Starting phenix.real_space_refine on Thu Mar 5 10:44:32 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7kvc_23046/03_2026/7kvc_23046.cif Found real_map, /net/cci-nas-00/data/ceres_data/7kvc_23046/03_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_23046/03_2026/7kvc_23046.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7kvc_23046/03_2026/7kvc_23046.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7kvc_23046/03_2026/7kvc_23046.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7kvc_23046/03_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-5986/lib/python3.9/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: 2.48, per 1000 atoms: 0.11 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: 1.66 Conformation dependent library (CDL) restraints added in 936.4 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: 0.67 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: 3.73 Time building geometry restraints manager: 2.21 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: 0.06 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: 0.890 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: 0.350 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 16.970 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.010 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:0.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.560 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8225 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 covalent geometry : bond 0.00479 (22290) covalent geometry : angle 0.83628 (30020) hydrogen bonds : bond 0.14957 ( 960) hydrogen bonds : angle 6.80853 ( 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 : 0.066 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: 0.0294 time to fit residues: 1.6336 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 : 0.085 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: ** E 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 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: 0.8016 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 covalent geometry : bond 0.00328 (22290) covalent geometry : angle 0.71286 (30020) hydrogen bonds : bond 0.04762 ( 960) hydrogen bonds : angle 5.25135 ( 2610) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4536 Ramachandran restraints generated. 2268 Oldfield, 0 Emsley, 2268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4536 Ramachandran restraints generated. 2268 Oldfield, 0 Emsley, 2268 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: 0.0365 time to fit residues: 2.3531 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 : 0.089 ------------------------------------------------------------------------------- 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: 0.0870 chunk 116 optimal weight: 6.9990 chunk 254 optimal weight: 1.9990 chunk 159 optimal weight: 0.0980 chunk 140 optimal weight: 30.0000 chunk 115 optimal weight: 6.9990 chunk 4 optimal weight: 20.0000 chunk 253 optimal weight: 0.4980 chunk 181 optimal weight: 0.6980 overall best weight: 0.2796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.071744 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.056562 restraints weight = 11062.747| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.058357 restraints weight = 7102.153| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.059854 restraints weight = 5244.161| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.060976 restraints weight = 4079.053| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.061757 restraints weight = 3341.188| |-----------------------------------------------------------------------------| r_work (final): 0.3145 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7940 moved from start: 0.2921 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= 0.124 Angle : 0.657 6.213 30020 Z= 0.329 Chirality : 0.043 0.127 3400 Planarity : 0.004 0.044 3800 Dihedral : 4.558 19.002 2900 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 11.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.95 % Favored : 94.05 % Rotamer: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % 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: -1.18 (0.16), residues: 2520 helix: 0.87 (0.17), residues: 890 sheet: -0.77 (0.26), residues: 350 loop : -2.07 (0.16), residues: 1280 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG J 215 TYR 0.014 0.002 TYR D 250 PHE 0.015 0.001 PHE H 226 HIS 0.005 0.001 HIS C 197 Details of bonding type rmsd covalent geometry : bond 0.00267 (22290) covalent geometry : angle 0.65688 (30020) hydrogen bonds : bond 0.04162 ( 960) hydrogen bonds : angle 4.92512 ( 2610) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4536 Ramachandran restraints generated. 2268 Oldfield, 0 Emsley, 2268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4536 Ramachandran restraints generated. 2268 Oldfield, 0 Emsley, 2268 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 : 0.094 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 13 LYS cc_start: 0.8663 (mmmm) cc_final: 0.8431 (mmmm) REVERT: E 85 PHE cc_start: 0.9329 (t80) cc_final: 0.9070 (t80) REVERT: E 222 ILE cc_start: 0.9033 (tp) cc_final: 0.8767 (tp) REVERT: E 250 TYR cc_start: 0.8192 (t80) cc_final: 0.7601 (t80) REVERT: E 253 ASP cc_start: 0.9413 (p0) cc_final: 0.9209 (p0) REVERT: E 295 LEU cc_start: 0.9381 (mm) cc_final: 0.9104 (mm) outliers start: 0 outliers final: 0 residues processed: 53 average time/residue: 0.0423 time to fit residues: 2.8176 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 : 0.092 ------------------------------------------------------------------------------- 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: 20.0000 chunk 78 optimal weight: 20.0000 chunk 219 optimal weight: 4.9990 chunk 195 optimal weight: 7.9990 chunk 227 optimal weight: 10.0000 chunk 109 optimal weight: 9.9990 chunk 129 optimal weight: 0.0770 chunk 32 optimal weight: 8.9990 chunk 81 optimal weight: 0.0870 chunk 1 optimal weight: 10.0000 chunk 154 optimal weight: 20.0000 overall best weight: 4.4322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3285 r_free = 0.3285 target = 0.069038 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2961 r_free = 0.2961 target = 0.054512 restraints weight = 11386.080| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.056367 restraints weight = 7275.173| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.057726 restraints weight = 5260.244| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.058760 restraints weight = 4058.379| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.059486 restraints weight = 3334.240| |-----------------------------------------------------------------------------| r_work (final): 0.3082 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8060 moved from start: 0.2920 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= 0.152 Angle : 0.642 5.503 30020 Z= 0.334 Chirality : 0.044 0.139 3400 Planarity : 0.004 0.043 3800 Dihedral : 4.857 20.492 2900 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 13.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.75 % Favored : 93.25 % Rotamer: Outliers : 0.00 % Allowed : 6.02 % Favored : 93.98 % 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: -1.10 (0.16), residues: 2520 helix: 1.05 (0.18), residues: 880 sheet: -1.13 (0.25), residues: 400 loop : -1.97 (0.16), residues: 1240 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 215 TYR 0.013 0.002 TYR F 214 PHE 0.017 0.002 PHE B 226 HIS 0.002 0.001 HIS F 77 Details of bonding type rmsd covalent geometry : bond 0.00329 (22290) covalent geometry : angle 0.64203 (30020) hydrogen bonds : bond 0.04045 ( 960) hydrogen bonds : angle 4.92143 ( 2610) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4536 Ramachandran restraints generated. 2268 Oldfield, 0 Emsley, 2268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4536 Ramachandran restraints generated. 2268 Oldfield, 0 Emsley, 2268 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 : 0.087 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 13 LYS cc_start: 0.8779 (mmmm) cc_final: 0.8525 (mmmm) REVERT: E 50 ASP cc_start: 0.8986 (p0) cc_final: 0.8729 (p0) REVERT: E 52 ILE cc_start: 0.9212 (mm) cc_final: 0.8799 (mm) REVERT: E 85 PHE cc_start: 0.9225 (t80) cc_final: 0.8951 (t80) REVERT: E 198 LEU cc_start: 0.9481 (mt) cc_final: 0.9243 (mt) REVERT: E 226 PHE cc_start: 0.8137 (m-10) cc_final: 0.7924 (m-10) REVERT: E 250 TYR cc_start: 0.8835 (t80) cc_final: 0.7924 (t80) REVERT: E 258 GLN cc_start: 0.7583 (mm-40) cc_final: 0.7135 (tp-100) REVERT: E 262 LEU cc_start: 0.8685 (mt) cc_final: 0.7882 (mt) REVERT: E 295 LEU cc_start: 0.9346 (mm) cc_final: 0.9070 (mm) outliers start: 0 outliers final: 0 residues processed: 50 average time/residue: 0.0348 time to fit residues: 2.2821 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 : 0.088 ------------------------------------------------------------------------------- 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: 3.9990 chunk 17 optimal weight: 5.9990 chunk 176 optimal weight: 8.9990 chunk 217 optimal weight: 20.0000 chunk 142 optimal weight: 4.9990 chunk 144 optimal weight: 6.9990 chunk 72 optimal weight: 10.0000 chunk 42 optimal weight: 3.9990 chunk 227 optimal weight: 9.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3273 r_free = 0.3273 target = 0.068473 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.053983 restraints weight = 11803.738| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.055807 restraints weight = 7393.462| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.057135 restraints weight = 5340.576| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.058061 restraints weight = 4147.343| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.058597 restraints weight = 3432.109| |-----------------------------------------------------------------------------| r_work (final): 0.3053 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8080 moved from start: 0.3095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 22290 Z= 0.156 Angle : 0.646 5.462 30020 Z= 0.337 Chirality : 0.044 0.122 3400 Planarity : 0.004 0.039 3800 Dihedral : 4.837 18.076 2900 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 16.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.14 % Favored : 92.86 % Rotamer: Outliers : 0.40 % Allowed : 4.82 % Favored : 94.78 % 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: -0.99 (0.16), residues: 2520 helix: 1.05 (0.17), residues: 890 sheet: -0.46 (0.27), residues: 350 loop : -2.05 (0.16), residues: 1280 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 272 TYR 0.016 0.002 TYR H 214 PHE 0.010 0.002 PHE D 226 HIS 0.002 0.001 HIS C 197 Details of bonding type rmsd covalent geometry : bond 0.00332 (22290) covalent geometry : angle 0.64591 (30020) hydrogen bonds : bond 0.04131 ( 960) hydrogen bonds : angle 4.93340 ( 2610) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4536 Ramachandran restraints generated. 2268 Oldfield, 0 Emsley, 2268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4536 Ramachandran restraints generated. 2268 Oldfield, 0 Emsley, 2268 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 : 0.088 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 13 LYS cc_start: 0.8764 (mmmm) cc_final: 0.8361 (mmmm) REVERT: E 50 ASP cc_start: 0.8953 (p0) cc_final: 0.8522 (p0) REVERT: E 52 ILE cc_start: 0.9193 (mm) cc_final: 0.8708 (mm) REVERT: E 85 PHE cc_start: 0.9165 (t80) cc_final: 0.8877 (t80) REVERT: E 191 MET cc_start: 0.9511 (tpt) cc_final: 0.9259 (tpt) REVERT: E 215 ARG cc_start: 0.8779 (ttt90) cc_final: 0.8562 (ttt90) REVERT: E 250 TYR cc_start: 0.8933 (t80) cc_final: 0.6812 (t80) REVERT: E 262 LEU cc_start: 0.8700 (mt) cc_final: 0.8468 (mt) REVERT: E 295 LEU cc_start: 0.9385 (mm) cc_final: 0.9143 (mm) outliers start: 1 outliers final: 0 residues processed: 55 average time/residue: 0.0417 time to fit residues: 2.8376 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 : 0.092 ------------------------------------------------------------------------------- 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: 0.9990 chunk 131 optimal weight: 8.9990 chunk 71 optimal weight: 1.9990 chunk 41 optimal weight: 0.0040 chunk 159 optimal weight: 0.3980 chunk 222 optimal weight: 0.8980 chunk 155 optimal weight: 7.9990 chunk 1 optimal weight: 2.9990 chunk 254 optimal weight: 0.9980 chunk 104 optimal weight: 20.0000 chunk 145 optimal weight: 5.9990 overall best weight: 0.6594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.072929 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.057531 restraints weight = 10845.526| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.059499 restraints weight = 6902.677| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.060979 restraints weight = 4998.154| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.062069 restraints weight = 3868.136| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.062892 restraints weight = 3177.626| |-----------------------------------------------------------------------------| r_work (final): 0.3151 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7902 moved from start: 0.3727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 22290 Z= 0.123 Angle : 0.663 6.356 30020 Z= 0.334 Chirality : 0.043 0.137 3400 Planarity : 0.004 0.046 3800 Dihedral : 4.428 16.415 2900 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 10.54 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: -0.57 (0.16), residues: 2520 helix: 1.19 (0.17), residues: 900 sheet: -0.64 (0.25), residues: 400 loop : -1.51 (0.16), residues: 1220 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG G 215 TYR 0.011 0.001 TYR B 250 PHE 0.009 0.001 PHE E 257 HIS 0.005 0.001 HIS C 197 Details of bonding type rmsd covalent geometry : bond 0.00272 (22290) covalent geometry : angle 0.66277 (30020) hydrogen bonds : bond 0.04219 ( 960) hydrogen bonds : angle 4.82987 ( 2610) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4536 Ramachandran restraints generated. 2268 Oldfield, 0 Emsley, 2268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4536 Ramachandran restraints generated. 2268 Oldfield, 0 Emsley, 2268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 59 time to evaluate : 0.087 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 13 LYS cc_start: 0.8735 (mmmm) cc_final: 0.8348 (mmmm) REVERT: E 50 ASP cc_start: 0.8797 (p0) cc_final: 0.8339 (p0) REVERT: E 52 ILE cc_start: 0.9218 (mm) cc_final: 0.8788 (mm) REVERT: E 85 PHE cc_start: 0.9206 (t80) cc_final: 0.8746 (t80) REVERT: E 121 PHE cc_start: 0.9175 (t80) cc_final: 0.8947 (t80) REVERT: E 191 MET cc_start: 0.9523 (tpt) cc_final: 0.9290 (tpt) REVERT: E 195 LEU cc_start: 0.9608 (pp) cc_final: 0.9398 (pp) REVERT: E 250 TYR cc_start: 0.8341 (t80) cc_final: 0.7486 (t80) REVERT: E 253 ASP cc_start: 0.9445 (p0) cc_final: 0.9243 (p0) REVERT: E 262 LEU cc_start: 0.8488 (mt) cc_final: 0.8202 (mt) REVERT: E 295 LEU cc_start: 0.9326 (mm) cc_final: 0.9040 (mm) outliers start: 0 outliers final: 0 residues processed: 59 average time/residue: 0.0438 time to fit residues: 3.1936 Evaluate side-chains 48 residues out of total 249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 48 time to evaluate : 0.086 ------------------------------------------------------------------------------- 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: 1.9990 chunk 135 optimal weight: 10.0000 chunk 191 optimal weight: 10.0000 chunk 106 optimal weight: 4.9990 chunk 220 optimal weight: 5.9990 chunk 177 optimal weight: 0.0370 chunk 47 optimal weight: 0.0370 chunk 1 optimal weight: 0.2980 chunk 244 optimal weight: 9.9990 chunk 13 optimal weight: 8.9990 chunk 124 optimal weight: 9.9990 overall best weight: 1.4740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.072400 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.056794 restraints weight = 11109.182| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.058624 restraints weight = 7270.373| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.060047 restraints weight = 5380.442| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.061079 restraints weight = 4225.875| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.061892 restraints weight = 3504.832| |-----------------------------------------------------------------------------| r_work (final): 0.3149 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7913 moved from start: 0.3956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 22290 Z= 0.123 Angle : 0.660 5.746 30020 Z= 0.335 Chirality : 0.043 0.136 3400 Planarity : 0.006 0.082 3800 Dihedral : 4.368 18.120 2900 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 12.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.16 % Favored : 94.84 % Rotamer: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % 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: -0.24 (0.17), residues: 2520 helix: 1.30 (0.17), residues: 900 sheet: -0.17 (0.26), residues: 400 loop : -1.30 (0.17), residues: 1220 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 215 TYR 0.010 0.001 TYR E 214 PHE 0.018 0.001 PHE F 247 HIS 0.003 0.001 HIS C 197 Details of bonding type rmsd covalent geometry : bond 0.00271 (22290) covalent geometry : angle 0.66001 (30020) hydrogen bonds : bond 0.03894 ( 960) hydrogen bonds : angle 4.79218 ( 2610) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4536 Ramachandran restraints generated. 2268 Oldfield, 0 Emsley, 2268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4536 Ramachandran restraints generated. 2268 Oldfield, 0 Emsley, 2268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 56 time to evaluate : 0.088 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 13 LYS cc_start: 0.8766 (mmmm) cc_final: 0.8387 (mmmm) REVERT: E 50 ASP cc_start: 0.8804 (p0) cc_final: 0.8362 (p0) REVERT: E 52 ILE cc_start: 0.9179 (mm) cc_final: 0.8752 (mm) REVERT: E 85 PHE cc_start: 0.9149 (t80) cc_final: 0.8680 (t80) REVERT: E 121 PHE cc_start: 0.9192 (t80) cc_final: 0.8977 (t80) REVERT: E 191 MET cc_start: 0.9541 (tpt) cc_final: 0.9318 (tpt) REVERT: E 246 THR cc_start: 0.8002 (m) cc_final: 0.7546 (m) REVERT: E 250 TYR cc_start: 0.8366 (t80) cc_final: 0.7562 (t80) REVERT: E 262 LEU cc_start: 0.8455 (mt) cc_final: 0.8171 (mt) REVERT: E 295 LEU cc_start: 0.9382 (mm) cc_final: 0.9096 (mm) outliers start: 0 outliers final: 0 residues processed: 56 average time/residue: 0.0410 time to fit residues: 2.9190 Evaluate side-chains 48 residues out of total 249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 48 time to evaluate : 0.093 ------------------------------------------------------------------------------- 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: 9.9990 chunk 233 optimal weight: 10.0000 chunk 139 optimal weight: 0.6980 chunk 31 optimal weight: 8.9990 chunk 169 optimal weight: 5.9990 chunk 207 optimal weight: 8.9990 chunk 171 optimal weight: 0.0070 chunk 96 optimal weight: 6.9990 chunk 181 optimal weight: 10.0000 chunk 177 optimal weight: 0.0370 chunk 210 optimal weight: 9.9990 overall best weight: 2.7480 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.071117 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.056146 restraints weight = 11466.139| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.058087 restraints weight = 7289.050| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.059457 restraints weight = 5251.510| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.060527 restraints weight = 4101.391| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.061324 restraints weight = 3364.464| |-----------------------------------------------------------------------------| r_work (final): 0.3128 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7950 moved from start: 0.3975 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= 0.124 Angle : 0.636 6.052 30020 Z= 0.322 Chirality : 0.043 0.134 3400 Planarity : 0.005 0.069 3800 Dihedral : 4.401 19.477 2900 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 12.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.16 % Favored : 94.84 % Rotamer: Outliers : 0.00 % Allowed : 1.20 % Favored : 98.80 % 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: -0.15 (0.17), residues: 2520 helix: 1.37 (0.17), residues: 900 sheet: 0.58 (0.29), residues: 350 loop : -1.44 (0.17), residues: 1270 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 215 TYR 0.012 0.001 TYR H 214 PHE 0.009 0.001 PHE I 247 HIS 0.002 0.001 HIS C 197 Details of bonding type rmsd covalent geometry : bond 0.00275 (22290) covalent geometry : angle 0.63569 (30020) hydrogen bonds : bond 0.03734 ( 960) hydrogen bonds : angle 4.62775 ( 2610) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4536 Ramachandran restraints generated. 2268 Oldfield, 0 Emsley, 2268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4536 Ramachandran restraints generated. 2268 Oldfield, 0 Emsley, 2268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 51 time to evaluate : 0.079 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 13 LYS cc_start: 0.8794 (mmmm) cc_final: 0.8406 (mmmm) REVERT: E 85 PHE cc_start: 0.9147 (t80) cc_final: 0.8667 (t80) REVERT: E 160 LEU cc_start: 0.9685 (mp) cc_final: 0.9461 (mp) REVERT: E 191 MET cc_start: 0.9568 (tpt) cc_final: 0.9348 (tpt) REVERT: E 250 TYR cc_start: 0.8384 (t80) cc_final: 0.7247 (t80) REVERT: E 262 LEU cc_start: 0.8507 (mt) cc_final: 0.8113 (mt) outliers start: 0 outliers final: 0 residues processed: 51 average time/residue: 0.0331 time to fit residues: 2.2397 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 : 0.053 ------------------------------------------------------------------------------- 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: 8.9990 chunk 66 optimal weight: 6.9990 chunk 75 optimal weight: 0.0020 chunk 146 optimal weight: 6.9990 chunk 31 optimal weight: 9.9990 chunk 104 optimal weight: 20.0000 chunk 142 optimal weight: 10.0000 chunk 26 optimal weight: 20.0000 chunk 144 optimal weight: 3.9990 chunk 132 optimal weight: 5.9990 chunk 39 optimal weight: 5.9990 overall best weight: 4.5996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3303 r_free = 0.3303 target = 0.069774 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.054752 restraints weight = 11787.830| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.056749 restraints weight = 7335.780| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.058216 restraints weight = 5214.705| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.059263 restraints weight = 4003.480| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.059927 restraints weight = 3267.791| |-----------------------------------------------------------------------------| r_work (final): 0.3089 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8006 moved from start: 0.3785 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= 0.158 Angle : 0.669 5.435 30020 Z= 0.348 Chirality : 0.044 0.141 3400 Planarity : 0.006 0.080 3800 Dihedral : 4.737 20.031 2900 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 15.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 0.00 % Allowed : 1.20 % Favored : 98.80 % 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: -0.26 (0.17), residues: 2520 helix: 1.14 (0.17), residues: 900 sheet: 0.71 (0.30), residues: 350 loop : -1.46 (0.17), residues: 1270 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 215 TYR 0.016 0.002 TYR H 214 PHE 0.012 0.002 PHE E 121 HIS 0.002 0.001 HIS B 77 Details of bonding type rmsd covalent geometry : bond 0.00343 (22290) covalent geometry : angle 0.66868 (30020) hydrogen bonds : bond 0.03896 ( 960) hydrogen bonds : angle 4.70432 ( 2610) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4536 Ramachandran restraints generated. 2268 Oldfield, 0 Emsley, 2268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4536 Ramachandran restraints generated. 2268 Oldfield, 0 Emsley, 2268 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 : 0.093 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 13 LYS cc_start: 0.8802 (mmmm) cc_final: 0.8421 (mmmm) REVERT: E 85 PHE cc_start: 0.9101 (t80) cc_final: 0.8839 (t80) REVERT: E 250 TYR cc_start: 0.8546 (t80) cc_final: 0.7463 (t80) REVERT: E 262 LEU cc_start: 0.8541 (mt) cc_final: 0.8224 (mt) outliers start: 0 outliers final: 0 residues processed: 52 average time/residue: 0.0278 time to fit residues: 1.9537 Evaluate side-chains 43 residues out of total 249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 43 time to evaluate : 0.084 ------------------------------------------------------------------------------- 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: 0.9980 chunk 180 optimal weight: 20.0000 chunk 144 optimal weight: 5.9990 chunk 215 optimal weight: 20.0000 chunk 155 optimal weight: 0.0670 chunk 135 optimal weight: 7.9990 chunk 65 optimal weight: 4.9990 chunk 21 optimal weight: 6.9990 chunk 209 optimal weight: 3.9990 chunk 166 optimal weight: 5.9990 overall best weight: 3.2124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.070886 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2988 r_free = 0.2988 target = 0.055661 restraints weight = 11372.016| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.057689 restraints weight = 7189.505| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.059158 restraints weight = 5114.394| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.060237 restraints weight = 3930.714| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.061026 restraints weight = 3197.896| |-----------------------------------------------------------------------------| r_work (final): 0.3117 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7964 moved from start: 0.3918 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= 0.131 Angle : 0.666 6.050 30020 Z= 0.337 Chirality : 0.045 0.145 3400 Planarity : 0.005 0.070 3800 Dihedral : 4.588 18.545 2900 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 12.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.16 % Favored : 94.84 % 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: -0.21 (0.17), residues: 2520 helix: 1.25 (0.17), residues: 900 sheet: 0.78 (0.30), residues: 350 loop : -1.50 (0.17), residues: 1270 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG G 215 TYR 0.015 0.001 TYR F 214 PHE 0.013 0.001 PHE F 121 HIS 0.002 0.001 HIS D 197 Details of bonding type rmsd covalent geometry : bond 0.00291 (22290) covalent geometry : angle 0.66553 (30020) hydrogen bonds : bond 0.03839 ( 960) hydrogen bonds : angle 4.54608 ( 2610) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4536 Ramachandran restraints generated. 2268 Oldfield, 0 Emsley, 2268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4536 Ramachandran restraints generated. 2268 Oldfield, 0 Emsley, 2268 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 : 0.085 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 13 LYS cc_start: 0.8799 (mmmm) cc_final: 0.8412 (mmmm) REVERT: E 85 PHE cc_start: 0.9115 (t80) cc_final: 0.8629 (t80) REVERT: E 250 TYR cc_start: 0.8455 (t80) cc_final: 0.7557 (t80) REVERT: E 262 LEU cc_start: 0.8452 (mt) cc_final: 0.8190 (mt) outliers start: 0 outliers final: 0 residues processed: 52 average time/residue: 0.0326 time to fit residues: 2.2336 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 : 0.093 ------------------------------------------------------------------------------- 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: 3.9990 chunk 52 optimal weight: 20.0000 chunk 14 optimal weight: 0.6980 chunk 259 optimal weight: 10.0000 chunk 229 optimal weight: 0.0010 chunk 228 optimal weight: 5.9990 chunk 22 optimal weight: 0.5980 chunk 46 optimal weight: 5.9990 chunk 5 optimal weight: 10.0000 chunk 69 optimal weight: 1.9990 chunk 35 optimal weight: 0.0370 overall best weight: 0.6666 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.074760 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.059285 restraints weight = 11265.688| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.061325 restraints weight = 7302.258| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.062865 restraints weight = 5265.725| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.064026 restraints weight = 4070.915| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.064911 restraints weight = 3312.910| |-----------------------------------------------------------------------------| r_work (final): 0.3197 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7837 moved from start: 0.4620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 22290 Z= 0.114 Angle : 0.659 7.062 30020 Z= 0.321 Chirality : 0.043 0.172 3400 Planarity : 0.004 0.049 3800 Dihedral : 4.274 21.808 2900 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % 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: 0.10 (0.17), residues: 2520 helix: 1.40 (0.17), residues: 900 sheet: 0.05 (0.28), residues: 420 loop : -0.96 (0.18), residues: 1200 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 215 TYR 0.008 0.001 TYR F 214 PHE 0.014 0.001 PHE C 121 HIS 0.004 0.001 HIS A 197 Details of bonding type rmsd covalent geometry : bond 0.00246 (22290) covalent geometry : angle 0.65855 (30020) hydrogen bonds : bond 0.03701 ( 960) hydrogen bonds : angle 4.39013 ( 2610) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1330.66 seconds wall clock time: 24 minutes 43.94 seconds (1483.94 seconds total)