Starting phenix.real_space_refine on Wed Mar 4 11:08:46 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8atg_15649/03_2026/8atg_15649.cif Found real_map, /net/cci-nas-00/data/ceres_data/8atg_15649/03_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 { model { file = "/net/cci-nas-00/data/ceres_data/8atg_15649/03_2026/8atg_15649.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8atg_15649/03_2026/8atg_15649.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8atg_15649/03_2026/8atg_15649.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8atg_15649/03_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-5986/lib/python3.9/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: 2.17, per 1000 atoms: 0.17 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: 1.16 Conformation dependent library (CDL) restraints added in 610.7 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: 0.45 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: 2.08 Time building geometry restraints manager: 1.48 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: 7528 26.06 - 52.13: 362 52.13 - 78.19: 85 78.19 - 104.26: 25 104.26 - 130.32: 25 Dihedral angle restraints: 8025 sinusoidal: 3350 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 8022 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: 0.03 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: 0.970 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.130 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 12.090 Find NCS groups from input model: 0.100 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:6.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.700 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5998 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 : 18.850 130.322 4975 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 covalent geometry : bond 0.00656 (13300) covalent geometry : angle 0.70913 (18095) hydrogen bonds : bond 0.20507 ( 560) hydrogen bonds : angle 6.86630 ( 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 : 0.570 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: 0.5180 time to fit residues: 139.0461 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 : 0.333 ------------------------------------------------------------------------------- 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... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.090232 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.065215 restraints weight = 38869.194| |-----------------------------------------------------------------------------| r_work (start): 0.3294 rms_B_bonded: 3.70 r_work: 0.3117 rms_B_bonded: 4.92 restraints_weight: 0.5000 r_work (final): 0.3117 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8375 moved from start: 0.2223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 13300 Z= 0.164 Angle : 0.680 6.519 18095 Z= 0.348 Chirality : 0.045 0.134 2040 Planarity : 0.005 0.037 2175 Dihedral : 20.423 138.354 2477 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.93 % Favored : 93.01 % Rotamer: Outliers : 2.88 % Allowed : 13.74 % Favored : 83.37 % 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: 1.68 (0.22), residues: 525 sheet: -1.75 (0.28), residues: 325 loop : -1.74 (0.24), residues: 695 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 109 TYR 0.016 0.002 TYR A 266 PHE 0.015 0.001 PHE D 37 TRP 0.007 0.001 TRP E 47 HIS 0.005 0.001 HIS A 235 Details of bonding type rmsd covalent geometry : bond 0.00373 (13300) covalent geometry : angle 0.68029 (18095) hydrogen bonds : bond 0.04056 ( 560) hydrogen bonds : angle 5.35055 ( 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 196 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 161 time to evaluate : 0.400 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 GLU cc_start: 0.8165 (pm20) cc_final: 0.7959 (tp30) REVERT: A 187 GLN cc_start: 0.9051 (mt0) cc_final: 0.8768 (mt0) REVERT: B 174 PHE cc_start: 0.7713 (p90) cc_final: 0.7274 (p90) REVERT: B 187 GLN cc_start: 0.9022 (mt0) cc_final: 0.8728 (mt0) REVERT: B 266 TYR cc_start: 0.8652 (m-80) cc_final: 0.8417 (m-80) REVERT: C 35 GLU cc_start: 0.7966 (pm20) cc_final: 0.7680 (pm20) REVERT: C 187 GLN cc_start: 0.8995 (mt0) cc_final: 0.8712 (mt0) REVERT: D 187 GLN cc_start: 0.9029 (mt0) cc_final: 0.8747 (mt0) REVERT: D 248 LYS cc_start: 0.9028 (mtmt) cc_final: 0.8676 (mttp) REVERT: E 187 GLN cc_start: 0.9034 (mt0) cc_final: 0.8733 (mt0) REVERT: E 213 TRP cc_start: 0.8736 (m-10) cc_final: 0.8407 (m-10) outliers start: 35 outliers final: 15 residues processed: 186 average time/residue: 0.5393 time to fit residues: 110.3375 Evaluate side-chains 142 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 127 time to evaluate : 0.468 ------------------------------------------------------------------------------- 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 36 THR 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 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: 0.7980 chunk 47 optimal weight: 5.9990 chunk 109 optimal weight: 5.9990 chunk 108 optimal weight: 9.9990 chunk 73 optimal weight: 7.9990 chunk 152 optimal weight: 9.9990 chunk 99 optimal weight: 0.0670 chunk 111 optimal weight: 5.9990 chunk 124 optimal weight: 10.0000 chunk 21 optimal weight: 1.9990 chunk 35 optimal weight: 8.9990 overall best weight: 2.9724 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 19 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.087880 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.063136 restraints weight = 39311.670| |-----------------------------------------------------------------------------| r_work (start): 0.3257 rms_B_bonded: 3.70 r_work: 0.3078 rms_B_bonded: 4.88 restraints_weight: 0.5000 r_work (final): 0.3078 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8489 moved from start: 0.3075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 13300 Z= 0.191 Angle : 0.650 7.165 18095 Z= 0.333 Chirality : 0.044 0.143 2040 Planarity : 0.004 0.035 2175 Dihedral : 19.595 145.630 2475 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.32 % Allowed : 6.99 % Favored : 92.69 % Rotamer: Outliers : 3.79 % Allowed : 15.06 % Favored : 81.15 % 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: -0.42 (0.22), residues: 1545 helix: 2.10 (0.22), residues: 520 sheet: -1.49 (0.28), residues: 330 loop : -1.53 (0.25), residues: 695 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 189 TYR 0.014 0.002 TYR D 102 PHE 0.015 0.001 PHE E 37 TRP 0.011 0.001 TRP B 213 HIS 0.005 0.002 HIS B 235 Details of bonding type rmsd covalent geometry : bond 0.00437 (13300) covalent geometry : angle 0.65038 (18095) hydrogen bonds : bond 0.03981 ( 560) hydrogen bonds : angle 4.86190 ( 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 191 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 145 time to evaluate : 0.451 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 163 GLU cc_start: 0.8301 (mp0) cc_final: 0.7980 (mp0) REVERT: A 187 GLN cc_start: 0.9106 (mt0) cc_final: 0.8727 (mt0) REVERT: A 205 MET cc_start: 0.9396 (ttm) cc_final: 0.9171 (mtt) REVERT: A 313 LEU cc_start: 0.9385 (OUTLIER) cc_final: 0.9119 (tp) REVERT: B 35 GLU cc_start: 0.8421 (pm20) cc_final: 0.8192 (pm20) REVERT: B 163 GLU cc_start: 0.8348 (mp0) cc_final: 0.7936 (mp0) REVERT: B 187 GLN cc_start: 0.9077 (mt0) cc_final: 0.8708 (mt0) REVERT: B 248 LYS cc_start: 0.9143 (mtmt) cc_final: 0.8928 (tppt) REVERT: C 187 GLN cc_start: 0.9014 (mt0) cc_final: 0.8670 (mt0) REVERT: C 248 LYS cc_start: 0.9153 (mtmt) cc_final: 0.8447 (tppt) REVERT: C 313 LEU cc_start: 0.9426 (mt) cc_final: 0.9004 (tp) REVERT: D 35 GLU cc_start: 0.8382 (tp30) cc_final: 0.8162 (tp30) REVERT: D 187 GLN cc_start: 0.9061 (mt0) cc_final: 0.8735 (mt0) REVERT: D 245 ASN cc_start: 0.9217 (m-40) cc_final: 0.8873 (p0) REVERT: D 248 LYS cc_start: 0.9056 (mtmt) cc_final: 0.8701 (mttp) REVERT: D 313 LEU cc_start: 0.9461 (mt) cc_final: 0.9048 (tp) REVERT: E 248 LYS cc_start: 0.9074 (mtmt) cc_final: 0.8849 (mttt) outliers start: 46 outliers final: 27 residues processed: 177 average time/residue: 0.5074 time to fit residues: 98.6322 Evaluate side-chains 160 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 132 time to evaluate : 0.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 VAL Chi-restraints excluded: chain A residue 19 ASN Chi-restraints excluded: chain A residue 32 ASP Chi-restraints excluded: chain A residue 36 THR 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 32 ASP Chi-restraints excluded: chain B residue 36 THR Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain C residue 18 VAL Chi-restraints excluded: chain C residue 32 ASP Chi-restraints excluded: chain C residue 36 THR Chi-restraints excluded: chain C residue 174 PHE 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 214 THR Chi-restraints excluded: chain E residue 255 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 26 optimal weight: 0.9990 chunk 68 optimal weight: 0.0030 chunk 146 optimal weight: 0.7980 chunk 34 optimal weight: 10.0000 chunk 69 optimal weight: 3.9990 chunk 132 optimal weight: 8.9990 chunk 67 optimal weight: 5.9990 chunk 45 optimal weight: 10.0000 chunk 153 optimal weight: 0.8980 chunk 82 optimal weight: 0.9980 chunk 84 optimal weight: 0.9980 overall best weight: 0.7390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 245 ASN E 245 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.088909 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.064280 restraints weight = 39133.817| |-----------------------------------------------------------------------------| r_work (start): 0.3288 rms_B_bonded: 3.69 r_work: 0.3113 rms_B_bonded: 4.85 restraints_weight: 0.5000 r_work (final): 0.3113 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8452 moved from start: 0.3228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 13300 Z= 0.118 Angle : 0.604 7.506 18095 Z= 0.309 Chirality : 0.043 0.157 2040 Planarity : 0.004 0.034 2175 Dihedral : 19.083 135.112 2475 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.32 % Allowed : 5.63 % Favored : 94.05 % Rotamer: Outliers : 2.39 % Allowed : 18.44 % Favored : 79.18 % 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: -0.26 (0.22), residues: 1545 helix: 2.20 (0.22), residues: 520 sheet: -1.40 (0.28), residues: 325 loop : -1.41 (0.25), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 189 TYR 0.011 0.001 TYR C 102 PHE 0.014 0.001 PHE E 37 TRP 0.007 0.001 TRP A 160 HIS 0.004 0.001 HIS B 235 Details of bonding type rmsd covalent geometry : bond 0.00274 (13300) covalent geometry : angle 0.60438 (18095) hydrogen bonds : bond 0.03409 ( 560) hydrogen bonds : angle 4.58264 ( 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 175 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 146 time to evaluate : 0.357 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 163 GLU cc_start: 0.8137 (mp0) cc_final: 0.7717 (pm20) REVERT: A 187 GLN cc_start: 0.9040 (mt0) cc_final: 0.8682 (mt0) REVERT: B 163 GLU cc_start: 0.8288 (mp0) cc_final: 0.8048 (mp0) REVERT: B 187 GLN cc_start: 0.9018 (mt0) cc_final: 0.8703 (mt0) REVERT: B 248 LYS cc_start: 0.8991 (mtmt) cc_final: 0.8663 (mmmt) REVERT: B 282 GLU cc_start: 0.9035 (mm-30) cc_final: 0.8517 (tm-30) REVERT: C 187 GLN cc_start: 0.8979 (mt0) cc_final: 0.8622 (mt0) REVERT: C 248 LYS cc_start: 0.9004 (mtmt) cc_final: 0.8714 (mtmt) REVERT: C 313 LEU cc_start: 0.9413 (mt) cc_final: 0.9106 (tp) REVERT: D 35 GLU cc_start: 0.8381 (tp30) cc_final: 0.8162 (tp30) REVERT: D 187 GLN cc_start: 0.8997 (mt0) cc_final: 0.8680 (mt0) REVERT: D 248 LYS cc_start: 0.9112 (mtmt) cc_final: 0.8797 (mttp) REVERT: D 313 LEU cc_start: 0.9429 (mt) cc_final: 0.9136 (tp) REVERT: E 187 GLN cc_start: 0.9019 (mt0) cc_final: 0.8613 (mt0) REVERT: E 248 LYS cc_start: 0.9075 (mtmt) cc_final: 0.8849 (mttt) REVERT: E 313 LEU cc_start: 0.9378 (mt) cc_final: 0.9087 (tp) outliers start: 29 outliers final: 15 residues processed: 164 average time/residue: 0.5596 time to fit residues: 100.0239 Evaluate side-chains 146 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 131 time to evaluate : 0.445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 ASP Chi-restraints excluded: chain A residue 36 THR 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 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 32 ASP Chi-restraints excluded: chain D residue 36 THR Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain E residue 32 ASP Chi-restraints excluded: chain E residue 36 THR Chi-restraints excluded: chain E residue 212 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 11 optimal weight: 6.9990 chunk 74 optimal weight: 9.9990 chunk 141 optimal weight: 4.9990 chunk 22 optimal weight: 0.9990 chunk 47 optimal weight: 20.0000 chunk 32 optimal weight: 20.0000 chunk 102 optimal weight: 30.0000 chunk 64 optimal weight: 4.9990 chunk 122 optimal weight: 5.9990 chunk 79 optimal weight: 8.9990 chunk 85 optimal weight: 6.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 19 ASN B 19 ASN B 245 ASN C 245 ASN D 19 ASN D 245 ASN ** E 19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.084979 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.061341 restraints weight = 39841.579| |-----------------------------------------------------------------------------| r_work (start): 0.3220 rms_B_bonded: 3.55 r_work: 0.3040 rms_B_bonded: 4.72 restraints_weight: 0.5000 r_work (final): 0.3040 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8583 moved from start: 0.3845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.056 13300 Z= 0.270 Angle : 0.686 8.235 18095 Z= 0.345 Chirality : 0.044 0.168 2040 Planarity : 0.004 0.031 2175 Dihedral : 19.000 126.999 2475 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.32 % Allowed : 7.51 % Favored : 92.17 % Rotamer: Outliers : 3.87 % Allowed : 17.86 % Favored : 78.27 % 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: -0.33 (0.22), residues: 1545 helix: 2.16 (0.21), residues: 520 sheet: -1.40 (0.27), residues: 325 loop : -1.49 (0.24), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 189 TYR 0.012 0.002 TYR B 102 PHE 0.013 0.002 PHE D 37 TRP 0.011 0.001 TRP E 213 HIS 0.005 0.002 HIS D 235 Details of bonding type rmsd covalent geometry : bond 0.00617 (13300) covalent geometry : angle 0.68593 (18095) hydrogen bonds : bond 0.03865 ( 560) hydrogen bonds : angle 4.74498 ( 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 181 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 134 time to evaluate : 0.456 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 GLU cc_start: 0.8392 (pm20) cc_final: 0.7899 (pm20) REVERT: A 163 GLU cc_start: 0.8073 (mp0) cc_final: 0.7615 (mp0) REVERT: A 187 GLN cc_start: 0.9107 (mt0) cc_final: 0.8733 (mt0) REVERT: A 205 MET cc_start: 0.9389 (ttm) cc_final: 0.9165 (mtt) REVERT: A 248 LYS cc_start: 0.9247 (mttt) cc_final: 0.8972 (mmmm) REVERT: B 163 GLU cc_start: 0.8302 (mp0) cc_final: 0.7865 (mp0) REVERT: B 187 GLN cc_start: 0.9118 (mt0) cc_final: 0.8747 (mt0) REVERT: C 248 LYS cc_start: 0.8955 (mtmt) cc_final: 0.8713 (mmmt) REVERT: C 313 LEU cc_start: 0.9447 (mt) cc_final: 0.9201 (tp) REVERT: D 187 GLN cc_start: 0.9066 (mt0) cc_final: 0.8685 (mt0) REVERT: D 245 ASN cc_start: 0.9191 (m-40) cc_final: 0.8908 (p0) REVERT: D 248 LYS cc_start: 0.9190 (mtmt) cc_final: 0.8851 (mttp) REVERT: D 313 LEU cc_start: 0.9475 (mt) cc_final: 0.9216 (tp) REVERT: E 187 GLN cc_start: 0.9067 (mt0) cc_final: 0.8668 (mt0) REVERT: E 248 LYS cc_start: 0.9128 (mtmt) cc_final: 0.8899 (mttt) REVERT: E 313 LEU cc_start: 0.9422 (mt) cc_final: 0.9198 (tp) outliers start: 47 outliers final: 25 residues processed: 163 average time/residue: 0.5633 time to fit residues: 100.3282 Evaluate side-chains 150 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 125 time to evaluate : 0.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 VAL Chi-restraints excluded: chain A residue 32 ASP Chi-restraints excluded: chain A residue 36 THR Chi-restraints excluded: chain A residue 255 THR Chi-restraints excluded: chain B residue 18 VAL Chi-restraints excluded: chain B residue 36 THR Chi-restraints excluded: chain B residue 255 THR Chi-restraints excluded: chain C residue 18 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 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 174 PHE 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 32 ASP Chi-restraints excluded: chain E residue 36 THR Chi-restraints excluded: chain E residue 174 PHE 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: 0.8980 chunk 84 optimal weight: 0.7980 chunk 109 optimal weight: 0.0070 chunk 53 optimal weight: 0.9990 chunk 51 optimal weight: 0.7980 chunk 46 optimal weight: 4.9990 chunk 60 optimal weight: 0.5980 chunk 148 optimal weight: 10.0000 chunk 122 optimal weight: 5.9990 chunk 133 optimal weight: 10.0000 chunk 62 optimal weight: 10.0000 overall best weight: 0.6198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 19 ASN ** B 235 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 19 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 = 0.3849 r_free = 0.3849 target = 0.088260 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.063693 restraints weight = 39020.493| |-----------------------------------------------------------------------------| r_work (start): 0.3281 rms_B_bonded: 3.64 r_work: 0.3110 rms_B_bonded: 4.76 restraints_weight: 0.5000 r_work (final): 0.3110 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8498 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 0.040 13300 Z= 0.121 Angle : 0.646 10.129 18095 Z= 0.325 Chirality : 0.043 0.145 2040 Planarity : 0.004 0.033 2175 Dihedral : 18.542 112.316 2475 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.32 % Allowed : 4.66 % Favored : 95.02 % Rotamer: Outliers : 2.80 % Allowed : 19.59 % Favored : 77.61 % 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: -0.09 (0.23), residues: 1545 helix: 2.34 (0.22), residues: 520 sheet: -1.27 (0.28), residues: 325 loop : -1.33 (0.25), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 189 TYR 0.011 0.001 TYR D 263 PHE 0.016 0.001 PHE A 37 TRP 0.010 0.001 TRP A 213 HIS 0.005 0.002 HIS D 235 Details of bonding type rmsd covalent geometry : bond 0.00289 (13300) covalent geometry : angle 0.64589 (18095) hydrogen bonds : bond 0.03304 ( 560) hydrogen bonds : angle 4.43884 ( 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 178 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 144 time to evaluate : 0.317 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 163 GLU cc_start: 0.8080 (mp0) cc_final: 0.7653 (mp0) REVERT: A 187 GLN cc_start: 0.9033 (mt0) cc_final: 0.8670 (mt0) REVERT: A 248 LYS cc_start: 0.9196 (mttt) cc_final: 0.8898 (mmmt) REVERT: B 163 GLU cc_start: 0.8285 (mp0) cc_final: 0.8001 (mp0) REVERT: B 187 GLN cc_start: 0.9034 (mt0) cc_final: 0.8632 (mt0) REVERT: B 248 LYS cc_start: 0.9279 (mmmt) cc_final: 0.9002 (mmmm) REVERT: C 174 PHE cc_start: 0.7900 (OUTLIER) cc_final: 0.7527 (p90) REVERT: C 187 GLN cc_start: 0.8958 (mt0) cc_final: 0.8566 (mt0) REVERT: D 187 GLN cc_start: 0.8979 (mt0) cc_final: 0.8587 (mt0) REVERT: D 245 ASN cc_start: 0.9204 (m-40) cc_final: 0.8886 (p0) REVERT: D 248 LYS cc_start: 0.9272 (mtmt) cc_final: 0.8763 (mmmm) REVERT: E 187 GLN cc_start: 0.9022 (mt0) cc_final: 0.8663 (mt0) REVERT: E 214 THR cc_start: 0.9641 (OUTLIER) cc_final: 0.9396 (m) REVERT: E 245 ASN cc_start: 0.9170 (m-40) cc_final: 0.8942 (p0) REVERT: E 248 LYS cc_start: 0.9143 (mtmt) cc_final: 0.8903 (mttt) outliers start: 34 outliers final: 20 residues processed: 165 average time/residue: 0.5448 time to fit residues: 98.2720 Evaluate side-chains 145 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 123 time to evaluate : 0.436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 ASP Chi-restraints excluded: chain A residue 36 THR Chi-restraints excluded: chain A residue 212 SER Chi-restraints excluded: chain B residue 18 VAL 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 212 SER 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 E residue 18 VAL Chi-restraints excluded: chain E residue 32 ASP Chi-restraints excluded: chain E residue 36 THR Chi-restraints excluded: chain E residue 174 PHE Chi-restraints excluded: chain E residue 212 SER Chi-restraints excluded: chain E residue 214 THR Chi-restraints excluded: chain E residue 305 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 26 optimal weight: 3.9990 chunk 20 optimal weight: 2.9990 chunk 31 optimal weight: 10.0000 chunk 62 optimal weight: 10.0000 chunk 68 optimal weight: 4.9990 chunk 85 optimal weight: 0.9980 chunk 71 optimal weight: 10.0000 chunk 98 optimal weight: 9.9990 chunk 89 optimal weight: 9.9990 chunk 139 optimal weight: 6.9990 chunk 73 optimal weight: 7.9990 overall best weight: 3.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 19 ASN A 307 ASN B 19 ASN B 245 ASN C 19 ASN C 245 ASN D 19 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.085717 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.060874 restraints weight = 39872.558| |-----------------------------------------------------------------------------| r_work (start): 0.3203 rms_B_bonded: 3.59 r_work: 0.3031 rms_B_bonded: 4.75 restraints_weight: 0.5000 r_work (final): 0.3031 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8591 moved from start: 0.4338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 13300 Z= 0.241 Angle : 0.707 9.246 18095 Z= 0.354 Chirality : 0.043 0.173 2040 Planarity : 0.004 0.032 2175 Dihedral : 18.467 99.477 2475 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.32 % Allowed : 7.25 % Favored : 92.43 % Rotamer: Outliers : 3.37 % Allowed : 20.16 % Favored : 76.46 % 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: -0.15 (0.22), residues: 1545 helix: 2.27 (0.22), residues: 520 sheet: -1.28 (0.27), 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 0.012 0.001 TYR C 251 PHE 0.011 0.001 PHE C 37 TRP 0.010 0.001 TRP B 213 HIS 0.005 0.002 HIS D 235 Details of bonding type rmsd covalent geometry : bond 0.00560 (13300) covalent geometry : angle 0.70677 (18095) hydrogen bonds : bond 0.03615 ( 560) hydrogen bonds : angle 4.58791 ( 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: 41 poor density : 128 time to evaluate : 0.474 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 163 GLU cc_start: 0.8138 (mp0) cc_final: 0.7688 (mp0) REVERT: A 187 GLN cc_start: 0.9083 (mt0) cc_final: 0.8588 (mm110) REVERT: A 248 LYS cc_start: 0.9000 (mttt) cc_final: 0.8741 (mmmt) REVERT: B 163 GLU cc_start: 0.8296 (mp0) cc_final: 0.7815 (mp0) REVERT: B 187 GLN cc_start: 0.9113 (mt0) cc_final: 0.8680 (mt0) REVERT: B 205 MET cc_start: 0.9239 (OUTLIER) cc_final: 0.8986 (mtp) REVERT: B 248 LYS cc_start: 0.9305 (mmmt) cc_final: 0.8988 (mmmm) REVERT: C 248 LYS cc_start: 0.9255 (mmmt) cc_final: 0.8981 (mmmm) REVERT: D 187 GLN cc_start: 0.9031 (mt0) cc_final: 0.8592 (mt0) REVERT: D 248 LYS cc_start: 0.9242 (mtmt) cc_final: 0.8759 (mmmm) REVERT: E 35 GLU cc_start: 0.8522 (pm20) cc_final: 0.8235 (pm20) REVERT: E 187 GLN cc_start: 0.9031 (mt0) cc_final: 0.8677 (mt0) REVERT: E 248 LYS cc_start: 0.9177 (mtmt) cc_final: 0.8933 (tppt) outliers start: 41 outliers final: 29 residues processed: 157 average time/residue: 0.5638 time to fit residues: 96.7900 Evaluate side-chains 150 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 120 time to evaluate : 0.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 ASP 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 174 PHE 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 174 PHE Chi-restraints excluded: chain D residue 212 SER Chi-restraints excluded: chain E residue 18 VAL Chi-restraints excluded: chain E residue 32 ASP Chi-restraints excluded: chain E residue 94 VAL Chi-restraints excluded: chain E residue 174 PHE Chi-restraints excluded: chain E residue 212 SER Chi-restraints excluded: chain E residue 255 THR Chi-restraints excluded: chain E residue 305 LEU 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: 7.9990 chunk 61 optimal weight: 5.9990 chunk 146 optimal weight: 0.9990 chunk 65 optimal weight: 10.0000 chunk 63 optimal weight: 5.9990 chunk 134 optimal weight: 8.9990 chunk 113 optimal weight: 0.7980 chunk 67 optimal weight: 10.0000 chunk 115 optimal weight: 0.6980 chunk 43 optimal weight: 7.9990 overall best weight: 2.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 19 ASN B 19 ASN C 19 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 = 0.3820 r_free = 0.3820 target = 0.086432 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.061664 restraints weight = 39537.946| |-----------------------------------------------------------------------------| r_work (start): 0.3222 rms_B_bonded: 3.61 r_work: 0.3044 rms_B_bonded: 4.79 restraints_weight: 0.5000 r_work (final): 0.3044 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8575 moved from start: 0.4500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 13300 Z= 0.184 Angle : 0.687 10.545 18095 Z= 0.342 Chirality : 0.043 0.212 2040 Planarity : 0.004 0.032 2175 Dihedral : 18.171 89.931 2475 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.32 % Allowed : 4.98 % Favored : 94.69 % Rotamer: Outliers : 2.96 % Allowed : 22.22 % Favored : 74.81 % 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: -0.06 (0.22), residues: 1545 helix: 2.33 (0.22), residues: 520 sheet: -1.17 (0.27), residues: 325 loop : -1.33 (0.25), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 109 TYR 0.011 0.001 TYR D 263 PHE 0.010 0.001 PHE C 37 TRP 0.009 0.001 TRP B 160 HIS 0.005 0.002 HIS D 235 Details of bonding type rmsd covalent geometry : bond 0.00438 (13300) covalent geometry : angle 0.68699 (18095) hydrogen bonds : bond 0.03364 ( 560) hydrogen bonds : angle 4.47515 ( 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 159 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 123 time to evaluate : 0.392 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 163 GLU cc_start: 0.8131 (mp0) cc_final: 0.7673 (mp0) REVERT: A 187 GLN cc_start: 0.9058 (mt0) cc_final: 0.8676 (mt0) REVERT: A 248 LYS cc_start: 0.9102 (mttt) cc_final: 0.8762 (mmmt) REVERT: B 163 GLU cc_start: 0.8274 (mp0) cc_final: 0.7798 (mp0) REVERT: B 187 GLN cc_start: 0.9087 (mt0) cc_final: 0.8657 (mt0) REVERT: B 205 MET cc_start: 0.9222 (OUTLIER) cc_final: 0.8980 (mtp) REVERT: B 248 LYS cc_start: 0.9303 (mmmt) cc_final: 0.8997 (mmmm) REVERT: C 248 LYS cc_start: 0.9264 (mmmt) cc_final: 0.9021 (mmmt) REVERT: D 187 GLN cc_start: 0.8994 (mt0) cc_final: 0.8552 (mt0) REVERT: D 248 LYS cc_start: 0.9271 (mtmt) cc_final: 0.8756 (mmmm) REVERT: E 187 GLN cc_start: 0.9008 (mt0) cc_final: 0.8658 (mt0) outliers start: 36 outliers final: 27 residues processed: 148 average time/residue: 0.5720 time to fit residues: 92.4187 Evaluate side-chains 147 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 119 time to evaluate : 0.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 VAL Chi-restraints excluded: chain A residue 32 ASP 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 174 PHE 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 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 32 ASP Chi-restraints excluded: chain E residue 94 VAL Chi-restraints excluded: chain E residue 174 PHE Chi-restraints excluded: chain E residue 212 SER Chi-restraints excluded: chain E residue 305 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 117 optimal weight: 0.0870 chunk 26 optimal weight: 0.6980 chunk 49 optimal weight: 9.9990 chunk 98 optimal weight: 8.9990 chunk 134 optimal weight: 8.9990 chunk 141 optimal weight: 30.0000 chunk 32 optimal weight: 20.0000 chunk 36 optimal weight: 6.9990 chunk 33 optimal weight: 6.9990 chunk 84 optimal weight: 0.0770 chunk 17 optimal weight: 1.9990 overall best weight: 1.9720 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3824 r_free = 0.3824 target = 0.086725 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.062107 restraints weight = 39265.077| |-----------------------------------------------------------------------------| r_work (start): 0.3234 rms_B_bonded: 3.60 r_work: 0.3056 rms_B_bonded: 4.74 restraints_weight: 0.5000 r_work (final): 0.3056 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8573 moved from start: 0.4659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 13300 Z= 0.155 Angle : 0.678 8.476 18095 Z= 0.340 Chirality : 0.043 0.199 2040 Planarity : 0.004 0.032 2175 Dihedral : 17.947 89.845 2475 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.32 % Allowed : 6.34 % Favored : 93.33 % Rotamer: Outliers : 2.55 % Allowed : 22.96 % Favored : 74.49 % 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: 2.32 (0.22), residues: 520 sheet: -1.05 (0.28), residues: 325 loop : -1.26 (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 0.012 0.001 PHE E 37 TRP 0.011 0.001 TRP A 213 HIS 0.005 0.002 HIS D 235 Details of bonding type rmsd covalent geometry : bond 0.00379 (13300) covalent geometry : angle 0.67830 (18095) hydrogen bonds : bond 0.03207 ( 560) hydrogen bonds : angle 4.39022 ( 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 151 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 120 time to evaluate : 0.399 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 33 LYS cc_start: 0.8745 (ttpp) cc_final: 0.8497 (tmmt) REVERT: A 35 GLU cc_start: 0.8061 (pm20) cc_final: 0.7827 (pm20) REVERT: A 163 GLU cc_start: 0.8181 (mp0) cc_final: 0.7699 (mp0) REVERT: A 187 GLN cc_start: 0.9048 (mt0) cc_final: 0.8570 (mm110) REVERT: A 248 LYS cc_start: 0.9166 (mttt) cc_final: 0.8783 (mmmt) REVERT: B 163 GLU cc_start: 0.8282 (mp0) cc_final: 0.7771 (mp0) REVERT: B 187 GLN cc_start: 0.9078 (mt0) cc_final: 0.8650 (mt0) REVERT: B 205 MET cc_start: 0.9232 (OUTLIER) cc_final: 0.8995 (mtp) REVERT: B 248 LYS cc_start: 0.9312 (mmmt) cc_final: 0.8950 (mmmm) REVERT: C 187 GLN cc_start: 0.8979 (mt0) cc_final: 0.8558 (mt0) REVERT: D 187 GLN cc_start: 0.9002 (mt0) cc_final: 0.8550 (mt0) REVERT: D 248 LYS cc_start: 0.9240 (mtmt) cc_final: 0.8747 (mmmm) REVERT: E 187 GLN cc_start: 0.9022 (mt0) cc_final: 0.8581 (mt0) REVERT: E 248 LYS cc_start: 0.9238 (tppt) cc_final: 0.8583 (tmtt) outliers start: 31 outliers final: 24 residues processed: 144 average time/residue: 0.5815 time to fit residues: 91.4764 Evaluate side-chains 144 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 119 time to evaluate : 0.463 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 VAL Chi-restraints excluded: chain A residue 32 ASP 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 212 SER 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 94 VAL Chi-restraints excluded: chain E residue 212 SER Chi-restraints excluded: chain E residue 305 LEU 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: 0.6980 chunk 117 optimal weight: 1.9990 chunk 153 optimal weight: 0.9980 chunk 111 optimal weight: 7.9990 chunk 6 optimal weight: 8.9990 chunk 149 optimal weight: 0.7980 chunk 25 optimal weight: 3.9990 chunk 81 optimal weight: 7.9990 chunk 10 optimal weight: 10.0000 chunk 62 optimal weight: 10.0000 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 19 ASN B 19 ASN ** B 235 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 19 ASN D 19 ASN E 19 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.086610 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.061968 restraints weight = 39471.835| |-----------------------------------------------------------------------------| r_work (start): 0.3233 rms_B_bonded: 3.61 r_work: 0.3068 rms_B_bonded: 4.73 restraints_weight: 0.5000 r_work (final): 0.3068 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8555 moved from start: 0.4761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 13300 Z= 0.147 Angle : 0.676 8.326 18095 Z= 0.341 Chirality : 0.043 0.181 2040 Planarity : 0.004 0.033 2175 Dihedral : 17.714 89.932 2475 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.32 % Allowed : 4.72 % Favored : 94.95 % Rotamer: Outliers : 2.47 % Allowed : 23.21 % Favored : 74.32 % 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 (0.22), residues: 1545 helix: 2.29 (0.21), residues: 520 sheet: -0.98 (0.28), residues: 325 loop : -1.25 (0.25), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG E 109 TYR 0.013 0.001 TYR D 263 PHE 0.010 0.001 PHE E 265 TRP 0.010 0.001 TRP A 213 HIS 0.005 0.002 HIS D 235 Details of bonding type rmsd covalent geometry : bond 0.00360 (13300) covalent geometry : angle 0.67569 (18095) hydrogen bonds : bond 0.03114 ( 560) hydrogen bonds : angle 4.32191 ( 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 152 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 122 time to evaluate : 0.483 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 GLU cc_start: 0.8072 (pm20) cc_final: 0.7816 (pm20) REVERT: A 163 GLU cc_start: 0.8207 (mp0) cc_final: 0.7719 (mp0) REVERT: A 187 GLN cc_start: 0.9047 (mt0) cc_final: 0.8562 (mm110) REVERT: A 248 LYS cc_start: 0.9179 (mttt) cc_final: 0.8772 (mmmt) REVERT: B 163 GLU cc_start: 0.8310 (mp0) cc_final: 0.7783 (mp0) REVERT: B 187 GLN cc_start: 0.9075 (mt0) cc_final: 0.8644 (mt0) REVERT: B 205 MET cc_start: 0.9241 (OUTLIER) cc_final: 0.9014 (mtp) REVERT: C 187 GLN cc_start: 0.8960 (mt0) cc_final: 0.8532 (mt0) REVERT: C 248 LYS cc_start: 0.9156 (mmmt) cc_final: 0.8770 (tppt) REVERT: D 187 GLN cc_start: 0.9004 (mt0) cc_final: 0.8555 (mt0) REVERT: D 248 LYS cc_start: 0.9200 (mtmt) cc_final: 0.8728 (mmmm) REVERT: E 187 GLN cc_start: 0.9024 (mt0) cc_final: 0.8576 (mt0) REVERT: E 248 LYS cc_start: 0.9226 (tppt) cc_final: 0.8616 (mmmt) outliers start: 30 outliers final: 25 residues processed: 142 average time/residue: 0.5841 time to fit residues: 90.2813 Evaluate side-chains 147 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 121 time to evaluate : 0.438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 VAL Chi-restraints excluded: chain A residue 32 ASP 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 212 SER 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 D residue 212 SER Chi-restraints excluded: chain E residue 18 VAL Chi-restraints excluded: chain E residue 94 VAL Chi-restraints excluded: chain E residue 212 SER Chi-restraints excluded: chain E residue 305 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 141 optimal weight: 9.9990 chunk 110 optimal weight: 9.9990 chunk 27 optimal weight: 0.7980 chunk 128 optimal weight: 10.0000 chunk 21 optimal weight: 3.9990 chunk 90 optimal weight: 10.0000 chunk 58 optimal weight: 5.9990 chunk 20 optimal weight: 1.9990 chunk 52 optimal weight: 0.9980 chunk 35 optimal weight: 10.0000 chunk 104 optimal weight: 5.9990 overall best weight: 2.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 19 ASN B 19 ASN ** B 235 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 19 ASN D 19 ASN E 19 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.085962 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.061613 restraints weight = 39236.411| |-----------------------------------------------------------------------------| r_work (start): 0.3220 rms_B_bonded: 3.57 r_work: 0.3049 rms_B_bonded: 4.68 restraints_weight: 0.5000 r_work (final): 0.3049 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8581 moved from start: 0.4912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 13300 Z= 0.183 Angle : 0.685 7.876 18095 Z= 0.346 Chirality : 0.043 0.179 2040 Planarity : 0.004 0.033 2175 Dihedral : 17.663 89.991 2475 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.32 % Allowed : 6.15 % Favored : 93.53 % Rotamer: Outliers : 2.30 % Allowed : 23.46 % Favored : 74.24 % 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: 2.28 (0.21), residues: 520 sheet: -0.96 (0.28), residues: 325 loop : -1.23 (0.25), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 109 TYR 0.016 0.001 TYR D 263 PHE 0.014 0.001 PHE A 37 TRP 0.011 0.001 TRP A 213 HIS 0.005 0.002 HIS D 235 Details of bonding type rmsd covalent geometry : bond 0.00441 (13300) covalent geometry : angle 0.68485 (18095) hydrogen bonds : bond 0.03193 ( 560) hydrogen bonds : angle 4.37063 ( 1725) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4000.07 seconds wall clock time: 68 minutes 45.69 seconds (4125.69 seconds total)