Starting phenix.real_space_refine on Tue Jul 29 02:00:17 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wbf_37423/07_2025/8wbf_37423_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wbf_37423/07_2025/8wbf_37423.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.99 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8wbf_37423/07_2025/8wbf_37423.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wbf_37423/07_2025/8wbf_37423.map" model { file = "/net/cci-nas-00/data/ceres_data/8wbf_37423/07_2025/8wbf_37423_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wbf_37423/07_2025/8wbf_37423_neut.cif" } resolution = 2.99 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= 0.137 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 6852 2.51 5 N 1958 2.21 5 O 2024 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 10914 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: 2819 Number of conformers: 1 Conformer: "" Number of residues, atoms: 352, 2819 Classifications: {'peptide': 352} Link IDs: {'PCIS': 2, 'PTRANS': 17, 'TRANS': 332} 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: 13.00, per 1000 atoms: 1.19 Number of scatterers: 10914 At special positions: 0 Unit cell: (114.75, 116.45, 110.5, 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 2024 8.00 N 1958 7.00 C 6852 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=2.03 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 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: 4.45 Conformation dependent library (CDL) restraints added in 2.0 seconds 2704 Ramachandran restraints generated. 1352 Oldfield, 0 Emsley, 1352 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2520 Finding SS restraints... Secondary structure from input PDB file: 31 helices and 20 sheets defined 18.7% alpha, 19.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.33 Creating SS restraints... Processing helix chain 'A' and resid 38 through 53 removed outlier: 3.726A pdb=" N ALA A 43 " --> pdb=" O PRO A 39 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ALA A 44 " --> pdb=" O ARG A 40 " (cutoff:3.500A) Processing helix chain 'A' and resid 61 through 70 removed outlier: 3.885A pdb=" N ASN A 65 " --> pdb=" O SER A 61 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ILE A 66 " --> pdb=" O ARG A 62 " (cutoff:3.500A) Processing helix chain 'A' and resid 71 through 82 Processing helix chain 'A' and resid 144 through 148 removed outlier: 3.645A pdb=" N ARG A 148 " --> pdb=" O LEU A 145 " (cutoff:3.500A) Processing helix chain 'A' and resid 226 through 230 removed outlier: 3.512A pdb=" N THR A 230 " --> pdb=" O LYS A 227 " (cutoff:3.500A) Processing helix chain 'A' and resid 244 through 248 removed outlier: 3.538A pdb=" N ALA A 248 " --> pdb=" O LYS A 245 " (cutoff:3.500A) Processing helix chain 'A' and resid 252 through 256 Processing helix chain 'A' and resid 341 through 345 Processing helix chain 'B' and resid 38 through 51 removed outlier: 3.867A pdb=" N ALA B 43 " --> pdb=" O PRO B 39 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N GLU B 51 " --> pdb=" O LYS B 47 " (cutoff:3.500A) Processing helix chain 'B' and resid 61 through 82 removed outlier: 3.630A pdb=" N ASN B 65 " --> pdb=" O SER B 61 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N VAL B 71 " --> pdb=" O MET B 67 " (cutoff:3.500A) removed outlier: 4.809A pdb=" N GLY B 73 " --> pdb=" O ARG B 69 " (cutoff:3.500A) removed outlier: 5.642A pdb=" N GLU B 74 " --> pdb=" O SER B 70 " (cutoff:3.500A) Processing helix chain 'B' and resid 144 through 146 No H-bonds generated for 'chain 'B' and resid 144 through 146' Processing helix chain 'B' and resid 180 through 183 removed outlier: 4.059A pdb=" N VAL B 183 " --> pdb=" O ASP B 180 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 180 through 183' Processing helix chain 'B' and resid 226 through 230 Processing helix chain 'B' and resid 237 through 241 removed outlier: 3.864A pdb=" N LEU B 241 " --> pdb=" O GLU B 238 " (cutoff:3.500A) Processing helix chain 'B' and resid 244 through 248 removed outlier: 3.697A pdb=" N ALA B 248 " --> pdb=" O LYS B 245 " (cutoff:3.500A) Processing helix chain 'B' and resid 252 through 256 removed outlier: 3.534A pdb=" N THR B 256 " --> pdb=" O HIS B 253 " (cutoff:3.500A) Processing helix chain 'B' and resid 341 through 345 removed outlier: 3.697A pdb=" N ASN B 344 " --> pdb=" O PRO B 341 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N LEU B 345 " --> pdb=" O GLU B 342 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 341 through 345' Processing helix chain 'a' and resid 38 through 53 Processing helix chain 'a' and resid 61 through 82 removed outlier: 4.970A pdb=" N GLY a 73 " --> pdb=" O ARG a 69 " (cutoff:3.500A) removed outlier: 5.088A pdb=" N GLU a 74 " --> pdb=" O SER a 70 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ASN a 82 " --> pdb=" O ILE a 78 " (cutoff:3.500A) Processing helix chain 'a' and resid 180 through 183 removed outlier: 3.920A pdb=" N VAL a 183 " --> pdb=" O ASP a 180 " (cutoff:3.500A) No H-bonds generated for 'chain 'a' and resid 180 through 183' Processing helix chain 'a' and resid 226 through 230 Processing helix chain 'a' and resid 244 through 248 removed outlier: 3.631A pdb=" N ALA a 248 " --> pdb=" O LYS a 245 " (cutoff:3.500A) Processing helix chain 'a' and resid 252 through 256 Processing helix chain 'a' and resid 341 through 345 removed outlier: 3.527A pdb=" N ASN a 344 " --> pdb=" O PRO a 341 " (cutoff:3.500A) removed outlier: 3.598A 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 53 Processing helix chain 'b' and resid 61 through 82 removed outlier: 4.835A pdb=" N GLY b 73 " --> pdb=" O ARG b 69 " (cutoff:3.500A) removed outlier: 5.056A pdb=" N GLU b 74 " --> pdb=" O SER b 70 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ASN b 82 " --> pdb=" O ILE b 78 " (cutoff:3.500A) Processing helix chain 'b' and resid 180 through 183 removed outlier: 3.859A pdb=" N VAL b 183 " --> pdb=" O ASP b 180 " (cutoff:3.500A) No H-bonds generated for 'chain 'b' and resid 180 through 183' Processing helix chain 'b' and resid 226 through 230 Processing helix chain 'b' and resid 244 through 248 removed outlier: 3.572A pdb=" N ALA b 248 " --> pdb=" O LYS b 245 " (cutoff:3.500A) Processing helix chain 'b' and resid 252 through 256 Processing helix chain 'b' and resid 341 through 345 Processing sheet with id=AA1, first strand: chain 'A' and resid 2 through 7 removed outlier: 3.777A pdb=" N GLU a 12 " --> pdb=" O ASP a 7 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N VAL a 2 " --> pdb=" O VAL A 6 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 33 through 36 removed outlier: 6.709A pdb=" N LYS A 170 " --> pdb=" O VAL A 155 " (cutoff:3.500A) removed outlier: 5.522A pdb=" N VAL A 155 " --> pdb=" O LYS A 170 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 56 through 57 removed outlier: 6.519A pdb=" N THR A 87 " --> pdb=" O PHE A 133 " (cutoff:3.500A) removed outlier: 7.329A pdb=" N VAL A 135 " --> pdb=" O THR A 87 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N VAL A 89 " --> pdb=" O VAL A 135 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 329 through 331 removed outlier: 4.700A pdb=" N PHE A 277 " --> pdb=" O LYS A 213 " (cutoff:3.500A) removed outlier: 9.243A pdb=" N LYS A 213 " --> pdb=" O PHE A 277 " (cutoff:3.500A) removed outlier: 5.583A pdb=" N LEU A 212 " --> pdb=" O GLU A 205 " (cutoff:3.500A) removed outlier: 5.964A pdb=" N GLU A 205 " --> pdb=" O LEU A 212 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ARG A 214 " --> pdb=" O GLU A 203 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ALA A 193 " --> pdb=" O SER A 204 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N GLU a 192 " --> pdb=" O LYS a 189 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ALA a 193 " --> pdb=" O SER a 204 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ARG a 214 " --> pdb=" O GLU a 203 " (cutoff:3.500A) removed outlier: 6.142A pdb=" N GLU a 205 " --> pdb=" O LEU a 212 " (cutoff:3.500A) removed outlier: 5.518A pdb=" N LEU a 212 " --> pdb=" O GLU a 205 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ALA a 325 " --> pdb=" O GLY a 328 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N GLY a 328 " --> pdb=" O ALA a 325 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 284 through 287 removed outlier: 6.235A pdb=" N LYS A 284 " --> pdb=" O TRP A 311 " (cutoff:3.500A) removed outlier: 7.535A pdb=" N CYS A 313 " --> pdb=" O LYS A 284 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N HIS A 286 " --> pdb=" O CYS A 313 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 2 through 6 removed outlier: 3.958A pdb=" N GLU b 12 " --> pdb=" O ASP b 7 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N VAL b 2 " --> pdb=" O VAL B 6 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 33 through 36 removed outlier: 6.512A pdb=" N LYS B 33 " --> pdb=" O VAL B 167 " (cutoff:3.500A) removed outlier: 7.739A pdb=" N LEU B 169 " --> pdb=" O LYS B 33 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N HIS B 35 " --> pdb=" O LEU B 169 " (cutoff:3.500A) removed outlier: 8.042A pdb=" N VAL B 171 " --> pdb=" O HIS B 35 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ASP B 157 " --> pdb=" O TRP B 168 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N LYS B 170 " --> pdb=" O VAL B 155 " (cutoff:3.500A) removed outlier: 5.294A pdb=" N VAL B 155 " --> pdb=" O LYS B 170 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 56 through 57 removed outlier: 6.800A pdb=" N GLY B 56 " --> pdb=" O ALA B 149 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'B' and resid 88 through 90 removed outlier: 6.526A pdb=" N VAL B 89 " --> pdb=" O VAL B 135 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'B' and resid 329 through 331 removed outlier: 4.565A pdb=" N PHE B 277 " --> pdb=" O LYS B 213 " (cutoff:3.500A) removed outlier: 9.014A pdb=" N LYS B 213 " --> pdb=" O PHE B 277 " (cutoff:3.500A) removed outlier: 5.449A pdb=" N LEU B 212 " --> pdb=" O GLU B 205 " (cutoff:3.500A) removed outlier: 5.993A pdb=" N GLU B 205 " --> pdb=" O LEU B 212 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ALA B 193 " --> pdb=" O SER B 204 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N GLU b 192 " --> pdb=" O LYS b 189 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ARG b 214 " --> pdb=" O GLU b 203 " (cutoff:3.500A) removed outlier: 5.896A pdb=" N GLU b 205 " --> pdb=" O LEU b 212 " (cutoff:3.500A) removed outlier: 5.352A pdb=" N LEU b 212 " --> pdb=" O GLU b 205 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 284 through 287 removed outlier: 6.231A pdb=" N LYS B 284 " --> pdb=" O TRP B 311 " (cutoff:3.500A) removed outlier: 7.897A pdb=" N CYS B 313 " --> pdb=" O LYS B 284 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N HIS B 286 " --> pdb=" O CYS B 313 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'a' and resid 35 through 36 removed outlier: 7.155A pdb=" N HIS a 35 " --> pdb=" O LEU a 169 " (cutoff:3.500A) removed outlier: 9.181A pdb=" N VAL a 171 " --> pdb=" O HIS a 35 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'a' and resid 56 through 57 removed outlier: 6.959A pdb=" N GLY a 56 " --> pdb=" O ALA a 149 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'a' and resid 87 through 89 removed outlier: 6.512A pdb=" N THR a 87 " --> pdb=" O PHE a 133 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'a' and resid 284 through 287 removed outlier: 6.130A pdb=" N LYS a 284 " --> pdb=" O TRP a 311 " (cutoff:3.500A) removed outlier: 7.616A pdb=" N CYS a 313 " --> pdb=" O LYS a 284 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N HIS a 286 " --> pdb=" O CYS a 313 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'b' and resid 35 through 36 removed outlier: 6.787A pdb=" N HIS b 35 " --> pdb=" O LEU b 169 " (cutoff:3.500A) removed outlier: 8.947A pdb=" N VAL b 171 " --> pdb=" O HIS b 35 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'b' and resid 56 through 57 removed outlier: 6.907A pdb=" N GLY b 56 " --> pdb=" O ALA b 149 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'b' and resid 87 through 89 removed outlier: 6.488A pdb=" N THR b 87 " --> pdb=" O PHE b 133 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'b' and resid 275 through 276 Processing sheet with id=AC2, first strand: chain 'b' and resid 284 through 287 removed outlier: 6.069A pdb=" N LYS b 284 " --> pdb=" O TRP b 311 " (cutoff:3.500A) removed outlier: 7.549A pdb=" N CYS b 313 " --> pdb=" O LYS b 284 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N HIS b 286 " --> pdb=" O CYS b 313 " (cutoff:3.500A) 263 hydrogen bonds defined for protein. 678 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: 7.36 Time building geometry restraints manager: 5.24 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3627 1.34 - 1.46: 2639 1.46 - 1.58: 4830 1.58 - 1.70: 0 1.70 - 1.82: 112 Bond restraints: 11208 Sorted by residual: bond pdb=" N LYS B 120 " pdb=" CA LYS B 120 " ideal model delta sigma weight residual 1.456 1.483 -0.027 1.22e-02 6.72e+03 4.81e+00 bond pdb=" N LYS A 120 " pdb=" CA LYS A 120 " ideal model delta sigma weight residual 1.456 1.480 -0.024 1.23e-02 6.61e+03 3.85e+00 bond pdb=" CB VAL B 188 " pdb=" CG2 VAL B 188 " ideal model delta sigma weight residual 1.521 1.490 0.031 3.30e-02 9.18e+02 8.80e-01 bond pdb=" CA LYS A 120 " pdb=" C LYS A 120 " ideal model delta sigma weight residual 1.524 1.513 0.011 1.26e-02 6.30e+03 7.38e-01 bond pdb=" CB GLU B 12 " pdb=" CG GLU B 12 " ideal model delta sigma weight residual 1.520 1.545 -0.025 3.00e-02 1.11e+03 6.82e-01 ... (remaining 11203 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.97: 14325 0.97 - 1.95: 687 1.95 - 2.92: 132 2.92 - 3.90: 34 3.90 - 4.87: 14 Bond angle restraints: 15192 Sorted by residual: angle pdb=" N GLY a 328 " pdb=" CA GLY a 328 " pdb=" C GLY a 328 " ideal model delta sigma weight residual 110.43 115.30 -4.87 1.35e+00 5.49e-01 1.30e+01 angle pdb=" CA LYS B 120 " pdb=" C LYS B 120 " pdb=" O LYS B 120 " ideal model delta sigma weight residual 120.81 117.82 2.99 1.15e+00 7.56e-01 6.78e+00 angle pdb=" N PRO B 144 " pdb=" CA PRO B 144 " pdb=" C PRO B 144 " ideal model delta sigma weight residual 110.40 114.31 -3.91 1.61e+00 3.86e-01 5.91e+00 angle pdb=" N LYS A 120 " pdb=" CA LYS A 120 " pdb=" CB LYS A 120 " ideal model delta sigma weight residual 109.83 113.36 -3.53 1.51e+00 4.39e-01 5.46e+00 angle pdb=" C ASP a 208 " pdb=" N THR a 209 " pdb=" CA THR a 209 " ideal model delta sigma weight residual 121.80 125.79 -3.99 1.71e+00 3.42e-01 5.44e+00 ... (remaining 15187 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.43: 6096 17.43 - 34.86: 513 34.86 - 52.28: 106 52.28 - 69.71: 17 69.71 - 87.14: 6 Dihedral angle restraints: 6738 sinusoidal: 2830 harmonic: 3908 Sorted by residual: 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 -172.89 86.89 1 1.00e+01 1.00e-02 9.08e+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 93.00 172.27 -79.27 1 1.00e+01 1.00e-02 7.81e+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 93.00 165.47 -72.47 1 1.00e+01 1.00e-02 6.71e+01 ... (remaining 6735 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 936 0.028 - 0.056: 427 0.056 - 0.084: 92 0.084 - 0.112: 114 0.112 - 0.141: 23 Chirality restraints: 1592 Sorted by residual: chirality pdb=" CB THR a 209 " pdb=" CA THR a 209 " pdb=" OG1 THR a 209 " pdb=" CG2 THR a 209 " both_signs ideal model delta sigma weight residual False 2.55 2.41 0.14 2.00e-01 2.50e+01 4.94e-01 chirality pdb=" CB THR b 209 " pdb=" CA THR b 209 " pdb=" OG1 THR b 209 " pdb=" CG2 THR b 209 " both_signs ideal model delta sigma weight residual False 2.55 2.42 0.13 2.00e-01 2.50e+01 4.51e-01 chirality pdb=" CA ILE A 57 " pdb=" N ILE A 57 " pdb=" C ILE A 57 " pdb=" CB ILE A 57 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.39e-01 ... (remaining 1589 not shown) Planarity restraints: 1956 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY A 119 " -0.006 2.00e-02 2.50e+03 1.26e-02 1.59e+00 pdb=" C GLY A 119 " 0.022 2.00e-02 2.50e+03 pdb=" O GLY A 119 " -0.008 2.00e-02 2.50e+03 pdb=" N LYS A 120 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 150 " -0.009 2.00e-02 2.50e+03 7.86e-03 1.55e+00 pdb=" CG TRP A 150 " 0.021 2.00e-02 2.50e+03 pdb=" CD1 TRP A 150 " -0.009 2.00e-02 2.50e+03 pdb=" CD2 TRP A 150 " 0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP A 150 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP A 150 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP A 150 " -0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 150 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 150 " -0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP A 150 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 71 " 0.006 2.00e-02 2.50e+03 1.22e-02 1.48e+00 pdb=" C VAL A 71 " -0.021 2.00e-02 2.50e+03 pdb=" O VAL A 71 " 0.008 2.00e-02 2.50e+03 pdb=" N GLU A 72 " 0.007 2.00e-02 2.50e+03 ... (remaining 1953 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 1466 2.76 - 3.29: 9525 3.29 - 3.83: 17133 3.83 - 4.36: 20761 4.36 - 4.90: 37488 Nonbonded interactions: 86373 Sorted by model distance: nonbonded pdb=" O LEU b 231 " pdb=" OG SER b 252 " model vdw 2.224 3.040 nonbonded pdb=" O LEU a 231 " pdb=" OG SER a 252 " model vdw 2.228 3.040 nonbonded pdb=" OG SER A 297 " pdb=" O TYR A 331 " model vdw 2.233 3.040 nonbonded pdb=" O GLY A 266 " pdb=" OG SER A 348 " model vdw 2.240 3.040 nonbonded pdb=" O MET b 97 " pdb=" OG1 THR b 222 " model vdw 2.255 3.040 ... (remaining 86368 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.03 Found NCS groups: ncs_group { reference = (chain 'A' 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: 14.130 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: 9.390 Check model and map are aligned: 0.110 Set scattering table: 0.150 Process input model: 49.580 Find NCS groups from input model: 0.780 Set up NCS constraints: 0.120 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: 0.020 Load rotamer database and sin/cos tables:39.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 113.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7956 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 : 0.002 0.031 11232 Z= 0.110 Angle : 0.510 4.870 15240 Z= 0.281 Chirality : 0.042 0.141 1592 Planarity : 0.003 0.027 1956 Dihedral : 13.353 87.141 4146 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.17 % Favored : 92.83 % Rotamer: Outliers : 0.08 % Allowed : 0.25 % 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 (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: -1.12 (0.23), residues: 1352 helix: 1.86 (0.43), residues: 148 sheet: -1.75 (0.31), residues: 302 loop : -0.82 (0.21), residues: 902 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 150 HIS 0.006 0.001 HIS b 164 PHE 0.010 0.001 PHE B 277 TYR 0.009 0.001 TYR A 331 ARG 0.003 0.000 ARG a 29 Details of bonding type rmsd hydrogen bonds : bond 0.22813 ( 263) hydrogen bonds : angle 9.38571 ( 678) SS BOND : bond 0.00168 ( 24) SS BOND : angle 0.82015 ( 48) covalent geometry : bond 0.00232 (11208) covalent geometry : angle 0.50857 (15192) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2704 Ramachandran restraints generated. 1352 Oldfield, 0 Emsley, 1352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2704 Ramachandran restraints generated. 1352 Oldfield, 0 Emsley, 1352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 1194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 219 time to evaluate : 1.289 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 157 ASP cc_start: 0.7828 (t0) cc_final: 0.7511 (t70) REVERT: A 261 ARG cc_start: 0.7795 (mtt90) cc_final: 0.7473 (mtp180) REVERT: A 329 CYS cc_start: 0.7703 (t) cc_final: 0.7385 (t) REVERT: B 103 ARG cc_start: 0.7620 (ptt90) cc_final: 0.7222 (ptt180) REVERT: B 251 LEU cc_start: 0.8800 (mt) cc_final: 0.8536 (mt) REVERT: B 286 HIS cc_start: 0.6971 (m170) cc_final: 0.6650 (m-70) REVERT: a 7 ASP cc_start: 0.8067 (t0) cc_final: 0.7828 (t0) REVERT: a 74 GLU cc_start: 0.6929 (mt-10) cc_final: 0.6390 (tt0) REVERT: a 82 ASN cc_start: 0.7339 (m110) cc_final: 0.7132 (m-40) REVERT: a 213 LYS cc_start: 0.8889 (ttpt) cc_final: 0.8666 (tttt) REVERT: a 258 GLU cc_start: 0.8096 (mm-30) cc_final: 0.7517 (mt-10) REVERT: a 274 GLU cc_start: 0.8772 (tt0) cc_final: 0.8469 (tt0) REVERT: a 284 LYS cc_start: 0.7260 (mttt) cc_final: 0.6882 (mmmt) REVERT: b 63 MET cc_start: 0.8131 (mmm) cc_final: 0.7777 (mmt) REVERT: b 69 ARG cc_start: 0.7745 (ttm-80) cc_final: 0.7534 (mtt-85) outliers start: 1 outliers final: 0 residues processed: 220 average time/residue: 1.3881 time to fit residues: 327.1626 Evaluate side-chains 150 residues out of total 1194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 150 time to evaluate : 1.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 114 optimal weight: 10.0000 chunk 103 optimal weight: 2.9990 chunk 57 optimal weight: 4.9990 chunk 35 optimal weight: 0.9990 chunk 69 optimal weight: 8.9990 chunk 55 optimal weight: 0.8980 chunk 106 optimal weight: 10.0000 chunk 41 optimal weight: 2.9990 chunk 64 optimal weight: 2.9990 chunk 79 optimal weight: 0.0070 chunk 123 optimal weight: 2.9990 overall best weight: 1.5804 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 ASN A 158 HIS A 254 HIS B 1 HIS B 95 ASN B 131 ASN B 207 ASN B 254 HIS a 35 HIS a 48 GLN a 195 HIS a 216 HIS a 254 HIS a 255 ASN a 286 HIS b 35 HIS b 48 GLN b 254 HIS b 255 ASN b 286 HIS Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.159835 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.124009 restraints weight = 11693.011| |-----------------------------------------------------------------------------| r_work (start): 0.3422 rms_B_bonded: 2.21 r_work: 0.3260 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3112 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.3112 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8082 moved from start: 0.1542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.093 11232 Z= 0.160 Angle : 0.589 15.224 15240 Z= 0.314 Chirality : 0.044 0.193 1592 Planarity : 0.004 0.044 1956 Dihedral : 4.496 19.248 1486 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.54 % Favored : 92.46 % Rotamer: Outliers : 3.43 % Allowed : 9.55 % Favored : 87.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.81 % 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: -1.01 (0.24), residues: 1352 helix: 1.88 (0.42), residues: 152 sheet: -1.59 (0.31), residues: 322 loop : -0.74 (0.21), residues: 878 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 232 HIS 0.005 0.001 HIS b 164 PHE 0.014 0.001 PHE B 277 TYR 0.009 0.001 TYR A 122 ARG 0.005 0.000 ARG B 257 Details of bonding type rmsd hydrogen bonds : bond 0.04372 ( 263) hydrogen bonds : angle 6.12273 ( 678) SS BOND : bond 0.00601 ( 24) SS BOND : angle 1.97805 ( 48) covalent geometry : bond 0.00394 (11208) covalent geometry : angle 0.57913 (15192) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2704 Ramachandran restraints generated. 1352 Oldfield, 0 Emsley, 1352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2704 Ramachandran restraints generated. 1352 Oldfield, 0 Emsley, 1352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 149 time to evaluate : 1.118 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 GLU cc_start: 0.5755 (tm-30) cc_final: 0.5354 (mt-10) REVERT: A 85 GLN cc_start: 0.7975 (mt0) cc_final: 0.7234 (mm110) REVERT: A 220 MET cc_start: 0.8100 (OUTLIER) cc_final: 0.6991 (mpt) REVERT: A 261 ARG cc_start: 0.8009 (mtt90) cc_final: 0.7469 (mtp180) REVERT: A 263 GLN cc_start: 0.8784 (OUTLIER) cc_final: 0.8030 (mt0) REVERT: B 103 ARG cc_start: 0.7862 (ptt90) cc_final: 0.7471 (ptt180) REVERT: B 286 HIS cc_start: 0.7032 (m170) cc_final: 0.6703 (m-70) REVERT: B 340 GLU cc_start: 0.7672 (tp30) cc_final: 0.7400 (tp30) REVERT: a 63 MET cc_start: 0.7883 (mmm) cc_final: 0.7551 (mpt) REVERT: a 74 GLU cc_start: 0.6944 (mt-10) cc_final: 0.6233 (tt0) REVERT: a 224 GLU cc_start: 0.8018 (OUTLIER) cc_final: 0.7619 (mt-10) REVERT: a 255 ASN cc_start: 0.8852 (t0) cc_final: 0.8634 (t160) REVERT: a 258 GLU cc_start: 0.8278 (mm-30) cc_final: 0.7527 (mt-10) REVERT: a 274 GLU cc_start: 0.8707 (tt0) cc_final: 0.8437 (tt0) REVERT: a 278 GLU cc_start: 0.6820 (mt-10) cc_final: 0.6350 (pt0) REVERT: a 284 LYS cc_start: 0.7174 (mttt) cc_final: 0.6693 (mmmt) REVERT: b 11 LYS cc_start: 0.7438 (OUTLIER) cc_final: 0.6639 (mmtt) REVERT: b 349 MET cc_start: 0.7309 (mmt) cc_final: 0.7025 (mmm) outliers start: 41 outliers final: 18 residues processed: 173 average time/residue: 1.2951 time to fit residues: 240.6036 Evaluate side-chains 159 residues out of total 1194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 137 time to evaluate : 1.154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 MET Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 220 MET Chi-restraints excluded: chain A residue 239 SER Chi-restraints excluded: chain A residue 263 GLN Chi-restraints excluded: chain B residue 30 ASP Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 136 ASP Chi-restraints excluded: chain B residue 139 THR Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain a residue 13 THR Chi-restraints excluded: chain a residue 106 VAL Chi-restraints excluded: chain a residue 220 MET Chi-restraints excluded: chain a residue 224 GLU Chi-restraints excluded: chain a residue 279 GLU Chi-restraints excluded: chain b residue 2 VAL Chi-restraints excluded: chain b residue 11 LYS Chi-restraints excluded: chain b residue 13 THR Chi-restraints excluded: chain b residue 67 MET Chi-restraints excluded: chain b residue 232 TRP Chi-restraints excluded: chain b residue 287 VAL Chi-restraints excluded: chain b residue 351 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 106 optimal weight: 10.0000 chunk 134 optimal weight: 7.9990 chunk 3 optimal weight: 5.9990 chunk 8 optimal weight: 1.9990 chunk 49 optimal weight: 6.9990 chunk 54 optimal weight: 0.6980 chunk 114 optimal weight: 10.0000 chunk 12 optimal weight: 0.0470 chunk 50 optimal weight: 3.9990 chunk 27 optimal weight: 4.9990 chunk 130 optimal weight: 3.9990 overall best weight: 2.1484 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 195 HIS B 254 HIS a 254 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.156296 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.119728 restraints weight = 11890.144| |-----------------------------------------------------------------------------| r_work (start): 0.3373 rms_B_bonded: 2.24 r_work: 0.3200 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3051 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.3051 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8105 moved from start: 0.1907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 11232 Z= 0.184 Angle : 0.670 19.566 15240 Z= 0.349 Chirality : 0.045 0.202 1592 Planarity : 0.004 0.042 1956 Dihedral : 4.774 22.110 1486 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.28 % Favored : 91.72 % Rotamer: Outliers : 3.94 % Allowed : 13.07 % Favored : 83.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.81 % 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: -1.20 (0.23), residues: 1352 helix: 1.80 (0.41), residues: 152 sheet: -1.65 (0.31), residues: 316 loop : -0.93 (0.21), residues: 884 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP B 232 HIS 0.005 0.001 HIS a 254 PHE 0.011 0.002 PHE B 277 TYR 0.012 0.002 TYR A 331 ARG 0.008 0.001 ARG b 261 Details of bonding type rmsd hydrogen bonds : bond 0.04384 ( 263) hydrogen bonds : angle 5.89766 ( 678) SS BOND : bond 0.00627 ( 24) SS BOND : angle 3.17347 ( 48) covalent geometry : bond 0.00448 (11208) covalent geometry : angle 0.64722 (15192) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2704 Ramachandran restraints generated. 1352 Oldfield, 0 Emsley, 1352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2704 Ramachandran restraints generated. 1352 Oldfield, 0 Emsley, 1352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 138 time to evaluate : 1.395 Fit side-chains revert: symmetry clash REVERT: A 26 GLU cc_start: 0.5532 (tm-30) cc_final: 0.5290 (mt-10) REVERT: A 80 GLU cc_start: 0.7559 (OUTLIER) cc_final: 0.6923 (tt0) REVERT: A 85 GLN cc_start: 0.8065 (mt0) cc_final: 0.7326 (mm110) REVERT: A 263 GLN cc_start: 0.8904 (OUTLIER) cc_final: 0.8080 (mt0) REVERT: A 342 GLU cc_start: 0.8042 (OUTLIER) cc_final: 0.7526 (mp0) REVERT: B 103 ARG cc_start: 0.7926 (ptt90) cc_final: 0.7504 (ptt180) REVERT: B 263 GLN cc_start: 0.8980 (OUTLIER) cc_final: 0.7429 (mp10) REVERT: B 274 GLU cc_start: 0.8681 (OUTLIER) cc_final: 0.8386 (tt0) REVERT: B 340 GLU cc_start: 0.7691 (tp30) cc_final: 0.7379 (tp30) REVERT: a 63 MET cc_start: 0.7908 (mmm) cc_final: 0.7519 (mpt) REVERT: a 74 GLU cc_start: 0.6842 (mt-10) cc_final: 0.6210 (tt0) REVERT: a 224 GLU cc_start: 0.8137 (OUTLIER) cc_final: 0.6972 (mt-10) REVERT: a 258 GLU cc_start: 0.8171 (mm-30) cc_final: 0.7433 (mt-10) REVERT: a 274 GLU cc_start: 0.8756 (tt0) cc_final: 0.8525 (tt0) REVERT: a 284 LYS cc_start: 0.7075 (mttt) cc_final: 0.6581 (mmmt) REVERT: b 63 MET cc_start: 0.7221 (mmt) cc_final: 0.6773 (mmt) REVERT: b 220 MET cc_start: 0.8156 (mpt) cc_final: 0.7933 (mpt) outliers start: 47 outliers final: 23 residues processed: 172 average time/residue: 1.5530 time to fit residues: 290.4956 Evaluate side-chains 154 residues out of total 1194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 125 time to evaluate : 1.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 CYS Chi-restraints excluded: chain A residue 15 CYS Chi-restraints excluded: chain A residue 63 MET Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 80 GLU Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 136 ASP Chi-restraints excluded: chain A residue 233 THR Chi-restraints excluded: chain A residue 239 SER Chi-restraints excluded: chain A residue 263 GLN Chi-restraints excluded: chain A residue 342 GLU Chi-restraints excluded: chain B residue 30 ASP Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 139 THR Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain B residue 263 GLN Chi-restraints excluded: chain B residue 274 GLU Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain a residue 13 THR Chi-restraints excluded: chain a residue 106 VAL Chi-restraints excluded: chain a residue 220 MET Chi-restraints excluded: chain a residue 224 GLU Chi-restraints excluded: chain a residue 279 GLU Chi-restraints excluded: chain b residue 2 VAL Chi-restraints excluded: chain b residue 13 THR Chi-restraints excluded: chain b residue 97 MET Chi-restraints excluded: chain b residue 287 VAL Chi-restraints excluded: chain b residue 351 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 82 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 chunk 50 optimal weight: 3.9990 chunk 47 optimal weight: 7.9990 chunk 73 optimal weight: 9.9990 chunk 118 optimal weight: 0.9980 chunk 55 optimal weight: 5.9990 chunk 59 optimal weight: 3.9990 chunk 63 optimal weight: 5.9990 chunk 88 optimal weight: 1.9990 chunk 31 optimal weight: 0.3980 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 254 HIS ** a 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 254 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.157017 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.119737 restraints weight = 11765.983| |-----------------------------------------------------------------------------| r_work (start): 0.3369 rms_B_bonded: 2.30 r_work: 0.3201 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3050 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3050 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8162 moved from start: 0.2071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 11232 Z= 0.152 Angle : 0.622 17.206 15240 Z= 0.325 Chirality : 0.044 0.220 1592 Planarity : 0.004 0.041 1956 Dihedral : 4.640 22.240 1486 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 4.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.99 % Favored : 92.01 % Rotamer: Outliers : 3.52 % Allowed : 15.41 % Favored : 81.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.81 % 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: -1.12 (0.23), residues: 1352 helix: 1.97 (0.42), residues: 152 sheet: -1.59 (0.32), residues: 306 loop : -0.92 (0.21), residues: 894 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP b 232 HIS 0.004 0.001 HIS a 254 PHE 0.011 0.001 PHE B 277 TYR 0.011 0.001 TYR A 122 ARG 0.009 0.000 ARG b 261 Details of bonding type rmsd hydrogen bonds : bond 0.03769 ( 263) hydrogen bonds : angle 5.62028 ( 678) SS BOND : bond 0.00493 ( 24) SS BOND : angle 2.90011 ( 48) covalent geometry : bond 0.00370 (11208) covalent geometry : angle 0.60119 (15192) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2704 Ramachandran restraints generated. 1352 Oldfield, 0 Emsley, 1352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2704 Ramachandran restraints generated. 1352 Oldfield, 0 Emsley, 1352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 140 time to evaluate : 1.145 Fit side-chains revert: symmetry clash REVERT: A 263 GLN cc_start: 0.8893 (OUTLIER) cc_final: 0.8017 (mt0) REVERT: A 342 GLU cc_start: 0.8065 (OUTLIER) cc_final: 0.7515 (mp0) REVERT: B 23 ASN cc_start: 0.8005 (OUTLIER) cc_final: 0.7694 (t0) REVERT: B 103 ARG cc_start: 0.7951 (ptt90) cc_final: 0.7549 (ptt180) REVERT: B 263 GLN cc_start: 0.9005 (OUTLIER) cc_final: 0.7505 (mp10) REVERT: B 274 GLU cc_start: 0.8679 (OUTLIER) cc_final: 0.8362 (tt0) REVERT: B 286 HIS cc_start: 0.7001 (m170) cc_final: 0.6677 (m-70) REVERT: B 340 GLU cc_start: 0.7652 (tp30) cc_final: 0.7450 (tp30) REVERT: a 63 MET cc_start: 0.7963 (mmm) cc_final: 0.7400 (mpt) REVERT: a 74 GLU cc_start: 0.6855 (mt-10) cc_final: 0.6238 (tt0) REVERT: a 224 GLU cc_start: 0.8222 (OUTLIER) cc_final: 0.7041 (mt-10) REVERT: a 258 GLU cc_start: 0.8196 (mm-30) cc_final: 0.7542 (mt-10) REVERT: a 274 GLU cc_start: 0.8778 (tt0) cc_final: 0.8574 (tt0) REVERT: a 284 LYS cc_start: 0.7133 (mttt) cc_final: 0.6646 (mmmt) REVERT: b 11 LYS cc_start: 0.7397 (OUTLIER) cc_final: 0.6633 (mmtt) REVERT: b 63 MET cc_start: 0.7598 (mmt) cc_final: 0.6870 (mmt) REVERT: b 178 GLU cc_start: 0.8133 (OUTLIER) cc_final: 0.7049 (mm-30) REVERT: b 316 CYS cc_start: 0.6926 (m) cc_final: 0.6572 (m) REVERT: b 349 MET cc_start: 0.7327 (mmt) cc_final: 0.7022 (mmm) outliers start: 42 outliers final: 22 residues processed: 168 average time/residue: 1.3214 time to fit residues: 238.4617 Evaluate side-chains 162 residues out of total 1194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 132 time to evaluate : 1.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 CYS Chi-restraints excluded: chain A residue 15 CYS Chi-restraints excluded: chain A residue 63 MET Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 239 SER Chi-restraints excluded: chain A residue 263 GLN Chi-restraints excluded: chain A residue 342 GLU Chi-restraints excluded: chain B residue 23 ASN Chi-restraints excluded: chain B residue 30 ASP Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 139 THR Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain B residue 263 GLN Chi-restraints excluded: chain B residue 274 GLU Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain a residue 13 THR Chi-restraints excluded: chain a residue 87 THR Chi-restraints excluded: chain a residue 89 VAL Chi-restraints excluded: chain a residue 106 VAL Chi-restraints excluded: chain a residue 220 MET Chi-restraints excluded: chain a residue 224 GLU Chi-restraints excluded: chain a residue 279 GLU Chi-restraints excluded: chain b residue 2 VAL Chi-restraints excluded: chain b residue 11 LYS Chi-restraints excluded: chain b residue 13 THR Chi-restraints excluded: chain b residue 97 MET Chi-restraints excluded: chain b residue 178 GLU Chi-restraints excluded: chain b residue 287 VAL Chi-restraints excluded: chain b residue 351 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 133 optimal weight: 5.9990 chunk 46 optimal weight: 8.9990 chunk 79 optimal weight: 0.7980 chunk 35 optimal weight: 6.9990 chunk 17 optimal weight: 4.9990 chunk 83 optimal weight: 6.9990 chunk 15 optimal weight: 3.9990 chunk 56 optimal weight: 2.9990 chunk 54 optimal weight: 0.9990 chunk 68 optimal weight: 0.9990 chunk 118 optimal weight: 0.7980 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 254 HIS a 95 ASN a 254 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.157516 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.120305 restraints weight = 11660.151| |-----------------------------------------------------------------------------| r_work (start): 0.3375 rms_B_bonded: 2.30 r_work: 0.3213 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3064 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3064 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8107 moved from start: 0.2171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 11232 Z= 0.133 Angle : 0.601 16.114 15240 Z= 0.315 Chirality : 0.043 0.200 1592 Planarity : 0.004 0.038 1956 Dihedral : 4.512 22.130 1486 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.77 % Favored : 92.23 % Rotamer: Outliers : 3.35 % Allowed : 16.50 % Favored : 80.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.81 % 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: -1.01 (0.23), residues: 1352 helix: 2.14 (0.42), residues: 152 sheet: -1.41 (0.32), residues: 300 loop : -0.91 (0.21), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP b 232 HIS 0.004 0.001 HIS a 254 PHE 0.011 0.001 PHE B 277 TYR 0.014 0.001 TYR A 122 ARG 0.009 0.000 ARG b 261 Details of bonding type rmsd hydrogen bonds : bond 0.03428 ( 263) hydrogen bonds : angle 5.44068 ( 678) SS BOND : bond 0.00436 ( 24) SS BOND : angle 2.80781 ( 48) covalent geometry : bond 0.00321 (11208) covalent geometry : angle 0.58119 (15192) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2704 Ramachandran restraints generated. 1352 Oldfield, 0 Emsley, 1352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2704 Ramachandran restraints generated. 1352 Oldfield, 0 Emsley, 1352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 147 time to evaluate : 1.148 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 6 VAL cc_start: 0.7546 (m) cc_final: 0.7325 (p) REVERT: A 26 GLU cc_start: 0.5879 (tm-30) cc_final: 0.5053 (tt0) REVERT: A 85 GLN cc_start: 0.8055 (mt0) cc_final: 0.7369 (mm110) REVERT: A 263 GLN cc_start: 0.8857 (OUTLIER) cc_final: 0.7984 (mt0) REVERT: A 342 GLU cc_start: 0.8040 (OUTLIER) cc_final: 0.7505 (mp0) REVERT: B 103 ARG cc_start: 0.7927 (ptt90) cc_final: 0.7543 (ptt180) REVERT: B 274 GLU cc_start: 0.8661 (OUTLIER) cc_final: 0.8332 (tt0) REVERT: a 63 MET cc_start: 0.7880 (mmm) cc_final: 0.7242 (mpt) REVERT: a 74 GLU cc_start: 0.6793 (mt-10) cc_final: 0.6210 (tt0) REVERT: a 224 GLU cc_start: 0.8180 (OUTLIER) cc_final: 0.7021 (mt-10) REVERT: a 258 GLU cc_start: 0.8103 (mm-30) cc_final: 0.7478 (mt-10) REVERT: a 274 GLU cc_start: 0.8775 (tt0) cc_final: 0.8545 (tt0) REVERT: a 284 LYS cc_start: 0.7076 (mttt) cc_final: 0.6597 (mmmt) REVERT: b 11 LYS cc_start: 0.7355 (OUTLIER) cc_final: 0.6607 (mmtt) REVERT: b 63 MET cc_start: 0.7570 (mmt) cc_final: 0.7248 (mmm) outliers start: 40 outliers final: 23 residues processed: 174 average time/residue: 1.2649 time to fit residues: 236.7443 Evaluate side-chains 163 residues out of total 1194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 135 time to evaluate : 1.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 CYS Chi-restraints excluded: chain A residue 15 CYS Chi-restraints excluded: chain A residue 30 ASP Chi-restraints excluded: chain A residue 63 MET Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 263 GLN Chi-restraints excluded: chain A residue 342 GLU Chi-restraints excluded: chain B residue 30 ASP Chi-restraints excluded: chain B residue 106 VAL Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 139 THR Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain B residue 274 GLU Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain a residue 13 THR Chi-restraints excluded: chain a residue 87 THR Chi-restraints excluded: chain a residue 106 VAL Chi-restraints excluded: chain a residue 220 MET Chi-restraints excluded: chain a residue 224 GLU Chi-restraints excluded: chain a residue 279 GLU Chi-restraints excluded: chain b residue 2 VAL Chi-restraints excluded: chain b residue 11 LYS Chi-restraints excluded: chain b residue 13 THR Chi-restraints excluded: chain b residue 51 GLU Chi-restraints excluded: chain b residue 97 MET Chi-restraints excluded: chain b residue 287 VAL Chi-restraints excluded: chain b residue 351 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 88 optimal weight: 1.9990 chunk 30 optimal weight: 2.9990 chunk 27 optimal weight: 4.9990 chunk 72 optimal weight: 4.9990 chunk 99 optimal weight: 6.9990 chunk 96 optimal weight: 5.9990 chunk 77 optimal weight: 10.0000 chunk 76 optimal weight: 1.9990 chunk 23 optimal weight: 6.9990 chunk 63 optimal weight: 5.9990 chunk 7 optimal weight: 6.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 254 HIS a 254 HIS b 147 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.152804 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.115108 restraints weight = 11882.286| |-----------------------------------------------------------------------------| r_work (start): 0.3313 rms_B_bonded: 2.26 r_work: 0.3148 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.2999 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.2999 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8190 moved from start: 0.2436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.069 11232 Z= 0.265 Angle : 0.736 20.011 15240 Z= 0.384 Chirality : 0.048 0.191 1592 Planarity : 0.005 0.042 1956 Dihedral : 5.085 23.407 1486 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.32 % Favored : 90.68 % Rotamer: Outliers : 3.85 % Allowed : 17.50 % Favored : 78.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.81 % 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: -1.36 (0.23), residues: 1352 helix: 1.85 (0.42), residues: 152 sheet: -1.72 (0.32), residues: 282 loop : -1.15 (0.20), residues: 918 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP a 28 HIS 0.006 0.002 HIS b 195 PHE 0.013 0.002 PHE a 323 TYR 0.016 0.002 TYR b 34 ARG 0.009 0.001 ARG b 261 Details of bonding type rmsd hydrogen bonds : bond 0.04476 ( 263) hydrogen bonds : angle 5.76573 ( 678) SS BOND : bond 0.00564 ( 24) SS BOND : angle 3.13052 ( 48) covalent geometry : bond 0.00659 (11208) covalent geometry : angle 0.71545 (15192) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2704 Ramachandran restraints generated. 1352 Oldfield, 0 Emsley, 1352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2704 Ramachandran restraints generated. 1352 Oldfield, 0 Emsley, 1352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 127 time to evaluate : 1.269 Fit side-chains revert: symmetry clash REVERT: A 26 GLU cc_start: 0.6035 (tm-30) cc_final: 0.5262 (tt0) REVERT: A 263 GLN cc_start: 0.9017 (OUTLIER) cc_final: 0.8132 (mt0) REVERT: A 342 GLU cc_start: 0.8107 (OUTLIER) cc_final: 0.7494 (mp0) REVERT: B 103 ARG cc_start: 0.8007 (ptt90) cc_final: 0.7596 (ptt180) REVERT: B 263 GLN cc_start: 0.9025 (OUTLIER) cc_final: 0.7447 (mp10) REVERT: B 274 GLU cc_start: 0.8705 (OUTLIER) cc_final: 0.8449 (tt0) REVERT: B 339 LYS cc_start: 0.7650 (tttp) cc_final: 0.7375 (mttt) REVERT: B 340 GLU cc_start: 0.7834 (tp30) cc_final: 0.7607 (tp30) REVERT: a 63 MET cc_start: 0.7976 (mmm) cc_final: 0.7116 (mpt) REVERT: a 74 GLU cc_start: 0.6933 (mt-10) cc_final: 0.6266 (tt0) REVERT: a 224 GLU cc_start: 0.8294 (OUTLIER) cc_final: 0.7893 (mt-10) REVERT: a 258 GLU cc_start: 0.8053 (mm-30) cc_final: 0.7420 (mt-10) REVERT: a 274 GLU cc_start: 0.8808 (tt0) cc_final: 0.8583 (tt0) REVERT: a 278 GLU cc_start: 0.6957 (mt-10) cc_final: 0.6416 (pt0) REVERT: a 284 LYS cc_start: 0.7053 (mttt) cc_final: 0.6517 (mmmt) REVERT: b 11 LYS cc_start: 0.7401 (OUTLIER) cc_final: 0.6636 (mmtt) REVERT: b 178 GLU cc_start: 0.8176 (OUTLIER) cc_final: 0.7076 (mm-30) outliers start: 46 outliers final: 28 residues processed: 159 average time/residue: 1.2675 time to fit residues: 216.7153 Evaluate side-chains 156 residues out of total 1194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 121 time to evaluate : 1.141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 CYS Chi-restraints excluded: chain A residue 15 CYS Chi-restraints excluded: chain A residue 17 THR Chi-restraints excluded: chain A residue 63 MET Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 136 ASP Chi-restraints excluded: chain A residue 239 SER Chi-restraints excluded: chain A residue 263 GLN Chi-restraints excluded: chain A residue 342 GLU Chi-restraints excluded: chain B residue 30 ASP Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 139 THR Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain B residue 263 GLN Chi-restraints excluded: chain B residue 274 GLU Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain a residue 13 THR Chi-restraints excluded: chain a residue 87 THR Chi-restraints excluded: chain a residue 89 VAL Chi-restraints excluded: chain a residue 106 VAL Chi-restraints excluded: chain a residue 220 MET Chi-restraints excluded: chain a residue 224 GLU Chi-restraints excluded: chain a residue 279 GLU Chi-restraints excluded: chain b residue 2 VAL Chi-restraints excluded: chain b residue 11 LYS Chi-restraints excluded: chain b residue 13 THR Chi-restraints excluded: chain b residue 51 GLU Chi-restraints excluded: chain b residue 67 MET Chi-restraints excluded: chain b residue 97 MET Chi-restraints excluded: chain b residue 162 VAL Chi-restraints excluded: chain b residue 178 GLU Chi-restraints excluded: chain b residue 287 VAL Chi-restraints excluded: chain b residue 351 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 104 optimal weight: 4.9990 chunk 39 optimal weight: 3.9990 chunk 81 optimal weight: 10.0000 chunk 83 optimal weight: 6.9990 chunk 92 optimal weight: 0.6980 chunk 111 optimal weight: 9.9990 chunk 26 optimal weight: 0.0470 chunk 110 optimal weight: 2.9990 chunk 88 optimal weight: 1.9990 chunk 18 optimal weight: 0.0470 chunk 34 optimal weight: 0.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 147 HIS B 254 HIS a 254 HIS b 164 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.157789 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.121207 restraints weight = 11882.722| |-----------------------------------------------------------------------------| r_work (start): 0.3387 rms_B_bonded: 2.29 r_work: 0.3207 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3056 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3056 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8099 moved from start: 0.2365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 11232 Z= 0.108 Angle : 0.590 14.732 15240 Z= 0.311 Chirality : 0.042 0.209 1592 Planarity : 0.004 0.037 1956 Dihedral : 4.560 21.216 1486 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.95 % Favored : 93.05 % Rotamer: Outliers : 3.10 % Allowed : 18.34 % Favored : 78.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.81 % 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: -1.03 (0.23), residues: 1352 helix: 2.27 (0.42), residues: 152 sheet: -1.45 (0.32), residues: 300 loop : -0.94 (0.21), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP b 28 HIS 0.004 0.001 HIS a 254 PHE 0.012 0.001 PHE B 277 TYR 0.018 0.001 TYR A 122 ARG 0.009 0.000 ARG b 261 Details of bonding type rmsd hydrogen bonds : bond 0.03231 ( 263) hydrogen bonds : angle 5.37313 ( 678) SS BOND : bond 0.00428 ( 24) SS BOND : angle 2.68936 ( 48) covalent geometry : bond 0.00253 (11208) covalent geometry : angle 0.57145 (15192) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2704 Ramachandran restraints generated. 1352 Oldfield, 0 Emsley, 1352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2704 Ramachandran restraints generated. 1352 Oldfield, 0 Emsley, 1352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 136 time to evaluate : 1.148 Fit side-chains revert: symmetry clash REVERT: A 26 GLU cc_start: 0.5723 (tm-30) cc_final: 0.5118 (tt0) REVERT: A 263 GLN cc_start: 0.8821 (OUTLIER) cc_final: 0.7948 (mt0) REVERT: A 342 GLU cc_start: 0.8041 (OUTLIER) cc_final: 0.7453 (mp0) REVERT: B 103 ARG cc_start: 0.7917 (ptt90) cc_final: 0.7509 (ptt180) REVERT: B 274 GLU cc_start: 0.8676 (OUTLIER) cc_final: 0.8327 (tt0) REVERT: B 340 GLU cc_start: 0.7607 (tp30) cc_final: 0.7388 (tp30) REVERT: a 74 GLU cc_start: 0.6843 (mt-10) cc_final: 0.6145 (tt0) REVERT: a 224 GLU cc_start: 0.8112 (OUTLIER) cc_final: 0.7608 (mt-10) REVERT: a 258 GLU cc_start: 0.8072 (mm-30) cc_final: 0.7434 (mt-10) REVERT: a 274 GLU cc_start: 0.8780 (tt0) cc_final: 0.8566 (tt0) REVERT: a 284 LYS cc_start: 0.7032 (mttt) cc_final: 0.6498 (mmmt) REVERT: b 97 MET cc_start: 0.7964 (OUTLIER) cc_final: 0.7499 (mtt) REVERT: b 279 GLU cc_start: 0.7277 (pt0) cc_final: 0.6670 (pm20) outliers start: 37 outliers final: 18 residues processed: 159 average time/residue: 1.2439 time to fit residues: 213.5375 Evaluate side-chains 149 residues out of total 1194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 126 time to evaluate : 1.178 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 CYS Chi-restraints excluded: chain A residue 15 CYS Chi-restraints excluded: chain A residue 63 MET Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 263 GLN Chi-restraints excluded: chain A residue 342 GLU Chi-restraints excluded: chain B residue 30 ASP Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 139 THR Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain B residue 274 GLU Chi-restraints excluded: chain a residue 106 VAL Chi-restraints excluded: chain a residue 220 MET Chi-restraints excluded: chain a residue 224 GLU Chi-restraints excluded: chain a residue 279 GLU Chi-restraints excluded: chain b residue 13 THR Chi-restraints excluded: chain b residue 51 GLU Chi-restraints excluded: chain b residue 97 MET Chi-restraints excluded: chain b residue 162 VAL Chi-restraints excluded: chain b residue 209 THR Chi-restraints excluded: chain b residue 351 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 76 optimal weight: 8.9990 chunk 78 optimal weight: 6.9990 chunk 27 optimal weight: 4.9990 chunk 2 optimal weight: 1.9990 chunk 135 optimal weight: 3.9990 chunk 117 optimal weight: 6.9990 chunk 114 optimal weight: 9.9990 chunk 129 optimal weight: 9.9990 chunk 23 optimal weight: 0.0770 chunk 1 optimal weight: 2.9990 chunk 59 optimal weight: 4.9990 overall best weight: 2.8146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 147 HIS B 254 HIS a 95 ASN a 254 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.153697 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.116291 restraints weight = 11742.905| |-----------------------------------------------------------------------------| r_work (start): 0.3325 rms_B_bonded: 2.30 r_work: 0.3156 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3008 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3008 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8225 moved from start: 0.2494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.071 11232 Z= 0.226 Angle : 0.703 18.686 15240 Z= 0.367 Chirality : 0.046 0.216 1592 Planarity : 0.004 0.040 1956 Dihedral : 4.921 22.632 1486 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.17 % Favored : 90.83 % Rotamer: Outliers : 3.52 % Allowed : 18.76 % Favored : 77.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.81 % 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: -1.28 (0.23), residues: 1352 helix: 1.96 (0.42), residues: 154 sheet: -1.71 (0.32), residues: 282 loop : -1.09 (0.20), residues: 916 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP a 28 HIS 0.006 0.001 HIS a 254 PHE 0.012 0.002 PHE a 323 TYR 0.018 0.002 TYR b 34 ARG 0.010 0.001 ARG b 261 Details of bonding type rmsd hydrogen bonds : bond 0.04137 ( 263) hydrogen bonds : angle 5.63269 ( 678) SS BOND : bond 0.00534 ( 24) SS BOND : angle 3.09447 ( 48) covalent geometry : bond 0.00559 (11208) covalent geometry : angle 0.68247 (15192) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2704 Ramachandran restraints generated. 1352 Oldfield, 0 Emsley, 1352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2704 Ramachandran restraints generated. 1352 Oldfield, 0 Emsley, 1352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 124 time to evaluate : 1.383 Fit side-chains revert: symmetry clash REVERT: A 80 GLU cc_start: 0.7641 (OUTLIER) cc_final: 0.6947 (tt0) REVERT: A 263 GLN cc_start: 0.9003 (OUTLIER) cc_final: 0.8115 (mt0) REVERT: A 342 GLU cc_start: 0.8146 (OUTLIER) cc_final: 0.7574 (mp0) REVERT: B 103 ARG cc_start: 0.8016 (ptt90) cc_final: 0.7617 (ptt180) REVERT: B 274 GLU cc_start: 0.8712 (OUTLIER) cc_final: 0.8436 (tt0) REVERT: B 340 GLU cc_start: 0.7800 (tp30) cc_final: 0.7495 (tp30) REVERT: a 63 MET cc_start: 0.7679 (OUTLIER) cc_final: 0.7183 (mpt) REVERT: a 74 GLU cc_start: 0.6970 (mt-10) cc_final: 0.6240 (tt0) REVERT: a 224 GLU cc_start: 0.8324 (OUTLIER) cc_final: 0.7915 (mt-10) REVERT: a 258 GLU cc_start: 0.8033 (mm-30) cc_final: 0.7445 (mt-10) REVERT: a 274 GLU cc_start: 0.8829 (tt0) cc_final: 0.8601 (tt0) REVERT: a 284 LYS cc_start: 0.7122 (mttt) cc_final: 0.6550 (mmmt) REVERT: b 11 LYS cc_start: 0.7404 (OUTLIER) cc_final: 0.6652 (mmtt) outliers start: 42 outliers final: 26 residues processed: 152 average time/residue: 1.3092 time to fit residues: 215.8024 Evaluate side-chains 150 residues out of total 1194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 117 time to evaluate : 1.173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 CYS Chi-restraints excluded: chain A residue 15 CYS Chi-restraints excluded: chain A residue 17 THR Chi-restraints excluded: chain A residue 63 MET Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 80 GLU Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 239 SER Chi-restraints excluded: chain A residue 263 GLN Chi-restraints excluded: chain A residue 342 GLU Chi-restraints excluded: chain B residue 30 ASP Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 139 THR Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain B residue 274 GLU Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain a residue 13 THR Chi-restraints excluded: chain a residue 63 MET Chi-restraints excluded: chain a residue 89 VAL Chi-restraints excluded: chain a residue 106 VAL Chi-restraints excluded: chain a residue 220 MET Chi-restraints excluded: chain a residue 224 GLU Chi-restraints excluded: chain a residue 231 LEU Chi-restraints excluded: chain a residue 279 GLU Chi-restraints excluded: chain b residue 2 VAL Chi-restraints excluded: chain b residue 11 LYS Chi-restraints excluded: chain b residue 13 THR Chi-restraints excluded: chain b residue 51 GLU Chi-restraints excluded: chain b residue 97 MET Chi-restraints excluded: chain b residue 162 VAL Chi-restraints excluded: chain b residue 209 THR Chi-restraints excluded: chain b residue 351 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 105 optimal weight: 0.7980 chunk 55 optimal weight: 4.9990 chunk 118 optimal weight: 0.7980 chunk 110 optimal weight: 9.9990 chunk 28 optimal weight: 10.0000 chunk 63 optimal weight: 6.9990 chunk 96 optimal weight: 0.9990 chunk 81 optimal weight: 10.0000 chunk 82 optimal weight: 0.9980 chunk 51 optimal weight: 3.9990 chunk 83 optimal weight: 5.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 147 HIS B 254 HIS a 254 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.155391 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.118321 restraints weight = 11840.533| |-----------------------------------------------------------------------------| r_work (start): 0.3355 rms_B_bonded: 2.24 r_work: 0.3189 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3039 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.3039 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8090 moved from start: 0.2476 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 11232 Z= 0.147 Angle : 0.659 17.087 15240 Z= 0.345 Chirality : 0.044 0.249 1592 Planarity : 0.004 0.039 1956 Dihedral : 4.725 22.192 1486 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.69 % Favored : 92.31 % Rotamer: Outliers : 3.02 % Allowed : 19.26 % Favored : 77.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.81 % 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: -1.17 (0.23), residues: 1352 helix: 2.27 (0.42), residues: 152 sheet: -1.69 (0.33), residues: 282 loop : -1.03 (0.20), residues: 918 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP a 28 HIS 0.004 0.001 HIS a 254 PHE 0.010 0.001 PHE B 277 TYR 0.016 0.001 TYR A 122 ARG 0.009 0.000 ARG b 261 Details of bonding type rmsd hydrogen bonds : bond 0.03557 ( 263) hydrogen bonds : angle 5.47793 ( 678) SS BOND : bond 0.00480 ( 24) SS BOND : angle 3.15090 ( 48) covalent geometry : bond 0.00353 (11208) covalent geometry : angle 0.63599 (15192) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2704 Ramachandran restraints generated. 1352 Oldfield, 0 Emsley, 1352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2704 Ramachandran restraints generated. 1352 Oldfield, 0 Emsley, 1352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 127 time to evaluate : 1.186 Fit side-chains revert: symmetry clash REVERT: A 26 GLU cc_start: 0.6155 (tm-30) cc_final: 0.5121 (tt0) REVERT: A 80 GLU cc_start: 0.7581 (OUTLIER) cc_final: 0.6885 (tt0) REVERT: A 263 GLN cc_start: 0.8871 (OUTLIER) cc_final: 0.7979 (mt0) REVERT: A 342 GLU cc_start: 0.8132 (OUTLIER) cc_final: 0.7586 (mp0) REVERT: B 103 ARG cc_start: 0.7912 (ptt90) cc_final: 0.7474 (ptt180) REVERT: B 274 GLU cc_start: 0.8637 (OUTLIER) cc_final: 0.8322 (tt0) REVERT: B 340 GLU cc_start: 0.7695 (tp30) cc_final: 0.7459 (tp30) REVERT: a 63 MET cc_start: 0.7499 (OUTLIER) cc_final: 0.7024 (mpt) REVERT: a 74 GLU cc_start: 0.6877 (mt-10) cc_final: 0.6188 (tt0) REVERT: a 224 GLU cc_start: 0.8147 (OUTLIER) cc_final: 0.7671 (mt-10) REVERT: a 258 GLU cc_start: 0.8039 (mm-30) cc_final: 0.7424 (mt-10) REVERT: a 274 GLU cc_start: 0.8755 (tt0) cc_final: 0.8528 (tt0) REVERT: a 284 LYS cc_start: 0.7031 (mttt) cc_final: 0.6487 (mmmt) outliers start: 36 outliers final: 23 residues processed: 149 average time/residue: 1.3550 time to fit residues: 217.4399 Evaluate side-chains 154 residues out of total 1194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 125 time to evaluate : 1.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 CYS Chi-restraints excluded: chain A residue 15 CYS Chi-restraints excluded: chain A residue 63 MET Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 80 GLU Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 263 GLN Chi-restraints excluded: chain A residue 342 GLU Chi-restraints excluded: chain B residue 30 ASP Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 139 THR Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain B residue 274 GLU Chi-restraints excluded: chain a residue 13 THR Chi-restraints excluded: chain a residue 63 MET Chi-restraints excluded: chain a residue 106 VAL Chi-restraints excluded: chain a residue 220 MET Chi-restraints excluded: chain a residue 224 GLU Chi-restraints excluded: chain a residue 279 GLU Chi-restraints excluded: chain b residue 2 VAL Chi-restraints excluded: chain b residue 13 THR Chi-restraints excluded: chain b residue 51 GLU Chi-restraints excluded: chain b residue 67 MET Chi-restraints excluded: chain b residue 97 MET Chi-restraints excluded: chain b residue 162 VAL Chi-restraints excluded: chain b residue 209 THR Chi-restraints excluded: chain b residue 228 SER Chi-restraints excluded: chain b residue 351 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 13 optimal weight: 6.9990 chunk 18 optimal weight: 2.9990 chunk 104 optimal weight: 2.9990 chunk 37 optimal weight: 0.8980 chunk 15 optimal weight: 0.9990 chunk 45 optimal weight: 4.9990 chunk 48 optimal weight: 9.9990 chunk 74 optimal weight: 7.9990 chunk 59 optimal weight: 3.9990 chunk 89 optimal weight: 3.9990 chunk 109 optimal weight: 4.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 147 HIS B 254 HIS a 254 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.154298 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.116970 restraints weight = 11770.742| |-----------------------------------------------------------------------------| r_work (start): 0.3335 rms_B_bonded: 2.29 r_work: 0.3170 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3021 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3021 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8165 moved from start: 0.2545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 11232 Z= 0.199 Angle : 0.702 17.864 15240 Z= 0.366 Chirality : 0.046 0.253 1592 Planarity : 0.004 0.040 1956 Dihedral : 4.864 22.257 1486 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.80 % Favored : 91.20 % Rotamer: Outliers : 2.93 % Allowed : 19.51 % Favored : 77.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.81 % 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: -1.28 (0.23), residues: 1352 helix: 2.09 (0.42), residues: 154 sheet: -1.76 (0.32), residues: 282 loop : -1.10 (0.20), residues: 916 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP a 28 HIS 0.006 0.001 HIS a 254 PHE 0.011 0.002 PHE a 323 TYR 0.017 0.002 TYR A 122 ARG 0.009 0.001 ARG b 261 Details of bonding type rmsd hydrogen bonds : bond 0.03932 ( 263) hydrogen bonds : angle 5.58533 ( 678) SS BOND : bond 0.00555 ( 24) SS BOND : angle 3.24034 ( 48) covalent geometry : bond 0.00488 (11208) covalent geometry : angle 0.67887 (15192) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2704 Ramachandran restraints generated. 1352 Oldfield, 0 Emsley, 1352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2704 Ramachandran restraints generated. 1352 Oldfield, 0 Emsley, 1352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 123 time to evaluate : 2.066 Fit side-chains revert: symmetry clash REVERT: A 26 GLU cc_start: 0.6131 (tm-30) cc_final: 0.5290 (tt0) REVERT: A 80 GLU cc_start: 0.7602 (OUTLIER) cc_final: 0.6903 (tt0) REVERT: A 263 GLN cc_start: 0.8947 (OUTLIER) cc_final: 0.8054 (mt0) REVERT: A 342 GLU cc_start: 0.8140 (OUTLIER) cc_final: 0.7580 (mp0) REVERT: B 103 ARG cc_start: 0.7958 (ptt90) cc_final: 0.7525 (ptt180) REVERT: B 274 GLU cc_start: 0.8678 (OUTLIER) cc_final: 0.8362 (tt0) REVERT: B 340 GLU cc_start: 0.7767 (tp30) cc_final: 0.7486 (tp30) REVERT: a 63 MET cc_start: 0.7590 (OUTLIER) cc_final: 0.6989 (mpt) REVERT: a 74 GLU cc_start: 0.6964 (mt-10) cc_final: 0.6238 (tt0) REVERT: a 224 GLU cc_start: 0.8258 (OUTLIER) cc_final: 0.7845 (mt-10) REVERT: a 258 GLU cc_start: 0.8031 (mm-30) cc_final: 0.7405 (mt-10) REVERT: a 274 GLU cc_start: 0.8785 (tt0) cc_final: 0.8562 (tt0) REVERT: a 284 LYS cc_start: 0.7091 (mttt) cc_final: 0.6542 (mmmt) REVERT: b 63 MET cc_start: 0.7891 (mmt) cc_final: 0.7628 (mpp) outliers start: 35 outliers final: 24 residues processed: 146 average time/residue: 1.4434 time to fit residues: 227.2448 Evaluate side-chains 150 residues out of total 1194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 120 time to evaluate : 1.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 CYS Chi-restraints excluded: chain A residue 15 CYS Chi-restraints excluded: chain A residue 63 MET Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 80 GLU Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 263 GLN Chi-restraints excluded: chain A residue 342 GLU Chi-restraints excluded: chain B residue 30 ASP Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 139 THR Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain B residue 251 LEU Chi-restraints excluded: chain B residue 274 GLU Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain a residue 13 THR Chi-restraints excluded: chain a residue 63 MET Chi-restraints excluded: chain a residue 106 VAL Chi-restraints excluded: chain a residue 220 MET Chi-restraints excluded: chain a residue 224 GLU Chi-restraints excluded: chain a residue 279 GLU Chi-restraints excluded: chain b residue 2 VAL Chi-restraints excluded: chain b residue 13 THR Chi-restraints excluded: chain b residue 51 GLU Chi-restraints excluded: chain b residue 97 MET Chi-restraints excluded: chain b residue 162 VAL Chi-restraints excluded: chain b residue 209 THR Chi-restraints excluded: chain b residue 228 SER Chi-restraints excluded: chain b residue 351 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 84 optimal weight: 0.7980 chunk 4 optimal weight: 0.7980 chunk 132 optimal weight: 2.9990 chunk 72 optimal weight: 0.6980 chunk 69 optimal weight: 0.9990 chunk 64 optimal weight: 1.9990 chunk 30 optimal weight: 4.9990 chunk 116 optimal weight: 0.4980 chunk 44 optimal weight: 6.9990 chunk 91 optimal weight: 5.9990 chunk 45 optimal weight: 0.0070 overall best weight: 0.5598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 147 HIS B 254 HIS a 254 HIS b 102 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.158914 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.122331 restraints weight = 11662.041| |-----------------------------------------------------------------------------| r_work (start): 0.3403 rms_B_bonded: 2.25 r_work: 0.3240 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3091 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3091 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8062 moved from start: 0.2509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 11232 Z= 0.103 Angle : 0.605 14.967 15240 Z= 0.318 Chirality : 0.042 0.223 1592 Planarity : 0.004 0.037 1956 Dihedral : 4.395 20.104 1486 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.95 % Favored : 93.05 % Rotamer: Outliers : 2.68 % Allowed : 19.85 % Favored : 77.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.81 % 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: -0.96 (0.24), residues: 1352 helix: 2.39 (0.42), residues: 154 sheet: -1.52 (0.32), residues: 304 loop : -0.86 (0.21), residues: 894 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP a 28 HIS 0.004 0.001 HIS a 254 PHE 0.012 0.001 PHE B 277 TYR 0.015 0.001 TYR A 122 ARG 0.008 0.000 ARG b 261 Details of bonding type rmsd hydrogen bonds : bond 0.03086 ( 263) hydrogen bonds : angle 5.28683 ( 678) SS BOND : bond 0.00431 ( 24) SS BOND : angle 2.86033 ( 48) covalent geometry : bond 0.00234 (11208) covalent geometry : angle 0.58375 (15192) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9069.84 seconds wall clock time: 158 minutes 8.20 seconds (9488.20 seconds total)