Starting phenix.real_space_refine on Sat Aug 23 08:23:05 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wbg_37424/08_2025/8wbg_37424_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wbg_37424/08_2025/8wbg_37424.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8wbg_37424/08_2025/8wbg_37424.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wbg_37424/08_2025/8wbg_37424.map" model { file = "/net/cci-nas-00/data/ceres_data/8wbg_37424/08_2025/8wbg_37424_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wbg_37424/08_2025/8wbg_37424_neut.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.086 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 80 5.16 5 C 6811 2.51 5 N 1947 2.21 5 O 2016 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 10854 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 2819 Number of conformers: 1 Conformer: "" Number of residues, atoms: 352, 2819 Classifications: {'peptide': 352} Link IDs: {'PCIS': 2, 'PTRANS': 17, 'TRANS': 332} Chain: "B" Number of atoms: 2759 Number of conformers: 1 Conformer: "" Number of residues, atoms: 345, 2759 Classifications: {'peptide': 345} Link IDs: {'PCIS': 2, 'PTRANS': 17, 'TRANS': 325} Chain breaks: 1 Chain: "a" Number of atoms: 2638 Number of conformers: 1 Conformer: "" Number of residues, atoms: 330, 2638 Classifications: {'peptide': 330} Link IDs: {'PCIS': 2, 'PTRANS': 16, 'TRANS': 311} Chain breaks: 1 Chain: "b" Number of atoms: 2638 Number of conformers: 1 Conformer: "" Number of residues, atoms: 330, 2638 Classifications: {'peptide': 330} Link IDs: {'PCIS': 2, 'PTRANS': 16, 'TRANS': 311} Chain breaks: 1 Time building chain proxies: 2.69, per 1000 atoms: 0.25 Number of scatterers: 10854 At special positions: 0 Unit cell: (109.65, 121.55, 111.35, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 80 16.00 O 2016 8.00 N 1947 7.00 C 6811 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=24, symmetry=0 Simple disulfide: pdb=" SG CYS A 4 " - pdb=" SG CYS A 15 " distance=2.03 Simple disulfide: pdb=" SG CYS A 55 " - pdb=" SG CYS A 143 " distance=2.03 Simple disulfide: pdb=" SG CYS A 179 " - pdb=" SG CYS A 223 " distance=2.03 Simple disulfide: pdb=" SG CYS A 280 " - pdb=" SG CYS A 329 " distance=2.02 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 312 " distance=2.04 Simple disulfide: pdb=" SG CYS A 313 " - pdb=" SG CYS A 316 " distance=2.03 Simple disulfide: pdb=" SG CYS B 4 " - pdb=" SG CYS B 15 " distance=2.03 Simple disulfide: pdb=" SG CYS B 55 " - pdb=" SG CYS B 143 " distance=2.03 Simple disulfide: pdb=" SG CYS B 179 " - pdb=" SG CYS B 223 " distance=2.03 Simple disulfide: pdb=" SG CYS B 280 " - pdb=" SG CYS B 329 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 312 " distance=2.04 Simple disulfide: pdb=" SG CYS B 313 " - pdb=" SG CYS B 316 " distance=2.03 Simple disulfide: pdb=" SG CYS a 4 " - pdb=" SG CYS a 15 " distance=2.03 Simple disulfide: pdb=" SG CYS a 55 " - pdb=" SG CYS a 143 " distance=2.03 Simple disulfide: pdb=" SG CYS a 179 " - pdb=" SG CYS a 223 " distance=2.03 Simple disulfide: pdb=" SG CYS a 280 " - pdb=" SG CYS a 329 " distance=2.03 Simple disulfide: pdb=" SG CYS a 291 " - pdb=" SG CYS a 312 " distance=2.03 Simple disulfide: pdb=" SG CYS a 313 " - pdb=" SG CYS a 316 " distance=2.03 Simple disulfide: pdb=" SG CYS b 4 " - pdb=" SG CYS b 15 " distance=2.03 Simple disulfide: pdb=" SG CYS b 55 " - pdb=" SG CYS b 143 " distance=2.03 Simple disulfide: pdb=" SG CYS b 179 " - pdb=" SG CYS b 223 " distance=2.03 Simple disulfide: pdb=" SG CYS b 280 " - pdb=" SG CYS b 329 " distance=2.03 Simple disulfide: pdb=" SG CYS b 291 " - pdb=" SG CYS b 312 " distance=2.03 Simple disulfide: pdb=" SG CYS b 313 " - pdb=" SG CYS b 316 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.71 Conformation dependent library (CDL) restraints added in 304.8 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 2686 Ramachandran restraints generated. 1343 Oldfield, 0 Emsley, 1343 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2506 Finding SS restraints... Secondary structure from input PDB file: 31 helices and 18 sheets defined 19.0% alpha, 19.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.30 Creating SS restraints... Processing helix chain 'A' and resid 38 through 53 removed outlier: 4.086A pdb=" N ALA A 44 " --> pdb=" O ARG A 40 " (cutoff:3.500A) Processing helix chain 'A' and resid 61 through 82 removed outlier: 4.923A pdb=" N GLY A 73 " --> pdb=" O ARG A 69 " (cutoff:3.500A) removed outlier: 5.709A pdb=" N GLU A 74 " --> pdb=" O SER A 70 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N ASN A 82 " --> pdb=" O ILE A 78 " (cutoff:3.500A) Processing helix chain 'A' and resid 144 through 146 No H-bonds generated for 'chain 'A' and resid 144 through 146' Processing helix chain 'A' and resid 226 through 230 Processing helix chain 'A' and resid 237 through 241 removed outlier: 3.529A pdb=" N LEU A 241 " --> pdb=" O GLU A 238 " (cutoff:3.500A) Processing helix chain 'A' and resid 244 through 248 Processing helix chain 'A' and resid 252 through 256 removed outlier: 3.681A pdb=" N THR A 256 " --> pdb=" O HIS A 253 " (cutoff:3.500A) Processing helix chain 'A' and resid 341 through 345 removed outlier: 3.544A pdb=" N ASN A 344 " --> pdb=" O PRO A 341 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N LEU A 345 " --> pdb=" O GLU A 342 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 341 through 345' Processing helix chain 'B' and resid 38 through 52 removed outlier: 3.615A pdb=" N ALA B 43 " --> pdb=" O PRO B 39 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N ALA B 44 " --> pdb=" O ARG B 40 " (cutoff:3.500A) Processing helix chain 'B' and resid 61 through 71 Processing helix chain 'B' and resid 71 through 83 removed outlier: 3.661A pdb=" N GLU B 80 " --> pdb=" O ASN B 76 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N GLU B 81 " --> pdb=" O ALA B 77 " (cutoff:3.500A) Processing helix chain 'B' and resid 226 through 230 Processing helix chain 'B' and resid 237 through 241 Processing helix chain 'B' and resid 244 through 248 Processing helix chain 'B' and resid 252 through 256 Processing helix chain 'B' and resid 341 through 345 removed outlier: 4.066A pdb=" N ASN B 344 " --> pdb=" O PRO B 341 " (cutoff:3.500A) Processing helix chain 'a' and resid 38 through 52 Processing helix chain 'a' and resid 61 through 82 removed outlier: 4.828A pdb=" N GLY a 73 " --> pdb=" O ARG a 69 " (cutoff:3.500A) removed outlier: 5.113A pdb=" N GLU a 74 " --> pdb=" O SER a 70 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ALA a 77 " --> pdb=" O GLY a 73 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N GLU a 80 " --> pdb=" O ASN a 76 " (cutoff:3.500A) Processing helix chain 'a' and resid 144 through 146 No H-bonds generated for 'chain 'a' and resid 144 through 146' Processing helix chain 'a' and resid 226 through 230 Processing helix chain 'a' and resid 237 through 241 Processing helix chain 'a' and resid 244 through 248 Processing helix chain 'a' and resid 252 through 256 Processing helix chain 'a' and resid 341 through 345 Processing helix chain 'b' and resid 24 through 28 removed outlier: 3.597A pdb=" N TRP b 28 " --> pdb=" O VAL b 25 " (cutoff:3.500A) Processing helix chain 'b' and resid 38 through 53 Processing helix chain 'b' and resid 61 through 82 removed outlier: 4.368A pdb=" N GLY b 73 " --> pdb=" O ARG b 69 " (cutoff:3.500A) removed outlier: 4.703A pdb=" N GLU b 74 " --> pdb=" O SER b 70 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ASN b 76 " --> pdb=" O GLU b 72 " (cutoff:3.500A) removed outlier: 5.523A pdb=" N ALA b 77 " --> pdb=" O GLY b 73 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N ILE b 78 " --> pdb=" O GLU b 74 " (cutoff:3.500A) Processing helix chain 'b' and resid 226 through 230 Processing helix chain 'b' and resid 237 through 241 removed outlier: 3.611A pdb=" N LEU b 241 " --> pdb=" O GLU b 238 " (cutoff:3.500A) Processing helix chain 'b' and resid 244 through 248 removed outlier: 3.659A pdb=" N ALA b 248 " --> pdb=" O LYS b 245 " (cutoff:3.500A) Processing helix chain 'b' and resid 252 through 256 removed outlier: 3.501A pdb=" N THR b 256 " --> pdb=" O HIS b 253 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 2 through 7 removed outlier: 3.531A pdb=" N ASP A 7 " --> pdb=" O GLU A 12 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N GLU A 12 " --> pdb=" O ASP A 7 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N VAL a 2 " --> pdb=" O VAL A 6 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 32 through 36 removed outlier: 6.672A pdb=" N SER A 166 " --> pdb=" O HIS A 158 " (cutoff:3.500A) removed outlier: 4.899A pdb=" N HIS A 158 " --> pdb=" O SER A 166 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N TRP A 168 " --> pdb=" O GLU A 156 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 56 through 57 removed outlier: 7.118A pdb=" N GLY A 56 " --> pdb=" O ALA A 149 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 87 through 90 removed outlier: 6.509A pdb=" N THR A 87 " --> pdb=" O PHE A 133 " (cutoff:3.500A) removed outlier: 7.288A pdb=" N VAL A 135 " --> pdb=" O THR A 87 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N VAL A 89 " --> pdb=" O VAL A 135 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 329 through 331 removed outlier: 3.616A pdb=" N GLU A 274 " --> pdb=" O ARG A 324 " (cutoff:3.500A) removed outlier: 7.128A pdb=" N GLU A 203 " --> pdb=" O LYS A 213 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N ALA A 215 " --> pdb=" O TRP A 201 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N TRP A 201 " --> pdb=" O ALA A 215 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ALA A 193 " --> pdb=" O SER A 204 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ALA a 193 " --> pdb=" O SER a 204 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N ARG a 214 " --> pdb=" O GLU a 203 " (cutoff:3.500A) removed outlier: 5.848A pdb=" N GLU a 205 " --> pdb=" O LEU a 212 " (cutoff:3.500A) removed outlier: 5.597A pdb=" N LEU a 212 " --> pdb=" O GLU a 205 " (cutoff:3.500A) removed outlier: 8.979A pdb=" N LYS a 213 " --> pdb=" O PHE a 277 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N PHE a 277 " --> pdb=" O LYS a 213 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N GLU a 274 " --> pdb=" O ARG a 324 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N PHE a 323 " --> pdb=" O TRP a 330 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 284 through 287 Processing sheet with id=AA7, first strand: chain 'B' and resid 2 through 7 removed outlier: 3.659A pdb=" N GLU B 12 " --> pdb=" O ASP B 7 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N GLU b 12 " --> pdb=" O ASP b 7 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N VAL b 2 " --> pdb=" O VAL B 6 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 34 through 35 removed outlier: 3.658A pdb=" N HIS B 35 " --> pdb=" O VAL B 167 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 328 through 331 removed outlier: 3.748A pdb=" N GLU B 274 " --> pdb=" O ARG B 324 " (cutoff:3.500A) removed outlier: 5.820A pdb=" N LEU B 212 " --> pdb=" O GLU B 205 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N GLU B 205 " --> pdb=" O LEU B 212 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ARG B 214 " --> pdb=" O GLU B 203 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N ALA B 193 " --> pdb=" O SER B 204 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N GLU b 192 " --> pdb=" O LYS b 189 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N SER b 204 " --> pdb=" O ALA b 193 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ARG b 214 " --> pdb=" O GLU b 203 " (cutoff:3.500A) removed outlier: 5.535A pdb=" N GLU b 205 " --> pdb=" O LEU b 212 " (cutoff:3.500A) removed outlier: 5.427A pdb=" N LEU b 212 " --> pdb=" O GLU b 205 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 311 through 313 Processing sheet with id=AB2, first strand: chain 'a' and resid 33 through 36 removed outlier: 6.109A pdb=" N LYS a 33 " --> pdb=" O VAL a 167 " (cutoff:3.500A) removed outlier: 7.213A pdb=" N LEU a 169 " --> pdb=" O LYS a 33 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N HIS a 35 " --> pdb=" O LEU a 169 " (cutoff:3.500A) removed outlier: 8.475A pdb=" N VAL a 171 " --> pdb=" O HIS a 35 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'a' and resid 56 through 58 Processing sheet with id=AB4, first strand: chain 'a' and resid 88 through 89 Processing sheet with id=AB5, first strand: chain 'a' and resid 284 through 287 Processing sheet with id=AB6, first strand: chain 'b' and resid 87 through 89 Processing sheet with id=AB7, first strand: chain 'b' and resid 153 through 154 Processing sheet with id=AB8, first strand: chain 'b' and resid 284 through 287 removed outlier: 3.787A pdb=" N TRP b 311 " --> pdb=" O LYS b 284 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N CYS b 313 " --> pdb=" O HIS b 286 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'b' and resid 298 through 299 removed outlier: 3.634A pdb=" N LEU b 298 " --> pdb=" O TYR b 331 " (cutoff:3.500A) 295 hydrogen bonds defined for protein. 726 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: 1.21 Time building geometry restraints manager: 0.96 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 3609 1.35 - 1.47: 2674 1.47 - 1.59: 4750 1.59 - 1.71: 0 1.71 - 1.83: 112 Bond restraints: 11145 Sorted by residual: bond pdb=" N VAL b 162 " pdb=" CA VAL b 162 " ideal model delta sigma weight residual 1.457 1.495 -0.038 1.15e-02 7.56e+03 1.11e+01 bond pdb=" N VAL A 25 " pdb=" CA VAL A 25 " ideal model delta sigma weight residual 1.459 1.497 -0.038 1.25e-02 6.40e+03 9.13e+00 bond pdb=" N PHE b 160 " pdb=" CA PHE b 160 " ideal model delta sigma weight residual 1.458 1.488 -0.031 1.30e-02 5.92e+03 5.59e+00 bond pdb=" N ASP A 24 " pdb=" CA ASP A 24 " ideal model delta sigma weight residual 1.460 1.493 -0.033 1.42e-02 4.96e+03 5.42e+00 bond pdb=" N ASN a 207 " pdb=" CA ASN a 207 " ideal model delta sigma weight residual 1.457 1.487 -0.030 1.29e-02 6.01e+03 5.42e+00 ... (remaining 11140 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.32: 14516 1.32 - 2.65: 479 2.65 - 3.97: 95 3.97 - 5.29: 14 5.29 - 6.62: 2 Bond angle restraints: 15106 Sorted by residual: angle pdb=" N ASP A 208 " pdb=" CA ASP A 208 " pdb=" C ASP A 208 " ideal model delta sigma weight residual 112.72 107.72 5.00 1.28e+00 6.10e-01 1.52e+01 angle pdb=" CA TRP A 28 " pdb=" C TRP A 28 " pdb=" N ARG A 29 " ideal model delta sigma weight residual 118.13 123.11 -4.98 1.28e+00 6.10e-01 1.51e+01 angle pdb=" N ILE b 242 " pdb=" CA ILE b 242 " pdb=" C ILE b 242 " ideal model delta sigma weight residual 111.48 107.94 3.54 9.40e-01 1.13e+00 1.42e+01 angle pdb=" CA ASP A 24 " pdb=" C ASP A 24 " pdb=" O ASP A 24 " ideal model delta sigma weight residual 122.27 117.95 4.32 1.16e+00 7.43e-01 1.39e+01 angle pdb=" C ASN a 207 " pdb=" CA ASN a 207 " pdb=" CB ASN a 207 " ideal model delta sigma weight residual 110.42 117.04 -6.62 1.99e+00 2.53e-01 1.11e+01 ... (remaining 15101 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.60: 6135 17.60 - 35.19: 444 35.19 - 52.79: 91 52.79 - 70.39: 24 70.39 - 87.98: 7 Dihedral angle restraints: 6701 sinusoidal: 2816 harmonic: 3885 Sorted by residual: dihedral pdb=" CB CYS b 291 " pdb=" SG CYS b 291 " pdb=" SG CYS b 312 " pdb=" CB CYS b 312 " ideal model delta sinusoidal sigma weight residual -86.00 -173.98 87.98 1 1.00e+01 1.00e-02 9.26e+01 dihedral pdb=" CB CYS b 313 " pdb=" SG CYS b 313 " pdb=" SG CYS b 316 " pdb=" CB CYS b 316 " ideal model delta sinusoidal sigma weight residual -86.00 -151.55 65.55 1 1.00e+01 1.00e-02 5.63e+01 dihedral pdb=" CB CYS a 313 " pdb=" SG CYS a 313 " pdb=" SG CYS a 316 " pdb=" CB CYS a 316 " ideal model delta sinusoidal sigma weight residual 93.00 156.86 -63.86 1 1.00e+01 1.00e-02 5.37e+01 ... (remaining 6698 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 1235 0.043 - 0.085: 214 0.085 - 0.128: 126 0.128 - 0.170: 7 0.170 - 0.213: 2 Chirality restraints: 1584 Sorted by residual: chirality pdb=" CA VAL A 25 " pdb=" N VAL A 25 " pdb=" C VAL A 25 " pdb=" CB VAL A 25 " both_signs ideal model delta sigma weight residual False 2.44 2.65 -0.21 2.00e-01 2.50e+01 1.13e+00 chirality pdb=" CA VAL b 162 " pdb=" N VAL b 162 " pdb=" C VAL b 162 " pdb=" CB VAL b 162 " both_signs ideal model delta sigma weight residual False 2.44 2.64 -0.20 2.00e-01 2.50e+01 1.01e+00 chirality pdb=" CB VAL A 25 " pdb=" CA VAL A 25 " pdb=" CG1 VAL A 25 " pdb=" CG2 VAL A 25 " both_signs ideal model delta sigma weight residual False -2.63 -2.47 -0.16 2.00e-01 2.50e+01 6.55e-01 ... (remaining 1581 not shown) Planarity restraints: 1945 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY A 100 " 0.031 5.00e-02 4.00e+02 4.72e-02 3.56e+00 pdb=" N PRO A 101 " -0.082 5.00e-02 4.00e+02 pdb=" CA PRO A 101 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO A 101 " 0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASP a 208 " 0.008 2.00e-02 2.50e+03 1.67e-02 2.78e+00 pdb=" C ASP a 208 " -0.029 2.00e-02 2.50e+03 pdb=" O ASP a 208 " 0.011 2.00e-02 2.50e+03 pdb=" N THR a 209 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASN b 95 " 0.025 5.00e-02 4.00e+02 3.73e-02 2.22e+00 pdb=" N PRO b 96 " -0.064 5.00e-02 4.00e+02 pdb=" CA PRO b 96 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO b 96 " 0.019 5.00e-02 4.00e+02 ... (remaining 1942 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 837 2.74 - 3.28: 10584 3.28 - 3.82: 16278 3.82 - 4.36: 20013 4.36 - 4.90: 36068 Nonbonded interactions: 83780 Sorted by model distance: nonbonded pdb=" OG SER B 322 " pdb=" NH1 ARG B 324 " model vdw 2.197 3.120 nonbonded pdb=" NH1 ARG b 299 " pdb=" O THR b 301 " model vdw 2.206 3.120 nonbonded pdb=" OG SER B 61 " pdb=" OE1 GLU B 219 " model vdw 2.228 3.040 nonbonded pdb=" OE2 GLU a 72 " pdb=" ND2 ASN a 76 " model vdw 2.236 3.120 nonbonded pdb=" OG SER b 322 " pdb=" NH1 ARG b 324 " model vdw 2.243 3.120 ... (remaining 83775 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 1 through 107 or resid 130 through 352)) selection = (chain 'B' and (resid 1 through 107 or resid 130 through 352)) selection = chain 'a' selection = chain 'b' } 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: 1.330 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.210 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 8.990 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.010 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:0.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.600 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7406 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 : 0.003 0.038 11169 Z= 0.154 Angle : 0.585 6.617 15154 Z= 0.344 Chirality : 0.042 0.213 1584 Planarity : 0.004 0.047 1945 Dihedral : 13.023 87.838 4123 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.99 % Favored : 94.86 % Rotamer: Outliers : 0.17 % Allowed : 0.17 % Favored : 99.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.81 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.10 (0.24), residues: 1343 helix: 1.10 (0.44), residues: 148 sheet: -1.73 (0.36), residues: 225 loop : -0.78 (0.21), residues: 970 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG a 338 TYR 0.010 0.001 TYR B 32 PHE 0.011 0.001 PHE A 123 TRP 0.023 0.001 TRP a 232 HIS 0.004 0.001 HIS b 254 Details of bonding type rmsd covalent geometry : bond 0.00280 (11145) covalent geometry : angle 0.58232 (15106) SS BOND : bond 0.00253 ( 24) SS BOND : angle 1.22673 ( 48) hydrogen bonds : bond 0.22758 ( 295) hydrogen bonds : angle 8.92144 ( 726) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2686 Ramachandran restraints generated. 1343 Oldfield, 0 Emsley, 1343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2686 Ramachandran restraints generated. 1343 Oldfield, 0 Emsley, 1343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1189 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 204 time to evaluate : 0.370 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 ARG cc_start: 0.8195 (tpp80) cc_final: 0.7669 (tpp80) REVERT: A 52 ASP cc_start: 0.6183 (t0) cc_final: 0.5978 (t0) REVERT: A 156 GLU cc_start: 0.7451 (pt0) cc_final: 0.7195 (pt0) REVERT: A 274 GLU cc_start: 0.8077 (tt0) cc_final: 0.7687 (mt-10) REVERT: a 207 ASN cc_start: 0.7381 (t0) cc_final: 0.6815 (t0) REVERT: a 208 ASP cc_start: 0.7873 (OUTLIER) cc_final: 0.6865 (t0) REVERT: a 251 LEU cc_start: 0.8657 (mp) cc_final: 0.8389 (mp) REVERT: a 311 TRP cc_start: 0.6507 (m100) cc_final: 0.6063 (m100) REVERT: a 315 GLU cc_start: 0.8065 (tt0) cc_final: 0.7557 (tp30) REVERT: b 67 MET cc_start: 0.6248 (tmm) cc_final: 0.6040 (tmm) REVERT: b 330 TRP cc_start: 0.6650 (m100) cc_final: 0.6196 (m-10) outliers start: 2 outliers final: 0 residues processed: 204 average time/residue: 0.1095 time to fit residues: 30.2244 Evaluate side-chains 121 residues out of total 1189 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 120 time to evaluate : 0.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 208 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 98 optimal weight: 9.9990 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 0.8980 chunk 66 optimal weight: 5.9990 chunk 130 optimal weight: 5.9990 chunk 124 optimal weight: 0.7980 chunk 103 optimal weight: 5.9990 chunk 77 optimal weight: 0.0050 chunk 122 optimal weight: 0.0570 chunk 91 optimal weight: 4.9990 chunk 55 optimal weight: 8.9990 overall best weight: 0.9514 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 48 GLN A 207 ASN B 35 HIS ** B 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 82 ASN a 76 ASN a 207 ASN b 35 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4389 r_free = 0.4389 target = 0.211759 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4023 r_free = 0.4023 target = 0.170529 restraints weight = 12184.742| |-----------------------------------------------------------------------------| r_work (start): 0.4004 rms_B_bonded: 3.32 r_work: 0.3735 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.3735 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7485 moved from start: 0.1601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 11169 Z= 0.132 Angle : 0.590 7.703 15154 Z= 0.313 Chirality : 0.043 0.168 1584 Planarity : 0.004 0.047 1945 Dihedral : 4.976 50.529 1478 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.10 % Favored : 95.76 % Rotamer: Outliers : 1.35 % Allowed : 6.64 % Favored : 92.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.81 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.97 (0.24), residues: 1343 helix: 1.43 (0.43), residues: 153 sheet: -1.69 (0.32), residues: 284 loop : -0.63 (0.22), residues: 906 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 261 TYR 0.014 0.001 TYR a 331 PHE 0.025 0.002 PHE B 277 TRP 0.019 0.001 TRP a 232 HIS 0.004 0.001 HIS b 254 Details of bonding type rmsd covalent geometry : bond 0.00307 (11145) covalent geometry : angle 0.58467 (15106) SS BOND : bond 0.00232 ( 24) SS BOND : angle 1.46986 ( 48) hydrogen bonds : bond 0.04029 ( 295) hydrogen bonds : angle 6.33710 ( 726) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2686 Ramachandran restraints generated. 1343 Oldfield, 0 Emsley, 1343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2686 Ramachandran restraints generated. 1343 Oldfield, 0 Emsley, 1343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1189 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 138 time to evaluate : 0.295 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 89 VAL cc_start: 0.8333 (p) cc_final: 0.8093 (m) REVERT: A 274 GLU cc_start: 0.8110 (tt0) cc_final: 0.7291 (mt-10) REVERT: A 333 MET cc_start: 0.6153 (OUTLIER) cc_final: 0.5564 (mtp) REVERT: B 339 LYS cc_start: 0.7389 (pttm) cc_final: 0.6787 (ptmm) REVERT: a 208 ASP cc_start: 0.8145 (OUTLIER) cc_final: 0.7933 (p0) REVERT: a 251 LEU cc_start: 0.8696 (mp) cc_final: 0.8461 (mp) REVERT: a 315 GLU cc_start: 0.8195 (tt0) cc_final: 0.7681 (tp30) REVERT: b 67 MET cc_start: 0.5846 (tmm) cc_final: 0.5584 (tmm) outliers start: 16 outliers final: 11 residues processed: 147 average time/residue: 0.0993 time to fit residues: 20.4382 Evaluate side-chains 129 residues out of total 1189 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 116 time to evaluate : 0.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 SER Chi-restraints excluded: chain A residue 333 MET Chi-restraints excluded: chain B residue 57 ILE Chi-restraints excluded: chain B residue 220 MET Chi-restraints excluded: chain B residue 283 THR Chi-restraints excluded: chain a residue 208 ASP Chi-restraints excluded: chain a residue 287 VAL Chi-restraints excluded: chain b residue 5 SER Chi-restraints excluded: chain b residue 7 ASP Chi-restraints excluded: chain b residue 13 THR Chi-restraints excluded: chain b residue 209 THR Chi-restraints excluded: chain b residue 252 SER Chi-restraints excluded: chain b residue 283 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 107 optimal weight: 4.9990 chunk 4 optimal weight: 1.9990 chunk 81 optimal weight: 0.6980 chunk 46 optimal weight: 10.0000 chunk 102 optimal weight: 7.9990 chunk 134 optimal weight: 9.9990 chunk 76 optimal weight: 9.9990 chunk 9 optimal weight: 4.9990 chunk 82 optimal weight: 4.9990 chunk 3 optimal weight: 3.9990 chunk 7 optimal weight: 2.9990 overall best weight: 2.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 254 HIS ** b 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 269 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4327 r_free = 0.4327 target = 0.204323 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.163275 restraints weight = 12411.761| |-----------------------------------------------------------------------------| r_work (start): 0.3928 rms_B_bonded: 3.35 r_work: 0.3651 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.3651 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7608 moved from start: 0.2118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.076 11169 Z= 0.248 Angle : 0.696 10.961 15154 Z= 0.365 Chirality : 0.047 0.246 1584 Planarity : 0.005 0.047 1945 Dihedral : 5.368 50.786 1478 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.48 % Favored : 93.45 % Rotamer: Outliers : 2.44 % Allowed : 8.92 % Favored : 88.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.81 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.34 (0.23), residues: 1343 helix: 0.98 (0.42), residues: 159 sheet: -1.77 (0.32), residues: 279 loop : -0.95 (0.21), residues: 905 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG b 336 TYR 0.019 0.002 TYR B 34 PHE 0.023 0.002 PHE B 277 TRP 0.026 0.002 TRP a 232 HIS 0.008 0.002 HIS b 254 Details of bonding type rmsd covalent geometry : bond 0.00604 (11145) covalent geometry : angle 0.68419 (15106) SS BOND : bond 0.00448 ( 24) SS BOND : angle 2.36087 ( 48) hydrogen bonds : bond 0.04651 ( 295) hydrogen bonds : angle 6.39173 ( 726) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2686 Ramachandran restraints generated. 1343 Oldfield, 0 Emsley, 1343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2686 Ramachandran restraints generated. 1343 Oldfield, 0 Emsley, 1343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1189 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 132 time to evaluate : 0.387 Fit side-chains revert: symmetry clash REVERT: A 12 GLU cc_start: 0.7561 (mm-30) cc_final: 0.7291 (mp0) REVERT: A 97 MET cc_start: 0.8449 (mtm) cc_final: 0.8128 (mtt) REVERT: A 324 ARG cc_start: 0.8405 (mpt180) cc_final: 0.7953 (mmt-90) REVERT: B 333 MET cc_start: 0.7039 (mtt) cc_final: 0.6679 (mtm) REVERT: B 339 LYS cc_start: 0.7342 (pttm) cc_final: 0.6935 (ptmm) REVERT: a 34 TYR cc_start: 0.7551 (m-80) cc_final: 0.7331 (m-80) REVERT: a 69 ARG cc_start: 0.7176 (ptp-170) cc_final: 0.6729 (tpp80) REVERT: a 146 LYS cc_start: 0.8123 (mtpt) cc_final: 0.7847 (mmtt) REVERT: a 208 ASP cc_start: 0.8320 (OUTLIER) cc_final: 0.8107 (p0) REVERT: a 311 TRP cc_start: 0.6782 (m100) cc_final: 0.6365 (m100) REVERT: b 67 MET cc_start: 0.6041 (tmm) cc_final: 0.5692 (tmm) outliers start: 29 outliers final: 21 residues processed: 149 average time/residue: 0.0947 time to fit residues: 19.9715 Evaluate side-chains 141 residues out of total 1189 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 119 time to evaluate : 0.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 GLU Chi-restraints excluded: chain A residue 59 SER Chi-restraints excluded: chain A residue 139 THR Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 165 THR Chi-restraints excluded: chain A residue 218 ILE Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain B residue 57 ILE Chi-restraints excluded: chain B residue 220 MET Chi-restraints excluded: chain B residue 283 THR Chi-restraints excluded: chain a residue 13 THR Chi-restraints excluded: chain a residue 93 VAL Chi-restraints excluded: chain a residue 208 ASP Chi-restraints excluded: chain a residue 287 VAL Chi-restraints excluded: chain b residue 5 SER Chi-restraints excluded: chain b residue 7 ASP Chi-restraints excluded: chain b residue 13 THR Chi-restraints excluded: chain b residue 17 THR Chi-restraints excluded: chain b residue 71 VAL Chi-restraints excluded: chain b residue 209 THR Chi-restraints excluded: chain b residue 252 SER Chi-restraints excluded: chain b residue 283 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 57 optimal weight: 0.7980 chunk 119 optimal weight: 1.9990 chunk 39 optimal weight: 9.9990 chunk 40 optimal weight: 9.9990 chunk 95 optimal weight: 9.9990 chunk 118 optimal weight: 0.9980 chunk 46 optimal weight: 0.0270 chunk 10 optimal weight: 0.7980 chunk 105 optimal weight: 3.9990 chunk 125 optimal weight: 7.9990 chunk 74 optimal weight: 8.9990 overall best weight: 0.9240 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 95 ASN a 344 ASN b 95 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4365 r_free = 0.4365 target = 0.208648 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.167889 restraints weight = 12347.303| |-----------------------------------------------------------------------------| r_work (start): 0.3985 rms_B_bonded: 3.30 r_work: 0.3704 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.3704 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7526 moved from start: 0.2383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 11169 Z= 0.118 Angle : 0.571 14.338 15154 Z= 0.298 Chirality : 0.042 0.220 1584 Planarity : 0.004 0.038 1945 Dihedral : 4.787 49.355 1478 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.62 % Favored : 95.31 % Rotamer: Outliers : 2.19 % Allowed : 11.27 % Favored : 86.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.81 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.26 (0.23), residues: 1343 helix: 1.13 (0.42), residues: 159 sheet: -1.81 (0.32), residues: 287 loop : -0.86 (0.21), residues: 897 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 40 TYR 0.012 0.001 TYR A 331 PHE 0.020 0.001 PHE B 277 TRP 0.013 0.001 TRP a 330 HIS 0.004 0.001 HIS b 254 Details of bonding type rmsd covalent geometry : bond 0.00280 (11145) covalent geometry : angle 0.56473 (15106) SS BOND : bond 0.00408 ( 24) SS BOND : angle 1.63523 ( 48) hydrogen bonds : bond 0.03424 ( 295) hydrogen bonds : angle 5.83340 ( 726) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2686 Ramachandran restraints generated. 1343 Oldfield, 0 Emsley, 1343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2686 Ramachandran restraints generated. 1343 Oldfield, 0 Emsley, 1343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1189 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 133 time to evaluate : 0.273 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 12 GLU cc_start: 0.7362 (mm-30) cc_final: 0.7123 (mp0) REVERT: A 40 ARG cc_start: 0.8330 (tpp80) cc_final: 0.7966 (tpp80) REVERT: B 54 ILE cc_start: 0.6335 (mp) cc_final: 0.6117 (mp) REVERT: B 186 THR cc_start: 0.8640 (OUTLIER) cc_final: 0.8308 (m) REVERT: B 333 MET cc_start: 0.6622 (mtt) cc_final: 0.6310 (mtm) REVERT: B 339 LYS cc_start: 0.7395 (pttm) cc_final: 0.7056 (ptmm) REVERT: a 146 LYS cc_start: 0.8148 (mtpt) cc_final: 0.7852 (mmtt) REVERT: a 208 ASP cc_start: 0.8257 (OUTLIER) cc_final: 0.8017 (p0) REVERT: a 333 MET cc_start: 0.8130 (mmp) cc_final: 0.6919 (mmm) REVERT: b 67 MET cc_start: 0.5835 (tmm) cc_final: 0.5543 (tmm) outliers start: 26 outliers final: 17 residues processed: 150 average time/residue: 0.0945 time to fit residues: 20.0579 Evaluate side-chains 140 residues out of total 1189 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 121 time to evaluate : 0.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 GLU Chi-restraints excluded: chain A residue 59 SER Chi-restraints excluded: chain A residue 139 THR Chi-restraints excluded: chain A residue 165 THR Chi-restraints excluded: chain B residue 4 CYS Chi-restraints excluded: chain B residue 12 GLU Chi-restraints excluded: chain B residue 57 ILE Chi-restraints excluded: chain B residue 186 THR Chi-restraints excluded: chain B residue 220 MET Chi-restraints excluded: chain B residue 280 CYS Chi-restraints excluded: chain B residue 283 THR Chi-restraints excluded: chain a residue 13 THR Chi-restraints excluded: chain a residue 208 ASP Chi-restraints excluded: chain a residue 287 VAL Chi-restraints excluded: chain a residue 302 THR Chi-restraints excluded: chain b residue 13 THR Chi-restraints excluded: chain b residue 71 VAL Chi-restraints excluded: chain b residue 209 THR Chi-restraints excluded: chain b residue 283 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 113 optimal weight: 5.9990 chunk 28 optimal weight: 0.8980 chunk 103 optimal weight: 0.9980 chunk 60 optimal weight: 8.9990 chunk 39 optimal weight: 9.9990 chunk 8 optimal weight: 10.0000 chunk 19 optimal weight: 5.9990 chunk 86 optimal weight: 4.9990 chunk 65 optimal weight: 1.9990 chunk 55 optimal weight: 0.5980 chunk 57 optimal weight: 2.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 95 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4352 r_free = 0.4352 target = 0.207073 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.166254 restraints weight = 12254.374| |-----------------------------------------------------------------------------| r_work (start): 0.3968 rms_B_bonded: 3.37 r_work: 0.3680 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.3680 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7564 moved from start: 0.2553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 11169 Z= 0.148 Angle : 0.584 13.225 15154 Z= 0.303 Chirality : 0.043 0.217 1584 Planarity : 0.004 0.039 1945 Dihedral : 4.779 49.117 1478 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.66 % Favored : 94.19 % Rotamer: Outliers : 2.69 % Allowed : 11.77 % Favored : 85.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.81 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.29 (0.23), residues: 1343 helix: 1.10 (0.42), residues: 159 sheet: -1.64 (0.33), residues: 283 loop : -0.96 (0.21), residues: 901 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 40 TYR 0.010 0.001 TYR A 331 PHE 0.016 0.002 PHE B 277 TRP 0.011 0.001 TRP b 68 HIS 0.005 0.001 HIS b 254 Details of bonding type rmsd covalent geometry : bond 0.00359 (11145) covalent geometry : angle 0.57730 (15106) SS BOND : bond 0.00410 ( 24) SS BOND : angle 1.67342 ( 48) hydrogen bonds : bond 0.03549 ( 295) hydrogen bonds : angle 5.82403 ( 726) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2686 Ramachandran restraints generated. 1343 Oldfield, 0 Emsley, 1343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2686 Ramachandran restraints generated. 1343 Oldfield, 0 Emsley, 1343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1189 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 127 time to evaluate : 0.416 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 12 GLU cc_start: 0.7375 (mm-30) cc_final: 0.7154 (mp0) REVERT: A 97 MET cc_start: 0.8443 (mtm) cc_final: 0.8102 (mtt) REVERT: A 331 TYR cc_start: 0.6815 (OUTLIER) cc_final: 0.5049 (t80) REVERT: B 339 LYS cc_start: 0.7541 (pttm) cc_final: 0.7217 (ptmm) REVERT: a 146 LYS cc_start: 0.8242 (mtpt) cc_final: 0.7962 (mmtt) REVERT: a 208 ASP cc_start: 0.8293 (OUTLIER) cc_final: 0.8056 (p0) REVERT: a 333 MET cc_start: 0.8143 (mmp) cc_final: 0.7187 (mmm) REVERT: b 67 MET cc_start: 0.5970 (tmm) cc_final: 0.5659 (tmm) outliers start: 32 outliers final: 24 residues processed: 149 average time/residue: 0.0874 time to fit residues: 18.7109 Evaluate side-chains 143 residues out of total 1189 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 117 time to evaluate : 0.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 GLU Chi-restraints excluded: chain A residue 59 SER Chi-restraints excluded: chain A residue 139 THR Chi-restraints excluded: chain A residue 165 THR Chi-restraints excluded: chain A residue 331 TYR Chi-restraints excluded: chain B residue 4 CYS Chi-restraints excluded: chain B residue 12 GLU Chi-restraints excluded: chain B residue 57 ILE Chi-restraints excluded: chain B residue 220 MET Chi-restraints excluded: chain B residue 280 CYS Chi-restraints excluded: chain B residue 283 THR Chi-restraints excluded: chain a residue 13 THR Chi-restraints excluded: chain a residue 93 VAL Chi-restraints excluded: chain a residue 157 ASP Chi-restraints excluded: chain a residue 208 ASP Chi-restraints excluded: chain a residue 287 VAL Chi-restraints excluded: chain a residue 302 THR Chi-restraints excluded: chain b residue 5 SER Chi-restraints excluded: chain b residue 7 ASP Chi-restraints excluded: chain b residue 13 THR Chi-restraints excluded: chain b residue 25 VAL Chi-restraints excluded: chain b residue 71 VAL Chi-restraints excluded: chain b residue 209 THR Chi-restraints excluded: chain b residue 240 ASP Chi-restraints excluded: chain b residue 252 SER Chi-restraints excluded: chain b residue 283 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 63 optimal weight: 9.9990 chunk 5 optimal weight: 3.9990 chunk 66 optimal weight: 6.9990 chunk 11 optimal weight: 10.0000 chunk 18 optimal weight: 0.9980 chunk 129 optimal weight: 8.9990 chunk 115 optimal weight: 9.9990 chunk 13 optimal weight: 5.9990 chunk 73 optimal weight: 9.9990 chunk 9 optimal weight: 3.9990 chunk 112 optimal weight: 0.3980 overall best weight: 3.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 95 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4315 r_free = 0.4315 target = 0.203022 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.162143 restraints weight = 12481.121| |-----------------------------------------------------------------------------| r_work (start): 0.3917 rms_B_bonded: 3.45 r_work: 0.3629 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.3629 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7633 moved from start: 0.2687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.083 11169 Z= 0.255 Angle : 0.692 13.026 15154 Z= 0.361 Chirality : 0.048 0.230 1584 Planarity : 0.005 0.044 1945 Dihedral : 5.222 48.623 1478 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.15 % Allowed : 7.74 % Favored : 92.11 % Rotamer: Outliers : 3.53 % Allowed : 12.87 % Favored : 83.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.81 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.59 (0.23), residues: 1343 helix: 0.79 (0.41), residues: 159 sheet: -1.69 (0.33), residues: 275 loop : -1.22 (0.20), residues: 909 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 148 TYR 0.014 0.002 TYR B 34 PHE 0.016 0.002 PHE A 133 TRP 0.015 0.002 TRP A 311 HIS 0.009 0.002 HIS B 254 Details of bonding type rmsd covalent geometry : bond 0.00616 (11145) covalent geometry : angle 0.68052 (15106) SS BOND : bond 0.00647 ( 24) SS BOND : angle 2.33630 ( 48) hydrogen bonds : bond 0.04263 ( 295) hydrogen bonds : angle 6.20944 ( 726) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2686 Ramachandran restraints generated. 1343 Oldfield, 0 Emsley, 1343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2686 Ramachandran restraints generated. 1343 Oldfield, 0 Emsley, 1343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1189 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 125 time to evaluate : 0.335 Fit side-chains revert: symmetry clash REVERT: A 12 GLU cc_start: 0.7528 (mm-30) cc_final: 0.7281 (mp0) REVERT: A 24 ASP cc_start: 0.8617 (t0) cc_final: 0.8356 (t0) REVERT: A 28 TRP cc_start: 0.7259 (m-10) cc_final: 0.6927 (m-10) REVERT: A 40 ARG cc_start: 0.8465 (tpp80) cc_final: 0.8263 (tpp80) REVERT: A 97 MET cc_start: 0.8512 (mtm) cc_final: 0.8181 (mtt) REVERT: A 125 ARG cc_start: 0.8439 (mmm-85) cc_final: 0.8238 (mmm-85) REVERT: A 331 TYR cc_start: 0.6973 (OUTLIER) cc_final: 0.5416 (t80) REVERT: B 339 LYS cc_start: 0.7615 (pttm) cc_final: 0.7337 (ptmm) REVERT: a 34 TYR cc_start: 0.7618 (m-80) cc_final: 0.7314 (m-80) REVERT: a 69 ARG cc_start: 0.7187 (ptp-170) cc_final: 0.6699 (tpp80) REVERT: a 146 LYS cc_start: 0.8220 (mtpt) cc_final: 0.7958 (mmtm) REVERT: a 208 ASP cc_start: 0.8267 (OUTLIER) cc_final: 0.8066 (p0) REVERT: a 311 TRP cc_start: 0.6804 (m100) cc_final: 0.6506 (m100) REVERT: a 333 MET cc_start: 0.8183 (mmp) cc_final: 0.7923 (mmp) outliers start: 42 outliers final: 33 residues processed: 153 average time/residue: 0.0950 time to fit residues: 20.8028 Evaluate side-chains 149 residues out of total 1189 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 114 time to evaluate : 0.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 VAL Chi-restraints excluded: chain A residue 26 GLU Chi-restraints excluded: chain A residue 59 SER Chi-restraints excluded: chain A residue 115 TRP Chi-restraints excluded: chain A residue 139 THR Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 165 THR Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 218 ILE Chi-restraints excluded: chain A residue 231 LEU Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 331 TYR Chi-restraints excluded: chain B residue 4 CYS Chi-restraints excluded: chain B residue 12 GLU Chi-restraints excluded: chain B residue 21 VAL Chi-restraints excluded: chain B residue 57 ILE Chi-restraints excluded: chain B residue 67 MET Chi-restraints excluded: chain B residue 220 MET Chi-restraints excluded: chain B residue 280 CYS Chi-restraints excluded: chain B residue 283 THR Chi-restraints excluded: chain a residue 93 VAL Chi-restraints excluded: chain a residue 208 ASP Chi-restraints excluded: chain a residue 287 VAL Chi-restraints excluded: chain a residue 302 THR Chi-restraints excluded: chain b residue 5 SER Chi-restraints excluded: chain b residue 7 ASP Chi-restraints excluded: chain b residue 9 SER Chi-restraints excluded: chain b residue 15 CYS Chi-restraints excluded: chain b residue 25 VAL Chi-restraints excluded: chain b residue 71 VAL Chi-restraints excluded: chain b residue 209 THR Chi-restraints excluded: chain b residue 240 ASP Chi-restraints excluded: chain b residue 252 SER Chi-restraints excluded: chain b residue 283 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 107 optimal weight: 40.0000 chunk 127 optimal weight: 0.9990 chunk 63 optimal weight: 9.9990 chunk 124 optimal weight: 0.5980 chunk 35 optimal weight: 6.9990 chunk 113 optimal weight: 1.9990 chunk 38 optimal weight: 6.9990 chunk 98 optimal weight: 1.9990 chunk 29 optimal weight: 6.9990 chunk 49 optimal weight: 6.9990 chunk 75 optimal weight: 0.8980 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 95 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4351 r_free = 0.4351 target = 0.206982 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.166107 restraints weight = 12289.969| |-----------------------------------------------------------------------------| r_work (start): 0.3958 rms_B_bonded: 3.49 r_work: 0.3678 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.3678 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7564 moved from start: 0.2822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 11169 Z= 0.141 Angle : 0.605 12.144 15154 Z= 0.313 Chirality : 0.043 0.209 1584 Planarity : 0.004 0.038 1945 Dihedral : 4.830 48.690 1478 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.06 % Favored : 94.79 % Rotamer: Outliers : 2.86 % Allowed : 14.63 % Favored : 82.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.81 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.46 (0.23), residues: 1343 helix: 0.89 (0.41), residues: 160 sheet: -1.71 (0.33), residues: 269 loop : -1.10 (0.21), residues: 914 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG b 261 TYR 0.009 0.001 TYR A 331 PHE 0.017 0.002 PHE B 277 TRP 0.012 0.001 TRP A 311 HIS 0.004 0.001 HIS b 254 Details of bonding type rmsd covalent geometry : bond 0.00344 (11145) covalent geometry : angle 0.59478 (15106) SS BOND : bond 0.00454 ( 24) SS BOND : angle 2.06308 ( 48) hydrogen bonds : bond 0.03464 ( 295) hydrogen bonds : angle 5.84253 ( 726) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2686 Ramachandran restraints generated. 1343 Oldfield, 0 Emsley, 1343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2686 Ramachandran restraints generated. 1343 Oldfield, 0 Emsley, 1343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1189 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 124 time to evaluate : 0.421 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 40 ARG cc_start: 0.8315 (tpp80) cc_final: 0.8102 (tpp80) REVERT: A 97 MET cc_start: 0.8437 (mtm) cc_final: 0.8090 (mtt) REVERT: A 331 TYR cc_start: 0.6926 (OUTLIER) cc_final: 0.5412 (t80) REVERT: B 141 LYS cc_start: 0.7504 (pptt) cc_final: 0.6761 (ttpp) REVERT: B 339 LYS cc_start: 0.7656 (pttm) cc_final: 0.7388 (ptmm) REVERT: a 69 ARG cc_start: 0.7168 (ptp-170) cc_final: 0.6663 (tpp80) REVERT: a 146 LYS cc_start: 0.8215 (mtpt) cc_final: 0.7956 (mmtm) REVERT: b 67 MET cc_start: 0.6001 (tmm) cc_final: 0.5719 (tmm) outliers start: 34 outliers final: 30 residues processed: 145 average time/residue: 0.0854 time to fit residues: 18.0746 Evaluate side-chains 146 residues out of total 1189 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 115 time to evaluate : 0.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 GLU Chi-restraints excluded: chain A residue 59 SER Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 139 THR Chi-restraints excluded: chain A residue 165 THR Chi-restraints excluded: chain A residue 231 LEU Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 331 TYR Chi-restraints excluded: chain B residue 4 CYS Chi-restraints excluded: chain B residue 12 GLU Chi-restraints excluded: chain B residue 57 ILE Chi-restraints excluded: chain B residue 67 MET Chi-restraints excluded: chain B residue 95 ASN Chi-restraints excluded: chain B residue 220 MET Chi-restraints excluded: chain B residue 280 CYS Chi-restraints excluded: chain B residue 283 THR Chi-restraints excluded: chain a residue 93 VAL Chi-restraints excluded: chain a residue 106 VAL Chi-restraints excluded: chain a residue 157 ASP Chi-restraints excluded: chain a residue 287 VAL Chi-restraints excluded: chain a residue 302 THR Chi-restraints excluded: chain b residue 9 SER Chi-restraints excluded: chain b residue 15 CYS Chi-restraints excluded: chain b residue 17 THR Chi-restraints excluded: chain b residue 25 VAL Chi-restraints excluded: chain b residue 71 VAL Chi-restraints excluded: chain b residue 209 THR Chi-restraints excluded: chain b residue 240 ASP Chi-restraints excluded: chain b residue 252 SER Chi-restraints excluded: chain b residue 283 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 17 optimal weight: 0.9980 chunk 3 optimal weight: 1.9990 chunk 121 optimal weight: 2.9990 chunk 47 optimal weight: 9.9990 chunk 2 optimal weight: 0.9990 chunk 5 optimal weight: 2.9990 chunk 32 optimal weight: 0.5980 chunk 87 optimal weight: 0.0870 chunk 30 optimal weight: 0.8980 chunk 105 optimal weight: 9.9990 chunk 40 optimal weight: 10.0000 overall best weight: 0.7160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 95 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4373 r_free = 0.4373 target = 0.209223 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.168643 restraints weight = 12323.457| |-----------------------------------------------------------------------------| r_work (start): 0.3989 rms_B_bonded: 3.43 r_work: 0.3718 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.3718 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7512 moved from start: 0.2978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 11169 Z= 0.109 Angle : 0.573 11.644 15154 Z= 0.293 Chirality : 0.042 0.193 1584 Planarity : 0.003 0.036 1945 Dihedral : 4.346 16.755 1476 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.21 % Favored : 94.64 % Rotamer: Outliers : 2.52 % Allowed : 15.22 % Favored : 82.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.81 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.33 (0.23), residues: 1343 helix: 0.96 (0.41), residues: 160 sheet: -1.65 (0.33), residues: 269 loop : -1.00 (0.21), residues: 914 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG b 261 TYR 0.009 0.001 TYR A 331 PHE 0.015 0.001 PHE B 277 TRP 0.009 0.001 TRP b 68 HIS 0.003 0.001 HIS b 254 Details of bonding type rmsd covalent geometry : bond 0.00263 (11145) covalent geometry : angle 0.56407 (15106) SS BOND : bond 0.00423 ( 24) SS BOND : angle 1.82851 ( 48) hydrogen bonds : bond 0.03088 ( 295) hydrogen bonds : angle 5.61025 ( 726) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2686 Ramachandran restraints generated. 1343 Oldfield, 0 Emsley, 1343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2686 Ramachandran restraints generated. 1343 Oldfield, 0 Emsley, 1343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1189 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 123 time to evaluate : 0.400 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 331 TYR cc_start: 0.6866 (OUTLIER) cc_final: 0.5397 (t80) REVERT: B 141 LYS cc_start: 0.7575 (pptt) cc_final: 0.6880 (ttpp) REVERT: B 339 LYS cc_start: 0.7737 (pttm) cc_final: 0.7437 (ptmm) REVERT: a 69 ARG cc_start: 0.7138 (ptp-170) cc_final: 0.6621 (tpp80) REVERT: a 146 LYS cc_start: 0.8191 (mtpt) cc_final: 0.7944 (mmtt) REVERT: b 67 MET cc_start: 0.6047 (tmm) cc_final: 0.5735 (tmm) outliers start: 30 outliers final: 23 residues processed: 142 average time/residue: 0.1000 time to fit residues: 20.3111 Evaluate side-chains 139 residues out of total 1189 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 115 time to evaluate : 0.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 VAL Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 139 THR Chi-restraints excluded: chain A residue 165 THR Chi-restraints excluded: chain A residue 231 LEU Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 331 TYR Chi-restraints excluded: chain B residue 4 CYS Chi-restraints excluded: chain B residue 57 ILE Chi-restraints excluded: chain B residue 67 MET Chi-restraints excluded: chain B residue 220 MET Chi-restraints excluded: chain B residue 280 CYS Chi-restraints excluded: chain B residue 283 THR Chi-restraints excluded: chain a residue 106 VAL Chi-restraints excluded: chain a residue 157 ASP Chi-restraints excluded: chain a residue 287 VAL Chi-restraints excluded: chain a residue 302 THR Chi-restraints excluded: chain b residue 9 SER Chi-restraints excluded: chain b residue 15 CYS Chi-restraints excluded: chain b residue 17 THR Chi-restraints excluded: chain b residue 25 VAL Chi-restraints excluded: chain b residue 71 VAL Chi-restraints excluded: chain b residue 240 ASP Chi-restraints excluded: chain b residue 283 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 85 optimal weight: 2.9990 chunk 128 optimal weight: 9.9990 chunk 86 optimal weight: 1.9990 chunk 116 optimal weight: 5.9990 chunk 4 optimal weight: 7.9990 chunk 81 optimal weight: 0.6980 chunk 2 optimal weight: 2.9990 chunk 22 optimal weight: 0.5980 chunk 3 optimal weight: 3.9990 chunk 42 optimal weight: 10.0000 chunk 26 optimal weight: 5.9990 overall best weight: 1.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 95 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4345 r_free = 0.4345 target = 0.206456 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.165218 restraints weight = 12309.828| |-----------------------------------------------------------------------------| r_work (start): 0.3949 rms_B_bonded: 3.44 r_work: 0.3676 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.3676 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7572 moved from start: 0.2991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 11169 Z= 0.174 Angle : 0.625 13.801 15154 Z= 0.321 Chirality : 0.044 0.199 1584 Planarity : 0.004 0.039 1945 Dihedral : 4.544 18.302 1476 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.55 % Favored : 93.30 % Rotamer: Outliers : 3.11 % Allowed : 14.47 % Favored : 82.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.81 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.45 (0.23), residues: 1343 helix: 0.90 (0.41), residues: 160 sheet: -1.72 (0.33), residues: 279 loop : -1.07 (0.21), residues: 904 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 29 TYR 0.010 0.001 TYR A 331 PHE 0.014 0.002 PHE B 277 TRP 0.013 0.001 TRP A 28 HIS 0.006 0.001 HIS B 254 Details of bonding type rmsd covalent geometry : bond 0.00423 (11145) covalent geometry : angle 0.61485 (15106) SS BOND : bond 0.00530 ( 24) SS BOND : angle 2.08088 ( 48) hydrogen bonds : bond 0.03569 ( 295) hydrogen bonds : angle 5.81859 ( 726) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2686 Ramachandran restraints generated. 1343 Oldfield, 0 Emsley, 1343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2686 Ramachandran restraints generated. 1343 Oldfield, 0 Emsley, 1343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1189 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 117 time to evaluate : 0.360 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 28 TRP cc_start: 0.7007 (m-10) cc_final: 0.6622 (m-10) REVERT: A 97 MET cc_start: 0.8501 (mtm) cc_final: 0.8171 (mtt) REVERT: A 331 TYR cc_start: 0.6966 (OUTLIER) cc_final: 0.5618 (t80) REVERT: B 141 LYS cc_start: 0.7569 (pptt) cc_final: 0.6863 (ttpp) REVERT: B 339 LYS cc_start: 0.7668 (pttm) cc_final: 0.7348 (ptmm) REVERT: a 69 ARG cc_start: 0.7166 (ptp-170) cc_final: 0.6629 (tpp80) REVERT: a 146 LYS cc_start: 0.8200 (mtpt) cc_final: 0.7968 (mmtt) REVERT: a 333 MET cc_start: 0.7944 (mmp) cc_final: 0.6915 (mmm) REVERT: b 67 MET cc_start: 0.6069 (tmm) cc_final: 0.5654 (tmm) REVERT: b 349 MET cc_start: 0.3244 (ptp) cc_final: 0.2955 (ptp) outliers start: 37 outliers final: 32 residues processed: 140 average time/residue: 0.0889 time to fit residues: 18.1379 Evaluate side-chains 143 residues out of total 1189 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 110 time to evaluate : 0.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 VAL Chi-restraints excluded: chain A residue 59 SER Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 139 THR Chi-restraints excluded: chain A residue 165 THR Chi-restraints excluded: chain A residue 222 THR Chi-restraints excluded: chain A residue 231 LEU Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 331 TYR Chi-restraints excluded: chain B residue 4 CYS Chi-restraints excluded: chain B residue 57 ILE Chi-restraints excluded: chain B residue 67 MET Chi-restraints excluded: chain B residue 95 ASN Chi-restraints excluded: chain B residue 220 MET Chi-restraints excluded: chain B residue 280 CYS Chi-restraints excluded: chain B residue 283 THR Chi-restraints excluded: chain a residue 93 VAL Chi-restraints excluded: chain a residue 106 VAL Chi-restraints excluded: chain a residue 157 ASP Chi-restraints excluded: chain a residue 208 ASP Chi-restraints excluded: chain a residue 287 VAL Chi-restraints excluded: chain a residue 302 THR Chi-restraints excluded: chain a residue 350 VAL Chi-restraints excluded: chain b residue 7 ASP Chi-restraints excluded: chain b residue 9 SER Chi-restraints excluded: chain b residue 13 THR Chi-restraints excluded: chain b residue 15 CYS Chi-restraints excluded: chain b residue 17 THR Chi-restraints excluded: chain b residue 25 VAL Chi-restraints excluded: chain b residue 209 THR Chi-restraints excluded: chain b residue 240 ASP Chi-restraints excluded: chain b residue 283 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 5 optimal weight: 0.9980 chunk 83 optimal weight: 0.0980 chunk 102 optimal weight: 0.9980 chunk 81 optimal weight: 6.9990 chunk 104 optimal weight: 0.9980 chunk 93 optimal weight: 3.9990 chunk 23 optimal weight: 0.8980 chunk 116 optimal weight: 0.8980 chunk 125 optimal weight: 8.9990 chunk 12 optimal weight: 10.0000 chunk 16 optimal weight: 9.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 95 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4366 r_free = 0.4366 target = 0.209419 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.167285 restraints weight = 12147.843| |-----------------------------------------------------------------------------| r_work (start): 0.3954 rms_B_bonded: 3.41 r_work: 0.3690 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.3690 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7409 moved from start: 0.3090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 11169 Z= 0.114 Angle : 0.579 13.161 15154 Z= 0.298 Chirality : 0.042 0.173 1584 Planarity : 0.003 0.038 1945 Dihedral : 4.366 21.488 1476 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.21 % Favored : 94.64 % Rotamer: Outliers : 2.78 % Allowed : 15.05 % Favored : 82.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.81 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.32 (0.23), residues: 1343 helix: 0.94 (0.40), residues: 160 sheet: -1.63 (0.33), residues: 279 loop : -0.97 (0.21), residues: 904 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG b 14 TYR 0.009 0.001 TYR A 331 PHE 0.015 0.001 PHE B 277 TRP 0.011 0.001 TRP a 311 HIS 0.004 0.001 HIS B 269 Details of bonding type rmsd covalent geometry : bond 0.00274 (11145) covalent geometry : angle 0.57128 (15106) SS BOND : bond 0.00464 ( 24) SS BOND : angle 1.81443 ( 48) hydrogen bonds : bond 0.03219 ( 295) hydrogen bonds : angle 5.63647 ( 726) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2686 Ramachandran restraints generated. 1343 Oldfield, 0 Emsley, 1343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2686 Ramachandran restraints generated. 1343 Oldfield, 0 Emsley, 1343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1189 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 119 time to evaluate : 0.342 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 331 TYR cc_start: 0.6930 (OUTLIER) cc_final: 0.5450 (t80) REVERT: B 141 LYS cc_start: 0.7566 (pptt) cc_final: 0.6916 (ttpp) REVERT: B 339 LYS cc_start: 0.7699 (pttm) cc_final: 0.7361 (ptmm) REVERT: a 69 ARG cc_start: 0.7155 (ptp-170) cc_final: 0.6553 (tpp80) REVERT: a 146 LYS cc_start: 0.8272 (mtpt) cc_final: 0.7929 (mmtm) REVERT: a 333 MET cc_start: 0.7896 (mmp) cc_final: 0.6863 (mmm) outliers start: 33 outliers final: 29 residues processed: 139 average time/residue: 0.0904 time to fit residues: 18.0995 Evaluate side-chains 144 residues out of total 1189 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 114 time to evaluate : 0.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 VAL Chi-restraints excluded: chain A residue 59 SER Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 139 THR Chi-restraints excluded: chain A residue 165 THR Chi-restraints excluded: chain A residue 231 LEU Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 331 TYR Chi-restraints excluded: chain B residue 4 CYS Chi-restraints excluded: chain B residue 57 ILE Chi-restraints excluded: chain B residue 95 ASN Chi-restraints excluded: chain B residue 220 MET Chi-restraints excluded: chain B residue 280 CYS Chi-restraints excluded: chain B residue 283 THR Chi-restraints excluded: chain a residue 93 VAL Chi-restraints excluded: chain a residue 106 VAL Chi-restraints excluded: chain a residue 157 ASP Chi-restraints excluded: chain a residue 208 ASP Chi-restraints excluded: chain a residue 287 VAL Chi-restraints excluded: chain a residue 302 THR Chi-restraints excluded: chain a residue 350 VAL Chi-restraints excluded: chain b residue 7 ASP Chi-restraints excluded: chain b residue 9 SER Chi-restraints excluded: chain b residue 13 THR Chi-restraints excluded: chain b residue 15 CYS Chi-restraints excluded: chain b residue 17 THR Chi-restraints excluded: chain b residue 25 VAL Chi-restraints excluded: chain b residue 209 THR Chi-restraints excluded: chain b residue 283 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 70 optimal weight: 0.6980 chunk 100 optimal weight: 0.8980 chunk 61 optimal weight: 6.9990 chunk 23 optimal weight: 4.9990 chunk 83 optimal weight: 6.9990 chunk 115 optimal weight: 9.9990 chunk 3 optimal weight: 0.9990 chunk 105 optimal weight: 9.9990 chunk 52 optimal weight: 2.9990 chunk 25 optimal weight: 0.9990 chunk 4 optimal weight: 1.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 95 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4371 r_free = 0.4371 target = 0.209375 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4006 r_free = 0.4006 target = 0.168518 restraints weight = 12322.811| |-----------------------------------------------------------------------------| r_work (start): 0.3987 rms_B_bonded: 3.45 r_work: 0.3712 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.3712 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7519 moved from start: 0.3103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.101 11169 Z= 0.160 Angle : 0.863 59.200 15154 Z= 0.479 Chirality : 0.044 0.495 1584 Planarity : 0.004 0.051 1945 Dihedral : 4.370 21.356 1476 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.99 % Favored : 94.86 % Rotamer: Outliers : 2.44 % Allowed : 15.31 % Favored : 82.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.81 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.30 (0.23), residues: 1343 helix: 0.95 (0.40), residues: 160 sheet: -1.62 (0.33), residues: 279 loop : -0.96 (0.21), residues: 904 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG b 14 TYR 0.009 0.001 TYR A 331 PHE 0.014 0.001 PHE B 277 TRP 0.010 0.001 TRP A 118 HIS 0.004 0.001 HIS b 254 Details of bonding type rmsd covalent geometry : bond 0.00354 (11145) covalent geometry : angle 0.85829 (15106) SS BOND : bond 0.00474 ( 24) SS BOND : angle 1.80419 ( 48) hydrogen bonds : bond 0.03235 ( 295) hydrogen bonds : angle 5.63833 ( 726) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2360.15 seconds wall clock time: 40 minutes 58.93 seconds (2458.93 seconds total)