------------------------------------------- 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 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 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 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 122 LEU 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 25 optimal weight: 2.9990 chunk 31 optimal weight: 2.9990 chunk 1 optimal weight: 0.0970 chunk 85 optimal weight: 0.7980 chunk 13 optimal weight: 1.9990 chunk 55 optimal weight: 3.9990 chunk 18 optimal weight: 0.6980 chunk 43 optimal weight: 0.9980 chunk 77 optimal weight: 1.9990 chunk 80 optimal weight: 1.9990 chunk 29 optimal weight: 0.5980 overall best weight: 0.6378 ------------------------------------------------------------------------------- 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 = 0.3241 r_free = 0.3241 target = 0.100166 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2929 r_free = 0.2929 target = 0.080090 restraints weight = 11762.590| |-----------------------------------------------------------------------------| r_work (start): 0.2935 rms_B_bonded: 2.32 r_work: 0.2815 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2678 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.2678 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8943 moved from start: 0.1797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 7953 Z= 0.230 Angle : 0.528 5.658 10845 Z= 0.284 Chirality : 0.045 0.133 1197 Planarity : 0.004 0.034 1422 Dihedral : 6.210 53.770 1088 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 4.29 % Allowed : 19.12 % Favored : 76.59 % 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: -1.69 (0.43), residues: 93 sheet: 0.70 (0.30), residues: 261 loop : -0.82 (0.25), residues: 642 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP B 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 253 ********************** 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 91 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 56 time to evaluate : 0.796 Fit side-chains REVERT: A 18 ASP cc_start: 0.7869 (OUTLIER) cc_final: 0.7580 (p0) REVERT: A 340 MET cc_start: 0.6811 (mtt) cc_final: 0.6459 (mpt) REVERT: B 18 ASP cc_start: 0.7943 (OUTLIER) cc_final: 0.7629 (p0) REVERT: B 159 ARG cc_start: 0.8596 (OUTLIER) cc_final: 0.8321 (mmt180) REVERT: B 253 ARG cc_start: 0.8922 (OUTLIER) cc_final: 0.8632 (ptp90) outliers start: 35 outliers final: 30 residues processed: 88 average time/residue: 1.1423 time to fit residues: 107.5085 Evaluate side-chains 86 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 52 time to evaluate : 0.804 ------------------------------------------------------------------------------- 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 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 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 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: 0.5980 chunk 66 optimal weight: 0.0030 chunk 76 optimal weight: 0.9980 chunk 63 optimal weight: 0.9990 chunk 40 optimal weight: 2.9990 chunk 6 optimal weight: 0.9980 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: 0.6790 ------------------------------------------------------------------------------- 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 = 0.3239 r_free = 0.3239 target = 0.100052 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2926 r_free = 0.2926 target = 0.080020 restraints weight = 11639.144| |-----------------------------------------------------------------------------| r_work (start): 0.2934 rms_B_bonded: 2.30 r_work: 0.2814 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2676 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.2676 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8939 moved from start: 0.1824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 7953 Z= 0.239 Angle : 0.528 5.658 10845 Z= 0.285 Chirality : 0.046 0.135 1197 Planarity : 0.004 0.035 1422 Dihedral : 6.211 54.047 1088 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 4.41 % Allowed : 19.12 % Favored : 76.47 % 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: -0.71 (0.26), residues: 996 helix: -1.70 (0.43), residues: 93 sheet: 0.69 (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 B 281 HIS 0.003 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 A 253 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6087.74 seconds wall clock time: 108 minutes 25.66 seconds (6505.66 seconds total)