Starting phenix.real_space_refine on Fri Jul 3 01:26:48 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9w21_65562/07_2026/9w21_65562.cif Found real_map, /net/cci-nas-00/data/ceres_data/9w21_65562/07_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_65562/07_2026/9w21_65562.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9w21_65562/07_2026/9w21_65562.map" model { file = "/net/cci-nas-00/data/ceres_data/9w21_65562/07_2026/9w21_65562.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9w21_65562/07_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-6108/lib/python3.11/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: 2.03, per 1000 atoms: 0.18 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: 0.85 Conformation dependent library (CDL) restraints added in 374.9 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: 0.32 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: 1.21 Time building geometry restraints manager: 1.15 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: 5.010 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: 0.030 Set scattering table: 0.030 Process input model: 9.590 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.060 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4166 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 : 0.102 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: 0.0858 time to fit residues: 5.6444 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 : 0.106 ------------------------------------------------------------------------------- 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... 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 = 0.4074 r_free = 0.4074 target = 0.097995 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.077722 restraints weight = 14396.490| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.080283 restraints weight = 10117.360| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.082181 restraints weight = 7677.890| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.083617 restraints weight = 6168.334| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.084746 restraints weight = 5187.421| |-----------------------------------------------------------------------------| r_work (final): 0.3804 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5448 moved from start: 0.3005 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 : 10.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 0.66 % Allowed : 4.61 % Favored : 94.74 % 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) ************************************************ 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 50 residues out of total 304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 48 time to evaluate : 0.111 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: 0.7200 (mmm) cc_final: 0.6863 (mmm) REVERT: a 166 ASN cc_start: 0.9439 (t0) cc_final: 0.8930 (t0) outliers start: 2 outliers final: 1 residues processed: 49 average time/residue: 0.0933 time to fit residues: 5.3108 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 : 0.109 ------------------------------------------------------------------------------- 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: 3.9990 chunk 127 optimal weight: 0.0000 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: 0.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... a 24 ASN a 107 GLN a 195 HIS 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 = 0.4038 r_free = 0.4038 target = 0.095402 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.073471 restraints weight = 15082.685| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.076079 restraints weight = 10666.956| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.078036 restraints weight = 8155.500| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.079499 restraints weight = 6583.089| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.080647 restraints weight = 5545.198| |-----------------------------------------------------------------------------| r_work (final): 0.3748 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5549 moved from start: 0.2784 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= 0.099 Angle : 0.545 5.480 15432 Z= 0.278 Chirality : 0.040 0.154 1644 Planarity : 0.003 0.034 1956 Dihedral : 3.792 14.883 1472 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 10.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % 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: -0.57 (0.21), residues: 1376 helix: 0.94 (0.40), residues: 188 sheet: -1.01 (0.31), residues: 276 loop : -0.41 (0.19), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 174 TYR 0.013 0.001 TYR b 158 PHE 0.016 0.001 PHE A 160 TRP 0.021 0.001 TRP A 168 HIS 0.001 0.000 HIS A 195 Details of bonding type rmsd/Z covalent geometry : bond 0.00207 / 0.10 (11352) covalent geometry : angle 0.54372 / 0.28 (15384) SS BOND : bond 0.00220 / 0.15 ( 24) SS BOND : angle 0.84176 / 0.53 ( 48) hydrogen bonds : bond 0.03381 / 2.12 ( 236) hydrogen bonds : angle 5.99059 / 4.24 ( 612) *********************** REFINEMENT MACRO_CYCLE 3 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 37 residues out of total 304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 37 time to evaluate : 0.115 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: 0.8206 (m-80) cc_final: 0.7531 (m-80) REVERT: a 69 LYS cc_start: 0.9060 (mttt) cc_final: 0.8767 (mttp) REVERT: a 123 MET cc_start: 0.7237 (mmm) cc_final: 0.6896 (mmm) REVERT: a 166 ASN cc_start: 0.9456 (t0) cc_final: 0.9077 (t0) REVERT: a 168 TRP cc_start: 0.9144 (m-90) cc_final: 0.8941 (m-90) REVERT: a 184 MET cc_start: 0.7011 (ppp) cc_final: 0.5664 (ptm) REVERT: a 219 GLU cc_start: 0.8171 (tm-30) cc_final: 0.7803 (tm-30) REVERT: a 323 TYR cc_start: 0.6204 (m-10) cc_final: 0.5980 (m-80) outliers start: 0 outliers final: 0 residues processed: 37 average time/residue: 0.1112 time to fit residues: 4.7043 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 : 0.119 ------------------------------------------------------------------------------- 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: 0.7980 chunk 80 optimal weight: 0.5980 chunk 127 optimal weight: 0.0870 chunk 129 optimal weight: 0.4980 chunk 12 optimal weight: 8.9990 chunk 62 optimal weight: 3.9990 chunk 33 optimal weight: 4.9990 chunk 54 optimal weight: 3.9990 chunk 59 optimal weight: 0.0970 chunk 25 optimal weight: 0.0970 chunk 35 optimal weight: 9.9990 overall best weight: 0.2754 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.4065 r_free = 0.4065 target = 0.096806 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.074638 restraints weight = 14245.908| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.077226 restraints weight = 10192.838| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.079156 restraints weight = 7842.123| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.080656 restraints weight = 6362.581| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.081817 restraints weight = 5366.919| |-----------------------------------------------------------------------------| r_work (final): 0.3780 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5474 moved from start: 0.3289 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= 0.098 Angle : 0.551 5.554 15432 Z= 0.284 Chirality : 0.039 0.124 1644 Planarity : 0.003 0.034 1956 Dihedral : 3.968 17.222 1472 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 9.62 Ramachandran Plot: Outliers : 0.29 % Allowed : 3.49 % Favored : 96.22 % Rotamer: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % 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: 1.04 (0.41), residues: 188 sheet: -1.40 (0.33), residues: 236 loop : -0.37 (0.19), residues: 952 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG b 322 TYR 0.023 0.002 TYR a 256 PHE 0.015 0.001 PHE B 160 TRP 0.033 0.001 TRP b 232 HIS 0.003 0.000 HIS A 254 Details of bonding type rmsd/Z covalent geometry : bond 0.00201 / 0.10 (11352) covalent geometry : angle 0.55045 / 0.28 (15384) SS BOND : bond 0.00400 / 0.28 ( 24) SS BOND : angle 0.76340 / 0.54 ( 48) hydrogen bonds : bond 0.03057 / 1.92 ( 236) hydrogen bonds : angle 5.71155 / 4.01 ( 612) *********************** REFINEMENT MACRO_CYCLE 4 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 38 residues out of total 304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 38 time to evaluate : 0.096 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 34 PHE cc_start: 0.8076 (m-80) cc_final: 0.7458 (m-80) REVERT: a 69 LYS cc_start: 0.9087 (mttt) cc_final: 0.8618 (mttm) REVERT: a 123 MET cc_start: 0.7204 (mmm) cc_final: 0.6850 (mmm) REVERT: a 166 ASN cc_start: 0.9335 (t0) cc_final: 0.9134 (t0) REVERT: a 184 MET cc_start: 0.6807 (ppp) cc_final: 0.5375 (ptm) REVERT: a 219 GLU cc_start: 0.8142 (tm-30) cc_final: 0.7720 (tm-30) outliers start: 0 outliers final: 0 residues processed: 38 average time/residue: 0.1143 time to fit residues: 4.8851 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 : 0.098 ------------------------------------------------------------------------------- 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: 0.0870 chunk 11 optimal weight: 3.9990 chunk 131 optimal weight: 8.9990 chunk 49 optimal weight: 0.1980 chunk 125 optimal weight: 0.0470 chunk 95 optimal weight: 1.9990 chunk 44 optimal weight: 0.5980 chunk 101 optimal weight: 7.9990 chunk 120 optimal weight: 4.9990 chunk 126 optimal weight: 0.6980 chunk 52 optimal weight: 7.9990 overall best weight: 0.3256 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.096470 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.074405 restraints weight = 14367.838| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.077063 restraints weight = 10113.163| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.079091 restraints weight = 7719.583| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.080593 restraints weight = 6237.317| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.081730 restraints weight = 5250.187| |-----------------------------------------------------------------------------| r_work (final): 0.3776 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5513 moved from start: 0.3625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 11376 Z= 0.104 Angle : 0.562 6.653 15432 Z= 0.284 Chirality : 0.040 0.140 1644 Planarity : 0.004 0.052 1956 Dihedral : 4.060 23.144 1472 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 11.73 Ramachandran Plot: Outliers : 0.29 % Allowed : 2.91 % Favored : 96.80 % 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: -0.46 (0.22), residues: 1376 helix: 0.98 (0.40), residues: 188 sheet: -1.34 (0.33), residues: 236 loop : -0.24 (0.19), residues: 952 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG b 257 TYR 0.010 0.001 TYR B 158 PHE 0.009 0.001 PHE a 160 TRP 0.029 0.001 TRP a 232 HIS 0.002 0.000 HIS A 195 Details of bonding type rmsd/Z covalent geometry : bond 0.00243 / 0.10 (11352) covalent geometry : angle 0.56088 / 0.28 (15384) SS BOND : bond 0.00252 / 0.18 ( 24) SS BOND : angle 0.83771 / 0.55 ( 48) hydrogen bonds : bond 0.03100 / 1.95 ( 236) hydrogen bonds : angle 5.46885 / 3.78 ( 612) *********************** REFINEMENT MACRO_CYCLE 5 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 36 residues out of total 304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 36 time to evaluate : 0.115 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 69 LYS cc_start: 0.9098 (mttt) cc_final: 0.8665 (mttm) REVERT: a 123 MET cc_start: 0.7227 (mmm) cc_final: 0.6935 (mmm) REVERT: a 184 MET cc_start: 0.6662 (ppp) cc_final: 0.5303 (ptm) REVERT: a 198 MET cc_start: 0.8706 (tpp) cc_final: 0.8481 (tpp) REVERT: a 219 GLU cc_start: 0.8043 (tm-30) cc_final: 0.7612 (tm-30) REVERT: a 288 THR cc_start: 0.9129 (p) cc_final: 0.8720 (p) outliers start: 0 outliers final: 0 residues processed: 36 average time/residue: 0.1033 time to fit residues: 4.2995 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 : 0.118 ------------------------------------------------------------------------------- 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: 3.9990 chunk 30 optimal weight: 0.0980 chunk 103 optimal weight: 5.9990 chunk 53 optimal weight: 3.9990 chunk 79 optimal weight: 6.9990 chunk 3 optimal weight: 0.0870 chunk 29 optimal weight: 2.9990 chunk 92 optimal weight: 2.9990 chunk 135 optimal weight: 0.0980 chunk 56 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 overall best weight: 0.8562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.4039 r_free = 0.4039 target = 0.094982 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.073029 restraints weight = 14385.028| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.075576 restraints weight = 10410.844| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.077489 restraints weight = 8045.334| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.078994 restraints weight = 6536.907| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.080085 restraints weight = 5522.798| |-----------------------------------------------------------------------------| r_work (final): 0.3737 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5540 moved from start: 0.3835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.017 11376 Z= 0.083 Angle : 0.490 5.861 15432 Z= 0.246 Chirality : 0.039 0.120 1644 Planarity : 0.003 0.032 1956 Dihedral : 3.731 21.882 1472 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 10.40 Ramachandran Plot: Outliers : 0.29 % Allowed : 2.91 % Favored : 96.80 % 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: -0.40 (0.22), residues: 1376 helix: 1.14 (0.41), residues: 188 sheet: -1.31 (0.34), residues: 232 loop : -0.23 (0.19), residues: 956 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 257 TYR 0.008 0.001 TYR a 158 PHE 0.006 0.001 PHE b 160 TRP 0.024 0.001 TRP A 232 HIS 0.001 0.001 HIS B 261 Details of bonding type rmsd/Z covalent geometry : bond 0.00182 / 0.08 (11352) covalent geometry : angle 0.48792 / 0.24 (15384) SS BOND : bond 0.00189 / 0.13 ( 24) SS BOND : angle 0.97674 / 0.64 ( 48) hydrogen bonds : bond 0.02745 / 1.74 ( 236) hydrogen bonds : angle 5.20123 / 3.57 ( 612) *********************** REFINEMENT MACRO_CYCLE 6 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 38 residues out of total 304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 38 time to evaluate : 0.103 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 69 LYS cc_start: 0.9140 (mttt) cc_final: 0.8848 (mttp) REVERT: a 123 MET cc_start: 0.7223 (mmm) cc_final: 0.6999 (mmm) REVERT: a 184 MET cc_start: 0.6388 (ppp) cc_final: 0.5350 (ptp) REVERT: a 198 MET cc_start: 0.8706 (tpp) cc_final: 0.8496 (tpp) REVERT: a 219 GLU cc_start: 0.8097 (tm-30) cc_final: 0.7709 (tm-30) REVERT: a 275 MET cc_start: 0.8583 (mmp) cc_final: 0.8338 (mmp) outliers start: 0 outliers final: 0 residues processed: 38 average time/residue: 0.1066 time to fit residues: 4.6521 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 : 0.105 ------------------------------------------------------------------------------- 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: 2.9990 chunk 75 optimal weight: 1.9990 chunk 11 optimal weight: 2.9990 chunk 83 optimal weight: 2.9990 chunk 100 optimal weight: 0.0170 chunk 108 optimal weight: 10.0000 chunk 41 optimal weight: 4.9990 chunk 9 optimal weight: 10.0000 chunk 110 optimal weight: 4.9990 chunk 17 optimal weight: 4.9990 chunk 84 optimal weight: 5.9990 overall best weight: 2.2026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** a 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 82 ASN a 107 GLN a 229 HIS ** a 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.091890 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.070471 restraints weight = 15391.103| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.072788 restraints weight = 11167.859| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.074569 restraints weight = 8691.125| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.075878 restraints weight = 7097.094| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.077054 restraints weight = 6068.218| |-----------------------------------------------------------------------------| r_work (final): 0.3687 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5633 moved from start: 0.4089 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= 0.112 Angle : 0.537 5.978 15432 Z= 0.270 Chirality : 0.039 0.122 1644 Planarity : 0.003 0.030 1956 Dihedral : 3.725 13.053 1472 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 13.33 Ramachandran Plot: Outliers : 0.29 % Allowed : 3.20 % Favored : 96.51 % 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: -0.13 (0.22), residues: 1376 helix: 1.25 (0.41), residues: 188 sheet: -0.49 (0.43), residues: 152 loop : -0.26 (0.19), residues: 1036 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG b 257 TYR 0.010 0.001 TYR B 323 PHE 0.007 0.001 PHE a 178 TRP 0.022 0.002 TRP A 232 HIS 0.003 0.001 HIS A 195 Details of bonding type rmsd/Z covalent geometry : bond 0.00248 / 0.11 (11352) covalent geometry : angle 0.53579 / 0.27 (15384) SS BOND : bond 0.00180 / 0.12 ( 24) SS BOND : angle 0.87190 / 0.56 ( 48) hydrogen bonds : bond 0.02712 / 1.76 ( 236) hydrogen bonds : angle 5.15255 / 3.54 ( 612) *********************** REFINEMENT MACRO_CYCLE 7 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 38 residues out of total 304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 38 time to evaluate : 0.146 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 34 PHE cc_start: 0.7970 (m-80) cc_final: 0.7227 (m-80) REVERT: a 69 LYS cc_start: 0.9158 (mttt) cc_final: 0.8713 (mmtt) REVERT: a 123 MET cc_start: 0.7161 (mmm) cc_final: 0.6876 (mmm) REVERT: a 184 MET cc_start: 0.6395 (ppp) cc_final: 0.5356 (ptp) REVERT: a 198 MET cc_start: 0.8815 (tpp) cc_final: 0.8569 (tpp) REVERT: a 219 GLU cc_start: 0.8180 (tm-30) cc_final: 0.7762 (tm-30) REVERT: a 275 MET cc_start: 0.8447 (mmp) cc_final: 0.8173 (mmp) outliers start: 0 outliers final: 0 residues processed: 38 average time/residue: 0.1211 time to fit residues: 5.2097 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 : 0.065 ------------------------------------------------------------------------------- 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: 0.9990 chunk 18 optimal weight: 6.9990 chunk 108 optimal weight: 6.9990 chunk 71 optimal weight: 0.9980 chunk 56 optimal weight: 0.5980 chunk 76 optimal weight: 0.0270 chunk 130 optimal weight: 6.9990 chunk 97 optimal weight: 0.4980 chunk 47 optimal weight: 0.0870 chunk 4 optimal weight: 0.7980 chunk 120 optimal weight: 3.9990 overall best weight: 0.4016 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** a 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 107 GLN a 263 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 = 0.4018 r_free = 0.4018 target = 0.094127 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.070425 restraints weight = 13733.670| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.073100 restraints weight = 9748.950| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.075224 restraints weight = 7485.433| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.076942 restraints weight = 6052.850| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.078284 restraints weight = 5078.861| |-----------------------------------------------------------------------------| r_work (final): 0.3731 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5588 moved from start: 0.4161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.017 11376 Z= 0.080 Angle : 0.487 5.772 15432 Z= 0.242 Chirality : 0.039 0.121 1644 Planarity : 0.003 0.040 1956 Dihedral : 3.438 13.047 1472 Min Nonbonded Distance : 2.636 Molprobity Statistics. All-atom Clashscore : 9.94 Ramachandran Plot: Outliers : 0.29 % Allowed : 3.49 % Favored : 96.22 % 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: -0.19 (0.22), residues: 1376 helix: 1.26 (0.41), residues: 188 sheet: -0.58 (0.37), residues: 172 loop : -0.28 (0.19), residues: 1016 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG b 257 TYR 0.006 0.001 TYR a 158 PHE 0.004 0.001 PHE B 160 TRP 0.020 0.001 TRP A 232 HIS 0.007 0.001 HIS A 229 Details of bonding type rmsd/Z covalent geometry : bond 0.00174 / 0.08 (11352) covalent geometry : angle 0.48603 / 0.24 (15384) SS BOND : bond 0.00194 / 0.14 ( 24) SS BOND : angle 0.82703 / 0.51 ( 48) hydrogen bonds : bond 0.02869 / 1.82 ( 236) hydrogen bonds : angle 5.21464 / 3.54 ( 612) *********************** REFINEMENT MACRO_CYCLE 8 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 41 residues out of total 304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 41 time to evaluate : 0.084 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 34 PHE cc_start: 0.8071 (m-80) cc_final: 0.7306 (m-80) REVERT: a 69 LYS cc_start: 0.9167 (mttt) cc_final: 0.8860 (mttp) REVERT: a 123 MET cc_start: 0.7198 (mmm) cc_final: 0.6925 (mmm) REVERT: a 184 MET cc_start: 0.6461 (ppp) cc_final: 0.5874 (ptp) REVERT: a 198 MET cc_start: 0.8927 (tpp) cc_final: 0.8702 (tpp) REVERT: a 225 TRP cc_start: 0.8693 (t-100) cc_final: 0.8449 (t60) outliers start: 0 outliers final: 0 residues processed: 41 average time/residue: 0.0985 time to fit residues: 4.6421 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 : 0.102 ------------------------------------------------------------------------------- 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: 0.0870 chunk 79 optimal weight: 6.9990 chunk 11 optimal weight: 0.8980 chunk 23 optimal weight: 1.9990 chunk 134 optimal weight: 9.9990 chunk 4 optimal weight: 0.9990 chunk 56 optimal weight: 2.9990 chunk 92 optimal weight: 0.0270 chunk 50 optimal weight: 0.0770 chunk 18 optimal weight: 6.9990 chunk 97 optimal weight: 0.0970 overall best weight: 0.2372 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.4056 r_free = 0.4056 target = 0.094805 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.073076 restraints weight = 15287.538| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.075623 restraints weight = 10944.901| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.077637 restraints weight = 8446.533| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.079102 restraints weight = 6871.721| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.080297 restraints weight = 5821.700| |-----------------------------------------------------------------------------| r_work (final): 0.3765 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5520 moved from start: 0.4456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 11376 Z= 0.093 Angle : 0.536 5.377 15432 Z= 0.266 Chirality : 0.040 0.123 1644 Planarity : 0.003 0.033 1956 Dihedral : 3.590 12.836 1472 Min Nonbonded Distance : 2.641 Molprobity Statistics. All-atom Clashscore : 9.21 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: -0.23 (0.22), residues: 1376 helix: 1.26 (0.41), residues: 188 sheet: -0.62 (0.34), residues: 200 loop : -0.30 (0.19), residues: 988 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 299 TYR 0.008 0.001 TYR a 331 PHE 0.003 0.001 PHE a 160 TRP 0.017 0.001 TRP A 232 HIS 0.003 0.000 HIS b 229 Details of bonding type rmsd/Z covalent geometry : bond 0.00204 / 0.09 (11352) covalent geometry : angle 0.53429 / 0.27 (15384) SS BOND : bond 0.00383 / 0.29 ( 24) SS BOND : angle 0.90755 / 0.57 ( 48) hydrogen bonds : bond 0.02742 / 1.75 ( 236) hydrogen bonds : angle 4.98733 / 3.36 ( 612) *********************** REFINEMENT MACRO_CYCLE 9 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 36 residues out of total 304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 36 time to evaluate : 0.119 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 184 MET cc_start: 0.6618 (ppp) cc_final: 0.5978 (ptp) REVERT: a 225 TRP cc_start: 0.8736 (t-100) cc_final: 0.8506 (t60) REVERT: a 333 MET cc_start: 0.7002 (pmm) cc_final: 0.6618 (pmm) outliers start: 0 outliers final: 0 residues processed: 36 average time/residue: 0.1032 time to fit residues: 4.2441 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 : 0.065 ------------------------------------------------------------------------------- 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: 0.0980 chunk 89 optimal weight: 0.1980 chunk 5 optimal weight: 0.0570 chunk 24 optimal weight: 0.9990 chunk 115 optimal weight: 0.7980 chunk 39 optimal weight: 0.7980 chunk 69 optimal weight: 0.6980 chunk 44 optimal weight: 0.0370 chunk 53 optimal weight: 0.5980 chunk 111 optimal weight: 20.0000 chunk 128 optimal weight: 0.0870 overall best weight: 0.0954 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** a 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 107 GLN a 263 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 = 0.4062 r_free = 0.4062 target = 0.096245 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.074413 restraints weight = 14880.598| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.077015 restraints weight = 10767.855| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.078968 restraints weight = 8322.698| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.080494 restraints weight = 6767.946| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.081532 restraints weight = 5709.133| |-----------------------------------------------------------------------------| r_work (final): 0.3768 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5509 moved from start: 0.4749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 11376 Z= 0.096 Angle : 0.586 6.352 15432 Z= 0.286 Chirality : 0.044 0.348 1644 Planarity : 0.004 0.039 1956 Dihedral : 3.578 13.864 1472 Min Nonbonded Distance : 2.639 Molprobity Statistics. All-atom Clashscore : 9.71 Ramachandran Plot: Outliers : 0.29 % Allowed : 3.49 % Favored : 96.22 % 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: -0.36 (0.22), residues: 1376 helix: 1.09 (0.42), residues: 188 sheet: -0.78 (0.37), residues: 184 loop : -0.38 (0.19), residues: 1004 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG a 192 TYR 0.005 0.001 TYR b 323 PHE 0.005 0.001 PHE A 247 TRP 0.015 0.001 TRP b 330 HIS 0.002 0.000 HIS b 229 Details of bonding type rmsd/Z covalent geometry : bond 0.00210 / 0.10 (11352) covalent geometry : angle 0.58531 / 0.29 (15384) SS BOND : bond 0.00291 / 0.22 ( 24) SS BOND : angle 0.85905 / 0.54 ( 48) hydrogen bonds : bond 0.03201 / 2.13 ( 236) hydrogen bonds : angle 5.24710 / 3.54 ( 612) ********************** REFINEMENT MACRO_CYCLE 10 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 37 residues out of total 304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 37 time to evaluate : 0.112 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 69 LYS cc_start: 0.9106 (mttt) cc_final: 0.8890 (mttt) REVERT: a 166 ASN cc_start: 0.9297 (t0) cc_final: 0.9062 (t0) REVERT: a 168 TRP cc_start: 0.9195 (m-90) cc_final: 0.8945 (m-90) REVERT: a 184 MET cc_start: 0.6377 (ppp) cc_final: 0.5948 (ptp) REVERT: a 225 TRP cc_start: 0.8734 (t-100) cc_final: 0.8527 (t60) REVERT: a 333 MET cc_start: 0.6970 (pmm) cc_final: 0.6538 (pmm) outliers start: 0 outliers final: 0 residues processed: 37 average time/residue: 0.0812 time to fit residues: 3.5232 Evaluate side-chains 31 residues out of total 304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 31 time to evaluate : 0.117 ------------------------------------------------------------------------------- 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: 0.1980 chunk 71 optimal weight: 4.9990 chunk 38 optimal weight: 0.5980 chunk 27 optimal weight: 0.0000 chunk 76 optimal weight: 0.9990 chunk 15 optimal weight: 0.8980 chunk 23 optimal weight: 1.9990 chunk 90 optimal weight: 0.0870 chunk 40 optimal weight: 1.9990 chunk 49 optimal weight: 0.9990 chunk 25 optimal weight: 2.9990 overall best weight: 0.3562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.4048 r_free = 0.4048 target = 0.095238 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.073989 restraints weight = 14626.477| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.076437 restraints weight = 10625.646| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.078309 restraints weight = 8276.106| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.079676 restraints weight = 6745.514| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.080880 restraints weight = 5735.731| |-----------------------------------------------------------------------------| r_work (final): 0.3761 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5521 moved from start: 0.4755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 11376 Z= 0.087 Angle : 0.545 7.180 15432 Z= 0.265 Chirality : 0.039 0.155 1644 Planarity : 0.003 0.035 1956 Dihedral : 3.456 14.018 1472 Min Nonbonded Distance : 2.635 Molprobity Statistics. All-atom Clashscore : 9.62 Ramachandran Plot: Outliers : 0.29 % Allowed : 3.78 % Favored : 95.93 % 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: -0.30 (0.22), residues: 1376 helix: 1.29 (0.42), residues: 188 sheet: -0.56 (0.37), residues: 180 loop : -0.41 (0.18), residues: 1008 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG a 192 TYR 0.014 0.001 TYR B 323 PHE 0.004 0.001 PHE B 277 TRP 0.015 0.001 TRP a 201 HIS 0.002 0.000 HIS b 229 Details of bonding type rmsd/Z covalent geometry : bond 0.00201 / 0.09 (11352) covalent geometry : angle 0.54363 / 0.26 (15384) SS BOND : bond 0.00242 / 0.18 ( 24) SS BOND : angle 0.83272 / 0.53 ( 48) hydrogen bonds : bond 0.02495 / 1.62 ( 236) hydrogen bonds : angle 5.28778 / 3.62 ( 612) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1209.13 seconds wall clock time: 21 minutes 56.83 seconds (1316.83 seconds total)