Starting phenix.real_space_refine on Mon Dec 30 12:45:19 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8atg_15649/12_2024/8atg_15649.cif Found real_map, /net/cci-nas-00/data/ceres_data/8atg_15649/12_2024/8atg_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8atg_15649/12_2024/8atg_15649.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8atg_15649/12_2024/8atg_15649.map" model { file = "/net/cci-nas-00/data/ceres_data/8atg_15649/12_2024/8atg_15649.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8atg_15649/12_2024/8atg_15649.cif" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/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: {'PHE:plan': 1, 'GLU:plan': 6, 'ASN:plan1': 3, 'ARG:plan': 3, 'ASP:plan': 7} 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: C, B, E, D Time building chain proxies: 5.65, per 1000 atoms: 0.43 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: 3.28 Conformation dependent library (CDL) restraints added in 1.6 seconds 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: 1.46 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: 3.80 Time building geometry restraints manager: 3.78 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: 0.00 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: 0.850 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.430 Check model and map are aligned: 0.090 Set scattering table: 0.120 Process input model: 28.160 Find NCS groups from input model: 0.460 Set up NCS constraints: 0.030 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:11.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.940 ------------------------------------------------------------------------------- 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= 0.400 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.011 0.001 TRP D 160 HIS 0.002 0.001 HIS B 127 PHE 0.027 0.002 PHE E 195 TYR 0.012 0.001 TYR B 194 ARG 0.004 0.000 ARG D 189 *********************** 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 : 1.420 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: 1.1442 time to fit residues: 307.9243 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 : 1.447 ------------------------------------------------------------------------------- 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 130 optimal weight: 9.9990 chunk 117 optimal weight: 7.9990 chunk 65 optimal weight: 9.9990 chunk 40 optimal weight: 20.0000 chunk 79 optimal weight: 1.9990 chunk 62 optimal weight: 10.0000 chunk 121 optimal weight: 6.9990 chunk 47 optimal weight: 20.0000 chunk 73 optimal weight: 1.9990 chunk 90 optimal weight: 5.9990 chunk 140 optimal weight: 20.0000 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6294 moved from start: 0.2941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 13300 Z= 0.412 Angle : 0.769 6.903 18095 Z= 0.390 Chirality : 0.047 0.146 2040 Planarity : 0.005 0.038 2175 Dihedral : 20.702 143.896 2477 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 9.74 Ramachandran Plot: Outliers : 0.32 % Allowed : 6.99 % Favored : 92.69 % Rotamer: Outliers : 3.79 % Allowed : 13.09 % Favored : 83.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.88 (0.22), residues: 1545 helix: 1.67 (0.21), residues: 520 sheet: -1.75 (0.28), residues: 330 loop : -1.76 (0.24), residues: 695 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 160 HIS 0.005 0.002 HIS A 235 PHE 0.013 0.002 PHE D 37 TYR 0.013 0.002 TYR E 102 ARG 0.004 0.001 ARG D 109 *********************** 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 199 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 153 time to evaluate : 1.494 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 35 GLU cc_start: 0.8395 (pm20) cc_final: 0.8016 (pm20) REVERT: B 187 GLN cc_start: 0.9067 (mt0) cc_final: 0.8683 (mt0) REVERT: C 187 GLN cc_start: 0.9083 (mt0) cc_final: 0.8729 (mt0) REVERT: C 248 LYS cc_start: 0.8879 (mtmt) cc_final: 0.8364 (tppt) REVERT: D 248 LYS cc_start: 0.8741 (mtmt) cc_final: 0.8419 (mttp) REVERT: E 174 PHE cc_start: 0.7830 (OUTLIER) cc_final: 0.7387 (p90) REVERT: E 187 GLN cc_start: 0.9102 (mt0) cc_final: 0.8739 (mt0) outliers start: 46 outliers final: 22 residues processed: 187 average time/residue: 1.1646 time to fit residues: 240.2110 Evaluate side-chains 152 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 129 time to evaluate : 1.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 THR Chi-restraints excluded: chain A residue 212 SER Chi-restraints excluded: chain A residue 255 THR Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain B residue 36 THR Chi-restraints excluded: chain B residue 205 MET Chi-restraints excluded: chain B residue 212 SER Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 271 ILE 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 C residue 271 ILE 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 36 THR 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 270 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 78 optimal weight: 8.9990 chunk 43 optimal weight: 7.9990 chunk 117 optimal weight: 3.9990 chunk 95 optimal weight: 20.0000 chunk 38 optimal weight: 2.9990 chunk 141 optimal weight: 1.9990 chunk 152 optimal weight: 5.9990 chunk 125 optimal weight: 20.0000 chunk 139 optimal weight: 2.9990 chunk 48 optimal weight: 0.0980 chunk 113 optimal weight: 0.6980 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 245 ASN D 245 ASN E 19 ASN E 245 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6257 moved from start: 0.3145 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= 0.220 Angle : 0.623 6.144 18095 Z= 0.318 Chirality : 0.043 0.146 2040 Planarity : 0.004 0.033 2175 Dihedral : 19.912 142.356 2475 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.21 % Favored : 93.66 % Rotamer: Outliers : 3.46 % Allowed : 16.30 % Favored : 80.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.46 (0.22), residues: 1545 helix: 2.16 (0.22), residues: 520 sheet: -1.64 (0.27), residues: 325 loop : -1.57 (0.25), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 160 HIS 0.005 0.002 HIS B 235 PHE 0.016 0.001 PHE E 37 TYR 0.013 0.001 TYR B 102 ARG 0.004 0.000 ARG A 189 *********************** 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 189 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 147 time to evaluate : 1.698 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 163 GLU cc_start: 0.7895 (mp0) cc_final: 0.7676 (mp0) REVERT: A 187 GLN cc_start: 0.9060 (mt0) cc_final: 0.8677 (mt0) REVERT: B 187 GLN cc_start: 0.9044 (mt0) cc_final: 0.8705 (mt0) REVERT: C 174 PHE cc_start: 0.7699 (p90) cc_final: 0.7226 (p90) REVERT: C 187 GLN cc_start: 0.9061 (mt0) cc_final: 0.8742 (mt0) REVERT: D 163 GLU cc_start: 0.7876 (mp0) cc_final: 0.7545 (mp0) REVERT: D 174 PHE cc_start: 0.7701 (OUTLIER) cc_final: 0.7145 (p90) REVERT: D 187 GLN cc_start: 0.9047 (mt0) cc_final: 0.8640 (mt0) REVERT: D 248 LYS cc_start: 0.8790 (mtmt) cc_final: 0.8433 (mttp) REVERT: E 187 GLN cc_start: 0.9029 (mt0) cc_final: 0.8665 (mt0) outliers start: 42 outliers final: 30 residues processed: 175 average time/residue: 1.1934 time to fit residues: 229.6751 Evaluate side-chains 155 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 124 time to evaluate : 2.491 ------------------------------------------------------------------------------- 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 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 212 SER Chi-restraints excluded: chain B residue 214 THR Chi-restraints excluded: chain B residue 255 THR 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 212 SER 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 19 ASN 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 214 THR 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 212 SER 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 139 optimal weight: 5.9990 chunk 106 optimal weight: 20.0000 chunk 73 optimal weight: 7.9990 chunk 15 optimal weight: 9.9990 chunk 67 optimal weight: 8.9990 chunk 94 optimal weight: 20.0000 chunk 141 optimal weight: 6.9990 chunk 149 optimal weight: 4.9990 chunk 134 optimal weight: 20.0000 chunk 40 optimal weight: 20.0000 chunk 124 optimal weight: 10.0000 overall best weight: 6.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 200 ASN C 245 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6412 moved from start: 0.4013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.072 13300 Z= 0.558 Angle : 0.776 6.540 18095 Z= 0.395 Chirality : 0.046 0.163 2040 Planarity : 0.005 0.029 2175 Dihedral : 20.080 139.403 2475 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 10.09 Ramachandran Plot: Outliers : 0.32 % Allowed : 7.51 % Favored : 92.17 % Rotamer: Outliers : 3.95 % Allowed : 17.28 % Favored : 78.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.55 (0.22), residues: 1545 helix: 1.97 (0.21), residues: 520 sheet: -1.57 (0.27), residues: 325 loop : -1.59 (0.24), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 213 HIS 0.005 0.002 HIS D 235 PHE 0.014 0.002 PHE B 238 TYR 0.016 0.002 TYR B 102 ARG 0.002 0.000 ARG B 189 *********************** 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 168 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 120 time to evaluate : 1.345 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 163 GLU cc_start: 0.7814 (mp0) cc_final: 0.7510 (pm20) REVERT: A 187 GLN cc_start: 0.9128 (mt0) cc_final: 0.8750 (mt0) REVERT: B 163 GLU cc_start: 0.8105 (mp0) cc_final: 0.7829 (mp0) REVERT: B 187 GLN cc_start: 0.9088 (mt0) cc_final: 0.8739 (mt0) REVERT: C 212 SER cc_start: 0.9537 (OUTLIER) cc_final: 0.9322 (p) REVERT: D 163 GLU cc_start: 0.7910 (mp0) cc_final: 0.7550 (mp0) REVERT: D 187 GLN cc_start: 0.9091 (mt0) cc_final: 0.8696 (mt0) REVERT: D 248 LYS cc_start: 0.8884 (mtmt) cc_final: 0.8552 (mttp) REVERT: E 187 GLN cc_start: 0.9127 (mt0) cc_final: 0.8701 (mt0) outliers start: 48 outliers final: 28 residues processed: 156 average time/residue: 1.2025 time to fit residues: 206.1721 Evaluate side-chains 143 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 114 time to evaluate : 1.438 ------------------------------------------------------------------------------- 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 174 PHE Chi-restraints excluded: chain A residue 205 MET 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 174 PHE Chi-restraints excluded: chain B residue 255 THR 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 174 PHE Chi-restraints excluded: chain C residue 205 MET 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 32 ASP Chi-restraints excluded: chain D residue 36 THR Chi-restraints excluded: chain D residue 174 PHE 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 212 SER Chi-restraints excluded: chain E residue 255 THR Chi-restraints excluded: chain E residue 270 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 85 optimal weight: 0.9990 chunk 2 optimal weight: 10.0000 chunk 111 optimal weight: 5.9990 chunk 61 optimal weight: 5.9990 chunk 127 optimal weight: 9.9990 chunk 103 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 76 optimal weight: 9.9990 chunk 134 optimal weight: 2.9990 chunk 37 optimal weight: 20.0000 chunk 50 optimal weight: 0.6980 overall best weight: 3.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 200 ASN D 245 ASN E 19 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6361 moved from start: 0.4253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 13300 Z= 0.312 Angle : 0.664 8.763 18095 Z= 0.334 Chirality : 0.044 0.146 2040 Planarity : 0.004 0.031 2175 Dihedral : 19.536 126.811 2475 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.26 % Allowed : 6.47 % Favored : 93.27 % Rotamer: Outliers : 3.87 % Allowed : 19.26 % Favored : 76.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.35 (0.22), residues: 1545 helix: 2.24 (0.22), residues: 520 sheet: -1.50 (0.27), residues: 325 loop : -1.53 (0.25), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 213 HIS 0.005 0.002 HIS E 235 PHE 0.014 0.001 PHE C 37 TYR 0.011 0.001 TYR D 102 ARG 0.004 0.000 ARG E 189 *********************** 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 178 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 131 time to evaluate : 1.467 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 35 GLU cc_start: 0.8423 (pm20) cc_final: 0.7492 (pm20) REVERT: A 163 GLU cc_start: 0.7912 (mp0) cc_final: 0.7547 (pm20) REVERT: A 187 GLN cc_start: 0.9114 (mt0) cc_final: 0.8618 (mm110) REVERT: A 248 LYS cc_start: 0.8944 (mttt) cc_final: 0.8713 (mttp) REVERT: B 163 GLU cc_start: 0.8089 (mp0) cc_final: 0.7745 (mp0) REVERT: B 187 GLN cc_start: 0.9054 (mt0) cc_final: 0.8624 (mt0) REVERT: C 187 GLN cc_start: 0.9099 (mt0) cc_final: 0.8671 (mt0) REVERT: C 248 LYS cc_start: 0.9069 (mmmt) cc_final: 0.8744 (mmmm) REVERT: D 163 GLU cc_start: 0.8020 (mp0) cc_final: 0.7648 (mp0) REVERT: D 187 GLN cc_start: 0.9064 (mt0) cc_final: 0.8670 (mt0) REVERT: D 248 LYS cc_start: 0.8908 (mtmt) cc_final: 0.8603 (mttp) REVERT: E 187 GLN cc_start: 0.9092 (mt0) cc_final: 0.8700 (mt0) outliers start: 47 outliers final: 28 residues processed: 162 average time/residue: 1.3371 time to fit residues: 237.5631 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 : 1.490 ------------------------------------------------------------------------------- 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 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 174 PHE Chi-restraints excluded: chain B residue 212 SER Chi-restraints excluded: chain B residue 255 THR 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 174 PHE 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 134 optimal weight: 7.9990 chunk 29 optimal weight: 3.9990 chunk 87 optimal weight: 0.6980 chunk 36 optimal weight: 7.9990 chunk 149 optimal weight: 4.9990 chunk 124 optimal weight: 10.0000 chunk 69 optimal weight: 10.0000 chunk 12 optimal weight: 9.9990 chunk 49 optimal weight: 1.9990 chunk 78 optimal weight: 20.0000 chunk 144 optimal weight: 1.9990 overall best weight: 2.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 245 ASN B 19 ASN C 19 ASN C 245 ASN D 245 ASN E 245 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6362 moved from start: 0.4453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 13300 Z= 0.277 Angle : 0.648 8.124 18095 Z= 0.327 Chirality : 0.043 0.145 2040 Planarity : 0.004 0.032 2175 Dihedral : 18.941 110.818 2475 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.26 % Allowed : 6.54 % Favored : 93.20 % Rotamer: Outliers : 4.28 % Allowed : 19.92 % Favored : 75.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.17 (0.22), residues: 1545 helix: 2.32 (0.22), residues: 520 sheet: -1.30 (0.27), residues: 325 loop : -1.43 (0.25), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 213 HIS 0.005 0.002 HIS D 235 PHE 0.014 0.001 PHE C 37 TYR 0.011 0.001 TYR B 28 ARG 0.002 0.000 ARG B 109 *********************** 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 181 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 129 time to evaluate : 1.295 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 35 GLU cc_start: 0.8047 (pm20) cc_final: 0.7659 (pm20) REVERT: A 163 GLU cc_start: 0.7956 (mp0) cc_final: 0.7640 (mp0) REVERT: A 187 GLN cc_start: 0.9082 (mt0) cc_final: 0.8712 (mt0) REVERT: A 248 LYS cc_start: 0.9053 (mttt) cc_final: 0.8824 (mttp) REVERT: B 163 GLU cc_start: 0.8098 (mp0) cc_final: 0.7734 (mp0) REVERT: B 187 GLN cc_start: 0.9041 (mt0) cc_final: 0.8601 (mt0) REVERT: C 248 LYS cc_start: 0.9038 (mmmt) cc_final: 0.8718 (tmtt) REVERT: D 163 GLU cc_start: 0.8064 (mp0) cc_final: 0.7709 (mp0) REVERT: D 187 GLN cc_start: 0.9034 (mt0) cc_final: 0.8630 (mt0) REVERT: E 187 GLN cc_start: 0.9072 (mt0) cc_final: 0.8643 (mt0) REVERT: E 248 LYS cc_start: 0.9044 (tppt) cc_final: 0.8630 (tmtt) outliers start: 52 outliers final: 33 residues processed: 165 average time/residue: 1.1905 time to fit residues: 216.3003 Evaluate side-chains 157 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 124 time to evaluate : 1.420 ------------------------------------------------------------------------------- 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 212 SER Chi-restraints excluded: chain B residue 255 THR Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain C residue 18 VAL Chi-restraints excluded: chain C residue 94 VAL Chi-restraints excluded: chain C residue 174 PHE 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 18 VAL 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 D residue 255 THR Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain D residue 305 LEU 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 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 16 optimal weight: 10.0000 chunk 85 optimal weight: 0.7980 chunk 109 optimal weight: 20.0000 chunk 84 optimal weight: 0.9990 chunk 126 optimal weight: 20.0000 chunk 83 optimal weight: 2.9990 chunk 149 optimal weight: 0.9980 chunk 93 optimal weight: 10.0000 chunk 91 optimal weight: 7.9990 chunk 68 optimal weight: 9.9990 chunk 92 optimal weight: 6.9990 overall best weight: 2.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 19 ASN C 245 ASN D 19 ASN D 245 ASN E 19 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6360 moved from start: 0.4625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 13300 Z= 0.268 Angle : 0.649 8.364 18095 Z= 0.328 Chirality : 0.043 0.174 2040 Planarity : 0.004 0.033 2175 Dihedral : 18.668 97.799 2475 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.19 % Allowed : 5.63 % Favored : 94.17 % Rotamer: Outliers : 3.46 % Allowed : 21.40 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.09 (0.22), residues: 1545 helix: 2.37 (0.22), residues: 520 sheet: -1.23 (0.27), residues: 325 loop : -1.37 (0.25), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 213 HIS 0.005 0.002 HIS B 235 PHE 0.012 0.001 PHE C 37 TYR 0.011 0.001 TYR D 28 ARG 0.004 0.000 ARG D 109 *********************** 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 165 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 123 time to evaluate : 1.448 Fit side-chains revert: symmetry clash REVERT: A 163 GLU cc_start: 0.7994 (mp0) cc_final: 0.7641 (mp0) REVERT: A 187 GLN cc_start: 0.9063 (mt0) cc_final: 0.8562 (mm110) REVERT: B 187 GLN cc_start: 0.9025 (mt0) cc_final: 0.8579 (mt0) REVERT: C 187 GLN cc_start: 0.9059 (mt0) cc_final: 0.8619 (mt0) REVERT: D 163 GLU cc_start: 0.8094 (mp0) cc_final: 0.7753 (mp0) REVERT: D 187 GLN cc_start: 0.9027 (mt0) cc_final: 0.8613 (mt0) REVERT: D 248 LYS cc_start: 0.9059 (tppt) cc_final: 0.8365 (tmtt) REVERT: E 32 ASP cc_start: 0.7647 (OUTLIER) cc_final: 0.7381 (m-30) REVERT: E 187 GLN cc_start: 0.9045 (mt0) cc_final: 0.8610 (mt0) outliers start: 42 outliers final: 31 residues processed: 153 average time/residue: 1.2572 time to fit residues: 211.4265 Evaluate side-chains 150 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 118 time to evaluate : 1.458 ------------------------------------------------------------------------------- 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 94 VAL Chi-restraints excluded: chain A residue 174 PHE Chi-restraints excluded: chain A residue 205 MET Chi-restraints excluded: chain A residue 212 SER Chi-restraints excluded: chain B residue 18 VAL Chi-restraints excluded: chain B residue 94 VAL Chi-restraints excluded: chain B residue 177 GLU Chi-restraints excluded: chain B residue 212 SER Chi-restraints excluded: chain B residue 255 THR Chi-restraints excluded: chain C residue 18 VAL Chi-restraints excluded: chain C residue 32 ASP 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 255 THR Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain D residue 18 VAL 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 D residue 255 THR Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain D residue 305 LEU 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 59 optimal weight: 9.9990 chunk 89 optimal weight: 5.9990 chunk 45 optimal weight: 5.9990 chunk 29 optimal weight: 8.9990 chunk 28 optimal weight: 8.9990 chunk 94 optimal weight: 20.0000 chunk 101 optimal weight: 20.0000 chunk 73 optimal weight: 0.2980 chunk 13 optimal weight: 4.9990 chunk 117 optimal weight: 0.9990 chunk 135 optimal weight: 6.9990 overall best weight: 3.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 19 ASN C 19 ASN C 245 ASN D 19 ASN D 245 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6391 moved from start: 0.4833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 13300 Z= 0.341 Angle : 0.695 8.022 18095 Z= 0.354 Chirality : 0.044 0.183 2040 Planarity : 0.004 0.033 2175 Dihedral : 18.500 89.783 2475 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.19 % Allowed : 6.99 % Favored : 92.82 % Rotamer: Outliers : 3.21 % Allowed : 23.54 % Favored : 73.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.07 (0.22), residues: 1545 helix: 2.34 (0.21), residues: 520 sheet: -1.23 (0.27), residues: 325 loop : -1.32 (0.25), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 213 HIS 0.005 0.002 HIS B 235 PHE 0.010 0.001 PHE E 265 TYR 0.011 0.001 TYR B 102 ARG 0.003 0.000 ARG D 109 *********************** 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 151 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 112 time to evaluate : 1.341 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 163 GLU cc_start: 0.8006 (mp0) cc_final: 0.7641 (mp0) REVERT: B 187 GLN cc_start: 0.9036 (mt0) cc_final: 0.8577 (mt0) REVERT: D 163 GLU cc_start: 0.8105 (mp0) cc_final: 0.7723 (mp0) REVERT: D 187 GLN cc_start: 0.9035 (mt0) cc_final: 0.8608 (mt0) REVERT: D 248 LYS cc_start: 0.8993 (tppt) cc_final: 0.8521 (tmtt) REVERT: E 32 ASP cc_start: 0.7734 (OUTLIER) cc_final: 0.7467 (m-30) REVERT: E 187 GLN cc_start: 0.9052 (mt0) cc_final: 0.8639 (mt0) outliers start: 39 outliers final: 31 residues processed: 143 average time/residue: 1.3081 time to fit residues: 204.5193 Evaluate side-chains 143 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 111 time to evaluate : 1.364 ------------------------------------------------------------------------------- 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 94 VAL Chi-restraints excluded: chain A residue 174 PHE Chi-restraints excluded: chain A residue 205 MET Chi-restraints excluded: chain A residue 212 SER Chi-restraints excluded: chain B residue 18 VAL Chi-restraints excluded: chain B residue 94 VAL Chi-restraints excluded: chain B residue 177 GLU Chi-restraints excluded: chain B residue 212 SER Chi-restraints excluded: chain B residue 255 THR Chi-restraints excluded: chain C residue 18 VAL Chi-restraints excluded: chain C residue 32 ASP Chi-restraints excluded: chain C residue 94 VAL Chi-restraints excluded: chain C residue 174 PHE 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 18 VAL 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 D residue 255 THR Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain D residue 305 LEU 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 143 optimal weight: 0.3980 chunk 130 optimal weight: 5.9990 chunk 139 optimal weight: 8.9990 chunk 83 optimal weight: 1.9990 chunk 60 optimal weight: 5.9990 chunk 109 optimal weight: 9.9990 chunk 42 optimal weight: 1.9990 chunk 125 optimal weight: 5.9990 chunk 131 optimal weight: 2.9990 chunk 138 optimal weight: 5.9990 chunk 91 optimal weight: 0.8980 overall best weight: 1.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 19 ASN C 19 ASN C 245 ASN D 19 ASN E 19 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6350 moved from start: 0.4925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 13300 Z= 0.231 Angle : 0.669 8.405 18095 Z= 0.342 Chirality : 0.043 0.195 2040 Planarity : 0.004 0.034 2175 Dihedral : 18.195 89.497 2475 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.19 % Allowed : 4.40 % Favored : 95.40 % Rotamer: Outliers : 2.55 % Allowed : 24.53 % Favored : 72.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.02 (0.22), residues: 1545 helix: 2.38 (0.22), residues: 520 sheet: -1.13 (0.28), residues: 325 loop : -1.27 (0.25), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 213 HIS 0.005 0.002 HIS B 235 PHE 0.013 0.001 PHE D 37 TYR 0.011 0.001 TYR D 263 ARG 0.003 0.000 ARG D 109 *********************** 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 155 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 124 time to evaluate : 1.684 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 163 GLU cc_start: 0.8005 (mp0) cc_final: 0.7627 (mp0) REVERT: A 187 GLN cc_start: 0.9060 (mt0) cc_final: 0.8574 (mm110) REVERT: B 187 GLN cc_start: 0.8998 (mt0) cc_final: 0.8547 (mt0) REVERT: D 163 GLU cc_start: 0.8114 (mp0) cc_final: 0.7742 (mp0) REVERT: D 187 GLN cc_start: 0.9015 (mt0) cc_final: 0.8588 (mt0) REVERT: D 248 LYS cc_start: 0.8999 (tppt) cc_final: 0.8603 (tmtt) REVERT: E 32 ASP cc_start: 0.7731 (OUTLIER) cc_final: 0.7454 (m-30) REVERT: E 187 GLN cc_start: 0.9034 (mt0) cc_final: 0.8581 (mt0) outliers start: 31 outliers final: 21 residues processed: 146 average time/residue: 1.2911 time to fit residues: 207.3892 Evaluate side-chains 137 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 115 time to evaluate : 1.456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 VAL Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 205 MET Chi-restraints excluded: chain A residue 212 SER Chi-restraints excluded: chain B residue 18 VAL Chi-restraints excluded: chain B residue 94 VAL Chi-restraints excluded: chain B residue 177 GLU Chi-restraints excluded: chain B residue 212 SER Chi-restraints excluded: chain B residue 255 THR Chi-restraints excluded: chain C residue 18 VAL Chi-restraints excluded: chain C residue 94 VAL Chi-restraints excluded: chain C residue 212 SER Chi-restraints excluded: chain D residue 18 VAL 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 305 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 147 optimal weight: 0.9990 chunk 89 optimal weight: 5.9990 chunk 69 optimal weight: 0.0670 chunk 102 optimal weight: 30.0000 chunk 154 optimal weight: 9.9990 chunk 142 optimal weight: 6.9990 chunk 122 optimal weight: 0.6980 chunk 12 optimal weight: 1.9990 chunk 94 optimal weight: 0.9980 chunk 75 optimal weight: 9.9990 chunk 97 optimal weight: 5.9990 overall best weight: 0.9522 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 19 ASN C 19 ASN C 245 ASN D 19 ASN E 19 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6331 moved from start: 0.5023 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= 0.209 Angle : 0.681 8.295 18095 Z= 0.346 Chirality : 0.043 0.193 2040 Planarity : 0.004 0.036 2175 Dihedral : 17.831 89.833 2475 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.19 % Allowed : 5.05 % Favored : 94.76 % Rotamer: Outliers : 2.06 % Allowed : 25.51 % Favored : 72.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.05 (0.22), residues: 1545 helix: 2.36 (0.21), residues: 520 sheet: -1.05 (0.28), residues: 325 loop : -1.23 (0.25), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 213 HIS 0.005 0.002 HIS B 235 PHE 0.013 0.001 PHE E 37 TYR 0.018 0.001 TYR D 263 ARG 0.003 0.000 ARG A 109 ********************** 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 146 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 121 time to evaluate : 1.483 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 163 GLU cc_start: 0.8029 (mp0) cc_final: 0.7644 (mp0) REVERT: A 187 GLN cc_start: 0.9028 (mt0) cc_final: 0.8535 (mm110) REVERT: B 187 GLN cc_start: 0.8977 (mt0) cc_final: 0.8525 (mt0) REVERT: C 187 GLN cc_start: 0.9017 (mt0) cc_final: 0.8565 (mt0) REVERT: D 163 GLU cc_start: 0.8157 (mp0) cc_final: 0.7793 (mp0) REVERT: D 187 GLN cc_start: 0.8991 (mt0) cc_final: 0.8576 (mt0) REVERT: D 248 LYS cc_start: 0.8977 (tppt) cc_final: 0.8603 (tmtt) REVERT: E 32 ASP cc_start: 0.7727 (OUTLIER) cc_final: 0.7486 (m-30) REVERT: E 187 GLN cc_start: 0.9034 (mt0) cc_final: 0.8568 (mt0) REVERT: E 248 LYS cc_start: 0.9125 (tppt) cc_final: 0.8606 (tmtt) outliers start: 25 outliers final: 22 residues processed: 138 average time/residue: 1.3471 time to fit residues: 202.5262 Evaluate side-chains 139 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 116 time to evaluate : 1.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 VAL 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 94 VAL Chi-restraints excluded: chain B residue 177 GLU Chi-restraints excluded: chain B residue 212 SER Chi-restraints excluded: chain B residue 255 THR Chi-restraints excluded: chain C residue 18 VAL 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 D residue 18 VAL 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 205 MET 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 130 optimal weight: 8.9990 chunk 37 optimal weight: 4.9990 chunk 113 optimal weight: 4.9990 chunk 18 optimal weight: 10.0000 chunk 34 optimal weight: 10.0000 chunk 123 optimal weight: 9.9990 chunk 51 optimal weight: 4.9990 chunk 126 optimal weight: 7.9990 chunk 15 optimal weight: 1.9990 chunk 22 optimal weight: 0.8980 chunk 108 optimal weight: 2.9990 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 19 ASN C 19 ASN C 245 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 = 0.3807 r_free = 0.3807 target = 0.085323 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.060547 restraints weight = 39801.397| |-----------------------------------------------------------------------------| r_work (start): 0.3213 rms_B_bonded: 3.63 r_work: 0.3033 rms_B_bonded: 4.78 restraints_weight: 0.5000 r_work (final): 0.3033 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8616 moved from start: 0.5124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 13300 Z= 0.310 Angle : 0.684 7.629 18095 Z= 0.349 Chirality : 0.044 0.191 2040 Planarity : 0.004 0.035 2175 Dihedral : 17.733 89.180 2475 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.19 % Allowed : 6.21 % Favored : 93.59 % Rotamer: Outliers : 2.06 % Allowed : 25.84 % Favored : 72.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.02 (0.22), residues: 1545 helix: 2.33 (0.21), residues: 520 sheet: -1.07 (0.28), residues: 325 loop : -1.26 (0.25), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 213 HIS 0.005 0.002 HIS D 235 PHE 0.015 0.001 PHE B 165 TYR 0.011 0.001 TYR D 263 ARG 0.003 0.000 ARG B 189 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4085.57 seconds wall clock time: 74 minutes 52.72 seconds (4492.72 seconds total)