Starting phenix.real_space_refine on Fri Jul 3 08:32:49 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8atg_15649/07_2026/8atg_15649.cif Found real_map, /net/cci-nas-00/data/ceres_data/8atg_15649/07_2026/8atg_15649.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/8atg_15649/07_2026/8atg_15649.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8atg_15649/07_2026/8atg_15649.cif" model { file = "/net/cci-nas-00/data/ceres_data/8atg_15649/07_2026/8atg_15649.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8atg_15649/07_2026/8atg_15649.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8atg_15649/07_2026/8atg_15649.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8atg_15649/07_2026/8atg_15649.map" } resolution = 2.9 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= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 25 5.49 5 S 20 5.16 5 C 8680 2.51 5 N 1960 2.21 5 O 2305 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 12990 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 2402 Number of conformers: 1 Conformer: "" Number of residues, atoms: 311, 2402 Classifications: {'peptide': 311} Incomplete info: {'truncation_to_alanine': 36} Link IDs: {'PTRANS': 18, 'TRANS': 292} Unresolved non-hydrogen bonds: 124 Unresolved non-hydrogen angles: 157 Unresolved non-hydrogen dihedrals: 93 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'GLU:plan': 6, 'ASP:plan': 7, 'ASN:plan1': 3, 'ARG:plan': 3, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 75 Chain: "A" Number of atoms: 196 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 196 Unusual residues: {'POV': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 64 Unresolved non-hydrogen angles: 64 Unresolved non-hydrogen dihedrals: 64 Planarities with less than four sites: {'POV:plan-1': 4} Unresolved non-hydrogen planarities: 8 Restraints were copied for chains: B, C, D, E Time building chain proxies: 2.43, per 1000 atoms: 0.19 Number of scatterers: 12990 At special positions: 0 Unit cell: (91.84, 92.66, 118.08, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 20 16.00 P 25 15.00 O 2305 8.00 N 1960 7.00 C 8680 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: 0.87 Conformation dependent library (CDL) restraints added in 579.1 milliseconds 3090 Ramachandran restraints generated. 1545 Oldfield, 0 Emsley, 1545 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3050 Finding SS restraints... Secondary structure from input PDB file: 40 helices and 20 sheets defined 37.9% alpha, 22.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.37 Creating SS restraints... Processing helix chain 'A' and resid 118 through 122 removed outlier: 3.533A pdb=" N ASP A 122 " --> pdb=" O TYR A 119 " (cutoff:3.500A) Processing helix chain 'A' and resid 178 through 180 No H-bonds generated for 'chain 'A' and resid 178 through 180' Processing helix chain 'A' and resid 196 through 201 Processing helix chain 'A' and resid 201 through 214 removed outlier: 3.634A pdb=" N MET A 205 " --> pdb=" O ILE A 201 " (cutoff:3.500A) Processing helix chain 'A' and resid 215 through 218 removed outlier: 3.829A pdb=" N SER A 218 " --> pdb=" O ALA A 215 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 215 through 218' Processing helix chain 'A' and resid 220 through 244 removed outlier: 3.978A pdb=" N THR A 244 " --> pdb=" O ILE A 240 " (cutoff:3.500A) Processing helix chain 'A' and resid 254 through 282 removed outlier: 3.639A pdb=" N ILE A 259 " --> pdb=" O THR A 255 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N PHE A 260 " --> pdb=" O GLY A 256 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N GLU A 282 " --> pdb=" O TYR A 278 " (cutoff:3.500A) Processing helix chain 'A' and resid 284 through 315 removed outlier: 3.942A pdb=" N ILE A 297 " --> pdb=" O ARG A 293 " (cutoff:3.500A) Proline residue: A 300 - end of helix Processing helix chain 'B' and resid 118 through 122 removed outlier: 3.532A pdb=" N ASP B 122 " --> pdb=" O TYR B 119 " (cutoff:3.500A) Processing helix chain 'B' and resid 178 through 180 No H-bonds generated for 'chain 'B' and resid 178 through 180' Processing helix chain 'B' and resid 196 through 201 Processing helix chain 'B' and resid 201 through 214 removed outlier: 3.634A pdb=" N MET B 205 " --> pdb=" O ILE B 201 " (cutoff:3.500A) Processing helix chain 'B' and resid 215 through 218 removed outlier: 3.829A pdb=" N SER B 218 " --> pdb=" O ALA B 215 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 215 through 218' Processing helix chain 'B' and resid 220 through 244 removed outlier: 3.978A pdb=" N THR B 244 " --> pdb=" O ILE B 240 " (cutoff:3.500A) Processing helix chain 'B' and resid 254 through 282 removed outlier: 3.639A pdb=" N ILE B 259 " --> pdb=" O THR B 255 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N PHE B 260 " --> pdb=" O GLY B 256 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N GLU B 282 " --> pdb=" O TYR B 278 " (cutoff:3.500A) Processing helix chain 'B' and resid 284 through 315 removed outlier: 3.942A pdb=" N ILE B 297 " --> pdb=" O ARG B 293 " (cutoff:3.500A) Proline residue: B 300 - end of helix Processing helix chain 'C' and resid 118 through 122 removed outlier: 3.533A pdb=" N ASP C 122 " --> pdb=" O TYR C 119 " (cutoff:3.500A) Processing helix chain 'C' and resid 178 through 180 No H-bonds generated for 'chain 'C' and resid 178 through 180' Processing helix chain 'C' and resid 196 through 201 Processing helix chain 'C' and resid 201 through 214 removed outlier: 3.634A pdb=" N MET C 205 " --> pdb=" O ILE C 201 " (cutoff:3.500A) Processing helix chain 'C' and resid 215 through 218 removed outlier: 3.830A pdb=" N SER C 218 " --> pdb=" O ALA C 215 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 215 through 218' Processing helix chain 'C' and resid 220 through 244 removed outlier: 3.978A pdb=" N THR C 244 " --> pdb=" O ILE C 240 " (cutoff:3.500A) Processing helix chain 'C' and resid 254 through 282 removed outlier: 3.639A pdb=" N ILE C 259 " --> pdb=" O THR C 255 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N PHE C 260 " --> pdb=" O GLY C 256 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N GLU C 282 " --> pdb=" O TYR C 278 " (cutoff:3.500A) Processing helix chain 'C' and resid 284 through 315 removed outlier: 3.942A pdb=" N ILE C 297 " --> pdb=" O ARG C 293 " (cutoff:3.500A) Proline residue: C 300 - end of helix Processing helix chain 'D' and resid 118 through 122 removed outlier: 3.534A pdb=" N ASP D 122 " --> pdb=" O TYR D 119 " (cutoff:3.500A) Processing helix chain 'D' and resid 178 through 180 No H-bonds generated for 'chain 'D' and resid 178 through 180' Processing helix chain 'D' and resid 196 through 201 Processing helix chain 'D' and resid 201 through 214 removed outlier: 3.634A pdb=" N MET D 205 " --> pdb=" O ILE D 201 " (cutoff:3.500A) Processing helix chain 'D' and resid 215 through 218 removed outlier: 3.830A pdb=" N SER D 218 " --> pdb=" O ALA D 215 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 215 through 218' Processing helix chain 'D' and resid 220 through 244 removed outlier: 3.978A pdb=" N THR D 244 " --> pdb=" O ILE D 240 " (cutoff:3.500A) Processing helix chain 'D' and resid 254 through 282 removed outlier: 3.639A pdb=" N ILE D 259 " --> pdb=" O THR D 255 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N PHE D 260 " --> pdb=" O GLY D 256 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N GLU D 282 " --> pdb=" O TYR D 278 " (cutoff:3.500A) Processing helix chain 'D' and resid 284 through 315 removed outlier: 3.943A pdb=" N ILE D 297 " --> pdb=" O ARG D 293 " (cutoff:3.500A) Proline residue: D 300 - end of helix Processing helix chain 'E' and resid 118 through 122 removed outlier: 3.534A pdb=" N ASP E 122 " --> pdb=" O TYR E 119 " (cutoff:3.500A) Processing helix chain 'E' and resid 178 through 180 No H-bonds generated for 'chain 'E' and resid 178 through 180' Processing helix chain 'E' and resid 196 through 201 Processing helix chain 'E' and resid 201 through 214 removed outlier: 3.634A pdb=" N MET E 205 " --> pdb=" O ILE E 201 " (cutoff:3.500A) Processing helix chain 'E' and resid 215 through 218 removed outlier: 3.830A pdb=" N SER E 218 " --> pdb=" O ALA E 215 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 215 through 218' Processing helix chain 'E' and resid 220 through 244 removed outlier: 3.979A pdb=" N THR E 244 " --> pdb=" O ILE E 240 " (cutoff:3.500A) Processing helix chain 'E' and resid 254 through 282 removed outlier: 3.640A pdb=" N ILE E 259 " --> pdb=" O THR E 255 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N PHE E 260 " --> pdb=" O GLY E 256 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N GLU E 282 " --> pdb=" O TYR E 278 " (cutoff:3.500A) Processing helix chain 'E' and resid 284 through 315 removed outlier: 3.942A pdb=" N ILE E 297 " --> pdb=" O ARG E 293 " (cutoff:3.500A) Proline residue: E 300 - end of helix Processing sheet with id=AA1, first strand: chain 'A' and resid 19 through 23 removed outlier: 6.066A pdb=" N ARG A 105 " --> pdb=" O VAL A 89 " (cutoff:3.500A) removed outlier: 5.285A pdb=" N VAL A 89 " --> pdb=" O ARG A 105 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N VAL A 94 " --> pdb=" O LYS A 64 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LYS A 64 " --> pdb=" O VAL A 94 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 27 through 28 Processing sheet with id=AA3, first strand: chain 'A' and resid 76 through 78 removed outlier: 4.928A pdb=" N VAL A 132 " --> pdb=" O SER A 182 " (cutoff:3.500A) removed outlier: 7.440A pdb=" N SER A 182 " --> pdb=" O VAL A 132 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N ARG A 189 " --> pdb=" O GLU A 163 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 76 through 78 removed outlier: 4.928A pdb=" N VAL A 132 " --> pdb=" O SER A 182 " (cutoff:3.500A) removed outlier: 7.440A pdb=" N SER A 182 " --> pdb=" O VAL A 132 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N LYS A 183 " --> pdb=" O LYS A 170 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 19 through 23 removed outlier: 6.066A pdb=" N ARG B 105 " --> pdb=" O VAL B 89 " (cutoff:3.500A) removed outlier: 5.285A pdb=" N VAL B 89 " --> pdb=" O ARG B 105 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N VAL B 94 " --> pdb=" O LYS B 64 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LYS B 64 " --> pdb=" O VAL B 94 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 27 through 28 Processing sheet with id=AA7, first strand: chain 'B' and resid 76 through 78 removed outlier: 4.927A pdb=" N VAL B 132 " --> pdb=" O SER B 182 " (cutoff:3.500A) removed outlier: 7.441A pdb=" N SER B 182 " --> pdb=" O VAL B 132 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N ARG B 189 " --> pdb=" O GLU B 163 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 76 through 78 removed outlier: 4.927A pdb=" N VAL B 132 " --> pdb=" O SER B 182 " (cutoff:3.500A) removed outlier: 7.441A pdb=" N SER B 182 " --> pdb=" O VAL B 132 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N LYS B 183 " --> pdb=" O LYS B 170 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 19 through 23 removed outlier: 6.066A pdb=" N ARG C 105 " --> pdb=" O VAL C 89 " (cutoff:3.500A) removed outlier: 5.284A pdb=" N VAL C 89 " --> pdb=" O ARG C 105 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N VAL C 94 " --> pdb=" O LYS C 64 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LYS C 64 " --> pdb=" O VAL C 94 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 27 through 28 Processing sheet with id=AB2, first strand: chain 'C' and resid 76 through 78 removed outlier: 4.928A pdb=" N VAL C 132 " --> pdb=" O SER C 182 " (cutoff:3.500A) removed outlier: 7.440A pdb=" N SER C 182 " --> pdb=" O VAL C 132 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N ARG C 189 " --> pdb=" O GLU C 163 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 76 through 78 removed outlier: 4.928A pdb=" N VAL C 132 " --> pdb=" O SER C 182 " (cutoff:3.500A) removed outlier: 7.440A pdb=" N SER C 182 " --> pdb=" O VAL C 132 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N LYS C 183 " --> pdb=" O LYS C 170 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 19 through 23 removed outlier: 6.066A pdb=" N ARG D 105 " --> pdb=" O VAL D 89 " (cutoff:3.500A) removed outlier: 5.284A pdb=" N VAL D 89 " --> pdb=" O ARG D 105 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N VAL D 94 " --> pdb=" O LYS D 64 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LYS D 64 " --> pdb=" O VAL D 94 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 27 through 28 Processing sheet with id=AB6, first strand: chain 'D' and resid 76 through 78 removed outlier: 4.927A pdb=" N VAL D 132 " --> pdb=" O SER D 182 " (cutoff:3.500A) removed outlier: 7.440A pdb=" N SER D 182 " --> pdb=" O VAL D 132 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N ARG D 189 " --> pdb=" O GLU D 163 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 76 through 78 removed outlier: 4.927A pdb=" N VAL D 132 " --> pdb=" O SER D 182 " (cutoff:3.500A) removed outlier: 7.440A pdb=" N SER D 182 " --> pdb=" O VAL D 132 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N LYS D 183 " --> pdb=" O LYS D 170 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 19 through 23 removed outlier: 6.066A pdb=" N ARG E 105 " --> pdb=" O VAL E 89 " (cutoff:3.500A) removed outlier: 5.285A pdb=" N VAL E 89 " --> pdb=" O ARG E 105 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N VAL E 94 " --> pdb=" O LYS E 64 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LYS E 64 " --> pdb=" O VAL E 94 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 27 through 28 Processing sheet with id=AC1, first strand: chain 'E' and resid 76 through 78 removed outlier: 4.927A pdb=" N VAL E 132 " --> pdb=" O SER E 182 " (cutoff:3.500A) removed outlier: 7.440A pdb=" N SER E 182 " --> pdb=" O VAL E 132 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N ARG E 189 " --> pdb=" O GLU E 163 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 76 through 78 removed outlier: 4.927A pdb=" N VAL E 132 " --> pdb=" O SER E 182 " (cutoff:3.500A) removed outlier: 7.440A pdb=" N SER E 182 " --> pdb=" O VAL E 132 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N LYS E 183 " --> pdb=" O LYS E 170 " (cutoff:3.500A) 600 hydrogen bonds defined for protein. 1725 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.26 Time building geometry restraints manager: 1.23 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1981 1.32 - 1.44: 3536 1.44 - 1.57: 7698 1.57 - 1.69: 50 1.69 - 1.81: 35 Bond restraints: 13300 Sorted by residual: bond pdb=" O12 POV C 401 " pdb=" P POV C 401 " ideal model delta sigma weight residual 1.657 1.605 0.052 2.00e-02 2.50e+03 6.85e+00 bond pdb=" O12 POV D 401 " pdb=" P POV D 401 " ideal model delta sigma weight residual 1.657 1.605 0.052 2.00e-02 2.50e+03 6.84e+00 bond pdb=" O12 POV E 404 " pdb=" P POV E 404 " ideal model delta sigma weight residual 1.657 1.605 0.052 2.00e-02 2.50e+03 6.81e+00 bond pdb=" O12 POV A 401 " pdb=" P POV A 401 " ideal model delta sigma weight residual 1.657 1.605 0.052 2.00e-02 2.50e+03 6.80e+00 bond pdb=" O12 POV B 404 " pdb=" P POV B 404 " ideal model delta sigma weight residual 1.657 1.605 0.052 2.00e-02 2.50e+03 6.71e+00 ... (remaining 13295 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.40: 17184 1.40 - 2.79: 722 2.79 - 4.19: 130 4.19 - 5.58: 47 5.58 - 6.98: 12 Bond angle restraints: 18095 Sorted by residual: angle pdb=" N VAL C 141 " pdb=" CA VAL C 141 " pdb=" C VAL C 141 " ideal model delta sigma weight residual 112.29 108.57 3.72 9.40e-01 1.13e+00 1.57e+01 angle pdb=" N VAL A 141 " pdb=" CA VAL A 141 " pdb=" C VAL A 141 " ideal model delta sigma weight residual 112.29 108.58 3.71 9.40e-01 1.13e+00 1.56e+01 angle pdb=" N VAL D 141 " pdb=" CA VAL D 141 " pdb=" C VAL D 141 " ideal model delta sigma weight residual 112.29 108.59 3.70 9.40e-01 1.13e+00 1.55e+01 angle pdb=" N VAL E 141 " pdb=" CA VAL E 141 " pdb=" C VAL E 141 " ideal model delta sigma weight residual 112.29 108.60 3.69 9.40e-01 1.13e+00 1.54e+01 angle pdb=" N VAL B 141 " pdb=" CA VAL B 141 " pdb=" C VAL B 141 " ideal model delta sigma weight residual 112.29 108.63 3.66 9.40e-01 1.13e+00 1.52e+01 ... (remaining 18090 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.06: 7438 26.06 - 52.13: 312 52.13 - 78.19: 85 78.19 - 104.26: 15 104.26 - 130.32: 25 Dihedral angle restraints: 7875 sinusoidal: 3200 harmonic: 4675 Sorted by residual: dihedral pdb=" C3 POV B 403 " pdb=" C31 POV B 403 " pdb=" O31 POV B 403 " pdb=" C32 POV B 403 " ideal model delta sinusoidal sigma weight residual 172.61 -57.07 -130.32 1 3.00e+01 1.11e-03 1.76e+01 dihedral pdb=" C3 POV A 403 " pdb=" C31 POV A 403 " pdb=" O31 POV A 403 " pdb=" C32 POV A 403 " ideal model delta sinusoidal sigma weight residual 172.61 -57.07 -130.32 1 3.00e+01 1.11e-03 1.76e+01 dihedral pdb=" C3 POV C 403 " pdb=" C31 POV C 403 " pdb=" O31 POV C 403 " pdb=" C32 POV C 403 " ideal model delta sinusoidal sigma weight residual 172.61 -57.09 -130.30 1 3.00e+01 1.11e-03 1.76e+01 ... (remaining 7872 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 1111 0.026 - 0.053: 566 0.053 - 0.079: 181 0.079 - 0.105: 116 0.105 - 0.131: 66 Chirality restraints: 2040 Sorted by residual: chirality pdb=" CA PRO D 204 " pdb=" N PRO D 204 " pdb=" C PRO D 204 " pdb=" CB PRO D 204 " both_signs ideal model delta sigma weight residual False 2.72 2.59 0.13 2.00e-01 2.50e+01 4.31e-01 chirality pdb=" CA PRO B 204 " pdb=" N PRO B 204 " pdb=" C PRO B 204 " pdb=" CB PRO B 204 " both_signs ideal model delta sigma weight residual False 2.72 2.59 0.13 2.00e-01 2.50e+01 4.19e-01 chirality pdb=" CA PRO A 204 " pdb=" N PRO A 204 " pdb=" C PRO A 204 " pdb=" CB PRO A 204 " both_signs ideal model delta sigma weight residual False 2.72 2.59 0.13 2.00e-01 2.50e+01 4.12e-01 ... (remaining 2037 not shown) Planarity restraints: 2175 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C28 POV E 404 " 0.043 2.00e-02 2.50e+03 4.27e-02 1.82e+01 pdb=" C29 POV E 404 " -0.042 2.00e-02 2.50e+03 pdb="C210 POV E 404 " -0.043 2.00e-02 2.50e+03 pdb="C211 POV E 404 " 0.043 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C28 POV B 404 " -0.042 2.00e-02 2.50e+03 4.25e-02 1.81e+01 pdb=" C29 POV B 404 " 0.042 2.00e-02 2.50e+03 pdb="C210 POV B 404 " 0.043 2.00e-02 2.50e+03 pdb="C211 POV B 404 " -0.043 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C28 POV A 404 " -0.042 2.00e-02 2.50e+03 4.25e-02 1.81e+01 pdb=" C29 POV A 404 " 0.042 2.00e-02 2.50e+03 pdb="C210 POV A 404 " 0.043 2.00e-02 2.50e+03 pdb="C211 POV A 404 " -0.043 2.00e-02 2.50e+03 ... (remaining 2172 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 2730 2.79 - 3.31: 12271 3.31 - 3.84: 20918 3.84 - 4.37: 24032 4.37 - 4.90: 41332 Nonbonded interactions: 101283 Sorted by model distance: nonbonded pdb=" O ILE E 25 " pdb=" ND2 ASN E 152 " model vdw 2.256 3.120 nonbonded pdb=" O ILE D 25 " pdb=" ND2 ASN D 152 " model vdw 2.256 3.120 nonbonded pdb=" O ILE A 25 " pdb=" ND2 ASN A 152 " model vdw 2.257 3.120 nonbonded pdb=" O ILE B 25 " pdb=" ND2 ASN B 152 " model vdw 2.257 3.120 nonbonded pdb=" O ILE C 25 " pdb=" ND2 ASN C 152 " model vdw 2.257 3.120 ... (remaining 101278 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: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.600 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 11.480 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.190 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5943 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.052 13300 Z= 0.309 Angle : 0.709 6.979 18095 Z= 0.336 Chirality : 0.043 0.131 2040 Planarity : 0.005 0.044 2175 Dihedral : 18.241 130.322 4825 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 13.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.44 % Favored : 92.56 % Rotamer: Outliers : 0.00 % Allowed : 0.41 % Favored : 99.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.00 (0.22), residues: 1545 helix: 1.34 (0.22), residues: 535 sheet: -1.41 (0.33), residues: 275 loop : -1.94 (0.23), residues: 735 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 189 TYR 0.012 0.001 TYR B 194 PHE 0.027 0.002 PHE E 195 TRP 0.011 0.001 TRP D 160 HIS 0.002 0.001 HIS B 127 Details of bonding type rmsd/Z covalent geometry : bond 0.00656 / 0.31 (13300) covalent geometry : angle 0.70913 / 0.34 (18095) hydrogen bonds : bond 0.20507 / 14.43 ( 560) hydrogen bonds : angle 6.86630 / 4.84 ( 1725) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3090 Ramachandran restraints generated. 1545 Oldfield, 0 Emsley, 1545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3090 Ramachandran restraints generated. 1545 Oldfield, 0 Emsley, 1545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 244 time to evaluate : 0.456 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 174 PHE cc_start: 0.7501 (p90) cc_final: 0.7247 (p90) REVERT: C 174 PHE cc_start: 0.7631 (p90) cc_final: 0.7380 (p90) REVERT: D 174 PHE cc_start: 0.7689 (p90) cc_final: 0.7436 (p90) REVERT: D 187 GLN cc_start: 0.8909 (mt0) cc_final: 0.8660 (mm110) REVERT: E 248 LYS cc_start: 0.8579 (mtmt) cc_final: 0.8317 (tppt) outliers start: 0 outliers final: 1 residues processed: 244 average time/residue: 0.4566 time to fit residues: 122.7042 Evaluate side-chains 131 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 130 time to evaluate : 0.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 291 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 98 optimal weight: 7.9990 chunk 107 optimal weight: 20.0000 chunk 10 optimal weight: 6.9990 chunk 66 optimal weight: 20.0000 chunk 130 optimal weight: 9.9990 chunk 124 optimal weight: 10.0000 chunk 103 optimal weight: 9.9990 chunk 77 optimal weight: 0.1980 chunk 122 optimal weight: 0.9990 chunk 91 optimal weight: 1.9990 chunk 149 optimal weight: 0.9990 overall best weight: 2.2388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.090298 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.065137 restraints weight = 39049.028| |-----------------------------------------------------------------------------| r_work (start): 0.3297 rms_B_bonded: 3.70 r_work: 0.3120 rms_B_bonded: 4.92 restraints_weight: 0.5000 r_work (final): 0.3120 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8310 moved from start: 0.2074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 13300 Z= 0.169 Angle : 0.672 6.977 18095 Z= 0.345 Chirality : 0.044 0.144 2040 Planarity : 0.005 0.038 2175 Dihedral : 19.054 136.908 2327 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.32 % Allowed : 6.08 % Favored : 93.59 % Rotamer: Outliers : 2.22 % Allowed : 14.57 % Favored : 83.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.85 (0.22), residues: 1545 helix: 1.66 (0.22), residues: 525 sheet: -1.74 (0.28), residues: 325 loop : -1.74 (0.24), residues: 695 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 189 TYR 0.015 0.002 TYR A 266 PHE 0.014 0.001 PHE D 37 TRP 0.007 0.001 TRP B 160 HIS 0.005 0.001 HIS A 235 Details of bonding type rmsd/Z covalent geometry : bond 0.00385 / 0.17 (13300) covalent geometry : angle 0.67171 / 0.34 (18095) hydrogen bonds : bond 0.04362 / 2.99 ( 560) hydrogen bonds : angle 5.37872 / 3.74 ( 1725) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3090 Ramachandran restraints generated. 1545 Oldfield, 0 Emsley, 1545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3090 Ramachandran restraints generated. 1545 Oldfield, 0 Emsley, 1545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 159 time to evaluate : 0.473 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 174 PHE cc_start: 0.7702 (p90) cc_final: 0.7260 (p90) REVERT: B 187 GLN cc_start: 0.9019 (mt0) cc_final: 0.8738 (mt0) REVERT: B 266 TYR cc_start: 0.8691 (m-80) cc_final: 0.8489 (m-80) REVERT: C 35 GLU cc_start: 0.7841 (pm20) cc_final: 0.7615 (pm20) REVERT: C 187 GLN cc_start: 0.8975 (mt0) cc_final: 0.8712 (mt0) REVERT: D 187 GLN cc_start: 0.9023 (mt0) cc_final: 0.8748 (mt0) REVERT: D 248 LYS cc_start: 0.9032 (mtmt) cc_final: 0.8685 (mttp) REVERT: E 187 GLN cc_start: 0.9032 (mt0) cc_final: 0.8721 (mt0) REVERT: E 213 TRP cc_start: 0.8739 (m-10) cc_final: 0.8355 (m-10) REVERT: E 248 LYS cc_start: 0.8977 (mtmt) cc_final: 0.8653 (mtmm) outliers start: 27 outliers final: 15 residues processed: 177 average time/residue: 0.4825 time to fit residues: 93.8891 Evaluate side-chains 141 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 126 time to evaluate : 0.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 THR Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain A residue 212 SER Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain B residue 36 THR Chi-restraints excluded: chain B residue 212 SER Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain C residue 212 SER Chi-restraints excluded: chain C residue 255 THR Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain D residue 205 MET Chi-restraints excluded: chain D residue 212 SER Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain E residue 36 THR Chi-restraints excluded: chain E residue 212 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 56 optimal weight: 0.9980 chunk 47 optimal weight: 0.9990 chunk 109 optimal weight: 0.9980 chunk 108 optimal weight: 0.5980 chunk 73 optimal weight: 8.9990 chunk 152 optimal weight: 7.9990 chunk 99 optimal weight: 0.0980 chunk 111 optimal weight: 0.9980 chunk 124 optimal weight: 10.0000 chunk 21 optimal weight: 7.9990 chunk 35 optimal weight: 10.0000 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.091293 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.066227 restraints weight = 39079.289| |-----------------------------------------------------------------------------| r_work (start): 0.3318 rms_B_bonded: 3.73 r_work: 0.3144 rms_B_bonded: 4.93 restraints_weight: 0.5000 r_work (final): 0.3144 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8294 moved from start: 0.2498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 13300 Z= 0.121 Angle : 0.621 6.444 18095 Z= 0.316 Chirality : 0.043 0.142 2040 Planarity : 0.004 0.034 2175 Dihedral : 17.949 139.311 2325 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.32 % Allowed : 5.63 % Favored : 94.05 % Rotamer: Outliers : 1.81 % Allowed : 17.12 % Favored : 81.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.59 (0.22), residues: 1545 helix: 1.88 (0.22), residues: 525 sheet: -1.63 (0.28), residues: 325 loop : -1.57 (0.25), residues: 695 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 189 TYR 0.012 0.001 TYR C 102 PHE 0.017 0.001 PHE E 37 TRP 0.006 0.001 TRP D 160 HIS 0.005 0.001 HIS B 235 Details of bonding type rmsd/Z covalent geometry : bond 0.00268 / 0.12 (13300) covalent geometry : angle 0.62073 / 0.32 (18095) hydrogen bonds : bond 0.03790 / 2.60 ( 560) hydrogen bonds : angle 4.87067 / 3.40 ( 1725) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3090 Ramachandran restraints generated. 1545 Oldfield, 0 Emsley, 1545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3090 Ramachandran restraints generated. 1545 Oldfield, 0 Emsley, 1545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 154 time to evaluate : 0.332 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 163 GLU cc_start: 0.8114 (mp0) cc_final: 0.7885 (mp0) REVERT: A 187 GLN cc_start: 0.8983 (mt0) cc_final: 0.8688 (mt0) REVERT: A 313 LEU cc_start: 0.9351 (mp) cc_final: 0.8989 (tp) REVERT: B 266 TYR cc_start: 0.8646 (m-80) cc_final: 0.8390 (m-80) REVERT: C 187 GLN cc_start: 0.8927 (mt0) cc_final: 0.8616 (mt0) REVERT: C 213 TRP cc_start: 0.8787 (m-10) cc_final: 0.8471 (m-10) REVERT: C 248 LYS cc_start: 0.9079 (mtmt) cc_final: 0.8320 (tppt) REVERT: D 187 GLN cc_start: 0.8954 (mt0) cc_final: 0.8657 (mt0) REVERT: D 248 LYS cc_start: 0.9012 (mtmt) cc_final: 0.8672 (mttp) REVERT: E 35 GLU cc_start: 0.8247 (pm20) cc_final: 0.7843 (pm20) REVERT: E 213 TRP cc_start: 0.8733 (m-10) cc_final: 0.8448 (m-10) REVERT: E 248 LYS cc_start: 0.9005 (mtmt) cc_final: 0.8762 (tppt) outliers start: 22 outliers final: 10 residues processed: 170 average time/residue: 0.4642 time to fit residues: 86.6953 Evaluate side-chains 135 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 125 time to evaluate : 0.483 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 THR Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain B residue 205 MET Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain C residue 36 THR Chi-restraints excluded: chain C residue 205 MET Chi-restraints excluded: chain C residue 214 THR Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain D residue 36 THR Chi-restraints excluded: chain D residue 270 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 26 optimal weight: 7.9990 chunk 68 optimal weight: 0.7980 chunk 146 optimal weight: 0.0980 chunk 34 optimal weight: 10.0000 chunk 69 optimal weight: 9.9990 chunk 132 optimal weight: 20.0000 chunk 67 optimal weight: 10.0000 chunk 45 optimal weight: 7.9990 chunk 153 optimal weight: 5.9990 chunk 82 optimal weight: 4.9990 chunk 84 optimal weight: 0.9980 overall best weight: 2.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 245 ASN D 245 ASN E 19 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.088384 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.063405 restraints weight = 39587.253| |-----------------------------------------------------------------------------| r_work (start): 0.3264 rms_B_bonded: 3.72 r_work: 0.3089 rms_B_bonded: 4.91 restraints_weight: 0.5000 r_work (final): 0.3089 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8425 moved from start: 0.3056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 13300 Z= 0.177 Angle : 0.626 6.302 18095 Z= 0.320 Chirality : 0.044 0.164 2040 Planarity : 0.004 0.037 2175 Dihedral : 17.352 136.080 2325 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.32 % Allowed : 6.73 % Favored : 92.94 % Rotamer: Outliers : 3.05 % Allowed : 16.79 % Favored : 80.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.22 (0.22), residues: 1545 helix: 2.22 (0.22), residues: 520 sheet: -1.29 (0.28), residues: 330 loop : -1.43 (0.25), residues: 695 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 189 TYR 0.013 0.001 TYR E 102 PHE 0.027 0.001 PHE D 116 TRP 0.013 0.001 TRP D 213 HIS 0.004 0.001 HIS D 235 Details of bonding type rmsd/Z covalent geometry : bond 0.00411 / 0.18 (13300) covalent geometry : angle 0.62565 / 0.32 (18095) hydrogen bonds : bond 0.03565 / 2.46 ( 560) hydrogen bonds : angle 4.70812 / 3.26 ( 1725) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3090 Ramachandran restraints generated. 1545 Oldfield, 0 Emsley, 1545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3090 Ramachandran restraints generated. 1545 Oldfield, 0 Emsley, 1545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 135 time to evaluate : 0.303 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 163 GLU cc_start: 0.7980 (mp0) cc_final: 0.7632 (pm20) REVERT: A 187 GLN cc_start: 0.9034 (mt0) cc_final: 0.8713 (mt0) REVERT: A 245 ASN cc_start: 0.9204 (m-40) cc_final: 0.8845 (p0) REVERT: A 248 LYS cc_start: 0.9055 (mtmt) cc_final: 0.8766 (mttm) REVERT: A 313 LEU cc_start: 0.9368 (OUTLIER) cc_final: 0.9098 (tp) REVERT: C 248 LYS cc_start: 0.9077 (mtmt) cc_final: 0.8799 (mmmm) REVERT: D 187 GLN cc_start: 0.9006 (mt0) cc_final: 0.8664 (mt0) REVERT: D 313 LEU cc_start: 0.9437 (mt) cc_final: 0.9048 (tp) REVERT: E 248 LYS cc_start: 0.8900 (mtmt) cc_final: 0.8674 (mmmt) outliers start: 37 outliers final: 24 residues processed: 155 average time/residue: 0.4621 time to fit residues: 78.7955 Evaluate side-chains 148 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 123 time to evaluate : 0.475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 VAL Chi-restraints excluded: chain A residue 36 THR Chi-restraints excluded: chain A residue 212 SER Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 313 LEU Chi-restraints excluded: chain B residue 18 VAL Chi-restraints excluded: chain B residue 36 THR Chi-restraints excluded: chain B residue 212 SER Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain C residue 18 VAL Chi-restraints excluded: chain C residue 36 THR Chi-restraints excluded: chain C residue 205 MET Chi-restraints excluded: chain C residue 212 SER Chi-restraints excluded: chain C residue 214 THR Chi-restraints excluded: chain C residue 255 THR Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain D residue 18 VAL Chi-restraints excluded: chain D residue 36 THR Chi-restraints excluded: chain D residue 212 SER Chi-restraints excluded: chain D residue 255 THR Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain E residue 18 VAL Chi-restraints excluded: chain E residue 36 THR Chi-restraints excluded: chain E residue 212 SER Chi-restraints excluded: chain E residue 255 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 11 optimal weight: 0.7980 chunk 74 optimal weight: 9.9990 chunk 141 optimal weight: 30.0000 chunk 22 optimal weight: 0.7980 chunk 47 optimal weight: 4.9990 chunk 32 optimal weight: 20.0000 chunk 102 optimal weight: 20.0000 chunk 64 optimal weight: 9.9990 chunk 122 optimal weight: 5.9990 chunk 79 optimal weight: 20.0000 chunk 85 optimal weight: 0.8980 overall best weight: 2.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 245 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.087446 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.062312 restraints weight = 40002.345| |-----------------------------------------------------------------------------| r_work (start): 0.3251 rms_B_bonded: 3.69 r_work: 0.3075 rms_B_bonded: 4.92 restraints_weight: 0.5000 r_work (final): 0.3075 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8463 moved from start: 0.3552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 13300 Z= 0.176 Angle : 0.626 8.123 18095 Z= 0.320 Chirality : 0.044 0.152 2040 Planarity : 0.004 0.033 2175 Dihedral : 16.864 123.775 2325 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.32 % Allowed : 6.47 % Favored : 93.20 % Rotamer: Outliers : 2.80 % Allowed : 18.68 % Favored : 78.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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 (0.22), residues: 1545 helix: 2.33 (0.22), residues: 525 sheet: -1.34 (0.27), residues: 325 loop : -1.35 (0.25), residues: 695 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 189 TYR 0.011 0.001 TYR D 102 PHE 0.016 0.001 PHE D 116 TRP 0.010 0.001 TRP B 213 HIS 0.004 0.002 HIS B 235 Details of bonding type rmsd/Z covalent geometry : bond 0.00415 / 0.18 (13300) covalent geometry : angle 0.62601 / 0.32 (18095) hydrogen bonds : bond 0.03513 / 2.41 ( 560) hydrogen bonds : angle 4.58646 / 3.19 ( 1725) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3090 Ramachandran restraints generated. 1545 Oldfield, 0 Emsley, 1545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3090 Ramachandran restraints generated. 1545 Oldfield, 0 Emsley, 1545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 132 time to evaluate : 0.313 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 163 GLU cc_start: 0.8019 (mp0) cc_final: 0.7654 (pm20) REVERT: A 187 GLN cc_start: 0.8998 (mt0) cc_final: 0.8656 (mt0) REVERT: A 245 ASN cc_start: 0.9219 (m-40) cc_final: 0.8877 (p0) REVERT: A 248 LYS cc_start: 0.9096 (mtmt) cc_final: 0.8797 (mttm) REVERT: B 35 GLU cc_start: 0.8313 (pm20) cc_final: 0.7982 (pm20) REVERT: B 187 GLN cc_start: 0.8994 (mt0) cc_final: 0.8729 (mt0) REVERT: B 245 ASN cc_start: 0.9235 (m-40) cc_final: 0.8911 (p0) REVERT: C 248 LYS cc_start: 0.8887 (mtmt) cc_final: 0.8607 (mmmt) REVERT: C 313 LEU cc_start: 0.9436 (mt) cc_final: 0.9092 (tp) REVERT: D 187 GLN cc_start: 0.8980 (mt0) cc_final: 0.8648 (mt0) REVERT: D 245 ASN cc_start: 0.9190 (m-40) cc_final: 0.8947 (p0) REVERT: D 248 LYS cc_start: 0.9217 (mtmt) cc_final: 0.8733 (mmmm) REVERT: D 313 LEU cc_start: 0.9464 (mt) cc_final: 0.9167 (tp) REVERT: E 313 LEU cc_start: 0.9392 (mt) cc_final: 0.9094 (tp) outliers start: 34 outliers final: 24 residues processed: 152 average time/residue: 0.4851 time to fit residues: 80.9528 Evaluate side-chains 146 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 122 time to evaluate : 0.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 VAL Chi-restraints excluded: chain A residue 36 THR Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain B residue 18 VAL Chi-restraints excluded: chain B residue 36 THR Chi-restraints excluded: chain B residue 212 SER Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain C residue 18 VAL Chi-restraints excluded: chain C residue 36 THR Chi-restraints excluded: chain C residue 205 MET Chi-restraints excluded: chain C residue 212 SER Chi-restraints excluded: chain C residue 214 THR Chi-restraints excluded: chain C residue 255 THR Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain C residue 271 ILE Chi-restraints excluded: chain D residue 18 VAL Chi-restraints excluded: chain D residue 36 THR Chi-restraints excluded: chain D residue 212 SER Chi-restraints excluded: chain D residue 255 THR Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain E residue 18 VAL Chi-restraints excluded: chain E residue 36 THR Chi-restraints excluded: chain E residue 212 SER Chi-restraints excluded: chain E residue 255 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 112 optimal weight: 0.9990 chunk 84 optimal weight: 0.7980 chunk 109 optimal weight: 20.0000 chunk 53 optimal weight: 0.9990 chunk 51 optimal weight: 0.6980 chunk 46 optimal weight: 9.9990 chunk 60 optimal weight: 0.6980 chunk 148 optimal weight: 10.0000 chunk 122 optimal weight: 0.6980 chunk 133 optimal weight: 20.0000 chunk 62 optimal weight: 10.0000 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 19 ASN B 19 ASN C 245 ASN D 19 ASN E 19 ASN E 245 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.088540 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.063453 restraints weight = 39233.566| |-----------------------------------------------------------------------------| r_work (start): 0.3274 rms_B_bonded: 3.67 r_work: 0.3102 rms_B_bonded: 4.87 restraints_weight: 0.5000 r_work (final): 0.3102 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8430 moved from start: 0.3695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 13300 Z= 0.119 Angle : 0.621 6.732 18095 Z= 0.317 Chirality : 0.043 0.155 2040 Planarity : 0.004 0.032 2175 Dihedral : 16.514 111.133 2325 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.32 % Allowed : 5.63 % Favored : 94.05 % Rotamer: Outliers : 2.30 % Allowed : 20.00 % Favored : 77.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 (0.23), residues: 1545 helix: 2.40 (0.22), residues: 525 sheet: -1.27 (0.28), residues: 325 loop : -1.31 (0.26), residues: 695 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 189 TYR 0.013 0.001 TYR D 263 PHE 0.018 0.001 PHE D 116 TRP 0.014 0.001 TRP A 213 HIS 0.004 0.001 HIS B 235 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.12 (13300) covalent geometry : angle 0.62062 / 0.32 (18095) hydrogen bonds : bond 0.03299 / 2.23 ( 560) hydrogen bonds : angle 4.42480 / 3.09 ( 1725) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3090 Ramachandran restraints generated. 1545 Oldfield, 0 Emsley, 1545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3090 Ramachandran restraints generated. 1545 Oldfield, 0 Emsley, 1545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 141 time to evaluate : 0.308 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 163 GLU cc_start: 0.8023 (mp0) cc_final: 0.7650 (pm20) REVERT: A 187 GLN cc_start: 0.8978 (mt0) cc_final: 0.8604 (mt0) REVERT: A 245 ASN cc_start: 0.9199 (m-40) cc_final: 0.8938 (p0) REVERT: A 248 LYS cc_start: 0.9095 (mtmt) cc_final: 0.8790 (mttm) REVERT: B 187 GLN cc_start: 0.8952 (mt0) cc_final: 0.8655 (mt0) REVERT: B 248 LYS cc_start: 0.9062 (mttt) cc_final: 0.8745 (mmmt) REVERT: C 248 LYS cc_start: 0.8750 (mtmt) cc_final: 0.8508 (mmmt) REVERT: C 313 LEU cc_start: 0.9428 (mt) cc_final: 0.9122 (tp) REVERT: D 174 PHE cc_start: 0.7834 (OUTLIER) cc_final: 0.7564 (p90) REVERT: D 187 GLN cc_start: 0.8943 (mt0) cc_final: 0.8574 (mt0) REVERT: D 248 LYS cc_start: 0.9280 (mtmt) cc_final: 0.8749 (mmmm) REVERT: D 313 LEU cc_start: 0.9456 (mt) cc_final: 0.9184 (tp) REVERT: E 248 LYS cc_start: 0.9285 (mmmt) cc_final: 0.8922 (tmtt) REVERT: E 313 LEU cc_start: 0.9389 (mt) cc_final: 0.9146 (tp) outliers start: 28 outliers final: 16 residues processed: 162 average time/residue: 0.4824 time to fit residues: 85.8870 Evaluate side-chains 139 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 122 time to evaluate : 0.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 VAL Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain B residue 18 VAL Chi-restraints excluded: chain B residue 36 THR Chi-restraints excluded: chain B residue 205 MET Chi-restraints excluded: chain C residue 18 VAL Chi-restraints excluded: chain C residue 36 THR Chi-restraints excluded: chain C residue 205 MET Chi-restraints excluded: chain C residue 214 THR Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain D residue 18 VAL Chi-restraints excluded: chain D residue 36 THR Chi-restraints excluded: chain D residue 174 PHE Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain E residue 18 VAL Chi-restraints excluded: chain E residue 36 THR Chi-restraints excluded: chain E residue 255 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 26 optimal weight: 1.9990 chunk 20 optimal weight: 4.9990 chunk 31 optimal weight: 10.0000 chunk 62 optimal weight: 10.0000 chunk 68 optimal weight: 7.9990 chunk 85 optimal weight: 5.9990 chunk 71 optimal weight: 9.9990 chunk 98 optimal weight: 8.9990 chunk 89 optimal weight: 4.9990 chunk 139 optimal weight: 10.0000 chunk 73 optimal weight: 6.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 307 ASN B 245 ASN C 19 ASN ** D 19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 245 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.086326 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.063641 restraints weight = 40205.399| |-----------------------------------------------------------------------------| r_work (start): 0.3207 rms_B_bonded: 3.44 r_work: 0.3019 rms_B_bonded: 4.73 restraints_weight: 0.5000 r_work (final): 0.3019 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8559 moved from start: 0.4294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.059 13300 Z= 0.296 Angle : 0.743 7.995 18095 Z= 0.376 Chirality : 0.045 0.209 2040 Planarity : 0.004 0.031 2175 Dihedral : 16.721 101.674 2325 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.32 % Allowed : 7.31 % Favored : 92.36 % Rotamer: Outliers : 4.12 % Allowed : 19.75 % Favored : 76.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.30 (0.22), residues: 1545 helix: 2.11 (0.21), residues: 520 sheet: -1.38 (0.26), residues: 325 loop : -1.41 (0.25), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 117 TYR 0.012 0.002 TYR A 23 PHE 0.015 0.002 PHE D 238 TRP 0.015 0.002 TRP B 213 HIS 0.005 0.002 HIS D 235 Details of bonding type rmsd/Z covalent geometry : bond 0.00681 / 0.30 (13300) covalent geometry : angle 0.74316 / 0.38 (18095) hydrogen bonds : bond 0.03953 / 2.73 ( 560) hydrogen bonds : angle 4.71844 / 3.27 ( 1725) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3090 Ramachandran restraints generated. 1545 Oldfield, 0 Emsley, 1545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3090 Ramachandran restraints generated. 1545 Oldfield, 0 Emsley, 1545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 119 time to evaluate : 0.295 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 163 GLU cc_start: 0.8093 (mp0) cc_final: 0.7688 (pm20) REVERT: B 187 GLN cc_start: 0.9084 (mt0) cc_final: 0.8655 (mt0) REVERT: B 205 MET cc_start: 0.9364 (OUTLIER) cc_final: 0.9125 (mtp) REVERT: B 248 LYS cc_start: 0.8691 (mttt) cc_final: 0.8421 (mmmt) REVERT: C 248 LYS cc_start: 0.8923 (mtmt) cc_final: 0.8572 (mmmm) REVERT: C 313 LEU cc_start: 0.9473 (mt) cc_final: 0.9176 (tp) REVERT: D 187 GLN cc_start: 0.9055 (mt0) cc_final: 0.8619 (mt0) REVERT: D 212 SER cc_start: 0.9732 (OUTLIER) cc_final: 0.9505 (p) REVERT: D 248 LYS cc_start: 0.9206 (mtmt) cc_final: 0.8739 (mmmm) REVERT: D 313 LEU cc_start: 0.9483 (mt) cc_final: 0.9229 (tp) REVERT: E 187 GLN cc_start: 0.9064 (mt0) cc_final: 0.8677 (mt0) REVERT: E 248 LYS cc_start: 0.9289 (mmmt) cc_final: 0.8762 (mtmt) REVERT: E 313 LEU cc_start: 0.9435 (mt) cc_final: 0.9232 (tp) outliers start: 50 outliers final: 25 residues processed: 158 average time/residue: 0.4555 time to fit residues: 78.7800 Evaluate side-chains 140 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 113 time to evaluate : 0.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 VAL Chi-restraints excluded: chain A residue 36 THR Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain B residue 18 VAL Chi-restraints excluded: chain B residue 36 THR Chi-restraints excluded: chain B residue 94 VAL Chi-restraints excluded: chain B residue 205 MET Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain C residue 18 VAL Chi-restraints excluded: chain C residue 36 THR Chi-restraints excluded: chain C residue 94 VAL Chi-restraints excluded: chain C residue 205 MET Chi-restraints excluded: chain C residue 214 THR Chi-restraints excluded: chain C residue 255 THR Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain D residue 18 VAL Chi-restraints excluded: chain D residue 32 ASP Chi-restraints excluded: chain D residue 36 THR Chi-restraints excluded: chain D residue 94 VAL Chi-restraints excluded: chain D residue 212 SER Chi-restraints excluded: chain D residue 255 THR Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain E residue 18 VAL Chi-restraints excluded: chain E residue 36 THR Chi-restraints excluded: chain E residue 94 VAL Chi-restraints excluded: chain E residue 214 THR Chi-restraints excluded: chain E residue 255 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 31 optimal weight: 10.0000 chunk 4 optimal weight: 9.9990 chunk 61 optimal weight: 6.9990 chunk 146 optimal weight: 0.6980 chunk 65 optimal weight: 8.9990 chunk 63 optimal weight: 6.9990 chunk 134 optimal weight: 2.9990 chunk 113 optimal weight: 0.7980 chunk 67 optimal weight: 30.0000 chunk 115 optimal weight: 0.9990 chunk 43 optimal weight: 6.9990 overall best weight: 2.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 19 ASN B 19 ASN C 19 ASN D 19 ASN D 245 ASN E 19 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.086533 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.062371 restraints weight = 39248.994| |-----------------------------------------------------------------------------| r_work (start): 0.3228 rms_B_bonded: 3.60 r_work: 0.3058 rms_B_bonded: 4.73 restraints_weight: 0.5000 r_work (final): 0.3058 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8528 moved from start: 0.4403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 13300 Z= 0.172 Angle : 0.664 7.648 18095 Z= 0.341 Chirality : 0.044 0.204 2040 Planarity : 0.004 0.032 2175 Dihedral : 16.461 90.429 2325 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.32 % Allowed : 5.44 % Favored : 94.24 % Rotamer: Outliers : 3.05 % Allowed : 21.40 % Favored : 75.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.11 (0.22), residues: 1545 helix: 2.33 (0.22), residues: 520 sheet: -1.25 (0.27), residues: 325 loop : -1.37 (0.25), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 109 TYR 0.012 0.001 TYR D 263 PHE 0.015 0.001 PHE A 37 TRP 0.022 0.001 TRP A 213 HIS 0.005 0.002 HIS D 235 Details of bonding type rmsd/Z covalent geometry : bond 0.00416 / 0.17 (13300) covalent geometry : angle 0.66399 / 0.34 (18095) hydrogen bonds : bond 0.03491 / 2.36 ( 560) hydrogen bonds : angle 4.48190 / 3.13 ( 1725) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3090 Ramachandran restraints generated. 1545 Oldfield, 0 Emsley, 1545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3090 Ramachandran restraints generated. 1545 Oldfield, 0 Emsley, 1545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 123 time to evaluate : 0.324 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 163 GLU cc_start: 0.8129 (mp0) cc_final: 0.7695 (mp0) REVERT: A 187 GLN cc_start: 0.9037 (mt0) cc_final: 0.8583 (mm110) REVERT: A 205 MET cc_start: 0.9395 (ttm) cc_final: 0.9183 (mtt) REVERT: B 35 GLU cc_start: 0.8265 (pm20) cc_final: 0.8017 (pm20) REVERT: B 187 GLN cc_start: 0.9050 (mt0) cc_final: 0.8624 (mt0) REVERT: B 205 MET cc_start: 0.9249 (OUTLIER) cc_final: 0.9004 (mtp) REVERT: B 248 LYS cc_start: 0.8866 (mttt) cc_final: 0.8548 (mmmt) REVERT: C 313 LEU cc_start: 0.9446 (mt) cc_final: 0.9221 (tp) REVERT: D 187 GLN cc_start: 0.9000 (mt0) cc_final: 0.8568 (mt0) REVERT: D 212 SER cc_start: 0.9697 (OUTLIER) cc_final: 0.9470 (p) REVERT: D 245 ASN cc_start: 0.9131 (m-40) cc_final: 0.8806 (t0) REVERT: D 248 LYS cc_start: 0.9229 (mtmt) cc_final: 0.8772 (mmmm) REVERT: E 187 GLN cc_start: 0.9001 (mt0) cc_final: 0.8562 (mt0) REVERT: E 214 THR cc_start: 0.9679 (OUTLIER) cc_final: 0.9355 (m) outliers start: 37 outliers final: 26 residues processed: 149 average time/residue: 0.4754 time to fit residues: 77.7597 Evaluate side-chains 148 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 119 time to evaluate : 0.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 VAL Chi-restraints excluded: chain A residue 36 THR Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 174 PHE Chi-restraints excluded: chain A residue 212 SER Chi-restraints excluded: chain B residue 18 VAL Chi-restraints excluded: chain B residue 36 THR Chi-restraints excluded: chain B residue 94 VAL Chi-restraints excluded: chain B residue 205 MET Chi-restraints excluded: chain B residue 212 SER Chi-restraints excluded: chain C residue 18 VAL Chi-restraints excluded: chain C residue 36 THR Chi-restraints excluded: chain C residue 94 VAL Chi-restraints excluded: chain C residue 205 MET Chi-restraints excluded: chain C residue 212 SER Chi-restraints excluded: chain C residue 214 THR Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain D residue 18 VAL Chi-restraints excluded: chain D residue 32 ASP Chi-restraints excluded: chain D residue 36 THR Chi-restraints excluded: chain D residue 94 VAL Chi-restraints excluded: chain D residue 212 SER Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain E residue 18 VAL Chi-restraints excluded: chain E residue 36 THR Chi-restraints excluded: chain E residue 94 VAL Chi-restraints excluded: chain E residue 212 SER Chi-restraints excluded: chain E residue 214 THR Chi-restraints excluded: chain E residue 255 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 117 optimal weight: 0.8980 chunk 26 optimal weight: 0.9990 chunk 49 optimal weight: 4.9990 chunk 98 optimal weight: 0.2980 chunk 134 optimal weight: 6.9990 chunk 141 optimal weight: 20.0000 chunk 32 optimal weight: 20.0000 chunk 36 optimal weight: 0.0970 chunk 33 optimal weight: 9.9990 chunk 84 optimal weight: 0.9980 chunk 17 optimal weight: 0.0980 overall best weight: 0.4778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 19 ASN B 19 ASN ** B 235 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 19 ASN D 19 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.087647 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.063601 restraints weight = 39121.668| |-----------------------------------------------------------------------------| r_work (start): 0.3263 rms_B_bonded: 3.59 r_work: 0.3093 rms_B_bonded: 4.73 restraints_weight: 0.5000 r_work (final): 0.3093 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8493 moved from start: 0.4494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 13300 Z= 0.128 Angle : 0.684 10.804 18095 Z= 0.345 Chirality : 0.043 0.185 2040 Planarity : 0.004 0.033 2175 Dihedral : 16.178 86.069 2325 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.32 % Allowed : 5.05 % Favored : 94.63 % Rotamer: Outliers : 2.06 % Allowed : 22.63 % Favored : 75.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.04 (0.22), residues: 1545 helix: 2.31 (0.22), residues: 520 sheet: -1.10 (0.28), residues: 325 loop : -1.32 (0.25), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 109 TYR 0.012 0.001 TYR D 263 PHE 0.015 0.001 PHE E 37 TRP 0.022 0.001 TRP A 213 HIS 0.005 0.002 HIS D 235 Details of bonding type rmsd/Z covalent geometry : bond 0.00316 / 0.13 (13300) covalent geometry : angle 0.68436 / 0.34 (18095) hydrogen bonds : bond 0.03217 / 2.17 ( 560) hydrogen bonds : angle 4.33400 / 3.03 ( 1725) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3090 Ramachandran restraints generated. 1545 Oldfield, 0 Emsley, 1545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3090 Ramachandran restraints generated. 1545 Oldfield, 0 Emsley, 1545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 124 time to evaluate : 0.480 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 163 GLU cc_start: 0.8151 (mp0) cc_final: 0.7675 (mp0) REVERT: A 187 GLN cc_start: 0.9005 (mt0) cc_final: 0.8575 (mm110) REVERT: A 205 MET cc_start: 0.9388 (ttm) cc_final: 0.9175 (mtt) REVERT: B 35 GLU cc_start: 0.7932 (pm20) cc_final: 0.7707 (pm20) REVERT: B 187 GLN cc_start: 0.9004 (mt0) cc_final: 0.8681 (mt0) REVERT: B 205 MET cc_start: 0.9231 (OUTLIER) cc_final: 0.8982 (mtp) REVERT: B 248 LYS cc_start: 0.9026 (mttt) cc_final: 0.8621 (mmmt) REVERT: C 187 GLN cc_start: 0.8941 (mt0) cc_final: 0.8521 (mt0) REVERT: C 248 LYS cc_start: 0.9242 (mmmt) cc_final: 0.8776 (mtmt) REVERT: D 187 GLN cc_start: 0.8948 (mt0) cc_final: 0.8529 (mt0) REVERT: D 248 LYS cc_start: 0.9219 (mtmt) cc_final: 0.8745 (mmmm) REVERT: E 187 GLN cc_start: 0.8984 (mt0) cc_final: 0.8559 (mt0) REVERT: E 214 THR cc_start: 0.9594 (OUTLIER) cc_final: 0.9279 (m) REVERT: E 248 LYS cc_start: 0.9233 (mmpt) cc_final: 0.8862 (tmtt) outliers start: 25 outliers final: 20 residues processed: 143 average time/residue: 0.4835 time to fit residues: 75.8506 Evaluate side-chains 140 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 118 time to evaluate : 0.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 VAL Chi-restraints excluded: chain A residue 36 THR Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 212 SER Chi-restraints excluded: chain B residue 18 VAL Chi-restraints excluded: chain B residue 36 THR Chi-restraints excluded: chain B residue 94 VAL Chi-restraints excluded: chain B residue 205 MET Chi-restraints excluded: chain C residue 18 VAL Chi-restraints excluded: chain C residue 36 THR Chi-restraints excluded: chain C residue 94 VAL Chi-restraints excluded: chain C residue 205 MET Chi-restraints excluded: chain C residue 214 THR Chi-restraints excluded: chain D residue 18 VAL Chi-restraints excluded: chain D residue 32 ASP Chi-restraints excluded: chain D residue 36 THR Chi-restraints excluded: chain D residue 94 VAL Chi-restraints excluded: chain E residue 18 VAL Chi-restraints excluded: chain E residue 36 THR Chi-restraints excluded: chain E residue 94 VAL Chi-restraints excluded: chain E residue 205 MET Chi-restraints excluded: chain E residue 214 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 73 optimal weight: 5.9990 chunk 144 optimal weight: 0.9980 chunk 117 optimal weight: 0.3980 chunk 153 optimal weight: 1.9990 chunk 111 optimal weight: 10.0000 chunk 6 optimal weight: 20.0000 chunk 149 optimal weight: 6.9990 chunk 25 optimal weight: 7.9990 chunk 81 optimal weight: 0.0470 chunk 10 optimal weight: 3.9990 chunk 62 optimal weight: 10.0000 overall best weight: 1.4882 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 19 ASN B 19 ASN ** B 235 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 19 ASN D 19 ASN D 245 ASN E 19 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.087925 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.063518 restraints weight = 39148.224| |-----------------------------------------------------------------------------| r_work (start): 0.3250 rms_B_bonded: 3.61 r_work: 0.3080 rms_B_bonded: 4.73 restraints_weight: 0.5000 r_work (final): 0.3080 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8505 moved from start: 0.4605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 13300 Z= 0.142 Angle : 0.687 10.879 18095 Z= 0.344 Chirality : 0.043 0.215 2040 Planarity : 0.004 0.033 2175 Dihedral : 16.080 86.184 2325 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.32 % Allowed : 5.11 % Favored : 94.56 % Rotamer: Outliers : 2.30 % Allowed : 22.47 % Favored : 75.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 (0.22), residues: 1545 helix: 2.26 (0.22), residues: 520 sheet: -0.99 (0.28), residues: 325 loop : -1.31 (0.25), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 109 TYR 0.015 0.001 TYR D 263 PHE 0.014 0.001 PHE D 37 TRP 0.027 0.001 TRP A 213 HIS 0.004 0.002 HIS D 235 Details of bonding type rmsd/Z covalent geometry : bond 0.00353 / 0.14 (13300) covalent geometry : angle 0.68651 / 0.34 (18095) hydrogen bonds : bond 0.03146 / 2.12 ( 560) hydrogen bonds : angle 4.31187 / 3.01 ( 1725) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3090 Ramachandran restraints generated. 1545 Oldfield, 0 Emsley, 1545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3090 Ramachandran restraints generated. 1545 Oldfield, 0 Emsley, 1545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 117 time to evaluate : 0.318 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 163 GLU cc_start: 0.8150 (mp0) cc_final: 0.7677 (mp0) REVERT: A 187 GLN cc_start: 0.9002 (mt0) cc_final: 0.8561 (mm110) REVERT: A 205 MET cc_start: 0.9405 (ttm) cc_final: 0.9196 (mtt) REVERT: A 248 LYS cc_start: 0.9290 (mtmt) cc_final: 0.9071 (mttp) REVERT: B 187 GLN cc_start: 0.9019 (mt0) cc_final: 0.8600 (mt0) REVERT: B 205 MET cc_start: 0.9257 (OUTLIER) cc_final: 0.9016 (mtp) REVERT: B 248 LYS cc_start: 0.9118 (mttt) cc_final: 0.8694 (mmmt) REVERT: C 248 LYS cc_start: 0.9180 (mmmt) cc_final: 0.8965 (mmmt) REVERT: D 187 GLN cc_start: 0.8985 (mt0) cc_final: 0.8559 (mt0) REVERT: D 248 LYS cc_start: 0.9197 (mtmt) cc_final: 0.8745 (mmmm) REVERT: E 187 GLN cc_start: 0.9005 (mt0) cc_final: 0.8575 (mt0) REVERT: E 214 THR cc_start: 0.9618 (OUTLIER) cc_final: 0.9310 (m) REVERT: E 248 LYS cc_start: 0.9255 (mmpt) cc_final: 0.8907 (mmmt) outliers start: 28 outliers final: 21 residues processed: 137 average time/residue: 0.4714 time to fit residues: 70.7600 Evaluate side-chains 136 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 113 time to evaluate : 0.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 VAL Chi-restraints excluded: chain A residue 36 THR Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 212 SER Chi-restraints excluded: chain B residue 18 VAL Chi-restraints excluded: chain B residue 36 THR Chi-restraints excluded: chain B residue 94 VAL Chi-restraints excluded: chain B residue 205 MET Chi-restraints excluded: chain B residue 212 SER Chi-restraints excluded: chain C residue 18 VAL Chi-restraints excluded: chain C residue 36 THR Chi-restraints excluded: chain C residue 94 VAL Chi-restraints excluded: chain C residue 174 PHE Chi-restraints excluded: chain C residue 205 MET Chi-restraints excluded: chain C residue 214 THR Chi-restraints excluded: chain D residue 18 VAL Chi-restraints excluded: chain D residue 32 ASP Chi-restraints excluded: chain D residue 36 THR Chi-restraints excluded: chain D residue 94 VAL Chi-restraints excluded: chain E residue 18 VAL Chi-restraints excluded: chain E residue 36 THR Chi-restraints excluded: chain E residue 94 VAL Chi-restraints excluded: chain E residue 214 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 141 optimal weight: 4.9990 chunk 110 optimal weight: 10.0000 chunk 27 optimal weight: 10.0000 chunk 128 optimal weight: 3.9990 chunk 21 optimal weight: 1.9990 chunk 90 optimal weight: 9.9990 chunk 58 optimal weight: 3.9990 chunk 20 optimal weight: 0.9990 chunk 52 optimal weight: 4.9990 chunk 35 optimal weight: 5.9990 chunk 104 optimal weight: 5.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 19 ASN B 19 ASN C 19 ASN D 19 ASN D 245 ASN E 19 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.086027 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.062851 restraints weight = 39333.446| |-----------------------------------------------------------------------------| r_work (start): 0.3233 rms_B_bonded: 3.52 r_work: 0.3052 rms_B_bonded: 4.66 restraints_weight: 0.5000 r_work (final): 0.3052 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8550 moved from start: 0.4782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 13300 Z= 0.203 Angle : 0.706 9.471 18095 Z= 0.356 Chirality : 0.044 0.225 2040 Planarity : 0.004 0.033 2175 Dihedral : 16.087 87.348 2325 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.32 % Allowed : 6.41 % Favored : 93.27 % Rotamer: Outliers : 2.14 % Allowed : 22.72 % Favored : 75.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.05 (0.22), residues: 1545 helix: 2.23 (0.21), residues: 520 sheet: -0.94 (0.28), residues: 325 loop : -1.35 (0.25), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 109 TYR 0.017 0.001 TYR D 263 PHE 0.014 0.001 PHE E 37 TRP 0.033 0.001 TRP A 213 HIS 0.004 0.001 HIS D 235 Details of bonding type rmsd/Z covalent geometry : bond 0.00482 / 0.20 (13300) covalent geometry : angle 0.70596 / 0.36 (18095) hydrogen bonds : bond 0.03326 / 2.25 ( 560) hydrogen bonds : angle 4.39648 / 3.05 ( 1725) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3367.70 seconds wall clock time: 58 minutes 9.92 seconds (3489.92 seconds total)