Starting phenix.real_space_refine on Sat Jul 4 15:11:34 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7kvc_23046/07_2026/7kvc_23046.cif Found real_map, /net/cci-nas-00/data/ceres_data/7kvc_23046/07_2026/7kvc_23046.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 { model { file = "/net/cci-nas-00/data/ceres_data/7kvc_23046/07_2026/7kvc_23046.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7kvc_23046/07_2026/7kvc_23046.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7kvc_23046/07_2026/7kvc_23046.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7kvc_23046/07_2026/7kvc_23046.map" } 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= 0.011 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 40 5.16 5 C 14120 2.51 5 N 3590 2.21 5 O 4170 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 110 residue(s): 0.02s 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: 21920 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 2192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 266, 2192 Classifications: {'peptide': 266} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 257} Chain breaks: 6 Restraints were copied for chains: B, C, D, E, F, G, H, I, J Time building chain proxies: 2.72, per 1000 atoms: 0.12 Number of scatterers: 21920 At special positions: 0 Unit cell: (136.85, 138.55, 99.45, 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 40 16.00 O 4170 8.00 N 3590 7.00 C 14120 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.78 Conformation dependent library (CDL) restraints added in 945.4 milliseconds 5040 Ramachandran restraints generated. 2520 Oldfield, 0 Emsley, 2520 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5060 Finding SS restraints... Secondary structure from input PDB file: 100 helices and 30 sheets defined 42.9% alpha, 12.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.59 Creating SS restraints... Processing helix chain 'A' and resid 52 through 62 Processing helix chain 'A' and resid 64 through 68 Processing helix chain 'A' and resid 80 through 101 removed outlier: 3.948A pdb=" N ILE A 99 " --> pdb=" O ASN A 95 " (cutoff:3.500A) Processing helix chain 'A' and resid 173 through 201 Processing helix chain 'A' and resid 203 through 208 removed outlier: 4.318A pdb=" N ARG A 207 " --> pdb=" O SER A 204 " (cutoff:3.500A) Processing helix chain 'A' and resid 211 through 213 No H-bonds generated for 'chain 'A' and resid 211 through 213' Processing helix chain 'A' and resid 214 through 227 Processing helix chain 'A' and resid 239 through 247 removed outlier: 3.748A pdb=" N PHE A 247 " --> pdb=" O GLN A 243 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 259 Processing helix chain 'A' and resid 271 through 276 removed outlier: 4.104A pdb=" N ASP A 276 " --> pdb=" O ARG A 272 " (cutoff:3.500A) Processing helix chain 'B' and resid 52 through 62 Processing helix chain 'B' and resid 64 through 68 Processing helix chain 'B' and resid 80 through 101 removed outlier: 3.949A pdb=" N ILE B 99 " --> pdb=" O ASN B 95 " (cutoff:3.500A) Processing helix chain 'B' and resid 173 through 201 Processing helix chain 'B' and resid 203 through 208 removed outlier: 4.318A pdb=" N ARG B 207 " --> pdb=" O SER B 204 " (cutoff:3.500A) Processing helix chain 'B' and resid 211 through 213 No H-bonds generated for 'chain 'B' and resid 211 through 213' Processing helix chain 'B' and resid 214 through 227 Processing helix chain 'B' and resid 239 through 247 removed outlier: 3.748A pdb=" N PHE B 247 " --> pdb=" O GLN B 243 " (cutoff:3.500A) Processing helix chain 'B' and resid 251 through 259 Processing helix chain 'B' and resid 271 through 276 removed outlier: 4.103A pdb=" N ASP B 276 " --> pdb=" O ARG B 272 " (cutoff:3.500A) Processing helix chain 'C' and resid 52 through 62 Processing helix chain 'C' and resid 64 through 68 Processing helix chain 'C' and resid 80 through 101 removed outlier: 3.950A pdb=" N ILE C 99 " --> pdb=" O ASN C 95 " (cutoff:3.500A) Processing helix chain 'C' and resid 173 through 201 Processing helix chain 'C' and resid 203 through 208 removed outlier: 4.318A pdb=" N ARG C 207 " --> pdb=" O SER C 204 " (cutoff:3.500A) Processing helix chain 'C' and resid 211 through 213 No H-bonds generated for 'chain 'C' and resid 211 through 213' Processing helix chain 'C' and resid 214 through 227 Processing helix chain 'C' and resid 239 through 247 removed outlier: 3.747A pdb=" N PHE C 247 " --> pdb=" O GLN C 243 " (cutoff:3.500A) Processing helix chain 'C' and resid 251 through 259 Processing helix chain 'C' and resid 271 through 276 removed outlier: 4.103A pdb=" N ASP C 276 " --> pdb=" O ARG C 272 " (cutoff:3.500A) Processing helix chain 'D' and resid 52 through 62 Processing helix chain 'D' and resid 64 through 68 Processing helix chain 'D' and resid 80 through 101 removed outlier: 3.949A pdb=" N ILE D 99 " --> pdb=" O ASN D 95 " (cutoff:3.500A) Processing helix chain 'D' and resid 173 through 201 Processing helix chain 'D' and resid 203 through 208 removed outlier: 4.319A pdb=" N ARG D 207 " --> pdb=" O SER D 204 " (cutoff:3.500A) Processing helix chain 'D' and resid 211 through 213 No H-bonds generated for 'chain 'D' and resid 211 through 213' Processing helix chain 'D' and resid 214 through 227 Processing helix chain 'D' and resid 239 through 247 removed outlier: 3.747A pdb=" N PHE D 247 " --> pdb=" O GLN D 243 " (cutoff:3.500A) Processing helix chain 'D' and resid 251 through 259 Processing helix chain 'D' and resid 271 through 276 removed outlier: 4.103A pdb=" N ASP D 276 " --> pdb=" O ARG D 272 " (cutoff:3.500A) Processing helix chain 'E' and resid 52 through 62 Processing helix chain 'E' and resid 64 through 68 Processing helix chain 'E' and resid 80 through 101 removed outlier: 3.949A pdb=" N ILE E 99 " --> pdb=" O ASN E 95 " (cutoff:3.500A) Processing helix chain 'E' and resid 173 through 201 Processing helix chain 'E' and resid 203 through 208 removed outlier: 4.318A pdb=" N ARG E 207 " --> pdb=" O SER E 204 " (cutoff:3.500A) Processing helix chain 'E' and resid 211 through 213 No H-bonds generated for 'chain 'E' and resid 211 through 213' Processing helix chain 'E' and resid 214 through 227 Processing helix chain 'E' and resid 239 through 247 removed outlier: 3.748A pdb=" N PHE E 247 " --> pdb=" O GLN E 243 " (cutoff:3.500A) Processing helix chain 'E' and resid 251 through 259 Processing helix chain 'E' and resid 271 through 276 removed outlier: 4.104A pdb=" N ASP E 276 " --> pdb=" O ARG E 272 " (cutoff:3.500A) Processing helix chain 'F' and resid 52 through 62 Processing helix chain 'F' and resid 64 through 68 Processing helix chain 'F' and resid 80 through 101 removed outlier: 3.949A pdb=" N ILE F 99 " --> pdb=" O ASN F 95 " (cutoff:3.500A) Processing helix chain 'F' and resid 173 through 201 Processing helix chain 'F' and resid 203 through 208 removed outlier: 4.318A pdb=" N ARG F 207 " --> pdb=" O SER F 204 " (cutoff:3.500A) Processing helix chain 'F' and resid 211 through 213 No H-bonds generated for 'chain 'F' and resid 211 through 213' Processing helix chain 'F' and resid 214 through 227 Processing helix chain 'F' and resid 239 through 247 removed outlier: 3.747A pdb=" N PHE F 247 " --> pdb=" O GLN F 243 " (cutoff:3.500A) Processing helix chain 'F' and resid 251 through 259 Processing helix chain 'F' and resid 271 through 276 removed outlier: 4.103A pdb=" N ASP F 276 " --> pdb=" O ARG F 272 " (cutoff:3.500A) Processing helix chain 'G' and resid 52 through 62 Processing helix chain 'G' and resid 64 through 68 Processing helix chain 'G' and resid 80 through 101 removed outlier: 3.949A pdb=" N ILE G 99 " --> pdb=" O ASN G 95 " (cutoff:3.500A) Processing helix chain 'G' and resid 173 through 201 Processing helix chain 'G' and resid 203 through 208 removed outlier: 4.318A pdb=" N ARG G 207 " --> pdb=" O SER G 204 " (cutoff:3.500A) Processing helix chain 'G' and resid 211 through 213 No H-bonds generated for 'chain 'G' and resid 211 through 213' Processing helix chain 'G' and resid 214 through 227 Processing helix chain 'G' and resid 239 through 247 removed outlier: 3.747A pdb=" N PHE G 247 " --> pdb=" O GLN G 243 " (cutoff:3.500A) Processing helix chain 'G' and resid 251 through 259 Processing helix chain 'G' and resid 271 through 276 removed outlier: 4.103A pdb=" N ASP G 276 " --> pdb=" O ARG G 272 " (cutoff:3.500A) Processing helix chain 'H' and resid 52 through 62 Processing helix chain 'H' and resid 64 through 68 Processing helix chain 'H' and resid 80 through 101 removed outlier: 3.949A pdb=" N ILE H 99 " --> pdb=" O ASN H 95 " (cutoff:3.500A) Processing helix chain 'H' and resid 173 through 201 Processing helix chain 'H' and resid 203 through 208 removed outlier: 4.318A pdb=" N ARG H 207 " --> pdb=" O SER H 204 " (cutoff:3.500A) Processing helix chain 'H' and resid 211 through 213 No H-bonds generated for 'chain 'H' and resid 211 through 213' Processing helix chain 'H' and resid 214 through 227 Processing helix chain 'H' and resid 239 through 247 removed outlier: 3.748A pdb=" N PHE H 247 " --> pdb=" O GLN H 243 " (cutoff:3.500A) Processing helix chain 'H' and resid 251 through 259 Processing helix chain 'H' and resid 271 through 276 removed outlier: 4.104A pdb=" N ASP H 276 " --> pdb=" O ARG H 272 " (cutoff:3.500A) Processing helix chain 'I' and resid 52 through 62 Processing helix chain 'I' and resid 64 through 68 Processing helix chain 'I' and resid 80 through 101 removed outlier: 3.950A pdb=" N ILE I 99 " --> pdb=" O ASN I 95 " (cutoff:3.500A) Processing helix chain 'I' and resid 173 through 201 Processing helix chain 'I' and resid 203 through 208 removed outlier: 4.318A pdb=" N ARG I 207 " --> pdb=" O SER I 204 " (cutoff:3.500A) Processing helix chain 'I' and resid 211 through 213 No H-bonds generated for 'chain 'I' and resid 211 through 213' Processing helix chain 'I' and resid 214 through 227 Processing helix chain 'I' and resid 239 through 247 removed outlier: 3.747A pdb=" N PHE I 247 " --> pdb=" O GLN I 243 " (cutoff:3.500A) Processing helix chain 'I' and resid 251 through 259 Processing helix chain 'I' and resid 271 through 276 removed outlier: 4.103A pdb=" N ASP I 276 " --> pdb=" O ARG I 272 " (cutoff:3.500A) Processing helix chain 'J' and resid 52 through 62 Processing helix chain 'J' and resid 64 through 68 Processing helix chain 'J' and resid 80 through 101 removed outlier: 3.949A pdb=" N ILE J 99 " --> pdb=" O ASN J 95 " (cutoff:3.500A) Processing helix chain 'J' and resid 173 through 201 Processing helix chain 'J' and resid 203 through 208 removed outlier: 4.319A pdb=" N ARG J 207 " --> pdb=" O SER J 204 " (cutoff:3.500A) Processing helix chain 'J' and resid 211 through 213 No H-bonds generated for 'chain 'J' and resid 211 through 213' Processing helix chain 'J' and resid 214 through 227 Processing helix chain 'J' and resid 239 through 247 removed outlier: 3.747A pdb=" N PHE J 247 " --> pdb=" O GLN J 243 " (cutoff:3.500A) Processing helix chain 'J' and resid 251 through 259 Processing helix chain 'J' and resid 271 through 276 removed outlier: 4.104A pdb=" N ASP J 276 " --> pdb=" O ARG J 272 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 13 through 17 Processing sheet with id=AA2, first strand: chain 'A' and resid 156 through 159 removed outlier: 4.127A pdb=" N LEU A 116 " --> pdb=" O LYS A 309 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N LYS A 309 " --> pdb=" O LEU A 116 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 279 through 285 removed outlier: 3.503A pdb=" N SER A 302 " --> pdb=" O GLY A 298 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 13 through 17 Processing sheet with id=AA5, first strand: chain 'B' and resid 156 through 159 removed outlier: 4.127A pdb=" N LEU B 116 " --> pdb=" O LYS B 309 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N LYS B 309 " --> pdb=" O LEU B 116 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 279 through 285 removed outlier: 3.504A pdb=" N SER B 302 " --> pdb=" O GLY B 298 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 13 through 17 Processing sheet with id=AA8, first strand: chain 'C' and resid 156 through 159 removed outlier: 4.127A pdb=" N LEU C 116 " --> pdb=" O LYS C 309 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N LYS C 309 " --> pdb=" O LEU C 116 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 279 through 285 removed outlier: 3.504A pdb=" N SER C 302 " --> pdb=" O GLY C 298 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 13 through 17 Processing sheet with id=AB2, first strand: chain 'D' and resid 156 through 159 removed outlier: 4.127A pdb=" N LEU D 116 " --> pdb=" O LYS D 309 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N LYS D 309 " --> pdb=" O LEU D 116 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 279 through 285 removed outlier: 3.503A pdb=" N SER D 302 " --> pdb=" O GLY D 298 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 13 through 17 Processing sheet with id=AB5, first strand: chain 'E' and resid 156 through 159 removed outlier: 4.128A pdb=" N LEU E 116 " --> pdb=" O LYS E 309 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N LYS E 309 " --> pdb=" O LEU E 116 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 279 through 285 removed outlier: 3.503A pdb=" N SER E 302 " --> pdb=" O GLY E 298 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 13 through 17 Processing sheet with id=AB8, first strand: chain 'F' and resid 156 through 159 removed outlier: 4.128A pdb=" N LEU F 116 " --> pdb=" O LYS F 309 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N LYS F 309 " --> pdb=" O LEU F 116 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 279 through 285 removed outlier: 3.503A pdb=" N SER F 302 " --> pdb=" O GLY F 298 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'G' and resid 13 through 17 Processing sheet with id=AC2, first strand: chain 'G' and resid 156 through 159 removed outlier: 4.127A pdb=" N LEU G 116 " --> pdb=" O LYS G 309 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N LYS G 309 " --> pdb=" O LEU G 116 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'G' and resid 279 through 285 removed outlier: 3.504A pdb=" N SER G 302 " --> pdb=" O GLY G 298 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'H' and resid 13 through 17 Processing sheet with id=AC5, first strand: chain 'H' and resid 156 through 159 removed outlier: 4.128A pdb=" N LEU H 116 " --> pdb=" O LYS H 309 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N LYS H 309 " --> pdb=" O LEU H 116 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'H' and resid 279 through 285 removed outlier: 3.503A pdb=" N SER H 302 " --> pdb=" O GLY H 298 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'I' and resid 13 through 17 Processing sheet with id=AC8, first strand: chain 'I' and resid 156 through 159 removed outlier: 4.128A pdb=" N LEU I 116 " --> pdb=" O LYS I 309 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N LYS I 309 " --> pdb=" O LEU I 116 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'I' and resid 279 through 285 removed outlier: 3.504A pdb=" N SER I 302 " --> pdb=" O GLY I 298 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'J' and resid 13 through 17 Processing sheet with id=AD2, first strand: chain 'J' and resid 156 through 159 removed outlier: 4.127A pdb=" N LEU J 116 " --> pdb=" O LYS J 309 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N LYS J 309 " --> pdb=" O LEU J 116 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'J' and resid 279 through 285 removed outlier: 3.503A pdb=" N SER J 302 " --> pdb=" O GLY J 298 " (cutoff:3.500A) 960 hydrogen bonds defined for protein. 2610 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: 3.38 Time building geometry restraints manager: 2.41 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 6996 1.34 - 1.46: 4253 1.46 - 1.57: 10971 1.57 - 1.69: 0 1.69 - 1.81: 70 Bond restraints: 22290 Sorted by residual: bond pdb=" C ASP C 329 " pdb=" N PHE C 330 " ideal model delta sigma weight residual 1.332 1.310 0.023 1.40e-02 5.10e+03 2.60e+00 bond pdb=" C ASP G 329 " pdb=" N PHE G 330 " ideal model delta sigma weight residual 1.332 1.310 0.022 1.40e-02 5.10e+03 2.57e+00 bond pdb=" C ASP D 329 " pdb=" N PHE D 330 " ideal model delta sigma weight residual 1.332 1.310 0.022 1.40e-02 5.10e+03 2.51e+00 bond pdb=" C ASP J 329 " pdb=" N PHE J 330 " ideal model delta sigma weight residual 1.332 1.310 0.022 1.40e-02 5.10e+03 2.50e+00 bond pdb=" C ASP B 329 " pdb=" N PHE B 330 " ideal model delta sigma weight residual 1.332 1.310 0.022 1.40e-02 5.10e+03 2.45e+00 ... (remaining 22285 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.21: 26992 1.21 - 2.43: 2312 2.43 - 3.64: 479 3.64 - 4.85: 186 4.85 - 6.07: 51 Bond angle restraints: 30020 Sorted by residual: angle pdb=" N GLU A 94 " pdb=" CA GLU A 94 " pdb=" CB GLU A 94 " ideal model delta sigma weight residual 110.16 116.23 -6.07 1.48e+00 4.57e-01 1.68e+01 angle pdb=" N GLU H 94 " pdb=" CA GLU H 94 " pdb=" CB GLU H 94 " ideal model delta sigma weight residual 110.16 116.22 -6.06 1.48e+00 4.57e-01 1.68e+01 angle pdb=" N GLU G 94 " pdb=" CA GLU G 94 " pdb=" CB GLU G 94 " ideal model delta sigma weight residual 110.16 116.21 -6.05 1.48e+00 4.57e-01 1.67e+01 angle pdb=" N GLU I 94 " pdb=" CA GLU I 94 " pdb=" CB GLU I 94 " ideal model delta sigma weight residual 110.16 116.20 -6.04 1.48e+00 4.57e-01 1.66e+01 angle pdb=" N GLU F 94 " pdb=" CA GLU F 94 " pdb=" CB GLU F 94 " ideal model delta sigma weight residual 110.16 116.20 -6.04 1.48e+00 4.57e-01 1.66e+01 ... (remaining 30015 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.05: 11842 17.05 - 34.11: 1398 34.11 - 51.16: 180 51.16 - 68.22: 30 68.22 - 85.27: 10 Dihedral angle restraints: 13460 sinusoidal: 5650 harmonic: 7810 Sorted by residual: dihedral pdb=" CA ASP B 50 " pdb=" C ASP B 50 " pdb=" N GLY B 51 " pdb=" CA GLY B 51 " ideal model delta harmonic sigma weight residual -180.00 -156.83 -23.17 0 5.00e+00 4.00e-02 2.15e+01 dihedral pdb=" CA ASP G 50 " pdb=" C ASP G 50 " pdb=" N GLY G 51 " pdb=" CA GLY G 51 " ideal model delta harmonic sigma weight residual 180.00 -156.84 -23.16 0 5.00e+00 4.00e-02 2.15e+01 dihedral pdb=" CA GLU F 271 " pdb=" C GLU F 271 " pdb=" N ARG F 272 " pdb=" CA ARG F 272 " ideal model delta harmonic sigma weight residual 180.00 -156.84 -23.16 0 5.00e+00 4.00e-02 2.14e+01 ... (remaining 13457 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 2198 0.038 - 0.076: 795 0.076 - 0.114: 260 0.114 - 0.152: 137 0.152 - 0.190: 10 Chirality restraints: 3400 Sorted by residual: chirality pdb=" CG LEU F 333 " pdb=" CB LEU F 333 " pdb=" CD1 LEU F 333 " pdb=" CD2 LEU F 333 " both_signs ideal model delta sigma weight residual False -2.59 -2.40 -0.19 2.00e-01 2.50e+01 9.01e-01 chirality pdb=" CG LEU J 333 " pdb=" CB LEU J 333 " pdb=" CD1 LEU J 333 " pdb=" CD2 LEU J 333 " both_signs ideal model delta sigma weight residual False -2.59 -2.40 -0.19 2.00e-01 2.50e+01 8.96e-01 chirality pdb=" CG LEU D 333 " pdb=" CB LEU D 333 " pdb=" CD1 LEU D 333 " pdb=" CD2 LEU D 333 " both_signs ideal model delta sigma weight residual False -2.59 -2.40 -0.19 2.00e-01 2.50e+01 8.96e-01 ... (remaining 3397 not shown) Planarity restraints: 3800 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR D 250 " 0.031 5.00e-02 4.00e+02 4.68e-02 3.50e+00 pdb=" N PRO D 251 " -0.081 5.00e-02 4.00e+02 pdb=" CA PRO D 251 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO D 251 " 0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR C 250 " 0.031 5.00e-02 4.00e+02 4.67e-02 3.49e+00 pdb=" N PRO C 251 " -0.081 5.00e-02 4.00e+02 pdb=" CA PRO C 251 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO C 251 " 0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR A 250 " 0.031 5.00e-02 4.00e+02 4.67e-02 3.49e+00 pdb=" N PRO A 251 " -0.081 5.00e-02 4.00e+02 pdb=" CA PRO A 251 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO A 251 " 0.026 5.00e-02 4.00e+02 ... (remaining 3797 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 4649 2.76 - 3.29: 25142 3.29 - 3.83: 39098 3.83 - 4.36: 43860 4.36 - 4.90: 66715 Nonbonded interactions: 179464 Sorted by model distance: nonbonded pdb=" NE ARG I 215 " pdb=" O ALA I 245 " model vdw 2.224 3.120 nonbonded pdb=" NE ARG C 215 " pdb=" O ALA C 245 " model vdw 2.224 3.120 nonbonded pdb=" NE ARG A 215 " pdb=" O ALA A 245 " model vdw 2.224 3.120 nonbonded pdb=" NE ARG F 215 " pdb=" O ALA F 245 " model vdw 2.224 3.120 nonbonded pdb=" NE ARG G 215 " pdb=" O ALA G 245 " model vdw 2.224 3.120 ... (remaining 179459 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: 0.08 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' } Set up NCS constraints Number of NCS constrained groups: 1 pdb_interpretation.ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' } 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: 1.000 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: 0.020 Extract box with map and model: 0.310 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 16.740 Find NCS groups from input model: 0.200 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:1.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.600 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8070 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 : 0.005 0.038 22290 Z= 0.229 Angle : 0.836 6.069 30020 Z= 0.460 Chirality : 0.049 0.190 3400 Planarity : 0.005 0.047 3800 Dihedral : 13.910 85.271 8400 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 33.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.71 % Favored : 89.29 % Rotamer: Outliers : 0.00 % Allowed : 0.40 % Favored : 99.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % 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: -2.46 (0.16), residues: 2520 helix: -0.42 (0.17), residues: 880 sheet: -1.75 (0.24), residues: 420 loop : -2.54 (0.17), residues: 1220 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG H 272 TYR 0.017 0.002 TYR E 305 PHE 0.021 0.002 PHE G 330 HIS 0.004 0.001 HIS B 197 Details of bonding type rmsd/Z covalent geometry : bond 0.00479 / 0.23 (22290) covalent geometry : angle 0.83628 / 0.46 (30020) hydrogen bonds : bond 0.14957 / 9.88 ( 960) hydrogen bonds : angle 6.80853 / 4.63 ( 2610) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5040 Ramachandran restraints generated. 2520 Oldfield, 0 Emsley, 2520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5040 Ramachandran restraints generated. 2520 Oldfield, 0 Emsley, 2520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 40 time to evaluate : 0.094 Fit side-chains revert: symmetry clash REVERT: A 85 PHE cc_start: 0.9433 (t80) cc_final: 0.9164 (t80) REVERT: A 198 LEU cc_start: 0.9390 (mt) cc_final: 0.9130 (mt) outliers start: 0 outliers final: 0 residues processed: 40 average time/residue: 0.0268 time to fit residues: 1.4644 Evaluate side-chains 37 residues out of total 249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 37 time to evaluate : 0.054 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 197 optimal weight: 4.9990 chunk 215 optimal weight: 30.0000 chunk 20 optimal weight: 0.9980 chunk 132 optimal weight: 5.9990 chunk 248 optimal weight: 1.9990 chunk 207 optimal weight: 3.9990 chunk 155 optimal weight: 3.9990 chunk 244 optimal weight: 40.0000 chunk 183 optimal weight: 9.9990 chunk 111 optimal weight: 30.0000 chunk 258 optimal weight: 20.0000 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.067960 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2962 r_free = 0.2962 target = 0.054067 restraints weight = 11622.800| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.055770 restraints weight = 7307.490| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.057140 restraints weight = 5347.737| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.058212 restraints weight = 4144.156| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.058946 restraints weight = 3375.618| |-----------------------------------------------------------------------------| r_work (final): 0.3076 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7870 moved from start: 0.2091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 22290 Z= 0.155 Angle : 0.713 6.125 30020 Z= 0.376 Chirality : 0.043 0.131 3400 Planarity : 0.005 0.054 3800 Dihedral : 5.550 20.844 2900 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 17.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.54 % Favored : 92.46 % Rotamer: Outliers : 0.40 % Allowed : 8.43 % Favored : 91.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % 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: -1.75 (0.16), residues: 2520 helix: 0.38 (0.17), residues: 880 sheet: -0.98 (0.26), residues: 350 loop : -2.42 (0.15), residues: 1290 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 215 TYR 0.033 0.003 TYR F 305 PHE 0.020 0.002 PHE A 226 HIS 0.007 0.001 HIS C 197 Details of bonding type rmsd/Z covalent geometry : bond 0.00328 / 0.16 (22290) covalent geometry : angle 0.71286 / 0.38 (30020) hydrogen bonds : bond 0.04762 / 3.10 ( 960) hydrogen bonds : angle 5.25135 / 3.60 ( 2610) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5040 Ramachandran restraints generated. 2520 Oldfield, 0 Emsley, 2520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5040 Ramachandran restraints generated. 2520 Oldfield, 0 Emsley, 2520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 48 time to evaluate : 0.089 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 13 LYS cc_start: 0.8672 (mmmm) cc_final: 0.8457 (mmmm) REVERT: E 85 PHE cc_start: 0.9360 (t80) cc_final: 0.9051 (t80) REVERT: E 198 LEU cc_start: 0.9458 (mt) cc_final: 0.9251 (mt) REVERT: E 250 TYR cc_start: 0.8258 (t80) cc_final: 0.7481 (t80) REVERT: E 253 ASP cc_start: 0.9371 (p0) cc_final: 0.9143 (p0) outliers start: 1 outliers final: 1 residues processed: 49 average time/residue: 0.0355 time to fit residues: 2.2984 Evaluate side-chains 44 residues out of total 249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 43 time to evaluate : 0.063 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 49 optimal weight: 0.0170 chunk 2 optimal weight: 3.9990 chunk 123 optimal weight: 0.5980 chunk 116 optimal weight: 4.9990 chunk 254 optimal weight: 1.9990 chunk 159 optimal weight: 0.0980 chunk 140 optimal weight: 30.0000 chunk 115 optimal weight: 8.9990 chunk 4 optimal weight: 20.0000 chunk 253 optimal weight: 0.4980 chunk 181 optimal weight: 0.6980 overall best weight: 0.3818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 238 ASN ** E 258 GLN ** 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 = 0.3350 r_free = 0.3350 target = 0.071659 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.056466 restraints weight = 11049.701| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.058428 restraints weight = 7044.491| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.059862 restraints weight = 5081.625| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.060927 restraints weight = 3962.530| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 17)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.061538 restraints weight = 3261.181| |-----------------------------------------------------------------------------| r_work (final): 0.3142 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7794 moved from start: 0.2912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 22290 Z= 0.122 Angle : 0.656 6.184 30020 Z= 0.329 Chirality : 0.043 0.127 3400 Planarity : 0.004 0.044 3800 Dihedral : 4.574 19.053 2900 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 12.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.16 % Favored : 94.84 % Rotamer: Outliers : 0.00 % Allowed : 5.62 % Favored : 94.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % 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: -1.12 (0.16), residues: 2520 helix: 0.93 (0.17), residues: 890 sheet: -0.72 (0.26), residues: 350 loop : -2.05 (0.16), residues: 1280 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG J 215 TYR 0.014 0.001 TYR G 250 PHE 0.015 0.001 PHE H 226 HIS 0.005 0.001 HIS C 197 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.12 (22290) covalent geometry : angle 0.65610 / 0.33 (30020) hydrogen bonds : bond 0.04155 / 2.70 ( 960) hydrogen bonds : angle 4.91871 / 3.41 ( 2610) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5040 Ramachandran restraints generated. 2520 Oldfield, 0 Emsley, 2520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5040 Ramachandran restraints generated. 2520 Oldfield, 0 Emsley, 2520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 52 time to evaluate : 0.056 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 13 LYS cc_start: 0.8661 (mmmm) cc_final: 0.8432 (mmmm) REVERT: E 85 PHE cc_start: 0.9322 (t80) cc_final: 0.9047 (t80) REVERT: E 222 ILE cc_start: 0.9024 (tp) cc_final: 0.8753 (tp) REVERT: E 250 TYR cc_start: 0.8189 (t80) cc_final: 0.7602 (t80) REVERT: E 253 ASP cc_start: 0.9417 (p0) cc_final: 0.9216 (p0) REVERT: E 295 LEU cc_start: 0.9389 (mm) cc_final: 0.9154 (mm) outliers start: 0 outliers final: 0 residues processed: 52 average time/residue: 0.0288 time to fit residues: 1.9020 Evaluate side-chains 45 residues out of total 249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 45 time to evaluate : 0.096 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 82 optimal weight: 0.7980 chunk 78 optimal weight: 20.0000 chunk 219 optimal weight: 0.0570 chunk 195 optimal weight: 10.0000 chunk 227 optimal weight: 8.9990 chunk 109 optimal weight: 9.9990 chunk 129 optimal weight: 0.0170 chunk 32 optimal weight: 8.9990 chunk 81 optimal weight: 0.0050 chunk 1 optimal weight: 0.8980 chunk 154 optimal weight: 20.0000 overall best weight: 0.3550 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.073242 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.057480 restraints weight = 10442.924| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.059357 restraints weight = 6991.649| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.060685 restraints weight = 5121.649| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.061747 restraints weight = 4062.825| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.062347 restraints weight = 3361.405| |-----------------------------------------------------------------------------| r_work (final): 0.3163 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7737 moved from start: 0.3646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 22290 Z= 0.117 Angle : 0.644 6.187 30020 Z= 0.320 Chirality : 0.044 0.134 3400 Planarity : 0.003 0.038 3800 Dihedral : 4.403 18.468 2900 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 10.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % 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: -0.61 (0.16), residues: 2520 helix: 1.44 (0.17), residues: 890 sheet: -0.81 (0.25), residues: 400 loop : -1.71 (0.16), residues: 1230 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 215 TYR 0.012 0.001 TYR G 250 PHE 0.014 0.002 PHE A 257 HIS 0.003 0.001 HIS F 197 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.12 (22290) covalent geometry : angle 0.64372 / 0.32 (30020) hydrogen bonds : bond 0.03911 / 2.53 ( 960) hydrogen bonds : angle 4.82559 / 3.35 ( 2610) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5040 Ramachandran restraints generated. 2520 Oldfield, 0 Emsley, 2520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5040 Ramachandran restraints generated. 2520 Oldfield, 0 Emsley, 2520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 55 time to evaluate : 0.067 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 50 ASP cc_start: 0.8807 (p0) cc_final: 0.8502 (p0) REVERT: E 52 ILE cc_start: 0.9231 (mm) cc_final: 0.8844 (mm) REVERT: E 191 MET cc_start: 0.9531 (tpt) cc_final: 0.9324 (tpt) REVERT: E 250 TYR cc_start: 0.8544 (t80) cc_final: 0.7345 (t80) REVERT: E 254 LEU cc_start: 0.9449 (mm) cc_final: 0.9120 (mm) REVERT: E 262 LEU cc_start: 0.8564 (mt) cc_final: 0.8259 (mt) REVERT: E 295 LEU cc_start: 0.9390 (mm) cc_final: 0.9135 (mm) outliers start: 0 outliers final: 0 residues processed: 55 average time/residue: 0.0339 time to fit residues: 2.4578 Evaluate side-chains 46 residues out of total 249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 46 time to evaluate : 0.090 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 195 optimal weight: 6.9990 chunk 94 optimal weight: 4.9990 chunk 209 optimal weight: 0.0270 chunk 17 optimal weight: 4.9990 chunk 176 optimal weight: 0.9990 chunk 217 optimal weight: 20.0000 chunk 142 optimal weight: 9.9990 chunk 144 optimal weight: 10.0000 chunk 72 optimal weight: 4.9990 chunk 42 optimal weight: 1.9990 chunk 227 optimal weight: 0.0060 overall best weight: 1.6060 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.071992 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.056970 restraints weight = 10857.938| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.058916 restraints weight = 7011.807| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.060351 restraints weight = 5088.376| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.061337 restraints weight = 3985.833| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 15)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.061947 restraints weight = 3295.759| |-----------------------------------------------------------------------------| r_work (final): 0.3166 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7782 moved from start: 0.3909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 22290 Z= 0.114 Angle : 0.636 6.592 30020 Z= 0.318 Chirality : 0.043 0.132 3400 Planarity : 0.004 0.034 3800 Dihedral : 4.288 19.356 2900 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 11.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.16 % Favored : 94.84 % Rotamer: Outliers : 0.40 % Allowed : 4.02 % Favored : 95.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.20 (0.17), residues: 2520 helix: 1.68 (0.17), residues: 890 sheet: -0.70 (0.26), residues: 420 loop : -1.34 (0.17), residues: 1210 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 215 TYR 0.013 0.001 TYR C 12 PHE 0.018 0.002 PHE E 85 HIS 0.004 0.001 HIS J 197 Details of bonding type rmsd/Z covalent geometry : bond 0.00254 / 0.11 (22290) covalent geometry : angle 0.63582 / 0.32 (30020) hydrogen bonds : bond 0.03964 / 2.57 ( 960) hydrogen bonds : angle 4.56605 / 3.16 ( 2610) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5040 Ramachandran restraints generated. 2520 Oldfield, 0 Emsley, 2520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5040 Ramachandran restraints generated. 2520 Oldfield, 0 Emsley, 2520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 54 time to evaluate : 0.093 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 50 ASP cc_start: 0.8826 (p0) cc_final: 0.8411 (p0) REVERT: E 52 ILE cc_start: 0.9141 (mm) cc_final: 0.8698 (mm) REVERT: E 85 PHE cc_start: 0.9332 (t80) cc_final: 0.8987 (t80) REVERT: E 94 GLU cc_start: 0.9065 (OUTLIER) cc_final: 0.8774 (mp0) REVERT: E 120 ASP cc_start: 0.8633 (m-30) cc_final: 0.7550 (t70) REVERT: E 121 PHE cc_start: 0.9208 (t80) cc_final: 0.8943 (t80) REVERT: E 195 LEU cc_start: 0.9586 (pp) cc_final: 0.9358 (pp) REVERT: E 250 TYR cc_start: 0.8318 (t80) cc_final: 0.7616 (t80) REVERT: E 262 LEU cc_start: 0.8606 (mt) cc_final: 0.8273 (mt) REVERT: E 295 LEU cc_start: 0.9371 (mm) cc_final: 0.9094 (mm) outliers start: 1 outliers final: 0 residues processed: 55 average time/residue: 0.0480 time to fit residues: 3.2399 Evaluate side-chains 47 residues out of total 249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 46 time to evaluate : 0.053 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 207 optimal weight: 0.8980 chunk 131 optimal weight: 8.9990 chunk 71 optimal weight: 0.0170 chunk 41 optimal weight: 0.0770 chunk 159 optimal weight: 0.0010 chunk 222 optimal weight: 4.9990 chunk 155 optimal weight: 4.9990 chunk 1 optimal weight: 8.9990 chunk 254 optimal weight: 0.8980 chunk 104 optimal weight: 20.0000 chunk 145 optimal weight: 0.8980 overall best weight: 0.3782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.075215 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.059233 restraints weight = 10716.629| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.061144 restraints weight = 7097.278| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.062643 restraints weight = 5245.910| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.063746 restraints weight = 4102.719| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.064551 restraints weight = 3386.227| |-----------------------------------------------------------------------------| r_work (final): 0.3207 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7690 moved from start: 0.4446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 22290 Z= 0.118 Angle : 0.647 7.414 30020 Z= 0.323 Chirality : 0.043 0.187 3400 Planarity : 0.003 0.034 3800 Dihedral : 4.197 20.411 2900 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 10.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.95 % Favored : 94.05 % Rotamer: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % 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: 0.03 (0.17), residues: 2520 helix: 1.83 (0.17), residues: 890 sheet: -0.14 (0.28), residues: 370 loop : -1.31 (0.17), residues: 1260 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG J 215 TYR 0.011 0.001 TYR J 12 PHE 0.012 0.001 PHE C 247 HIS 0.004 0.001 HIS F 197 Details of bonding type rmsd/Z covalent geometry : bond 0.00256 / 0.12 (22290) covalent geometry : angle 0.64725 / 0.32 (30020) hydrogen bonds : bond 0.03874 / 2.50 ( 960) hydrogen bonds : angle 4.66179 / 3.27 ( 2610) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5040 Ramachandran restraints generated. 2520 Oldfield, 0 Emsley, 2520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5040 Ramachandran restraints generated. 2520 Oldfield, 0 Emsley, 2520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 54 time to evaluate : 0.092 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 13 LYS cc_start: 0.8552 (mmmm) cc_final: 0.8259 (mmmm) REVERT: E 15 GLU cc_start: 0.8572 (pp20) cc_final: 0.8268 (pm20) REVERT: E 50 ASP cc_start: 0.8808 (p0) cc_final: 0.8396 (p0) REVERT: E 52 ILE cc_start: 0.9124 (mm) cc_final: 0.8645 (mm) REVERT: E 85 PHE cc_start: 0.9363 (t80) cc_final: 0.9059 (t80) REVERT: E 120 ASP cc_start: 0.8561 (m-30) cc_final: 0.7525 (t70) REVERT: E 121 PHE cc_start: 0.9156 (t80) cc_final: 0.8935 (t80) REVERT: E 195 LEU cc_start: 0.9596 (pp) cc_final: 0.9382 (pp) REVERT: E 250 TYR cc_start: 0.8274 (t80) cc_final: 0.7765 (t80) outliers start: 0 outliers final: 0 residues processed: 54 average time/residue: 0.0451 time to fit residues: 3.0083 Evaluate side-chains 47 residues out of total 249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 47 time to evaluate : 0.061 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 41 optimal weight: 2.9990 chunk 135 optimal weight: 9.9990 chunk 191 optimal weight: 20.0000 chunk 106 optimal weight: 3.9990 chunk 220 optimal weight: 10.0000 chunk 177 optimal weight: 0.0470 chunk 47 optimal weight: 0.0270 chunk 1 optimal weight: 0.4980 chunk 244 optimal weight: 7.9990 chunk 13 optimal weight: 6.9990 chunk 124 optimal weight: 5.9990 overall best weight: 1.5140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.074453 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.058912 restraints weight = 11220.092| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.060927 restraints weight = 7283.207| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.062451 restraints weight = 5301.323| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.063521 restraints weight = 4098.906| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.064365 restraints weight = 3360.049| |-----------------------------------------------------------------------------| r_work (final): 0.3183 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7743 moved from start: 0.4612 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 22290 Z= 0.110 Angle : 0.595 5.555 30020 Z= 0.305 Chirality : 0.041 0.120 3400 Planarity : 0.003 0.027 3800 Dihedral : 4.153 21.639 2900 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 10.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.16 % Favored : 94.84 % Rotamer: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % 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 (0.17), residues: 2520 helix: 2.08 (0.18), residues: 890 sheet: -0.39 (0.27), residues: 420 loop : -0.95 (0.18), residues: 1210 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 215 TYR 0.011 0.001 TYR G 214 PHE 0.008 0.001 PHE J 85 HIS 0.005 0.001 HIS C 197 Details of bonding type rmsd/Z covalent geometry : bond 0.00248 / 0.11 (22290) covalent geometry : angle 0.59518 / 0.31 (30020) hydrogen bonds : bond 0.03710 / 2.41 ( 960) hydrogen bonds : angle 4.51679 / 3.16 ( 2610) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5040 Ramachandran restraints generated. 2520 Oldfield, 0 Emsley, 2520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5040 Ramachandran restraints generated. 2520 Oldfield, 0 Emsley, 2520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 55 time to evaluate : 0.082 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 13 LYS cc_start: 0.8647 (mmmm) cc_final: 0.8336 (mmmm) REVERT: E 15 GLU cc_start: 0.8510 (pp20) cc_final: 0.8239 (pm20) REVERT: E 50 ASP cc_start: 0.8853 (p0) cc_final: 0.8553 (p0) REVERT: E 52 ILE cc_start: 0.9158 (mm) cc_final: 0.8790 (mm) REVERT: E 85 PHE cc_start: 0.9364 (t80) cc_final: 0.9035 (t80) REVERT: E 120 ASP cc_start: 0.8576 (m-30) cc_final: 0.7542 (t70) REVERT: E 121 PHE cc_start: 0.9211 (t80) cc_final: 0.8945 (t80) REVERT: E 195 LEU cc_start: 0.9611 (pp) cc_final: 0.9402 (pp) REVERT: E 250 TYR cc_start: 0.8319 (t80) cc_final: 0.7792 (t80) REVERT: E 262 LEU cc_start: 0.8615 (mt) cc_final: 0.8379 (mt) outliers start: 0 outliers final: 0 residues processed: 55 average time/residue: 0.0558 time to fit residues: 3.6475 Evaluate side-chains 46 residues out of total 249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 46 time to evaluate : 0.097 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 220 optimal weight: 5.9990 chunk 233 optimal weight: 9.9990 chunk 139 optimal weight: 20.0000 chunk 31 optimal weight: 10.0000 chunk 169 optimal weight: 3.9990 chunk 207 optimal weight: 6.9990 chunk 171 optimal weight: 1.9990 chunk 96 optimal weight: 7.9990 chunk 181 optimal weight: 20.0000 chunk 177 optimal weight: 9.9990 chunk 210 optimal weight: 6.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 90 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.071519 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.056286 restraints weight = 11355.963| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.058247 restraints weight = 7246.085| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.059593 restraints weight = 5242.462| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.060784 restraints weight = 4093.184| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.061544 restraints weight = 3355.588| |-----------------------------------------------------------------------------| r_work (final): 0.3125 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7870 moved from start: 0.4180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 22290 Z= 0.166 Angle : 0.647 5.421 30020 Z= 0.338 Chirality : 0.043 0.120 3400 Planarity : 0.006 0.102 3800 Dihedral : 4.923 32.249 2900 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 17.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % 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: 0.12 (0.17), residues: 2520 helix: 1.83 (0.18), residues: 900 sheet: -0.22 (0.27), residues: 370 loop : -1.18 (0.18), residues: 1250 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 215 TYR 0.014 0.002 TYR F 214 PHE 0.015 0.002 PHE C 247 HIS 0.002 0.001 HIS C 197 Details of bonding type rmsd/Z covalent geometry : bond 0.00356 / 0.17 (22290) covalent geometry : angle 0.64739 / 0.34 (30020) hydrogen bonds : bond 0.04024 / 2.61 ( 960) hydrogen bonds : angle 4.61328 / 3.22 ( 2610) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5040 Ramachandran restraints generated. 2520 Oldfield, 0 Emsley, 2520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5040 Ramachandran restraints generated. 2520 Oldfield, 0 Emsley, 2520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 47 time to evaluate : 0.091 Fit side-chains revert: symmetry clash REVERT: E 13 LYS cc_start: 0.8679 (mmmm) cc_final: 0.8317 (mmmm) REVERT: E 15 GLU cc_start: 0.8533 (pp20) cc_final: 0.8212 (pm20) REVERT: E 52 ILE cc_start: 0.9214 (mm) cc_final: 0.8908 (mm) REVERT: E 121 PHE cc_start: 0.9282 (t80) cc_final: 0.9010 (t80) REVERT: E 160 LEU cc_start: 0.9678 (mp) cc_final: 0.9364 (mp) REVERT: E 250 TYR cc_start: 0.8518 (t80) cc_final: 0.7865 (t80) outliers start: 0 outliers final: 0 residues processed: 47 average time/residue: 0.0356 time to fit residues: 2.1463 Evaluate side-chains 42 residues out of total 249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 42 time to evaluate : 0.091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 135 optimal weight: 6.9990 chunk 66 optimal weight: 0.9990 chunk 75 optimal weight: 20.0000 chunk 146 optimal weight: 5.9990 chunk 31 optimal weight: 10.0000 chunk 104 optimal weight: 20.0000 chunk 142 optimal weight: 9.9990 chunk 26 optimal weight: 20.0000 chunk 144 optimal weight: 2.9990 chunk 132 optimal weight: 10.0000 chunk 39 optimal weight: 3.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 90 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.071643 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.056046 restraints weight = 11513.733| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.058065 restraints weight = 7393.329| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.059561 restraints weight = 5316.975| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.060746 restraints weight = 4117.698| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.061549 restraints weight = 3339.250| |-----------------------------------------------------------------------------| r_work (final): 0.3140 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7841 moved from start: 0.4203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 22290 Z= 0.159 Angle : 0.692 6.169 30020 Z= 0.363 Chirality : 0.044 0.127 3400 Planarity : 0.005 0.078 3800 Dihedral : 4.917 34.795 2900 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 15.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.95 % Favored : 94.05 % Rotamer: Outliers : 0.00 % Allowed : 0.80 % Favored : 99.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % 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: 0.02 (0.17), residues: 2520 helix: 1.60 (0.17), residues: 900 sheet: 0.23 (0.28), residues: 350 loop : -1.26 (0.18), residues: 1270 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 215 TYR 0.017 0.002 TYR A 214 PHE 0.014 0.002 PHE D 85 HIS 0.001 0.001 HIS C 197 Details of bonding type rmsd/Z covalent geometry : bond 0.00348 / 0.16 (22290) covalent geometry : angle 0.69193 / 0.36 (30020) hydrogen bonds : bond 0.04297 / 2.77 ( 960) hydrogen bonds : angle 4.94230 / 3.48 ( 2610) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5040 Ramachandran restraints generated. 2520 Oldfield, 0 Emsley, 2520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5040 Ramachandran restraints generated. 2520 Oldfield, 0 Emsley, 2520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 50 time to evaluate : 0.092 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 13 LYS cc_start: 0.8674 (mmmm) cc_final: 0.8338 (mmmm) REVERT: E 85 PHE cc_start: 0.9229 (t80) cc_final: 0.8884 (t80) REVERT: E 250 TYR cc_start: 0.8580 (t80) cc_final: 0.7714 (t80) REVERT: E 262 LEU cc_start: 0.8722 (mt) cc_final: 0.8509 (mt) outliers start: 0 outliers final: 0 residues processed: 50 average time/residue: 0.0418 time to fit residues: 2.6297 Evaluate side-chains 42 residues out of total 249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 42 time to evaluate : 0.082 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 113 optimal weight: 9.9990 chunk 51 optimal weight: 30.0000 chunk 180 optimal weight: 9.9990 chunk 144 optimal weight: 0.4980 chunk 215 optimal weight: 20.0000 chunk 155 optimal weight: 9.9990 chunk 135 optimal weight: 10.0000 chunk 65 optimal weight: 6.9990 chunk 21 optimal weight: 0.7980 chunk 209 optimal weight: 0.0020 chunk 166 optimal weight: 0.0980 overall best weight: 1.6790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.073726 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.058387 restraints weight = 11600.820| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.060418 restraints weight = 7545.918| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.061964 restraints weight = 5442.285| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.063058 restraints weight = 4190.580| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.063817 restraints weight = 3398.253| |-----------------------------------------------------------------------------| r_work (final): 0.3178 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7743 moved from start: 0.4572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 22290 Z= 0.132 Angle : 0.704 6.738 30020 Z= 0.364 Chirality : 0.044 0.132 3400 Planarity : 0.005 0.065 3800 Dihedral : 4.830 36.549 2900 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 12.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.06 (0.17), residues: 2520 helix: 1.61 (0.17), residues: 900 sheet: -0.15 (0.28), residues: 370 loop : -1.09 (0.18), residues: 1250 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 215 TYR 0.014 0.002 TYR C 214 PHE 0.016 0.002 PHE D 85 HIS 0.004 0.001 HIS F 197 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.13 (22290) covalent geometry : angle 0.70365 / 0.36 (30020) hydrogen bonds : bond 0.04179 / 2.67 ( 960) hydrogen bonds : angle 4.80222 / 3.39 ( 2610) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5040 Ramachandran restraints generated. 2520 Oldfield, 0 Emsley, 2520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5040 Ramachandran restraints generated. 2520 Oldfield, 0 Emsley, 2520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 53 time to evaluate : 0.063 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 13 LYS cc_start: 0.8657 (mmmm) cc_final: 0.8301 (mmmm) REVERT: E 15 GLU cc_start: 0.8603 (pp20) cc_final: 0.8339 (pm20) REVERT: E 50 ASP cc_start: 0.8790 (p0) cc_final: 0.8460 (p0) REVERT: E 52 ILE cc_start: 0.9293 (mm) cc_final: 0.8973 (mm) REVERT: E 85 PHE cc_start: 0.9248 (t80) cc_final: 0.8900 (t80) REVERT: E 250 TYR cc_start: 0.8369 (t80) cc_final: 0.7725 (t80) REVERT: E 262 LEU cc_start: 0.8635 (mt) cc_final: 0.8418 (mt) REVERT: E 306 LEU cc_start: 0.9100 (mm) cc_final: 0.8457 (mp) outliers start: 0 outliers final: 0 residues processed: 53 average time/residue: 0.0450 time to fit residues: 2.9495 Evaluate side-chains 44 residues out of total 249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 44 time to evaluate : 0.087 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 175 optimal weight: 0.2980 chunk 52 optimal weight: 20.0000 chunk 14 optimal weight: 3.9990 chunk 259 optimal weight: 30.0000 chunk 229 optimal weight: 0.0000 chunk 228 optimal weight: 6.9990 chunk 22 optimal weight: 3.9990 chunk 46 optimal weight: 9.9990 chunk 5 optimal weight: 9.9990 chunk 69 optimal weight: 10.0000 chunk 35 optimal weight: 10.0000 overall best weight: 3.0590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 90 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.072559 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.057518 restraints weight = 11940.332| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.059485 restraints weight = 7797.657| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.060917 restraints weight = 5629.567| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.061999 restraints weight = 4349.665| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.062878 restraints weight = 3547.015| |-----------------------------------------------------------------------------| r_work (final): 0.3159 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7781 moved from start: 0.4570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 22290 Z= 0.138 Angle : 0.677 6.209 30020 Z= 0.353 Chirality : 0.043 0.132 3400 Planarity : 0.005 0.066 3800 Dihedral : 4.995 42.863 2900 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 12.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.16 % Favored : 94.84 % Rotamer: Outliers : 0.00 % Allowed : 0.40 % Favored : 99.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.06 (0.17), residues: 2520 helix: 1.56 (0.17), residues: 900 sheet: 0.19 (0.28), residues: 350 loop : -1.16 (0.18), residues: 1270 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 215 TYR 0.015 0.002 TYR B 214 PHE 0.013 0.002 PHE G 121 HIS 0.002 0.001 HIS A 197 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.14 (22290) covalent geometry : angle 0.67674 / 0.35 (30020) hydrogen bonds : bond 0.04013 / 2.57 ( 960) hydrogen bonds : angle 4.77233 / 3.36 ( 2610) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1475.12 seconds wall clock time: 27 minutes 17.79 seconds (1637.79 seconds total)