Starting phenix.real_space_refine on Thu Jun 4 07:02:40 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9w21_65562/06_2026/9w21_65562.cif Found real_map, /net/cci-nas-00/data/ceres_data/9w21_65562/06_2026/9w21_65562.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9w21_65562/06_2026/9w21_65562.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9w21_65562/06_2026/9w21_65562.map" model { file = "/net/cci-nas-00/data/ceres_data/9w21_65562/06_2026/9w21_65562.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9w21_65562/06_2026/9w21_65562.cif" } resolution = 4.7 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 84 5.16 5 C 6992 2.51 5 N 1916 2.21 5 O 2072 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 22 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6079/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 11064 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 2766 Number of conformers: 1 Conformer: "" Number of residues, atoms: 346, 2766 Classifications: {'peptide': 346} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 329} Chain: "a" Number of atoms: 2766 Number of conformers: 1 Conformer: "" Number of residues, atoms: 346, 2766 Classifications: {'peptide': 346} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 329} Chain: "B" Number of atoms: 2766 Number of conformers: 1 Conformer: "" Number of residues, atoms: 346, 2766 Classifications: {'peptide': 346} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 329} Chain: "b" Number of atoms: 2766 Number of conformers: 1 Conformer: "" Number of residues, atoms: 346, 2766 Classifications: {'peptide': 346} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 329} Time building chain proxies: 2.80, per 1000 atoms: 0.25 Number of scatterers: 11064 At special positions: 0 Unit cell: (95.953, 122.122, 108.702, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 84 16.00 O 2072 8.00 N 1916 7.00 C 6992 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=24, symmetry=0 Simple disulfide: pdb=" SG CYS A 4 " - pdb=" SG CYS A 15 " distance=2.03 Simple disulfide: pdb=" SG CYS A 55 " - pdb=" SG CYS A 143 " distance=2.03 Simple disulfide: pdb=" SG CYS A 179 " - pdb=" SG CYS A 223 " distance=2.03 Simple disulfide: pdb=" SG CYS A 280 " - pdb=" SG CYS A 329 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 312 " distance=2.03 Simple disulfide: pdb=" SG CYS A 313 " - pdb=" SG CYS A 316 " distance=2.03 Simple disulfide: pdb=" SG CYS a 4 " - pdb=" SG CYS a 15 " distance=2.03 Simple disulfide: pdb=" SG CYS a 55 " - pdb=" SG CYS a 143 " distance=2.03 Simple disulfide: pdb=" SG CYS a 179 " - pdb=" SG CYS a 223 " distance=2.03 Simple disulfide: pdb=" SG CYS a 280 " - pdb=" SG CYS a 329 " distance=2.03 Simple disulfide: pdb=" SG CYS a 291 " - pdb=" SG CYS a 312 " distance=2.03 Simple disulfide: pdb=" SG CYS a 313 " - pdb=" SG CYS a 316 " distance=2.03 Simple disulfide: pdb=" SG CYS B 4 " - pdb=" SG CYS B 15 " distance=2.03 Simple disulfide: pdb=" SG CYS B 55 " - pdb=" SG CYS B 143 " distance=2.03 Simple disulfide: pdb=" SG CYS B 179 " - pdb=" SG CYS B 223 " distance=2.03 Simple disulfide: pdb=" SG CYS B 280 " - pdb=" SG CYS B 329 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 312 " distance=2.03 Simple disulfide: pdb=" SG CYS B 313 " - pdb=" SG CYS B 316 " distance=2.03 Simple disulfide: pdb=" SG CYS b 4 " - pdb=" SG CYS b 15 " distance=2.03 Simple disulfide: pdb=" SG CYS b 55 " - pdb=" SG CYS b 143 " distance=2.03 Simple disulfide: pdb=" SG CYS b 179 " - pdb=" SG CYS b 223 " distance=2.03 Simple disulfide: pdb=" SG CYS b 280 " - pdb=" SG CYS b 329 " distance=2.03 Simple disulfide: pdb=" SG CYS b 291 " - pdb=" SG CYS b 312 " distance=2.03 Simple disulfide: pdb=" SG CYS b 313 " - pdb=" SG CYS b 316 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.86 Conformation dependent library (CDL) restraints added in 413.0 milliseconds 2752 Ramachandran restraints generated. 1376 Oldfield, 0 Emsley, 1376 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2568 Finding SS restraints... Secondary structure from input PDB file: 24 helices and 15 sheets defined 17.6% alpha, 14.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.37 Creating SS restraints... Processing helix chain 'A' and resid 38 through 53 Processing helix chain 'A' and resid 61 through 82 Proline residue: A 73 - end of helix Processing helix chain 'A' and resid 114 through 121 Processing helix chain 'A' and resid 226 through 230 removed outlier: 3.599A pdb=" N HIS A 229 " --> pdb=" O PRO A 226 " (cutoff:3.500A) Processing helix chain 'A' and resid 244 through 248 Processing helix chain 'A' and resid 267 through 271 Processing helix chain 'a' and resid 38 through 53 Processing helix chain 'a' and resid 61 through 82 Proline residue: a 73 - end of helix Processing helix chain 'a' and resid 114 through 121 Processing helix chain 'a' and resid 226 through 230 removed outlier: 3.599A pdb=" N HIS a 229 " --> pdb=" O PRO a 226 " (cutoff:3.500A) Processing helix chain 'a' and resid 244 through 248 Processing helix chain 'a' and resid 267 through 271 Processing helix chain 'B' and resid 38 through 53 Processing helix chain 'B' and resid 61 through 82 Proline residue: B 73 - end of helix Processing helix chain 'B' and resid 114 through 121 Processing helix chain 'B' and resid 226 through 230 removed outlier: 3.599A pdb=" N HIS B 229 " --> pdb=" O PRO B 226 " (cutoff:3.500A) Processing helix chain 'B' and resid 244 through 248 Processing helix chain 'B' and resid 267 through 271 Processing helix chain 'b' and resid 38 through 53 Processing helix chain 'b' and resid 61 through 82 Proline residue: b 73 - end of helix Processing helix chain 'b' and resid 114 through 121 Processing helix chain 'b' and resid 226 through 230 removed outlier: 3.599A pdb=" N HIS b 229 " --> pdb=" O PRO b 226 " (cutoff:3.500A) Processing helix chain 'b' and resid 244 through 248 Processing helix chain 'b' and resid 267 through 271 Processing sheet with id=AA1, first strand: chain 'A' and resid 88 through 90 removed outlier: 3.959A pdb=" N ILE A 57 " --> pdb=" O LEU A 134 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N GLY A 56 " --> pdb=" O ALA A 149 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 153 through 155 Processing sheet with id=AA3, first strand: chain 'A' and resid 329 through 330 removed outlier: 3.550A pdb=" N ASP A 276 " --> pdb=" O ARG A 322 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N GLU A 274 " --> pdb=" O ARG A 324 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N PHE A 277 " --> pdb=" O GLU A 213 " (cutoff:3.500A) removed outlier: 8.977A pdb=" N GLU A 213 " --> pdb=" O PHE A 277 " (cutoff:3.500A) removed outlier: 5.359A pdb=" N ILE A 212 " --> pdb=" O ALA A 205 " (cutoff:3.500A) removed outlier: 5.896A pdb=" N ALA A 205 " --> pdb=" O ILE A 212 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N ILE A 202 " --> pdb=" O HIS A 195 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N HIS A 195 " --> pdb=" O ILE A 202 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LYS A 189 " --> pdb=" O ARG A 192 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N VAL A 194 " --> pdb=" O ALA A 187 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ALA A 187 " --> pdb=" O VAL A 194 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N ALA A 186 " --> pdb=" O ILE a 188 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ILE a 188 " --> pdb=" O ALA A 186 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ILE A 188 " --> pdb=" O ALA a 186 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N ALA a 186 " --> pdb=" O ILE A 188 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ALA a 187 " --> pdb=" O VAL a 194 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N VAL a 194 " --> pdb=" O ALA a 187 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LYS a 189 " --> pdb=" O ARG a 192 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N HIS a 195 " --> pdb=" O ILE a 202 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N ILE a 202 " --> pdb=" O HIS a 195 " (cutoff:3.500A) removed outlier: 5.896A pdb=" N ALA a 205 " --> pdb=" O ILE a 212 " (cutoff:3.500A) removed outlier: 5.359A pdb=" N ILE a 212 " --> pdb=" O ALA a 205 " (cutoff:3.500A) removed outlier: 8.977A pdb=" N GLU a 213 " --> pdb=" O PHE a 277 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N PHE a 277 " --> pdb=" O GLU a 213 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N GLU a 274 " --> pdb=" O ARG a 324 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ASP a 276 " --> pdb=" O ARG a 322 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 284 through 287 removed outlier: 6.036A pdb=" N THR A 284 " --> pdb=" O TRP A 311 " (cutoff:3.500A) removed outlier: 7.645A pdb=" N CYS A 313 " --> pdb=" O THR A 284 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N VAL A 286 " --> pdb=" O CYS A 313 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'a' and resid 88 through 90 removed outlier: 3.958A pdb=" N ILE a 57 " --> pdb=" O LEU a 134 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N GLY a 56 " --> pdb=" O ALA a 149 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'a' and resid 153 through 155 Processing sheet with id=AA7, first strand: chain 'a' and resid 284 through 287 removed outlier: 6.036A pdb=" N THR a 284 " --> pdb=" O TRP a 311 " (cutoff:3.500A) removed outlier: 7.645A pdb=" N CYS a 313 " --> pdb=" O THR a 284 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N VAL a 286 " --> pdb=" O CYS a 313 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 4 through 5 removed outlier: 4.065A pdb=" N CYS B 4 " --> pdb=" O CYS b 4 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N CYS b 4 " --> pdb=" O CYS B 4 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'B' and resid 88 through 90 removed outlier: 3.958A pdb=" N ILE B 57 " --> pdb=" O LEU B 134 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N GLY B 56 " --> pdb=" O ALA B 149 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 153 through 155 Processing sheet with id=AB2, first strand: chain 'B' and resid 329 through 330 removed outlier: 3.549A pdb=" N ASP B 276 " --> pdb=" O ARG B 322 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N GLU B 274 " --> pdb=" O ARG B 324 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N PHE B 277 " --> pdb=" O GLU B 213 " (cutoff:3.500A) removed outlier: 8.976A pdb=" N GLU B 213 " --> pdb=" O PHE B 277 " (cutoff:3.500A) removed outlier: 5.359A pdb=" N ILE B 212 " --> pdb=" O ALA B 205 " (cutoff:3.500A) removed outlier: 5.896A pdb=" N ALA B 205 " --> pdb=" O ILE B 212 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N ILE B 202 " --> pdb=" O HIS B 195 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N HIS B 195 " --> pdb=" O ILE B 202 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LYS B 189 " --> pdb=" O ARG B 192 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N VAL B 194 " --> pdb=" O ALA B 187 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ALA B 187 " --> pdb=" O VAL B 194 " (cutoff:3.500A) removed outlier: 4.673A pdb=" N ALA B 186 " --> pdb=" O ILE b 188 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N ILE b 188 " --> pdb=" O ALA B 186 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N ILE B 188 " --> pdb=" O ALA b 186 " (cutoff:3.500A) removed outlier: 4.625A pdb=" N ALA b 186 " --> pdb=" O ILE B 188 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ALA b 187 " --> pdb=" O VAL b 194 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N VAL b 194 " --> pdb=" O ALA b 187 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LYS b 189 " --> pdb=" O ARG b 192 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N HIS b 195 " --> pdb=" O ILE b 202 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N ILE b 202 " --> pdb=" O HIS b 195 " (cutoff:3.500A) removed outlier: 5.896A pdb=" N ALA b 205 " --> pdb=" O ILE b 212 " (cutoff:3.500A) removed outlier: 5.358A pdb=" N ILE b 212 " --> pdb=" O ALA b 205 " (cutoff:3.500A) removed outlier: 8.976A pdb=" N GLU b 213 " --> pdb=" O PHE b 277 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N PHE b 277 " --> pdb=" O GLU b 213 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N GLU b 274 " --> pdb=" O ARG b 324 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ASP b 276 " --> pdb=" O ARG b 322 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 284 through 287 removed outlier: 6.036A pdb=" N THR B 284 " --> pdb=" O TRP B 311 " (cutoff:3.500A) removed outlier: 7.645A pdb=" N CYS B 313 " --> pdb=" O THR B 284 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N VAL B 286 " --> pdb=" O CYS B 313 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'b' and resid 88 through 90 removed outlier: 3.959A pdb=" N ILE b 57 " --> pdb=" O LEU b 134 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N GLY b 56 " --> pdb=" O ALA b 149 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'b' and resid 153 through 155 Processing sheet with id=AB6, first strand: chain 'b' and resid 284 through 287 removed outlier: 6.036A pdb=" N THR b 284 " --> pdb=" O TRP b 311 " (cutoff:3.500A) removed outlier: 7.644A pdb=" N CYS b 313 " --> pdb=" O THR b 284 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N VAL b 286 " --> pdb=" O CYS b 313 " (cutoff:3.500A) 236 hydrogen bonds defined for protein. 612 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.53 Time building geometry restraints manager: 1.18 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2227 1.33 - 1.45: 2805 1.45 - 1.57: 6200 1.57 - 1.70: 0 1.70 - 1.82: 120 Bond restraints: 11352 Sorted by residual: bond pdb=" N ASP b 190 " pdb=" CA ASP b 190 " ideal model delta sigma weight residual 1.457 1.484 -0.026 1.29e-02 6.01e+03 4.14e+00 bond pdb=" N ASP B 190 " pdb=" CA ASP B 190 " ideal model delta sigma weight residual 1.457 1.483 -0.025 1.29e-02 6.01e+03 3.89e+00 bond pdb=" N ASP A 190 " pdb=" CA ASP A 190 " ideal model delta sigma weight residual 1.457 1.483 -0.025 1.29e-02 6.01e+03 3.83e+00 bond pdb=" N ASP a 190 " pdb=" CA ASP a 190 " ideal model delta sigma weight residual 1.457 1.483 -0.025 1.29e-02 6.01e+03 3.81e+00 bond pdb=" CD GLN A 47 " pdb=" OE1 GLN A 47 " ideal model delta sigma weight residual 1.231 1.207 0.024 1.90e-02 2.77e+03 1.61e+00 ... (remaining 11347 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.36: 14787 1.36 - 2.72: 447 2.72 - 4.08: 106 4.08 - 5.44: 24 5.44 - 6.80: 20 Bond angle restraints: 15384 Sorted by residual: angle pdb=" N GLN B 47 " pdb=" CA GLN B 47 " pdb=" CB GLN B 47 " ideal model delta sigma weight residual 110.30 116.53 -6.23 1.54e+00 4.22e-01 1.64e+01 angle pdb=" N GLN A 47 " pdb=" CA GLN A 47 " pdb=" CB GLN A 47 " ideal model delta sigma weight residual 110.30 116.49 -6.19 1.54e+00 4.22e-01 1.61e+01 angle pdb=" N GLN a 47 " pdb=" CA GLN a 47 " pdb=" CB GLN a 47 " ideal model delta sigma weight residual 110.30 116.48 -6.18 1.54e+00 4.22e-01 1.61e+01 angle pdb=" N GLN b 47 " pdb=" CA GLN b 47 " pdb=" CB GLN b 47 " ideal model delta sigma weight residual 110.30 116.43 -6.13 1.54e+00 4.22e-01 1.58e+01 angle pdb=" CA GLN b 47 " pdb=" CB GLN b 47 " pdb=" CG GLN b 47 " ideal model delta sigma weight residual 114.10 120.90 -6.80 2.00e+00 2.50e-01 1.15e+01 ... (remaining 15379 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.11: 6109 16.11 - 32.23: 559 32.23 - 48.34: 112 48.34 - 64.46: 24 64.46 - 80.57: 12 Dihedral angle restraints: 6816 sinusoidal: 2836 harmonic: 3980 Sorted by residual: dihedral pdb=" CB CYS a 291 " pdb=" SG CYS a 291 " pdb=" SG CYS a 312 " pdb=" CB CYS a 312 " ideal model delta sinusoidal sigma weight residual -86.00 -158.06 72.06 1 1.00e+01 1.00e-02 6.64e+01 dihedral pdb=" CB CYS b 291 " pdb=" SG CYS b 291 " pdb=" SG CYS b 312 " pdb=" CB CYS b 312 " ideal model delta sinusoidal sigma weight residual -86.00 -158.03 72.03 1 1.00e+01 1.00e-02 6.64e+01 dihedral pdb=" CB CYS A 291 " pdb=" SG CYS A 291 " pdb=" SG CYS A 312 " pdb=" CB CYS A 312 " ideal model delta sinusoidal sigma weight residual -86.00 -158.02 72.02 1 1.00e+01 1.00e-02 6.64e+01 ... (remaining 6813 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 980 0.029 - 0.058: 461 0.058 - 0.088: 100 0.088 - 0.117: 87 0.117 - 0.146: 16 Chirality restraints: 1644 Sorted by residual: chirality pdb=" CB ILE a 335 " pdb=" CA ILE a 335 " pdb=" CG1 ILE a 335 " pdb=" CG2 ILE a 335 " both_signs ideal model delta sigma weight residual False 2.64 2.50 0.15 2.00e-01 2.50e+01 5.34e-01 chirality pdb=" CB ILE A 335 " pdb=" CA ILE A 335 " pdb=" CG1 ILE A 335 " pdb=" CG2 ILE A 335 " both_signs ideal model delta sigma weight residual False 2.64 2.50 0.15 2.00e-01 2.50e+01 5.33e-01 chirality pdb=" CA GLN a 47 " pdb=" N GLN a 47 " pdb=" C GLN a 47 " pdb=" CB GLN a 47 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.15 2.00e-01 2.50e+01 5.28e-01 ... (remaining 1641 not shown) Planarity restraints: 1956 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP a 225 " -0.017 2.00e-02 2.50e+03 1.76e-02 7.73e+00 pdb=" CG TRP a 225 " 0.048 2.00e-02 2.50e+03 pdb=" CD1 TRP a 225 " -0.021 2.00e-02 2.50e+03 pdb=" CD2 TRP a 225 " 0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP a 225 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP a 225 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP a 225 " -0.009 2.00e-02 2.50e+03 pdb=" CZ2 TRP a 225 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP a 225 " 0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP a 225 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 225 " -0.017 2.00e-02 2.50e+03 1.75e-02 7.69e+00 pdb=" CG TRP B 225 " 0.048 2.00e-02 2.50e+03 pdb=" CD1 TRP B 225 " -0.020 2.00e-02 2.50e+03 pdb=" CD2 TRP B 225 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP B 225 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP B 225 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP B 225 " -0.009 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 225 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 225 " 0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP B 225 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP b 225 " 0.017 2.00e-02 2.50e+03 1.75e-02 7.62e+00 pdb=" CG TRP b 225 " -0.048 2.00e-02 2.50e+03 pdb=" CD1 TRP b 225 " 0.021 2.00e-02 2.50e+03 pdb=" CD2 TRP b 225 " 0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP b 225 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP b 225 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP b 225 " 0.009 2.00e-02 2.50e+03 pdb=" CZ2 TRP b 225 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP b 225 " -0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP b 225 " 0.000 2.00e-02 2.50e+03 ... (remaining 1953 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 3166 2.81 - 3.34: 10848 3.34 - 3.86: 18294 3.86 - 4.38: 20616 4.38 - 4.90: 34653 Nonbonded interactions: 87577 Sorted by model distance: nonbonded pdb=" NZ LYS B 172 " pdb=" OD1 ASP B 176 " model vdw 2.292 3.120 nonbonded pdb=" NZ LYS b 172 " pdb=" OD1 ASP b 176 " model vdw 2.292 3.120 nonbonded pdb=" NZ LYS A 172 " pdb=" OD1 ASP A 176 " model vdw 2.292 3.120 nonbonded pdb=" NZ LYS a 172 " pdb=" OD1 ASP a 176 " model vdw 2.292 3.120 nonbonded pdb=" O ALA a 43 " pdb=" OE1 GLN a 47 " model vdw 2.334 3.040 ... (remaining 87572 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: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'a' selection = chain 'B' selection = chain 'b' } Set up NCS constraints Number of NCS constrained groups: 1 pdb_interpretation.ncs_group { reference = chain 'A' selection = chain 'a' selection = chain 'B' selection = chain 'b' } Set refine NCS operators NCS operators will be refined. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.480 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: 0.000 Extract box with map and model: 0.240 Check model and map are aligned: 0.050 Set scattering table: 0.030 Process input model: 10.790 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.840 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4377 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 : 0.002 0.029 11376 Z= 0.121 Angle : 0.621 6.796 15432 Z= 0.332 Chirality : 0.041 0.146 1644 Planarity : 0.003 0.032 1956 Dihedral : 12.386 80.569 4176 Min Nonbonded Distance : 2.292 Molprobity Statistics. All-atom Clashscore : 12.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 0.00 % Allowed : 0.82 % Favored : 99.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.67 (0.22), residues: 1376 helix: 0.62 (0.39), residues: 188 sheet: -1.17 (0.29), residues: 296 loop : -0.35 (0.20), residues: 892 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG a 272 TYR 0.007 0.001 TYR A 32 PHE 0.005 0.001 PHE a 279 TRP 0.048 0.002 TRP B 225 HIS 0.002 0.000 HIS B 224 Details of bonding type rmsd/Z covalent geometry : bond 0.00231 / 0.12 (11352) covalent geometry : angle 0.62066 / 0.33 (15384) SS BOND : bond 0.00208 / 0.15 ( 24) SS BOND : angle 0.67700 / 0.42 ( 48) hydrogen bonds : bond 0.21102 / 13.67 ( 236) hydrogen bonds : angle 8.54070 / 6.21 ( 612) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2752 Ramachandran restraints generated. 1376 Oldfield, 0 Emsley, 1376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2752 Ramachandran restraints generated. 1376 Oldfield, 0 Emsley, 1376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 57 time to evaluate : 0.122 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 123 MET cc_start: 0.7317 (mmm) cc_final: 0.7026 (mmm) outliers start: 0 outliers final: 0 residues processed: 57 average time/residue: 0.0948 time to fit residues: 6.1911 Evaluate side-chains 30 residues out of total 304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 30 time to evaluate : 0.104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 98 optimal weight: 4.9990 chunk 107 optimal weight: 0.1980 chunk 10 optimal weight: 0.0570 chunk 66 optimal weight: 4.9990 chunk 130 optimal weight: 0.2980 chunk 124 optimal weight: 0.9990 chunk 103 optimal weight: 9.9990 chunk 77 optimal weight: 10.0000 chunk 122 optimal weight: 0.9980 chunk 91 optimal weight: 10.0000 chunk 55 optimal weight: 0.0170 overall best weight: 0.3136 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 24 ASN a 77 HIS a 107 GLN a 254 HIS a 263 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4068 r_free = 0.4068 target = 0.097612 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.077111 restraints weight = 14253.092| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.079648 restraints weight = 10046.967| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.081540 restraints weight = 7618.123| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.083041 restraints weight = 6130.278| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.084201 restraints weight = 5135.725| |-----------------------------------------------------------------------------| r_work (final): 0.3797 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5513 moved from start: 0.3085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 11376 Z= 0.110 Angle : 0.582 5.335 15432 Z= 0.298 Chirality : 0.042 0.194 1644 Planarity : 0.004 0.042 1956 Dihedral : 4.294 20.675 1472 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 10.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 0.66 % Allowed : 4.93 % Favored : 94.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.58 (0.21), residues: 1376 helix: 0.93 (0.40), residues: 188 sheet: -1.05 (0.31), residues: 268 loop : -0.41 (0.19), residues: 920 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG a 322 TYR 0.011 0.001 TYR a 158 PHE 0.022 0.002 PHE A 160 TRP 0.012 0.001 TRP A 225 HIS 0.001 0.000 HIS a 269 Details of bonding type rmsd/Z covalent geometry : bond 0.00231 / 0.11 (11352) covalent geometry : angle 0.58041 / 0.30 (15384) SS BOND : bond 0.00264 / 0.18 ( 24) SS BOND : angle 0.90501 / 0.56 ( 48) hydrogen bonds : bond 0.03565 / 2.27 ( 236) hydrogen bonds : angle 6.33429 / 4.51 ( 612) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2064 Ramachandran restraints generated. 1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2064 Ramachandran restraints generated. 1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 47 time to evaluate : 0.112 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 123 MET cc_start: 0.7193 (mmm) cc_final: 0.6855 (mmm) REVERT: a 166 ASN cc_start: 0.9440 (t0) cc_final: 0.8931 (t0) outliers start: 2 outliers final: 1 residues processed: 48 average time/residue: 0.0988 time to fit residues: 5.4197 Evaluate side-chains 26 residues out of total 304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 25 time to evaluate : 0.087 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 134 optimal weight: 0.9980 chunk 105 optimal weight: 0.7980 chunk 31 optimal weight: 10.0000 chunk 63 optimal weight: 7.9990 chunk 127 optimal weight: 0.1980 chunk 72 optimal weight: 8.9990 chunk 68 optimal weight: 10.0000 chunk 103 optimal weight: 0.9980 chunk 110 optimal weight: 9.9990 chunk 120 optimal weight: 8.9990 chunk 14 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 107 GLN a 195 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4028 r_free = 0.4028 target = 0.095475 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.073867 restraints weight = 15123.947| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.076415 restraints weight = 10787.432| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.078395 restraints weight = 8297.872| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.079928 restraints weight = 6702.032| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.081087 restraints weight = 5626.013| |-----------------------------------------------------------------------------| r_work (final): 0.3746 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5570 moved from start: 0.2825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 11376 Z= 0.094 Angle : 0.539 5.525 15432 Z= 0.274 Chirality : 0.040 0.150 1644 Planarity : 0.003 0.034 1956 Dihedral : 3.741 14.764 1472 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 10.49 Ramachandran Plot: Outliers : 0.29 % Allowed : 3.20 % Favored : 96.51 % Rotamer: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.72 (0.21), residues: 1376 helix: 0.79 (0.40), residues: 188 sheet: -1.10 (0.30), residues: 276 loop : -0.50 (0.19), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 174 TYR 0.014 0.001 TYR A 158 PHE 0.016 0.001 PHE b 160 TRP 0.020 0.001 TRP A 168 HIS 0.001 0.000 HIS A 195 Details of bonding type rmsd/Z covalent geometry : bond 0.00201 / 0.09 (11352) covalent geometry : angle 0.53767 / 0.27 (15384) SS BOND : bond 0.00238 / 0.16 ( 24) SS BOND : angle 0.85584 / 0.54 ( 48) hydrogen bonds : bond 0.03347 / 2.09 ( 236) hydrogen bonds : angle 5.92335 / 4.18 ( 612) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2064 Ramachandran restraints generated. 1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2064 Ramachandran restraints generated. 1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 37 residues out of total 304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 37 time to evaluate : 0.134 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 34 PHE cc_start: 0.8156 (m-80) cc_final: 0.7484 (m-80) REVERT: a 69 LYS cc_start: 0.9063 (mttt) cc_final: 0.8753 (mttp) REVERT: a 123 MET cc_start: 0.7187 (mmm) cc_final: 0.6834 (mmm) REVERT: a 166 ASN cc_start: 0.9409 (t0) cc_final: 0.9022 (t0) REVERT: a 168 TRP cc_start: 0.9121 (m-90) cc_final: 0.8874 (m-90) REVERT: a 184 MET cc_start: 0.6963 (ppp) cc_final: 0.5496 (ptm) REVERT: a 219 GLU cc_start: 0.8199 (tm-30) cc_final: 0.7866 (tm-30) REVERT: a 323 TYR cc_start: 0.6137 (m-10) cc_final: 0.5915 (m-80) outliers start: 0 outliers final: 0 residues processed: 37 average time/residue: 0.1038 time to fit residues: 4.3832 Evaluate side-chains 29 residues out of total 304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 29 time to evaluate : 0.118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 95 optimal weight: 0.0370 chunk 80 optimal weight: 0.8980 chunk 127 optimal weight: 0.0980 chunk 129 optimal weight: 1.9990 chunk 12 optimal weight: 10.0000 chunk 62 optimal weight: 0.0770 chunk 33 optimal weight: 10.0000 chunk 54 optimal weight: 0.9980 chunk 59 optimal weight: 4.9990 chunk 25 optimal weight: 4.9990 chunk 35 optimal weight: 4.9990 overall best weight: 0.4216 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 107 GLN a 145 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4052 r_free = 0.4052 target = 0.096216 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.073809 restraints weight = 14094.620| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.076449 restraints weight = 9992.416| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.078392 restraints weight = 7638.992| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.079916 restraints weight = 6177.583| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.081080 restraints weight = 5205.501| |-----------------------------------------------------------------------------| r_work (final): 0.3756 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5590 moved from start: 0.3330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 11376 Z= 0.097 Angle : 0.541 5.511 15432 Z= 0.280 Chirality : 0.039 0.124 1644 Planarity : 0.003 0.034 1956 Dihedral : 3.899 16.807 1472 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 0.29 % Allowed : 3.78 % Favored : 95.93 % Rotamer: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.81 (0.21), residues: 1376 helix: 0.80 (0.40), residues: 188 sheet: -1.53 (0.33), residues: 236 loop : -0.52 (0.18), residues: 952 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 322 TYR 0.021 0.002 TYR a 256 PHE 0.014 0.001 PHE B 20 TRP 0.031 0.001 TRP b 232 HIS 0.001 0.000 HIS a 254 Details of bonding type rmsd/Z covalent geometry : bond 0.00201 / 0.10 (11352) covalent geometry : angle 0.54039 / 0.28 (15384) SS BOND : bond 0.00469 / 0.33 ( 24) SS BOND : angle 0.74417 / 0.52 ( 48) hydrogen bonds : bond 0.03021 / 1.90 ( 236) hydrogen bonds : angle 5.68289 / 3.97 ( 612) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2064 Ramachandran restraints generated. 1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2064 Ramachandran restraints generated. 1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 38 time to evaluate : 0.080 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 34 PHE cc_start: 0.8154 (m-80) cc_final: 0.7524 (m-80) REVERT: a 69 LYS cc_start: 0.9093 (mttt) cc_final: 0.8790 (mttp) REVERT: a 123 MET cc_start: 0.7217 (mmm) cc_final: 0.6850 (mmm) REVERT: a 166 ASN cc_start: 0.9380 (t0) cc_final: 0.9008 (t0) REVERT: a 184 MET cc_start: 0.6819 (ppp) cc_final: 0.5441 (ptm) REVERT: a 288 THR cc_start: 0.9078 (p) cc_final: 0.8655 (p) outliers start: 0 outliers final: 0 residues processed: 38 average time/residue: 0.1071 time to fit residues: 4.5716 Evaluate side-chains 28 residues out of total 304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 28 time to evaluate : 0.083 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 60 optimal weight: 0.6980 chunk 11 optimal weight: 4.9990 chunk 131 optimal weight: 7.9990 chunk 49 optimal weight: 10.0000 chunk 125 optimal weight: 0.8980 chunk 95 optimal weight: 0.9980 chunk 44 optimal weight: 0.9990 chunk 101 optimal weight: 10.0000 chunk 120 optimal weight: 4.9990 chunk 126 optimal weight: 0.9990 chunk 52 optimal weight: 6.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 107 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4037 r_free = 0.4037 target = 0.095098 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.073107 restraints weight = 14369.512| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.075603 restraints weight = 10375.013| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.077546 restraints weight = 8019.570| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.079037 restraints weight = 6525.021| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.080196 restraints weight = 5512.486| |-----------------------------------------------------------------------------| r_work (final): 0.3738 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5593 moved from start: 0.3677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 11376 Z= 0.102 Angle : 0.548 6.506 15432 Z= 0.278 Chirality : 0.039 0.136 1644 Planarity : 0.004 0.043 1956 Dihedral : 3.930 21.561 1472 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 13.29 Ramachandran Plot: Outliers : 0.29 % Allowed : 4.07 % Favored : 95.64 % Rotamer: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.96 (0.21), residues: 1376 helix: 0.64 (0.40), residues: 188 sheet: -1.76 (0.30), residues: 280 loop : -0.49 (0.19), residues: 908 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG b 257 TYR 0.011 0.001 TYR B 158 PHE 0.009 0.001 PHE a 160 TRP 0.027 0.001 TRP b 232 HIS 0.001 0.000 HIS a 254 Details of bonding type rmsd/Z covalent geometry : bond 0.00241 / 0.10 (11352) covalent geometry : angle 0.54706 / 0.28 (15384) SS BOND : bond 0.00192 / 0.13 ( 24) SS BOND : angle 0.83929 / 0.55 ( 48) hydrogen bonds : bond 0.03034 / 1.90 ( 236) hydrogen bonds : angle 5.50972 / 3.81 ( 612) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2064 Ramachandran restraints generated. 1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2064 Ramachandran restraints generated. 1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 34 residues out of total 304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 34 time to evaluate : 0.130 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 123 MET cc_start: 0.7132 (mmm) cc_final: 0.6801 (mmm) REVERT: a 166 ASN cc_start: 0.9347 (t0) cc_final: 0.8985 (t0) REVERT: a 184 MET cc_start: 0.6718 (ppp) cc_final: 0.5651 (ptp) REVERT: a 198 MET cc_start: 0.8657 (tpp) cc_final: 0.8414 (tpp) REVERT: a 219 GLU cc_start: 0.8100 (tm-30) cc_final: 0.7694 (tm-30) outliers start: 0 outliers final: 0 residues processed: 34 average time/residue: 0.1031 time to fit residues: 4.0569 Evaluate side-chains 27 residues out of total 304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 27 time to evaluate : 0.106 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 25 optimal weight: 0.6980 chunk 30 optimal weight: 0.6980 chunk 103 optimal weight: 4.9990 chunk 53 optimal weight: 9.9990 chunk 79 optimal weight: 7.9990 chunk 3 optimal weight: 1.9990 chunk 29 optimal weight: 0.0570 chunk 92 optimal weight: 0.0980 chunk 135 optimal weight: 8.9990 chunk 56 optimal weight: 4.9990 chunk 7 optimal weight: 0.0770 overall best weight: 0.3256 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 82 ASN a 107 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4051 r_free = 0.4051 target = 0.096062 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.073748 restraints weight = 14231.047| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.076359 restraints weight = 10185.435| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.078334 restraints weight = 7833.397| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.079856 restraints weight = 6326.056| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.081049 restraints weight = 5331.898| |-----------------------------------------------------------------------------| r_work (final): 0.3759 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5590 moved from start: 0.3940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 11376 Z= 0.086 Angle : 0.509 5.494 15432 Z= 0.258 Chirality : 0.039 0.121 1644 Planarity : 0.003 0.035 1956 Dihedral : 3.819 20.207 1472 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 10.36 Ramachandran Plot: Outliers : 0.29 % Allowed : 4.36 % Favored : 95.35 % Rotamer: Outliers : 0.33 % Allowed : 2.30 % Favored : 97.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.50 (0.22), residues: 1376 helix: 0.86 (0.41), residues: 188 sheet: -0.42 (0.36), residues: 200 loop : -0.55 (0.19), residues: 988 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 257 TYR 0.009 0.001 TYR B 158 PHE 0.008 0.001 PHE B 20 TRP 0.023 0.001 TRP A 232 HIS 0.001 0.000 HIS A 195 Details of bonding type rmsd/Z covalent geometry : bond 0.00185 / 0.09 (11352) covalent geometry : angle 0.50766 / 0.26 (15384) SS BOND : bond 0.00212 / 0.15 ( 24) SS BOND : angle 0.80651 / 0.53 ( 48) hydrogen bonds : bond 0.02851 / 1.81 ( 236) hydrogen bonds : angle 5.28858 / 3.61 ( 612) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2064 Ramachandran restraints generated. 1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2064 Ramachandran restraints generated. 1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 36 residues out of total 304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 35 time to evaluate : 0.108 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 69 LYS cc_start: 0.9132 (mttt) cc_final: 0.8745 (mttm) REVERT: a 123 MET cc_start: 0.7192 (mmm) cc_final: 0.6965 (mmm) REVERT: a 184 MET cc_start: 0.6532 (ppp) cc_final: 0.5525 (ptp) REVERT: a 198 MET cc_start: 0.8727 (tpp) cc_final: 0.8517 (tpp) REVERT: a 288 THR cc_start: 0.9196 (p) cc_final: 0.8828 (p) outliers start: 1 outliers final: 1 residues processed: 35 average time/residue: 0.1081 time to fit residues: 4.2986 Evaluate side-chains 29 residues out of total 304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 28 time to evaluate : 0.116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 40 optimal weight: 0.6980 chunk 75 optimal weight: 2.9990 chunk 11 optimal weight: 2.9990 chunk 83 optimal weight: 0.4980 chunk 100 optimal weight: 0.9980 chunk 108 optimal weight: 7.9990 chunk 41 optimal weight: 0.0170 chunk 9 optimal weight: 0.0870 chunk 110 optimal weight: 0.0870 chunk 17 optimal weight: 0.7980 chunk 84 optimal weight: 0.9980 overall best weight: 0.2774 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 107 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4064 r_free = 0.4064 target = 0.096776 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.074892 restraints weight = 14710.418| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.077376 restraints weight = 10602.693| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.079251 restraints weight = 8239.310| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.080676 restraints weight = 6731.701| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.081751 restraints weight = 5721.177| |-----------------------------------------------------------------------------| r_work (final): 0.3766 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5568 moved from start: 0.4267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 11376 Z= 0.093 Angle : 0.536 6.080 15432 Z= 0.273 Chirality : 0.040 0.125 1644 Planarity : 0.004 0.049 1956 Dihedral : 3.723 15.335 1472 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 9.16 Ramachandran Plot: Outliers : 0.29 % Allowed : 4.36 % Favored : 95.35 % Rotamer: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.65 (0.21), residues: 1376 helix: 0.69 (0.40), residues: 188 sheet: -0.68 (0.38), residues: 180 loop : -0.61 (0.18), residues: 1008 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG b 257 TYR 0.008 0.001 TYR b 331 PHE 0.007 0.001 PHE b 20 TRP 0.019 0.001 TRP b 232 HIS 0.001 0.000 HIS B 131 Details of bonding type rmsd/Z covalent geometry : bond 0.00197 / 0.09 (11352) covalent geometry : angle 0.53466 / 0.27 (15384) SS BOND : bond 0.00327 / 0.25 ( 24) SS BOND : angle 0.82425 / 0.53 ( 48) hydrogen bonds : bond 0.02936 / 1.84 ( 236) hydrogen bonds : angle 5.42909 / 3.70 ( 612) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2064 Ramachandran restraints generated. 1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2064 Ramachandran restraints generated. 1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 38 time to evaluate : 0.112 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 69 LYS cc_start: 0.9107 (mttt) cc_final: 0.8737 (mttm) REVERT: a 123 MET cc_start: 0.7243 (mmm) cc_final: 0.7016 (mmm) REVERT: a 184 MET cc_start: 0.6641 (ppp) cc_final: 0.5771 (ptp) REVERT: a 225 TRP cc_start: 0.8652 (t-100) cc_final: 0.8431 (t60) outliers start: 0 outliers final: 0 residues processed: 38 average time/residue: 0.0690 time to fit residues: 3.0864 Evaluate side-chains 27 residues out of total 304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 27 time to evaluate : 0.106 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 51 optimal weight: 0.0070 chunk 18 optimal weight: 6.9990 chunk 108 optimal weight: 8.9990 chunk 71 optimal weight: 3.9990 chunk 56 optimal weight: 0.9990 chunk 76 optimal weight: 0.8980 chunk 130 optimal weight: 0.0030 chunk 97 optimal weight: 0.9990 chunk 47 optimal weight: 0.2980 chunk 4 optimal weight: 0.9990 chunk 120 optimal weight: 4.9990 overall best weight: 0.4410 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 107 GLN a 229 HIS a 263 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4056 r_free = 0.4056 target = 0.096277 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.073366 restraints weight = 13966.131| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.075916 restraints weight = 10170.563| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.077932 restraints weight = 7928.680| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.079474 restraints weight = 6483.177| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.080734 restraints weight = 5500.910| |-----------------------------------------------------------------------------| r_work (final): 0.3767 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5578 moved from start: 0.4550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 11376 Z= 0.084 Angle : 0.523 5.331 15432 Z= 0.259 Chirality : 0.039 0.121 1644 Planarity : 0.003 0.035 1956 Dihedral : 3.620 12.148 1472 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 10.13 Ramachandran Plot: Outliers : 0.29 % Allowed : 3.49 % Favored : 96.22 % Rotamer: Outliers : 0.00 % Allowed : 0.66 % Favored : 99.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.65 (0.21), residues: 1376 helix: 0.80 (0.40), residues: 188 sheet: -0.62 (0.38), residues: 172 loop : -0.65 (0.18), residues: 1016 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 257 TYR 0.006 0.001 TYR B 158 PHE 0.007 0.001 PHE a 20 TRP 0.017 0.001 TRP A 232 HIS 0.002 0.000 HIS A 254 Details of bonding type rmsd/Z covalent geometry : bond 0.00181 / 0.08 (11352) covalent geometry : angle 0.52119 / 0.26 (15384) SS BOND : bond 0.00262 / 0.19 ( 24) SS BOND : angle 0.85828 / 0.57 ( 48) hydrogen bonds : bond 0.02810 / 1.78 ( 236) hydrogen bonds : angle 5.14626 / 3.47 ( 612) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2064 Ramachandran restraints generated. 1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2064 Ramachandran restraints generated. 1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 39 residues out of total 304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 39 time to evaluate : 0.116 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 69 LYS cc_start: 0.9158 (mttt) cc_final: 0.8700 (mttm) REVERT: a 123 MET cc_start: 0.7229 (mmm) cc_final: 0.7005 (mmm) REVERT: a 184 MET cc_start: 0.6609 (ppp) cc_final: 0.5847 (ptp) REVERT: a 219 GLU cc_start: 0.8102 (tm-30) cc_final: 0.7717 (tm-30) REVERT: a 225 TRP cc_start: 0.8656 (t-100) cc_final: 0.8447 (t60) REVERT: a 333 MET cc_start: 0.6857 (pmm) cc_final: 0.6472 (pmm) outliers start: 0 outliers final: 0 residues processed: 39 average time/residue: 0.0903 time to fit residues: 4.0402 Evaluate side-chains 29 residues out of total 304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 29 time to evaluate : 0.083 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 107 optimal weight: 10.0000 chunk 79 optimal weight: 5.9990 chunk 11 optimal weight: 3.9990 chunk 23 optimal weight: 0.0570 chunk 134 optimal weight: 0.3980 chunk 4 optimal weight: 0.9990 chunk 56 optimal weight: 0.9980 chunk 92 optimal weight: 1.9990 chunk 50 optimal weight: 0.0670 chunk 18 optimal weight: 5.9990 chunk 97 optimal weight: 0.2980 overall best weight: 0.3636 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 107 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4060 r_free = 0.4060 target = 0.096583 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.074620 restraints weight = 15044.144| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.077217 restraints weight = 10794.087| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.079171 restraints weight = 8285.025| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.080721 restraints weight = 6705.621| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.081928 restraints weight = 5652.088| |-----------------------------------------------------------------------------| r_work (final): 0.3771 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5568 moved from start: 0.4750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 11376 Z= 0.090 Angle : 0.525 5.356 15432 Z= 0.259 Chirality : 0.039 0.154 1644 Planarity : 0.003 0.035 1956 Dihedral : 3.724 14.130 1472 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 10.77 Ramachandran Plot: Outliers : 0.29 % Allowed : 4.07 % Favored : 95.64 % Rotamer: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.76 (0.21), residues: 1376 helix: 0.85 (0.41), residues: 188 sheet: -1.06 (0.33), residues: 224 loop : -0.64 (0.19), residues: 964 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 257 TYR 0.011 0.001 TYR B 323 PHE 0.007 0.001 PHE a 20 TRP 0.017 0.001 TRP A 232 HIS 0.009 0.001 HIS b 229 Details of bonding type rmsd/Z covalent geometry : bond 0.00206 / 0.09 (11352) covalent geometry : angle 0.52398 / 0.26 (15384) SS BOND : bond 0.00255 / 0.19 ( 24) SS BOND : angle 0.76417 / 0.49 ( 48) hydrogen bonds : bond 0.02347 / 1.51 ( 236) hydrogen bonds : angle 5.21732 / 3.58 ( 612) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2064 Ramachandran restraints generated. 1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2064 Ramachandran restraints generated. 1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 39 residues out of total 304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 39 time to evaluate : 0.115 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 69 LYS cc_start: 0.9146 (mttt) cc_final: 0.8700 (mttm) REVERT: a 184 MET cc_start: 0.6333 (ppp) cc_final: 0.5611 (ptp) REVERT: a 219 GLU cc_start: 0.8025 (tm-30) cc_final: 0.7663 (tm-30) REVERT: a 333 MET cc_start: 0.6948 (pmm) cc_final: 0.6318 (pmm) outliers start: 0 outliers final: 0 residues processed: 39 average time/residue: 0.0943 time to fit residues: 4.2631 Evaluate side-chains 26 residues out of total 304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 26 time to evaluate : 0.089 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 1 optimal weight: 0.8980 chunk 89 optimal weight: 0.0270 chunk 5 optimal weight: 7.9990 chunk 24 optimal weight: 3.9990 chunk 115 optimal weight: 5.9990 chunk 39 optimal weight: 7.9990 chunk 69 optimal weight: 9.9990 chunk 44 optimal weight: 4.9990 chunk 53 optimal weight: 7.9990 chunk 111 optimal weight: 20.0000 chunk 128 optimal weight: 0.0070 overall best weight: 1.9860 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 107 GLN ** a 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3994 r_free = 0.3994 target = 0.093097 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.070803 restraints weight = 15082.718| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.073231 restraints weight = 10870.678| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.075094 restraints weight = 8429.166| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.076544 restraints weight = 6879.244| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.077681 restraints weight = 5822.755| |-----------------------------------------------------------------------------| r_work (final): 0.3690 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5711 moved from start: 0.4941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 11376 Z= 0.109 Angle : 0.543 5.647 15432 Z= 0.271 Chirality : 0.039 0.142 1644 Planarity : 0.003 0.031 1956 Dihedral : 3.665 15.336 1472 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 14.16 Ramachandran Plot: Outliers : 0.29 % Allowed : 3.20 % Favored : 96.51 % Rotamer: Outliers : 0.00 % Allowed : 0.99 % Favored : 99.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.79 (0.21), residues: 1376 helix: 0.82 (0.40), residues: 188 sheet: -1.03 (0.35), residues: 220 loop : -0.68 (0.18), residues: 968 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 257 TYR 0.009 0.002 TYR A 323 PHE 0.019 0.002 PHE B 217 TRP 0.026 0.002 TRP A 232 HIS 0.006 0.001 HIS b 229 Details of bonding type rmsd/Z covalent geometry : bond 0.00246 / 0.11 (11352) covalent geometry : angle 0.54148 / 0.27 (15384) SS BOND : bond 0.00208 / 0.15 ( 24) SS BOND : angle 0.93722 / 0.64 ( 48) hydrogen bonds : bond 0.02658 / 1.73 ( 236) hydrogen bonds : angle 5.00082 / 3.44 ( 612) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2064 Ramachandran restraints generated. 1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2064 Ramachandran restraints generated. 1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 36 residues out of total 304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 36 time to evaluate : 0.120 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 34 PHE cc_start: 0.7983 (m-80) cc_final: 0.7710 (m-80) REVERT: a 69 LYS cc_start: 0.9226 (mttt) cc_final: 0.8797 (mttm) REVERT: a 88 ILE cc_start: 0.9246 (tt) cc_final: 0.8531 (tt) REVERT: a 198 MET cc_start: 0.8663 (tpp) cc_final: 0.8279 (tpp) REVERT: a 219 GLU cc_start: 0.8148 (tm-30) cc_final: 0.7774 (tm-30) REVERT: a 333 MET cc_start: 0.6972 (pmm) cc_final: 0.6219 (pmm) outliers start: 0 outliers final: 0 residues processed: 36 average time/residue: 0.0871 time to fit residues: 3.6875 Evaluate side-chains 28 residues out of total 304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 28 time to evaluate : 0.107 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 78 optimal weight: 8.9990 chunk 71 optimal weight: 5.9990 chunk 38 optimal weight: 0.9980 chunk 27 optimal weight: 0.0000 chunk 76 optimal weight: 0.0370 chunk 15 optimal weight: 0.9990 chunk 23 optimal weight: 3.9990 chunk 90 optimal weight: 0.0870 chunk 40 optimal weight: 0.0980 chunk 49 optimal weight: 0.9990 chunk 25 optimal weight: 4.9990 overall best weight: 0.2440 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 107 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.094204 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.070633 restraints weight = 13661.462| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.073255 restraints weight = 9744.296| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.075237 restraints weight = 7526.904| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.076760 restraints weight = 6147.766| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.078031 restraints weight = 5228.539| |-----------------------------------------------------------------------------| r_work (final): 0.3738 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5623 moved from start: 0.5103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 11376 Z= 0.088 Angle : 0.537 5.291 15432 Z= 0.263 Chirality : 0.041 0.178 1644 Planarity : 0.003 0.039 1956 Dihedral : 3.605 13.999 1472 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 12.05 Ramachandran Plot: Outliers : 0.29 % Allowed : 4.07 % Favored : 95.64 % Rotamer: Outliers : 0.00 % Allowed : 0.66 % Favored : 99.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.79 (0.21), residues: 1376 helix: 0.93 (0.40), residues: 188 sheet: -0.87 (0.34), residues: 216 loop : -0.75 (0.18), residues: 972 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 257 TYR 0.011 0.001 TYR B 323 PHE 0.012 0.001 PHE b 217 TRP 0.070 0.002 TRP B 225 HIS 0.004 0.000 HIS b 229 Details of bonding type rmsd/Z covalent geometry : bond 0.00199 / 0.09 (11352) covalent geometry : angle 0.53647 / 0.26 (15384) SS BOND : bond 0.00233 / 0.18 ( 24) SS BOND : angle 0.79331 / 0.53 ( 48) hydrogen bonds : bond 0.02361 / 1.52 ( 236) hydrogen bonds : angle 4.95393 / 3.36 ( 612) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1197.28 seconds wall clock time: 21 minutes 42.04 seconds (1302.04 seconds total)