Starting phenix.real_space_refine on Thu Jul 31 05:18:13 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8atg_15649/07_2025/8atg_15649.cif Found real_map, /net/cci-nas-00/data/ceres_data/8atg_15649/07_2025/8atg_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_15649/07_2025/8atg_15649.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8atg_15649/07_2025/8atg_15649.map" model { file = "/net/cci-nas-00/data/ceres_data/8atg_15649/07_2025/8atg_15649.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8atg_15649/07_2025/8atg_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-5711/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: 5.98, per 1000 atoms: 0.46 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: 3.31 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: 1.56 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: 3.84 Time building geometry restraints manager: 3.91 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: 0.10 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'E' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.390 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.570 Check model and map are aligned: 0.110 Set scattering table: 0.120 Process input model: 29.250 Find NCS groups from input model: 0.230 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:12.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.520 ------------------------------------------------------------------------------- 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 (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 Details of bonding type rmsd hydrogen bonds : bond 0.20507 ( 560) hydrogen bonds : angle 6.86630 ( 1725) covalent geometry : bond 0.00656 (13300) covalent geometry : angle 0.70913 (18095) *********************** 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 : 1.444 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: 1.0944 time to fit residues: 294.3794 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 : 1.515 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.087103 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.062185 restraints weight = 39060.748| |-----------------------------------------------------------------------------| r_work (start): 0.3231 rms_B_bonded: 3.65 r_work: 0.3053 rms_B_bonded: 4.84 restraints_weight: 0.5000 r_work (final): 0.3053 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8519 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= 0.282 Angle : 0.769 6.903 18095 Z= 0.390 Chirality : 0.047 0.146 2040 Planarity : 0.005 0.038 2175 Dihedral : 20.702 143.895 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 Details of bonding type rmsd hydrogen bonds : bond 0.04282 ( 560) hydrogen bonds : angle 5.46953 ( 1725) covalent geometry : bond 0.00630 (13300) covalent geometry : angle 0.76854 (18095) *********************** 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 : 1.483 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: 0.8506 (pm20) cc_final: 0.8054 (pm20) REVERT: B 187 GLN cc_start: 0.9146 (mt0) cc_final: 0.8774 (mt0) REVERT: C 187 GLN cc_start: 0.9149 (mt0) cc_final: 0.8802 (mt0) REVERT: C 248 LYS cc_start: 0.9123 (mtmt) cc_final: 0.8450 (tppt) REVERT: D 163 GLU cc_start: 0.8540 (mt-10) cc_final: 0.8226 (mp0) REVERT: D 248 LYS cc_start: 0.9090 (mtmt) cc_final: 0.8790 (mttp) REVERT: E 174 PHE cc_start: 0.7790 (OUTLIER) cc_final: 0.7243 (p90) REVERT: E 187 GLN cc_start: 0.9157 (mt0) cc_final: 0.8794 (mt0) outliers start: 46 outliers final: 22 residues processed: 187 average time/residue: 1.1541 time to fit residues: 237.8270 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 : 1.156 ------------------------------------------------------------------------------- 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 93 optimal weight: 10.0000 chunk 94 optimal weight: 5.9990 chunk 138 optimal weight: 7.9990 chunk 28 optimal weight: 3.9990 chunk 134 optimal weight: 5.9990 chunk 50 optimal weight: 2.9990 chunk 83 optimal weight: 4.9990 chunk 59 optimal weight: 0.9990 chunk 91 optimal weight: 0.9990 chunk 71 optimal weight: 30.0000 chunk 4 optimal weight: 9.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.087396 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.062810 restraints weight = 39141.945| |-----------------------------------------------------------------------------| r_work (start): 0.3247 rms_B_bonded: 3.64 r_work: 0.3067 rms_B_bonded: 4.88 restraints_weight: 0.5000 r_work (final): 0.3067 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8520 moved from start: 0.3224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 13300 Z= 0.180 Angle : 0.636 6.076 18095 Z= 0.325 Chirality : 0.043 0.137 2040 Planarity : 0.004 0.033 2175 Dihedral : 19.981 142.857 2475 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.26 % Allowed : 7.06 % Favored : 92.69 % Rotamer: Outliers : 3.62 % Allowed : 15.97 % Favored : 80.41 % 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: -0.50 (0.22), residues: 1545 helix: 2.12 (0.22), residues: 520 sheet: -1.65 (0.27), residues: 325 loop : -1.59 (0.24), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 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 Details of bonding type rmsd hydrogen bonds : bond 0.03821 ( 560) hydrogen bonds : angle 4.91836 ( 1725) covalent geometry : bond 0.00421 (13300) covalent geometry : angle 0.63553 (18095) *********************** 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 188 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 144 time to evaluate : 1.437 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 163 GLU cc_start: 0.8054 (mp0) cc_final: 0.7793 (mp0) REVERT: A 187 GLN cc_start: 0.9143 (mt0) cc_final: 0.8759 (mt0) REVERT: B 187 GLN cc_start: 0.9124 (mt0) cc_final: 0.8791 (mt0) REVERT: B 212 SER cc_start: 0.9658 (OUTLIER) cc_final: 0.9454 (p) REVERT: B 248 LYS cc_start: 0.8967 (mtmt) cc_final: 0.8744 (mmmt) REVERT: B 313 LEU cc_start: 0.9467 (mt) cc_final: 0.9081 (tp) REVERT: C 187 GLN cc_start: 0.9127 (mt0) cc_final: 0.8781 (mt0) REVERT: C 313 LEU cc_start: 0.9423 (mt) cc_final: 0.9094 (tp) REVERT: D 163 GLU cc_start: 0.8545 (mt-10) cc_final: 0.8258 (mp0) REVERT: D 174 PHE cc_start: 0.7720 (OUTLIER) cc_final: 0.7465 (p90) REVERT: D 187 GLN cc_start: 0.9127 (mt0) cc_final: 0.8771 (mt0) REVERT: D 248 LYS cc_start: 0.9133 (mtmt) cc_final: 0.8778 (mttp) REVERT: D 313 LEU cc_start: 0.9466 (mt) cc_final: 0.9104 (tp) REVERT: E 187 GLN cc_start: 0.9109 (mt0) cc_final: 0.8729 (mt0) REVERT: E 248 LYS cc_start: 0.8900 (mtmt) cc_final: 0.8694 (mmmt) REVERT: E 313 LEU cc_start: 0.9394 (mt) cc_final: 0.9048 (tp) outliers start: 44 outliers final: 30 residues processed: 173 average time/residue: 1.3929 time to fit residues: 264.4012 Evaluate side-chains 156 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 124 time to evaluate : 1.547 ------------------------------------------------------------------------------- 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 255 THR Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain C residue 271 ILE Chi-restraints excluded: chain D residue 18 VAL Chi-restraints excluded: chain D residue 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 80 optimal weight: 9.9990 chunk 17 optimal weight: 20.0000 chunk 87 optimal weight: 3.9990 chunk 36 optimal weight: 8.9990 chunk 133 optimal weight: 6.9990 chunk 8 optimal weight: 9.9990 chunk 131 optimal weight: 9.9990 chunk 113 optimal weight: 0.8980 chunk 152 optimal weight: 9.9990 chunk 60 optimal weight: 3.9990 chunk 2 optimal weight: 10.0000 overall best weight: 4.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 245 ASN B 245 ASN C 200 ASN C 245 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.084288 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.061210 restraints weight = 39795.879| |-----------------------------------------------------------------------------| r_work (start): 0.3213 rms_B_bonded: 3.48 r_work: 0.3032 rms_B_bonded: 4.71 restraints_weight: 0.5000 r_work (final): 0.3032 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8574 moved from start: 0.3732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.061 13300 Z= 0.278 Angle : 0.686 6.176 18095 Z= 0.350 Chirality : 0.044 0.169 2040 Planarity : 0.004 0.030 2175 Dihedral : 19.726 137.829 2475 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.32 % Allowed : 7.51 % Favored : 92.17 % Rotamer: Outliers : 3.70 % Allowed : 16.95 % Favored : 79.34 % 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: -0.45 (0.22), residues: 1545 helix: 2.11 (0.22), residues: 520 sheet: -1.54 (0.27), residues: 325 loop : -1.57 (0.24), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 160 HIS 0.005 0.002 HIS C 235 PHE 0.011 0.001 PHE B 238 TYR 0.014 0.001 TYR A 102 ARG 0.002 0.000 ARG A 109 Details of bonding type rmsd hydrogen bonds : bond 0.03883 ( 560) hydrogen bonds : angle 4.83519 ( 1725) covalent geometry : bond 0.00636 (13300) covalent geometry : angle 0.68606 (18095) *********************** 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 174 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 129 time to evaluate : 1.478 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 163 GLU cc_start: 0.7966 (mp0) cc_final: 0.7647 (mp0) REVERT: A 187 GLN cc_start: 0.9177 (mt0) cc_final: 0.8819 (mt0) REVERT: B 163 GLU cc_start: 0.8251 (mp0) cc_final: 0.7921 (mp0) REVERT: B 187 GLN cc_start: 0.9158 (mt0) cc_final: 0.8842 (mt0) REVERT: B 248 LYS cc_start: 0.8899 (mtmt) cc_final: 0.8690 (mmmt) REVERT: B 313 LEU cc_start: 0.9502 (mt) cc_final: 0.9179 (tp) REVERT: C 187 GLN cc_start: 0.9143 (mt0) cc_final: 0.8755 (mt0) REVERT: C 212 SER cc_start: 0.9699 (OUTLIER) cc_final: 0.9495 (p) REVERT: C 248 LYS cc_start: 0.8965 (mtmt) cc_final: 0.8705 (mmmm) REVERT: C 313 LEU cc_start: 0.9451 (mt) cc_final: 0.9139 (tp) REVERT: D 174 PHE cc_start: 0.7911 (OUTLIER) cc_final: 0.7702 (p90) REVERT: D 187 GLN cc_start: 0.9113 (mt0) cc_final: 0.8757 (mt0) REVERT: D 212 SER cc_start: 0.9735 (OUTLIER) cc_final: 0.9504 (p) REVERT: D 248 LYS cc_start: 0.9215 (mtmt) cc_final: 0.8873 (mttp) REVERT: D 313 LEU cc_start: 0.9489 (mt) cc_final: 0.9179 (tp) REVERT: E 187 GLN cc_start: 0.9148 (mt0) cc_final: 0.8732 (mt0) REVERT: E 313 LEU cc_start: 0.9452 (mt) cc_final: 0.9174 (tp) outliers start: 45 outliers final: 27 residues processed: 161 average time/residue: 1.4670 time to fit residues: 259.8364 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 : 1.463 ------------------------------------------------------------------------------- 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 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 C residue 271 ILE 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 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 61 optimal weight: 10.0000 chunk 148 optimal weight: 6.9990 chunk 154 optimal weight: 9.9990 chunk 43 optimal weight: 3.9990 chunk 28 optimal weight: 9.9990 chunk 88 optimal weight: 0.8980 chunk 51 optimal weight: 0.9990 chunk 70 optimal weight: 9.9990 chunk 5 optimal weight: 30.0000 chunk 111 optimal weight: 4.9990 chunk 130 optimal weight: 9.9990 overall best weight: 3.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 19 ASN A 245 ASN B 245 ASN C 200 ASN D 19 ASN D 245 ASN E 19 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.084581 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.061531 restraints weight = 39633.811| |-----------------------------------------------------------------------------| r_work (start): 0.3227 rms_B_bonded: 3.47 r_work: 0.3048 rms_B_bonded: 4.67 restraints_weight: 0.5000 r_work (final): 0.3048 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8575 moved from start: 0.4101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 13300 Z= 0.211 Angle : 0.651 7.004 18095 Z= 0.332 Chirality : 0.043 0.145 2040 Planarity : 0.004 0.031 2175 Dihedral : 19.349 125.231 2475 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.99 % Favored : 92.88 % Rotamer: Outliers : 3.95 % Allowed : 18.68 % Favored : 77.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.34 (0.22), residues: 1545 helix: 2.25 (0.22), residues: 520 sheet: -1.49 (0.27), residues: 325 loop : -1.54 (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 D 235 PHE 0.009 0.001 PHE A 265 TYR 0.012 0.001 TYR A 102 ARG 0.002 0.000 ARG C 189 Details of bonding type rmsd hydrogen bonds : bond 0.03670 ( 560) hydrogen bonds : angle 4.73117 ( 1725) covalent geometry : bond 0.00493 (13300) covalent geometry : angle 0.65142 (18095) *********************** 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 184 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 136 time to evaluate : 1.520 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: 0.8066 (mp0) cc_final: 0.7667 (pm20) REVERT: A 187 GLN cc_start: 0.9154 (mt0) cc_final: 0.8788 (mt0) REVERT: A 248 LYS cc_start: 0.9282 (mttt) cc_final: 0.9069 (mttp) REVERT: B 163 GLU cc_start: 0.8262 (mp0) cc_final: 0.7879 (mp0) REVERT: B 187 GLN cc_start: 0.9134 (mt0) cc_final: 0.8734 (mt0) REVERT: B 313 LEU cc_start: 0.9504 (mt) cc_final: 0.9261 (tp) REVERT: C 313 LEU cc_start: 0.9441 (mt) cc_final: 0.9228 (tp) REVERT: D 187 GLN cc_start: 0.9100 (mt0) cc_final: 0.8696 (mt0) REVERT: D 248 LYS cc_start: 0.9256 (mtmt) cc_final: 0.8955 (mttp) REVERT: D 313 LEU cc_start: 0.9475 (mt) cc_final: 0.9238 (tp) REVERT: E 187 GLN cc_start: 0.9115 (mt0) cc_final: 0.8702 (mt0) REVERT: E 248 LYS cc_start: 0.9316 (mmmt) cc_final: 0.8944 (tmtt) outliers start: 48 outliers final: 29 residues processed: 167 average time/residue: 1.1286 time to fit residues: 207.1536 Evaluate side-chains 151 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 122 time to evaluate : 1.464 ------------------------------------------------------------------------------- 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 A residue 255 THR Chi-restraints excluded: chain B residue 18 VAL 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 205 MET 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 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 Chi-restraints excluded: chain E residue 270 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 5 optimal weight: 7.9990 chunk 68 optimal weight: 20.0000 chunk 90 optimal weight: 10.0000 chunk 94 optimal weight: 8.9990 chunk 20 optimal weight: 0.7980 chunk 120 optimal weight: 6.9990 chunk 115 optimal weight: 0.7980 chunk 100 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 37 optimal weight: 20.0000 chunk 128 optimal weight: 10.0000 overall best weight: 4.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 19 ASN A 245 ASN B 19 ASN C 19 ASN D 19 ASN D 245 ASN E 245 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.084542 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.061463 restraints weight = 40042.760| |-----------------------------------------------------------------------------| r_work (start): 0.3212 rms_B_bonded: 3.58 r_work: 0.3029 rms_B_bonded: 4.73 restraints_weight: 0.5000 r_work (final): 0.3029 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8602 moved from start: 0.4415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.058 13300 Z= 0.239 Angle : 0.678 10.671 18095 Z= 0.342 Chirality : 0.043 0.158 2040 Planarity : 0.004 0.030 2175 Dihedral : 18.890 112.415 2475 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.31 % Favored : 92.56 % Rotamer: Outliers : 4.36 % Allowed : 19.67 % Favored : 75.97 % 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: -0.28 (0.22), residues: 1545 helix: 2.27 (0.22), residues: 520 sheet: -1.39 (0.27), residues: 325 loop : -1.51 (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 D 235 PHE 0.013 0.001 PHE D 37 TYR 0.012 0.001 TYR A 102 ARG 0.002 0.000 ARG D 192 Details of bonding type rmsd hydrogen bonds : bond 0.03710 ( 560) hydrogen bonds : angle 4.66692 ( 1725) covalent geometry : bond 0.00556 (13300) covalent geometry : angle 0.67754 (18095) *********************** 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: 53 poor density : 128 time to evaluate : 2.778 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 GLU cc_start: 0.8583 (pm20) cc_final: 0.8136 (pm20) REVERT: A 163 GLU cc_start: 0.8102 (mp0) cc_final: 0.7688 (mp0) REVERT: A 187 GLN cc_start: 0.9166 (mt0) cc_final: 0.8785 (mt0) REVERT: A 248 LYS cc_start: 0.9307 (mttt) cc_final: 0.8764 (mmmm) REVERT: B 163 GLU cc_start: 0.8279 (mp0) cc_final: 0.8033 (mp0) REVERT: B 187 GLN cc_start: 0.9160 (mt0) cc_final: 0.8733 (mt0) REVERT: B 248 LYS cc_start: 0.9353 (mmmt) cc_final: 0.9010 (mmmm) REVERT: B 313 LEU cc_start: 0.9512 (mt) cc_final: 0.9288 (tp) REVERT: C 248 LYS cc_start: 0.9253 (mmmt) cc_final: 0.8976 (mmmm) REVERT: C 313 LEU cc_start: 0.9455 (mt) cc_final: 0.9242 (tp) REVERT: D 187 GLN cc_start: 0.9125 (mt0) cc_final: 0.8703 (mt0) REVERT: D 248 LYS cc_start: 0.9271 (mtmt) cc_final: 0.8957 (mttp) REVERT: D 313 LEU cc_start: 0.9480 (mt) cc_final: 0.9279 (tp) REVERT: E 187 GLN cc_start: 0.9163 (mt0) cc_final: 0.8723 (mt0) outliers start: 53 outliers final: 38 residues processed: 165 average time/residue: 1.8074 time to fit residues: 330.9944 Evaluate side-chains 158 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 120 time to evaluate : 2.040 ------------------------------------------------------------------------------- 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 205 MET Chi-restraints excluded: chain A residue 212 SER Chi-restraints excluded: chain A residue 255 THR Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain B residue 18 VAL Chi-restraints excluded: chain B residue 94 VAL 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 94 VAL Chi-restraints excluded: chain C residue 174 PHE Chi-restraints excluded: chain C residue 177 GLU 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 36 THR Chi-restraints excluded: chain D residue 94 VAL Chi-restraints excluded: chain D residue 174 PHE Chi-restraints excluded: chain D residue 177 GLU 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 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 270 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 0 optimal weight: 10.0000 chunk 88 optimal weight: 0.8980 chunk 48 optimal weight: 8.9990 chunk 95 optimal weight: 10.0000 chunk 138 optimal weight: 5.9990 chunk 37 optimal weight: 9.9990 chunk 34 optimal weight: 9.9990 chunk 153 optimal weight: 7.9990 chunk 141 optimal weight: 0.0980 chunk 104 optimal weight: 5.9990 chunk 6 optimal weight: 7.9990 overall best weight: 4.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 19 ASN A 245 ASN C 19 ASN C 245 ASN D 19 ASN D 245 ASN E 19 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.084304 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.060139 restraints weight = 39872.813| |-----------------------------------------------------------------------------| r_work (start): 0.3192 rms_B_bonded: 3.62 r_work: 0.3021 rms_B_bonded: 4.75 restraints_weight: 0.5000 r_work (final): 0.3021 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8603 moved from start: 0.4654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.058 13300 Z= 0.242 Angle : 0.688 10.526 18095 Z= 0.350 Chirality : 0.044 0.184 2040 Planarity : 0.004 0.031 2175 Dihedral : 18.599 98.419 2475 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.38 % Favored : 92.49 % Rotamer: Outliers : 3.70 % Allowed : 21.48 % 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 (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: -0.25 (0.22), residues: 1545 helix: 2.26 (0.22), residues: 520 sheet: -1.34 (0.27), residues: 325 loop : -1.48 (0.25), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 213 HIS 0.005 0.002 HIS D 235 PHE 0.011 0.001 PHE E 265 TYR 0.011 0.001 TYR A 102 ARG 0.005 0.000 ARG D 109 Details of bonding type rmsd hydrogen bonds : bond 0.03645 ( 560) hydrogen bonds : angle 4.62704 ( 1725) covalent geometry : bond 0.00562 (13300) covalent geometry : angle 0.68804 (18095) *********************** 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 170 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 125 time to evaluate : 1.995 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 163 GLU cc_start: 0.8160 (mp0) cc_final: 0.7767 (mp0) REVERT: A 187 GLN cc_start: 0.9153 (mt0) cc_final: 0.8633 (mm110) REVERT: A 248 LYS cc_start: 0.9295 (mttt) cc_final: 0.8975 (mmmt) REVERT: B 163 GLU cc_start: 0.8280 (mp0) cc_final: 0.8036 (mp0) REVERT: B 187 GLN cc_start: 0.9145 (mt0) cc_final: 0.8700 (mt0) REVERT: B 313 LEU cc_start: 0.9512 (mt) cc_final: 0.9304 (tp) REVERT: C 248 LYS cc_start: 0.9229 (mmmt) cc_final: 0.8893 (mmmm) REVERT: D 187 GLN cc_start: 0.9118 (mt0) cc_final: 0.8677 (mt0) REVERT: D 248 LYS cc_start: 0.9264 (mtmt) cc_final: 0.8941 (mttp) REVERT: E 187 GLN cc_start: 0.9123 (mt0) cc_final: 0.8668 (mt0) REVERT: E 248 LYS cc_start: 0.9326 (mmmt) cc_final: 0.9075 (mmmm) outliers start: 45 outliers final: 37 residues processed: 160 average time/residue: 1.6728 time to fit residues: 292.6121 Evaluate side-chains 150 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 113 time to evaluate : 1.525 ------------------------------------------------------------------------------- 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 212 SER Chi-restraints excluded: chain A residue 255 THR Chi-restraints excluded: chain B residue 18 VAL Chi-restraints excluded: chain B residue 94 VAL 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 94 VAL Chi-restraints excluded: chain C residue 174 PHE Chi-restraints excluded: chain C residue 177 GLU 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 177 GLU 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 Chi-restraints excluded: chain E residue 270 VAL 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 63 optimal weight: 7.9990 chunk 25 optimal weight: 0.8980 chunk 122 optimal weight: 8.9990 chunk 98 optimal weight: 7.9990 chunk 89 optimal weight: 6.9990 chunk 44 optimal weight: 9.9990 chunk 92 optimal weight: 6.9990 chunk 121 optimal weight: 6.9990 chunk 34 optimal weight: 9.9990 chunk 147 optimal weight: 0.6980 chunk 77 optimal weight: 10.0000 overall best weight: 4.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 19 ASN A 245 ASN B 19 ASN ** B 235 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 19 ASN D 19 ASN D 245 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.084508 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.059806 restraints weight = 40424.913| |-----------------------------------------------------------------------------| r_work (start): 0.3174 rms_B_bonded: 3.69 r_work: 0.3001 rms_B_bonded: 4.81 restraints_weight: 0.5000 r_work (final): 0.3001 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8623 moved from start: 0.4882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.060 13300 Z= 0.260 Angle : 0.720 9.142 18095 Z= 0.365 Chirality : 0.044 0.190 2040 Planarity : 0.004 0.032 2175 Dihedral : 18.270 89.786 2475 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 8.73 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.57 % Favored : 92.30 % Rotamer: Outliers : 3.62 % Allowed : 23.46 % 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: -0.22 (0.22), residues: 1545 helix: 2.24 (0.21), residues: 520 sheet: -1.33 (0.27), residues: 325 loop : -1.42 (0.25), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 213 HIS 0.006 0.002 HIS B 235 PHE 0.012 0.001 PHE D 37 TYR 0.011 0.001 TYR A 102 ARG 0.003 0.000 ARG D 109 Details of bonding type rmsd hydrogen bonds : bond 0.03692 ( 560) hydrogen bonds : angle 4.64138 ( 1725) covalent geometry : bond 0.00603 (13300) covalent geometry : angle 0.72004 (18095) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3090 Ramachandran restraints generated. 1545 Oldfield, 0 Emsley, 1545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3090 Ramachandran restraints generated. 1545 Oldfield, 0 Emsley, 1545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 116 time to evaluate : 1.395 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 163 GLU cc_start: 0.8216 (mp0) cc_final: 0.7804 (mp0) REVERT: B 163 GLU cc_start: 0.8283 (mp0) cc_final: 0.8036 (mp0) REVERT: B 187 GLN cc_start: 0.9153 (mt0) cc_final: 0.8692 (mt0) REVERT: B 248 LYS cc_start: 0.9330 (mmmt) cc_final: 0.8990 (mmmm) REVERT: C 248 LYS cc_start: 0.9254 (mmmt) cc_final: 0.8957 (mmmm) REVERT: D 187 GLN cc_start: 0.9111 (mt0) cc_final: 0.8666 (mt0) REVERT: D 248 LYS cc_start: 0.9249 (mtmt) cc_final: 0.8934 (mttp) REVERT: E 187 GLN cc_start: 0.9138 (mt0) cc_final: 0.8656 (mt0) REVERT: E 248 LYS cc_start: 0.9304 (mmmt) cc_final: 0.9067 (tmtt) outliers start: 44 outliers final: 34 residues processed: 150 average time/residue: 1.2295 time to fit residues: 201.4058 Evaluate side-chains 146 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 112 time to evaluate : 1.380 ------------------------------------------------------------------------------- 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 A residue 255 THR Chi-restraints excluded: chain B residue 18 VAL 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 177 GLU 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 177 GLU 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 270 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 93 optimal weight: 10.0000 chunk 8 optimal weight: 1.9990 chunk 63 optimal weight: 8.9990 chunk 2 optimal weight: 8.9990 chunk 111 optimal weight: 1.9990 chunk 34 optimal weight: 10.0000 chunk 57 optimal weight: 0.7980 chunk 132 optimal weight: 6.9990 chunk 79 optimal weight: 3.9990 chunk 94 optimal weight: 7.9990 chunk 122 optimal weight: 7.9990 overall best weight: 3.1588 ------------------------------------------------------------------------------- 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 D 245 ASN E 19 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.085022 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.060732 restraints weight = 39796.626| |-----------------------------------------------------------------------------| r_work (start): 0.3196 rms_B_bonded: 3.66 r_work: 0.3023 rms_B_bonded: 4.81 restraints_weight: 0.5000 r_work (final): 0.3023 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8606 moved from start: 0.5003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 13300 Z= 0.199 Angle : 0.713 10.538 18095 Z= 0.357 Chirality : 0.043 0.200 2040 Planarity : 0.004 0.033 2175 Dihedral : 17.997 89.684 2475 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.70 % Favored : 92.17 % Rotamer: Outliers : 3.05 % Allowed : 24.53 % 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: -0.14 (0.22), residues: 1545 helix: 2.29 (0.22), residues: 520 sheet: -1.28 (0.27), residues: 325 loop : -1.37 (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 B 235 PHE 0.012 0.001 PHE D 37 TYR 0.011 0.001 TYR E 102 ARG 0.003 0.000 ARG D 109 Details of bonding type rmsd hydrogen bonds : bond 0.03516 ( 560) hydrogen bonds : angle 4.57154 ( 1725) covalent geometry : bond 0.00477 (13300) covalent geometry : angle 0.71317 (18095) *********************** 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 153 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 116 time to evaluate : 1.344 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 163 GLU cc_start: 0.8202 (mp0) cc_final: 0.7776 (mp0) REVERT: A 187 GLN cc_start: 0.9145 (mt0) cc_final: 0.8637 (mm110) REVERT: A 248 LYS cc_start: 0.9315 (mmmt) cc_final: 0.9033 (mmmm) REVERT: B 163 GLU cc_start: 0.8289 (mp0) cc_final: 0.8034 (mp0) REVERT: B 187 GLN cc_start: 0.9135 (mt0) cc_final: 0.8681 (mt0) REVERT: B 248 LYS cc_start: 0.9275 (mmmt) cc_final: 0.8965 (mmmm) REVERT: C 248 LYS cc_start: 0.9254 (mmmt) cc_final: 0.8990 (mmmt) REVERT: D 187 GLN cc_start: 0.9097 (mt0) cc_final: 0.8644 (mt0) REVERT: D 248 LYS cc_start: 0.9260 (mtmt) cc_final: 0.8996 (mmmm) REVERT: E 187 GLN cc_start: 0.9143 (mt0) cc_final: 0.8669 (mt0) REVERT: E 248 LYS cc_start: 0.9304 (mmmt) cc_final: 0.9078 (tmtt) outliers start: 37 outliers final: 32 residues processed: 147 average time/residue: 1.2639 time to fit residues: 202.7219 Evaluate side-chains 141 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 109 time to evaluate : 1.482 ------------------------------------------------------------------------------- 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 212 SER Chi-restraints excluded: chain B residue 18 VAL 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 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 177 GLU 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 177 GLU 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 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 270 VAL 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 43 optimal weight: 9.9990 chunk 26 optimal weight: 0.6980 chunk 136 optimal weight: 0.8980 chunk 51 optimal weight: 0.9990 chunk 35 optimal weight: 20.0000 chunk 41 optimal weight: 5.9990 chunk 145 optimal weight: 1.9990 chunk 96 optimal weight: 9.9990 chunk 60 optimal weight: 7.9990 chunk 36 optimal weight: 9.9990 chunk 81 optimal weight: 0.8980 overall best weight: 1.0984 ------------------------------------------------------------------------------- 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 D 245 ASN E 19 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.085385 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.062286 restraints weight = 39324.344| |-----------------------------------------------------------------------------| r_work (start): 0.3244 rms_B_bonded: 3.51 r_work: 0.3069 rms_B_bonded: 4.65 restraints_weight: 0.5000 r_work (final): 0.3069 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8570 moved from start: 0.5086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 13300 Z= 0.140 Angle : 0.702 11.003 18095 Z= 0.353 Chirality : 0.043 0.223 2040 Planarity : 0.004 0.035 2175 Dihedral : 17.625 89.925 2475 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.50 % Favored : 94.37 % Rotamer: Outliers : 2.30 % Allowed : 25.10 % Favored : 72.59 % 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: -0.02 (0.22), residues: 1545 helix: 2.37 (0.22), residues: 520 sheet: -1.13 (0.28), residues: 325 loop : -1.32 (0.25), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 213 HIS 0.005 0.002 HIS B 235 PHE 0.015 0.001 PHE D 37 TYR 0.010 0.001 TYR B 102 ARG 0.004 0.000 ARG D 109 Details of bonding type rmsd hydrogen bonds : bond 0.03239 ( 560) hydrogen bonds : angle 4.36519 ( 1725) covalent geometry : bond 0.00349 (13300) covalent geometry : angle 0.70211 (18095) ********************** 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 159 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 131 time to evaluate : 1.362 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 163 GLU cc_start: 0.8219 (mp0) cc_final: 0.7783 (mp0) REVERT: A 187 GLN cc_start: 0.9116 (mt0) cc_final: 0.8640 (mm110) REVERT: A 248 LYS cc_start: 0.9279 (mmmt) cc_final: 0.8994 (mmmm) REVERT: B 163 GLU cc_start: 0.8335 (mp0) cc_final: 0.8065 (mp0) REVERT: B 187 GLN cc_start: 0.9100 (mt0) cc_final: 0.8648 (mt0) REVERT: B 248 LYS cc_start: 0.9260 (mmmt) cc_final: 0.8993 (mmmm) REVERT: C 248 LYS cc_start: 0.9259 (mmmt) cc_final: 0.9029 (mmmt) REVERT: D 187 GLN cc_start: 0.9031 (mt0) cc_final: 0.8582 (mt0) REVERT: D 245 ASN cc_start: 0.9101 (m-40) cc_final: 0.8695 (m110) REVERT: E 187 GLN cc_start: 0.9115 (mt0) cc_final: 0.8633 (mt0) REVERT: E 248 LYS cc_start: 0.9297 (mmmt) cc_final: 0.9050 (mmtt) outliers start: 28 outliers final: 23 residues processed: 152 average time/residue: 1.2126 time to fit residues: 201.7264 Evaluate side-chains 141 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 118 time to evaluate : 1.513 ------------------------------------------------------------------------------- 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 212 SER 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 177 GLU 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 177 GLU Chi-restraints excluded: chain D residue 212 SER Chi-restraints excluded: chain E residue 18 VAL Chi-restraints excluded: chain E residue 36 THR Chi-restraints excluded: chain E residue 94 VAL Chi-restraints excluded: chain E residue 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 89 optimal weight: 6.9990 chunk 86 optimal weight: 9.9990 chunk 38 optimal weight: 0.6980 chunk 18 optimal weight: 8.9990 chunk 115 optimal weight: 0.7980 chunk 24 optimal weight: 3.9990 chunk 93 optimal weight: 10.0000 chunk 141 optimal weight: 2.9990 chunk 136 optimal weight: 5.9990 chunk 33 optimal weight: 4.9990 chunk 21 optimal weight: 10.0000 overall best weight: 2.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 19 ASN A 245 ASN B 19 ASN C 19 ASN D 19 ASN E 19 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.084376 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.061182 restraints weight = 39895.010| |-----------------------------------------------------------------------------| r_work (start): 0.3217 rms_B_bonded: 3.54 r_work: 0.3040 rms_B_bonded: 4.67 restraints_weight: 0.5000 r_work (final): 0.3040 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8600 moved from start: 0.5211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 13300 Z= 0.184 Angle : 0.708 10.183 18095 Z= 0.356 Chirality : 0.043 0.195 2040 Planarity : 0.004 0.036 2175 Dihedral : 17.476 89.749 2475 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.28 % Favored : 93.59 % Rotamer: Outliers : 2.06 % Allowed : 26.42 % Favored : 71.52 % 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: -0.06 (0.22), residues: 1545 helix: 2.29 (0.21), residues: 520 sheet: -1.14 (0.28), residues: 325 loop : -1.31 (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 D 235 PHE 0.015 0.001 PHE D 165 TYR 0.010 0.001 TYR B 102 ARG 0.007 0.000 ARG E 109 Details of bonding type rmsd hydrogen bonds : bond 0.03341 ( 560) hydrogen bonds : angle 4.40381 ( 1725) covalent geometry : bond 0.00448 (13300) covalent geometry : angle 0.70827 (18095) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8787.91 seconds wall clock time: 157 minutes 33.82 seconds (9453.82 seconds total)